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X-ray Diffraction by Disordered

and Ordered Systems


Coverng X-rey Diffraction by Gases. Liquids
and Solids and Indicating How the Theory o/
Diffraction bV These Different States 01
Matter is Re/oted ond How It Can Be Used to
Solve Structural Problems

-----Relatell

--Ttdes o Jnterest

Book.
ASHBY
Dislocatlon ModeUlng of Physical Systems

BATA
Advances In Uquld Crystal Research and Apphcations (2 Vals )

CARTER

MetaJHc Shilts in NMR


GRAY & GOODBY
Uquid C<ystols

Preface

HOPKINS
The Mechanlcs of Solids
KRISHNAN el 01
ThermaJ Expanslon of Crystals
PAMPUN
CrystaI Growth 2nd edition
TANNER
X-ray Oiffraction Topography
WHmAKER

Crystal~aphy (An lntraduction for . ~ 5dence (and Other Solid State) Students)

Joumal.

This book i a Lntended pr i mar ily f or t hose reade r s , espec i ally beqinnlng re March students, "ho " ish to use X-ray diffraction to investigate specimens which
. .y not be crystal line.
Beqinners need to understand how inter fe r ence e f fec t s
arLae in X-ray dlfEr action patterns and t he underlyinq pri ncipIe s involved Ln
developing st~uc tural mode l a .
A general a pp r oach t o these topic s . and diff raction
geometry, a ppears in the fir s t four chaptErs o f t he book.
Nex t thE general ldeas
are applied to the scatterlng of X-rays by isolated a toms a nd molecules .
In s~
aequent chapters the ~ay9 l n whlch interference oodifies the pattern oE scattered
X-rays, when the atoes and molecules aggregate i n various states of matter , are
considered.
Such sta tes o f matter include l i quida, amo rphous sol i da and liquid
cryata l. as well as crystal s.
Each state gives rise to characterLstic i nterfer ence effects which inf luence the appearance and a ny $ubsequent a nalysis o f the re8ultlng X-rey d i ffrac t ion pattern .
The final chapt ar demonstrates t hat tha lnterpretation of X-ray dlf f r act i on pattern s i5 s imply an application o E physical opt ics.

Journal .of Physics and Chemistry of Solids


Materials ~nd 50dety
Materials Research BuIletin

Progress in Biophysics and Molecular Bialogy


Progress In Materlals Science
Progress in Crystal Growth and Characterization
Salid State CommunlcaHons

Full detaUs af any Pergamon publlclltion/ free specimen copy of lIny Pergamon
pumal avallabJe on request from your neares!: Pergamon offlce

Although readers will have a common intere s t in inter preting X-r ay dlf fractian
patterns, thelr backg r ound s are likely to be very dlf fe r ent.
The technique o f
X-ray diEfractlon ls used by b i ologists, b iochemLsts, geologists , chemlsts , physi~
ciat. and matariaLs scient is ts.
1 have , t here fore, t ried to e xpla in all except
the ~.t e lementary physical concept5 which arise .
But 1 have usuall y kept these
explanations fair ly ter se i n an attempt t o avoid boring r eader s with a str ong background i n physlcs .
Similar l y 1 have often supplemented rnathematics with desc r iptlons in words.
On occasion 1 have avoided mat hema t ics , such as exp l icit use of
tbe Dirac delta function . where it might have distracted SomB r eede rs.
Neverthel s aathematical ideas are used wherever 1 believe t hey are needed for a c l ear and
concis. explanation.
Ny intentlon i s that thi s book ~ i ll also be u sefu l to ad va n ced undergraduates
and students attend~ng post-graduate lecture courses.
Books o n dlf fraction by
crystal a can be seriou sly mislea d Lng for theae students because they often c r eate
thll fa l .. 1aIpresslon that X-ray diffrac tlon patterns can only be recorded frOlll
Cryatal a.
If they avol d this trap , students rlsk being caught by a not her - t he
ai.cenc_ption that there mu st be somethinq resembllnq a l attice Ln systems such as
liquida or qe ls iE l nterEerence effects are to modulate the pattern of ~ - rays scat tarad by t beir constituent molecules. _ 1 hope that tbis book wil! help t o pr event
tb. s pread of the se mi s understanding s.

CEETPS - F' TEC - SP


v

BiBLI"TEL'.\

_ _________-______________________________. _

L~
. ~
~(L~---O~~
~~
_ I

Preface
SI units are used throughout .
Units can cause confusion when comparing f ormulaa fer the intensity of X-raya scattered by an e l ectron given in different
I:xx:lks - some of the bocks "Usted in the bibliogr aphy use egs units .
Similar difficu lties occur when relating the i ntensity of scattered light te mol ecular polar i sabilLty - C9S units are used ln many books on 11ght scatter ing and the formulae
are differe nt .
Wavelenqths and distances between atems are Ilea sured ln nanolletres
(1 n.m 10- 9 m) or pi.c clletres (1 p:!l _ 10- 12 m ) .
Many col leagues and f riends have i nfluenced this book - either 1ndirectly, by
the1r influence en my ideas , or direct ly, by he1p1ng w1th var i ous s tagea in its
production.
Hy i d e as owe much te the influence of struther Amott who taught me
the va1ue oE analyaing d iff raction patterns fr om specimens which ara not s1ngle
crystals.
Conversations with John Woodhead-Galloway helped me to understand mo re
about the liquid s t ate : our col laborative research has also 1nfluenced the treatment
of Section I X.6.
A meeting wLth Alan MacKay, when t he book was being p I anned,
proved encouragLng and i n f luenced i ts contenta.
Richard Aapden read the whole book,
as Lt waa being wr1tten, and apotted many errors and ambiguitLes - sorne may rema1n
because 1 hava net aLways taken his advice.
Marqaret Adama , Stuart Gr undy and
Steve 8ickey kindl y provided photogr a ph s.
Karen Oavies helped to obtain many of
the diffraction pa t ter ns as well as photographing a ll the other illustratLons which
were drawn by Percy HUkins , my f ather.
'!'he typescript was produced by Laurel
Henfrey Business Services of Bramball , Cheshire.
Celia HukinSl . my wife, helped me
with the indexo
1 am very grat e f ul both to al1 of them and to the many o the r s who
have, in some vay , h e1ped te determine the f inal fonn of thia txJok.

Contents

CHAPTER 1

SCATI'E RING BY AN ELECTRON


LL

1.2
1.3
1.'
1.5
1.5
CHAPrER Il

,
L

3
4

5
6

OIFFRACTION AS FOURIER TRANSf'QRMATI ON

ILl
II . 2
IL 3
II .4
ILS
Ir.6
Ir . 7

CHAPTER III

Introduction
X-Ray beanas
Polar ised X-ray s
Unpol a rised X-rays
COmpwn effect
S1Jl1lllary

Intr oduction
Scatte ring hy an electron
density distrihution
Represent ation oE sc atte r ed waves
8
Properties of the Fourier transforDl LO
Light
l3
Neut rons and electrons
lO
Sl.lrnmary

L5

PRINCIPIES OF STRUcrURE reTERMlNATlON


III . l Introduction
IlI . 2 Phase problell
III.3 Patterson f\:f1ction
III.4 Solution hy deducti on
III. S Trial - and- e rror s o lu tion
III .6 Resolution
IlI.7 Loss of i n fo rmation at l o,",
Q values
III.a Chirality
III.9 Summary

vii

L7
L7
L8
LO
24
24

,.
27

30

viii
CHAP'JER IV

O{APTI!R V

s~'Y

39

lnt:roduction
Atoms
MOlecules
Molecules at l o w resolution
Anomalous scattering
Determination of dhlrality
5urnmary

'O
'42O

Introduction
5cattered intensity dist r i bution
Intensi ty at low Q va1ues
Solutions oi macromolecul es
Deduction oi molecular s tructure
Guin i er ' s la.
Snear ing
S~'Y

VII.S
VII.6

I n troduction
I ntemp1ecu1ar interfet"ence
Appearance o i di ff r llction pattems
Detennina tion of the Ilrrlll'lgenent
of molecules
Theories of g(rl for liquids
5wmnary

CflAPTER X

x.,

50
50

x.S
X. 6

51
51

O\1!.PTER Xl

56
58
62
63
Q(M'TER XII

72
73
75

76
76

80
85
86
87
87

89
90
93

In troducti on
In tensi ty distrillution
Di ffract ion geomt.ry
Detennination of cry stal
structures
Symmetry
Summary

Xl. 2
XI. 3
Xl. 4

Introduction
Powder method
Crystalline fibres
In terpretation o f crysta1Line
flbre patterns

XI. 5

S~'Y

119
119
125
129
13 1
133

134

lO'
136
139
141

RELA.TlOOSIlIP ro HICROSCOPY
XII . l In troduction
XII.2 Fourier transfo rmation ~d
microscopy
XII. 3 Atomic reso1ution
XI 1. 4 Electron micros copy and
diffraction
XII . 5 SU!IIIIary

64
65
70

9'
94
102
107
110
115
117

CRYSTALLINE POWDERS A....p CRYSTAlLINE FIBRES


:0. 1

54
54

Int.roduction
Ccn t inuous helix
Discontinuous he l ix
1obl ecu1ar helix
Ne matic organisation
SmecUc organisation
SUl!lIIlary

THREE-DlMENSIONAL CRYS'IALS
x.l
x.2
X. 3

4J
45

(NE-OlMENS l OOAL CRYSTALS


VIII. 1 In troduction
VIII. 2 lnterference effects
VIII. 3 Formation of the diffract ion
pattem
VIII. 4 I ntensi ty of the laye r lines
VIII. 5 Deduction of eleetron density
VIII. 6 Bragg's law
VIII. 7 Disorder
VIII . 8 Mosaie spread
VIII. 9 Lorentz corre ction
VIII.IO S~ry

HELlCE5 ANO LIQUIO CRYSTALS


IX.1
[x. 2
IX.3
IX.4
IX.S
IX.6
IX . 7

33
37

UQUIDS AN O AmRPHOUS SOLlOS


VILl
VII. 2
VII.3
VII. 4

CHAPTER VIII

31
31

IDEAL GASES ANO SOLUTIONS


VI.1
VI. 2
VI. 3
VI. 4
VI . 5
V1.6
Vl. 7
VI.8

OfAPTER VII

Int:roduction
EloIald sphere
Q-space
5illlu1ation by oplica! diffraction

ATOMS ],NO K)LECULES

V.l
V.2
V.3
V.,
v. 5
v.6
V. 7
CHAPTER VI

CHAPTER IX

OIFFRAcrlaq GEOMETRY
IV.l
IV . 2
IV.3
lV.4
lV. S

ix

Contents

Content.s

142
142
145
1 47
151

BIBLlOGRAPHY

152

INlEX

1 57

CHAPTER I

Scattering by an Electron

1 .1. I ntroduction
X-Ray diffr.ctlon l a usad to inve stlgate the structure ol matter at t he qolecular level.
Probabl y the mast common applicat i on ls t a d et ermine the poaltions
o f atoms in c r ystal s .
If thea8 atoms are chemic ally bonded ta each o ther, t he
technique yields the posit l ens o f the atoms in a malecule le. the mol ec ular struct ure.

The determination o f molecular structures in thls va)' 18 a r o ut!ne p r o ce-

dure in cheDistry and , inc r easingly, in b ioehemi stry .


Bowaver , t he t echnique of
X-ray diffractlon 15 far more versa t i ! e than th is common applica tion might SU9gest.
Useful data can be obtained from a wide variety of stete s a f matter and the analyala of these data 15 not reatrlcted ta the determlnatlon of molecular structure .
Applicatl ons include invest i gation ot the ~ran9eme nt of atoms and mol ecules
i n varLous phases and i n sub-microscopic s tructures which are a ssemblie s ot molecules.
Examples are p r ovlded b y the lnvest i qa tion o f t he struc ture of l iquid s by
physic lsts and of the preferre d orienta t ions o f polymer mol e cu les ln fibres a nd
tlIm. by maeerlals scientists.
Biologlsts use X-ray diffraction to determine the
a rranqements o f molecules ln 8u ch compllcated ane diver se ay stems as mu s c l e , vlruses
and cell membranes .
technique can a 1so be used a s a s imple and rapid methad f or identify lnq unReference X-ray diffrac t ion pat t ern s a re r ecorded from a range
of s~le . and t hese are compared v lth t he pattern from the unidentified substance .
!he s ubstanoe 15 identifl ed if Lts pattern coincides with one of t he re ference pattems.
Thi s procedure is a common analytica l method for identlfylng t he chemical
composit i on o f microcrystal s in povders and ls frequently used for this purpose by
enemists and geol ogists - lt i 8 even somet lmea used by pathologlsts who wlsh to
identify the crystalllne deposita vhich appear i n certain disease s ego sadium ura te
which i s deposi ted in cases o f gout.
The

known 9Ubstances.

X-Raya are scattered by the eIectrons in matter; t his chapter deaI s with these
aepects of X-ra y seattering by an electron which f oem t he foun dation f or the &naIysl. of X-ray di ffr actLon patterns from real syste~.
Although scattering by elec trons and atoms ceuld be rega rdad as a problem ln quantum meeh anics , the quan tum
na ture of these phenomena will l arge ly be ignored here - exc.pt that the shortcomings of cIasslcal theory viI I be noted where neeessary .
Clas si cal theo r y pr o vides a . i aple phy sical pletur. ef the .catterlng procesa whlch is in. surprisingly

X- Ray

D if f ra~tion

Scattcri ng by an El ectron

>-

>-

ELEc.TR.rc FIEL!) OSC l lLATrNC


I N THE XZ PLANE.

"'Zw

>Z

Fig. r. 2 .

rS4- PM

Fig. 1.1 .

WAVE L E~CT~ ----..:;::..

Intensity of X-rays from a typical generator as


a fun~ t ion of wavel enqth; the wavelenqth of Ka
X-ra ys produced w1th a copper anode 1s marked.

good agreeme nt wi t h quantum mechanics and , more importantly , experimental obser vati ons.
1.2 . X- Ray beams
In this book the X-ray beam which is incident on a specimen will alway s be considered te be monochromatic ano collimated: p r oduction o f such a beam i8 reascnably
simple.
F i gure 1.1 show$ t he intensity oI the X-rays produced by a t ypical generator , with a copper anode , as a function o f wavelength.
X-Rays e mi tted w1th the
"characteristic" wavelength5, marked Ka and Ka in the figu re, a re considerab l.y more
i n tense than the r adiation at other waveleng t hs - the so- called 6bremsstrahlung " .
An ef f ecti vely monochr omatic beam c an be obtalned by filte rlng out t he Ka X-rays
with a s heet o f a suitaole metal foil - nickel in the case oE X-rays generated at a
copper Anade o
(This f ilter exploits the sharp discontinuity i n the absorption coefficient of nickel - its -absorption edge - - which occurs at a wavelength between
those o copper Ko and Ka X- raya: further details ar e q i ven i n Se ct i on v.5. )
The
r esul t ing monochr omatjc beam can then be col limated by a series of pio-holes which ,
typical ly, have a diaceter of around 100 ~m.
Details of the appara tus used for X-ray di ffraction expericents are beyond the
acope o f t his book.
Such details are a lready widely available ano, with t he except ion ot the cameras and dltt r act ometers used to reco rd diffract i on patterns f r om
singl e c rystals, the apparatus is conceptual ly very simpl e.
An i dea o f th1 s concept ual s i mplicity can be gai ned froo Figs . rV.4 and 111.6 of Sect.LQ't Iv . 3. The descr iption in the preceding paragraph wa5 i ntended mere ly to give some indi catlon o f
the lllethods which are adopted.
SUitable beams can alao be obtained by foeusing the
x-rays usi ng e ither of two different methods.
One expl oits the total internal

Polar1sed X-ray beam incident on an electr on .

r eflection o f X-rays i n air at suitable sur f acesl t he glancing ang le at a glass surt ace f or copper 1<0. X-rays is Q. 25 0
The other exploits "Brag9 reflection by a
c r yatill (sect ion X.2).
A c r ystal a150 acts as a IOOnochromator since X-rays with
cUffe rent wavelengths are " reflected " at different angles; t hus Ko. and Ka radiat10n
can be s epara ted and the Ko. line can even be aplit into its two closely spaced comrf the ref lector is bent, the beam can be focused.
ponents - Kal and K .
a2
1. 3. i'Olari sed X-ra ys
I n Fig. 1. 2 a singl e electron d e f ines the origin , O, o f a coordinate system .
A beam of plane polarised X- raya is inc idant o n thia electron and its direction of
propagatlon defines t he x - axi s.
lts piane of polarlsation , le. the plane in which
ita e Lectr i c vector oscillates, de fines too z-axla and the y-a xis i5 defined so as
te form a right - hand ed Cartesian coordlnate system.
The apparent azrbiguity in the
defl n ition of the z-axis (should it poin t up or down in Fig . I . 2? ) is of no concern
because the system being investigat ed has mi r ror symmetry in the xy pl aneo
Becau seof its electric charge, the electron osci l late s up and dovo the z-axis
with the same fr equency as the electric vector of the i ncioent X-ray beam conse quent l y it acts a s a source of X-rays itse lf since accelerating charges are the
source of e lectromagnetic r adiation .
lf E is the clectric field a t the elec tron
(where ~ acts up or down the z-axis) , at sorne instant in time, the force acting o n
This force can be
i t i s e~ where e i5 the electr on ' s charge (-1.6 x 10-19 ej .
equated with the mass, m, of t he e l ectron (9.1 x 10- 31 kg) multiplied by its accel eration - wh i ch is, therefore , (e/m ) ~ .
Since e i 5 negative , the a cce lerat i on o l
t he electr on is in the opposite direction te ~ thU5 the oscillati ng electr on , and
bence the X- rays it emits, are,. radians out of phase with the incident X-r ays .
The em1tted X- raya vill have the sane frequency as the incident heam - and, t here fore , the same vavelength.
The i nt ens ity of X-raya f r om the oscillating electron de tected by an observer
at P can be calculated fr om c l assical ele c t r odynarnics.
l f l o i s the i ntensity inci~nt . on the electron, the intenslty detected by the observer is given, i n SI units,

by

U. 1I

" re R is the modulus of the vector , ~. which defines the posit i on of P and vhich

Scat ter ing by a n E1ectron

X- Ray Dlffr act i on

makes an a ngle 'z with the z-axis ~o 15 the permeabi lity of free space ( 4~ x 10 - 7

H m- l ) .

Equation 1.5 de f i nes the Npolarisation f actor", p , of X-ray diffr<!lction ana1yA conventi onal X-ray . generator produces unpolarised X-rays ane so the 10wer
expression for p, in equation 1 . 5, ls usual ly applic able.
Hovever, an unpola rised
beam of X- rays may b e partially plane polari sed by a cryata! monochromator .
SynchrOtron s and stor<!lge r inga , Vhich are increa8ingl y beinq e x:ploited as 50urces o f
lntense X-rays, also produce plane polarised radia t ion ; the X-rays are emitted by
electrons or pesitrons which a r e constantly accelerating beca use they a re moving in
a circula r path.
The speed of the particles, electr ons or pos i trons , in a syncbrotren or storaqe ring approaches that of l ight.

.!S.

Equa tlon 1.1 explai ns why ve are able to disrega rd the scattering o f X-rays by
the protons in matter.
The pr operty of the electr on which causes lt to act as a
secondary source, i n a beam cf incident X-rays , 15 its chacge .
We might expect
that t he protoo , which has 4n equal but opposite charge te that cf an electron ,
would have this SalDe property .
However , the mass of a proton (1 . 7 x 10- 27 Kg) la
very considerably greater than that of 4n e lectron .
Since I s 18 i nversely pr oportional te the square of the mass of the charged partlcle, the intensity of X-raya
p ropagated by an oscillating pr oton ia negligibly low when compared vlth tbat from
an electron.
X- Raya are propagated by the osci11ating electron in all directions ; t hus the
ele ctron can be con sidered to scatter the incident X-ray bearn.
lbeae scattered
X-rays are also plane polarised .
l t ia not in tended te prov ide any justificatien
f or thi a 5tateroent or te prove equation 1. L.
The scatter i ng of plane polarised
X-rays by an electron is the starting peint f r eID which mest of the analysia in t he
rest e f this book proceeds .
Only i n Section v.S wil1 there be any need to consider
the derivation of equation 1 . 1 any further .
1 . 4. Unpo1arised x-rays
lf the incident X-ray beam ia not polarised , its electric vector can, neverth e l es8 , be resolved into two components which are perpendicular to each other ; each
One component defines the zcomponen t t hen behaves l ike aplane polarised beam.
axis , as in Fig. 1 .2, and the other oscill ates in the y -axis direction , defined in
the same way as before - since they are perpendicular , they may be txe ated i ndepend ent1y.
Each independent component has an equal amplitude , and ~ence an equal intenaity , if the beam i 8 oomp 1e t ely non-polarised.
Since the overall intensity of
this beam is denoted by lo , each component has a n i ntensity af (1 o /2). Equ ati on 1.1
can then be app1 ied to ea ch component separately and the total scatt ered in tensit y ,
the sum o f the tvo results, is g iven by
2422.2
l s .. (Io/2 ) (lJo/4If) (e 1m R ) (nn

'z

2
+ s in 4>y)

(1. 2)

I f , i s the angle
R ."i th the y- ax:is a s in Fig. 1. 2 .
which R makes with the x:- ax:is , - then , from the properties of the direction 005ines
of P,

"""re 'y il5 the ang l e made by

cos 2, +

COS 2Q

+ cos2tz : 1

(1.3)

The angl e , will be enoountered frequently in the rest of this book beca use 1t can
be u sed to desc ribe the d irection of scatter1 ng with respect to the direction of the
incident beam .
From equations 1.2 and 1.3, it f ollows that
(1.4 )

1.5. c ompton etfect


According to c lasaical ele ctrodynamics , X-raya are acattered by electrons
witbout their wavelength being changed; quantum theo r y predicts a slight comp1ication .
In order to explain quantum effecta , it ia necessary to thinx o f the
X- ray beam as a stream o f photons .
Each photon has a n energy of hC/A where h is
Pl<!lnck ' s constant (6 . 6 x: 10- 34 J sl , c is the speed of electromagnetic vave s in a
vac uum 13 . 0 x 108 m s - l) and A i s the wavel ength of t he X-rays in the wave description .
Some photons col l i d e elast i eally with electrons i e. they do not lose
energy - re t u rni ng to the wave descri ption , A i5 unc hanged by scat teri ng . Another
photon may impart some o f its energy to an electron in a collision and consequently
th. re is an increase in 1.
This incr ease i s cal led the Compton effect.
Ho wever ,
it n.ver amounts to mor e than a few percent of A for the copper Xu X- rays usually
uaed fer X- ray d1ffra ction experiments .
X- Rays scattered without change of wavelength are coherent Le . if a n i nc ident

beam i6 scattered by several e lectrons, ther e i s a de f inite phase relationship bet ween the scattered waves ; Compton scattered X-r a ys are i ncoherent .
Interferenc e
cannot occur between i ncohe r e nt X- raya ana so, in general , it ~ight appear neces sary te determine t he propor t ion of the i nc ident beam scattered by each process;
in practice such a ri90reus approach i s unnecessary .
In this book it ia assumed that, in an assembly of electrens , each ene scatt e ra X-raya without a change of wavelenqth; physical optics then predicts that the
r eaultant scattered beam, from sorne systems, contains a proportion of incoherent
r ad iation.
The re sults from this approach agree with those from quantum t heory
tor ~ greater than about 20 pm ie. fer all ....avelengths used in X-ray di ffr action.
lt might be argued that such a treatment is unsa t isfactory because it attribute s
80ae of tne incoherent s c a tter incorr ect l y .
Quan tum theery tel ls us that inceherent scatter can a ri se from t he interaction of X- rays vith electrons .
Class i cal
el.ctr odynamics predicts that this interact ion gives r ise onl y to coherent scat t er
~e incoherent scatter must then arise froro the properties e f t he re sulting wave s .
lthough thi s l atter approaeh may be considered unsatisfac t ory , it has the adva n taqe that i t is easy to apply .

The results obtained for real systems , u sing c l assieal theory , do no t di ffer

fr~ the' predictions of quantum theo ry and are in aecord with exper ioental obserEquations 1 . 1 and 1.4 diff er o nly in the form of a trigon~e tric factor which
depends on the state of pol arisation of the incldent X-ray beam.
Rence they can
both be combined in the genera l form :
',. 1

(u

/4rr)2(e 4 / m2 R2)p

, polarised
p

, unpolarised

II .5)

vatlona.
"Quantum theory has not made the earlier t heories and t echn iques superfluous; rather it has brought out their l imit<!ltions a nd defined thei r range of
~al Ldity" (H. Born and E . Hel f , PrincipI es of Optic s" , 5th ed ., Pergamon Pr f!!SS
975 , p xxi).
Further d1scussion cf this topi c and a detailad compariaon e f t~e
quantUD..""I!Iechanlcal and classical approaches are given in t he book by J ames (see
BIBLIOGRAPBY Saction 2) .
lt i5 interesting that there will be negl i gible i nco her'ent scatter from the e lectron s i n a cryat al because of it s regular, r epetitive
atructure.

X- Ray Diffraction

1.6. S1\TOOl" ry

X-rays are scatte red by the electrons in matter.


Classical electr odynamics
can be used to calculate the scatter froe a single electron: scattered i ntensity
depends on the intens lty and state of polar isation of the l nc i dent beam .
The expresslons f or scettered intensity , for unpolarised and p lane polarised X-rays, dlffer only in a trlqonometric factor which ls usually referred to as the polarisatlon
fac tor .
SOme of the X- rays scattered by en electron are incohere nt , accordinq to
quantum theory, but t his comp licetion may be neqlected in practice when dealinq
with r eal sys te ms.

CHAPTER

[J

Diffraction as Fourier Transformation

11.1. Introductlon
If X-ray diffraction ls to be applied to understand l ng the structure of catter
at the molecular l evel , it ls necessary to develop the theory of Chapter 1 to dea l
vith assemblLes of very many electrons.
The str ue tural information provided by
scatte red X-raya coneerns the distribution of electrons since it is the electrons
in aattar which acatter X-rays.
50 far only scatterLng by a single electron has
been considered.
When an assembly of electrons scatters X-rays , i nterferenee
effects are llkely to occur .
lt is the se lnterference effects which lead to the
features of the diffraction pattern.
1[. 2.

5catterlng by an electron density dlstributlon

In Flq. 11. L a paral lel beam of monochromatic X-rays,


dant on a body.
A fraction of this incident beam will be
angle. .
Th~ point O 1s an a rbitrarily def1ned or1g10 on
Unit vectors
ano. ~ are defined by the directions of the
scattered through an angl e ~ , respe ctively.

&

of w8velength X, is ioeiscattered through an


the scattering body.
i ncident beam and that

Initially consideration of scatter will be restricted to that froro a volume


ele.ent , 6r, at a peint P; the positlon o f P in Fl g . 11.1 ls defined by the vector
~.
There-wll1 be a path difference between waves scattered throuqh ~ by e lectrons
at P and O of

and hence a phase difference of

<2'11 /X ) !.. <& - ~)


" vector

2.

is defined by

2. (211' /1,) <& -

~)

( H. l)

so that the phase difference simply becomes

~ .2.

Now lf there were only a single electron a t P the vave scattered by the

vol~

Offrac tion as Fouricr lransformation

X-Ray Diffraction

INCIDENT

8EAM

SCATTEA:EO

6EAM

Flg . II.l.

Scattering by

<'.lo

body.

element wou l d have an amplitude oE


Aa

p; (uo/4~)

Flg . Il.2.

(e / mR)

according ta equat ion I.5 ",here "o 18 the amplitude af the inc ident X- ray beam.
Note that t his result follows from equation r.s bec<'.Iuse th!! intensity oE <'.lo wave la
g i ven by th!! square af lts hl? litude.
(Tllis 15 not strictly true for the reb.t ionship between the QOdulu8 o f the electric vector and the lntenslty c f an electromaqnetlc wave. For llOre d e t<1li ls of why the approach adopted here ls valid see Sect ion V.S . )
If p{~) 18 the e l ectron density at P the number 01 e lectrons in the
volume e l ement ..,11 1 be p(~) o ~.
Sinee interference effects are belng con s i dered,
amplitudes of waves haya to be a dded - with regard ta phase differe nces.

The

electrons at P a11 ha ve the same posltlon ln spAce and so t he X-rays they s c atter
ln a given dlrection v i ll be ln phase.
Hence the amplitude scatter ed by these
electrons ls

Now that both the aroplltude ano phase of the wave scatter e d thr ough an angle
lt may
be represente!!! by

Thus , f o r the purposes of this book, the resulta n t wave scatter ed through an
anqle ~ by a body can be represented, both i n ampl1tude and pllase , by

F (~)

2
0 e
- , o P, "
"4 nmR

~ by

the entire body ls the n qive n" by

dr

(11. 2)

v here the limits of ln tegration are over the enti re voiume of the s catte rlnq body.
11.3. Representation of scattered vaves

Equation 1].2 l ncorporates the dependence of the scatt ered vave on a nuzbe~ of
facters vhic h are uSl,lally of llttle concern.
The quantltles e, m and \.L o are fundamental constantS the appearance of R smply takes into accaunt the inve r se
square dependence af intensit y on distance.
Aa acts only as a scale factor. All

p {!.) exp ( i

!...2.)

dr

(1l.3 )

12.1 -

(41T/~) sin (4'/2)

(Il .4 )

If the inteqral a f equatlon 1l. 3 were evaluated l t 'llQuld , i n gene:t:al, be a


coaplex number of the form A exp ia .
The modulus, A, cf thls complex number repre sents the "amplitude of the wave and ~ ft s phase.
Note thllt
A

p {r)
r. n )
_ e xp (1 _lIL

,.,

Equation 11. 3 follows from equation Il. 2 t he lnteqratlon is ayer the whole of the
8cattering sample.
Two parameters, 2. and " have so far been used ta describe
t he direction of the scattered beam and it ls essential to relate them .
Figure
1l.2 shows 2. as defined by equation 11.1.
I t is clear from thls figure thllt 2.
defines a 9pace whose orlgin 1s at O', whlch 15 dlstant 2w/~ f r om the or iqin , O,
of "real" space, and that

; , by the volume element at P , a re known the wave ls compl etely speclfied.

The re sultant wa ve scattered through an angle

oefinition af 2.

al these facters can be ignored because , ln thls book, onl y t he relat i ve lntensitles al the X- rays scattered In d i fferent dlrections by a body need be considerad;
in aany appllcatlons a f X-ray diffractl on lt 15 unnecessary to measu~e scattered
intenslty on an absolute scale.
lf the polarlsaclan factor, p, 19 s ufflcientl y
dlfferent from unlt y, it 15 usual to correct the observed data t o reaove lts effect.

exp la -

cos a + 1

ao that the lmag lnary part of


the phase.

F ( ~)

sin a

divided by t he real part yields the tangent of

The intenslty o f X-rays reaching a unit area of detector , ln a g lven time ,


depends on the power transmitted by a unl t c r oss- section of t he bea.m .
For a wave
vhich is represented by a complex number, F(2.) , this intensit y la given by
, (2) P- (2), vhere p. 1. the complex conjugate of F.
Thus i f 1 c.~.l 1& the !!!etectad
-ray lntenslty scattered throuqh an angle ,

X-Ray Diffraction

10
1 (2)

=o

(Il.5)

F(1() F(~

rE the inteqration of equa tion 11 . 3 15 taken ayer all space, then F(~) 15
called the Fouri er transform of p(r) .
When this equation was derived, the scatter10g body vas considered to "be the ~ly source of electron density in accessible
space~ hence integration Qver the extent of the body 15 the same as integration
oyer all space.
Thus F (2) may be considered to be the Fourier transform of p (E,.)
In consequenoe the properties of the Fourier transform may be used to explain the
properties oE scattered waves.

"z

[1.4. Propertie s o i the Fourier transform

In t his section 1 shal ! simply list sorne properties of the Fourier t r ansform o
No proofs are given, either beca use these properties follow simply frem the definition of the transform or because they are g1ven elsevhere; the book by Champeney
(see BIBLIOGRAPHY Sect10n 4) 1s a part1cularly useful source of proofs .
For the
p urposes of th1s sect1on, the Four1er t r ansform, F(gJ, of a funct1on, p(~}, is defined by
F(Q)

(~)

exp

(i

~. 2.)

0-.

"'"

-0-2
Fig . 11 . 3 .

The simplest properties concern addition and rotation.


lf two functions are
added the transform of their sum i6 simply the sum of the transforms of the two
functions.
Note that in general F (2.) w1l1 be a complex numbe r so that addition of
Four ier transforms involves mainta1ning the correct phase relationship bet ween them.
The need to maintain this phase relationship a llovs the transform to be used te represent a wave.
Rere the addition p r operties of F(2.) coincide exactly with the
"PrincipIe of Superposition" as described in elementary text- books dealing with
vave phenomena.
If a function is rotated , then an equal rotation . in the same
direetion about a parallel axis, has to be applied to its Fourier transformo

lE equation 11.6 defines F(g) as the Fourier tcansform of p{:) , then the

~n

ver sion theorem sta tes that

F (2) exp ( - i E. Q)

~~

:JC

(lI.6)

dr

where s at the foot of the integral sigo denotes iotegrat10n over all space .

..

P (E)

11

Diffraction as Fourier Transformation

dQ

(11. 7)

The funetion sine x.

Suppose p (!..) depends only on r , the modulus of E! and i5 indepe nden t of its
dLreetion.
Since roost of the applieations de5cr1bed in thls book vill involve
three-dimenslonal exalllples of p (r) , it viII then have spher1ca l symmetry.
This
spherieally symmetric electron d;nsity can be represented by p(r) and it turns out
that F (~) depends only on the modu lus of ~ and not on 1ts directlon.
F(2.}, the
spherically symrnetr1c Fourier transformo i5 then g1ven by
F(Ql

la'"

sine x

4nc
-1

le

p {r ) sine

(Qrl dr

(1 1. 8)

sin x

The funct ion sine x is plotted in Fig. 11.3; its values can be either pos1tive or
negative.
Note that F(Q) is no longer eomplex but it 5tl11 conveys phase information.
In Section 11.3 F(~) was r epresented in the form

The integral in equation 11.7 is often termed the i nverse Fourier transform, if
equation 11.6 defines the Fourier transform o
Str ietly the integral should be mult iplied by (2n)-3 when it appl i es t o a three- dimensiona l spaee .
I n Section 1 11 . 3
it was stated that, in this book , F(Q) w1l1 not be eonsidered to be measured on an
absolute scale.
Thus equat10n 11.7 v11 1 not re turn p(~) from F(Q) on an absol~te
seal e - so that the scale factor of (21f) -3 whieh a rises on inverse transformation
viII be neglected in the rest of this book.
l t makes no difference whic h of
equation 11 . 6 or 11 . 1 is the form of integral defininq the Fourier transforw s~nce
the other automatieally becomes the inverse transformo
80th equations 11.6 and
1 1. 7 have the sama properties and fo r many purposes it does not matte r wh1 c h 1s
used.
The tillO forms of integral differ only in the sign of their phases.
Thus
p I ( ~) calc ulated frem
p ' {!..) ,.

F (2.)

exp (i

~.~)

d~

dlffers from p (r ) . caleulated uslng equation 1 1.7 , o n ly in that one 1s lnverted ln


the orig1n with-respect to the other .

A cos o + i A sin a
but here F(Q) i5 real so that
A sin a

0=

Th1s conditlon ls only met if a is g1ven by


o = nTT

n=0, 1:1, :!:2

Since phases are measured by t he displacement of one wave relat1ve to a nother, a


r eal value o f F{Q) then i mplies a p hase of zero or TT rad1ans.
(Throughout this
book phases vill be measured vith respect to a vave scattered wlth a zero va lue of
Q. )
If the phase ls zero then A cos o is pos itive and hence F(Q) is positive;
if the phase ls n then A cos a i5 negative and he nee F (Q) ls negative. Thus, for
a spher1eally symmetr1e p ( r ) , F(Q) w11I always be real and can be posl tive
(corresponding to a phase of zero for the wave seattered in t he direetlon
speclf1 ed by Q) or negat1ve (corresponding to a phase of n).

X- Ray Diffraction

12

Diffraction as Fourier Transformat i on

13

' ,0

T
"

.....0

O"

(}2

O
Fig. II.5.
- (}2

TIlus p (!.) ls smeared out in a way which ia dictated by the forro of rj(r ) .
Equation
11. 1 1 ls particularly easy to understand physlcally if Ve::) is non-zero only at a
.. t of polnts.
Figure 11.5 ShOW8 a two-dimensi onal example where the convolution
operation consists simply of 8etting down p (::) with its or igin at each o f the poi nts.

- (} 4

Fig. II.4.

The function J

(x).

n. 5. Light

In Chapter IX SOlDe cyl indrically symmetric systems will be encountered; in


these systems p(r) 19 independent of the dlrection of r in projection.
The
Fourier transfoim of these two-dimensional projections-also depends only on the
modulus of ~ and not on its direction.
F(Q), the cylindrically symmetric Fourier
transform 1 5 then given by
F(Q ) ..

Jo'"

2nr p(r) Jo (Qrl dr

(1I.9)

Jo . ln equation 11.9, ls the zero-order Bessel function o f the first kind and 15
p l att ed in Flg. I1.4.
The 8essel function of the first kind , of arder n, may be
defined by

Jnixl -

m-o

( _ U m (X/2)n+2m
(II LO)

m!

(n + m)!

In general the series oE equation 11 . 10 does not converge rapidly and this function
is usually cowputed uslng a recurrence relation .
Further lnformatlon on Bessel
functions appear s ln Section IX.2 ~nd ln the book by Watso n (see BIBLIOGRAPBY Sec tion 4).
Before contlnuinq, it 19 perhaps worth noting that. just as a spherically symmetric function could be consldered as a series of concentric spherical
shell s, so a cylindrically symmetrlc function could be considered as a series of
coaxial cylindrica l she11s.
If two functions are multiplied, then the Fourier tranaform of their product
is given by the convolution of the Fourier transforms of the two functlona.
The
convo l utlon of two functions p (!.) and ~ (::) ls wrltten p (::) ) 1Ji (!J and la defined by
pe::)

) 1jI(!.) ..

Two- dimensional example of the convolut ion of a


function with a set of poi nts.

J
s

p(~) 1#>(:: -~) d~

(n . U)

This section and the next a r e dig r essions from the main theme of the book and
may be omitted without 1055 of contlnuit Yi here the appllcatlon of X-ray diffrac tion theory to the diffraction of 11ght wil1 be discussed .
Since light is simply
el ectromagnetic radiation with a longer wavelength (0.4 to 0.7 ~m) t han X-rays, it
migh t appear that a separate section on its propertles 15 unnecessary .
However
the r e are t wo reasons f or consldering the behaviour of light ln some detail.
Pirstly , lnterference effect s observed when 1ight i5 scattered by macromolecules
and calloidal particles are commonly expl o l ted in polymer and colloid science but
the theory i8 often presented as if it were unrelated t o X-ray diffraction.
Secondly, for scattering bodies whose dimensions are much greater than the wavelength , A, of the scatt ered radiation, the theory breaks down for ligh t but not for
X-raya .
Since A for 11ght 15 of the order of 10 3 times greater than that of x - rays
t here will be no appreciable interference effects for scattering bodles which are
as large as small molecules ie. which contain several electrons .
Therefore ,
equatlon 1.5 may be written in t he form
(1I. 12)
where p 18 the polarisation factor and R 15 the distance of t he detector from the
8catterer as ln Chapter l .
Here ~o and c also have the same meaning as in Chapt er li they are both fundamental constant s whose values are given in Sectlons I.3
and 1 .5 .
(Note that most text- books which deal with 11ght scattering do not use
SI units and equation I1 . 12 is then slightly d i ffe r ent . )
Molecular polarisability,
a , re1ate~ t he dipole moment, ~, induced i n a molecule to the applied elect ric fie l d,
! . and is defined by

, aE " P

The phenomenon represented by equatlon 11 .12, le. sca ttering without interfer ence,

=
18 often called "Raylelgh 8catterln9~ after Lord Ray le1g h who publlshed ilccounts
o f its theo ry in the l ate nineteenth an early twen t ieth c enturies .

F'o r l arger IIIOlecules <1.nd col1oidal particle s , lnterference '0'1111 occur be t .... e e n
light waves scattere d in the same direct ion by different parts oE the same body .
I nterference effects may be calculated by the method of Section 11. 2 ; 6catterinq
frem a vo lUlDE' e lemen t o oS r , ls considered fi.rst.
l f V 1 s the volume a f the s cat -

teri ne; body, the mole cul ar po larisabi lity o f the e l ement .... 111 be

lf a does not vary over the body and , from equation 11.1 2 , t he amplitude of the
wave lt scatters in a given d lrection ls
A p~ (c2 ~ ) [wa 6 r/~2 RV]

By analoqy wlth equatlon 11. 2 , the resultant


wave s cattered by the entire body through a n anqle , wi ll be represe nted , both in
~plitude and phase , by

'",here Aa 18 the incident ampl itude.

dr

( II . 13J

where Q and ~ are related by equat ion 11. 4 .


Rere, as before, the integrat i on 15
te be t a ken over the entire scattering body - pos itions vithin the body are r epr esented by~.
When a pplied to light, this approach is called the Ra yleigh-OebyeGans t heor y (often abbreviated ta R.D.G. theory in the literature af collold
s c i ence) .
Although this t heo r y is effect i vely exact for X-rays it is an approximatLon
f or 11ght scattering .
In Fig . 11.1, l ight scattered t hrough a n angle , by dLff e r ent parts aE the body wil l have ta pass through diff ering thicknesses of it.
Sup pose t hat fo r two points t h e difference in th1ckness Ls t , then the r e wil l be
an opt 1ca1 path d1ffere nce of

betveen the light s cattered by t hese peints, where n and no are the refractive 1n dices of Che body a nd the surrounding rnediun.
Thi s path difference l eads t o a
pha se dif f e rence of
(2 rr t !) (n

15

Diffract on as l'our ier Tr a nsfo r rnation

X-Ray Di ffracti on

14

- no)

which has been ignore<"! until now.


For K-raya both n a.n d no wi1 l be so close to
un ity that this phase difference will be negligible .
s ut for light equation
11.12 i5 at best an approximation.
The a ppro xl oati on is only adequate i f n i s
not mueh gre a ter than no and the 5cattering body ls no t too lar ge .
Exact theories of l l ght scattering nave only been worked out for a few siBple Sh3peS;
details are given in t he book by Kerke r (see BIBLIOGRAPII'l Section 4) .
11. 6 . Neutrons and elect rons
Neutron and eleetron diffraction can be used as a lternatives to X- r ay diffr3 ction f o r invesc igating the structure of matta r at the molecular l evel ; the a im
of t hi s sect i on 15 te iruU cate how the theory deve loped so fU" can be appl ied to
these te c~~iques.
Pa rtic l ea o f mass m, movi ng with a s peed v, C3n be cons idered
aa a wave vhase vavelenqth ls given by

(II.14 )

). - h! (mv)

where h is Planek: ' s consta nt (whose value 15 glven in Sectlon 1. 5) .


Neutrons and
e l eetrons can be made to atta in speeds leading te wavelengths whlch are comparable
te those of X-rays.
Neutrons are scatt ered by atooLc nucle i - usually elastical ly l e . without loss
of ener gy .
The 1n tensity o f neutrons scattered by a nucleus bears no simple relat ionship to its a toroi c numbe r and is not the same for dl fferent Lsotopes of the
same elemento
In contras t the int ensLty of X-rays sca c tered by an atom increases
wlth the number o f e lectron s Le . with atomic number, also the scattered intensity
15 t he same f or differen t i sotapes of t he s&me element beca use they have the same
number o f electrons .
Neutron diffraction i5 thus complementary t O X-ray dLffraction - a particularly common application 15 the accurate deterrnination o f hydrogen
atom positions in molecule5 since these atoms contain only a single e l ectron a nd
consequently are very we ak X- ray scatterers.
A nuclear react or Ls a suitably intense source of neutrons for diffrac tion
experiments; facilit i es f o r neutron diffraeti on are ava l1able a t rea ctors in
England, France and the U.S.A .
Eaeh degree o f t r ans lational fr eedoc of the neutron
l s associated ..dt h a DQst probable energy of k eT/ 2 vhe re kB 15 BoltzlI'lann' s consUlnt
(1.4 x 10 - 23 J K-l) and T i s a temperature measured on the Kelvin sc .. le .
Since the
neutron has thre e tra nslational degrees of freedom lts klnetic enerqy 1s given by

(Il . 15 )
whe re now v is the roo c-mean- square v elocity and ID is the mass of the ne utron
From eq uations 11 .14 and II.l S, t he wavelength of a neutr on
(1. 7 x 10- 27 kg ) .
belllll is g iven by
). '" h/ (J!tST m) '::!

The temperat ure o f the neutrons from a reactor is typ1cally of the order of lOOoC
thus A 15 af the a rder o f 0 . 1 1llIl .
Eleetrons are scattered by e l ectrostatic fie l d s in the ma tte r of the 5catter 1ng body.
A suitable beam is provided by acceleratlng the electrons through a
potential differen ce , V; the y then acquire kinetic energy of
mv 2 !2 "' Ve

(II .16)

where e and m a r e the c harge and rest mass of an e1ect ron as in Seet ion 1.3.
equations 11. 14 and 11.16 the wavelengt h o f an electron bearn i5
( II.l7)

1. = h/ (2Vem) 1:.

l f the electron 1s accelerated through 10 kV, it s wavelength l s o f the ord er of


0 . 1 n~.
In practice an electron microscope i5 the usual source o f e l ectrons for
diffraction experiment s ; further detail s are given 1n Sec tion X11.4.
Typically
this instrument accelerates e lectrons through 100 kV and so their wav elength ls
ahort compared with eg o eopper Ka x-rays .
The methods of this chapter are applicable to weak, elastic scattering of
neutrons and electrons.
Equation 11.3 t he n takes the general form

F(~)

v(!..) exp

(L

!:2.)

dr

(I I.181

16

X-Ray Diffraction

where V(r ) 18 sae appropriate scatterlng potenti al function.


Comparison of equatiORS ]I~2 and II . 3 showa that the l attar neglects the fundament81 ccnstants whlch
place F (2.l on an absolute ocaleo

A simi lar neglect 1 5 involved ln equation 11.18:

a dtfferent aet of constants has to be used f er X-rays , neutrons and e lectrona because the underlylng physlcs oE the scatterlng procesa la different ln each case.
Equat lon 11.18 represents an aPPrQximate theory whlch ls ooly adequate f or
weak Bcatter inq - the Born approximatlon.
This approximation la analogous to the
Raylelgh-Debye-Gana theory ef l ight scattering (Sect ion 11 . 5).
Tbe R.O . G. theory
la a r easonable approxiaation for amal l scatterers when n l a not very ~ lfferent
freD no
Light scatt e r ing intensity is rela ted to t he oolecular polar 18abll lty,
a , of the scat terer whlc h in turn 18 r e l ated t o n, tor molecule8 ln the gas phase ,
by

CHAPTER 111
a _ (n 2 _ll!N

Principies of Structure Determination

whe r e N ls the m.mer ef scatterer 8 per wlit volUIIle .


Bence ",hen n ia not very
dl f ferent from
the scatterlnq la weak and the R.D.G. theory i8 se en to provide
an exan:p l e of the Born approximatlon tor vea}( scs.tter ing .

no

11. 7. 5lUlmary

111 . 1. lntroduc tlon

I nter feren ce effects occur bet"'een X-rays scattered in the same d lrec tlon by
dlfferent electr ons in a scatterlng body.
Tbe scattering dlrectlon 15 def ined by
a vector 2 who se modulus 18 a function of scatterlng angle .
The re 8ultant beam
scattered with a glve n 2 ls repre se nted, both ln ampl itude and phase , by F(2l _
the Fourier trans fom o f t he electron density, o(r }.
When thi s beam 15 detected
its i nten s ity a t the de tector i8 glven by F(2)F" (Q:l Where F* l s the complex conju:
gate of F.
Recognltion that the scattered vaves may be represented by a Fourier
transform a llovs the pr ope rtles o f th18 function to be used to expla in d lffraction
effects.

The previous chapter descrlbed how te calculate the resulta nt X- r ay wave scat t erad ln a particular directlon from the electro n denslty dis t ribution o f a scatter 1ng body.
However the only means available for investlqating th1s e lectron dens1ty
dlstr1butlon , p (rl . 1s by the ..,ay lt scatters radia tion .
ThU8 the a1lll o f An X- ray
diffractlo n expe;iment 15 tO . easure F (2} , whlc h represents t he scattered wave , eve~
space defined by many 2 vectors , and hence te obtain lnfermat10n about p (~) .
Thus the previous c hapter considered the technique in reverse .
In al l appli catlons of X-ray diffraction one seeks to gain information about p (~l from F(~) ;
the aim o f the present chapter is to inve stigate the probl ems which then ari se.
These problems vl11 be con s i de red very gener a lly withou t undue regard elther t o t he
particul a r state s ef .att er which might be investl gated in a n X-ray diffractio n experiment or to any speci f ic applications.
X- Ray d.iffractien experiments may be performed elther to measure P (r) or to
answer some r estrlcted set o f questions about its form; this chapter l s concerned
predomina ntly with the f lrst kind of application .
Measuring p(r) amounts to deterc1nlng a s truc t ure.
8igh r eso l ution measurement of p(r) gives pasitions of a toms
ego in a molecule.
At lower resolution p(r ) shows the-posi tions o f mol ecule8 .
X-Ray diff raction can ansve r more r estr icted kinds of questions - two examples
follov.
One: are the polymer molecule s ln a r esin or iented (i9 p(r) anisot rop1c)7
'l'Wo:
dees a sampl e of c ry8t als consist of eg. sodium ura te (L8 p (r)-the same as in
sodium urate c r ystals)?
Some i nd1cation of the variety o f application s app eared i n
Saction 1.1 - but it may not always be clear how te categorise a problem..
Nevertheless soma restric ted questions may be IOOre easil y answe red than this c hapter
might imply, answeri ng s uc h questl on s usual l y depends on understanding the difErac tLon properties o f partlcular s ystems as d escr ibed i n Chapters VI to XI.
IIl.2. Phase probl ea

At f i rst aight it might appear that the lnversion property of the Four ier
described in Saction 11.4 , prevides t he key to t he problem of calculatlng
P (!..} from F(2).
Given the definition oE F {~.> l n equatlon Il. 6, it follows froID
thla property that
transfo~ .

17

18

Princ ipl @s of Structure Oetermi na t ion

X-Ray DiffractLon

p (!:.)

F (2.) exp (-1

!o-R.'

dQ

f,

(III.l )

pl!.l ) p (!.. + !.l)

d~

19

( IIl.l)

necessary te know whether tt 15 pos i tive or negative te apply equation 111.1 (see
Section 11 .4) but this lnformati on la lost when I{Ql is measured .

This operation produces a function which has high values whenever h1qh value s o f
pe!) ) and p {!.. + El) coincide.
Bl qhest peak s occur when ooopLete overlap of the
two functions occurs.
Thus the operation ueasures the correLation between a function and itself translated .
If p (r) repeats itse lf regula r l y it w111 coincide
with itself , with the repeat periodLcity, when translated past itself .
Thus autocorreLat i on provides a sensitive method for the analysis of periodlcities in pic tures - such as e l ectron microqraphs - where p(r ) in equation III . J represents t he
tve-dimensional distribution of qrey levels in the "black and white " p1cture .
(It
is perhaps surprising that equati on 11.6 , vhich involves more computational steps
t han equation 111.J, is so frequently us~ for this purpose by electron microscopists. )

Since only the modulus of F(Q) can be measured, it is only the ampl itude and
not the phase oE the resul tant X-ray wiI:!Ive scattered in the directien speclfied by
.Q. .... hich c an .be obtained.
Hence the phases of the scattered X-rays are lost IoI'hen
a diffraction pattern i8 recorded .
This loss of phase information constitutes the
so-called "pha8e problem " of X-ray diffraction analysis.

A successEul X- r a y diffraction experiment always yi@lds l(~) even lf F(~) cannot be completely specified.
What happens 1f l(~), which can be measured, is subs t ituted f o r F(Q) , whi ch generally cannot be, l n equatlon II I.l ?
The re sulting
inteqral i$ usually calLad the Pat terscn function , P (!.) , and is defined by equat ion 1II.4

Equation In . l 15 identlcal te equation 11. 7 but 15 reproduced he re because lt 19


essentlal te the argumenta ef this chapter.

A probleo arises ln that only the modulus af P QI can be obtained from a diffra ction e~periment and, in consequence , equation 111 . 1 cannot be applled directly
te caLC"Ulllte p (E.)'
The reason ter this difficul ty 1s that an X-ray detector, be
it a photoqraphic fi ~ or a counter, mea sures the lntensity, 1(2.', as deflned by
equation 11.5 .
In general F eQ) will be complex and measurement af 1 (2.> does not
all ow lts rea l and i~a9inary parts te be separa ted .

Even when F(Q) 18 real lt 15

What i5 t he physical reason for the phase problem?


For X-rays wit h a vavelength ~ - 154 pm the time period of oscillation of the electric vector is
19
5 )( 10s.
A detector of practical sensitivity loI'i11 then obtain information
over a time covering very nany oscillations.
It viII there fore be insensitive to
when the vaves arrive at the v aricus peints over its surface and therefore te the
relativa phases c f the resultant waves scattered in different directions.
The
only vay te rneasure these phases would .be by inte rference with a reference beam .
SUch an interference method requires a coherent X- ray SQurce , ego an X- ray laser,
but such a source has yet te be developed.
Determina t ion of a structure by x- ray diffraction thus amounts to overcoming
the phase problem so that, at least in principIe , p( r) could be calculated froro
the compl etely specifled F( ~) .
There a re tvo appr~ches to overcoaing this problem and hence so Lving struc tures: deduction or trial-and-error.
Before each oE
these approaches i5 considerad in detail it is worth describinq the properties of
a use fuI function - the Patterson function .
I II .l . Patterson func tion
The cross -corr elation of tvo real functions P{~' and ~(~) is denoted by and
defined by

P(!.l)

"(~ + ~l)

dE..l

iIII.2)

Note the 8imil arity to convolution a s d@fined by equation II.Il.


Th@ only differ ene@ i5 that , ln the convo Luti on operation , ,(r +!J ) is replaced by ~I~ - El)'
The two operations are of course equivale nt if-~(r + El) and ~(E. - El' are the 5arne
ie . if ~(~l l s an even function or can be transformed to one simply by translation
a l onq the d.1 .rection of !J. .
By an~llo;y with equation 111.2 , the autocorre l ation of pi!.) i5 defined by

P(!..)

f
,

I (Q) ex.p ( - i

!: ~) d~

F(2.) F - (2.) exp (- i !.. 2.)

(III.4)

d2.

[eqn,II.5)

The final line is a property of the inverse transform of F(2)F (~) known as the
Wiener-Khintchine theorero which 15 proved in the book by Champeney (see BIBLIOGRAPHY Section 4).
Thus the Patterson function yields the autoco rrela tion of the
eLectron density in the scatterer .
The Patterson function i s particularly use f ul when a structure centains a few
atams of high electron density .
Consider wha t happens when p(E..) is translated
past ltself .
Any peak,s which a.rise froro the coincidence o f one of these atomic
pos1tions with another wilL dominate the autocorrelation function beca use the peak
height wilL then be given by the product of their electron den sities.
Hence the
autocorrelation functl on will be do~nated by periodic it ies arising frero the
positions of the electron -dense a t oms ie. the Patterson function essentially yields
a .ap of vectors between any electron-dense atoros.
Thus the r elative pasitions o f
these atoms i n a molecule may be deduced (using t he term "molecule" in the g ene raL
sense of an assembly of a toms as i n Section v . 3) .
111.4. SOLution by deducti on
If p(r) is to be deduced from an X-ray dif fr actlon pattern , some method l s required to deduce F(~) frem l(~) .
In q eneral this deduction will invoLve finding
the real and imaqinary parts of the complex F(R).
Two different approaches have
been adopted and both are convent i onalLy described in considerabLe detall in textbooks of X-ray crystal lography such as those recommended in Seetion 12 of BIBLIDGRAP~Y.
The adm of t h is section ls merely te compleroent these standard a ccounts
by drawing a ttention to how these methods re l ate t o the pr incipIes descr ibed in

20
'rABIE Ir!.1.

Alqoritlu!l for the "heavy atom" lIlethod


I {~l .

over a range of Q

l.

Collect exper i mental data ,


values.

2.

Calculate

3.

Deduce pas1tlons of electron-dense atoms from P (E.)

4.

Use positleos oE electron-dense atoms 115 first


approldllation to p (!.) .

P(~)

from

I(~l

usi oq equation 111 .4.

2.-

5.

Define an initlal vector

6.

Calculate

7.

Cal culate phase . a (2,l , o f t he compl ex F(,2.) .

8.

Calc:uLllte better approxima t lon te the complex F {W

F(~l

f r om p (!.) using equation 11 . 3 .

TABLH UI.2.

IncrelDent 2,.

2.

10.

lf

11 .

Calculate better approltimation te p (!.l from F (2,)

12.

1 11. 1.

repl acement~

I ( ~)

1..

Collect experi mental data,


a range o f Q values.

2.

Collect corres pondi ng dat a, ID(~)' t r oro der i vative.

3.

Calculate P(EJ frOlll ID(~) using equation Ill . 4.

4.

Deduce position s of electron-dense atoms in derivat ive


from P{r ); de note the contr ibution of these atoros to
the electron densit y of the derivative by P a(~) '

from specilllen. over

5.

Define an LnLtial vector 2..

6.

Calculate Fa (2.) , the contribut ion of the e l ectrondense atoms to the scatter from the derivative, from
PHI!) uslng equation 11 .3.

7.

Noting that the compl ex FO(~ i5 given by

within r ange cl experimental data 90 ta 6.

using equation

A1qoriUm tor the "isomorphous

The ambiguity in step 7 can be resolved if the whole process 15 repeated with a s econd de ri vative.
Each derivative yie l ds two sol utions; the one which appears in both
cases is the required resul t o

F(SP ., 1 ' (2,1 exp (1 a(~) J

9.

21

Pr i nc ipIes of Structure Determination

X- Ray Diffra ct ion

F O (R.) .. F (Q.)

lf better approxi matlon r equired 90 te 5 .

F H (SlJ

calcula te t he compl ex F (Il.) froto Fa (I), 1"(12.) and


la (!tI as in Fig. UL L
Chapter n .

B.

The fir st approach r equlres the p r esence of a few electron-dense IltomS in a


moLecul e.
1'heir pas1tions can be located by the Patterson function desc rl bed ln
Sectlon III.J.
Since 8uch electr on- dense atoms make an important contribution to
p(r ) they t end, ln favourable cases , to dominate the X- ray scattering and their
positlons can then be used as a f irat step in an iter ative solution of the phase
problen (Table II I. l ) which is called the "heavy atoo" method.
The "isomorphous
replacement h method can be used if electron-den5e atoms can be attached to a specimen without disrupting its s tructure .
X- Ray diffraction experiments perf ormed on
both the speciDen and tbis chuica l derivative can then be used to sol ve the phase
problem (Table 111 .2 and Fig. 111. 1). 80th "heavy atom~ and "lsomorphous replac ement" l'IethOOs are described i n considerable detai l in crysta110graphic texts and
there la little need to discuss them further here .

9.

Increment 2..
If 2. stl11 within range of experimental data go to 6 .
A

!'1

l ,"(g l

-<
~
~

l ",(g l

O~~~;;;;;;~R~E~A~L~A~X~15~===:~~

The seoond deductive approach i9 to recover the missing phase i nformation by


so-cal led "dlrect methods" .
Oirect methods are i llustrated here by a simpl e onedimensional example which shows how F(~) can be completely deduced frOP I(~) in
f avourable clrcumstances.
The electron dens i ty distribution along a l ine can be
r epr esented by p (r) - since a pei nt on the 11ne can be defined . with respect to
some origin, by a scalar r.
From equation 11.6 the Fourier transform of p (r ) i5
F(Q )

.. j

""p (r) exp

(i

r Q) dr

which. f or oux present purpose, can usefully be written i n the form

"

Fig. III.1.

Oetermination of F(~, by the method of i 50morphous replacement , shown on an Argand dia gram o F (2.) 15 rep re sent ed both in amplitude
H
and phase by OP. A circle of radius lO (2.) is
drawn with O as origino Another ci r cle of
radius 1" (2.) l s dravn with P as orig in o These
circles i nter sect a t 11 and B. ThU5 elther PA
or PB could r e present F(~ in both amplitude
and phase by sati afy in; t he r elation ship
FD( ~ - F(2.) + F U{2.>

..

Principles oE Structur e Determination

X-Ray Diffraction

"
r{Q) - l

:p<cl eKp

Jf

o r ) has

" P (- d

(1

r Q)

exp (- i

centre of symmetry

dr

rQ)

F(Q)

+l

'"'p(r ) exp

dJ:: + i

(i

Q) dr

oop (r l exp (1 rQ) dr

(111.5)

ls real; the problem of recovering the

lost phase l nformat lon then r.educes to find ing wher F {Q) 15 positive and when lt 15
negative - according to Sectlon 11. 4 .
For every teature ln a centrosynnetr i c p (r)
thece wl11 be an identi cal feature on the other side of the centre cE s Y!fllletry.
lE the centre of symmetry ls cho sen as the or191n, p{r) becomes an even funetien
ie. piel 15 identical to p(- el .
Equation 111.5 then becomes
""p(e l exp (- i r Q) dr +

F(O) -

'" 2

[ .p

.()

'"'Plr) exp (1 r Q) dr

OL-----~~--~L--f,.0~~~~15
Q(""'-t ) ~

(r)

cos

(1:: Q) de

(IlI.6)

Fl g. III . 2 .

The final form of equat i on I l1.6 f0110W5 t r om the identit y

An

observed intensity distrLbution 1 ( Q)

exp ( 1 X) ces X + i sin X

Accor ding to eGUatLon I11 . 6, reo} ls r eal when p(r) 1s centros~etric.


Tne
Four1er transforc 1.5 also r eal tor centros~etr ic functions in two and three
d imensions; the Fourier tra n s f orn of t he spherically symmetric functlon in Sect ion
11 . 4 delDOflstrates a spee1a1 case of this pr operty.
lt vas a1so explained in Sect ion 11 .4 t hat a positive value for F {Q) i mplies a phase of zero far ene scattered
X-rays and a negative val ue implies a phase o f To radians .

10

o
05

Figure II1 . 2 shov,s the one-dimensional I{Q) - ho,", can Lt be used to deduce
t he sign of F(Q)?
The f l rst peak in I(Q), whien oceurs when Q equa1s zero , must
arise ran a posit ive value of F (Q) .
The reasen ls, f rom equation 11.6 , that
1"'(0) .. 2

OOp{r) dr

which is positive because i t representa the number of scattering e1ectrons. Suppose t hat F(Q) 18 a sDOothly va rying function which never has a value of zera at
an y of its minina - whLeh 15 the case far the Feu rier trans f orDs of many simple
f unctiol'ls .
When I (Q ) is zaro , F{Q) must pass through the Q-axis ie. i t changas
signo
TRua the sleond peak in I{Ql must arise frOIll a nega tive value a f F(Q) .
lf F(Q ) changes sigo every time I(Q) passes through zera its f o rm can be deduced
with t he resu lt shown in Fi q. lIr.3; the phases carrespond i ng to the peak s and
t roughs are ~rked .
Phase$ are defined with respee t to a bean scatt ered through
a l:ero angle ~hieh. s1nee F {O) is ;:ositive, Ls defined te be zero.

- <>5

Oirect nethods ~re not con f ined to ane-dimensional or eentrosymmetrie cas~s;


the ezamp1e here vas chosen so that it wou ld be easy tO i11ustrate and exp1ain.
The methods Are mast simpl y appliad te centr asyrnmetrie systems but they have been
extended to diffraetion da t a from single crystals where this eondition does no t
app1y.
Once ~gain further detaila are g i ven i n text-books on X-ray ery s tallography.

Fi9. r ll.3.

~ oooa

.e

The Fourier transform, F(Q) , inferred froe the


observed intensity distri bution, I(Q}, of
Fig. II I. 2.
Phases aE peaks a r e markad.

23

X-Ray Diffrac t ion

24

Princ i pIes of Struc t ure_ Determination

25

The problelll wit h all deductiva l3et-hods of solving the ?hase problem 15 that

they can only be appl led in favourable cases .


Usually these favourable cases are
the diffraction patterns from near - perfect, three-dinens i onal crysta ls .
For Bueh
systems the phase problen 15 scarcely a problern at a l L - as 15 demonstrated by the
routLne deteraination af crysta l structures .
In Chaptar VI we sha ll see t hat the
deductive approach can a1so be applied te investigat ing the structures ol aolecules
in ideal gases and solutions - but here only the spherically averaged electron density can be deduced because of the natura of the specllJ1en.
Otheoo'se Lt Is only
in a very few speclal cases that X-ray diffraction data can be interpreted ~
deduction.

111.5. Trlal-and-error solution


The !irst step here i5 te i nfer a trial model for p (r) by inspectien ef 1 (5().
This approach te the preblem clearly require5 seme knowledge of the forms of the
Fourier transforms of functions which miqht resemble p{r), if lt le to be successfuI .
Calculation of the Patterson function frem 1 (5() ;;;ay also help in the deve l opment ef a trial modal.
From the trial model for p (E.) the expected I(5(J can be
calculated uslng equatiens 11.3 ane lI.S.
The observed and calculated I{5() are
then compared.
en the basis of this camparison three different oonclusions might
be reached .
One: reject t he model for p(!:.) as being unsatisfactory. Two: accept
the mociel.
Three: modify the model to improve the agreement .

[f the trial model is not re j ected outright the thlrd possible course of
action nearly always has to be adopted.
A new calculation of [(~) has then te
folloy and the oomparison repeated .
Eventually, by a process of it~ration , the
modal will be icproved enough that the comparison i5 sufficLently favourable for
the model to be accepted.
This iterative process i5 termed "refLnement". Often
several trial nodels wLII have to be considered.
Those that cannot be re jected
outr i ght have to be refined and the one which gives the best account of the
observed 1 (,2) accepted.

0-2

-2-0

-1-5

- o

1-0

-0'5

' 5

20

r~

Pi g. III.4 .

Square peak.

The unsatis factory feature of trial-and-error solution Ls that one cannot be


sure that al l posslble models have been considered.
Thus the true strUcture may
have been overl ooked.
In consequence the resulting models cannot be established
with the same degree of certainty as can deductive models .

III.6. Resolution

2. -0

It follD\ll s frODl equation 11.4 that the maximum value oE Q fo r which F(R) can
be meaBured 15 qiven by

1-5
1-0

In practice it may no t pr ove convenient , o r even possible , to measure F(~) for Q


val ues which are so g re llt as even te approach 2max'
Acoording to equatlon 111. l ,
in order to ca I c~late p(!) from F(~ lt ls necesaary to integrate over a ll the
apace defined by 2 vectors whose moduli range between Mlnus and plus lnflnity.
lnteqration bet~een these limita Ls clearl y impossibIe beC4Use of the limited
extent of the space over which F(~ values can be measured.
What ia the effect o f truncating the ranga of integration in equatlon III . l?

0-5

-50 - 4 O -3 0

Figure 11].4 shows a square peek


sents p (r) : 1'19. Irl.5 ahows its
here ia centroaycmetric, P {Q) is
Application of equatlon 111.1 to

whose height, as a function of dLstance, repreFourier t r ansform, P (Q)


(Not e that, since p (r)
real and can be plotted en a single graph.)
F(Q) but with Q restricted te the range of -20 te

20

3 0

4 0

Q~

The an.wer to this que.tion wll1 be illustrated by a si~ple one-d ~nsional &xaaple .

Piq. III.5.

Fourier transform, P(Q), oE the square peak


in Flg. 111.4.

50

2.

PrincipIes of Structure Detenmination

X-Ray Diffraction

27

+20 units essentially reoovers the original p(r).


As the extent of Q-space used to reconstruct p(r] ls decreased so the sharp
square peak becoDes less well def1ned .
In Fig . 111 . 6 the range of Q-space 15 so
limited that the reconstructed p(r) appears as a bread peak; the sharp edges
characterising the square peak are 10st.
Thus X-ray waves scattered at h i gh Q
values carry high resolution information whereas waves scattered at lower Q values
carry only general information about the rough shape of p(r).
Further discussion
of this point occurs in Section v.4.

o-

0-.

C'
~

Q.. 0-"

0-2

-2-0

- 1-5

-10

- 05

0 5

'0

'5

20

r~

FiC}. 111 . 6 .

Square peak reconstructed from F(Q) of Fig.


111 .5 with Q in the range - 5 te 5 reciprocal
length units.

Another problem associated with resolution is il l ustrated in Fig. 111 . 7 .


This figure shows that restricting the range of Q can produce spurious peaks in
p(r) reconstruc t ed from F(Q).
In the figure peaks appear which were not present
in Fiq. 111 . 4.
These peaks have arisen solely because a limited range of F(Q)
values was used ta calculate p(r) .
The airo of an experiment is to find an unkna~n
p<~ from measurements of F<Z) ayer a limited range of Q values.
lt is tempting
to assign peaks, which might appear when equatian 111.1 is applied, to structural
features in p(r).
This example shows that such a conclusian might be incorrect
and that the peaks could simply arise froro truncation errors.
In consequence refinement is best carried out as described in Section 111.5
ie . ln Q-space.
In principIe a trial model p (r) can be used to appcrtion real and
imaginary parts te F(~) whose modulus was measured experimentally.
Thus the
experiment cauld provide a source of amplitudes for the scattered waves and the
trial model could produce phases .
The experimental amplitudes and mode l phases
could be used to compute a better approximation to p (r) .
This is the basis of the
heavy atom methad of Section 111.4 - where the trial mQdel consists of the positions of the electron-dense atoms.
Such a procedure can be mls1eading if only low
resolution data are available because spurious peaks could be produced in p(~).
The approach described in Section 111.5 is not subject to such errors since the
model p<~} i5 pre5umed te be defined at suff icient resolution for F(~) values to be
cal culated reliably in the range of Q values far whic h the diffraction pattern is
to be analysed .
III.7. Loss of information at low Q values
Figure 111.2 illustrates a general observation - that l(~) is very much higher
at low Q values than elsewher e.
A practical detector , such as a photographic fi lm
o r a counter, has a limited dynamic range which then often precludes measurement of
l(~ at 1010' Q values if the rest of the pattern ls ta be measured accurately.
1ndeed 1(~) is SQ great , for very 1010' Q values, thalt, when it 15 detected by a photographic film, it exposes much of the surrounding area.
X- Rays scattered at very
low Q val ues a re usually prevented from meeting the film by intercepting their path
with a lead stop - which accounts for the white circles in the centres oi the diffrac t ian patterns in this book.

QoS

:
~C>6

'"

0.4-

<>2.
-2<>

+s

FiC}. 111.7.

-o.,

Qos

zo

Square peak reconstructed from F(Q) of Pig.


111.5 with Q in the range -6 to 6 reciproca!

length units

What ls the effect of omitting F(~ corresponding to very low Q values froro
the integral in equatiol). III. l ?
The same example is used as in Section 111.6;
Fig. III.4 represents the true structure and Fig. llI.5 is its Fourier transformo
Figure 11 1 . 8 shows p(r) reconstructed from F(Q) omitting the F(Q} values in question.
Two effects are apparent .
Firstly, a roughly constant background, in this
example about 0.2, is subtracted from p( r ) .
Thus the lowest reconstructed values
of p(r) are negative instead of being zero .
Since in most experlments F(~) will
not be measured on an absolute scale (see Section 11.3), this scaling error is
usually of ltttle concer n.
Secondly , edges in the reconstructed p(r) are enhanced

2.

X- Ray Diffraction

29

Pr inc i ples o E Struc tur e Determinati on

'0

C~----;;,.A

os

e
o
B

-1 -0

r-5

05

lb)

(0.)

r~

Fig. 111 . 9 .

Flg. 111.8.

Squa~ pe~k

reconstructed froc

(e)

2:0

~(2)

F (-

e f Fig .

j oc!.)

Q.)

lnversion of a chiral structure.

exp (- i

!.: 2.)

dr

111. 5 omitting Q ln the ranga - 0.2 to 0.2


reciprocal length units.

( III. 7)
.. F" (2.)

by a
thls
Fig.
p(r)

peak on one side and a trough on the other .


lt 1s important to note that
peak a nd trough are not real structural features , le. they do not appear ln

111. 4 , but arise because a limited range of f{Q) values was u sed te compute
l n equatlon 111.1.

111.8. Chlrality
A chiral structure 15 cne which cannct be superimposed on its mirror ioage:
from the theory g lven so far lt eoerges that X-ray di f fraction cannot generally
distingulsh a structure troro lts mirror image le. the determination of chlral
structures 18 ambiquous .
lt may not be immediately apparent that whether or not
a .stJ:ucture 19 chiral can depend on the resolution at which it is being eX4l:Iined.
Consider a protein unit which iB ~de of four identical large molecules or subunits.
An experiment ~y be performed to determine whether these four sub- units
a re arranged at the corners of a tetrahedron or at the corners of a aquare - ta
make up a unit.
Only lov resolution data are required te answe r this question
i e. Ff2.) may be confined t e lov Q values.
lf, st this low resolution, the subunits are roughly spherical then the tetrahedral and square-planar structures are
both achiral ie. they ~e identical te their mirror images.
Thus the structure
can be solved Wl4llIbiguously.
However each sub-unit consists of a pol ymer chain
wound lnto some specific three-dimensional shape - rather like a somewhat irregular hall o f wool.
At this resolution the structure 1 5 chiral .
[ f further dif fract lon data, corresponding to higher Q values, are added to the original set and
used to determine the high resolution molecular structure of a sub- unit, they viII
be unable te distinquish the t rue structure frem its mirror iroage.
The ambiquity which occurs when determlning chiral structures arises beciluse
From equation II. 3 it
follows ehae

since p (~) is real.


The di ffraction pattern, according to equatlon 11.5. is a
map of F(2.)F" (2.) which, according to equa tion 111.7 is identical to F (-~)F *(-~)
(Friedel's Law ) .
Inspection of the diffra ction pattern cannot then distinguish
the "top - which yields F(2.) - from the "bottOIll - which yields F(-SV
Hence it
15 never clear. even i f a structure is solved by deduction , whether cne has detected F (Q.l or F ( - R) .
Sinca F (-.Q.l is identical te T*(Rl, it is not known vhi ch o f
F (2.1 o r F* (~V has b een determined t:he fO[1l.er represents the correct see of phases
but the latter r epresents the phases with their signs changed .
What happens if F"{2.l is used instead of F(R) in equation II!.!?

y* (2.) e:xp (- i

~ R)

The result

dI(

(eqn.llI.71

1",,- ""

f.

-<

! ", -< F(R' )

exp

(i

!.:~')

dQ.'

,,,.. - '"

p (2.) and F* (2.) cannot 'be distlnguished experimentally.

"'p(-!.)

[eqn . l1I.ll

X-Ray Dif fr action

30

Bence , 1f F"(2.l 15 used , equatlon 111 . 1 returns the stcuct ure inyectad ln the

or191n.
If a ch1%al structure 15 inver ted in a poi nt the result 18 an upside-down mlrrcr image.
Flqur e 111 . 9 s~s a chiral oolecule (a ) in whic h A, B, e and o e r e at
the cornera o i a tet ra hedroo .
InversLon af this molecul e in the cent r a l black
abaD y ields (b ) .
When lb ) 18 turned the righ t way up and sultably rota ted as in
(e) . lt can be seen to be the a irr c r imaqe o f (a).
Thus an exper iment to deter -

mine an unknown chlral structure oould yield not the correct result but lts mirro r
image .
In cer tal n cases the ambiguity can be resolved by exploitinq the propertles ef anooalous scatter ing (Sections V. S and V. 6) .

CHAPTER IV

UI.9. SUlIID4ry

Slnce the r eal and imaqinary pa r ts of F{Ql cannot be measured separ ately , the
inversion property ot t he Fourier transform cannot be used directly to ca l cul a t e
p (r).
This d i ff i cul ty i s terllled the "phase problem" and has to be overcome by a
procesa of deduc t i on o r by t rial - and-error.
Deduct ive methods a r e onl y applicable
in certain favourabl a c ase s but t he resulting model s for p( r) are es tabl ished with
grea ter certainty than in the t rial-and-e rro r approach .
SOth appr oaches can be
aided by calculating the i nve rse Fourier transform of I(Ql te yield the a u tocorrelation ot p (.!.)
X-Rays scattered a t low Q values provide informa t i on about the rough shape of
p (r) I'l1gh resolution information i9 carried by the X-rays scat tered at higher Q
value9.
When cal culatlng p (r) frQm l oy resolution data some of the peak s wh i ch
appear may ari sa froe truncatlon errors and not be true structural t eatures .
Om.1ss1on ot experilr:ent aI da ta corr espondlng t o very loy Q values from such a ca lculation leads to subtr act ion of a roughly constant backgr ound f r om p {~) edges
are aIso enhanced by the appearance of peaks and tro ughs wh ich are also not true
structural teatures.
X- Ray diff racti on cannot normal l y d istingu l sh a structure
from lts mirr o r i mage .

Diffraction Geometry

IV. l. Introductl on
I n Chapter 11 lt vas established that scattered yave s can be specified in bot h
a.mplitude and pha5e by F(2.).
The direction of the vector 2, i5 r elated to the sca t t ering direct i on - lts ~ulus . Q. i5 a function of the angle through which the yave
is scatte r ed.
~l so it was establi 5hed that a d etector measures 1 (2 ) whic h ls the
product of F {2,) with lts complex conj ugate.
The practica l pr oblem which then arises i 5 te r e l ate the patte rn o f detected
intensities to I {2,) .
Te r ephr ase t he probl em, each posit i on on the detector has
te be converted to a ve ctor ~ if the t heory presented in Chapte rs 11 and 111 i5 t o
be appl l ed to the analysis o f the diff r act i on p att e rn.
The purpose o f this chapte r is te aho .... hoy position s on a detect o r correspond t o positlons in Q-spac:e. Thus
it serves t o relate the theory of t he previou5 chapters to a rea l diff r act i on pattern o
IV.2. Ewa ld s phere
An a lternative interpreta t ion of ~ i5 i mp licit i n Sectlon 11. 3 whlc h leads to
the idea of an inte ns ity distr i bution exi5tlng throughout an unlimited e xtent o f a
continuous Q-space - i n much the same way as e l ectron de n sity ls di s t rlbuted in
real space.
To make the argument simpler, con slder a one-dimensi onal Fourier
transform whlc:h, from equation 11 . 6, i5 given by

F(Q )

p(r) exp (i r Q) dr

We cou l d represent F (O) by plot tlng a g raph l ike Pig. l II.S o f Section 111 . 6 .
(Figure 111 .5 actual l y r epresents an example where F (Q) is real and can be p lotted
on a s Ingle graph . )
COnsidered In this way. Q 15 simp l y the abscissa a gai nst
whlch the transform has t o be plot ted as ordinate - lt can have a ny val ue between
plus and minus infin lty.
F(O} "exists R in the apace defi ned b y t h is infinite
extent of O va lues l n mucb the same vayas o( r ) exists i n a space d efined by an
infinite extent o f r value s .

31

X-Ray Diffraction

32

Diffraction Geometry

33

In tbree dimensions 2 15 simply the vector which defi nes a po i nt at whlch we


can compute the three - dimensional Fourier transfarm, F(2J .
The space defined by
these vectors ~ 15 called Q-space - ve can define its origin (le. the origin of
the vectors) at the point O' of Fig. IV.l - just as in Section 11.3 .
From the
relat ionship between

I(~)

and

F{~).

represented by equation 11.5, ve can consider

that I (~) 15 capable of existing throughout the whole of this same Q- space . Thus
there ls a distribution of intensity which exists in Q-space , surrounding the orig1n O', much as the re 15 a distrlbutlon of electr ons s urroundi ng the or i g1n , O, of
real 5pace.
Sc..,.o"TlERED

BEAM.5

By measur ing the intensity of scattered X- raya we can e~plore the distribution
oE intensity in Q-space .
Since a diffraction experiment measures I (~), a diffr actio n pattern is a reco r d of intensi ty distribution i n a region of Q-space.
But ,
as we shall see , not all of Q-space ls accessible to a diffractlon experiment o
Figure I V . l shows an X- r ay beam which i s incident on a sp ecimen whose origin
is at O.
I n gene ral the specimen viII scatter X-rays in a11 directions.
Each
of these scattered directions corresponds to a vector~.
According to Section
11. 3 , the origin o f all these vectors is at O' which is distant 2~/X from O along
the dlrection of the incident beam.
Also accord1ng to this section , each of the
vectors meets the scattered beam to which it corresponds at a distance 2~/A away
from O.
Fi gure I V.l then shovs that, vhatever the scattering direction , the vectors 2 defined by scattered beams vill describe a spher e of radiua 2n/A whose origin is a t O - the Ew&ld sphere.

I NC rDE NT-----o_-t~Io...::"l\<i?:_~~O'

BEAM

Fig . IV . l.

Ewald sphere.

SCATT ERED B EAM

I NCIDE.NT

&EAM

-';o--j-----~~'F--_.;.,c17J--_j

--.

O'

IV. 3. Q-space
"\PI-IERLC,',L

SUR~ACE

1llROUGI-I
POlNT5 IN Q SPACE "'ITH
THE 5AME VALUE Of g

E-WALO 5P'i-lERE

Fig. IV.2.

Diffraction

geo~etry

In consequence a diffraction e xperiment only provides values oE 1 (2) at those


peinta in Q-space which lie on the surface of the Ewald sphere - taklng the incident beam to be f i xed.
The reason ls that scattered X-rays can only correspend
to those 2 vectors which terminate at the surface oE this sphere.
We can thereEore consider a diffraction pattern as being formed by the interaection of the
Ewald sphere with the distributlon o f i ntensit y in Q-space this model explains
the appearance of diffraction patterns from gases, liquids and amorphous solida.
It ",ill be seen, i n Chapters VI and VII, that , to r these systems , P (r) has spher ical symmetry albeit of a sta t istical nature.
Consequently 1 (Q.) dep;nds anly on
the modulus of Q, not on its direction , and can be written as I(Q) .
Figure I V.2
sOo"'s a s pherical shel l in Q- space if I(Q) is spherica lly symmetric , it will have
the same value a11 over this ahell.
In the figure the she l l intersecta t he Ewald
sphere at A and 8; in three dimensions A and 8 wil l lie on a circle , whose centre
la a t P, which wil l have a uni f orm intenslty.
To make thi s description clearer the circle encloses aplane surface which is perpendicular t o the plane of Fig.
IV.2 .
Thus , for a sca tterer with spherical symmetry, t he diffraction pattern has
circular symmetry .
~igure IV. 3 s hows an example oE suc h a pattern the distri bution of intensity along a radius of this pattern i5 ana logous to a graph of 1 (Q)
p l atted against Q as , for example , in Fig . 111 . 2 .

for a spherically-averaged
scatterer.

Figure IV. 4 shows an X-ray beam lncident on a specimen.


Much oi this bearo
continues , in a straight line, to a peint e on a p lane detector (usual ly a photographic film) which ls perpendicula r te the inci dent beam direction .
Some radiation wilL be scattered so that it meets the detector at other peints.
Consider
a scatter ed beam which meets the detector at the peint E; this peint may be defined by the vector X.
The probl em i s to relate the vector x on the detector to the vector 2. which
speci f ies the sca ttered beam.
Figure IV~4 shows that x 15 in the same plane as
the incident and scattered beams as , according to lts definition, is 2.
Thus the

35

Diffract i on Geometry

X-Ray Diff ra c t ion

34

FILM

,/
C

SPECIMEN

INCIDENT BEAM

Fig . I V. S .

F1q. IV.).

X-Ray d i ffractlon pattern o f para ff Ln wax.

Rel ation ship bet ween a point on the fi l m a nd a


point in Q-space.

C'(lINDER AX l5

FILM CU~VfO INTO


CYLINDRICAL 5URF'AC.E

~oJ<::::::-b-':"""""

INCt DENT
8EA""

Flg. lV.4.

Recordinq & dlffraction pattern on a flat film


perpend.lcullU" to the incident X-ray beUl.

Fiq. IV.6.

Re cording a dlffractlon pattern froro a sphe rically s~ tr ic spacimen on a cyl indri cal film .

37

Diffraet i on Geoaetry

X-Ray Oif f raction

36

=-

directi on o f x on the filo indica tes ehe direction cf the vector ~ fro~ O' to
polnt en the Evald aphere l n Vigo IV.l.
More rigorously, x 11es in ehe same direction as the projection of ~ on ta ehe detect or - see Fig. IV.S.
The DOdulus of 2. can be calclIlated from x, the modulus of x.
tance f r OD the speclcen to the film , chen
,

_ tan - 1 ( x /R )

(4'ftJ l ) sin [(1/2) tan -

lf R 19 t he dis-

(IV .1)

Equation IV .l fol l ows from Flg. IV.4.


Q .

UElIX AXIS

From equations 11.4 and IV.l


1

( x !R) J

Thus both the d i rectlon and the modulus cf

R can

(IV . 2)

INCI DENT

be deduced from t h e dif~actlon

Figure IV . 6 shows 8 comroon arrangeme nt for measuring the diffracti on pattern


speci~ n with spherical symmetry .
Such a pat tern has circular symmetry ,
as shown l n the eKAmple of Fig. I V.3, tor the r easons given ln Saetfon IV. 2. The
dlstribution of intensity a l ong any r adius of the diffr action pattern then conta lns
all the r equlred i nformation concerning the dependence of I(Q) on Q.
A dlameter
of the pat tern can be recorded on a strip of photographlc film.
If the film is
bent inte a cyl i nder wit h the specimen on its axis, aS shown in Fig. IV . 6, it is
t r ivial to caleuLate from the radiu s , R, and the a r c length, CE: Q can then be
ca.lculated freo. usi ng equation 11 . 4.
A coWl.t er 15 aften used inste<Jod of a
photoqraphie fi l n with this arrangeoent.
The eounter rota tes in a circular a r c
centred on the specicen and thu s measures intensity as a function o f angle . Equations whlch fore the basis f or calculating Q from a variety of other detector
geooetries are glven ln Volume 11 of tne ~l nternational Tablea fo r X-Ray Crystal logr aphy" (see BIBLIOGRAPHY Sectlon 2) .

DIRE CT JON

froa a

What un.lts are used to measure distances i n Q-space?


Three difEe r e n t s ys tems
are used .
'!'he one adopted in this book ls commonly used in solid- ana liquidsUte physics where 2. is sOllletimes denoted by K.
Accor ding to equation 11.4, Q
has the units of reciprocal length (usually nm=I l .
Crystallographers t ena to use
a vector ~ which 15 re lat ed te 2. by

2.

2(211

S al50 has the dimensions oE reciprocal length but it makes the interpretation oE
diffrac t ion patter ns Eran periodic structures s impler.
In Section VIII . 3 it \o/iLl
be shown tha t the a lff raction pattern from a series oE 1dentical scatter e r s spaced
a dis tance c apart l s con f inad to lines spaced 2w/c apart in Q-space .
Now 1f the
p a tte rn is described by the vec t or S, these lines are l/e apart ln S- spaee.
Thus
distanee6 in S- space can be irrPedlately inverted to yield r epeat di5tances in regularly periodie struct ures.
This simplifying feature l eads to its adoption by
crystallogr aphe r s IoIho refer to S- space as ~reclproca l spece".
A few crystallographic texts oake the diffract10n space dimen5ionless by definlng

n -space i5 also referred to as recipr ocal space and is measured ln the dimension l ess ~raciproca l lattlce units".
When using fOI'lllUlae '~hich relate distances in
Q-space te spacings in a scatterer, it 15 essential to convert measurements from
t he dif fraet10n pattern i nto the corr ect space ie . the one whlch the formula
appl l es to.
l o thl s book all formulae a re developed ln Q- space (as opposed to
S-space or n-space) .

- ->-----"l,--- -->JI

SEA ""

pattern.

Flg. IV. 7.

~~TECTOR

X-Ray beam inc ident at r ight ang l es to the


axis of a heLix oE atoms.

IV . '. StDul ati on by opti eal d ifEraction


Diffraetion of l ight by an array o f apertu r es can be used te simul ate the diffraction of K-rays by an array oE atoms or molecules .
Thls simulation i5 part1cularly useful in those cases where F (R) , and hence 1 (2.) , \%uld be difficult to compute.
Using Huygen's constructlon, an ape r ture can be cons idered as a source of
secondary waves in the same \o/ay tha t electrons emit secondary X-rays when they are
exclted by an inciden t beam .
The region o E interest in the optlcal simulat ion i5 eon f ined to 10\0/ Q values .
Although ~ for X-raya is of the order oE d istan ces be tween atoms , the d imensions
oE the apertures used fo r opt ieal diEfr aetion are conventiona lly ebout 104 t~mes
greater then A for light.
Thus apt ical diffraction data can provlde higher resolution information abo ut the arrangement of these apertures than X-ray diEfraction
can provide abcut en arr angement of atoms.
Section 111.6 provides the detalled
justification for thi s statement - t he maximurn value of Q whieh can be mea sured,
and which therefore determines the ultimate re solution of a d i ffraction experiment,
15 inversel y proportional to A.
If we are to compare our optical diffraction
analoque with an X-ray diff raction pattern ...e need only eonsider the lower Q values
which are theoretically accessible to light .
In the optical case the a rray of apertures ls two- d i llensional \o/hereas in the
X-ray case the array o f ato~s is th ree-dimensional; this difference does oot iovalidate the s imu l at i on.
we need only consider very low Q values in the optical
case .
The area of the Ewa l d s pher e Eor light which gives rise to this region of
the diffraction pattern is so small that it is effectively planar.
Thus the optical diffraction pat tern can be considered te be formed by aplane intersecting 1(~) :
thie; p lane pasatla through O' , a distance 2"/A fran the or i q !n of real space , and ls

X-Ray Oiffraction

39

Diffra ction Geometry

39

normal to the incident beam - from Section IV.2.


A property oE the Fourier transform 15 that aplane section through F(~}. which centaios the origin o Q-space, 15
equivalent to the transform ef p(r) projected on to a parallel plane in real space.
Therefore the aptical d iffraction-pattern froc a three-dimenslonal scatterer 19
exactly the same as that fram the projectlon oE its structure on to a plane perpendicular to the incident directi on.
The compllcation arising in the dlffraction of
11ght from large bodies , discussed in Section 11.5, does not arise here because the
medium of propagation ls unchanged by passage through an aperture ln an opaque
screen .

Fig. IV. S .

Apertures punched in ao opaque screen to represent the arrangement oE atoms in the helix of
Fig. IV.7 projected on te apl ane perrendicular
te the incident beam direction.

How 1s the technique used in practice?


Suppose an K-ray diffraction pattern
which has been recorded from a specimen has to be solved by trial - and-error, as in
Section III.S .
PI trial model has also been proposed - that the structure 18 a
helix of atoms whose axis is perpendicular to the incident X-ray beam, as in Flg.
Iv . 7.
What does the X-ray diffractlon pattern of this trial model look like? We
could build an actual scale model, using suitable spheres to represent atoros, and
eKamine the way it scattered a beam of light incident at right angles to the helix
aKis.
Apart freID the theoretical problems ralsed ln Section 11.5, this experiment
would be extremely tedious to perfonn.
All we need do is to punch a set of apertures which represent the positions of the atoms in the structure projected on to a
plane perpendicular to the inc i dent beam direction - as in Fig. Iv. B.
The optlcal
diffraction pattern of this "mask:" , in Fig . Iv . 9, has the appearance we would expect from the X-ray diffraction pattern of Qur trial model - if the model is accepta ble.
Optical diffraction can a 180 be uiOed to investigate the propertles of
Fourier transforms in two dimeniOions in the 8arue way and is use fuI in cases where
calculation might be unduly complicated.
IV. S. Surnrnary
An X-ray diffractlon pattern can be considered to be formed when a sphere of
radius 2n/A, centred at the orig1n of real space, intersects Q-space.
This sphere
ls called the Ewald sphere.
The pattern is recorded by projecting this intersection on to the detector .
Far a specimen with spherical symmetry, like a liquid or
a gas, the pattern will therefore have circular symmetry and be centred about the
point where the undeflected beam meets the detector.
The direction and magnitude
of the vector 2. can be measured from the geometry of the detector system .
Diffraction of light by a two-dimens10nal mask can be used to investigate the properties of Fourier transforms and to simulate X-ray diffraction .

Fig. IV.9.

~ical

diffractlon pattern froc the array of

apertures in Fiq. IV.a.

Atoms and Molecules

4l

CHAPTER V

Atoms and Molecules

V.l. Introduction
The wavelengths of X-rays are of the arder of the distances between ato~s i n
molecules ego copper Kn X-rays have A ~ 154 pro and the carbon-to-carbon single bond
15 also around 154 pm long .
Thus, if data are col1ected to sufflciently high Q
values, an X-ray diffraction experiment can provide information on the arrangernent
of atoms in molecules.
X-Ray diffraction data which are restr icted to l ower Q
values provide information on the structu re of the scatterer at lower resolution

(Section II1.61.

Hence these "lo..... anqle" data are sensitive to the grass shapes

of molecul es and te their arrangements in scattering specimens.


In consequence X-ray diff r action ls used to investigate the structure of matter
at the mo lecular level.
Such investigations inc lude the arrangement of atoros in
molecules (ie . ~lecu lar structure), the overal l shapes of molecules (eg . whether a
particular mac romolecule i s rod-shaped or globular) and the way molecules are
arranged in systems.
In order to pursue these investigations it is necessary to
understand how atoms and molecules scatter K-rays.

V. 2 . Atorns
Suppose that the electron density ln an atom has spherical symrnetry.
This
symrnetry can be con5idered as a tlme average over the course of an X-ray diffractlon
experiment o
lts Pourler transform will , according to Section 11 . 4, also have
spherical symmetry and ls consequently a function of the modulus of ~ but not it s
direction.
This Fourier t r an5form i5 usually denoted by f(Q) a nd 15 called the
"atomic 5cattering factor~ .
Accordlng to equation 11.4 it 15 given by
f (Q) '"

lo

"'41!r

Plr) slnc (Qr) dr

Atomic scattering Eactors for oxygen , carbon and


hydrogen

in Section 1 . 5 .
Applica tion oE the quantum theory at this late stage 1n the calculation oE f(Q) i6 not , therefore , really j U6tifiable ; a tborough account of the
rigorous calculation is given in the book b y James (see BIBLIOGRAPHY Sect ion 2) .
It 1s perhaps worth noting that the classical t heory used here proves useful only
becau5e the scat tering electrons in matter a re bound in atoms.
Volume IV of the
"1nternational Tables for X-Ray Crystal1ography" (see BIBLI OGRAPHY Section 2) lists
at~1c scattering factors and also glves estima tes oE their r eliabl1ity .
For
aluminium the experimenta l and theoretical va lues of f(Q) differ by several percent; differences of this kind could i ntroduce sruall systematic errors into the
determina tion oE mol ecul ar structures.
Figure V.l shows a few examples of the
dependence oE atomic scattering Eactors on Q.
Fortunately it ls possible to deduce most of the propertles of the atomlc
scattering fac t or slmply by inspectinq the fOrIn of equatlon V.l .
Since the atom
is considered t o have spherica l symmetry , E(Q) is real.
Also it is always positive which neans that, according to Section 11.4 , all atoms scatter X- rays with
the sane phase for al1 Q values.
In Section V. S a complication will be described
but 1t usually only aE f ects the analysis of X-ray dlEEraction patterns when a
chiral structure is to be distlngulshed from 1ts mirror image.

(V.l)

where there 15 considered to be only the one atom in accessible space.


In principIe P (r) can be calculated for an atom of each element; equation V. l
can then be used to calcu l ate f(Q) .
Calculation of p(r l i5 clearly a quantum
mechanical problem but equation v.I was derived by ignorlng complica tions arising
froIn the quantum theory of s~atte ri nq - these complicat1ons are discussed briefly

'0

F1g. V.l.

As might be expected, the greater the number of electr ons in t he atom - the
greater i5 the scattering fac tor; in partic ular when Q equals zero the scattering
fact o r i s equal to the number oE electrons ln t h e atom.
The number oE electr ons
at a distance r from the centre oE an atom ls given by
(v . 2)

From equations v.l and v . 2 the atomic scatter1nq factor becomes

X-Ray Diffra ction

"
f (Q) '"

"'t: (rJ sine

(Qr l :jr

Atoas and Molecules

ev. )

I n the limit as x tends t o zero, sinc(x ) ten s te unity - s o that


f O) '"

>u(:;> er '"

...'here Z 1 5 the number o E e lectrons in the atom .


Thus the ampl1tude $c a tte red with
a zero value oE Q b y a ro atom 1 5 e qu a l to its n wnbe r o f e l ectro n s - g ive n the definition o : f'(Q ) in equa tio:l 1 1 . 3 ~h ic;, n eglec ts sollle fundamen t al consta nte .

The fa1 1- off oE f (2 ) with increas ing Q la c aused by i nt erference between


X-rays scatterea in the salte directlon by diff e rent parts of the same atom .

In

contrast the at~ic scattering f a ctor for therma l neutrons does not dec rease apprec iably as Q i ncreases .
The reason l s simfly cha t neutro ns . unl i ke X- rays , are
s cattered by che atomi c n uc leus whL c h 15 very 5111&11 compat."ed with A ln tarference
effects between neutro ns sc at~ered by the sane ato~ are therefo re negl i gible.

v. 3 . Molecules
The terlD. "oolecule " here simply iap lies a n assembl y of atoms in c l ose association which it is convenient to consider together for t he purpose of c alc ulating
F{Q).
Thus a molecu l e in thie context does not necessari l y iroply a covalently
bonded structure.
In Cha ptere VIII and X the theory deve lope here for a n01ecule viII be applied to the ent ire structure which repe ats i tself regularly ta form
a c rys tal .
EIsevhere in this book , however, the theory wili usually be appliad to
molecul es in the chaDlcal sanse ie. a coval ently bonded assembl y of atems .

lt fo1.10ws, from equation V.4, that a chiral ool ecule cannot be distinqulshed
fr oa its nirror !mage since f(Q) 15 rea l And positive.
In Saction II1.8 it vas
shovn that F(~) cou l d not be distinguished experimentally froa F ( - gl - b ecause the
number of electrons ln a unit volume of space, ie. p(r), must always be ?Qsitive.
OOnsequencly a chiral structure could no t be distingulShed froa its cirrar lma;e.
Exact ly t he sama reasoning appl i es here - thus the expression for F(~) o f a QOlecule ln equati on V.4 has the general property described previously .
Section V.5
describes circ~stances under which the simple approach used so far breaks down
and the chirallty of a molecule can then be determined using X-ray diffracti on data
from a suitab le systec .
V.4. Mo l @cules at l o ..... resolution

According t o Se ction 11 1 .6, F(~) vill be insensitive to detailed molecular


structure at sufficiently low Q values.
To rephrase this statement - waves scat tered at these lo.., values o f Q correspond to a low resolution view of the structure.
In o rd~r to explaln these " 10...,-angle " diffraction data, lt is often sufficien t to consider the molecule to haya SODe simple shape with a unlform electron
density le. to ignore those detai l s of the structure which cause variations of p( r )
within the molecul e .
Thus soma globular macromolecules, such as certain enzymes~
may be considered as spheres and certain polymers simply as reds in the analysis
of low- angle X-ray diffraction patterns.
X-Ray scattering by spheres of uniform electron density is particularly appli cable as . . . i ll be seen in Seetion VI . 3.
Prom Seetion Il . 4 it follows that the
Fourler transferm of the sphere depends only on the modulus of ~ and is independent
of lts direction.
Than, according te aquatien II.e

F(Ql ..

When an assembly of atoms scatters x - rays , interference effects wi ll occur


betwean those X-rays s cattered in tl".e sama direc tion by different atolD.s .
'I'his
inter-atomic interference i s in addition to the intra - atomic interference effect s
.... hlch lead to the f a l l-off in f (Q) with increasing Q values.
Accord ing to Section II .4 the Fourier tra nsform of a molecule is simply obt ained by adding together
the transforme af its constituent a to~s with due regard to the phase differences
introduced by the positions of the a tome .
Then , for a mole cul e contain i ng N atoms,
the molecular transform ls glven by
N

F (~)

.,

fj (Q) exp

(i

~.2)

43

4n r 2 " si ne (Qr) d r

for a sphere of radius a with a uniform electron density, p.


evaluates to

'" (x )

3( sin x - x cos x }!x

Thi s integral

(V .S )

Equation V.5 may be simplifled to


(v . 4 l

jo ,

FeQ )

., n t(Qa }
(V.6 )

where ~j i s the pasition of the j th atoa, r e l a t ed to some a rbitrarily cho sen


origin, and fj is lts a tomic scattering factor.

noting that n, in equation v . 6, ls the number of elec trons in the sphere .


The complex F ( ~l i n equation V.4 represe nt s t he amplitude and phase o E the
X-rays scattered , ..,i th A particula :r vector 2., by a nolecu le .
lts f orre a l l ows for
interferenc e effects between X-rays scatter ed by di fferen t atons vhi l e f , wh lch
depends only on the modul us of 1(, Allows for interference e ffects be t ween X-rays
scat tered by different parts of the same atom.
Note tha t t he phase, but no t the
amplit ude, of F(l(l depe nds on where the origin i s chosen - th i s property is physi ca l1. y reascnable sinca defi n i tion of phase, but not of anpl itude , raquire s soce
arbitra r iLy chosen refe r e nc e.
Whe n Q equals ze ra, F(~) is s impl y t he sum o f all
the atocie scatter ing fa c tor s '""hich, accor ding ta Secti on V. 2 i5 equal to the nUIIIber of e lectrons ln the ~lecule.

Equat i on V. G s hows the same kind o f behaviour a s t he exact express ion for the
Four i er t ra nsform o f a molecul e at l ow Q vAlues.
Figure V. 2 show$ the fcm of t he
function O(x).
Note that, as x tends to zero, ~ ( x ) tends te unity.
'I'herefore ,
vhen Q eqpals zero, F(Q} , in equation V.G, 15 simply equa l to the number of electrons.
this approximate foro. for the molecular transform yields the sarna
result as the exac t expression of equation V.4 in the 11mitinq case of Q equal s
zero.
T e depenC!ence o f F(Q) for a sphere o n Q, which arises mathemat ica l l y fralD.
the form bf ~ in Fig. V.2, can be considered physically as the result of interference effebts between X-rays scattered in the sama direction by different parts of
the sphere.
As this simple model fer the molecular transform ignores the fact

EUS

Atoros and Ho l ecu les

X-Ray Oif fraction

45

that molecules eonsist of a t~s , it bec~es a peo r e r a pproximation for higher re solutLon diffraction data le. at higher Q values.
Figure VI.I of Saction VI.3 provides an example which demonstzates the appl icat ion of equation V.6 as an approxLmation to tbe molecular transforc and shows how its val ldity depends on Q.
Thr ee further propertles o f t he Fourler transforID o f a sphere can be simp l y
ded\lCad tron equation V.6.
Flrstly , although F(Q} in equation v . 6 i5 not collplex
it st i ll convey5 phase information .
In Fi g . V. 2 , t (x) c r osSes the x axis periodical l y.
Thus F {Q) must cross che Q axls - eorresponding to a changa in phase
of the scattered X-rays as explalned in Sectlon 11.4.
A change from a positive
t o a negative value of F(Q) corresponds t o a phase change froro O to T radians and
v ice versa.
Secondly, since ~(x) i5 equal to Q (- x }, F(Q) in equat ion v.6 18 the
same as F(-Q) .
The thlrd property o f F(Q) in equatlon V. 6 providas an example oE a general
property of Four ier transfor ms .
Fi gure v.l , vhieh was computed using equat10n
v. 6 , s how5 that F(Q) varies more for a larga sphere than for a small e r s pher e .
This observation ls a speclal casa of a general property - that large dimens i o ns
ln real s pace give r ise to rapidly varying ehanges in F(Q) .
Conversely, gentle
vari atlons i n F (Q) eorrespond to small distances in real space.
lt 15 thi s
property whieh l e ads to tha Observation of See tion 111 .6 - that F (~} does not carry
hlgh r esolution infor mation at low Q v alues .
Gentle variations in F(~) can only
be detected if a w1de r uge of Q val ues 1s examinad; if the ex~nat i on o f Q-space
15 restricted t o l ow Q values these variations wi ll be undetected and hlgh r esol ut10n information l ost .

0 -4

X-_~)

Fig. v.2 .

The function

~(x )

V. 5. Anomalous scattering

de f ined in equation V. 5.

This section ls concerned with a phenomenon whi ch may be used to distlnguish


a chlra l structure from it s mirror i mage in favourable clr cumstanees ; in the cour se
oE axplainlng this phanomenon sorne of the statements of Sections 1 .3 and 11. 2 vii i
be justified.
Both this sect ion and Seetia n v. 6 may be omitted by readers who a re
not intere5ted in de t ermin ing the chiral ity of s truc tures; rea der s who a r e 1nterested i n t his topie, but who dis like ~themat ieal e xplanatlons, can pr oc eed dlrectly
t o Secti o n v.6 .
Explanations in th i s section r ely, as far a s po5sible, on classi cal theory Eor the reasons given in Section 1. 5 ; t he quan tum t heory of anomalous
scattering is described , and com~red with olassie a l theory , in the book by James
(see BIBLI<XiRAPH'l Section 2).
I n Fi g . 1. 1 of Seet ion 1. 3 the electron osc illates up and down the z-axis as
it i5 accelerat ed by the oscl1 l ati ng electric Ei e ld of the incident r adiation .
Sinca the electric vector underqoes s i mple harmonie oscl l 1ation , ve mlght also
expect t he electron to be a simple harmonic oscillator.
The equa tion of IIIOt ion
f er en undamped, undriven electron oscll latlng along t he z-a xis i n thi s fa.shion i 5
simply

os .

,-o
" - ... .. ..

',5

2 -0

-o
Fig . v.3.

Comparlson oY F (Q) for spheras of r a d i us 2.5 nm


(dbtted l i ne) and 10 nm (continuous lloe) comp uted froP equation V.6 wi t h n equal to unity .

(V.7)
where Wo 1s its natural angul ar frequency ie . the value in the a b sence of damping
or driving torces.
However the motion of an electron 1n an atom will be damped
eg. by the a ttract ive force e xerted by tne nucleu5.
In roany similar pheoome na
this damping is proportional to the veloclt y of the osel l1ator ; t hus equation V. 7
hu to be modified to
(V. S )

X-Ray

46

Atoms and Molecules

D i ff ~action

where le: 15 a constant f o r a particular electron - the "da.mping facto r " .


Now the
electron 18 belnq constantly d r iven by the osci l lating f i eld o f the incident X-raya .
Sinee we are considering oacil1atlons which are confined te the z -a~ is . t he fte l d
st some lnstan t in time , t , can be denoted by a scaiar, E, whose oscillatory nature
can be shown by writ ing it in the fon

47

30

E - Eo exp (1 w t l
..mere 11,1 ls the ugular frequen cy and Ee the amplitude ef the oscillation .
The
force whl ch a f i eld E exerta on the charge, e, cf the e l ectron 15 sioply eE .
If
a 18 the malls cf an electron, its acceleration ls theo

eE/m -

( e /~)

Ea

e~p

(1 w tl

The r efor e equat ion V. S has te be f ur ther modified te


2
2
d z / dt + le: dz/dt +

w~

z = (e/m) Ee exp (1 w t)

Equation V.9 can be solved f or the displacement , z , of the electr on .


(e/ m) Eo exp (i w

2 -

t )/(W~

- w

+ i k w)

(V . 91

The r esult

(V .IO)

\-5

can easily be v e r i f i ed by subatLtu tion into equation V. 9.


Equat i on v.IO will be used te de rlve the amplitude oE the X- ra ys emitted by
the oscl11~t i n9 el ectron .
Ae cording to elassieal electrodynamics , the elect rLc
Ei"eld o f the radi atlon emitted by an eleetron with an aeceleration of d 2 z/dt 2 Ls
given by
B

( \.1 1 411) (e/R)

(sin .ji ) d z/dt


z

(V . l l )

Oiffer entiating equation V.IO


where ~Q ' R and $ 2 are de f ined in Section 1. 3.
twice with r espect to time and substltuting t h e result into equation V. 1I yields
the e l ectr i c field of the emitted e lectromagnetlc wave
E

2
2
2
Cw J (w _ w + i

k wl

O plotted against

WJIIIO for 1II0/k equal to 5


(cont inuous line ) and 50 (dotted line).

lncident X-rays l s great e r than the nat ural angular frequency of the electron l n
its atom.
As w approachas wo ' ls wil l suddenly i ncrease - beca use o f the b ehaviour
of O 8hown in F l g . V.4.
Thus 1110 can be cons ide red as an angula r r esonant frequency.
This resonanee a ffect can be used to explain the dlscontinuities in the absorption coef fie i ent of an element (it s ahsorption edges) descr i bed i n Section 1.2.
The ab8orpti on coefEici ent of an element is dafined empLrieally.
tf a monochromat ie X-ray beam oi intensi ty l o i5 incident on a thiekness, T, of mater ial, the
&mergent intensity L& given by

(V .12 )
(V.14)

- E (110/411') (l "/mR) sin ';>z

The i ntens ity oE the X-raya scattered by the eleetron can be calculated from
equation V. 12.
Followi ng Seetion 11. 3 the re sult i8
l a - nlo

Fig. v.4.

(~0/4T1)2

2 2

(e / m R ) sin

0z
(V.l3 l

where l o is the i neident inten 81ty; in t h is approaeh Es L8 taken to represent a


(Unfortunately this approach i gnor es the
wave whos a i ntensi ty 15 gLven by EsE;.
contribution oE the magnetle v8ctor to the intensity.
Becau se of the relationship betv een t he electr ic s nd magnetic vectors a con8t a nt of proportionalLty then
srise s i n obtainlng l s from E. and lo from E.
Of cour se thi s constant appears o n
both sides of equation V.l3 an~ he n ce cancels out.
De talls a re given in the bcok
by Bleaney lUId Bleaney - pp. 260 to 265 - see BIBLIQGRAPHY SecUon 7).
Equation
V.l) 18 ldent ical to equatlon 1 . 1 - apart from the appearance of O.
Provi ded Iol
is greater tban k. Flg. V.4
that O 15 very close to unlty ",hen w 19 greater
than 11,10'
'l'hUI5 equation 1.1 gLve. l a provided that the angular f requency of the

.how.

where ].J ls a eonstant f o r a given material - Lts "abso rption coefficient" .


A
mat erl a l which has a high value o f ].J absorbs a high proportion of the Lncident
X-raya .
According to Section 1. 5 we can consider an X-ray beam as fl stream of
photons oE energy hC /A where h ls Planek 's constant , e i s the speed of electr omagneti e rad i a tion in a vacuum and A ls the wflvelength of t he X-rays in t he vave
deacrlption .
Thus the greater the value of A, t he lover is the energy o f t he
X-ray p~otons and, consequently, t he le ss easl1 y the y would be expected t o pass
through matter.
Flgure V.5 shows that, as expected, ].J incraases with A - excep t
tbat its value suddenly drops when A equals a critlcal value, Ao.
In Flg. V. 6
this behaviour o f V ia combined \lith Fiq . 1.1 to ahov how a nickel filter can be
used t o remove coppe r KS X-rays .
He", is the sudden decr ease of U i n Fig. v. 5 expl alned by resonance?
The
transm1tted i n tensity can be a ttributed te scatter f o r which Q equals zero and
obtsined from equat ion V. 13 by giving +z the val ue of 900 le . sln .jIz becomes unity .
For a given incldent intenslty, lo' t he tra n ~itted lntenslty then i ncreases ",hen
lf the
n incr ealles i e., f or a high val ue oE w, when !al dee r ea ses te approach- 1110 '
transmitted i n tens ity i n ereallea, the absor ptlon eoefflc lent, ~ . will d acr se.

4.

~-Ray

80.... can the dec rea.se in

i
!

ti)

"

()

and IIlO

'"

2T.v - 2'1c!).

Thus a wave lenqth }. o 1s associated wlth Wo and hence with the decrease in 1J - >"0

..

!
:

S i nce

can be usad ta define the posLtlon of the sudden decrease, or absorpt ion edge ,
whlch appeara in Fiq. V. 5.
Resonanee occurs when }. 18 sueh that the enerqy of an
incident X-ray photon equals t he bindinq energy of an e l ectron in an atom: t he
e l ectron 16 then emitted , fol l awinq callision with a photon, and another falls
from a higher energy level to take its place.
(When the photon enerqy exceeds
the binding energy auch an event beoomes les8 probable and resonance does not
P'or elements
occur.)
ThUB each enerqy le1.7el has its corresponding 1.7alue o f A. '
o
whose atol'llic number is below about So, t he so-called ~K-edqe" i9 the close5t to
the X- ray wa vele nqths used for diffraction experiments.
Also A.o , for the K-edge,
i5 greater than A. of copper Ka ~-rays (ie. w is greate r than wo ] for elements up
to atemic nucber 27 (cobaltl.

2
><
zw .4
~

when 111 approaches 1110 ' be related to }.?

]J ,

are angular freguene!es, they are related to frequency, v , and hance to }. by

iJ
;;:

49

Atoms and Molecules

DiffractioD

::1

o-.z.

00,3

WA,VE~GTW

Fiq. V.S.

004-

J\o_l-4-9pm

Absorp~lon

( f'I"')---+

coefficient ter nickel as a f unetion


o f wavelength.

NIC.KEL

lf the wa1.7elength, X, of the X-raya incident en an atom is close to AO' the


positlon of its ab sorption edqe, the atomic scattering factor becomes complexo
The atomic seatterlng factor was showo to be real in Seetion V. 2 .
In fac t this
r esult arase from the assumption, in Sectlon 11.2, that the arnp11tude of t he
X-rays s cattered by an electron in matter was real ie. it was assumed that the
amplitude , Es. in equation v.12 vas real.
By taklng the pos1ti1.7e square root it
vas inevitable tha.t f (Q) in Section v.2 would be real and positive.
In secUon
11.2 the 1mmediate result of tak ing the positive square root was that F(2} would
always be r e al and positive when Q equalled zero le. the X- rays scattered wlth Q
equal te zero were asslqned a phase of zero radians; this scat tered bea.n:l became
the referanee f or a ll phase measurements a nd, aceording to Section 1. 3 , the phase
of the lnci de nt beam became -n r adians .
But, according to equat10n V. 12, Es ls
complexo
When Xo i 5 greater than A.. f(Q) is real and positive and 1s given by equa tlon
v . l.
Figure V.4 shows that Q tends to unity when tu is greater than 1010 ie. AO Ls
greater than A..
Also the theory used te explain absorption edges depends en w
be1ng greater tban k.
When tu is much greate r than wo Iwhich la the case far
atoma of lov atomic number), the only way Q, as defined in equat10n V.13 , can then
approach unlty i s for wo and kw to becorne effectively zero.
Then Es ln equation
V.12 wl11 be real Ilnd reduces to the positive square root of ls in equatian 1.1.
~ccording to the prev1aus paragraph, f(Q) is then given by equat lon V.3.
When troI o
ia much greater than w, w~ will be very much greater than k and , once again , the
1maginary part af f(Q) in equat1an V.14 disa pe ars .
In thls case Es for the elect~ans in questlon \oIill be negative - since (&)0 in equation v . l:! ls much greater than
tu.
However, 1.110 will be much greater than W only for atom9 cf high atornic number.
Tbe scatter f reo all the other electrons will then predominate and far most of then
I.ol
Consequently f(Q ] is still real and positive.
o \01111 be much less than w .

I f ). is close to Ao' f(Q) is complex and equation v.3 has tO be modified.


Figure V.4 show$ that n is very auch greater than unity when tu 19 clase t o 1.110 ie .
X ls elose to X
thus k cannot be negleeted in equ.atlon V.12.
Since n ls l arge
and Bs 1s eOlllpl~x, the contrlbut1on of the resonating electrons to f(Q} i8 complexo
Also the maqnitude o f the real part oE Es will be affected.
It i5 therefore customary te correct f{Q ) for anomalous scatt er1ng by writ1ng

l54-pm
Flq. V.5.

Filtering copper

WAVELf.NGTM ---:JIoo

fe lO} .,
X-rays with nickel.

f{Q}

+ f ' (2) + 1 f" (2)

(V.15]

X-Ray Diffraction

50

Values ef f ' and ftl are given ln \lolUDe 111 ef the "Inte rnational Tabl es for X- Ray

crystallography (see BIBLIOGRAPHY Seet1an 2) but for many purposes they are ne9l1gible.

v.e. DetermLnat ion Di chirality


It

f eo)

19 real, le . when the wavelenqth of the incident X-raya 15 far from

an abso rption edge ef the aten, a chiral IlIOLecu l e cannot be distinguished frOlll its
~ror iaage le . its chirallty cannot be determined .
Suppose a structure 19
determined by a methad ef the kind descrlbed in Chapter 111 .
I n Sectlon 111.8 lt
vas shown that lt 19 not then clear whether the resulting electron density, pl rl,
or its inverse, p( -~l , r epresents t he true structure.
One yields the true s tructure of a IIIOlecule: the other gives its mirror 1l1lo!11ge.
The rea son f o r the arnbigulty was snovn te be that, since p (~) 19 real, it is impossible to distingui5h
l{~ from I {- 21 experimentally.
It a11 the atomic scatt ering hctors , fj (Q), in
equati on V. 4 are real , the argumenta o f Section 111.8 still apply .

'I'he chiral1ty of a DO l ecule c an be determined when one , or more , o f the


atomic scatter ing lactors la complex ie . when i t contain s an atom with a n absorption edge which 15 close to the wavelenqth of the incident X-raya.
Then t he
argumenta of Section 111.8 do not apply to ~(~) , as defined by equation V.4 , and
there is no longer any conditlon for 1 (2) te equal l(~).
How 1a the ch1rality ol a molecule determined in pract ice ?
A structure
letermination yields two solutions - o (!..) and p (-!...).
A set of F (~) values is
then calculated lrom each 901utlon , f er positive and negative values of Q, using
equation V.4; these calculations empl ey the complex atomic scatter1nq fac tor s of
equation V.IS.
Each set o l F(~) values 1s used to ca l culate a set of le~) v a lues
using equation IJ.S - once agaln for both positive and negative values of Q.
The
set of calculated I(~ values which agrees better with these measured experimenta lly
must have bee n calculated from the bettar mode l for t he structure.
The application o f anoaalous scattering to the determination of chirallty ls
u8ually restricted te X-ray diff ractlon data from crystals.
The r eason is that
1 (2) and 1 (-21 mU8t not overlap on the diffraction pattern - other....ise they cannot
be separated far co~rison with calculated values .
Because of the arrange~ents
of molecules in mest pha8es ol matter, Ie~ and I ( -~) will overlapI but they can
be separated experimentally when recordlng d i ffr acti on patterns from c rystals .

V.7 . SUlUDary
The resultant X-ray vave scatter ed by a given type o f atom depends only on
the modulu5 of the vector 2.
11.11 atoms scatter a re s ulta nt wave ....lth the same
phase which does not vary with Q.
For a given a toro type t h e wa ve 15 repre sented
by the atonlc 5catt erlng factor fjeQ) which has a n amplitude egual te the atomic
num.ber of j when 2 equals zero.
The behaviour of the atomic scatter ing f actor is
compl l catel vhen t he wavelength of the incident X-rays 18 close to an - a bsor ptlon
edge of the atom thls compllcation can be usad to dlstinguish a chlral molecule
from lt s mlrror image 'u s1ng X- r ay dittraction data from a crystal.
The r esul tent X- ray vave scattered by a mol ecule depends on the direction of
as vell as en ita magnitude and can be represent ed by a complex number which is
ullually denotad by F (2l
Wben Q equals zero, F (2) equals the total number of.
electro n. ln the molecul e.
At sufficiently l ow Q values ft ls pDsslble to approxim.ate P (2) by SOlH geometrlcal shape which closely reselllbles the shape of the mo1ecule vhen viewed at low resolutlon.

CHAPTER VI

Ideal Gases and Solutions

VI.l. lntroduction
In a n ideal ga s there a re no int eTac tion s bet .... een the molecules .
This view
of an ideal gas has i t s orlgins in the kine tic theory of gases .
Por a real gas to
approach ideal behaviour, its concentrat ion of molecules must be so low that they
are unlikely to approach sufficiently closely f or any appr eciable interaction.
Thi8 view may be extended t o X-r ay scattering.
Then a gas is i deal if its mol ecular concentratlon i5 so lov that no appreciabl e i nterfer ence occurs between
X- rays scattered by dlfferent molecules ie. intermolecular interfere nce is neg11 glble.
Inter feren ce effects in the X- ray diffraction pattern of an i deal gas can
only a rise , by definitio n , between X-rays scattered ln the 8ame directi on by differ ent parts of the same molecule i e . a l l interference is intramolecular.

By analogy, an ideal solution contains solute molecules which can be con s i dered
to behave ln the same way as the molecule s in an ideal gas.
lf a real solution is
to &pproach ideal behaviour, its solute mo lecu les cannot interact appreclably either
v ith e a cn other or with salve nt DOlecules .
For the present purposes , a solution
can be considered te be ideal if the X- ray scatte r f Tom the sal ute molecule s i s not
modified by i ntermolecular interference.
I t t urns out that a dilute solut l on in
which the solute molecul es are very rnuch larger than the solvent mol ecules 15 ideal,
in t hi s sense, at l ow Q values .
Thus, by analogy with an ideal ga s, i nterfe r ence
ca n only a ri se between X-rays scattered, i n t he same directlo n, by diffe rent parts
ot the same solute molecule.
8ecause interference between X-rays scattered by differen t molecul es can b e
neglected, tne scattering properties of i deal gases and solution s a r e particularly
simple; the y are, there f ore, the first systems whose speci al pr operties are considered i n this book.
The absenc e of in t ermolecular inte rference effec ts makes i t
poasible to deduce informa t ion about molecular structure witho ut the need t o cons i der the compl i cation o f lntermolecular interference .
Unfortunately t he i nformation which can be deduced is 1 1mited by t ne ra ndom orie n tation s oi t he molecules
ln gases and solutions.
VI.2 . Scattered intensity distr lbution
lf a gas consi sted of only a sing le stationary molecule , the i nten sity of t he
X- r ays which it scattered would be g iven by

51

Ideal Gases and So l ucion s

K-Ray Oiffraction
1 ( ~) = F

[eqn . lI.S]

(Q) p. (\2.)

f j (Q ) exp ( i

~ .2.)

(Q)

exp (- i

.Ql

(eqn. V. 4J

L L

fj

(Q)

k (Q) exp

{i

(E.j - :4;.1 .Q)

(VIol)

k
~here

both summat10ns a re taken over a11 the atoros in the mo1ecule.


Here r ls
the position of the j th atom in the mo1ecule, with respect to sorne arbitrar!lY
chosen origin, and fj is its atomic scattering factor.

Now suppose that the gas contains N of these same molecules .


Interference
effects bet~een X- rays scattered by different molecu1es are considered to be neg11gible and so the resu1ti ng diffraction pattern is obtained by adding the intensity
contribution from each.
(Rad interference not been neglected it would have been
necessa ry to add the amplitudes of the X-ray waves scattered by each molecule ~ith due regard to phase differences.)
Adding a11 these intensity contributlons ,
the total ls given, according to equation Vl.l , by
I (Q) '" N

L L

fj ( Q) fk(Q) exp

(i

!1k Q)

('11.2)

where E.jk is the vector separation


molecu1e .

bet~een

Thus equation '11.2 has te be spher i cally averaged i f it i5 to represent t he


intenslty of the X- rays scattered by mol ecul es in the gas phase .
This equation
ls analogous t o the ~ourier transforID as defined ln equatlon II.6 - except that the
summati on of equation VI.2 ls over a set of atoms rather than over infinitesimal
scattering elements .
By analogy with equati on 11.8 , ~hich ls the Fourler transfoem of a functlon wlth spherical symmetry, equatl on VI.2 has then t o be repl aced
by

LE

Follo""ing the convention


IIo6, from an elemental length, dr, in equatlon lI . S .
of this book, r
is the modulus of ~jk ie. it is simp1y the istance between the
ik
jthandkth atoms in a molecule.
According to equatien VI.3, the intensity of X-rays scattered by a gas is independen t of the direct ion of R thus, accordlng to Section VI.2, its dlffracti on
pattern has circular symmetry - Like che example of Flg . IV.).
Then I(Q) can be
obtained by measuring the intensity distribution a10ng a radius of the pattern an
converting radial distance into a dlsc ance in Q-space by the mechads of Section
IV.3.
Note that equatlon VI . ) contains "self t erms" which a r i se when j equals k,
and "crOES terms" ""hich arise when they are not equal .
Sine e rjk, is equal to r kj ,
the cross terro between j ano k is identical to that between k ano J.
These properties are often emphasised by ~riting equation VI.] i n the form
I(Q)

N {

f~(Q}

+ 2

L
>

fj(Q) fk(Q) sine (Qr jk ) }

Equation VIo] can be used to determine the structures of molecules in i deal


gases.
It 15 parti cularly easy to understand how t hese structures can be de t ermined by trial - and-error.
A model has first to be proposed for the molecular
structure ; I(Q) ls then calculated froro the atoroic scattering factors and coordi nates of the model using equation VI . 3.
The result of this calculation ls compared with the experimentally determined intensity distribution and, if necessary ,
the model 15 adjusted to improve the agreerr.ent between the observed and cO!l;lculated
results.

the j th and k th atoms in a single

The mc1ecules in a gas have random orientations; this randomness was ignored
in the derlvation of equatlon '11 . 2.
Since the angles which vectors 11ke E.jk make
~lth
depend on the or i entation of the molecule, so does the value of ~lk.R and,
hence, I(~) .
At an inst ant in t~me , the contribution which each molecu e wll1
make to I(R) then depends on its orientatlon at that time.
Since a ga s contalns
very many molecules, every possible orientation ~ill be represented at that instant.
If Che intensity contribution from each of these orientations is added, the resultant lntensity wlll be characterlstic of a spherically averaged molecule.
Furthermore the cont rlbutions for each lnstant in time have to be summed over the time
periad durlng whl ch the diffraction pattern i5 recorded .
Durlng this period each
molecule is likel y to assume every possible orientatien - which also leads to the
scattered X- rays conveyi ng information about a mol ecule which has been spher i cally
averaged.

1 (Q)

53

f j (Q) f (Q) s i nc (Qr )


k
jk

(V1.3)

The f a ctor 4 ~ r2 appears on1y in the lntegral formu latlon - lt represents the surface area of a sphere of r adius r and genera tes a volume element , d~, in equatlon

In pract i ce e l ectron dlffraction is generally used for thls purpose because


electrons are more strongly scattered than X-rays.
For mast states of matter
electrons are so strongly absorbed thO!l; t very thin specimens have to be used - the
need to produce very thin speci mens can be a dlstlnct disadvantage of electron diffractlon.
Absorption is much l e ss of a problem for a gas because of the low concentration of absorbing molecules.
Note that for electron diffraction a high
vacuum is required throughout mast of the apparatus to eliminate scatter by air
the need for a high vacuum is usually a further disadvantage of the technique.
This appl icat i on can be used to introduce the idea of a scal e factor whlch
usually arises when interpreting X- ray di f fraction patterns from real systems .
lt is not usuall y worthwhile to attempt to record I(R) on an absolute scale by comparing it with 1 (O) .
So:ne indication of the d i fficulty of measurlng 1 (O ) , in
general, ls given in Se ction 111.7.
If l(Q) of equation VI . ) is measured on an
arbitrary scale , N c annot be oetermined and so it acts as ao empirical scale factor .
Then its value must be adjusted to obtaln the best agreement between an intenslty dlstribution calculated from a mode l and that obtained experimentally .
Note that , when Q is very close to zero, the theory used in this chapt er
breaks down .
According to Sect i on V.4 , the scattered X-rays wil l convey information about very large distances wlthin the specimen at these very low Q va1ues.
They wi l l then be sensitive te distances between molecules ie. intermoleculO!l;r interference will be detectable .
The complete theory is given by Guinier and by
James (see BIBLIOGRAPHY Sectian 2) .
Ho~ever. for d i lute gases and macromolecular
solutlons, the vO!l;lues of Q at ~hich intermolecu1ar interference i5 detectable are
so close ta zero that they are not usually measurable - therefore this effect will
be neglected ln the rest of the chapter.

54

X-Ray Diffraction

'OOr~

[ dea l Gases and Solutions

55

___
'or""-';::::- -- - - - - - - - - - - - -- - - WATER

10

10

15

05

.20

Flq. VI.l.

10

1 5

20

0 r-----~----~----~~~~

Q (.",-1) ----iI>

PROTE IN

Cooparison ef I {Q) for a spherLcally averaged


water mol ecule calculated using equation VI . 3
(continuous line) and equatlon VI.6 (dotted

Fl g. VI .2.

l1ne)

Compar lson oE f {Qa) f or spheres the siza of


proteln and water mol ecules.

VI. 3 . Intensity at low Q va lues


At l oy Q values the diffractlon pattern 16 insensitive te deta!l s of oolecular
structure and the calculat ion of I{Q} can be simplified .
Thi s LnsensLtivity vas
discussed in Sactlan v.4 .

There the Fourier transfonn o f a sphere , of r adius a,


and te be given by

vas shown to be independent ef the di rection cf


F(Q ) ., n CO(Qa)

(VI. 4)

whece CO (x) 1s defined ln equation v. 5 and the sphere contalos n electrons


Now
FeQ) already has spherical symmetry ~nd 15 rea l ; according t e Section II. ) the i otensity sca ttered by the sphere 15 F (Q).
The intensity sc~ttered by an ideal gas
oE N spheres is then obtained by ~ddi nq the intensity contri bution from each ie.
1 (Q)

., NF (Q)

(VI.5)
Equation VI . 5 could be ocnsidered as an a lternative r epresentation o f equation VI.3
where F(Q) represents the Fourier trans f orm of a spherically aver4qed molecule .
Here we a re oonsiderinq the low resolution case where the molecules can be treated
a s s phe r es so tha t , fro~ equati ons Vl.4 and Vl . S
I(Q) ., Nn

(Qal

(VI. 6)

F igure VI . I compares the predictions of equations VI . 3 and VI.6 , a t low Q


values, f o r a water molecule in the ~deal gas phase.
The difference between the se
predictLons is negligible at sufficlently low Q values.
For calcula t ing scatter
from an assembly of molecules with random orientatLons, the Fourier transform o l a
sphere can be a particularly use fu l function.
In the e xample s hown in F19. VI.I,
the sphe r e was assigned a r adlus of 96 pm vhich is compa.r abl e with the length o f an
0-8 bond .
VI.4. Solutions o f maeromoleeules
The purpose of thia seetlon 1$ to shov that dllute solutlons of macrcoolecule$
a pproach ideal behavlour at low Q values ie. the X-rays scatter ed by the SOlute

roolecules do not interfer e with those scattered by othe r solute or solvent moleeul es .
Cle~rly intarference with X-rays seattered by other solute molecule s wl1 1
be neqligible lf the salute ls suffl ciently dilute.
But how can interferenee
wlth K-rays scattered by the surroundinq solvent molecules be ignored?
Suppose that the solute molecules i n the solution are very much larger than
the solvent oolecules .
For low va lues o f Q, F{Q}, and hence I (Q} , will be insensltive to t he detailad s tructure of the solut ion for the r easons given ln Sectl on
V.4,
If Q l s restricted t o sufficient ly low Q values, I (Q) vill be sen s it ive to
the dimensions of t he large solute molecules vithout being sensit ive to the relatively small distances between the solvent moleeules .
Thus t he scattering f r om
the solvent can be considered mer ely as a featureless background which has to be
subtrac ted from t he experimentally determlned intenslty distribution to obtai n I(Q)
for the solute molecules alone.
Bow can ve determine, exper i menta ll y , wh ether a solution i8 ideal?
If I (Q )
is modfied by intermolecular l nter ference, its form vi l l depend on the conc entration of tha solutlon.
Thus, when I{Q) is measured from a solution whl eh is
presumed to be ideal, t he experiment s hould be repeated at a different coneentration.
The magnltude of the l ntensity distribution viI I change bec:ause the number of s cattere rs has e hanged.
But if lts shape le unehanged ie. the distributions a r e reLated s l mply by a scale factor - then t he presumption of i deal ity is
confirmed.
Figure VI.2 illustrates an example of the insensltivity of F(Q) to d etail, if
it i s restricted to low Q values.
Here t (Qa) ol equati on VI.4 is plotted for
spheres whose r adii a r e 2.5 nm a nd 0 . 096 mu.
The former could be consldered as
protain nol ecules and the latter as water aolecules i n which they are dissolved
Fiq. VI.l shows tha t a sphere o f this latter radi uS i8 a good model tor calculatlng the scatter from water molecu les at these low Q values.
N and n 2 , ln equa tion VI.6 , can be ignorad , for the present, as they simply adjust t he relative
scale of the two curves.
Althouqh the Pourier transform of the larga r s phere

X DOQ S I!

i
Ideal Gases and Solutions

X-Ray Diffraction

57

falls off fair l y r a pidly, in the region of Q-space shown , t hat of the smaller
sphere i 5 effectlvely fla t and featureless.
VI. 5. Deductien ol ool ecular structure

The atructurea of seall aolecules in ideal gases can often be solved using
the Patterson function of Section 111.3.
According to Sectlon Vl. 2, the intensity of X-rays scattered by an idea l gas or solution provides i nfermation about a
spherically averaged molecule and is independent of the direct ion of~.
The
Pa tterson func t i on is the Fourier t ransforM of I(Q) and, according to equations
11. 8 and 111.4, it CAn therefore be defined, for our present purposea by
P (r)

1""

4lfQ2 1 (Q) sinc

(Qr)

dQ

(VI. 7)

Now P(r) is independent of di rection and is a one-dimensional function.


Thus
peaks in P(r), computad from I{Q), now represent distances rather thAn v ector
separatlons.
If l (Q) la measured to sufficiently high values of Q, P(rJ will
the n yield interatomic distances.
Each peak will represent the di5tance between
two atous in a molecule - distances between atoms in different molecules are very
great, ie . they would appear at very high r values , which, in any case, would not
be detectable because 1 (0) i& i ndependent of intermolecular interference effects
for an ideal gas.
The height is r elated to the product of the electron densities
of the two atoms ~hese interatomic dLstance the peak represents - AS explained in
5ection 111 . 3.
Por smal l molecules, containing only a few atoms , the structure
can then be reeonstrueted from these distances.
This aethod is confined t o molecul es in the gas phase because solutions are only ideal at low Q values and then
I(Q} i5 insensitive te detall s of molecular structure .

Deduction of moLecular s tructure has two potential disadvantaqes: both a r ise


~our i er tran5formation of experimental data - P {r} of equatl on VI. 7 is a
~eur i er transformo
Accerding te this equation, P Ir) is an integra l whlcn luIs te
be evaluated between the limits of zero and infinity.
In practice, I (Q) can only
be mea5ured over a finite range of Q-space, as described in Seetion 111. 6.
Furthermore it ~as shown in tbis section that , if Q i5 too restricted in range, spurious peaks can ari 5e in P {r} .
The secend disadvantage arises because meaaurement
of I{Q) is subject te experimental noi5e.
Fourier t ransfermation ia very sensitive te noLee whlch, in this case , could distort the appearance of P{r).
For this
reason , vhen a molecular structure has been solved by deduction , the expected intensity distribution ahould alvays be computed froro its coor dina t es and compared
with that observed - as a check on its validity.
Altheuqh this caLculation also
involvea Fourler transformatlon , the function which i9 transformed l a now a set ef
model parameters with no exper imental noise.
frem

The structure of a spherical scatterer can be deduced by the direct method of


5ectLon 111.4; this approach can sometimes"be usefully applied to macromolecules
in ideal solut ions.
Figure VI . 3 shows that I(Q} for a 5phere passes through a
series o f peaks separated by zero values of the intensity.
The structure of a
sphere i $ independent o f the direction of a vector , r, in real spaca and its
Fourier transform l s independent o f the direction of- Q as described for a spheri cal ly symmetric funct10n in Section 11.4; the problem of determinlnq the structure
ef a spherical scatterer La thus identical te the example of Sacti on 111.4. Other
spherically averaged shapea closely resemble spher es at low O values - so does the
IDetbod work f or thelll too?
SUppose 1 (Q) is carefully measured and the necessary
correct1en s applied .
Ii it pa.ae& smoothly through zero bet_en peaks. the
spher~cally averaged ~.tte re r c l osely resemble s a .phere at th~ s resolution .
The

o+-------~5----~--~,O~~~--~15~------c
20
Q 4

Fig. vr.3.

__

r(Q ) for a sphere of radius a (on a n a rbitrary

scale )

method can then be appl ied.


r f 1 (Q) does not pass through zero ne ither does F(Q) and the method br eakg down .
Note that this approach ignores intermolecular interference, i e . it i8 Lnvalid for non-ideal solutions, and is subject te the potential
disadvantages of the previous paragraph - resulting modela should, therefore, be
c:hecked. in the same way.
VI, 6. Guinier' s law
Guinier ' s l aw provides a method for deduciog some informatie n on the structure
of solute molecules in ideal solutions - whatever the ir 8hape.
Note that the law
applies only te ideal solutions since its derivation ignores interference becween
X-raya scattered by different malecule s .
Thus its validity i5 r estricted to
di lute solution5 of macromal ecules and application te concentrated soluti ons , ge 1s
and fibres is inva lido
FUrthermore it ls specifically derived for very low Q
values at which diffraction data are insensitLve te detaLls of molecular structure .
Readers who are not interested in the derivation of the law should skip the next
five paraqraphs.
In Fig. V1 .4 a beam ef X-rays is incident on a scat terinq body which ls presuced to be in an ideal solut lon .
The reason for this presumption is that, i f
dlffractien effects at very low Q values are to provide informat ion en its structure, the body must be at least as large as a ~croQOl ecule - it cannot, the refo r e,
exist i n the gas phalJe and can only attain the ideal behaviour o l thill chapter in a
dilute 8OLution .
consider the scattered beam shown in the figure; the l - axis ls
defined to be perpendicular to the incident beam ln the plane def ined by the incident and .cattered bea.nls.
How 2. tertUnates at t he sur face o E the Ewald sphere
(Section rV.2) which, at very low Q values, is e f fectively apl ane which i8 perpen-

X-Hay Diffraction

58

59

I deal Gases and Solutions

Note thAt equation VI, 11 15 net concerned with the direction of 2. because t his vect or 15 now consldered to be coplanar with the -axis as we l l as with the incident
and scattered beams ie. tbe prob l e~ ls ene-dimensional .

Equation VI.lI can be simplifi ed further.


notlng that
ex p

I
AlU'

This simplification la achieved by

+ x + ( x /2l + - - -

( x ) ., 1

Slnce Q ls very 5ma11 we can neglect higher t erms when expanding equation VI . lI
and the r esult ls
F{Q) '" P

o{t)

di +

Q p

o{tl

dL -

(Q2 pj2l

J e
aa.l

di

(Vr.1 2)

SCATIERED

r_~______~__-c!-__==~====&EE=A:M~d Q

INCIDENT

&AM

If tbe or ig in, O, of t he body l s defined to be at i ts centroid

IJ

(.e,

t dt

<=

(VI. 131

s ince the centroid ls defined as the point about which the integr al aYer al1 the
elementa l f1rst !IIOments is zero.
The volume, V , of the body 15 given by
(V1. l4 )
Fig. VI . 4 .

Figure for the derivation ef Guinier's law .

and a functien, Gi. ' i5 defined by

J e'

diculllr te the incident beam because such 11 SIDall fraction of its surface is be1ng
considered .
'l'hus 2. is roughly perpendicular to the incident beam and, therefore ,
para 11el te the i - axis.

di.

o (i)

(V1.15)

Fr om equat10ns V1.12 to V1.15


At 10w Q va1ue s the Fourier transEorm oE the body vill be insensitive to t he
fluctuations in the e1ectron de nsity .
Thus the electron density of the bady is
effectively constant and the Fourier transEorm becomes
F (2)

'"

exp (i

E.,..g.l

(VI.8)

dr

where t he integratien is take n ayer t he whale body and r represents a peint within
it , with respect te an erigin O.
Since t he {-axis is ;early paral1el to ~
(V1.9 )
where 1. is the projection of E.. on to the l - axis .
lE the resu it of equation V1.9
we r e to be substituted i nto equat i on VI . 8, it would be necessary to 1ntegrate with
respect to f..
Nov, if r 1s a volume element in the body, it can be expressed,
in terms oE t, as
-

oSE.. '" o (l) . 6.l

(V1.1O)

where o(l! is the cross -sectional area of the body at a dis t ance t from O and 5t
is an elemental distance as ln Fig. VI . 4.
From equations VI.8 , VI.9 and VI.lO,
the Four ier transforrn o f the body becomes
F (Q) - p

oCe)

exp

(i

Ql

di

(V1.11)

(V1.16)
Now the [bracketedl funct1en could be considered as the first two terms i n the
expansion of an exponential .
If Q i s so small that only the first three terms are
requ ired for the expansion of equation VI.ll i nt o equat ion VI . 12 , Q2 vi l 1 be so
much smaller that equation VI. 16 can be rew ri tten in the form
F (Q) =

,,

pV exp (- Q G /2)

(V1. l7)

For an ideal so1ution, consisting oE N such scattering bodies , the resultant


intensity wili be given by
IlQ)

NF

[eqn . VI.5]

[2)

2 2
NP v exp (1(0) exp (-

Q2G~)

, ,)
Q
G

(eqn. V1.17]
(VI.18)

~e re I(O) ls the va1ue predicted for I(Q) when Q equals zero.


lt ls introduced
to avoid writing NP 2 v2 as well as te emphasise that , in pract1ce, this composi te
term will act roere1y as an empirical scale factor, since I(Q) will not usua l ly be
~asured on an abso1ute scale.

In a solution the scattering bodles 101111 have 11.11 posslble orient ations and
so equat ion VI.18 has to be sphe r ical ly averaged.

TABLE VI.L

Gl,

Gt

(VI.191

_ G

+G

(.(.2 ... p 2 + q2) dr

2
2
+ G
p
q

(3 / 5) 1: a

Sph ere

Radlus a

Ellipsold

Semi-axes a, a and ya

Long , thin r ed

Length l

Random coil

Mean-square end-to-end

TwO further a xes, p and q, Mve to be de f ined so tMt l , p and q are mutually perpendi cular .
If t , p and q a r e the proj e ctions c f r on to these a:xes

G2 _ UN>

Radl 1 of qyration for bodles of simple shape

Since t he on1)' terro in equa.-

tion VI.18 wh ich depends on the structure of the body 15


thia il.veraging can be
achieved simply by replacing lt with lts spherical average - denoted by <
>.
It vill no ... be ahown that <
> 1 5 related. to the rad1us o f 9yr o!lotion oi t he body ,
whlch 15 defin ed by

el

61

I deal Gases and So l ution5

X- Ray Oiffrac ti on

60

distance

{ (2 + / ) / S}I:! a

.l/121:!

~) ~/6~

See C. Tanford, "Physica1 Chemistry of Macromolecu1es,"


Wi1ey, 1961, pp. 150- 154 where a "completely unrestr lcted
po l ymer c hain~ 19 a "randoO'l coii " .

(eqo. VI. 19 ]

leqos. VI . IO a nd VI . 15 1

and th<i! re for e


(V I. 2a )

2
alnce G , as defined in equation VI . I9, ls independent oE the orientation o the
body and ls , consequently , ide ntical to lts spherlca l average.
When the body has
been spherically aver aqed its properties mus t be isotr opic and 80
<

G't

(VI. 211

> -

From equ ation s VI .20 and vI.21


<

c:;1

(VI. 22)

> - G /3

Substituting this result into equat i on VI.IB yle ld s


(VI. 23l
Equation VI.2 3 ls a statement of C:;uinler's 1aw.
Tab1e VI. 1 llst s a f ew f orwhich al l ow the radi us of gyratlon , G, to be calculated for a few dlf fe r ent
shapes.
How good an approximatlon i5 Guin ler ' s 1aw?
Flgure VI . 5 compares an
exact c a 1culation o f 1 (2) f or a sphere o f rad i us 2 . 5 nm wlth the pred ictlon of
equation VI . 23 ; raaders who have fo l lowed the de rl vatlon should note that, for the
purpose o f thi s c~pa r lson. the scale fac t o r

~u l ae

a,...

10

'H
~.
~+

o-z

1(0) ., M,2

was set egual to unity .


va1ues .

Guinle r' s law prevides a goOO approxlroa.t l on at 10w Q

0 '5

10

2.0

15
Q,(nm- I )

-----.

In practice Guin i er ' s l aw l s qenerally used to deduce the radius oE gyrati on


of the mol ecules in a solution .
Takl nq logarithcs o f both sidas of equation
VI.23 gives

Conve nt ionally tn [I(Q) ls plotte~ against Q? - a "Guinier plot ~ .


The slope of
the graph the n y lel da a valu e for G - assuming that al1 the l arqe scat tering

Fiq . VI . 5 .

Compar ison of I (Q ) for a s phere calculated


using equat l on VI . 6 (continuous ilne ) and
Guinier' s l aw (dotted lille) .

62

X-Ray Diff raction

l deal Gases and SOl u t i ons

bodi es in the solution a re ldentical.


Note that a11 intensity t:DE!asurements ha'le
to be corrected by subtracting the salvent cont ribution. fer the r e asons q lven in
Sectlon VI.4: this contribution can be measured ln a separate eKperi~nt.
1900rance a l the v alue of I {O) does not affect the determination of G.

Although Guinier's l aw a llows the radius of gyration a f a body te be deduced ,


its diDlenslons cannct be deduced unless its shape 19 known.
'I'he mathematical
reason 19 that the rel a tio nshi p between G and t he d imensions oE a body depel'.d on
its shape Guinier 's law pr o v ides a value tar G but no shape i nformation.
Physically this lqnorance ef shape arises because the experioental data p rev ide 1nformatLon on a spherlca lly a ve raged scatterer.
At the best ef times it is difficult
to distingu ish, eg . II sphere from a s pheric/l lly averaged red.
For the 1 0\1 Q
values , ie . low resolu t i on , /lt which Gui nier' s law appl i e s the distinction ls not
possible in the absence of further informat ion .

In equati on VI . 24, D(x ) 1s meAsured and h (x ) is ~easurable: l(x) is r equired to


calcul ate I(~). by th; methods oi Section Iv.3, in o rder to relate exper iment to
tbeor y .
l(~) can be recove r ed f r CII. D(x) and b (x) by reversing the process o f convolution in equation VI. 24 ie . by deconvolut ion .
The need for deconvolutlon oc curs
in m&ny areaa of science and engineering - the methad described here exploits the
properties o f the Fourier trans formo
If T de notes the operation o f Fourier trans formation , t ra ns forming bath s i des o f equation VI. 24 yields

T {D(~)} - T {I( ~)
T (I(~)

a coording to Section II.4.


gives

VI . 7 . Smear i ng
l t has already been indicated, i n Section v l.2 , that , i n a gas , t here are so
few mo lecules that the intens ity o f ecattered X-rays ie weak; a similar pr oblem
arises i n experiments on dilute solut ions where there wi ll be few salute mo l ecules .
In the case o f so lutions the probl e~ cannot be solved by using electrons , as in
Section VI. 2 , because the large number of salvent malecules woul d lea d to considerable absorption.
The anly way to obtain a d i ffract i on pattern in a r easona b le
time is to use as intense an X-ray beam as possible.
Synchrotrons are increasingly
beinq used as intense X-xa y sources for investigating solutions but the more traditional approach is to use an X-ray beam with a large cross - sect iona l area .
Haw does i nc r easing t he cross-sectional area of the beam i ncrease the scattered 1ntensity?
The int ensity of X- rays from a conventional generator is d ictated by the number of electrons striking the anade and is limit ed by the rate at
which the anade can be coaled.
If t he electrons strike a large Area t he cool ing
will be more efficient and it i s possible to generate a higher total intensity.
aut the cross-sectional a r ea o f the X- ray beam is a lso i ncreased.
Thus, although
the X-ray i ntensity per uni t a rea i s l imited , the total lntensity can be increased
by using a bellO with a larger cross-seetional area .
The theory in this book has been de r ived fo r a high ly ool l imat ed i ncident
X- ray beam whi c h ~eet s the dete c t o r at a peint o f negligible dimensions i f a beam
of larger crosa -sectional area i s used, a correction has t o be appli ed.
I n practice a very narrow rectangula r beam cros s -sect ion is general ly used and a variety
of correcti on procedure s has been app l ied .
The purpose o f this section ie not t o
ca ta logue these va r ious procedures but to ind i cate , in general , how beac shape
affects diffraction patterns.

A pin-hole coll ~~te d X-ray beam meets t he detector at a paint - but a beam
with a larger cr o ss-sectional area vill be r ecor ded a s some inte n sity distri bution,
h (x ) .
This vide beam can be consid ered as a parallel bundle o f h ighl y col limated
be~ each of .m.i ch gives rise t o the s ame intensity distribution, I (!.) , at the
detector, but with respect to a slightly different origin; the or i gin i5 de fined
by the polnt vhere each collimated beam meets t he detector as in Secti on I V.) .
A
wlde beAll, therefore , smears Ollt the i ntensity distribution , I (!.), whi ch would be
expected froID a colliaated beam .
According to Section 11 . 4 , the de t ected i ntens i ty,
D{!.) , is then given by
(V:I. 24)

63

h(~

T (h(~)}

Rearra ngi ng and applying the inverse tra nsform, T- l ,

vh1ch is simply

I (~ "" T- l [T{ D {~)}/'r{ h(~) } l

(VI. 25)

Equation VI.25 prevides a method for recovering l (x ) fr om D( x ) if t he inte ns1ty


d1atribution of h(x ) i s measured it i s not necessary to mea;ure the intensity of
either h (x ) or D(x) o n the same scale, as an absolute measur ement o f I ( ~) wil l not
uSually ~ required.
Accurate representa tion of h (x ) may sometimes be complic ated by t he obligue
incidence of the sca tte red x-rays .- Suppose h(x) is measured by detecting the undeviated X- r ay beam on a fl at f i lm vhich is perPendicular to it - as in Fig. IV .4 .
Tben h(x ) i a the inte nsity distribu t i on around the origino
If the beam were
scattered wlthout change of c ross -sec t ional shape to some other peint on the fil~
it \IOuld not be incident at r i ght angles.
Then the a rea o f fl1m blackened by
this scatter ed beam would net be exactly the same as that b lackened by the undevi ated beam , the shape obtained with the undeviated beam vould be distorted, in the
scattered case , by obl ique i neidence.
This effect has to be allowed for if equation VI. 25 'ls to be used to recaver an accura te r epresentation o f I (~) .

VI . 8. Summary
In an i deal gas lnterfe r enee betwee n X-rays scattered by different molecules
i a considered te be negligible.
'l'Ilus all inter ference e ff ects arise between
X- rays scattered by diffe rent par ts of the same molecule .
Since t he mol ecules
in a gas have random orientations , the diffraction pattern has circular symmetry
and conveys information on the structure of a spherically ave r aged molecule.
A solution i s considered to be i deal i f the scattering pr ope rti es of its
solute molecules are identical to those o f a molecule in a n ideal ga s .
Dilute
solutions of macromalecules are ideal, in this sense , at l ow Q values. Guinle r' s
l a\l provi des a methad for deducing the radi us o f qyrati on of solute mol ecules in
an ideal sol ution.
An X-ray bell.lll of larqe cross- sectional area may be used, in stead of a p in-hole collima t ed beam, to increase the i ntenaity of the diffraction
pattern - a correction then has to be app11ed to the intensity d istribution at the
detector before 1 (Q) can be cal culated.

Liquids and Amorphous Solids

65

technique cannot detect the changing positions of the molecules in a 1 iquid but
only t heir averaged, irregular positiens .
Consequently the same effects are observad ln X-ray diffraction patterns from both liquida and amorphous solid5.
X-Ray diffraction studie6 of these a ystems are usually performed to investi gate how the consti tuent POlecul es are arranged in them .
SLnce thL5 arrangement
15 so irregular, it w:Juld be jX)intless to attempt to speclfy t he position of each
malecule - especially as there wl1l be around 1023 malecules ln a real sample !
Thus the descrlption of the moleeular arrangement must be a statist i cal one.
VII. 2 . Intermoleeular interferenee

CHAPTER VII

Liquids and Amorphous Solids

VII . l. Introduction
When X- rays are seattered by the molecules in a liquld oc a solid, interference occurs bet~een the waves scattered, in the sarue direction, by different moleculea.
l ntermolecular lnterferenoe 19 now important because the mo l eeules are
much eloser together than they ~uld be in an ideal gas .
Consequently the theory

for ideal gases has to be extended to include inter- as well as intra-molecular


interference if lt 15 to be applied te liquids and solids.
In Chapters VIII and
X lt viII be shown that this extenslon 15 partlcu l a r ly easy f o r c rystalline solids
because their molecules are reqularl y a rranged in space.
The molecules in liquids

are i rregularly arranged and ~ve no preferred orLentation.


Amorphous sol i ds ,
ofte n cal led "gla55e6". are characte rised by a similarly irreqular arranqement oE
molecules and lack of molecular orientation.
Ne vertheles5 ene approac h to calculating intermolecular lnterference effects, for these irregular systems , treats
t.heQ a.s d1sordered crystals - this i8 the "paracr ystal titeor}' for disorder o f the
second kind" as CSescr1bed, for eK.1l1llple , by Bosemann (see BIBLIOGRAPHY Seetion 9 ) .
I n eo~lete contrast, the more modern approach, which is adopted here, aetually
expl oits the irreqularl ty which i s eharaeteristic of these s y stems for eaIculating
intermolecular interference effects.
Liquida are mueh more l1ke dense gases than disordered crystals .
A c rystal
which 15 subjected to shear stress stores the defo rmation energy and r eturns to i ts
original snape when the stress is removed - it i s elast ic .
In contrast 11quids
and gases both Eloy when a shear stress is app lied and do not s tere their deformatlon energy - they are viscous.
'I'hus the interactions between IIlOlecules must
be similar in liquids and gases , althouqh in a crystalline solld they a re very dif f erent .
This distinetion is emphaslsed by the symmetry changes yhich accompany
phase trans ltions.
Whe n a crystal melts a loss of symmetry occurs but no symmetry
change accoqpanles vapour l sation oE a l i quido
Indeed the only clear distinction
between a liqui~ and a dense gas i5 thst the formar is bounded by a surf ace tha t
has one f ace which is not defined by a container.
Why cons ider l iquids and amorphous sollds together?
Both a re charaeterised
by a seeningly haphazard arrangement o f molecules - the only difference L6 t hat the
IIIOlecules in a liquid are free to laOVe around so that their positions are cons ta ntly changinq .
An X- ray diffractlon pattern conveys information about the
structure of a scatt erer averaged over the time taken te r ecord it .
Therefore the

64

Liquids and solids consist of a.n assembly of POlecules in space .


Accordlng
to Section 11 . 4 the Fourier transform of this assemOly i5 the n given by the sam of
the trans forms of the individual molecules.
Remember t hat phase dlfferences, 1ntroduced by each molecule havin; a different position, have to be taken into
account - just as they dld yhen a tomic scattering factors were added to obtaLn a
molecular transfOrD i n Sectlon V. 3 .
Taking lnto account the se phase differences
allows for interference between X-raya scattered by different molecules .
In
liquids and amorphous solids the moleculas have random or ientations.
~oll owinq
essential ly the sama argumenta as in Section VI . 2, the calculated intensity dis tribution is then gLven by
I {Q}.

L L::
j

Fj{Q}Fk(Ql sine (Qrjk)

(VII .!)

Sere Fj (2) is the spherically averaged Fourler transform of the j th molecule yhich
i5 glven by e~tjon VI.3; &t 10'07 2 values the approximate form of equati on VI.6
may be applicable.
The spherlcall y averaged transtorm 15 appropriate here because ,
as in a gas, the molecu les have random orientations - for further details see Section VI . 2 .
(Note that , whe n calculating the sphericaliy averaged molecular transform in Section VI.2, the atomic 9cattering factors dLd ROt have to be spherical ly
averaged because, according to Section V.2, they already had spherical symmetry.)
The intensity distribut ion, I(Q), ot equation VII.l is independent of the
direction o f 2. and, hence , di ffraction patterns from liquids and amorphous solids
have ci r cular symmetry for the reasons discussed Ln Section IV. 2.
Figures VII . l,
VII.2 and VII . 3 provide examples of such d lffra ction patternS .
When the intensity
distribution &long & radius of one of these patterns ia converted into Q-space , it
gives I(Q} for the sample .
I{Q} does not depend on the direction of ~ because o f
the irregulari t y of the structure.
A lIlOlecule viII hAve some arrangement o f molecules around it wh ich , in total, might be expac ted to give rise to soma scattered
intens ity distribution, 1(2.),
SOme other molecule viii have the sama arrangement
of neighbours but with a different over all orlentation - because the re are so rnany
molecules in a macrosco pic sa.mple.
For the entire sample the diffraction pattern
then provides Lnformation about the structure of such a molecular c lus ter averaged
over .11.11 possible orientationSI thus I(Q} ia independent of the direct i on oE 2. for
essential ly the same reason as described in Section VI.2 for an ideal gas .
Noy that the applicabillty of equation VII.l has heen establlshed, it may be
manlpulated into a more useful formo
The first stage 15 to rewrlte it as

Li qui ds ana Amorphous Solids

X-Ray Diffr action

66

Fig. VI I . 3 .

67

X-Ray dif fracti on pa ttern of nOrmAL human


costal cart ilage.

lf tne gas consists of N identical molecules, this equation can be simplif ied ta
Fi g. VII .l .

X-Ray dtffrac t ion pa tte rn of water


(taJ:.en by 0.5. Hickey).

2
1 (Q) .. NF {Q} S (Q)

S(Q)

1 + (l/N)

L L:
,

(VIl.2)

sine (Qrjlt)

Equa tion VI l. 2 15 identical to equation VI.5 far an ideal gas - except f e r the
appearance cf S (Q) .
The on l y diff e r ence between the derivation s of equations
VI.5 and VI I.2 15 that the latt er does not ignore inte rmolecular interference ;
therefore, 5(Q) nust allow far t h is effect and 15 called the interference function .
( l t ls also somet imes called tne " s tru cture f actor" but this nomenc l ature c an be
con fus ing because the term 1s used in a different way by c rystallographers.)
Thus ln termolecula r interference effects can be repre sented by a n i nterfer ence funetion, S(2) ; t he ne xt s tep is to derive a more useful form for S(2) than
t hat in equation VII . 2.
Suppose that every molecule in the sample could be considered to ha ....e an "average" rel ationship with its nelghbours.
Then each o f the
N moleeules could lnteract vith IN - 1) others a nd t here would be H(N - 1) ident ieal interac tions.
As a resu lt , the definitlon of S(Q) l n e quation VII.2 could
be rewritten as
S(Q) - 1 + (N - 1)

sine IQrk)

1 + N

L
k

Fig. VlI.2.

x-Ray dLffractlon pattern of rubber (un stretched) .

sine (Qt"k )

(VIL3)

69

Liquids and Amorphous Solids

X-Ray Dif f raction

68

The secand line f0 1 10...5 froro the f i rst since N and (N - 1) are essentially the

sane f or an assembl y of around 1023 molecules.


Note that , in equat10n VII.J, rk
1s t he distance of the k th mol ecul e from the centre of sorne arbitrarily chosen
molecule .
Thus an arbitrarily chosen molecular centre has become the origin of
eur ooordina te system .
However every molecule in a liquid o c amorphous sol ld caes not have exactly
the same relationship wi th fts neighbours - thus the derivation of equation VII.3
was somewhat premature .
The statistical nature of the structure can be allowed
for proper ly by introducing the radial distribution function, g(r), which 1s the
probabi l lty of f1nd1ng a molecule at sorne distance , e , from the origino
Consider
an element , or , of the radial distance, r; this elemental length defines an elemental vol ume of

'"

a nd the p r obability of findi ng each molecule within t his volume is


{4nr

Sr /V } g(r)

where V is the total volume of the liquid or amorphous salid.


Now g(r) does no t
exist only at a series oE points - it 1s a eontinuous function .
Thus the summation oE equation VII.3 has te be replaced by an integral , now that a definite
molecular position has been rep1aced by the probability of finding the mo1eeule at
that point .
The result is

s (Q)

1 + no

2
411 r g(r ) sine (Qr) dr

0-2

Fig . VIl .4.

(VIl.4)

In Section VIl.4 it viII be seen that {S{Q) - l} and {g(r) - l} are rela ted
by Fourier tra nsformation.
~t1cipating this resu1t, cansider the effect oE replaclng g(r) in equat 10n VI I.4 by

/'0

Radial distribution fu netion , g(r) , of water .


(The data used t o produce this figure were
taken f ram A.B. Narten and H.A. Levy, J . Chem .
Phys . ~, 2263-2269 , 1971 . )

no '" N/v
vhere no is t he number oE molecules per unit volume.
The limits of integration
are betwen zero and i nfinity if the liquid is considered to be of effeetively infinite e xtent on the mo l ecular scale.

008

O~

1 .. {g(r) - 1}
which yields
s(Q) - l + no

411r

sine (Qr ) dr + no

4wr

(g(r) - l} sine (Qr) dr (VIl.S)

The first i n teg ral in equation VIl.S 1s a l most exactly the same as the integra l
which arase in the de r ivation of equation V.5 in Section V . S; here the constant
no r e p l a ces the efEectivel y constant electron density, p, which appeared previ ously .
Also in equation VII . S the upper limit of integration is infinity. Equa tton V.S shows that the value of this integral then tends to zero - because as x
in equation V.S tends to infin ity t he va1ue of ~(x) tends to zaro.
Therefore the
first integral i n equation VIl . S can be neqlected.
In sUllU!lary , for a liquid or !lIOOrphous solid, the scattered intensity distribution is given by

zo

40

60

80

100

Q(nm-')Fig . VII.S.

lnterferenee Eunetion, S(Q), for water. (The


data used to produce this figure were taken
froro A.H. Narten and H. A. Levy, J . Chem.Phys.
~! 2263 - 2269, 1971.)

X- Ray Diffraction

70

1 (Q)

NF

Liquids and Amorphoul Solid5

l O.

5(Q) '" 1 + no

(VII.6)

4n

{g(t) - 1)

'l'"

(Q1S (Q )

sine (Qr) d r

fro~ equations VII.2 and VII.5.


The interference funeton, S(Q), allow$ for lntermolecular lnterfer ence effects and , not unexpectedly , depends on the radial distributlen function, gfr) , whlch describes the statistical arrangement o f molecules in
the sacple .
Figure VII.4 ahows an example of g(r) for a liquid and Flg. VII.S

shows the correspondinq interference function 5(2) .

Both functions tend to

'"

~41ues

ef unlty - q(r) at high r values and S{Q) at high Q values .


Since 5(Q) contains peaks , so will the intenslty distribution, I{Q).
Thus
interference qives rise to the appearance ef peaks in a diffraction
partern.
S{Q) dependa on the number of molecules per unit volurne, no' but th@
dependene@ is rath@r complieated beeause g (r) depends on no too - the overall
effect and lts influence on ICQ) wlll be dlscussed in the next section.
i n termole~lar

~,

The d lscussion in this next section will use the idea of the packing fraction,
whlch 15 related to Ro by
11 ""

( 4 /31'/l"&3 n

(VII.7)

Mer@ a is the r adius of a spherical molecule ie. ~ ls strictly deflned onl y fo r


spheres (in thzee dimensions).
It is often oonvenient to tbink of the molecules
in a liquld or solld as spheres and then n i5 the fractlon of space actual1y occupied by molecul es - as opposed to the space between them.
Unlike no ' n does oot
depend on the slze of the molecules; consequently it 16 more suitable for A general
di scuss ioo on the appearance o f the dlffractloo pattern from a liquid or amorphous
solid.

Fig. VII.6.

ro

12.
o.~_

lnterference function , S(Q) , for spheres of


r a dls a at differe nt values of the packing
fraction , n.

20

VII . 3. Appearance of diffractlon patterns

"

Inter ference effects appear ln the lnteoslty dlstrlbutlon , I{Q), because the
Arraoqement of DOlecules in a llquld, or amorphous sol id , ls not completely
fei!!ltureless .
There will always be order of a statlstical klnd, ie. the arri!llngement of mo:e cules 15 not truly random, beca use eaeh molecule excludes the others
from the space which lt occuples itself.
Figure VII.6 shows how the lnterfe rence
function , S(Q) , depeods on the packlng fractlon, ~ , as a result of this "shortrange order w
The f lgure was computed for an assembly of spheres whlch only lnteract ln so far as each sphere , of ri!!ldlus a , exeludes the others from the volurr.e ~bich
it ceeupies - the theory ls glven in Seetion VII . S.

"

The eifect of interference is that 1 (2) ls no l onge r given by the squared,


sphericall~ averaged molecular transform, F 2 (Q) , of the i deal gas case , but is modulated by S{Q) - it ean then exh lbit one or more fairly sharp peaks .
Note, however,
that the modulation leads to the retention of some lntenslty between these peaks.
Figure VI . ) shows the relatively slowly varylnq form of F 2 (Q) for a sphere, 00 4n
arbltrary $cale: Fig. VI I.? shows the appearaoce cf I(Q) when F 2 {Ql 15 multlplled
by 5(2) as l n equatl on VII.6.
Peak5 appearing ln I(Q) can be more clcsely s paced
than the peaks in F2(Q).
The reason is that F2(Q) conveys lnformatlon o n molecular structure but seQ) conveys ioformatlon on an arrangement of molecules. Stnce
dlstances between molecules are much greater thao the distances between atoms ln a
molecule, S(Q) 1s i!II DOre o8cil latory function than p2{Q) - o!IIccordlnq te Section V.4.
Therefore peaks in I ( Q) can be IDOre closely speced thao t he peaks in F2 (O )

Fig. VIL7.

lICDOS

Intensity distribution, I(Q), for spherea of


radlus a when Che packing frection, ~ ,
equals 0.6.

14

X-Ray Diffraction

Liquids anrl Amorphous Solids

Figure VII.7 ShoW8 ~~W successive peaks in l(Q) become progresslvely broader
with Lncreas1nq Q - this behaviour 1& characteristlc al dlffractlon pattern9 fro~
irregular assecblies cf moleeules.
lt arises from the properties of S(Q) whose
peaks become progres8Lvely brcader and less intense, as shown in Flg . VII.6. Consequently peaka in l{Q) tend to become less intense a1so, although this tendency

-experimental" form of 5(Q) i~ obtained from the measured intensity distribution,


I(Q) , following division by F (2) - as before .
Caleulated and experimental forms
of 5(Q) are ~pared as a test of the tri a l modelo
Alternatlvely the calculated
form of 5 (Q) can be Dultiplied by F 2 (Q) to yield a predicted I (Q) which i$ compared
vith the experimental d.istribution te test the modelo
Further detall$ on this
approach to deternining structures were glven in Sectlon 111.5.

Figure VII.6 shows that, as ~ Lncreases , the peaks in S(Q), and hence in l(Q),
becaDe aharper : and the first peak , in particular, ai S(Q) shifts to a slightly
hlqher Q value.
The sharpness arlses because, as n Lncreases, the oolecules move
closer toqether aOO lnterference effects become more marked.
When 1'1 reaches Lts
maxlmum value (0.74) the spheres wil l become close pac~ed and the arrangement will
be crystalline - we ahall see later (in Section V1II.2) that 5(2), for a crystal ,
consista aolely of a series of equally sharp peaks.
At the other extreme, of very
low n values, 5(2) ha s the form expected for an ideal gas, ie. by comparison of
equations V1.5 and VII.6 it has a constant va lue of unity, and no peaks appear.
1ncreased eloseneas al80 explalns the peak shift when n increases .
The cloaer
together the nolecules move, the higher the resolution of the diffraction data required to me8sure their separatlon ie. the information on their spaclng ls oonveyed
at higher Q values.
Nov that the diffraction pattern from a liquid or an amorphous salid can be recoqnised - hew can 9 (r) be determlned?

VIl.5. Theories of g (r ) for liquida

72

can be Itodified by the behaviour o f F 2 (O) .

YII.4 . Determlnation ef the arrangement of molecules


It la alvays possible, at least In principIe, te deduce the radial distrl bution functlon, 9 (r), vhich describes the arrangement of molecules in a liquld o r
amorphous sol i d, froa the scattered Lntenslty dist~lbutlon, I {Q) .
The spherlcally
averaqed molecular transfoml, F {Q}, can be calculated, presuminq that the structure
of the Dolecules is knovn, uslnq equation VI. 3.
Dlvls10n of I{Q) , whlch ls
measuxed experimentally, by F2(Q) yields S{Q) acoordlng to equation VII. 6.
The
effect of N can be neglected as Lt acta simply as a scale factor.
Appl ication of
the Lnvers10n property of the Fourier transform, deacribed in Section 11.4, to the
definition ol S(2) in equation YII . 6 yields
9

(r) - 1

(l/no)

41fQ2 {s (2) - l} sine (Qr) dQ

(VIL8 )

The limits cf integration should be between zero and lnflnlty but . aceordlng to

Sectien 111 .6, there 15 a limit to the extent of Q-space which 19 measurable.
In
practlce, therefore, the upper l i mit has te be truncated.
No phase problem arises
in the i nversion of equation VII.6 because S(Q) is real a nd a lways positive - llke
I(Q) and F2{Q) from whieh it is calculated.
Although S(2) and , hence, the result
from equatlcn VII.8 will usually be obtained on an arbitrary scale, lt is possible
to obtain absolute values for g(r) .
lt i9 only neces9ary to scal e t.he result obtainBd for (g (r) - l} so that q(r) tends t.o unity at. hlgh r values , te achieve the
required resulto
Deduction of g{r) In thi s way has two disadvantages: spurious peaks can appear
ln q(r ), if an insufficient range of Q-space is used ln equation VII.S, and the
result ia very sensitive te experimental noise.
These di9advantages were dis cusaeCI In SectLon VL5.
the advantage of the deductive approach ls that lt can
yl eld a. posslbl y imperfect , trial model for g{r), if no other la avai l able , as ~
aid te solutlon by trial-ana-error.
Trial - and - error determination of q (r) does not involve Fourie r transfonlation
ol noiay data arad the truncatlon effects should not ariae for the reason given in
SectlDn 1U.6 .
"trialllOdel for g(r) i8 used to compute S (Q).
'I'hen the

73

X-Ray diffraetion data froD liquids are often used to test theories of the
liquid state; the purpose of this section i5 te indicate how these theories are
related to q(r) and thence, by equation VII.6, to S(2).
It ls not intended to
give a thorough account of liquid state physlcs or even to justify all of the
statements made both wculd be far beyond the scope ol this book.
The interested
reader ia referred to tne book by Croxton (see B1BLIOGRAPHY Section 9) lor further
detalls.
The total correlation function , h(r) is defined by
(VIL9)

h(r) - 9(r) - 1

Figure VII.4 shows that h(r) then representa fluetuations of 9 (r) about the va lue
vhlch it approaches at large r values.
In order te proceed further, consider how
one molecule lnfluences the position of another.
The first molecule can interact
directly with the second but it can alsa influence the posit1on of a third molecule
the pasitlon ef the third then exerts a further inlluence on the position of the
aecond.
Thus the influence of one colecule on another can be either direct or 10direct .
ThLs idea leads te the relationship
h(r) .. C {r ) + no h( r ) 0

C(r}

(VII.10)

which ls known as the Ornstein-Zernike equat.ion and can be used as a definltion of


the direct correlatlon function, C(r) .
There is a simple relationship between the interference function, 5(Q), and
the d1rect correlation function.
Remember that the Four ier transform of the convolutlon of two functions is equal to the product c f their individual Fourier
transforma - as in Section 11.4 .
Fourier transformation of equation VIL 10 yields

h(Q) C(2) + no h(Q}C(Q}


vhere h(Q) and e(Q} are the tra nsforms of h(r) and C(r) , respectively.
tions Vll . 6, YI1.9 and VII.ll it follows that
5 (Q)

( - no

e- (2)) -1

(VILll)
From equa-

(VII. 12)

Equation VII.12 allows S(Q) to be calculated from the Fouri er tranaform of C(r) if
no i8 knoWJ'\.
The direct correlation function, C(r), can be related te the intermolecular
potential functien. ~ ( r), vhich describes t he i nteraction between tvo molecules.
"t Large valuea of r . strictly as r tends to 1nfinity, C(r) 1s qiven by
(VII. 13)
vhere k B 18 Boltzmann's constant and T i8 the temperature, on the Kelvin scale, as

X-Ray Diffraction
TABLE VII.l.

Liquids and Amorphous Solids

Pereus-Yevick Hard-Sphere 01rect Correlation


Funetion
a + 6(r!2a) -+ y(r/2aI

C(Q) and no can be calculated from equations VII.16 and VII.7 respectively.
Finally S(Q) can be calculated from C(Q) and no using equation VII.12.
VII.6. Snrrmary

<:

2a

2.

C(r)
O

2fl)2(1

(1 -+

.:ifl {l

(fl/2) }2

-f

"
(l

(fl/2) Cl -+ 2n) 2 (1

Liquids and amarphous solids have an irregular arrangement of molecules. But,


in contrast to ideal gases , these molecules are sufficiently close for interference
to QCcur between X- rays scattered in the same direction by different molecules.
Thus ,the intenslty distribtion, I(Q}, expected of an ideal gas, is rnodulated by an
intexference function, S(Q) .
Beeause the moleeules nave random orientations, I(Q)
is independent of the direction of Q and the diffraction pattern has circ ular symmetry.
Diffraction patterns from liquids and amorphous solids can be recognised
because peaks in I (Q) becoroe increasi ngly broader with lnereasing Q.

-4
-4

" -4
"

in Section 11.6.
A theory oE the liquid state amounts to an expression far ~(r)
which at large r values is simply related to C{r) by equation VII.13.
According
to equation VII.12, S(Q} can be predieted from C(r) - sueh a prediction can be
tested by compar1son w1th experiment as deseribed in Section VII.4.
A surprisingly successful agreement between theory and experiment ean oEten
be aehieved by assuming that the only interaetion between molecules i5 mutual exclusion - eaeh excludes the others from the volume it oceupies .
Then ~(r) i5
given by

2a

<:

2a

(VII . 14)

Q (r)

Equation VI1.14
where the molecules are oonsidered to be spheres oE radius a.
represents a "hard sphere" model fo r the van der Waals' interaetion bet\o/een two
identical rnolecules. Better functions are available to represent van der Waals'
interactions but they diEfer mainl y in including a small. long-range attractive
termo
Long- range forces do not appear to contribute much to the structures of
most liquids - although for water, long-range dipole - dipol e interactions have to be
taken into account if S(Q) is te be explained satisfactorily .
Combination of the hard sphere model with a very successful approximate theory
(the Percus - Yeviek approximat ion ) allows S(Q) to be cornputed readily .
The PercusYevick approximation neglects certain kinds oE interactions between mo1ecules.
A
polynomia1 representation for C(r ) can then be developed \o/hich, accarding to equations VII .l 3 and VII . 14 has the property that
C(r)

2a

(VIl . 1Sl

The polynornial is given in Table VII . l; unlike the e~pression for C(r) in equation
VIL13, th1s polynomial representation is valid for all r values.
It follows from
equations 11. 9 and VII.15 that the ~ourier transforID of C(r) is given by
2.

e (Q) .. [ o

41fr

e (r ) sine (Qr) dr

75

(VIL 16)

since C(r) must be the same in a11 direetions ie. it has spherica1 symmetry.
n and a are knoWD, C (r ) can be obtained using the equa tions in Table VII.l.

lf
Then

The interference funct ion . S(Q), c an be calculated froro the structure of these
irregular systems.
Such structures are described by a radial distribution func tion, g(r), which 1s the probability of f i nding another molecule at a given di stance fram an arbitrarily chosen molecul ar centre.
S(Q) 1s re lated to g(r) by a
Fourier transfarmation .
If the molecular structure 15 known. S(Q) can be calculated fram I(Q) - g(r ) can then be obtained by inverse transformation.
Because o f
the errars which may be introduced by inverse transformation , it is preferable to
develop a model for g(r), calculate S(Q) and compare the result with that observed.
For liquids, theories have been developed which relate g{r), and hence S(Q). to
intermoleeular potential fun ctions .

One- Dimensional Cr ys t als

77

e - AXIS

CHAPTER VIII

.....
.. ...

One-dimensional Crystals

VIII.l. Introductian
A crystal i s a salid with a regularly repetitive structure.
As in any solid ,
interference wi ll oceur between X-rays scattered in the same direetion by different
moleeules because these mol ecules are pae~ed together so closely.
The regularity
oE this paeking makes the interferenee effeets partieularly easy to calcul ate .

Fig . VIII.l.

...-

._...... ,

...--

lATTI CE

VIII.2. Interference effeet s

lAYE Il

According to section II.4, the Fourier transform oE a one-dimensional erystal


is then given by the tr~sform of a layer , F(Ql, multipl i ed by the tran sform of a
Suppose that N points are r equ1red to generate the
one-dimensional lattice , ~{Q).
crystal.
In order to ealeulate the Fourier transform oE this rov of diserete
points , the integral of equation Ir .3 can be replaced by the summation

76

One-dimensional crystal .

A one-dimensional erystal has a regularly repeating strueture in one direetion


but this regular repetition 15 not a Eeature oE the structure in other directions.
One-dimensional erystals are considered in this book for three different reasans.
Flrstl y , the ane - dimensional crysta l provides a simpl e system tor 11lustrating the
properties of crystals in general eg o in Seetion VIII.6 .
Secondly, the theory of
dlffraetion by a one-dimensional crystal provides an essential background to understanding diffra etlon by three-dimensional crystals in Chapter X.
Thir dly, one dimensional crystals aetually occur a nd their diffraetlon patterns have to be interpreted in practice.
Sorne examples oE one-dimensional crystals viII be encountered
in Chapter !lL

Figure VII I.I shows a sehematic example of a one-dimensional crystal it consists of layers of bodies vhose arrangement repeats regularly in one direction but
not in others.
In reality sueh a structure would be three-dimenslonal with the
lines of bodles in the figure extending over planes which were perpendicular be the
plane oE the page - i t ls left te the reader's imagination te supply the third
dimension o
The bodies might be atoms or molecules or even structures made up of
many rnolecules.
The repeat direction will be designated the e-axis vhere e is the
repea t dlstanc:e.
Figure VIII.2 shows how Fi g . VIII.l can be generated by the convolution of a layer of bodies with a row of points - as in Fig. II.S.
This row oE
points ls t he one- dimensional lattice oE the c:rystal.

.t

...............

t:
"
o

Fig. VIII.2.

Gener ation oE a one-dimensional crystal by


eonvolution.

,.

X-Ray Diffractton

"

One - Dimensiona l Crystals

'(2) .,

L:

exp {l

!..:1-2.1

(VIlI . l)

j-l
where!.j 18 the pos ltlon of the j th point with respect to soma or i gln .
In F19_
VIII . 2 the erigin 18 arbitrarl1y placed at the end of the lattice and each point

ls separated !rom lts predeces90r by a

Now , when equation VIII.l 18

vector~.

written Ollt in full , l t can be seen te be a geometrical proqresslon whlch can be

summed , in tbe usual way, as follows:

'(2)

-+ exp

30

i z.o

G
~

(1 ~ . Q.l + exp (1 2~.~) +

(O

- - - - + exp (l{N - l } ~.~V


- {l - exp (1

Ns..Q.1 J/{l - exp (1 s..Q)}

e.p (1 N~.:2!2)

{ e.p
e.p

eKp ti S.~2)

(- i

Ns..2!2)

s..212)

exp (1 Ns.212)

exp (1

s.2121

CieN -

1)

S.2./2}

F(2..). ( ~

5"

12(VIII.2 )

sin (s.212)

The lntenslty el X-rays scattered by the crystal can now be calculat ed.

lts Fourler transform 1& given by

4"

Q.C _ _

,in (Ns 21 2 )
., eKp

Since

the scattered intenslty 19 g i ven , acoor-

ding to equa tion 11.5 , by

~ IIJ

.,

(VII!.J )
where P-CR'

ls the oompleK eon jugate of F (Rl .


IC21 - SCS(lF(R)F-(2)
S(~)

sin

(~.212)/sin

(~.g2 )

Prom equatlons VI II . 2 and VIII . )

4n

1T

Q.C _
(VIII.4(

N = 50

Here 5(2) 15 tne lnterferenee function for a one-dimensional erystal.


Sinee the
1ntens1ty seAttered by A 81n9l8 l ayer in isolation would be F(R)F-(2' the interferenee funet10n shows the effeet of staeking N layers on top of each other, a distanee e apart, to form a one-dimensionally perlodic structure.
lt can be shown analyt1eally that , as N tends to lnfinlty, 5(2) t ende to zero exeept in those reqlons of Q-epaee whieh satisfy the equation
~.:2.

O ~---L~--~----~~--c

2'lfl

(VIII. 5 )

fT

2n

311

4- n

5 rr

Bere l i8 any integer whieh ean have positive, negatlve and zera values,
Rather
than de riving equat ion VIII.5 analytieally , a numerieal approaeh ls adopted bece.
The analytlcal apprOAch ls deserlbed by Lipson and Taylor (see BIBLIOGRAPHY Seetlon 10).
In Flq. VII I.J, the 1nterference function 15 pletted aqainst Qc (le.
~.,2 when the twa vector8 Are parallel) for dlfferent values ef N.
When N 110 Slllall ,
the hlghest peaks in S(R! are regularly spaeed a distanee 2T1 / c apart 1n Q-spaee;
these peaka all nave the SlUlIe helght and w1dth.
As N increases the maln peak s
beCOIDe very nueh hiqher and s harper.
When N ls larga , S<2.) Cons18ts of sharp
peUII .paced 2./c aparto

F19. VIII . J.

Crystal lnterferenee fu nct1on , S(,2), deflned


by equation VIII.4 as a function of Qc.

X- Ray Diffraction

80

C-A ( S

-1

1.1

,,<L '

,:::

one-dimenslonal

I--+-- - -- ~

~::.

-- -.

"'",

Fig. VI I I.4.

The

(, -AXI S

"
E WAl D 5PHERE

81

One-Dimens i onal Crystals

,.,

2 ~c

'!.

INCID ENT X- RAV

BEAM

\ 2 ., O

--

"

Equation VIII.5 defines a set ef planes in


Q-space which are perpendicular t o the
e - axis direction .
requl~rity

acts as a very unu8ual amplifier fo r t he 1n-

tenaity whic h would be aeatter ed by a s ingle layer in isolatlon.


Fr~ Flq .
VIII.3 it appeer s that S(~) lncreases this lntens lty by an enormous factor, of t he

order of N2. in a fev selected regions o f Q-space.


all intensity 15 e f f ectively o blite rated .

But

in the majori ty of Q-space

Fi; . VI II . 5 .

Because t her e 15 e l most no acatter in

mest directiona, thls hiqhl y s elective amplification doe s not violete the principi e
ef conservation ef energy - despite t he magnit ude o l the gaLn .
Th.1. ampl i fLcat i on has

ilfI

perpendicular te c since only then can their dot produc t be zaro: ~ and 2s in the
f iqure previde exampl es.
All such vectors l1e on a pl ane perpendicular to ~.
Vectors like R6 and~, f o r which 2. . ~ equals 2~ (henee t .. 1) , al L end in aplane
whieh 15 parallel to the l .. aplane and distant 2w/c frotll lt.
Sirnilar1y the vector li Ra and 29 define another p1ane with l .. 2 .
For Rl. , ~ and Q) . the dot product ~.2 equals - 23 .
Hence these vectors define apl ane ",h i eh i B d istant 2~/c
from t he t .. O plane, but i n the opposlte direct ion to the l .. 1 plane; thls plane
has t .. - 1.
Since S (2) ls nan-zero anl y on these planes, lt follo,",5 from equa t i on
VII I.4 , ehat I( ~) too is non-zero only an them .

importan t consequence, whi c h 15 oft e n over l ooked,

far .yatees wh i cn are mixtut es of o rdered and disor dered phase s .


The amplified
region of Q-spac e , f or the or der ed phase , vill be very int ense compared with the
scatter from the d i sordered phase.
r n the r elative ly short time period r e quired
to aeallUre the former , the latt er m.ay remain undeteeted.
Thus X-ra y diffr/lction
is very insensitive to t he pr e senee o f disordered pha ses i n eueh systems .
The interferenee f uneti cn for a c rystal is very dilferent from th/lt tor an
i rregula r syetem such as a liquid c r a n amorphous sol ido
Pigure VIII.3 show$
that, f or 4 eryatal, the peaks a r e /lll equal ly sharp - in complete contrast te
~i9 . VII . 6 whe re successive peaks inerease in vidth.
HQw does tne sharpness of
S{~l affect the /lppearance of the diffraction pattern?
Befor e t nis que s tion can
be answer~ we ahal l have to consider how the diffra ction pattern from a onedimen s i onal cryatal i 9 f ormed .
VI I I.J . Format i on of the diffraction pattern
lt follows froa equation VIII.5 that the intensity 01 X-rays, I(2l, scattered
by a one -d~nsional cryatal i5 non -zero only on a set o f planes, spaced 2 ~/c apart
in Q- ~ce, which a r e perpendicular to the e- axis d i rect ion.
'I'he i nterference
lunct i on, S(~), of equation VII I.4 is effeetively non-zero onl y when equation
VIII . 5 i 8 satlsfied .
Figure VIII.4 shows t hat equa tion v rII . 5 defines a set of
paralL.l p larles per pendicular to t he e-axis; remember that

and thllt the dot product 01 tvo vectors is t he p rojectl oo o f the flrse. on t.o the
IIeCOnd - ...-ultiplied by the I eng e.h of the second.
Wh.elnever t i. zero, 2 must be

Formation o f the diffr action pattern from a


one-dimens10nal c r ystal.

Fi gura 'VI I I .S 9hows that the diffraetion pattarn i9 confined to a ser ies of
l inee, knovn a s "layer l ines"; these lines are formed when tne planes , on whleh
In the figure a beam
1 (2.) i 8 non- zero, interseet the surface of tne Eva ld sphere .
of X-raye ls incident at rlght angles ta the e - axis of a one-dimensional erystal .
Here O, the origin of real space, i5 defined by the i nter section of the beam with
t he e -axi s .
By definitian O', the ori gin of Q- space , is dista nt 2~/~ from O along
the dlr ection of the undef 1eeted ream.
1 (2.) i8 non-ze r a only o n a set of planes ,
sp&ced 2~/c apart in Q-space , whi eh are perpendicular te the e - axis dlrection. As
shovn in Fig. VI II.5, the pl anes interseet the Ewa1d ephere a l ong a ser ies af lines.
These lines , referred to as "l ayer lioes", ean be specl f ied, or "indexed", by t he
value of t .
By definition the plane eontai ning O ' has a z e r o va l ue of t.
The
oorresponding layer 1i ne, vith t _ O, ls often ealled the "equator" t he 1ine on
the d iffrac tlon pattern which is pera11e1 to the e-a xis, and therefore perpendic ular ta the equator, i5 called t he "mer1dian" .
In Fi g. VIII.5 t he e - axis of Q-spaee i5 de finad to be paral l el to the e-axis
of real space, naturally 1t passes through O the or i gin of Q-apa.ce .
The planes
on which I (2.1 is non-zero are perpendicular te the e-axis and, therefore , te t he
t -axis .
The t th plane of Q-space crosses the c-axis at a dls t ance
(VIII.61

One-Dimensional Cry stals

X-Ray Diffract ion

82

TABLE VIl I. l .

83

Relationship between film (x cY) and Q-space

(t . C) coor dLnates tor a fla t film Ferpen dLcular te t he lncident X- ray beam .
E""'''LD

{The axis of the one-dimensional erys ta! 15 perpendicular


to the X- ray belUll whose ..... avelenqth 15 Al

SP..jEIU.

x
y " 2R(r;:"/2n)/y

y _ 2 -

(tl/2wl 2 _ ((1/2,)2

FLg. VIII.6.

Definition of t and

~.

A devi ce called a Berna l char t can be used to measure ~ frcm the diff r aetion
even .... hen e is small - equation VIII. 6 can then be used to ca l culate c f r om
1'; .
Figure VIII.6 shows a vector R vhieh termina tes a t A - the intersection of t he
EWald sphere with a peint on the l th p l ane on ....hieh 1 (2.) is non-zera.
Thus t he
intensity a t A gives rise to a point on the diffraction pattern .
If the pattern
is recordad on a flat fi lm , the distance af this paint from the centre of the pattern (the intersection of the equator and merid!an) is relat ed to Q by equation
IV.2 .
Now Q. has components ; a nd e . . hieh a re, respeetivel y, par allel and perpendicular to ,the t-axis.
{J;; is the distance of A fram B - B i5 the point .... here the
l th plane i ntersects the ~-axis , as shown in Fig. VIII . 6 . }
Similarly the corresponding peint on the film has equatori al and meridional components x and y.
(Note
that he r e x is a component of x a nd not its modulus - in contrast to the usaqe in
equ<1.tion I V.2 . )
Figure IV.S showed hov the diffraction pattern a r ose f r oo. projecti nq Q-spa ce on a flat fil~.
OOnsiderable trigo nometric manipulati on is required to relate the components in Q-spaee to those on the film - see Volume 11 oE
the "International Tables for X-Ray Crystallography " (BIBLIOGRAPH'f Section 2) . The
re sults are glven in Table VIII.L

15

~ttern

-5

FLq_ VII!.7.

from O' .
Except tor the trivial case when
equals zero , the r; - axis dees not
touch the surface cl the Ewald sphere.
However, Lf e 15 sufflcle ntly large, r;
.... nl be very small for the f i rst fe .... planes of non-zero 1 (Q.)
Consequently these
lntersect such a limlted region of the surface of the Ewald sphere, ar ound O' , that
lt i 5 effectively aplane which is perpendicular to the incident beam d irection .
Then t e ffectively lies on the sur fa ce of the sphere for small values of 'l .
As a
resu lt the me r idian of the diffracti on pattern corresponds to the ;: -axis of Q- gpace ,
f or layer lines with low i values , provided c i5 sufficiently larqe .
The distances between layer l ines can be measured on t he diffraction pattern and converted
into Q-space uslng equation IV.2: t hey can then be equated with t oE equation
VIII. 6 in order to determine c.

-10

10

15

Bernal ahart lor the diffractlon pattarn


fro~ a one-dlmenslonal erystal where the
lncident X-ray beam le perpendicular to the
e-axis recorded on a llat photographic film
with a spaciman-to-fl1m dlstance of 10 cm .

Figure VI II .? shows a Be r nal chart: it i5 essentia lly a two-dimensional ruler


for rneasurlng ~ and ~ directly from the diffraction pattern.
For a given value
of R. the re lationships of Tabl e VIII.l can be used to pl ot line s whieh pass
throuqh equal values of 1'; and ~ on the film.
R, the dis tance between t he specimen
a nd the film, can be readily rnea5ured during an experiment o
In praetice the
measurements of ~ and e are best made on a phot oqraphic enlargement of t he dif fract lon pattern.
(8ut measur ement s of intenslty must always be made on the original
pattern . )
'I'he scale oE the enlargement can be measured and the Berna.! chart
enlarqed by the same fact or.
TOen the chart 15 la id DO the pattern and the value
of t eorre spondinq to the layar 11ne separ ation 151 read directly.
The spacinq e

One- Dimens ional Crystals

X-Ray Diffraction

8'

85

VII1 . 4. I"tensity of the l aye r l i nes

~ - AXIS WI-IEN PERPENDICULAR

TO INC IOENT

The l ayer l ines in ~ig. V111 . 6 need not a l l have t he same intensity.
According te equatien VII1.4, a non-zera value ef S{~) only determines that the lines
are allowed .
The intensity o f a line i5 qiven by P (R.)F* ( ~ ampl1fied by t he value
of S (R} - which i5 t he same for every layer l i ne but zero elsewhere.
Sinee F ( ~)
i8 the ~ourier transform of the e lectron density in a layer o f the one-dimens ional
crystal , it is the s tructure ef one of the se layers , shown in Fiq. VI II.2, ~hich
determines t he intensity along a layer lineo

~EA,",

T llTED AXIS

EWALD SPHERE

INCIDEN T

X- RAY BEAM

Fig. v III. a.

Seetan of the Ewald s phere showing the


e f fect of tilting t ne

can be c alculat ed

fr~

The equat o r pr ovides lnformAtion about t he structure of the one-dimensional


crystal proj ected on to the plane o f a l a ye r ie. perpendicular te its e -axis.
Seetion IV.4 i ndi cated that aplane section o f Q-6pace, vhic h passes tbrough O',
prevides informatlon a bout the scatter1nq speclJl'\en projected on te a paralle l plane
ln real space.
This pr operty follove dlreetly from the definitlon of the Fourie r
transform in equation II.6 and leads te the specia l case descr ibed here .
As in
Seetion 11.4, it l s not intended te prove the general propertle s of the Fourier
transform he re - the reader is referred t e books by Bracewe ll and Champeney (see
BIBLIOGRAPBY Sectl on 4) .

~-axls.

e uslnq equatlon VIII. 6 .

The intensity di s tribution a10n9 t he e - axis can be reoorded by ti lt ing tne


one-dimensional c rystal so that its e - axis 1 5 no longer perpe ndi cular to the beam.
Figure vIII. a 18 a section through the Ewald sphere.
It shows tha t t he e-ax is
10'111 touch the Ewald sph ere on the l th layer 11ne Lf lt ls t ilted through an
appropriate angla ,
sin

01. ,
-

",here

(1;/2)/(2,./),)

(VI II. 7)

Proa equatlons VI II.6 a nd VIII. ? :


a sin - 1 (l.)./2c)

(V I n.S )

A separate ti l t angle 1 5 required fo r each of the planes on ",hieh 1(2) ls non - ~e ro ,


~~cordin9 be equati on VIII.S, sinee l has a different value f or eaeh plane.
Ho~
n t.he C-axis be tilted?
lt f o l lOW8 from the r otation pr oper ties of the Fourie r
transform, in Section 11 . 4, that a tilt in r eal s paee ls accompani ed by an equal
tilt , in the same d ireetion, a bout a parallel axis in Q- 5pace .
Thu8 , in order te
tilt the t -axis as required, the erys tal e - axis is tilted so that it departs , by an
angle a , fre. the perpend icular te the ineident beam .
knovn~ these meaaurements re ly on two presumptiona .
ORe : that t he speeimen i 8
be a one -dilDensional eryst al.
Two : tha t the specime n can be set up so
that its e-axis ia perpendicu lar to the i ncident X- r ay beam.
If the pat ter n consillta ef a s er i es o f 1 ayer line ll of comparable shar pness , then the specmen can be
aSllumed to be a one-dimensional crystal.
According to Seeton III .8 I (n) i5
i dentLeal te I (_n)
- prov ided t ha t th ere are no atoms present ",ith an ' a b serption
~
edg

e el ose te the 1.neLdent wavelength ie. if a nomalous 5eattering la neg l iqible


'l'hua vhen the 1; -ax1 s, and hence the e-axis, is pe r pendicular to the X-ray beam
~~ intenaity distribution w11 l con f orm to the cand iticn t hat I (~l is ident i cai to
~l .
The t1lt. of tba specimen can be adju!>ted , u n t.il t.his condition i5 lllet te
:NI. e the e - axis perpendicular to the inc ident beam .
'

Similarly the ~ -axi s prevides i nformation about the s truc ture e f t he c r ystal
pro j ected on t o the e-axis.
Thls result fo llows frem exaetly the sama proper t y
of the Fourier transformo
Now a l ine in Q- s pa ee , vhieh passes through O', pro vldes information a bout the scat te r ing speeimen projected on to a parallel l i ne in
real space.
once again this property f ellows directly from the def inition of t he
~ourier transform in equation II.6 .
An expression will now be derived f er the ~our ier transform along the C-axl s note that the corresponding i nte nsity distrlbution only corresponds to the me ridian
of the diffraction pattern if e 16 very l arge and , even then , only at 10v l values.
We have s e en t hat the ~ouri er transforID ef a one-dimensional cryatal is glven by
F(~l v (~) ",hare V (~) simply l ead s to the intensity , and he nce the transform, F( ~} ,
of a layer in the one-dimensional crystal being amp l ified a l ong certain p l anes of
Q-space but ob litera ted elsevbere .
Thus, i n or d er te ealculate the Fourier transf o re of a one -d imensiona l e r ystal, ve need only calculat e t he t r ansf orm of a 8ingle
layer - and t he cal culation can be confined to the planes in Q- space which a re
specified by i ntegral val u es of l .

Since ve are concerned with t he transform a l o ng the ~ - axis , we need to calculate the Four l er transform of the electron density , o f a single l ayer o f the onedilUensional crys tal, projected on te the e-axis .
'I'he p rojected electron dens ity
in a single l ayer is deno ted by p (Z) ; where a di splacement along t he e - a xis is
denoted. by
r

Zc

(VIll .9)

Bere Z ie a fra c tional translat ion since e, as i n ~ig. VIII . l , is the distance between the crys tal l a yers; i f Z were grea ter tha n uni t.y we would be considering the
structure of the next. laye r.
Since we are on l." calculating the ~ourler transform
alo ng the C- axis , which ls parallel te e , the dot product , which a rises in t he
deflnition of the Fourier tra n s f orm , becomes
~.~ - rQ - ZcC 2nlz

(VUI. IO)

froa equationll VIII.6 and VIII.9.


Equat ion VIII.IO gives the values of :... ~ along
the ~ -axis where the Fourier transform of the one-dimensional crystal ill non-zero.
ThUII, fro~ equatienll 11.6 and VII I .IO, the Fourier transform ot a single l a ye r

86

X-RBy DiffTBction

Ooe-Dimensional Crystals

projected on te the e - a xis direction, when lt forme part ef a one-dlmenslona l c rys-

Therefere it is not n eceasarlly valid to attribute peaks in the calculated


p ( zl te featur es ln the scatteri ng specimen.
Suppose thAt a peak appears ln p (z ) ,
like that i n P ig . I I L 7 - doea it represent a t rue structural feature?
Thl s lDOdel
f or p ( Z) can be used te cOlQpute the expected ceridlenal intens ity dist r ibution ,
rcl ). from equations VIl L ll and I LS , to compare with that observed .
other
mode ls , in whlch the peak i 5 ~thed out , cOuld al so be used to calculate va l ues
of l(!) and the levels of agreement with e xperimental data compared te the agreement for the peaky model.
The re would only be evidence f or the peak rep r esentlng
a r e al structural feature lf tne level o f agreernent for the peaky model were s ig nificantl y better than for t he others.
A suitable stati s tica l test , t o determine
whether such a difference ls aignlficant, i 8 described in Volume IV o f the -Inte rnati onal Tabl e s for X-Ray Cryatallo<raphy" (see BIBLIOORAPHY SecUon 2).

tal, 15 given by
F

(tl -

1 p [ Z) exp

(2'1111z) dZ

(VIII.ll)

Note chat point s 410ng the e-axis , where P (2) 18 non-zero , a re speci f i ed by values
of l and so the transforID at the se polnts c an be wrltten as F(!l .
VII I .S . Deduction el electro" density
[n the diffr.ction pa tterns fro~ many r eal ex&mples of one -d imensional cr ystala, r(gJ 19 r e asonably intense only on the e-ax is and on the plane vi th l _ O.
lf e 19 large , the e-axis appears on the meridiano
Since I(~) decreases rapidly ,
in lntensity, off the e-axis , the merld!an theo appea r s as a rov cf spots .
These
epots will have spac ings which correspond to srr""ll va lues of t a nd are often referred to as -LOIo/-angla meridiona l" patterns .
~ne e lectron denaity of a layer proj ected on to the e-axis direction , p(Z) ,
can be deduced from a l ow-angle ceridional pattern - p rovided that t he phase problem , of Secti on 111.2, i 5 soluble .
Four ler inversion of e quatlon VIII .II y i eIds ,
according to SectiOIi 1[.4:

VIlL 6 . Bra99's law


Bragg ' s lav 18 often used to expla in X-ray diffractlon patterns f rom crystals.
COn s ider the X-ra ys scattere d SO that \( 15 para llel to the vector ~ which aeparates the points in Fig. VIII.2.
(In t hls experiment the inc ldent beam wauld not
be perpendicular to the e-axis.)
Thi s r ow o E polnts la the one-dimenslonal l attice o f t he c rystal.
For t hese X- rays the dot product ~. 2. becomes Qc and equat i on VI I I. 5 becomes
(VIII . 13)

Q 2Tillc
E'{tl exp (- 21'Tiiz)

p(Z) -

(V IIL 12 )

Compari son o! equations 11 . 4 and VIII. 13 yle lds


( 4Ir/:\)

Sere a sumcation, r ath e r than an integral, is app ropr ia te because F (I) i8 confi ned
t o a series o f d iscre te points .
In practice the inten s ity, ICI) , is neasured at
these peints -~ the r ea l and imaginar y parts of F(I) then have to be recove red from
ita modul us, I (i ) , by one of the methods of Section III .4.
Recovery of these
parts cons ti t utes a solution to the pha5e problern.
Note that , aince F{i) i5 not
a smoothly varying functio n, the so- called "direct methods " which are approp riate
in this case ar e fax more subtl e than the simple example gi ven i n Sec t ion 111 .4.
Omiss i on of F (O) does not distort the focm of p eZ) cal cul ated using equatian
VIIl.l 2 .
Thus it i s of no COIicern that the inten s ity of the undefl ected beam 1 5
no t measured.
Equation VII Ll2 can be rea rranged to give
p (Z) F(O) +

.L

Fel) exp (- 2iZ)

,lo
Tbe r esult s hows t ha t F (O) a cts only as a constant background which daes nat a ffect
the form of p eZ) - it s omission has t he effect o f removing a const ant background
from the cal culated ~lectron den5i ty .
In the gene ral case of Section I 1J. 7 the r e
v as the pos s ibility of scattered i nte ns ity very close to the undeflected beam which
~a~ried i nformation abo u t fluc tua tiens in the structure.
Removal ef the und efl ec e beam l eo to remova l of the neighbouring acatter , a t very l ew Q values with t he
con sequent l os s of s truct ural i nformation .
Here the information carr ied ' bY t he
scattered X-rays ls con fi ned t o the layer lines and is easily separateo.
0 1 d The cal cu.l ated e l ectron dens ity dist ribu tion , P (Z) , can be distorted by loss
1 ~ffraction da ta at high Q values .
Strict l y equation VIII.12 should include
a 1
val ues betwee n minus and plus infin ity.
Loas of higher t values corresponds to limit ing t he e xtent oE Q-space which i a used .
According te Section V. 4 ,
th. electron density can then only be calcul ated at l ey resolu tlon.
More seriously, s purieus peaks can appear in p eZ) - as ~ hown in Section 111 .7.

87

sin (+/2) - 2lfIlc

where ~ 19 the ang le through wbich the X- r a y s a re scattered.


defined as ~/2 . equati on VII 1. 14 becomes
2c sln e _

(VI II . l4 1
If the angle

is

i~

which is the Eorm o f Bragg ' s law whlch oonventl onally appears ln books 01'1 X-ray
crystallagraphy.
Thus Bragg's law arises a utonat ically froa tne Fourier transform of a crystal.
Wby adopt thls a pparently more complicated approach instead of d e riv ing Bragg ' s
l aw by the simpl e met hod given in elementa ry phy slcs textbooks?
The reason is
that Bragg ' s law o nly describes wnen I(\() might be expecte d to be non- zero; lt p r ovides no f ur t her i nformation about I (~ and give s no clue a s to how a structur e
might be de t ermined.
Furthermore the use o f Bragg'a l aw to explain interferenc e
effects can be ver y mis l eading because it applles onl y to crys tal s .
The approach
a dopted in th.is book shows how structure can be determined. (as d escri bed in Chapter III ) and is perfectly general - it appl ies to a11 statea o f matter.
VIII.;. Dl sorder
No crystal ia perfecto
In ~ig. VII I .l the bodies cannot a ll be expected to
l l e exactl y on the planes spaced a distance e apart.
For one r e ason or another a
body IlIight have a displ a c e.ment, r, a10ng the c - axis directlon - aboye or bel ow its
p l ane.
Flqure VIII;9 shows the resulting, one-diDIen s lonal cryatal.
Let the
root-mean- square displacement be o.
If the di 5trlbutlon i 5 Ga ussian , a reprelents
the standard deviation of the displaced diatancea whose diatributlo n 15 then given
by

(VlII . lS )

l<0D0I!i G

BB

X-Ray DiCfraction

One-Dimensional Cryst all

B.

e -AXIS

ef the speeimen .
No more energy ls absorbed: X-rays are absorbed by matter when
e l eetre ns are prometed to higher energy levela - so a b80rption by a giv en number of
i dentieal bodi es is l argely i ndependent af their pasltlons.
If the principle cf
e onservatien oE energy ia not te be vl01ated, the energy lost f rom the layer lines
must be used ta scatter X- raya ln other direct i ons - whLch leads to the appeara nee
of weak, dlffuse intenslty between them.
A rigorous account of dlffuse intensity
ls glven by Gu1nler, for a three -dimensional erysta1; James glves far ~ re det ail
(see BIBLIOGRAPBY Sect ion 2 ) .


...,
'\'
.....

.. .-..

.-.. .-..
.-..
..- .

Fiq. VIII.9 .

~perfect

one-dimensional crystal .

The lattice o f an imperfect crystal la generated by convolution cf the perfect


one-dimensional l attlce In Flq. VIII.2 wlth O{r } .
I n this figure the rov cf points
now represents the mean positions cf the bodies alonq the e-axis dlrectlon - the
c onvolution generates the distri butlons cf pos!tions about these means .
Foll owing
the oethod cf Section VIII.2 , lt 18 necessary to calcul a te the Fourier transform
cf thls lmperfect lattlce in crder to derive the interference function tor an imperfect, one-dicensional crystal.
The Fourier t r an sform cf the imperfec t lattice
ls obtained by multiplyinq t he transform of the perfect lattiee by the transfora af
Or).
Fourier transfo~ti on of Or) yields
(VIll.16)
Equation VI II . 16 is derived from equation VIII.IS uslng a general expressl on f o r
the Fourier transform of an exponential fune tion given by Champeney (see BIBLIOGRAPHY Sect ion 4 ) .
The l nterferenee funetion f or a perfeet one-dimensional erystal vas obtalned , in Section VIII . 2, by mult iplying t he Fourier transform of the
perfeet l a ttice by its ooapIex eonjugate.
For an imperfeet one-dimens i onal crystal we have te aultiply ~he Fourier t r ansform e f the imperfect Iattiee by its complex con juqate .
Since O(Q) i5 real, tbe result i s simply the int erference func tion for a perfect l a t tiee mul tiplied by the square of O(Q) .
The e f fect of this disorder La to dee r ease the i nt ensity ef tbe layer lines
without altering their sharpnes8.
It 15 , therefore , very dLfferent from the
ef!ect of dlsturbing the arrangem@nt of bodies , in the e - ax is di r ectl on, untLl it
re semblea an amorpnous sol id, the n tne peak s i n S{Q) would lncrease in wid th witn
increasing Q - see Fiq. VII.6.
When a i s zero , tne value of D{Q) is u nity And the
lntensity i s unchanged , t his result is physically reasonable because a zero value
of a correspolJds to a perfect ene-dLmensi onal c rystal.
As a departs frQJI zero ,
the value e f D{Q) d ecreases very rapidly, because Lt is an exponential, Eunction ,
so that the in~ensity of the layer lines is grea t l y r edueed.
Nultiplication by
the square of O{Q) can ' never lncrease the value of the Lnte r ferenee fun ctien of the
perEect crystal and so tne peak width in Fig. VIII.3 , and hence the shar pness of
the layer 11nes , is unehanged.
Oiffuse lntensLty appeara between the layer l ines oE the diffraetlon pattern
from an imperfeet one-dlmensional crystal .
When tha i ntensity of a layer 1ine
decrease. , the X- raya 8cattered in th~s ~reetion trans=it 1eS8 energy.
The
energy s uppl i ed te the spec:imen, by the lneldent beam, i. unehanged by the nature

We have seen that tne dl80rder d eseribed he r e i8 distinct frem the str uc tural
irreqularity of a n amorphous solid; it can a r i se Ln two ways - " thermal vibration
&nd random d ispIaeement of bodies about l a ttiee pasit i ons .
In the paracrystal
t heory of d isordered s ys t ems , the randoro displacement about lattLee points i5
called ~disorder of the tirst kind " .
Thermal vi bration and this structur al di splaeement can enly be distinquished experimentally by measurinq diffractlon patt erns at a var iety ef temperatures.
ExtrapalatLon t o a bsolute zero temperature ,
at whieh there is no thermal vibratlon , then gives the s truetural di aplac ement
alone.
VI I I. S. MosaLe spread
Imper f eetion c an ari se in another way - the e-axLs of Fig. VII I . l ~y not
point i n exactly t he same dlreetion all over the crysta1.
Th is kind of Lmperfection ls a one-dimensional example of mosaic spread - a lthough i n the one-dimensional case Lt 15 usua lly re f erred to as ~Lmperfec t orientation".
We can con.ider t he meaaie one - dimensLonal crystal to consi st of a n a9seCbl y o f perfect ong dimensional c r ystall ltes , each with a dif fere nt c-axis dlrect ion .
The diffr actLon pattern o f a mosaie crystal is formed by adding the inte ns ity
eontribution from each ie . Lnterfer enee effects between X-rays scattered by different crystallites are negl i gLble.
A priori we might have considered a naed f or
both intra- and inter-crystal11te ~te r ference functi ons; S(~) of equation VIl I.4
is the former.
However , tne erystallites are so large, compar ed wLth the d istancea bet ween their constltuent scattering b odies, that i nte r-erystallit e inter fe rence effect 5 wil l be appreeLahl e enly at very low Q value s - fraro t he r easoninq e f
Section V. 4.
TRere is no reason to suppose t hat the e ry stal lites vill be regularly
arranged in the crystal.
By analogy with the interference function of a liquid ,
in Fig. VII.S and VII.6 , the inter-erystal lnterference function wi ll have settled
to a val ue of unity for the region of Q-space i n whi ch i ntra-erystallite Lnterference effeets are observed"
Since inter-crystallite interference is neqlLgible ,
the diff raetion pattern is f ormed by addi nq t he intensity contributions e E t he
crysta l l i tes - as i n the ideal gas theory o f Section VI. 2 .
In the mosaLe eryst al the e - a xes o f the crystallltes wi l l be d i str ibuted about
aame pre ferred direction; consequent l y a eorrespend i ng distribution of vee t ors
occurs in Q-space.
For a per fect one-dimensional crystal the distribution oE
tLlts ls inf1n itely narrov ie. there is a unique e - axis as in Fiq . VII I . l.
lf the
e-axis of a crystaI 1Lte is ti lted lt fo llows, from Section I I . 4, that an equa l tilt ,
in the same dlrection, abollt a paralle1 axis through O ', must be applied t o lts
Fourier tra nsf ormo
Slnce there is a diatr~butlon of t ilts , a peint in Q-space l s
spread over a region.
Although the e - a xis t Llt s are a pplied to diEferent regions
of real space , a l l tilts in Q-space ar e r eferred to the same oriqin , O' .
The
reaaon 15 that, according to the defini tion of equation 1I.6, a shift of real s pace
positlon, r , enly affee ts the phase of the Fouri er t r ansform, F(2), a nd not tne
point 1n Q-=-space at which I {21 , g 1ven by equation II.S, has a particular value.

One-Dimen5ional Ccys tals

X- Ray Diffrac t i on

90

.5ECTION OF VQL UI>IE OVER


,'WHIeI" INTEN5ITY Ol 5TRI &UTE O

SURFACE DEFlNED
BY 9 VECTORS

eECTION OF
E'W'ALD

:;;<1.----

91

SPH ER

CURVE O N
WH ICH SURFACO:S
INTERSECT

"

o'

Flg. VII I.lO.

Suppose a vector

2.

Mosaic spread distributes the intensityat


the point TI. of Flg. VIII . 6 over a sur face
in Q-space this s urface i nter sect s the
Ewald sphere a10ng an are.

would have termina ted at a po i nt A, in Q-space, f o r a per-

fact one-dimensional crystal , lt terminates on a portion o f a spherlcai s urface ,


in Q- apace, for a mosaie one - dimensional crystal.
In the perfect erratal 2 had a
unique directlon now this direction 19 not unlque but l B merely preferred. There
la a family of ~ vectors, a l l wlth the same modul u s Q. but wlth a distrlbution of
t i lts about the preferred directi on, i n the mosaie case .
The intensi ty, I(~). oE
the point ln the perfect e ryata! will not be evenIy distributed over thls surface
but will have lts maximum va l ue at the original point which now corresponds te t he
prefe rred, rather than the unique, directlon of the e - axis.
Pointa on the diffract ion pattern of a perfect one-dimensional c rystal a r e
d rawn into ares on the diffract ion pattern o f a mosaic one -dimensional crystal.
Flg. VIII.IO shows a paint A on the surface of the Ewald sphere - as ln Fig .
VIII . 6. Now there 15 a faa l 1y o f vectors, all of modulus Q, terminating around A.
These vectors descrlbe a portion of the surface o f a sphere of radius Q centred at
the er ig in of Q-spaee, O'.
A lies both on this portion of spherieal surface and
en the aurface o f the Ewald sphere .
Figure VIII.IO shows that the two sur fa ees
l ntersect along an are through A.
en a dlffraction pattarn an are wl 11 appear
lnlltead of a point.
Furthermore , on l y a part e f 1(2,) wi ll be recorded on the
pattarn because only part of the surf aee ever which it is distributed intersect s
the surface of the Ewald sphere.
VIII.9. Lorentz correctlon
The need for the so-called "LQrentz correctien" ar ises because dlffer ent
points in Q-space have dlfferent opportunitie s to toueh the surface of the Ewald
sphere .
Figure VIII.S prevides an example.
The intensity dlstribution along 1';
cannot be recordad, except on the l - O p l ane, unlells the spec1men 15 tilted.
Bven then the required i ntenaity information 15 only given on the layer 11ne whos e
val ue of ls related te the tilt angle, a , by equation VIII.a .
Mosaic s pread, aescr1bed in Section VIII . a, cause. a further c~licatl on for
real systellls.
'I'hi. effect causea a point i n ;rspace te be dlstributed over part

Fig. VIII . 1I.

Figure for the derivatlon e f the Lorentz


f actor.

of the sur f~c e o f a sphere , of radius Q, as shown in Pig . VII I. IO.


Por a given
spec1men this surface area v l 11 increase in preportio n to ~ .
But enly an are,
wbose length viII be proportional to Q, lntersscts the surface of t he Evald sphere
and can appear on the dlffractLon pattern.
Thu s the f rac tlon of I(~) which i6
r ecorded decrease6 as Q increases .
Note that this spread has another e f fect .
ORce again Fig. VIII. S providas an example.
SoQe po ints a long the ~ -&Xi8 may be
apread out so much that they actually touch t he surface of the Ewald s phere. Then,
although the theory for a per tect one-dimensional crystal predicts that they cannot appear on the d i f fractio n pat tern, they may appear in practice.
However only
11 seall fract i on ot the to ta l 1 (-) .... i11 be r ecorded.
Rotat.1o n of Q- space about an axis , through O' , perpend icular te the plane of
Fi g . VII I . S , cight appear to slmpl ify t he analys i . of the intensity d istribution
along the meridian ln favourable cases .
Accor di ng to Section 11 . 4, t his r otation
oould be achieved by an equal r otatlon o f real aPlIca about a paralle l axis through
O.
I n many real examples of one-dimensional crys tals, the lntensity distribution
along the ~ -axis is much more lntense t han in the 9urroundi ng r egion ol Q- s pace.
The rota tion wou1d ensure that all of tbe lntensity o f the paints along the , -ax is
would pass through the surface of the Ewald sphere .
All passible values ot the
tilt angle, a, in Fig. VIII. a, would be used whlle r ecordlng a single diffraction
pattern.
lUternatively, Q-spaee eould be oscillated, backward s and forwards,
through the surface of the Ewald sphere, over a suff ic ient angular r a nge , to ensure
that all o f the intensity over t he peints woul d pass t h r ough.
In each case the
only l~ itation o f the peinta that could be recorded i8 t hat their Q value does not
exceed the maxLmum value which can be recorded f or radiation o f the wave l e ngth
being med - see Section 111 .6.

An anal ysls of thi s r ota t i o n shoyS how the Lorent ~ factor ar Lses and alloys
its form te be calcul ated.
~ints are apread over part of the surface o f a sphere,
i n Q-sp4ce, by mosaic epread, and the planes en which the intensity ie non-~ero
have a finite width - as shown in Fig. VIII.3.
Thus, although theory yiel ds the
intensity at a paint in Q-space . this lntensity ls actual1y spread over a vol~ e f
Q-space - where the intensity di stribution per unit volume is q(R), sayo
Figure
VIII.11 shows a secti on through tbe Ewald sphere.
In this figur e the volume of
o-space , over Wh1ch the lntensity assoclated w1th the peint P is distributed,

-'2

X-Ray Diffraction

One-Dimen sional Crystals

intersects the surface over an area which subtends a solid angla 01 Q at O, the

'3

VIII. lO. Summary

or1g1n of real space.


SUppose the volume cf Q-space la rotated through the surface of the Ewald
sphere about an axis, pass!nq through O ', which ls perpendicular te the plane ol
Fig. VIII.ll .
Consider an element, 50 , of the solid angle~.
lt corresponda te
an a rea on the surface of the &vaId sphere of

For an inerease, 68 . in the angle

e of

Fiq. VIII . lI , an are of length

Q6B

passes through the su r face of tbe sphere .


The volume when an ele~ntal area
passes through the surface la qlven by the product ef this area and the component
ol this are ...meh 18 perpendicular te lt.
From the figure this componant la

A one-dimensional erystal has a regularly repeat1ng structure in a single


direct10n {Lts c-axi s l .
[ts Fourier transfora and, hence, the intensity o f the
X-rays which it scatters are non-z:ero only en a set of p lanes in Q-5pi!loce.
These
planes interseet the surfac e of the Ewald sphere along lines - when these 1inlla
appear en ths d i ffractian pattern. they are called layer lines.
'!'he layer l1ne
whieh lneludes the undefleeted incident beam is called the equator and is assigned
a zero value of an integer t ; the distribution of scattered . intensity along t he
equator prevides informat10n about the structure o f the one-dimensional erystal
projeeted 01'1 to a plane perpendicular to the e - axis.
Succesaive layer l!nes, and
the planes which gave rise to them are ass igned l values o f 1, 2 , 3 - - - 01'1 one
side of the equator and -1, - 2, -3 - - - 01'1 the oUer .
Layer l ines 01'1 the d1t traetien pattern are perpendicular to the e -axis of the one-dilllensional erystal
anO are 2~/c apart when converted into Q-space, where e is the repeat distance a f
Che strueture along the e-axis .
The line on the diffraction pattern which is parallel to the e-axis is cal led
lf the e-axis is suitably tiltad , the structure of the one-dimensional eryatal, in projeetion 01'1 te the e - axis , ean be deduced frem the mer idional
!ntensity distributions of a series o f patterns.
Tilting may not be neeessary
ter specimens with large e values if only 10100' resolution information about the
etructure is required.
A Lorentz correetion has te be applied to the meaaured
intensity distribution - in part because a point in Q-spaee ia drawn into an are
en the d iffraetien pattern by mosaie spread.
In a real ane-dimensional eryatal
the seatterinq bodies are uaually distributed about the positions of the ideal
case.
'!'his d1 s tribution leada te a dtminut10n of the 1ntensity of the layer lines
and tbe appearaRce of weak diffuse intensity between them - the pattern does not
r emble that of en amorphous 501id if the displacements are smal l and distr1buted
about the ideal positions.
the meridiano

Thus the v o lum4! eLement in Q-space which pa sses through the surface of the Ewald
sphere 15 given by
6V .. (2'11/;\. ) 2 60 Q6B

cos (1jl/21

From equations II.4 (whieh relates Q to


6v -

(VIII. L7)

~)

and VIII.17

(~ /l)3 sin , ~8 611

(VIII. L8)

'!'he rotatlon allow5 the 1oO'hole volume of Q-spaee, over whieh the intensLty of
the point is spread , to pass through the surface of the Ewald sphere.
Thus the
i ntensLty recorded en the diffractLon pattern ls qlven by
I(Q..) ..

f !

q(Q) d ll dB

(VIII .19)

where the subscripts 8 and 11 denote integratLon over the whole ro tation as well as
over the whole solid angle subtended by the surfaee through whlc h the volune pasaes.
From equations VIII.18 and VIII.19:

I(~

- ()'/2w)3 (l /sin

~)

f f

q(2.) dv

'" ()' / 2,,)3 (l/sin .) F{2.)F * (,2)

(VIII.20)

since the Fourler transform, F(21 , multiplied by its eomplex conjugate, gives the
total i nten sity over thLs volume of Q-spaee.
In an experiDent we may w15h te deduce the modulus of F(~) from the intensity,
1 (.2) . of a spot whose centre 15 given by the vector .2.
l t ia then necessary to
qultiply this exper~ental lntenslty by sin " the Lorentz factor, before thls
lIOdulus can be equaU!d 1oO'lth l~ (2)
The ()./ 2,,) terlll can be ignorad as i t ls a constant f or a given X-ray wavelength.
The Lorent... factor ceon be calculated from Q
by usinq equation [[.4 whieh relates' te Q.

95

Helices and Liquid Crystals

HELlX MIS

1
CHAPTER IX

Helices and Liquid Crystals

IX.l. Introduction
This chapter 15 concerned with dl ffr actl on by systeus which prov i de r eal
exampl es o one~e n slcnal c rystals.
Many polymer molecules are one-dlmensional
c rystal51 themselves.
The reason 15 that , under sultable conditions, many o t hese
mol ecules are helleal - and a he l lx has the r epetitive structure in a single direction whlch c::haracteri ses a cne-dimensional crystal.
Several biological structu res
are helle. l - SOIne , such as the "thin filaments" of muscle. cons ist of g l obul a r
macromolec ules arranqed on a h el ix .
Befar e the diffraction propertie s of any of
these he~lces can be dLscussed , Lt viIi fir st be necessary te conslder the Fourier
t ransforms of two geanetric entities - the continuous hel ix and the discontinuous

Fig. IX.l .

Generation of a continuous

heli~

by convolut ion .

helix.

Smectic Iiquid crystals provide a furtner example o f one-d imensional crystals althouqh Bome types of smecti c have a degree of order in three dimens ions . Although
the nematic liquid crysti!lls, described in Section IX.5, a r e not at ell crystel l ine,
even in one dime n sion , r eesons will be qiven for consideri nq the ir diffr~ction
propert ies in this chapter.
There ls ~Iso a practical r e a son f or their i nc l usion
after helices .
A discus5ion o f diff raction by helical molecules will be i n separa ble f rom conslderat ion of polymers.
An important a pplicat lon of X- ray diffrac tion in polymer scienee 15 the determination ot any prefe rred dlrectlons in which
polymer cha ins are oriented in a sample .
The least ordered arranqeaent o f molec u l es in an oriented po l ymer saIllPle is the same as that in 4 nematic liquid crystal.

IX.2. Conti nuous h elix

g
Figure IX.l shows that the fami liar cor kserew shape of a continuous heli~ can
be generat ed by the convolution of a sinqle turn with a lattioe of points , spaced
p apart , where p i5 the hel ix piteh; comparison with Fiq. VII I. 2 5hows that the
helix ls a one-dimenslonal crystal.
Convolution of a function vith a set o f points
v iI I be considered f r equently in this chapter - the operat ion is repr esented pic torially in F i g. 11. 5.
Because the heli~ i5 a one-dimensi onal crysta l , its Fourier
transforn i s non-z erC only on a set of plane s , spaced 2T/p apart in Q- space, whieh
are perpendicular to the direction of i ts axis - provided the hel ix is of effectivel y infinite extent.
Raeh plane is speclf1ed by the va lU of the integer f and
gives r is8 to a l ayer line on the dlffraction pattern as deacr1bed in Section
VIII . 3; the undeflected X-ray beam defines the centre of the d1ffra ction pattern

.r
9J ',~

r"

'"

Ii!:~A L

Fiq. IX . 2 .
94

:Z
,

~'J

S PAC(

:t

fJ ~ ~

...

f --..11

Q - SPACE

Coordinate systems i n real space and Q-epaee .

X-Ray Diffraction

96

and l1es on the layer 11ne with l o.

(: .. (0

F igure

sLn'li .. B/l0 2 + S21~

IX. 2 defines the Carteslan (x ,y,z) and cylindrical polar (r,e ,z l coordlnates which
can be usad to describe

paint on the helix whLch 18 defined by the vector r. In


this sectLon tbe heL lx v l l1 be considered to have infinitesimal thickness - l1ke a

2 + S2) "

co. ~ .. a/(02 + B21~

Accordln9 to Section YIII.4, the Fourier transform of the helix 15 obtained


by calculatinq the transforlll ol a single t urn on each 0 1 these p lanes _
il

corkacrev made ef inf1nltely thin v i re.

Note that here r 16 the projection ef r

from Fiq . IX.2.


Thus the {bracketed } term in equation IX.4 can be multlplled by
un1ty in the fOml

en to a plane perpendicular to the hel1x axis (the z-axls ) and not lt9 lDOdulus;

also the symbols x and y are unrelated to their uSo!lge in Sections IV.3 and VIII . 3.
The value of r 18 constant for a glven helix vbich la conpletely speclfied by the
va lues ef r &nd p.
~19ure IX.2 a190 shovs the correspondlng Cartealan (a,B ,; )
and cylindrlcal polar (e,~ , ~) coordlnates which will be uaed to describe a point
in Q-space delinad by the vector~.
The ~-axis of real space and the t-axls oE
Q-space are defined to be p5rallel as ln Fig. VIII.6~ the direetion ol an X-ray
beam, which la incldent at rlght angles to the helix axis, could be taken to de fine
the directlona ol the x-axis and the a-axis.
However all that ls necessa ry is for
these axes te be dellned to be parallel.
Once again G and S are unrelated to
their usage ln Sectlons VIII.) and VIII.9 .
Readers who do not wish te follow the
detaLled derlvation of the Fourler transform of the continucus helix should skip
the next four paragraphs.

(/(0 2 + S2)~

to yield
er cos (2nz/p - 111) + zt
uslng the identity
cos CA - B) .. cos 1\ ces B + sin
Therefore equation IX.4

c~

11.

sin B

be rewrLtten as

(IX. 5)

In Fig. IX.2 the cOQpcnent s of ~ are the Carteslan coordina tes of the point
which it definea; thus it can be represented by

r ces 2 . . / . ]
r sin 211Z/ p

L-

(IX.I )

F(~.~,l)
(IX.21

Since, by delinition, the a-axis is parallel to the x-axi s, the ; - axis ls parallel
to the z-axls and, consequently, the S-axis 15 parallel to the y-axis, lt lellows,
from equatLons IX.l and IX.2, that

!,..2, - or cos (2n/p) + Sr sin (2'/1z/p) + tz

exp iCor ces (2wz / p ) + Br sin (2u/p) ... tz} d:

(IX.4)

froa equations 11.6 .ud 1%.3 - notlng that che only real .pace varlable i n equation
IX.) L. z.
Equation 1X.4 wil1 nov be tran15formed into cyllndrlca1 polar c:oordinates.
Simple tr 1qonometry yleld.

..

[P

exp i{(r cos C2lfz/p -

~l

2w.tz/p} d z

(IX.6)

Now that the Fourier transferm 1s non-zero only on a set of planes, whose positlon
ln the ;-axis direction i8 denoted by t . it can be considered ae a functlon ef e,
l and t rather than o f ( , ti and t .
The next atage of the calculatlon ls to evaluate the integral in equatien IX.6.
Ita form can be slmplifLed somewhat by introducinq the fractional coordinate Z, ef
Section VIII.4, where Z equals z/p .
Notlng that

(IX . 3)

(Remelllber the eO!lJl1ents on the dot product of vectors in Sectlon VIII. 3.)
The dlstrlbutlon of matter 15 constant along the helleal path but zero elsewher e. AssLqning the electron denslty along this path a value of unity, en some arb1trary scale,
the Fourler transform of a s1n91e turn ef hel1x becomes

fP

Me now find the values of p' ( e, ~ ,~ l on a set of planes vhich are spaced 2w/p
in Q-space aneS are perpendicular to the z-axla and, hence, to the t -axls le.
_ obUin an expreaaion for the Fourler transform of the entire helix.
Noting
that P ls the distance between l attlce points in Fig. IX . l ve substitute the expre sslon tor t for a o ne-dimenslonal crystal, from equa tion VIII. 6 , inte equation
:IX . S to obtaln
~t

since the helix turna through an angle of 2w radlans withi n a singl e pitch.
SiDllarly

P' la,B , ;) -

97

Helices and Liquid Crystals

dZ/dz - l /p
aquatlon IX.6 can be rewrltten as

l"(~, , , ,ll

.. P [ 1 exp

Heqlectlng p.
arranging

F(e,~,l)

~hich

i{~r

ces (2wZ - lit ) .. 21ft Z} dZ

acts as a constant scaling factor for a given helix, and re-

.. [ 1 exp i{f;r ces (2"Z - 1II ) } exp H211tzl dZ

"e l i ees and Liquid Cr ystal5

X-Ray Diffraction

9.
we now make the substitutlons

x-

*' -

and

~r

2wZ -

'JI

trom which Lt follows that


dt/dZ -

2 ..

n =7

and F(t !1 can be written aa

When the integral i5 evaluated (aee paga 31 of the book by Watson reoommended in
8IBL I OGRAPHY Sectlan 4) this express ion becomes
i

exp (lt~) Jt(X

n=6

---

n =5
/"',

where JnlX ) 18 the n th arder Bessel function of the fir st kind, definea in equation 11.9.

This result ls usually e xpressed in the fOml

n =4-

exp LiC. + _/2 ) Jt ' X)

/'.

sinee
exp (iln/2) - coa Ctw/21 + i sin (tn/21
whlch has the same value as 1 i

n =3

(The reason l a to force al1 the phase lnformation

into the exponential term . )

Now that the integral in equation IX.6 has been evaluated the Fourler t ransform cf t he l\elix CI'ln be written as

n = 2.

/\
(IX.7)

Equatlon IX.7 ls the Fourler transform ef a continuous helix.


From equations Il . S
ond IX.7, the lntenslty on the t th plane of Q-space i8 glven by

n=1

!\ ~

(IX.S)

tne lntensity eE X-xaya scattexed by a oontlnuaU5 hellx 15 independent cE


le. lt has cylindrical symmetry.

ThU8

On eaeh plane aE Q-space wa ves, repxesented by the Fouriex transEorm oE equatLon IX.', spread out rather 11ke the ripples en the surEaee o E a pond when a stone
15 dropped into it .
In thla case the dls turbance emanates frorn the I;-axl s.
The
lntensity on the t th p l ane, aceording te equatlon IX.S, 15 qiven by a squared
Dessel funetLon whase fortl 15 shown, Eer several t values , in Fiq. IX.3.
Note
that en the t th plane this Lntenaity is independent aE dlreetian, le. aE V, and
dependa only on the radius , r, af the helix and the dlstance, ~ , from the r;-axls.
Slnee lt fellows froa equatlan 11.10 that
J

-n

(X)

(-

n=O

l}n J (X)
n

the i nten.lty on the - l th plane 15 the same as o n the t th.


{Thls result oould
have been deduced f r om the cylindrLeal 9ymmetry and the general property ef diEEractlon pattRrnS discussed ln SectLan III.B . )

cA

10

Fiq. IX.3.

20
---+

Squared Besael functions.

99

Helices and Liquid Crystals

X-Ray Diff r action

100

..

____....... S

CA

1
2

OA

__ .

~._~=

IX.). Discontinucus he1ix

~._

4ft

A.

.,AA . .,
o
-1

-2
-3

AA.
.4
eA

Fl q. IX.4.

l (C,!) for

t _

4ft

*.
~

A discontinuoua helix consists o f a series of pelnts ~hich a r e regularly


&paced along a hel i cal path Fig. IX.5 shows an exampl e where the s pacing of peint s
along the helix axis (z-axis l direction 15 q.
Por the sake of s i lllpl i city we shall
initia1 ly con.ider the apecial case where the helix pitch, p, 1& an integral multiple of q - a so- called "integral he1 i x".
In the figure p/q _ 4 thus the
example o E an integral helix chesen here is a four-fold helix.
This figure also
ShOW8 that a discontlnuous helix can be generated b y multlplying a continuo us helix
by a set of planea the planes are perpendicular ta t he z:-axi s , a distance q apart ,
and represent a three- dimensianal func t ion which has a value of zera elsewhere in
.pace.
In the figure the helix and the planes are shown in pro j ection so that
the y appear as a sinuso i dal wave and a set of lines, respec t i ve1y - lt 19 left to
the reader ' s imagin ation te picture what is happenlng in three dimensions .
The Fourier trans form of a discon t i nuous hel i x is glven by the convolutlon of
the transform of the contlnuous helix with the transforlll of the set o f planes .
Thls result f ollo..... & from the property of the Feur ier t r ansform of the product of
two functlona, descr i bed i n Secti o n II.4, since the discontinuous helix could be
generated by multiplying two func t ions together.
The t r an sta rm of a set of planes,
spaced q apart, which are perpendicular to the z-axis, i9 a get of peints, spaced
2n/q apart , along the ( - axis.
This result fol l ows frolll the form of the Fo urier
trans form of a set of peints, discussed in Sections \111[ . 2 and VII I. ) and the inversion property of the Fourier t r ansform , described l n Secti on II.4.

As

CA

101

continuous helix.

Figure IX.4 shows the intensity, I (( , el , in 4 section of Q-space which contalns the e-axis.
The three-dimensional I(C,!) can be genera t ed by r otating the
flqure about the ~ -axls because af lts cylindrical sytlDetry .

Figure IX ,4 does

nat quite represent the dlffraction pattarn to be expected from a continuous hellx
beca use the Ewal d sphere cannot generally be considered as aplane sectlan ol Qspace and because af the distortion introduced when a d i ffr actLon pattern 15 recordad - see Sect i on V1II.3 ,
The figure was produced by plotting the squared Bessel
functions a f F ig. I x.3 on to a series e f layer 1ines.
Intensity maxima on the laye r lines lie on the arma of a diagonal cross and
decrease as the magnitude o f l increases .
Notice that intensity only appear s on
the e- axis ..... hen l equal s z:ero .
Mathematica1ly this r esul t arises because only
the z:ero order Bessel funct i o n in Fig. IX .3 is non-zero ..... hen X equals zero . Phys ically the diffraction pattern must have non-zero i ntensity at this poin t because
it i9 defi ned by the undeflected X- ray beam .
The equatorial Fourier transform
oould have been ebtained ..... ithout r ecourse te the mathematica1 derivation of this
section .
Accordi ng to Section \lIII.4 the equaterial transforlll is e qui val ent to
the transEorm o E the pr oj ection of the hellx on to a plane perpendicular te its
z-axls.
This pro j ection ls a circle, le. an annulus of infinitesimal thlckness,
so that its Fourier transform, by analogy .....ith tlle integral of equation II.9, is

en the equator Q, the rnodulus of ~, is identical to ( so that this result is equivalent to equation IX.i when t 15 set equal to zero.

, ,.
/

Flgure IX .6 represents a sectlon, containing the t - axis, through the intensity


distribution , I (( ,!l , for a di5cont inuous heli~ - ooly the DOr e prominent intenaity
maxil!lal are s hown.
In principIe t hls figure l s generate<'! by setting down the
Fouri er transforD of a continuous helix at each of the pein ts g i ven by the Fourler
transform of the set of p l ane s .
Kultiplicatlon of the result by its complex conjuqate yields Plg. l X.6 - olIccordinq to equa. tion 11.5.
In practlce t he figure i s
generated by aetti ng down Pig . IX.4 (somewhat simplilied here for the sake of
c 1arltyl at each of the peint s , spaced 2w/q apart, aa origino
Note t hat Fi q. IX.6 dees not correspond exactly to the d ilfract ion patter n o f
the discontinuoU9 hel ix.
The diffraction patt ern is formed by the intersection e f
Q-space with the surfollce of the Ewald sphere, as shewn in Fig. VIII. 5, and is also
somewhat distorted when it is recorded, as described i n Sect10n VII I. J.
In par ticular i t viI I b e necessary te tilt the helix, from t he per pendicular to the X-ray
beam, to measure t he intens i ty a t any peint on t he e - axis - other tha n on the equatoro
If p and q are very large (compared with the wavelength of the radlatl on)
the intensity distribution of Fig . I~.6 will appear a t ~ery l o..... Q values .
Then
the Ewald sphere 18 effective1y a plane perpendicular to the X-ray beam and t he
d i ffractien pattern .....111 close1y resemb1e this figure.
I n principIe many order s of Bessel function might be expected on each layer
11ne ol F1g. IX.6 but, as can be seen from Fig. IX.3 , only t he lower orders wi1l
glve ri se to appr eciable intensity.
The t - O layer 1ine correspends te an origin
defined by the undeflected X-ray b eaR and contains a zero- orde r Bessel funct10n
term o
lt al so coinci des vith the t - -4 1ayer line from t he transform o f a cont l nuous helix Who6e oriqin ls place<'! 2w / q up the e- axis and the l - 4 layer line
~rOlll an or1qin s1tuollted 2w/q down the ~-axis - since , in this example , p / q - 4.
Therefore this OOQposite equator i5 formed by Bessel functlons of order O, t 4 olIS
well a6 seme much h igher, and theref ore negligible, order s ariai ng frOlll setting the
origln of the continuoua hel ix down ~t further peints, 2ft/q apart , alon9 the ~ -axis.
These otber orders are only of ver]f low lnt ensity - furthermore t he ir ~xima also

Helic es and Liqui d Crystal s

X-Ray Di ff raction

102

1 03

ip

Flg . IX. 5.

i,

t 5
4

-1

-z
-3
-4

-5
-i.
-7
-8
F' l g. IX. 6.

] {( ,f)

:le

'f
e

1>

T
..
2 'X

q,

'f"

j,

Generation of a discontinuous helix by mul tiplication .

20/p

'f

--? E
INTECRAL

NON -INTEGRAL

F'lg. n.1.

for a four-fold he lix.


llOOOS _ ti

Comparison of int egral ana non-i n tegr al helices.

X-Ray

104

Dif f ~a ctio n

Helices and Liq u id Cr ysca l s

105

appear at very high ~ values .


Inspection oE the figure yields the result tha t
the Dessel function ardera, whlch mlght appear on the l th layer l ine , are given
by

n " l ... 4m

0, 1, 2 -

This selection rule can be generalised t a


n .. l + ( p ! q) m

TABLE IX . l.

Bessel function order s contributinq t o l ayer


l ines t or the non- integral helix ot Fig . I X.7.

provided p/q 1 5 an integer.

we now consider the general case where p 1s not necessarily an integra l multiple of q.

Figure IX . 7 campares two helices, one in tegral and the other non -

integral, with the sarue true repeat of c.

For the integral helix e 15 ident lcal

l.

te the piteh , p , but for the non-integral helix e 15 greater thao p.


How e must
be an i ntegr al lDllltiple of q and some other i ntegral ~ltiple of p - otherwise the

structure oould not repeat ltself exactly &10n9 thls distance.

""here N anO t are lntegers for an integral helix t - l .

80th the int egral and


non - integral heliees of Fig . IX . 7 haye N - 8.
Aeeording to Section VIII . 3 the
diffraetion pattern consists of layer lines spac ed 2n/e apa r t - it just happens
that for an integral helix e a.oo p a re identical .
The Fourier trans forID o f the
disoontinuous helix can stil1 be generated by setting down t he transform o f a <::ontinuous helix at points spaced 2w/q apart a10 ng the ~- axi s - for exac tly the same
reasons as before.
WOrking out the Bessel function orders that will be expected
on each layer line is now more eumbersome beeause p is not an integral multiple of
q.
The result is glven by the integral values of n obtained from
n

(f - Nm) It

for an integral helix t


previousl y.

1 and this result reduces to the selection rule obtained

'"'

Jn{(r) exp i

n(~

(.t

- 1

2
3

- 2

D "' 0 , ! 1 , ! 2

where all m values whieh do not l e ad to insignificantly small Sessel fu nction contrlbutions are to be i ncluded.
This res ult 15 simpl y the sum o f a11 the contribu ti ng continUOll$ heLix transforms whose origins are spaced. 2T/q apart along ehe
{ - axis.
Figure I)C.8 representa the intensi ty distributions e>o:pected frem the
helices of Flg. IX.?; lt show$ sections, containing the ~ - axis , of l ( , t) and is
analogolls to Fig. IX.6.
Bessel fun ction orders coneributin~ to the l ayer lines ,
in the non-integral case, are l is ted in Table IX. l .

- 5

- 6

2
- 1
- 4

- 7

- 6

- 2

- 7

- 5

I\'D. )/t.

- 4

rr/21
(Oc. 10)

- 2

- 1

-3

- 3
.,.

n
n -

The general express ion for the Fourier transform of a discontinuous helix can
now be given .
Fr oc equation IX . 7 the result is

F (, ,~ , tl

II1=O , 1,:l:2

Thus
(IX.9 )

e - Nq '"' tp

- 5
- 8

3
O

HeI i ces a nd Liquid erysraI s

X-Ray Diffrac ti on

106

1,,
7

4
3
2

O
-1

-2
-3
-4
~

-,

-7
-6

INTEGRAL
Fiq. IX . a.

,,
2ft/<.

IX.4. Molecular hel1x

T*

lf

7
,
5

Z'e

107

2
1

-1

-2

The s i~plest kind of molecular helix te i~gine consi sts o f globular macromolecule s arranged a 1o!\g a helical path.
Exaoples a re provided by too Mth in fi18o ments~ of c UBe l e and by the struc t ures o f cartain vlruses.
The se s truetur es are
the same as the discontinuous helix o f Fig. l x.5 - except that t he peinrs in the
figure now represent t he posit i ons of the globu l a r sub-units.
A mo l ecular he l ix
oE thi s kind may be re?resented by the convoluti on of a sub- unit .... ith the discont inuoua helix of peints .
Consequently the Fourier transform of such a molecular he llx 15 obtained by
multiplying the transform o f a globul ar sub-uni t , F (2.) , by the t ra nsform of the d iscontinuous helix - given by equation IX.IO.
F(Q) can be ealculated by the methad
of Seetion v.3 or , at l o.... reso l utien, Section V.4.
The Fourler transform of the
molecular helix ie then giv en by

-3

F((, ~ ,e)

-4

.. F(2.1

-5
~

-7
-8

NCH-INTEGRAL

made from a real diffraction pattern , the procedures descrlbed in 5ection VIII . 3
have to be adopted.
According ta Section rX. 2, a conclnuQus helix only r ie lds
non- zero i n t ensit y on che ( - axis at the origin oE Q-space; therefore, a discontlnuous helix only yields non-zero intensity a10n9 t h i s axis at lnterval s of 2T/q in
Q-space .
rf the lntensity distribution a10ng the ~ -ax is can be recorded, usually
from a series of diffraction patterns f r om tilted specimens , a nd t he distances betveen non- 2ero points eonverted into Q-space , q can be ca l culated.
Both intens i ty di s tributions in Fig . IX . e have certain s i milarities ; both eorrespond to the s&me valuE!s of e and q .
They can on1y be distinguished .... hen the
orde r s of the Bessel functlons .... hich contribute te eaeh layar 1ine are disentangled.
A good idea of the nature oE the scat tering helix can be gained by inspec t ion of
the patterns.
Te unders tand the patter n5 properly r must be known, sioee the
&rgument of t he Bessel funetions i5 ( r, ie. a model for the he llx ls required.
When a model i s ava i lable, which has the correct values o f e and q , the expected
diffraction pattern can be ca l culated and compared vith that observed .
The problem in interpretlng the patterns of Fig . IX . e is to decide whether c 15 identical
te p (an integr al heli.x) or is gr eater than p (a non-integral helix ) .
SO far
ve have ignored the hand of the helix.
Either helix in Fig. IX. 7 could b e rightor 1eft-handed, but according to Section I II. e, we are unable to determine this
hand Erom t he dlffractlon pattern alone - in the absence of anomalous 5catter i nq .

exp i

nN + rr/2)

(I X. ll)

trOl'll equat ion I X.IO which aloo gives the seleetlon rule for n.
]f r in equa tion
IX.l l corresponds to the radius of the helix which passes through the cent res of
the sub-un i t s , then a sub-unit centre must be u sed as the origin for the ealculation of F(Q> .
From equations 11.5 and IX.l I the intenslty dlstribution i5 given
by

l i t ,! )

s Ce ,l ) F (2.) F* (2.)

SI ( ,!l z

I ( ,!) f or integra l and non-integral hel i ces.

Values of e, the structural repeat, and q. the axial separation of points ,


can icmedlately be deduced f~m F ig . IX . B.
Layer l i ne s are separated. in Q-space,
by 2~ / c and he n ce ~a$urement of this spacing rields c.
When measure~ents are

Jn( ~ r)

(r) exp { i

(IX . l2 )

n ( rp + n/2) }

n
x

Jn(~r ) exp {-

n(~ +

nn)}

Thus arra nglng the s ub-units on a helix i ntroduces an interference function,


S(t , l) , which glve s the positlon s in Q-space wh ere intensity i s allo ....ed .
These
allowed positions enable c and q to be calculated as described in Section IX . J .
Since the int'ensity distribution depencs on F (~.>' the str uctur e of a sub-unit can
be dete rmined, at least in principIe, by the rnethods of Chapter 111.
Polymer mo1ecules cften forro helices.
Figure IX . 9 sho.... s the structura l fo r mula of poly-L-alanine - a single residue of this polymer is boxed in by dotted
lines.
Tbe mo1ecule can exist in a conformation known as the "a-he lil<" - the
cylindrical polar coordinates of the atorns in a single residue are listed in
Table IX.2.
If the j th atOlll in thi s residue has cylindrical polar coordinares
(r j. e j , 2 j) ' the coordinates of the corre sponding atom in successive residues a r e

cj

+ 2I1 t /N

rj

j
0j + 2 (2nt/ N),

cj

ej +

J (211t /N) ,

Zj +q
Zj + 2q
Zj

+ 3q

lIel i ces and Liquid Crys t als

X- Ray Diffrac t ion

l 06

The result fer the azlou tha l

109

(angular ) coordi nate fol lo....!:! because the hellx turns

through 2nt radians in . a repeat distance , e, whlch conteins N residues; the result
fer the axial coordinate follo\o,'9 direct ly frOlll the defini t ion of q - the axial rise

from one point on a helix to the next equivalent point le . in the ca se of a hel i cal
polymer it is the axial rise per residue.
Thus the a-helix can be considered as a set of coaxial atomic helices - with
one atomic helix for each atom i n a residue .
The radii oE the atomic helices,
as well as the relati ve a2imutha l and axial p:Js it i ons o f t he i!!Itoms on then, are
given by Table IX.2.
Al l the atomic helices lIIust have the same values ol e and
q if the relatlonship be t ween correspondlnq atoas is to be t he same i n all residues
ie. if covalent bond lengths etc. are to be preserved from one residue t o t he next .
For the a -helix c .. 2. 7 nlll and q ~ 0 . 15 nlll.
As we might expect, from Section
IX. 3 , these paraneters can be measured from a diffraction pattern - !urther deta ils
are given in Section I X. 5 .
Paul ing and Corey proposed a model Eor the o-helix ,
based on 5tereochemlcal pr incipIes, in which p!q .. 18/5; values oE N and t the n
follow from equation Ix .9.
The coordinates of Table IX.2 >lere obtained by refining the Pau1ing and Corey Dade l agi!!llnst the intensity distribution of an X-ra y diffraction pattern.
Fiq. IX.9.

Poly- L-~lanine.

By

analoqy w1th equation IX . ll the Fourie r transform of a single atomic he 11x

would be
F ((, v , l) .. !(Q)

(Er) exp i

(IX . 13)

n(1/I + ,,/2)

TABLE IX . 2.

cylindrical pola~ coordina tes of the atoms in


a sin91e residue of the a-hel l~ of pcly L
alanine

(Data published by S. Arnott and S.D . Oover, J. Hol ee.


Biol. 30, 209- 21 2 , 1967)

r {mn)

e (deqrees)

0.2268

(on e l

0.3013

1 3 . 54

0 . 0485

(roethyl)

0 .3294

17.63

O. OSOS

0.1906

78.33

0.0761

0.1664

72.41

0.0441

0.1548

27.35

0 . 0906

0 . 1539

18,5 7

0.1878

z (nm)

where f( Q) is the atomic scattering factor of Seetion V.2, whi c h i5 independent af


the direction af~.
But a problem arises when we come ta derive an expres510n for
the e ntire molecular hel1x - F ( , , ~ , t) ls complex and so the correct phase relatianshipa have to be maintained when a dding the cant r ibutions Eram the atomic helices
ie . eaeh h elix nust be referred te a common o r igi no
Once t he orlg i n la defl ned
for o ne atomic helix , the s&me one must be used for all the a the rs.
In Table IX. 2
the pasit l on of a carbon a t om was used to define an origino
The j th a tom i n the
residue l s related to the a~imuthal a nd axii!!ll coordi nat es o f t h i s origin by a
rotation , e j , and an axia l trans lat lon , Zj'
As in Sec t i on V.J , the eff ect of a
trans latlon, when add1ng atoml c scattering factors t o obtain a molecular transform,
1s to multiply fj(Q) by a tero
exp

(carbonyl )

(on N )

(i !.;.~)

"'here E.j is the vector pos1ti o n of the j th a t om le. r has the same meaning as in
F1g. IX. 2.
According to equation VIII. lO , t hi s tern- has the form
exp (2" i t Z j ) '" exp (2':'1 1 t ~lc )
tor a n axial translation i n a one-dimens iona l crys taL ; we now have to ge t the
orlgin ef the atomlc helix te the same azimuthal coordlnate as the origin le. it
has to be ratated by - Sj about the z-axis .
According to Section 1 1.4 , the effec t
on the Fourier transfort'll i5 to apply an equa l rotation about its I; - axis ie . \1 in
equAtion IX . U has to be replaced by (1JI - 91 ),
When equation 1)(.13 i5 5uitably
modi fied and the contrihutions af a1l the atomic helices are added, the Fourie r
transform oE a heli cal molecule becomes

F( E; ,v , t l '"

L ,L
n

fj J

(I;:r ) exp i {n(Ito - a


j
j

+ lr/2) ... 2T l

z / c}

( I X.14 )

110

Relices and Lqud Crystah

X-Ray Diffraction

"'FOLO AXIS

2-FOIJ) AXIS

*-e
f

Fig. IX.LO.

Effect o f a u-faLd rotation axis of synnetry

on the repeat distance of coaxial helices.


Here the summations are Qver a11 a toms in a residue and over al1 the Bessel function o rdecs which make A significant oontribution on t he layer 11ne - the possible
o r ders be1ng given ~y the selectlon rule of equation I X.IO.
In some polyruers twa o c more helical chains are wound about a coauaon axis the tIlUch publ lcised " double helix of DMA provides /ln exampl e.

Fig. [K. Il .

Nematic organlsation .

AA 4ssembly of u

coaxi al helices 15 sometimes called a "u - start" helb:.


Notice that a polyrller
chaln l ike poly-L-aLanine, in F'ig. IX . 9 15 not the sll!I'.e /lt both ends and so, like
/ln &rro,"" it def i nes a direction .
Thus a 2 - start helix could consist of "parlll-

l el" chains, ",here both point in the same di rection , o r so-called "anti - par./lllcl "
chains, like ctlA. which po1nt in diEfe r ent directions .
IE the constituent chains
of a u-start hel1x are pa.u.llel (as opposed to anti-parallell, they may be r elated
by a u-fold rotation axis of symmetry ie. a point on one helical chatn may be related to an equi valent point on anotlJ er chain by a rotation o f 211/u radians about the
helix axis.
o</hcn e denotes the rcpeat distance oE one of the eonstituent helices ,
i n l solatiOIl, Fig. IK . IO shows that. the repeat dist.ance for t h e e ntlre u-start
parallel helix: is reduced to elu - if the ehains are rel ated by a rotation axis .
Symmetry can then cause layer lines te be absent froro the diffraction pattern.
The absence of intensity at otherwise allowed positions in Q-spaee, as a result of
symmetry in real space . is a eornmon feature in K-ray diffraetion by crystals - and
one-dimens i ona l erystals are no exception .
In particular iE the parallel chains
o f a u -start helix are rel ated by a u-fold r otation axis oE 5~etry , the layer
l ines expected fro~ a single helix of the sace pitch vill disappear except when l
i5 a lIIultip1e of U.
The reason is that the repea t d i stanee ls r educed froo. c to
c/u .
Consequent1y the layer line spacing of the d1ff r action pat t ern is lncreased
to 2nu/ c in Q-spaee.
The possib il ity of coaxial, parallel helices. which are rel ated by symmetry, leading to absent l ayer l ines has to be considered when formul ating molecul ar oode1s te expla1n diffraetion patterns .
lX. 5. Hematc organisat ion
The helical polymer mo1ecul es considered in the pr evious section have an overall rod- like ahapel as a r esult they can often be oriented so that their long axes
a re para llel as sho"," i n Fig. IX . 11.
Orientation can be achieved by a variety of

Fig. IX.12.

Nematic org3nisation of rod,s projected on to a


plane perpendicul ar te the 2,-axis.

111

X-Ray Oif fraction

112

He lices and Liqu i d Cr ys ca ls

113

lHIans, 5uch as shearing or extrudlng concentratoo solutiona or gels , And 18 often


a desirable feature in synthetlc material s because of lts effect on mechanical

propertles .
Such b i ological s ystens as muscle and tendon 011.150 cantaln orlented
polymers for much the 8~e r eaaons.
Por studies of mol ecular struc ture 4n orien ted samp le 1s pre fe rred te a dlsor iented assembly of rods because the X-ray d iffrac tien pattern wilI no 10nger be spherically averaged.
In ~y systecs the l ong axes of the r od-shaped ~olecu l e5 Are reasonably perallel but the molecules have random r otat lons about these axes.
Furthernore there
need be no r egular side-ta-sid e spacings between molecules le. although they are
oriented , their urangenent la not c rysta lllne .
Then t he structure projected on

to a pl ane perpendicular t o the z - axls of Flq. IX.ll resemble s a r andom array of


dll1cs - as shown ln Flg. IlC. 12.
Of course the molecu lee are not really solid
rods , they conslst of arrangement8 o f a toms , and so Flg. IX.12 represents ooly a
Because the molecules are not
l ow re50lutlon vlew of the projected s tr uct ure.
slmply roda , tlle term "parallel" 15 often used 10 a speciallsed and restrLcted
sense.

A polymer chain, 11ke poly-L- alanlne ln Fig. IX. 9 , has a direction and can
peint up or dowo.
Then, when t he molecular axes a.r e paralleL , molecules themselves cauld e ither a ll peint Ln the sarne direction ("paralleL" - as opposed to
"anti- paral l eL") or p::Iln t randOllll y up and down.
Fig . lX .13 .
ne:natic 11quid crystal consists of r od-shaped IIIOlecules "'hich a r e oriented,
pointinq rando~y up and down, with no regular side-to-side arrangement Le . in pro jection Lt resembles Pig. IX.L2.
'Ih! can therefor e ca l 1 such en a rrangement of
r ods "nematic or gani sation".
The terms "oriented gel~ and "uniaxial orientatien~
are SODet1rnes used for this same arrangement but t hese t erms have becerne lmprecise
because both are used in a variety of slightl y differ e nt ways.
In a nema t i c
l iquid crys tal the r ods need not be pol}'lllers - they can be relatively SlIIall rodshaped mol ecules .
By analogy with Fig. IX.2, the direction of orientation wil l
be r eferred to as che z-axi s and the t-axis i5 parallel to it in Q- space.
A

An X-ray dlffract ion pattern

a nema tic provides information about a


cylindr ically averaged molecule.
The reason ls that all possible rotatlons abou t
the long luces of t he 1IQ1ecules "d ll be represented i n the sample and each 0 1 these
molecules wi lL scatter X-rays.
Suppose, for the sake o f arqument, that interfer ence between X-rays 5cattered by diffe rent molecule s i s negligible .
Then the systelll reseJDbles the ideal gas of Sectlon VI.2 except that the intensity 15 now not
spheri caLly averaged but, accorOing te the r otation proper ty of the Fourier trans lf F{-) is the Fourier
form in Secti on 11.4 , 15 OIlly ilwraged about the t-axis.
transform o f a molecule, ald there are N !lDlecules in the s ample , the lncensity
distribut 1.on is gi ven by
1 {2:l

N < F' (2:l F'*

(~.l

X-Ray dlffractioo patt ern from a l esion in


&g1ng hucan costal cart 11age.

lf t he organisation of rods is truly nematic, ie . the r e is no regu lar lty ln


the arrangement of molecules but onl y orientatio n, interference effect s can be
a l lowed for in much the same way as for a liquid or an amorphous solid,
The on ly
difference bet ween equati on VI.4 (ideal gas) and equa t ion VII. 6 (liquid or amorphous solid) i5 the appearance of en interference function .
By ana l ogy equation
l X.16 can be med1f i ed to
(I X.17)

f r~

>

( rX.1S l

by analoqy with tbe derivat10n o f equation VI.2.


Here < br ackets > denote a
cylindrical average about the ~ - axis , which is equival ent to an average over all
, valuas - see Plg. I X.2.
Thus, if ~ ( w) 1 5 some general fun ction of ~ ,

The lf.ean1.ng of equation IX. 15 i 8 perhaps c l earer if it L9 rewritten , in cyl ind.ric a l polar coordl nates , as
(IX.16)

to al l o", for intermolecu l ar lnterference.


Here S ((,~ l must be independent o f ~
if the intenslty distribution is to retain cyl i ndrical symcetry.
This lndependence arises beca use the arrangement of or iented rods in t he nema tic is independent of the azimuthal coardinate (8 in Fig. I X.2 l of real space.
The dlffraction patt ern wili be formed by the intersection of t he cylLndrically symmetric intensity distribution, l ( ,~l , with the surface of the Ewald
sphere as shown in Pig. VIII . S ; note that the X-ray beam i s c:onsidered to be
r oughly perpendicul ar to the z - axis .
Because the diffraction geanetry ls so
simi l ar , nemati cs are considered ln the same chapter as one-di mensi onal crystals .
The intensity distrl bution a l ong the ~ -axis o f Q-space p r ovides l nformation about
the structure projected on to the para l lel z-axis o f real space - for exactly the
same reason given in Section VII I. 4 .
A s bef o r e the mer idian of the diffraction
pattern ls still defined to be parallel to the z - axi s le. the direction i n which
the r ods are oriented.
The equato r i s defined to be perpe ndlcular tO the mer l dian and provides informa t ion on the structure projected on to a plane perpendi cular to the z -axi s - once again for exactly the same reason as in Section VlII .4.
The di ffrac t ion pattern from an ori ented a ssembly ef rod-shaped molecule s can
be used to determine the direction of or ientation .
A disorlented ar r ay of rodl ike molecul e s gives a d i ffraction pattern with circular symmetry - like Pig.
VII. 3 where the macr ODOlecul ar constituents ol the spec1men have no preferr ed
orientation .
Figure IX.I) does not have circu lar ayume try because the polyme r

X-Ray Diffrac t i on

114

Helices and Li quid Cr ystals

molecules in th l a specLmen are partial ly oriented.


The d irection o f preferred
orlentation 15 parel l aL to the merldian o f the pae tern.
la the meridian vertical
oc horizontal in ~lg. lX.1 3?
Fortunately X-rey dlffractlan patt e rns of the poI ymer ln questi on (eoilagen) have been obtained fron fibres wher e the orLentat i on vas
known and ve ca n i dentL!y the meridlan as vertical .
As the molecu l ar structure l a
aLBO k~~ ve cautd have calculated I (( . ~) traro Lts coordinates and i dentified the
Ileridian by compartao n of observed and calculated pattern s.

lt 18 relatLvely s tralqhtforward ta calcula t e the Lnterfer ence function of


equation IX.17 on the aquater.
Ne have seen that the equator prevides infor maticn aboue the kind oE projected structure shown ln Flg . IX.12.
This s tructure
i5 like a liquid or en amorphous solid except that it l a two- , racher t hao th~ee
dimensional.
l e can, therefore, be deacribed by a two-dimens lonal radia l distrlbution func c ion, q(r), whi ch is i ndependent of direction - e~cept in so far as it
is confined to the p lane of the figure.
By analogy with the three-~imenslonsl
definition in 5ectLa n VII . 2, g(r ) Ls simpl y the probability of f i ndlng s cen t r e of
one projecte d mol ecule st a qiven distance trom another.
In the three-dimensional
case of a l iquid o~ an amorphous solid, the interference function , 5(2) , wa s ~e
lated ta q {c) by equat ion VII.6.
Thls equatian contains the Four i e r t~ansform of
(t;( r l - 1)
fo~ a systelJ. wi t h 8phe~ical symmetry.
According to equllt i on II. 9 , the analogous
equation for a system with cylindrical symcetey is

S IC) 1 + n

r '"
Jo

2rrr (g(r) - l} J

( r ) dr

(IX. IB)

Bere S ( } ls t he equatoria l interference function and, ai nce ~ ls zer o en the equa tor , lt is a fun c tion o f ( only ; "o i 8 now the number of discs per un it area. Thus,
lf a model can be formulated for g(r ) , the interference f unc tion and intens ity di stribution ean be ca lculated en the equator ; the a nalysis of the equa torial intenaity distribution i5 analoqous to the liguid and amo rphous sol i d case of Sectian
VII.4.
There i9 a simple method of calculating the equatorlal Four i e r tran5form at
low (values.
Acoording to Section V.4 , t he transform is then only sensitive to
the proj e ct e ~ structure s t low re solution and the discs o f Flg. lX.1 2 become a good
approximation to the p rojected structures of the moleeules .
The Fourier tr ansform
of a d lsc , oE radius a , can be calculated trom equation 11. 9 , in the same way as
the Fourier tean aform of a aphere W8S calculated from equa tion 11 . 9 i n Seetion V.4.
In the case of the d isc the problem is two-dimensiona l in s t e ad of three-dlmensi onal;
the reault is
F '~ l

(Ix. 19)
In Section VI. J Lt was shown that consideri ng roughly s phe rical molecules to be
spheres was an excel lent approxillation, at 10'<0' Q values , f or calculat ing the scattared inten.Lty fren a 8yst~ where the arrangement of molecules had spherical symr
metey.
The approxiaation g l ven here t urns out to be equally good f or cylindri cally ave r aged i ntensity st sufficiently low va l ues of t .

115

Pa ra ~xlca lly, helical molecules, which are themselves one - dimensional c rys ta le , c an exhibit nematic o r qanisation ie. their arrange~nt in space need not be
crystalline.
Now F( ~ , ~ , t) in equation IX. 17 has to be repl a ced by F ( ' , ~ , {I of
equatlon lX.14 because the Fourier transforc e f a ~lecule ia confined to planes
in Q-space ~hLch are perpendicular t o the e -axis.
The d iffrac t ion pattern 18
exactly what one would expect of a cylindrically averaged he Lical ~lecule modif ied by an interference funct i on .
Note that

+ 2

LL
n

(~rk)Jn (E r j )

cos (n( Sk - 9 j )

k>j

whlch i s , of course , independent of V, but does depend on Si'


The dependence on
8 arises because i ntramo lecular interference ef fects depe na on t he r e l a tive azij
muthal posit ion s of different a to~s in the same mol ecule.
The layer line spacing
can be used te measure c , the axial repeat dstance of the he lices remembering that
conplication s can occu r for paral lel , ooa~ial heli ces - see Section IX. 4 .
I f the
a~ia l r ise per residue, q, is to be measured, the specimen wil l nave to be ti lted
so that a pelnt on the ~-axis can touch the surface of the Eweld s phere , as explaine~ l n Section VI II. J , and appear on the meri dian of the x- ray diffr~ction pattern o
SOIIle i dea o f the intensity distribution along the ~ -axls can usually be
obtained because t he inte n s ity distribution af Q-spa ce is blu.r red out by Desaic
spread, as described in Secti an VIIl.B , s u fficient ly f or maxi ma on t his a~is t o
touch the sur fa ce of the Ewa,ld spher a.
Mosaic spread a lso leads t he intensity
which i5 calcul ated a t a peint i n Q-space be appear dissipated over an arc on the
diffraction pa t tern.
In princip Ie chiral molecules canoot exhibit nematic orga nisat i on in practice
this restrict ion can be ignor a d for the very long r od5 of polymer s.
Chir a l llIo1ecules distort the nematic arrangement so that the molecul ar a x es are no longer a ll
paralle l sach s uccessive molecula r axis acquires a slight r otation or ~tw is t"
about the ~-x i a direction - as shown in Fig . IX . 14.
The result i 9 called a
"twi sted nematic " or "cholesteric" l iquid cryst.al; the l atter name arose because
this phage i 5 c ommonly forrned by ester s of cholesterol, although not by cholesterol
itself .
Belices are chiral and so a helical molecu l e cannot form a perfectly
oriented nematic.
Bowever, for a long rod, the rotat ion between a molecule and
its neighbour i5 e xtremely small ; the net twi st o f a molecule a t the surface of a
macroscopic s peclmen i s only a few degrees wlth re spect to e molecule at the centre.
Then the e ff ect on the dlffraction pattern wil l be indlstingu isheb le frolO the mosaie
spread of Section VI I I . B.
IX. 6 . Smectl c o r gan isat i on
A smectic liqu id crysta l nas a more ordered arrangement o f molecules thao a
nemat ic i the least ordered sroe c tics are true one-dimensional crystals.
Figure
IX.1 5 shows the errangeoent of molecules in a type A smecti c; the mol ecul es are
oriented and confined to l a yer s .
The l ayers .,.1 1 have the same thickness , e, so
that the wtructure repeats it sel f regul arly in the c-axis direction o f the figure.
Bowever there i 8 no r egularity in the side-to - side arrangement of the rods. Figure
IX.1 2 there fore representa t h e structure of a type A smscti c , pro)ected on to a
plane perpendicular to the e - axia, as well as t he projected s tructure of a nematic.

116

Hel ices a nd Liquid Crystals

X-Ray Di f fr act i on

117

i
-----+x

Fig . 1)(.16.
Fig. IK.14.

Schematic diaqram aE the "tvi st" ln a choLes-

terie liquid erystal.

X-Ray dtffract lon pattern from a fish fin-ray o

In oontrast a type B smectic has a regular side- ta-side arrangement of molecules


vithln the layers - ve are not conce r ned with such regular structures ln thls

chapter .
Figure 1X. 16 ShOW8 the X-ray d i ffra c tion pattern froro a system vhich reseobIes Fig. 1X.15 in having a l arered structure but no regular Side-te - side arrangement of molecu l es .
apart in Q- space.

e - AXIS

1111
IIIII 1
111 1
F iq . 1X . 1 5 .

Smectic type A orqanlsatlon.

The meridian 16 confin ed to layer lioes which are spaced 2~/c


The r e vas no need be tllt the specimen to obtain thls pattern

because the layer thickness 1s so gr eat (6? nm) tha t the pattern appears at very
low Q values.
At these l ow Q values the Ewald sphere is essentia l ly aplane saetion oE Q-spaee, perpendicular to the ineident X-ray beam, and so the intensity
distribution along the e-axis can be recorded without tilting.
Notiee that tha
intensity fades at higner ( val uas beeause the plana r Ewald sphere approximation
breaks down.
Then tne ( -axis, alonq whieh the intensity happens to be mueh s t ronger than els'ewhere in Q-spaee, becoces further from t he surEaee of the Ewald sphere,
as shown in Fig. VIII.S; Seetion VII I. 9 gives a detailed explanation oE this effect.
AIso notice tha t the meridional intensity distribution is not quite symmetriea l
about the equator , presumably beeause the speeimen was not quite perpendicular to
tne X- ray beam ; this effect is discussed in Section V I I ! . ) .
The equl!ltor is
entirely diffuse beeause, as in a nematie, it eonveys informa t ion about an array
of projeeted moleeules like Fig. IX.12.
Interference effeets on the e quator can
be explained in the same vay as fo r a nematie.
Thus Fig . IX.16 corresponds to the
diffraetion patter n of a true one-dimensional crystal .
I X. ?

SlJIDI[Iary

Some biologieal structures cons i st oE globular maeromol ecules arra nged on a


hel ical path cany polymer roolecul es are helical .
If their structures repeat ,
with a periodieity of e , along the helix axis, their di ffrae t10n patterns are eonfined to l ayer lines spaced 2 ~/ c apart in Q-space .
Note that e may be greater
than the piteh of t he helix .
A rotation axis of symmetry coinc1dent with the axis
of coaxial helices viII lead to the absence of seme layer line s which would b e ex peeted i n the diffraction pattern of a single heI ix .

118

X-Ray Diffcac t i on
The diffraction pattern cf 8 halleal molecule can also be used to Deasure q

the aXial r ise ef each Nresidue" which repeats itself 810ng the t.elical path.
Intensity only appears on the ~-8xis ef Q-space , which is parallel tO the helix
axis , at peints spaced 2~/q aparto
The helix axis has qenerally to be t Llted

fro~ the perpendicular to the lnci dent X-ray beam for a point on the ~ -ax is to
appear on a diffractlon pattern .

Rod-shaped rr~lecules, eg. helleal po l yu.ers , can often be lnduced to 8ssembl e


In the Iea st ardeced , oriented array there 15
And they can have
no side-te-side r e qularity ln the arrangement ef molecu les.
:a~dOl!l rot.ations about theLr long axes.
'l'he dLffraction oattern then pro',rides
,n,ormatian about the structure ef cylindrically averaged mo1ecule - interferen ~e
e e cts On the equator c.n be exp1 a i n ed b y a tvo- dimensional version "
of the theory
given in Chapter VII.
Such patterns can be used to dete~ine the d i rection of
preferred orien tation af polymer chains in ~ter iala.

~lth their a xe s oriented parall e l .

CHAPTER X

Three-dlmenslonal Crystals

X.l . Introduction
A true cryatal has a atructure which is repetitive in three dicensiona.
Extan.ion ol the theory ef diifraction by one-dimen.ional cryatala into three
dimen.iona ia all that is required to underatand the diffraction patterna froe
cryatala - i n princip1e .
I n practice X-ray crystallography involve. speciali.ed
tachniques and haa aome of ita own jargon .
Tbie specialisation ha. ari.an because
X-ray diffraction data can be u.ed te determine the repeatinq arrangE!ment of atoms
in a cryatal , and hence molecular atructure., vlth considerable eccurecy.
Conaequently X-ray cryste1logrephy has ateracted far more attention than any other
application ef X-rey diffraction.
The principal a i m of ehi . chapter i9 to indicate how the theory which has been
dave10ped .0 far can be applied te analysinq X-ray diffraction data froc enree dimensional crystals .
lt ie only intended to ~ive a sketchy account of X-ray
cryatalloqraphy as it is actuel1y practisad - there are already so nany books on
eni. aubject that it would be pointless to give yet another account of it . Tbere fore thi a chaptar .erves to l ink the theory presented in the rest of thia book to
the many accounts of X-ray cry . tallography ~hich are already available.
X.2. Intensity d i stribution
The arranqement of atoma which repeats itself regularly within e crysta1 is
called the "unit cell" .
Fiqure X.l then shows lIow 4 crystal can be generated by
the convolution of the unit ce11 contents with a three-dimenaiona l l attice o f
peints_
The figure actually demonstrates the propert ies o f a tvo-dimensional
crystal - the bebaviour in a third dimension ia ioplied by that in the other two.
This simple approach to explaininq the properties of three-dimensional cry.tal a
will be usad. throughout this section .
Flo;-urfl X.l ia analogous t o ;Oig. VIll.2
which ahowed how a one- dimen.ional crystal could be generated by convolution. The
only diffe r ence i. that, here, the structure is regularly repetitive in three
dimensiona CId, therefore, the latt ice conslst.S of an array of points in three
<Umenlliona inatead of a row of point.S .lon9 a Une.
A three-dimena ia"lal lattice ia Oefined by three vector s , a , b and c. aa shown
in F'ig. x.2.
In the one-dimenllional can of Section VIII . 2 , the-lattiCe vas
~f1ned a01111y by the vector ~ - its IDOdu1us, e , was the repeat diatance and i ta
directlon defined ehe orientat ien of ehe lattice in real space .
lIeee both the
119

120

Three-Oimensional Cryltala

X- Ray Oiffraction

0000
0000
000 0
0000
Flg . X.l.

moduli 01 !., ~ and ~ and the &nglee: bet..,een thu are required te define the l attica.
ne &nql . . between the pairs ef vectors !. with ~ :!2. w1th ~ and !.. w1th ~
are o!ten denotad by y , o And 8 . note that the usaq_ cf B and 8 la completely diffarene to that 1n Chaptar a VIII and IX.
In Fig. x.2 the intersectlon 01 the twc
vectora a vlth b 1. taken te be the or191n cf th. un1t cell PAa~ ln thr dlnensiona a vector ~ intar cta th. othar two, also at P, anel point. out el the plane
o! thi. flqure
cut not nace arl1y perpendicular to lt.
The posltlon ol the
j th atom in the unit eell is given by

(X.l )

Generation cf a crystal atructure by convolutlon.

Bera Xj Y1 and Zj are translatiene along the veetors ~, ~ and ~ expressed as fractions of the1r len;th Zj had exaetly the game meanin; in Chaptar VIII.rhese
fraetiona l tran.lationa are often called "fractional unit ce ll coordlnatea".
It
wlll be convenient to define tha vector

(x.2 )

=
P19 X.2.

Ceneratien el a two-d1cenalonal lattlca by convolutlon .

!! -->

Flqure X.2 alBO ahova that a thrse-dimenslonal lattlce 1. the convolutlon of


three one-dimenalonal latticee Fig. X.3 ahov a thet ita Fourler transform le nonzero only at a .et of pelnts ca l lad the M rec lprocal lattiee".
The rea l- space
lattice in Flg. x. 2 can be generated by convolutl on.
Considar a aln;le rov of
pelnt. vhere each le a dlstancs b apart; the lattlee le generatad when eaoh of
~e. pelnta acta a a an ori;ln for ancther rov of pelnta whleh are .paced a apart .
Accord1nq to Saction 11.4, tha Fourier transform of the thre.-dimenBlcnal latties
le then glvan by the produot of the t raneforme ol ea ch of the three one -d imens iona l
lattlcea.
Plgure x.3 shows that the transforms of the one-dimeneional l attic es
are non-zero only on a set of planes - spaced 2~ /a apart and perpendicular to a,
2rr/b apart and perpendicular t o b, and 2'1f / c apart and perpendicular to e .
ThIs
r.sult va. derivad in Saction VIII.3.
The product of the three transforma can
only be non-zero in thoaa regiona of Q-epaoe where eaeh o! t h. three i e itael! nonzero ie. where their planea interseot.
Figure x.3 showa that the planea interaect
at a aet of pointe.
The reciprooel lattiee can be defined by three vectors, which are conventionally denoted by a , b and c as shown in Fig. x.3; in contrast to the uaage i n the
rast of this book, the 8upe~8cript has nothing whatevar to do with cocplex conju;atee.
An;les between the pairs of vectora a with b+, b+ with c , and a+ with
~. are often r epreaentad by y+, a and S+ respectively.- I Fig. X~3 ~+ .~ l s ehe
pro jectlon of a+ on to the horizontal direotlon, which equals 2n/a, multiplied by
a - ehe re.ult-i . 2w.
Similarly

.. . ,.

1'1; . X.3.

121

Cenaration cf th. reciprocal latelca by multl-

pl1c&tlon.

b.b

f.. ,S

,."

a.b

~. f.

b.a

~. f.

c.a

s+ .~

O
O

(X.3 )

The dot product. whoaa values are zero arise ego because ~. l ies alon; ona of the
planea whlch 1. perpandicular te b.
Equation X.3 talla us that, from tha conatruct10n ol F1q. X.l,
i. alwa~s perpendlcular to both b .nd c, b. la al.aya
perpendicular to both .!.-and.=.. whlle ~. la .lway. perpendi(;,,lar te botb !.. and ~.

.+

122

X-Ray Diffra ccion

Three-Dimensional CrYltall

Moat crystals have geometrically more regular unit cells


be .impl1f1ed..

(Il,-I)

A iqnlnq indices to reciprocal lattie. points.


~lr.ct lon

el

~.

when rlq.

Reciprocal l att1es peine. are epecifiea by th e val usa ol thr inteqera - h,


k &nd l .
The vector. 2 whlch termnate st reciprocal latties pointB are qlven by

2-

h!.* + ~* +

!sil'

(X.4 1

where h, k ena l are integral &nd all three have valus of Z8ro at eh. orlq l n of
Q-apace , O'.
Figure X.4 ahowa a two-dl~n.ion.l example where only tvo of thea.
i n tec;e ra, h a nd k, a re requir~.
It will ofeen be convenlent t o define th. vector

The Fourier tranaform of the crystal can be obtained by multiplying the transform of the electron density dia tribution ln a unit cell by the transform of t he
l.ttlea.
Thia reault ariaes because tha eryatal atructure can be generat.a. by the
oonvolution of the unlt call content s with the lattic a.
Tha Four i er tranaform of
the eleetron deneity ln a unlt eell 19 given by equation V. 4.
Jl.lthouqh this equation has been taken to repreaent the Fouriar transform ol a molacule, it l. valid
for any assembly of atoms provided their relative po.itions are f ixad. - a. ia
clear from the derivatlon of Seetion V. 3.
Sine. the transform of the lattice ha.
a value of unity . t the r eciprocal lattice peinte and zero elsewhere, ve 8imply
hay. te calcula te the valuee of the "molecular transform" of equation V.4 at th.
reciproca l lattLee pointa in order to obtaln th. Pourier transform ot a eryatal.
~rom equations X. l and X. 4:
~.2. (Xj !. + Yj~ + Zj='.l . (h!." + kb - +

2"(hX j + kY, +
- 2"h!;

h -

equation X. 6 can then

w.

(2, ')

Thua th.ae aquatiOll& cay help the re.dar to plcture th.


x.3 1 . extended into thr dimensiona.

an~

What ls the valua of t h. Fourier tranlfo~ of the lattice at the rec iprocal
lattiee peints?
Aeeording te Flq. VIII. 3 the peak. in the Pouri.r tranlform of a
one-dimensi onal lattlce, ol effeetively infinlte extent , all have th a~ h.lght.
eon.equently the value of the Fourier tran.fora of a three-dimensional lattice vi l l
be the aame at all the recipr oc al lattice point..
This value viII be very large,
110 that the erys tal acta aa a n Amplifier for the Fourler transform of the unit eell
contente, at the rec i proc al lattiee peint., as d18cusaed Ln Section VIII.4.
Its
absolute value viII be e f no concern sinee
ahall not be conceroed with absolute
".lIurements of Lntenslty in thLs book. .
Consequently the Fourier tran.form ol the
l.ttice may be aSlligned a value of unLty, on some arbitrary scale, at eaeh of the
reciprocal lattiee peint .

ca,O}

rig . X.4.

123

(x . S)

t =.*>

tz j )
(X.7 )

Bere the second line fo llowe from equation x.3 and the third line from equations
X.2 and X.5 .
Then, trom equa tlons V. 4 and X.7 , the Fourler tranetorm ol the crystal 111 given by
(x.S)

who.. co~pon. nt. ~J.t be integra l i i the Fourier tranaform of th. latt ies 1. te be
non-zaro .

Note tlu.t
Icb* + t~*

- ( Ih!,*

..

kb* ...

l~" ) . (h!.- + k~- + ts- )}'J

(h 21L",2 + k. 2b_ 2 + l2 c ",2 + 2hka-b- COII ""(-

(x . 6 )

+ 2ktb-c* COII 0* + 2hl.-c* COII S*) ~


Equatlon X.6 L. the general .xpre ion vhlch glve. tha value. of Q corre.pondLng
to eh. rllciproclIl lattice polntll lt thllratore appli.1I to lIo-callad "triclinic"
cry.talll whlch are characterl.ed by

where the 8\lJ11C4tion haa to be t aken over all the atana ln a unit cell.
Now the
Fourier traoeform i, only non-zero at those pointa in Q-llpace which are given by
integral ccmponenta of h - it can, theretore , be written ae F (h) in.tead of .s
P' (.Q.l
Remember that the .tomle aeiLtterLnq factor, f j , d.ependa on Q which, Ln
;eneral, le related to the componente of h by equat ion x.6.
The values 01 the Fourier transform ol a cry.tal, F(h), at the reciprocal lattiee pointa are often called "atructure factor." by eryslloqraphera - althouqh
~timell thia term la applied to the modulu. of F{h).
seattered intenaity i.
ccnfinad te reciprocal lattic. peints and , aeoordin; te equatlon 11.5, la qlven by

'24

Three-Oimensional eryatals

X-Ray Diffraction

'25
(x.9)

where f'(h,l is qiven by equation K.S and F"'(!l) 19 1t. complex conjugate.
The point
on 11. diffraction pattern where 11. value of 1 (h) 18 recorded is often called a "rel.ctien".
This nomenclature arlses frora. 9r599'8 law, oE Section VIII.5 , whlch le

e - AXIS

EWALO
5P~ERE

~-AXIS

represented by equation VIII.6.


For 11. three-dLmen81onal crystal en equation like
equation VIII.6 can be deriv.d by conslderlng X-reya to be reflected by planes of
atoma in the c:rystel - hance the term "ref1.ection".

X.3. Diffraction geometry

Fig. x.5.

Sactlon through the Ewald sphere showinq reciprocal lattice pointa.

rE the crystal re~in9 atationary, Fiq. x.5 shaws that few reciprocal lattice
peints will touch the Slurfaee ol the Bwald aphere.
An exeeption oeeurs if the
unit cell ia very large - then the reoiprocal lattice points vill he so cloaely
.paced that some are bound te touch its surlace.
But the diffraction pattern wil l
depend on the precise position oE the erystal and may be difficult to interpreto
Figure X.S ia a aeetion through the Ewald aphere when c ia perpendicular to the
incident X-ray heam.
The cylindrical polar coordinates (~,*,') of a peint in
Q-apace are defined in Fig. IX.2.
In the rest cf this aBction, and indeed in the
remainder ol the book, the ~-axis will he defined to be parallel to e.
Figure x.6
ahowa a aeetion oE the Ewald sphere which is perpendicular to the e -axis, ie. to
the plane oE Fig. x.5, and so passee throuqh pointa in Q-space with the sama values
oE e.
lf few reciprocal lattice pointa toueh the Burface of the Evald sphere,
there vill be zero intensity on nearly 11.11 of the diffraction pattern.
An informative pattern can be reoorded if the cryatal in Figs. x.S ancl X. 6 i9
rotated about the direction ol c - which iB generally called its "c-axis". Accordin; to Section II.4 F(h) and, therefore, I(h) are rotated abcut the paraUel
e-axia of Q-space.
Reciprocal latt!ce points then pass throuqh the surface of the
Ewald sphere and the correaponding values of I(h) appear as apots on the diffraction
pattern.
Consider the reciprocal lattice pointa, like P, R, S and T ef Tl;. X.6,
vh1ch have the aAme values of ( and e.
They wi11 11.11 pass thrO\Jgh the allID8 pointa,
A and 8, on the Burface of the Ewald sphere.
Censequently the aependence of the
acatterea intensity en ~ cannot be detected.
A diffractlon pattern recorded ln
this way ls called 4 "rotation pattern" of the crystal.

Rotation patterns can be easily un~erstood lf they are converted into Q-space
coordinateSf the result is called a "reciprocal lattice rotation diaqram" and an
example is qiven here fer an orthorhombic unit cell.
An orthorhombic cell has the
folloving properties:
EWALD SPI-lERE

a,ob,oc
(I-6-y-90"

e-AXIS

Flg. K.6.

Secticn throuqh peinta in Q-space with the same


; vlllue .

Th1a example i8 a compromise - it i8 not 80 complicated as the general, or triclinic, case but it is not too regular in its dimensions.
As before the crystal
11 considered to rotate about ita c-axis so that lts Fourier transform ia rota tea
&bout the parallel e-axis.
For an orthorhombic cell c la parallel te c le. it is
coincldent with the !;-axia.
The e-axis can be locatad in practica hyadjusting
th. tilt of the cryatal until the tour quadrants of its rotation pattern are identical - more detalla latero
Note that, accerding to Section VIII.J, the intensity
diatrlbution alonq the ~-axia vill not be recorded when this Axis is perpendicular
te the incident beam the position deflned by the undeflected beam i8 an exception
but ita lntenaity will be too great to record wlth the rest ef the pattern - accordin; te S.ction III.7.

Il the diffraction pattern is recorded on a tLst film, the method d escribed


in S.ctlan VIII.) can be ~.ed to convert th. coordinates of eaeh point en th. filn
lnto coordinates in Q-space.
However rotation patterna are uBually recordad en
a cyllndrical film whlch 1. coaxiaL with the rotatlon axis .
The trana!ormat Lon
between film and Q-apace coordinatea, and th. correapondinq Bernal chart, are then
qlven 1n Vol.II el the " Intarnational Tablea for X-Ray crY8ta llography~ (se8 BIB-

uae. different un1t. for g...apace


(corr pondinq to the O-.pace el Sectlen IV.J) - th. conversion factor can be found
by ocmparlnq i ta equatl ons for a tiat film with thos. in Tabla VIII.l .
Notice
a I so that in "International Table." the I;-ax i. 1. deUned more generally than here :
ln th. tablea lt ia parallal to the ax l. about whlch the cryatal ls rotated.
In
thh boolt the ayatAl. b conaidered tQ be r otated about its c-axis but thiB 1. not
nece arily the cas. - lt coulCl equal ly vell be rotated about the a-axls or the
b-axi .

l.IOGRAPRY Section 2) .

But "International Tal:llea"

po.lelona ol the spots on the orthorhomblc rotation diagram will now be


Slnce !J ~ and ~ are mutua11y perpendicular, in t hls case, so are !.. , ~*
and e*,
A1ao !.* 19 now parallel to !.J .e.* b parallel to ~, and ~* ls parellel to
~ so thae equatlon X.J qives
a*

' Iu.' ....

It..o I ...D b><


1

.1

12 T

(1' l O.'

."

ao

0. 1. 0

6..1 ,,1 I,ooi

0,1,1

0. 1.1

l Ioz;

Fiq. X.7.

Prom equatlon X.IO


(X.ll )

1nclI the t-axlll now Ile. along the c!irectlon ol c*.


Sinee a , 6 and y are all
.qual to 9OP, so are 0*, S* end y* ,
Therefore equation x.6 become.
(X.12 )
and it also follov. that
(122 _ ;2) ~
(h 2 a*2 + k2b*2)~

0.1,.1 ~o:t ~ IJ:

\11 1,0,' O"

"

,,~

lo.l

o.u

1.2.2

1e..,1 OJ Iltl Iaz., II.LI Z.O.l

0,0,0

10..,0 ",O

2.0 1. 2.0

~""

cU,i

I,or i' CU TI"o

2,0.1

Ql.l

h... 1.11 o.z.l 1.1.!

2.0.1

,lO

(lCIO)

c* - 2:1 / c

- le'"

~ .. l~t Ql '

~.l

2rr/e

b* - 2rr/ b

127

Three-n iIt.ensional Crys tals

X-Ray Diffraction

126

(x.l3)

whera the final 11ne of equation X,13 follows from equations X.ll and X.12.
If
a, b 'and c are known, equatlon. x. lo , X. 11 and X.13 can be used to calculate where
the reciprocal lattlce point. viII appear - lnformation about ~ 15 lost when the
cry.tal 1. rotated becau all reclprocal lattice points vith ehe same values oE ~
and ; pa..s through the .ame tvo points on the surlace of the Ewa1d sphere.
Figure x.7 shove the orthorhombic, reclprocal lattlce rotation dleqram.
In
thl xample a* ha. been cheaen to be greater than b* ie. a ls less than b .
Note
that the po.itions of the apot. on the rotatlon diaqram are the same in all four
quadrants.
The sama will be true of the dilfraction pattern since the recording
proceas distorts a11 four quadrant. equally.
Thle diagram conEorms to the general
rule, diacuaaed ear lier ln thls section, that a reclproca l lattice peint sppaar. in
two placa. on the diflraction pattern.
Previoualy this reault wa. obtainad pictcrially - now we can see that th. two positions correapenO to the positlve and
neqatlve .quare roct s In equation X. l3 .
Reciprocal latt ic. points denoted by
(h,k,t), ( -h.k,t) , (h , -k,t) and (-h,-k,l ) all paaa thrcugh the peints marked with

Positiona of spets (h,k ,t) on an orthorhombic


reciproeal lattiee rotation_diagram (negative
valuea of l are denoted by t)

valu of (h,k,t) in Fiq. X.7 - because all four sets of indiees lead to the sarna
value. of ~ end 1; eecordin; to equations X.ll and X.13 .
In practice the posltiona ol the apets on an X-ray diffraction pattern are
usad te measure the unlt eell dimensionsl then Flg. X.7 19 obtained experiment.lly
and the construction of the reciprocal lattl e e ls reveraed to obtain the required
reeu lts.
'I'he first step le to assiqn values of h, k aOO t te each spot l e. tO
"index" the pattern.
Indexinq uBually preceea. by erial-and-error.
From Flq .
X.1 lt mlght appear straightforward but aeveral anega can occur: tvo examples viII
be qiven,
For a tetragonal crystal , vhich le the same as the orthorhombic case
except that a and b are equal, palrs of spets like (1,2,1) and (2 ,1 , 1) vill overlap,
lf y* la not 900, ~ 1. a functlon of y* - vhich compl ieatea the positlona
ol the spots.
Theae resulta can be derived from equation x.6, once the reciprocal
latt ice has been eonatructed , but they are summarleed by equations in Vol.II ol
"lntern.tional Tablea".
"llen the many spote heve been indexed, and t he ir Q values
meaaured, there ere more than enough da ta to determine the aix unknown. - a, b-,
c* , 0 - , 8* and y* .
In our orthorho~ie example equatlons X.11 and x . 13 would be
uaed te obtaln a- , b. anl c * lrom 1; end r; .
Tha constructlon of t he r e ciprocal
lattlee can then be rever aed - lf neceaeary vith the aid of equetions i n Vol.II ol
"lnternationa1 Tables".
In our example a, b and c can be ca1culated from a-, b"
and e . u.in; equation X.IO.
If equetlons x . IO, X.ll and X.13, which r epresent a
apecial caae, are to be used lt must flrst be reeoqnised that the unit can la lndeel orthorhombic i e . that o, S and y are a11 equal to 9aP .
In our orthorhornWhat can be pre~ieted about the lntenslties of the apots?
blc example of Fiq. x.1 the intensity of each apot marked (1,2,1) le r lly the
.um ol the lntensltiea at the (l , 2,l), (-1, 2 , 1), (1 , -2 , 1) and {-1, -2,l} reciprocal
lattiee point..
The inten.itiea of the sace reclproca1 1attice paints contribute
te both the (1 ,2,1) spot. so they mu.et have the lame net iptenslty.
S1.m11arly
the spots marked (1,2,-1) are re.lly a composite of the intenslti.a at the

".

Ihree-Dimensional Cry8tall

X-lay Diffract ion

"8

with larg8 unit cell. the .;:cts ue

tOQ

clo"ly epaced ter a counter to me.aur. the

inten.Lty ol e.eh paret.iy - so film then has te be ud.


X.4. Determlnation el erratal structurea
W& have en th&t the positiona el t he apota which cOn8titute the 41ffraction
pattarn of a eryatal can ba u.ed te meaaure ita unit cell dimensiona, th.ir relativa
inten_Lti can be u.ed to m.aaure th. electron den.Lty dietribution wlthin a un1t
cell.
Sinea the ~ourler transtorm ol a cryatal 18 non-zaro only at a s.t ol pointa,
tn. integral ol equation II.7 can be written
a summation.
The reeult ia

.a

p (!.)

F (!!) exp (- 1

!..~l

(X.14 )

where the integral campenents el ~ ran;. in valus from mlnua te plus lnfinity le.
lnformatlon tren an infinite number ol dlttraction apota ia required.
Fram equadona x.i and X.14

P(!.) . LP (~)
Fiq . x.e.

X-Ray diffraction pattern of a cryatal of the


enzytte 6-phoaphoqlucenata dehydroqenaae, extractad from aheap 1iver, obtained by the precessien
mathod (taken by Dr. M.J . Adama).

(-1,-2,-1), (1,-2,-1), (-1,2,-1) and (1,2,-1) reciprocal latUce pointa.


Thua tha
apeta marked (1 ,2,1 ) are the lum ot a aet of l(h) valuea and thoae marked (1 ,2,-1 )
are a aum of the correapondinq 1(-h) valuea.
Accordinq to equation X.4, if h corresponda tO a vector \2.. then -h, correapond.a to -Q and accorcUnq te SecHon IlI. e
1(2) ar:d 1(-g,) are eq.al.
Conaequantly the spota marked (1,2,ll and (1, 2 ,-1 ) have
tha .~e intenaity.
When this arqumant ia applied te othar pairs of apotl, (h,k,l )
with (h,k,-l), it can tal .un that the inteneity diatribution of a11 four quadranta
of the rotation pattem ia the same.
Thia r eault ia trua whatever the a hape of
the unit cell.
lf the intensity were not the aame in al l four quadranta, ie. if
Ilh) were not evarywhere equal to 1 (- hl , anomalous acatterinq. discua.ed in Sectlon
v.S vould be apprec iable - then, accordinq to Section V.6, the chira llty of the
unit call contenta could be eeterminad.
Overlap of spota on the diffraction pattern can be preventad by oscillatinq
the cryatal back ar~ torth throuqh a a~ ll angle.
The r esulting "oacil1atien patterna" allow the inteneitiea of each of the apota which were auperimpoaed in the
diffractlon pettem te be measured aaparately.
If the cryatal vere oacl llated
throuqh n/4 radiana from its poaition in Piq . X.6, enly the reciprocal lattice
peint marked P wOl.lld contribute to A and only that Dlarked S would contribute te B.
A aecond oacillatien pattern, afeer the cry.tal had been rotated by T/2 radiana,
vould allov points lika R and T to pasa through the surface ol the Evald aphere .
Thare are oany other methoda for recordinq X-rey diffraction petterna from
cryatala.
Tha preceaaio n methad is particularly intereatin; becaue. it recorda
undlatorted aections throuqh Q-apace.
It achieves thi. r eault by preceaain; the
film over the aurfaca of a aphera, whlch ia concantric with t he Ewald aphare, while
tn. crystal rotate..
By co11actio; a aariaa ot aectiona, thlll intenaity at _ch
reclproel lattice peint can be recordad.
An axample of a preceaaion photoqraph
ia ahovn in Fie. X.e.
Por accurate inten.ity maaaurementa counter. are often uaad
inataad of pbotoqraphic film to racord Che diffraction pattern.
But for cryatala

exp (-2w i!!..!l

(X .1S )

NOta that the alectron density diatrlbutlon need enly be calculated wlthln
unit callo
Ro_var, the poaitj~"\ll.a of the atoma are unknown - the a1m of
periment 1s to find them.
There.fore p (!.) ha. te be calculated at a larqe
of closely .paced points in the nepe that atemic poaltionl can be lnferred
regiona ot high electron denaity.

a ainqle
tha axn~r

from

The application of equation X.1S rail ea two problema: the phaae problem of
Section 111.2 and the unavailability of an infinite numbar of apots.
In eaaence
the phaee problem arise. becauae, in general , F(!!.) ia a complex nuchar and 1 ( ~) ,
which l e measured experimentally, can provi~e only ita modulue.
Mathoda f or solvin9 t he phase problem were given in Sections 111.4 and 111.5.
Note that the aimple
'idir.ct mathad" provided as en example in Section IIl.4 i. not applicable te cry.tal _ bacauae ita Pourier tranaform is not a amoothly varying function but i a re.tricted to peinte in Q-ap&ce.
Cirect methoda for cryatals are more aubtle and are
de.c ribed in the book by woolfaon taee BIBLIOGRAPHY Sact ion 12 1 .
What are tha oon.equencea o!-the numbar of apeta bain; limited?
Accordinq to Section 111.6, if
only a limited extent of Q-apace, ie . a limitad number ot spots, can be recordad,
tha raault ia that the reselution of the technique ia limited.
However, the
theoretic al reaolution is pertactly adequate to determine atomic poaitiona with the
X-ray wavelengtha qenerally used in diffraction experimenta.
Prota1n cryatal. are
u.ually imperfece, in the sena. deacribed in the one-di menaional c a a. ol Section
VIII.7.
The intenaity of their diffraction spets then decreases with increaainq Q
anel. it may not be f.a8lb l e, or even po.aibls , to record the intensities ol those
vhich convey hiqh re aolution intormation. St.receh.mical infermatlon, ie. covalent
bond lenqthe anC!. anqles, van der waals' radii etc., then has te be combined with
tha calculated electr~~ denaity distribut ion in order to find the poaltiona of atoma.
Remamber that, if the resolution ia severely limited, apurious peaka may appear ln
p(~l aa demonstrated in Section 111.6.
Why il X-ray cryatalloqraphy auch a uaaful techniqua for determininq molecular
atructura?
The principal reaaon ia that the diffraction data ~ not correapend to
a molacular struoture which ha. been apherical1y or cylindricallY avaraqed - in
centraae te Che ayatellla dillCU.aad in Chaptera VI to IX.
Ol coura. che intenaity,
I(~), at a.ch reciprocal lattlca polnt haa te ba meaaurad aeparatalY I tha intanaltiea of the compoaita apote ln a rotation pattarn provide cylindrically avaraqad

X-Ray

130

rhree- Dimens i onal Cryetala

D i ff ~ act ioD

inlormat l cn - because the dapendence ef the acatt.red inten.lty o n ~ 1. lost.


X-Ray crystalloqraphy has tbre. furthe r advantages.
Accurate inten.lty ~ a.ur.
ments are po lbl. because th. inten.lty dlstributlon conalats ef discrete apots on
a background whlch, tar a perfect cryatal, la fea turele...
Alao , t er a perfect
cryatal , lntermolecular interIar.nca effects do not leed the lnten81ty to fa l 1 o ff
wlth l n creaslng Q - in contrast to the case el a l i qu id or aoorphOU8 sol i d o
Measurement cf hlqh r e.al utian ~&ta 18 then straiqhtforwAr.
Al thouqh re.l c rystal. a re no t perfect , they are often sufficlently near perfect tar thes. advantaqe s
to apply.
'['he thlrd advantaqe 1. that, in practica, i t 18 vlrtually al_YII fea8ibls to apply the deductiva methoda el atructure determination , de.cribed in Section 1Ir.4 a cry.tal st ructure can , therefore , be ~termined with a hiqh deqree of
certalnty .

If acc urate atcmi c poslt i en. are to be determined, it ls nec e s 9ary te correct
th. m.a.ured intensi ties of the diffraction .pots for three difterent effects.
Firet the intenslty of each apet has to be divided by the polarisation factor, p,
delined in equat10n 1 .5 , for tbe reaBon glven ln Se ctlon II. 3.
Next the Lorentz
correction , of Sectlon VII I.9, has be be appliedl further detalle of the Lorentz
tactor are qLven in Vol . I I of t he "Internatlonlll Tabl es tor X-Ray Crystalloqrapr,y".
Fina11y , if very aocurate r esulta are requlred, 4n absorptlon oorrectlon must be
applled.
This correction recoqniaes thAt X-ray be~s scattered vith difter ent Q
valuBs, lB. at d1fferent scatterinq anqles , pass throuqh diffe rinq thickneases of
the speeimen .
Then , according t o equatlon V. l4, absorption can r e duc e the lntensity of each by a eliqhtly different fac tor.
Note that , further tO Sectl on II.J,
ve are ooly concerned with corre cticn faetora which are a function of O - since ve
are not oonc erned with measu r~ents on &n absolute scale (see al so 5ection V[. 2).
Methods which can be usad to place intensity mea.urementa on an abaolute scale a r e
deacr lbed i n IDOSt books en X - ra~' crystalloqraphy.
Equatio ~ X.l5 can be eesily modified t o al l ow for the kind of cryatal lmperf .et1en ~escr1be~ in Sect10n VIII.7; crystal lographers usually attribute t hi. iRperfection to thermal vi brations but Sect lon VI[I. i augqests that this ia otten an
overaimplification.
Suppoae that the atoma l n a eryatal vibratB lndependent ly,
t hen t he Fourier t ranaloro of each atoo, le . lts a toml c acatterlnq factor, haa t o
be multiplled by a f une tion wlth the fo rm of O(Q} in equatien VII[ .16 .
~he reault
ls that equation x.a haa to be r aplacad by

l'Ch,)

fj (O ) exp (- 020j/2) exp 21fi

h.'!:I

131

0'1

vibration parametare (correapon~inq to e1ther


or che ani.o tropic t ~perature
factora ) of eaeh atom. and oftan en overall
e f.ctor (see Sec t ion V[.2). Tbie
refin~nt i. beat carrlad out ln Q-apaee - for the reason 9iven in Section I[ [.6 .
When the number of .pot. who.e inten.ity ha. baen me.aured 9reacly exceed. tha numbar 9l variable parameter., very preci tructural information c an be obtained.
If th. data do not extend te aulf1ciently hiqh Q valuea for individual atcmic
poaition. te be re.olved, thi. approach ia not v.l i d.
Atalllc poe i cion. eh.n hava
to be v.rie~ .Ubject to the conditioo that they are rel.tad by r ea.onable bon~
lan9th. and anql vhila non-bondad atome do not approach cloae r than tha aun of
their van d.r Wa.l. ' r.dii , furthermcr e lt would be unr aon.bl. to att.mpt to
obtain individu.l the~l vibratlon peram.t.rs for .ech atom , in .ueh c , eo
that overall valua. hava tO be .a.iqned to entira mol.cul

.c.

X.5. S)'!!:!.try
Th. unit c.ll po e ~.try if the positione of all it. atom. can be
g.neret.d by the operation of symmetry .lamant. on a .ub t oE tba .e position .
Thi ub t, from vhich all t he other po.itions can be qen.ratad, i. c.llad the
"aeyatlMltr1c unit" of th. unit cell.
Symmetry el.ment. reflect, rotete or tran.l.t pe1nt to .n .quivalent peint.
So~e eymmetry elamenta actually parform a
combination of two oE the.a oparetion. eg. e riqht-handed u- l old .crev exi. tren.late peint throuqh a d i.tanc. p / u, wh.re p ie a repeat di.tanc. i n the axial
dir.ction, and rotat l t by 2w/u radian. .
Thu e pei nte which ere r.latad by a
u-fold .crev axia lie on a u- fold helix of p itch p.
Tha preparti of .ymmetry elemant. w111 be i llu.trated by u.in; a 2-fold
rotaclon axi. a. an .xaepla .
If th. j eh atom in a un1t cel l ha . fraccional unit
c.llooordinat (X" Yj, Zj ) ' a 2-tol d rctetion axis which i. coinci dent with the
c -exi. q.narate. another, equival.nt atom at (- Xj , -YI.' Zj) '
lf ehe po.1tlon of
th. original atora i . d.noted by !j. of equaHon 1.2 , he operat1on of the rotaHon
axis can ba repr ntad. by the matrix

o
1
O

(X.16l

In r ea1ity the ato~9 do not vibrate i ndependent ly but neither ~o they vibrate in
Uni80n the book by Janaa (8ee BIBLIOGRAPHY Section 2) qives a more ~Btailed
account of themA l vibrat 10 ns in crystals.
Furthermore there le no r eason to suppoae that . at e qLven t empe rat ure , t he amp litude of an atooic vibration will be
th. same i n all directicn. in a crystal .
Crystalloqraphers acmetime. make an
empirlcal a ttempt te de al vith thi. letter problen by replacing Q2a j / 2 in equation
X.16 with

The ree.on ia that


Oo1y 230 cambin.tlona of symmatry alaments are a llowed.
th. oombinetion of two or mora aymmetr y e l .mant. can qenerate further . ymmetry
Suppose that Il unic
.lement. and only eertaln combinacion a are then compatible.
Can hu
a._S _ y _ goo

where b ll , b22
are cellad "anisotropic t emperatura factor ." .
The f orm of
t he dependenoe on h , k and t arisea fro~ ueinq equation X. 6 to axpand O.
Refinanent of the atoDic po.ition. , i nfarred from the calculated e l ectron den.ity di.tr i b~tion, forms tha fin.l ataqe of a .tructure det armJnation .
Tha
meter. to be varla~ in ehi. r eflnement may lnclude tha positlen ~j and thermal

par.-

with 2- fold rotat ion exe. along the c- and b-axe . J tha .ffect ol ch e i. to mul t iply th. v.ctor !j' whlch d. fine e th. po.itlon of eh. j th atom, f ir. t by

X-,Ray Diffraction

132

[and th.n by eh. analogou8

1
O

ma~r1x

S~4etry can be uaad te aimplify expreaaiona for P(h) in equatLons X.e and
X.16 aa well aa fer p(x) in equatlon x.15.
In the ceae-of P (h) the aummatlon 01

tor a rotation axis colncident with th. b-axia -

which la

o
1
O

Therefore the nst operat1cn ia represented by multiplying


tvo matricel.
The reBult i .

133

in Vol.I of the "lnternational T!lblea for X-Ray Cryatalloqraphy": theae tablea


allow the apace qroup aymme try of th. unit cell to be determined.

I h ree-Dimensional Crystala

~j

by the product of the

- 1

which, by analogy vith the matrices fro~ which it ia qenereted , representa a


2-fold axis along ehe a-axis directlen; the evo 2- fol d exe. generate a third.
Similar &r9UQenta show that any one el the three can ba generated from th. other
tvo.
Thi. kind oi behaviour 18 not confined t o 2-fo1d rotation exe. but appliea
to any combination ef 8}'l!11'letry elements actlnq on a body.
Any set whos. elements
ean be qenera't.ed from each other in th18 wey h called a group.
Given the kinda

of aymmetry alements which can ba appItad t o a repetitive etructure like a eryatal,


1t turns out tMt therca are 230 possible greups o f elements - called "space qroups-.
The aa 230 spece groupa include the case vith no symmetry elements.
The symcetry eKetlpl1f1ed by certaln space groupa can only be observed 1f the
unit cel l of the cryatal has a particular shape.
In the example ot the previ ous
paragraph it vas presumed that
a - S_y_900

Actually no other comblnation of values for a , S and y is compatible w1th the only
aymmatry alemants of the unlt call be1ng three, non-parallel 2-fold rotation axes .
Then the unit cell must haye autually perpendicular edgea Le . its shape ia orthorhombic ( a~c ) , tetragonal ( a-~c ) or cubic (a-b-c ) .
11 the three rotation aKes
were neithar parallel nor perpendlcular , the1r rotatLons would be coupled so that
they woul d be Lncapable of BctLn; accordlnq to the i r definitions ie. they could
not existo
If tha ato:ns in the unit ca11 are reh,ted by certain canbinations of symmetry
elements some apots, wh1ch mlqht be predicted te appear in the diffraction pattern ,
viII actually be absent .
Coaxial, parallal helicea , in Saction IX.4, proyida sn
example.
There the preaence ot a u-told rotation axis alon9 the helix axLa (which
w. now recogoise as a acrew exia) lea to the abaence 01 layer lLnes unleaa t wa. an
Lnteqral ~ltiple o f u .
In qeneral , aymcetry may lead apota to be aystematically
Lbaent unl ea. the three lnte;ral coaponent. 01 h (1e. h and k a a well aa t ) obey
aimilar rulaa .
The pettern of abaences for each 01 the 230 apace qroupa La liatad

aquationa X.8 and X.16-nead only extend OYer the atoma in a aiqle aaymmetrlc unit ;
the contr ibutions 01 the other atoma can be generated by aymmetry.
Tha uaua l
practice i a to m04ily the form of p (h) to allow lor theae oontributions .
Sim ilarly it is cnly necaaaary to calculate p(X) ovar an aayametric unit and the elec tron dena i ty in ehe ra.t of the unlt cell can be qenerated by symmetry .
Often
many 01 the valun of f' (h l wh1ch contrihute to the a~tLon of equation x.15 wil l
be zaro.
lt la known, for a qiyen apace group aymmatry, whlch valuea of the componenta 01 h wll1 lead to a zero value for F (h ) ; conaaqu.ntly the .xpreaaion tor
p (xl can be - modified so that the valuea 01 F (h) which are ayatamatlcally uro do
not have to be Lncludad.
Special forma 01 equati ona X.8 and X.15, ler each ot
tha 230 apaea qroupa, are l iated in Vol.I 01 "International Tables".
Note that
aquatLona x.8 and X.15 are actually the lorma appropriete for the apace qroup with
no aymmetry elementa.

x.6.

SUItlDary

A crystal atructure is reqularly repetitiva in three d~enslona; the repeating unit ia called its "unit c ell".
The Fourier tranaform of a cryatal 111 conlined to peLnts in Q- apace - the "reclprocal lattice peints" .
Each reciprocal
lattice pelnt can b. specifiad by th. yaluea 01 three inteqers - denotad by h, k
and l.

Th. intenaity dlatribution 01 the dilfraction pattern from a Single atation8ry cryatal corresponda to an insufficient ext.nt of Q-spa ce to provide ~uch ulefuI information.
To record a uselul dlffraction pattern the cryatal haa te be
rotated or oacillated - ln some techniquea the film (or other detector) moyea alaco
The dillraction patt.rn la confinad to diacrete apota .
Each apet correaponda to
one, or mora , reciprocal lattice points and can be aasigned valuea ot h , k and !
by inapection - precise details depe~ on the experimental technique uaed to
record eh. pattern.
When the apots have been "indexad" Ln this way, and tbeir
po.itiona converted into Q- space , the unit cell dimenaiona can be calculated.
11 the phaae problem can be 8Olved, the elactron densLty distribution wlthin
a un1t cell can be calculate~ lrom the intenaltiea 01 th. spets which conatitute
tha diffraction pattern.
Poaitions of atoma wLthin the unit cell, and hence molecular atructures, can be inferred lrom the calculated electron density distribut10n - the coordinataa of the inferred atomic poaitions haya to be ref i nad to
obtain accurate molecular modela.

Crystalline Powders and Crystalline Fibres

135

CHAPTER XI

Crystalline Powders and Crystalline F1bres

XI.l. Introductlon

Flg. XI.l.

The a1m of thia chapter le te d.scribe the X-ray diffraction efEecte observed
tvo .yetama whlch althouqh cryatalline do not con.lst eimply of a single eryatal - cryatalllne powdara and cryatalllna fibra..
A partial . in a finely qround
powder ia typlcally l.s. than 1 ~m acro , yat in many powdars eaeh particle 1. a
fro~

eryatal.

Thare vill ba 110 many oE th tlny eryltal. in a macro8=plc apacilT.en

that e.eh ha. an effectively random orientation in .pace.


Crystalllne fibra. contaln orientad polymer molecules but , 1n centrase te the nematic and type A .mact l e
orqanlaatlona ef Chaptar IX, th.ir mol.culea have a regular 81~e - to - alde arrangemento
NO new theory ia introduced in this chapter - a11 that i9 neededo i5 te show
Before
hew the theery ef Chapter. VIII te X can be applied te these 5ystemB.
starting SectLen XI.3 it miqht be u.eful te lcok baek at Fig. I~.2.
This figure
definea the cylindrical polar ccordinatee l(,~ ,t) which are used te define the
po.ltien ef a peint in Q-epace - theee coordinates are particularly helpful when
describing the d1ffraction properties ef crystal1ine f ibres.
As we shall see, the
diffractlen pattern. fro~ crystalline powders and cryatalline fibres are e f considerable practicai value.
~I.2.

Pewder method

Perhaps the majer appl icatien ef the powder methed ie the identification of
unknown substances.
A sample of the crystal line aubetance which 18 to be i dentified ia greund into a fine powder 50 that it consiste ol a vast number of mierceryatal " these micro-eryatals wili have random orientations in spaee.
The diffraction properties ol this eryatallins powder can be understood usinq
the theory develop ed for a D088ic eryatal in Section VIII.B.
In three dimenaions
the cryatallitee, of which the melaie eryatal ie compased, will be tiny threedimensional crystal. .
A perfect three-dimensional eryatal eonsiats o! these crystallite tac~ed togethar neatlr, like a pila ef brieks.
Mosaic ' .pread conslsts
o! the erystallites bein; ran~mly tilted fro~ perfaet alignment about the three
axe. of a Cartasian cocrdinata aystem.
~ pa~ered apecimen then representa an
extreme caaa ol DOsaic apread where th. tilt about eaeh axia can ranga f r om zara to
2. ra~i4na, wlth auch a larga number ol tiny eryataI., avery poaslbla tilt wl11 be
l34

X-Ray diffraet10n pattern of a m1ero-crystalline depos1t in abone marrow biopsy; the


posltions of the rlngs and their relative inten sities showed that the miero-erysta1s eonsisted oE calcium oxalate .

equally represented.
A diffract ion pattern from a erystalline powder eonsists of sharp , concentr1c
rings - as i llustrated by the examp1e of Fig. XLl.
According to Seetion VIII.8;
the intensity at a reciprocal lattice paint is distributed over part of the surface of a sphere by mosaie spread.
The radius of the sphere is given by the value
of Q corresponding to the reeiprocal lattice paint a nd the area over whieh the intens1ty i5 sprea d depends on the deg ree of t l 1ting of the erystallites in the
mosaie erystal.
In this extreme case, where the tilt can be as great as 2~ radians , a nd a ll possible tilts are equa11y represented, the intensity of a reciprocal
lattiee paint will be evenIy distributed over an entire spherical surface in Q_
space.
The intens1ty dlstribution in Q-space is, therefore, confined to a series
of concentrie spherieal shells.
Each shell intersects the Ewald sphere around a
eircle - as deseribed in Sectlon IV.2.
Consequently the diffraetlon pattern consiats of concentric rings.
The radius of each r1ng depends on the value of Q for
the corresponding reciprocal lattice peint and henee, according to equation X.6, on
the unit ce11 dimensions.
Relative intensities of the r1ngs depend on the pasitions of the atoros within a unit ce1l - accordinq to equations ~.8 and x.9.
Thus the radii and relative intensities of the rings can be used as a "finger
print" to identify both the ehemieal const1tutien and the crystal form of an unknown substanee.
Several compilatlons of radl1, cenverted into Q-spa ee, and re1ative intensities are avai1able from pavaer patterns of standards which consist of
known substances in known erystal forms.
A substance ls 1dentified when the
medsurements froro its powder pattern coincide with those from a standard.

>topos _ J

Cr ystal l i ne Povders and Crystalline Fibres

X-Ray Diffraction

136

137

about their e - axe..


Since the crystallites are very sma l l, there viII be very
many in a maerOBeopi e specimen; all r otations, about the e -axi s, betveen zer o and
2y rad ians viI I then be equally represented.
A eryatalline fibre l a, therefor e , a very speeial kind ef mosale c rystal.
Aceording to Seetion VIlI . 8, its diffractlon pattern is then fenled by adding the
intensity contrlbution of eaeh erystall ite.
Each erystallite ro tation about the
e-axis i5 assoclated vith &n egual r otation of its Fourler tr&nsform about a parallel axi s in Q-space - from Section 11 .4.
As in Seetion X.3 the ~ -axis of Q-space
is defineo. to be parallel to the e-axes of the crystallites .
The rotated Four ier
transform , multiplled by its ~plex conjuqate , givea the correspondinq intens lty
d istri bution fer the r otated crystal l ite .
When the contr ibutions from a11 the
erystallites are added, the resultant intensity distr ibution ls eylindrieally averaged ie. the dependenee of the scattered intensity on ~ ls lost.

Fiq. XI.2.

Molecular packlnq in a cryatalline fibre.

At thi s peint it may help to compare t he diff r aetion propert ies of crystal line
In a crystalline powder the erystalf ibres vith these of erystalline powders.
lites have all poasible orientations in spaee .
As a resu lt the intensity at a
reciprocal 1attiee peint is distributed over the surface of a sphere oE radius Q
ie . the intenslty distribution is spherically a veraged .
In a erystalline fibre
the erystal lites have all possible r o tations about their e-axes.
When the con tributions to the seattered intensity from all the crysta1 1ites are added , the net
lntensity 1. eyl indrically averaged ie . if I(~ , ~ , C) i5 Che intensity distribution
scattered by a single crystallite, expressed as a functlon of eylindrieal pola r
coordinates , the intensity distr i butlon from the entire fibre is given by

XI. 3 . CryBtaLline fibres


[ (~ , ; l

Polymer IDOleculea have hellcal symmetry when they are oriented.


Con s ider a
slngle pol ymer molecule ln an or iented assembly.
Jf the mo l ecule 18 capabl e of
being orientad as descr1.bed in Seetian I X.S Lt must have a rod- l1ke shape.
In
such a IDOlecule eAch auccesaLve resldue .must have the same confornation.
A s lngle
residue which had a very different conforuati on would produce a kLnk - such a klnk
would prevent the mol eculea f r om becocing oriented.
Similarly a 9uccession of
resldues with wl1dly dLfferent conf ormatlons would lead t o a polymeI chain whlch
vas in no senae rod-l i ke and would be Lncapable al orientation.
If the residues
in a rod-like polymer molecule have the same conformation they vill be related by
a screw axis as defined ln Sectlon ~ . 5 le. the polymer molecule has hallcal symmetry .
Such rnol ecules need not resemhle eork- screws - a l tbough some do eg. the
a -he l lx of poI y-L-al anlne ln Sectlon IX.4.
AII that is i mplled by the descrlption
"heliea l" 18 that the c yllndrlcal pol ar coordlnates of corresponding atoms, in sue cessive residues, are r eIa ted as described in Section IX. 4 - a 2-fold heli ca l molecule, le . one i n whleh residues are related by a 2- fo ld scr ev axis , 18 dls t inctly
ribbon -like in ahape .

Many polymers fom crystalline fibres, whieh consist of assemblies of erystallites, wben their molecules are oriented.
One of the uni t cell a xes , conventi onally designated the e-axis, 15 deEined by t he periodicity of the mol ecular helix .
A s i ngle pol~~r ehain is so lonq that it may pass t hrouqh several erystal l ites.
Sinee the col ecules are or ie nted, and their hel ix axes define the e-axis, the
c - axes of the e r ystallites must then be , at least rouqhly, parallel.
Bowever
there ia no reaaon for any such cootinuity betveen erystal li tea in o t her directions .
,~i~re XI.2 repr esent a the QDlecular packinq i n a erystall i ne f i bre projected on to
a plane per pendicular to t lle e-axis direction.
'l'he projected molecules are r epresente<!. as diaca and the bounc!arles o f crystallites are marked.
Here t he ooduli of
.!. and ~ are aqual, the twc vect or s are perpendicular and there ia enly one molecule
in the unit ce11 - but none ol these preper t i es is a n ece.sary feature of crystal lina fibres.
The 1nportant point i a th5t the crystallltea are r&ndomly ro tated

.. (1/2'/1)

1"
O

I (C ~ , r;) d oJ

(see Seetlon IX.S ) .


Consequently a recipr ocal lattice paint a t ( , y , ~ ) has its
i ntensit y distrlbuted around a eircl e of radius ( who5e centre li es on the t - axis ,
at a distance ~ from O', the origin of Q-space: the surface enclosed by this eircle
ia, of course , perpendicular te the C-aKis.
Diffraction qeometry from a crystalline fi bre 15 just the 5ame as for a rotating sinqle crystal .
The reason i9 that all reci procal lattiee points with the
SAme values oE t and t are distributed around the same elrcl e in Q-spaee .
They
viI I then pass "through the same two points on the surfaee of the Ewald sphere ,
exactly as in Seetion X.3 , when the d i ffract ion pattern is formed.
Altern atlvely
t his result eoul d have been eKpl ai ned by appeallng to the inabi lity of K-r ay d i ffra etlon te diatinquish betveen systems whlch are averaged in spaee and time - as
in Seetion VILI.
The single crystal rotation method give s a diffraction pattern
which is e y lindrically averaqed in time; the diffraction pattern from a crystalline
flbre is cylindrically averaqed , about t he same axis, in spaee.
Pigure XI.3 provides an e xample of a diff r action pattern from a crystalline
fibr e) the spets can be indexed as described in Seetion x . l.
Notiee two featu r es
of these apots .
One: they are rather broad - ind.ieating, frau F iQ. VIII.J, tllat
there is a limited number o f un1t cells in a crystallite.
TWo: they are distinetly are-shaped - indicat ing . frOlll Section VIlLa , that the e - axes of t h e erystal lites are only r oughly parallel le. the pol ymer moleculea are imperfeetly ori ented .
Ares reduce the resolution of diffraction patterns from erystalline libr es.
Aecordinq te Section VIII.S , the are length inereases with 2 - t hen the intensity
01 a apot ia dissipated over an increasingly large area of p hotograpllic fl1m ie.
the intenaity falling on a unit area of film l s decreased.
Consequently it viII
beco~ lmpossible to detect the intensity of spots whose pasition s correspond to
high Q values - according te seetion V.4 thls limits the r e801ut ion of the dlffrac-

Crystall ine Powders and Crystalline Fib r es

X-Ray Diffracdon

De

139

tion pattern.

Flq. Xl. 3.

X-Ray diffractlon pattern of stretched r.lbber

the e-axis vas tilted s lightly from the perpendicular to the lncident K-ray beam (takan by
:l.E. DAvles).

Flq. XI. 4.

A "statist ical." crystalllte structure .

Interference effects, betveen X-rays seattered by different molecules are


much ea51er to calculate than vas the case fer necatle organ isation of oriented
polymers - see Sectlon IX.5.
However, a conpllcation, which frequently arises ,
18 tha t crystallites hava " statistleal" structures .
Figure XI.4 prevides a achematle example - ln projection on to a plane perpendicular to the e-axis.
Bere
eaeh molecular site 15 ranOomly occupied by a molecule with one of two possible
erientations.
Anether particularly common kind ef statistical crysta11ite structure consista of molecules which point randomly up or down the e-axis direction.
Statisti eal structures also invc lve moleeulea v ith dlfferent translations a10ng
the e -axis.
AnO. each site can be randomly occupied by IDOre than two differe nt
possibilities.
Each molecule scatters X-raya and the intensity at each r eciprocal
lattlce point refers to the structure ef an average unit cell .
Furthermore diffuse
lntenslty appaars between the reciprocal l attice points - its appearance vill now be
explained.
Figure :n.5 could be considerad as a "perfect" crystalli te structure.
Then the protruberances on some of the projected molecules in Fig. Xl.4 are slightly
displaced from the i dea l positions of Fig. X[.5 - according te Sectlon VIII .', diffu se lntenslty then appears between r eciproca l lattlce palnt s.
Nhen indexing diffractlon patterns frem crystalline fibres it ls impartant not te attribute maxima in
the diffuse i ntensity to intensity at reciprocal lattice peints.
Xl.4. lnterpreta tion of diffraction patterns from crxstalline fibres
The intensities of the spets in the diffraction pattern of a crystalline f ibre
can be used te determine the three-dicension.lll stnlcture of its polymer mol acules.
At first sight there may appear to be three difficulties.
ene i5 low r eso lution but this can easily be overcome, as de9cribed ln Section X.4, by supplementing the
diffractlon data with stereochemical inforca tion in the form of covalent bond
lengths, bond angles etc.
Another is that, in practice , ths deductive method5 oE
determining structure, de9cr ibed in Seetion 111.4, are r a rely applicable so that the
trial-and-error approach of Section 111.5 has to be used instead; fortunately, aa we
shall see in the next paragraph, this approaeh i9 partlcularly effec ti~e for helical
molecules.
The t hird apparent difficulty is that the intensi ties of the ditfraction spets previde lnformation about a cylindrically averaged st ruc ture ie. the dependenee of the intensity scattered by a crystall1te on It is lost .
Bowev.er, lf the
trial-and- error approach la te be used, cylindr ical averaqlng presents no real
problems.
Development of models for the three-dimenaional structures of polymer molecules
in crystalline fibres is reasonahly straightforward - because the molecules are
helieal .
Wben a helix ls packed ln a cryatallite its Fourier t r ansform 15 amplifled at the rec iprocal lattlce pelnt5 but beoomes zero elaewhere.
Thus its transforro l s sacpled at those peints in Q-space whlch correspond t o the reciprocal lattiee points; the relative i ntens l tles at these peints are unchanged by molecular
packing - exeept fe r interference between X-rays scattered by different helices in
the same unlt eell.
Therefore the intensity distribution along the e - axis can be
used to determine the axial rise per residue of the helix, as ln Seetion IX.4, and
t he layer line spac ing provides a value for the helical repeat, c .
Remember th4t
the lntenslty distributlon aloog the ~-axis has to be inspec ted o n diffraction patterns frcm suitably t ilted fibres.
But, becau se the orientation v il 1 usually be
imperfect, a good idea of this distribution can be gained without tilting - as described in Saetion VllI.9.
Also the relat ive intensitles of the spets provide a
valuable clue a. te whether integr al or non-integral helical modals should be considered; Sectlon IX . ) provides furthe r detaile.

Fiq. XI.5.

A perfect cryseallite structure.

140

X-Ray Oiffr3ction

Models have to be produced for the helleal mol ecule and for the packing al
helices in a c:ystallite .
Befere & ~lecular model can be devel oped , the structural formula ef the polymer, like that cf poly- t-alanine in FLq. IX.9, must be
knovn.
'nle confoI"llatlon ef residue ls then adjUBted, incorporatLng the stereochenical information which 18 to supplement the dLtf ractLon data, 80 that succes-

81ve [esidues iol0 together to t ore & helix el the required d ~en. ions.
Thls procedure 15 usually carr led out by computer .
Next a model 18 deve loped for the
packing cf the halices Ln a unit cell; the unit cell dimensiona can be determined
frcm the pos itLoos el the diffractlon spots .s seon as the pattern 15 indexed - a8
ln section X.J.
R~r that statlstlcal crystal lite modela, desc r ibed in Sect ion x. 1 , may be approprLate.
Next the intensity di strlbutlon , calcula ted from
the coordir~tes of the model, LB compared wlth that Observed - Btructure determlnat1cn, lncluding reflnement, proceeds as ln Sect i on 111 .5.
Novadays refinement
ia usually carried out in a computer , where the variable paramete ra ef the modal
are automat ically adjusted to Obtain the best fit bet...een ca1culated and observad
i ntensity dlatribu t lens.
Ouring the trial-and-error atructure determination , the hand of the helical
oolecules is usual ly deternined.
Fev polymers have achLral residues.
A rLght handed oclecular he llx of chirel residues ls not the mirror image of a lefthanded helix conaietlng of the sane residues.
Denoting the chirality o f a residue by L, and that ef its mirrer image by D, the mirrer image ef a 1eft-banded
hellx of L residues ls a rlq ht - handed he11x of o rasidues .
But if our palymer i s
knawn t o contain L residues, the r e are no valLa modela containinq O r esidue s. Any
competing left- and r i ght-handed helical modela must both contain L resLdues and
viII not be relatad as object to mirror tmage .
The arguments ol Section 111 . 8
are not applLcable to these modela and the better of the tlolO can be deteruined as
in Section 111.5.
An essential feature of the t rial-end-error method is the calculation ol the
expected intensity dlstributLon from the coordina tes of a codel fo r the structure haw ie this ealculetion performed?
When a molecular model has been built and a
aehece for packing the molecules in a unit cell developed , a set of trial coordi nates will be available for all the atoms in a unit cell.
11 these are expressed
as fractiona1 unit cell coordinates , equation X.16 can be used to calculate F{hl .
Thi s calculatlon i a performed fo r each reciprocal lattice paint which contributes
te the diffraction pattern.
Equation X. 9 is than used to calculate I(~) frOlll F(~.
Values o f I(h) for overlapp lng reciprocal lattice points are dded; overlapping
paints have the same values 01 t and t .
Tne r esult 15 a cylindrically averaged
intensity dlstri bution wh i ch can be compared with that observed.
lf a statistical
crystallite model 15 being de veloped, the suuaation of equation K.16 viII lnclude
atocie coordinates for every molecular pasition whic h can appear in tne structurel
the atcmi c scattering factor, f /, then has te be multiplied by the probability that
an atom v ill appear at tbis pos tion 1n a single unit cell - thi s probability ia
90IDetimes termad the "occupancy" o f the slte .

Equation X. 16 i a still valid, even tboug h the molecules are helieal .


There
i8 no real need to develop expr e8sions whieh take lnto aecount the h elical symmetry
o f the molecules i n a unit cell.
Such expre ss i ons wil l reduc e the number of atoms
lncluded in t h e summation - s lnee a ll the atomic positions in a unlt ce l l can usually be generated traro the coordinates of the aeoma ln a s i ngle residue of the hel icel molec;Ule.
Hovever , using a modern co!llpUter, cOl!lpUta.tion and sUJIIM.tion of ehe
terms ln equation X.l6 15 extreme ly rapid - so very little tiDe wi ll be saved if
en alternative expression is u sad .

Crys ta ll ine Povders and Crystalline Fibres

141

XI.5. Summarv

In the di f lractien pattern from a crystal l ine powde r the i ntensity associated
with a reciprocal lattice point 18 distributed over a cir cle.
The pattern then
consiate 0 1 concentric ringa - the radii oE these r ings converted into Q-space, and
their relativa intensities , are characterlstic of a particular c hemica1 substance
in a particular crystal forro.
Comparlson cf the radil and intensities , ~a9ured
lrem the diffraction pattern 01 an un~nown povde r, wLth the results from powders
of known compoaition, previde s a useful method 01 chemical analysls.
Many oriented polymer samples are crystalline fibres .
These fibres consist
of crystal lites vhose c-axes are defined by the axes ef the helLcal polymer chains.
Crystallites have randam rotation~ about their c-axes ; diffraction qeometry lor a
A difc rys talline libre 15 then ide ntical to that lor a r otating single crystal .
fraction pattern from a crystalline fibre can be used to determine the conformatlon
of its palymer chains .

Relationship to Microscopy

143

CHAPTER XII
EYE-PlfCf LfNS

Relationship to Microscopy

"
",
,"
"

XII.l . ln troduction
One purpose o f cnis chapter 15 te show hoy the Abbe theory o the microscope
provides a useful aid te understandinq the forcation and analysls of X-ray dlffractian patterns .
The Mlbe t.heory emphasi ses the rela t lonship bet ween an object , its
diffraction patter n and an ~qe of the object - a relationship whicb la fundamen tal te X-rey d iEfract l o n analysis.

~rmation

of a dlffractlon pattern la an inter-

mediate stage In the formatlon of en image by a microscope.


Since microscopes can
!mage irregular specimens , the illusion , often fosterad by X-rey diffractlon teKts,
that regul &rity in the object 15 necessar y for the farmatian of a dlffraction pattern, 1$ innediately dispelled.
Thls chapter . therefore, s\lJIIIM.r ises much tha t has
already appeared in e arI ier chapters by presenting tne material in a rather d i fferent way; tne theory oE the microscope provides a use fuI model f or X- ray diffraction
analysis.
Another purpose oE this chapter i 5 to indicate how the methods used in the
analysis of X- ray diffr action patterns can be applied to e lectron microscopy and
the att e nd&nt technique of electron dlff raction .
Detaila ef image analysls and
the reoonstruction of three-dimensional images Eroa electron micrographs are beyand
the scepe oE this bcoK - as a re detaila oE the variou5 diffra ction techniques
assoclated wi th alectron microscopy .
But much oE the underl ying theory of these
techniques is II!Issenth.lly the sane as that used in the analysis oE X-ray dlffr actlon pattll!lrns.
The Abbe theory e f tne microscepe emphasises the relationshlp of
electron microscopy to electron dlffraction and X-ray dlffraction.
Once thls
re l ationship 15 recognised, much of the contents of t hls book could be considerad
as an introduction to the theory which 15 applie d to the anal ysis of electron
micrographs .
XII.2 . Pourier eransforuatlon and microscopy
F igure XII.l shows hov a cicroscope forms a magnifled imaga . A'B'. of an
object, AB .
A peint SQurce oE 11ght ls positioned at the fecus 01 the condenser
l ens, i n order t o pr ovi de a para l lel beam o f l ight.
Sinca monochromatic X-rays
are u sual ly enployed in dilfraction exper iments , the sour ce w1l1 be assumed to be
~nochromatic here - te make comparison easier.
The object scatters the lnc1dent
llght beaa .
Al l scattered beams which are parallel are facused at the sama polnt
by tbe objectlve lens; the pattern of scattered l lght. which ia forced at the back
142

",'"
'"
",
,,'
,,',,'

":",

"
X

S'

Fig. XII . l.

~I

, ,~
"" ,
,"
,"

,"

:~~ OIF=r:RACTICt4 MmRN


"
'" ", 08.JE.C.TIVE LEN~

,","
"

'.:

Or.JECT

~
) CO"DE"~ER LE~
\

1,

,5OUIICE
( VIRTUAl.)

I~GE

I mage formation in the microscope.

focal plane ~f the Objective , is called the Fraunhofer diffr actlon pattern of the
object.
Throughout t hi s chapter "Fr aunhof er diffraction patt ern" wl1 l be abbreviated to "dlffraction pattern" .
A mi croscope forma an image in two stages: first a diffraction pattern is
formed and then en image.
Consider the formation of the diffraction pattern first .
The amplitude; and phases of the scattered vaves depand on the denslty o f scattering
matter ln the Object.
When the principIes of X-ray 8cattering vere discussed . in
Chaptere I and II, it eJOerged that the amplitudes and phaue could be c alculated
from the e l ectron density diatrlbution, p(~l ; when 11ght acattering la being considered lt ls usual te think in terms of molecular polarisabllity - t he relationship between molecular polarisability and refractive l ndex ie described in Saet ion
I I .6.
In Fig. XII.I the objaet1ve lens takes all wavee whlch are scatter ed in t he
aame di r ection and through the same ang l e, ie. a11 waves with the 84JlIe 2, and
focusea them at a point .
Each point ln the beck focal plane of the objectlve lens
then corresponda to a peint ln Q-space le . the dlffractlon patt ern ls focused ln
thia planeo
Slnce the diffractlon pattern l s not r ecor ded ln the micr o.cope , the phase
relatlonahip betveen the scattered waves 15 mal ntained.
There vill be a phase

Re lationship [O Kicroacopy

X- Ray Oiffraction

144

.a.ociated wlth the vaves focused !lt eaeh peint on the back focal plane of the
objective .
If a photoqraphlc film were used to record the diffractlon pattern,
a11 phase information would be Lost - as described in Seeton 1[[ . 2.

But, in the

microscope, the waves continue throuqh this plane and the correct phase relation.hipa betwaen vaves focused at different points, le. at different points in Q- space,

are

4n/c ~ ~x

145

(XII.2)

P'rem equations XII.l and XII.2 the condition that the holes are resolved ia

e > ,

malnt4i.ned.

The mlcroscope then synthesises an icaqe from the scattered l1qht.

In Plq.

XII. L the scattered vaves pass throuqh the bI!IIck foca l plana of the objective lens
and eventually a11 the ....aves ema.natlnq from A mest at one point and all those frOl!!
B Deet at another.
Thus the objective lens acts as & ~qnifyinq gl&88 to form
first a dlffrll.ctlon pattern and then a.n iDaqe .
In the Dlcroscope the eye-piece

lena mag'ni!les tilis lntercediate imaqe to fom the flnal image A'B'.

lens is

needed if a11 the waves scatter ed by A a re to i1Ieet at a single point le. no imaqe
can be lormed wlthout a lens.

An image is forced from a dlflraction pattern by inverse Fourier transformation.


Accordlng to Sectlon 11.3 the di!fractlon pattern 15 represented by the
Fourier transformo F(2), ol p(~) .
From Section 11.4, an ~ge of the object can
then be obtained by inverse tran5forcation of F(~).
Note that here ~diffractlon
pattern" relers to the waves passinq tlu::ough the back focal plane of the object lve
info%"lDation is conveyad both by their amplitudell and phases.
Thus the lIIicroscope transforms P' (2.) rather th&n 1 f2.1
Consequently the transformation ylelds an il1&ge,
as in Section 11.4 , rather than the sutocorre1ation lunction, as in Sectlon 111.3.
Accordlng to Sectlonll V.4 and 111.6, the re solution ol the mlcroscope depends
en the extent of Q-space Yhich ls used to syntheslse an image.
If the objectlve
aperture ol the microscope 15 decreased. yaves scattered at high Q values cannot
appear in the diffractlon pattarn and so the resolutlon of the nicroscope is

diminished, if the apertura is so rsduced that the extent of Q-space is severe1y


l~ited, spurious detall oay appear in the image - as descrlbed in Section 111.6.
Saction 111 . 6 alao ahows that the maximum value of Q which is accessible wl th a
given wavelength, A, ls
(XII .1)
Thus if the wavelength of the 1i ght i5 reduced, a greater extent of Q-space can be
ayntheslsed into an image an~ the re501ution of the microscope ls improved.
Reaolution viII now be treated more quantltative l y.
Suppose we wlsh to lmage
a rew of holes , which are equally spaced a dlatance c apart, in an opaque screen.
What vavelenqth ls required fer eaeh hole to be separated in the image le. for the
holes te be resolved?
lf the di!fraction pattern were recorded, at the back tocal
plane ot the objectlve , lt vould consist of linea apaced 2w/c apart ln Q-space a ccording to Sectlen VIII.3.
Each line i5 aasiqned an integer index, l.
The
1108 yhlch passes throu~h t he centre ol the diffraction pattern, perpendicular to
the plane ol Fiq. XII.l, has azaro value of l.
I f the adjacent lines can also be
s een the difEractlen pattern appears as a set ef lines: the two nearest adjacent
lines correapand to l values of plus and minus unlty.
The extent of Q-space whlch
is required to detect them ls
2 (2'11'/c) - 4",/c

This .ame extent of Q-apace DUst be synthesised i nto an image if the nature ot the
ob'ect i. to be revealed - a greater extent p%Qvide. more detall.
Equatlon XII.2
.w:mariMII the result :

ie. the theoretical resolution ol the microscope ia ol the same erder aa ehe vavelenqth of the light.
There are speciallaed technlques in mlcroacopy fo r adjustlng contrast by manipulating the diffractlon pattern before the !mage ia synthesised.
In -dark-field"
microacopy -the contrast ia enhanced by preventing vaves scattered at very lov Q
valusa from contributlnq to the 1mage.
If Fig. lII.4 represente the den!iity of
scattering matter in an objeet, Fiq. III.5 represents F (Q) and Fiq . 111.8, which i5
the inverse transform omittinq F(Q) at low Q va l ues, then representa the amplitude
of the light across the image formed by the dark-field microscope.
Figure III . e
ahowa that the dark-field technlque subtracts a constant background from this amplitude - and hence from the lntenslty of the image.
Suppose that an object consists
of bodles which scatter very little more light than their surroundlng medium - the
contrast i n the !mage wl l 1 be poor.
But the dark-field technlque can be used to
subtract a constant background from this llMge ..mlch corresponds to the intensity
contrlbution frOlll t he medilD surroundi.ng the bodies .
They will then appear as
light areas on a black background.
unfortunately Flg. III.S also showa thAt spuriQUB detail, which yas not present in the original object, can appear in the darkfield image.
What ls the effect of the thickness, t, of the object in Fig. KII.l?
Suppose
that the mlcroscope is r equired te lmage details whose dimensions are ot the order
of A le. it is operatlng near the llmit of its resolution.
In Sectlon lV.2 it was
shown that the region ef Q- space whlch can be explorad by scattered r ad l ation is
restrlcted to the surtace of the Evald sphere.
Tbus only that part of Q-space
which lie s en tbis spherical surfa ce is used te syntheaise an 1maqe of the ob'ect.
It aplane sectlen of Q-apace, which contained its . origln , O' , were used, the 1mage
would oorrespond to a projection of the object on t o a plane perpendicular to the
inci dent beam - as described in Sections IV.4 and VIIX,4 .
SUch a projection would
superimpose informatlon frcxn all polnts aboye and belo.., A , along the di rection of
the incident beam . threuqhout the thlckness, t, of the specimen.
But the diffraction pattern i5 not aplane section of Q-spaee and so the image does not correspond
to a magnified projection of the ebject.
lnstead the mlcroscope magnifies a se lected section of the objeet eg. threugh A and B.
Most ol the material yithln the
thickneas t does not appear in the image - the mleroscope is said ta possess a
limited depth of He Id.
XII.3. Atomic re501ution
Suppose that we wished to form en image with a resolution of about 0. 1 JUl , in
order to determine the posltions of atoms in an object.
According to Sect i on
KII.2 ve vou1d need a source of waves whose vavelength, ~ , yas comparable with this
required resolution.
Tbree kinds of yaves can have ~ values of around 0.1 JUl:
electrens (Sectlon lI . 6) , thermal neutrons (Section 11.6) and X-rays (Seetion 1.2).
Electron mlcroscopy has three drayMcks .
One: only very thln obj ects wi11 not
absorb the e lectron s _ see Section VI. 2.
Macroacopic speclmens have te be dispersed into tiny fragments or sectioned to produce objacta yhich are abo~t 100 nm
t hlck.
Both technique s, but particularly eectioning , involve extensive chemica l
and/ or mechanical treatoent yhlch may produce an object which bears little resemblanee to the original speciaen.
TWo: elemente ol 10\1 atooic number scatter inaufficient e lectrons te previde mueh centra lit ln the imaqe .
Th1s problem can be

Relat i onsh ip to MicroBcopy

X-Ray Dif fra ct i on

146

DI "AALTI OH PLANE

={j~~::==================================~I~to DIAMETER
"AM

F1g. XIl .2.

..

R-------~

01spens ing with an obj e ctive l @ns fer recordi nq a diffraction pattern whe n R ls large .

overco1!le by att6chinq atons whieh scatter st r onq l y to the object - but this " s ta i!lLng" wl11 change the original arrangeoent of atom B.
Three: the obj ect must be
s urrounded by a vacuun in the Di~ro5C Ope, ~ause ai r acatters appreclably (a very
4
Low pressure o l a round 10- N n- 15 required to p roduce a suitabLe be~) .
Thus

objects which contain l iqu i ds cannot be examined; the liquid wouid evaporate, d1sruptinq the struct ure o f the objec t and ruining the vacuum.

Neutron and X-ray

micros copy are i npossible b ecause of the absence of l enses.


Sorne oE the statements in the previous paraqraph ought, strictly, te be qualifi ed; many r eader s will not be unduly concerned wlth these qualifications and may
wish to oRlt this pa ragraph.
Firstly, sorne progres s i a being made towards exami ning ~wet~ spec imens in the e l ectron microscope.
The ob ject 1s enclosed in a cell
so that 11quld cannot evaporate i nto the hlgh vacuum of the microsoope.
Very hl gh
voltages [ar ound 1 MV ) are used, ln special mlcroscopas , to accelerate the electrons
so that they ecqu lre s ufficl ent e nerqy te pass through "windows " ln t he ce l 1Second ly, lenses are available for those X- rays whlch have suff iclently h i gh A
values - so - cal l ad "so ft" X-rays .
However, thes e wavelengths are f a r too hlgh for
an X-ray Ricroscope to resolve atomic pos1tlons in an object.
Even for l ow resol ution s tructure determinatlon , the X-ray mlcr oscepe has serioas d isadvantages
arislng from soft X-rays be lng very strongl y absorbed.
C&n we ~lspense with any of the l enses i n Fig . XII . l?
Although the r est of
th1s saction is concerned explicltl y wlth X-rays, mast o f t he a r guments app ly
equally well t o neutroos - neutro n d iffraction is a l ess com=on technique because
few re actors a r e available ... 9 sour ces.
A per allel beam of X-r ... ys can be produced
by the methoda desc r ibed in Sect ion 1. 2 - so there is no need for a condenser lens .
FurtherlllCre no lena is required to form the diffractlon pattern becaus e the erOiUs&et1onal dia.me ter o f the beam , which i 8 typically a:round 0 .1 1m, i a small comparad
with a typlca1 .pecimen-to- f ilm distence of several cent1=etres .
Piqure XII.2
then ahcwa t hat vaye cattered with the same ~ valuea will all arrive at effec-

141

tively the same ?Cint on aplane even in tlle absence of a lens.


Note that , i n
reality , the del init ion oi the peints is better than t h i s fi gure rnlght s uggest
But without
bec a use i t Bhows an exaggerated diaoeter for t he beam c r oss- section .
a lens "'e eMnot fOrll M 1.mage.
[n the absence o f a suitable X-ray lens , we a re r educed to analysing a d iffractlon pattern ol the object .
The obvlou$ method of analysl s l s to c~pute an inver se Fourier transform. to obtaln an image .
R~ember that the phase infermation
iB lost when t h e di ffraction pattern iB recorded.
But if th1 s information ca n be
deduced , by o ne c f the methods glven in Sectlon 111 . 4 , an image can be computed.
A structural model obtained by X-ray diffraction then has the same s tatus a s an
image observe d in a mlcroscope; in Section x.4 lt vas shown that structural mode l s
of this kLnd are most readily obta i ned, at atomic re solueion , whe n the object l s ...
crystal.

Analysis of X-ray diffraction patterns 15 not a lvays so str aightforward.


In
Seetion XII . 2 we saw that spurious details can appear when a limited range el
Q-space ia usad to form. an image.
Limit ing the range of Q-space te obtain low
resolutlon structural informatlon, which i5 equivalent to r edueing the objective
aperture of a microscope , is comrnon in X-ray diffraction sometimes this limitation
ls d lctated by the nature o f the specirnen because there la no detectable scatter
approaehing Qmax of equati on XII.l.
Care must then be taken not to a t t rlbute
spurious details, which arise from examinlng an insuff icient extent o f Q-space, to
s truetura l fea tures in the object.
Another complieation a r ises b ecause the trlal-and-err or approach , of SectloD
II l . 5 , may be necessary to determine s t ructure .
In this approach a trial ocdel i9
developed in the absence of phase i n f Orllat10n .
Deve l opment o f a model in this way
amounts to making impl icit assumptions about the phases ol t he scatter ed waves .
Of course these assumpt ions may have t o be medifled dur ing t he course of the s tructure determin ation~ nev e rthe less in it iai phases have implicitly t o be assuoed.
Structural mode la derived by the trial-and-erro r a pproa ch do no t then have quite
the same s tatus as the images formad by a mlcroscope.
5everal alternative models
may be p roposed.
The best is the simplest te p r ovide a satisfactory exph.nation
o f exper i ment a l observations - these obser vations sheul d not be re9trlcted to those
arlsinq from X- ray dlff ractlen e xperime nta .
XII . 4. Electron micr08copx and dlffr a ction
Ele ctron lenses can be used to foeus electrons to f orro an image in the electron
microscope: unfort unately electron lenses have severe aberrations so that the t heoretical reso l ut i on of around 4 pm is not achieved by a real mic ro!lcope .
Because
e le ctrons a r e charged , an electron beam can be defl ected by a magnetic fle ld .
An
electron lens 15 an e lectromagnet which focuses a pera l l e l bearn o! eleetrons to a
poi nt on a focal plane - jU5t like an optic al lens f ocuses Light.
The electro n
beam i s produced by accelerating the e l eetrons through a potential difference vhich
has a typical yal u e o f 100 kV.
According to equation ll. 1 7 o f Section 11. 6 , thelr
vavelenqth ls then 4 pm.
From Section XII . 2 ve woul d expect the resolution o f the
mieroscope to be of the same order .
Unf or tuna tely l enses cannot be ~anufactured
with suffic i ent accuracy for suc h a hiqh resolution t o be achieved l n practice.
With a auitable specimen , s u ch as a thi n f ilm of gold, t he resolution o f co nt~por
a r y microscopes ia no better than about 0.1 ODI.
of course , i! we have some prior knovledge ol eg . the arra ngemen t o f atoms in
a film o f gold. we may be &.ble t o obtain more detai l ed i nforma t ion than th Ls resolution might suqgest .
In Section X. 4 we s aw that X-ray cr ystal lography usual ly
only yields a l ov - r eso l utien pl cture of the e l ectron densit y 1n a prote i n molecule .

,.6

X- Ray Diffraction

Re l ationshi p t o Hi c r oacopy

B' (REAL) IMAGE

PROJEC.YOR LENS

O&JEC.TlVE LENS

Fig . XI I .4.

Electron micrograph o f a mica c rystal l ite .


The bar represents a distanc e of 10 ~m
{taken by S. M. W. Grundyl.

Fig. XI I.S.

El ect ron diffra ction pat tern of a part o f the


mlca crystal lite ahovn in rig . XII. 4 (taken
b y S. M. W. Grundy).

OBJEGT
CONDENSER LEN5

SOURCE

Fig . XI I. 3.

I mege f orma tion in the project ion micro5cope.

But, by comblning this picture with stereochemical information , the posltions o f


Essentlally the sace approach can be
a t oms i n the colecul e can be deternined .
u sed t o obtain detal l s ot atcole posltion s in meta l e and minerals by electron

ml croscopy .
Figure XI [.3 s h ows how the image form ed i n t he 11ght mlcroscope can be p r ojected by repla cing t he eye-piece vith a projector lens; a comparable optical
arra ngement has to b e ~sed in the electron microsoope - the a rrangement o f Fl q.
XI I.l cannot be used because the eye l s unable to detect electrons.
The acuree,
in an e l ectron :n1c r osc:ope , 15 a cathode.

Electrons f r om the cdthode a r e ac:celer-

atad tovards an anode by a h1g h potential difference - many o f them pass through a
hole in the anode t o produce a divergent electron beam.
The beam can only be pro~uced i n a very high vacuUD i e. a very l o .... pressure - this vacuum i s ma1ntaine d
throughout the instrumento
~ fluorescent ac ree n a llows the 1mage t o be visua l ised.
i'nlen el ectrons 5trike a point on the scree n , l i g ht 15 emitted; the 1ntensiey of chi s
light depende on the number c f e l ect rons strik ing the point .
Electr on micrographs
U:8 r~ rd e d by repl acing t.he fluorescent screen w1th a photogra ph1c f ilm .
The image, produced b y an electron microscope . corresponds te a magni f led pro'ection of the object l e. both tne top and the bottOll, as ....ell a s the i n.ide , appear

149

150

Rela tionship to Hicroscopy

X- Hay Dffraction

super1D:posed in the 1lMqe.


In other words the electrcn microscope has a cons i derable depth ol f Leld.
This property arises beoause the microscope ls always operated far from ita theoretical l1mlt of resolution.
The Q values ol the vavas which

of SectLon 11 .6 can break down for the conditions whlch occur in the electron
micrescope .

form the dLffractLon pattern are then ~uch less than Qmax of equation XII.l le. mueh
less than 2" /1 - the rad i us of the Ewald sphere.
At theae low Q vaLues the Ewald
sphere 18 effec tively a plane sect10n of Q-space , passlnq through the o r ig1n O',
which 15 perpendicul ar to the direction of the Lncident electr on beam .
AcoordLng
to Seeton XII.2. the lmage formed from this diffraction pattern 15 a magn ifled
projectlon ol che object on to a plane perpendicular to this beam d irection.

XII.S. sua:raa.ry

Mueh srnaller objects can be used 1n diffractlon experimenta wlth electron s


than with X-raya.
Figure XII.4 shovs an electron microqraph of a 81ng1e mica
crysta1l ite - in the orlginal microqraph the maqnifi cation was about 2 , 500 times.
Because 40 object of this aize can be imaged in the electron micro8cope, we know
when there i5 a s lngle crysta111te in the electron beam; this beam can have a dia~e ter o f on1y abcut 20 nm a t the object.
The object is placed on a supporting
stage and can be moved into view by suitably sma11 d Lsp1acements because the stage
i5 manipulated by the operator via a geared-down mechanical linkage.
When the
object is sul tably positioned its diffraction pattern can be vLewed instead of
forming an lmage.
HcnoI do electrons pass through the stage?
They do not hava
to - the objec t ls actualLy supported by a thin (20 nm) carbon film which apana a
hole i n a specimen grld vhlch, in turn, spans an ape r ture in the staqa.
Fiqure XII.5 i a the electron diffr action pattern of a selected area of the
object .
This area oould be selected by l!miting the condenser aperture of the
microscope .
In Fiq. XII .4 the crystallite is positiened 80 t hat one of its crystal axes points in the incident beam dlrecti on.
Suppose ve l abel th1s axis as the
c-axis.
Then the plane section of Q-space which vas used to f orm Fig. XII.5 Ls
the plane defined by the reciprocal lattiee vectors a~ and b~ o f Seceion x.2 sinee c 1s perpendicul a r to both a" and b.
In thLs e:z.ample the electron diffrac tion pattern contains the !U\llIe information as the precelilsion method provides in
X-ray c r ystalloqr aphy - an undistorted seetion of the reciprocal lattice.
But
here an undlstorted section of Q-spaee can be recorded from very much smaller
speclmens than are required for X-ray diffraction.

151

Formation of a diffraction pattern ls an lntermediate stage in the formation


of M image.
In a uic roscope the diffraction pattern i5 fo~ in the back focal
plane of the objective lena ; the lens focuses all waves from a scatterLng ObjEct
which hava the sallle 2 vectors a t a point in this plane.
HO\oiever ehe diffraction
pattern 18 not recorded so that the vaves continue with their 'phase relationship
undisturbed.
Because the lens causes the paths of these vaves to converge, an
image i9 formad.
I n a mlcroscope the eye-piece lens maqni!i es this intermediate
image to form a greetly magnifled final image.
No suitable lenses exi8t for X-rays - we can then record a diffraction pattern
but not an imaqe.
The diffractlon pattern can be recorded without a l ens by mak1ng the distance from the scattering object te the detector sufficient l y lar~e.
Since an lmage cannet be formad we have to record the diffr action pattern.
The
phase problem" arise8 because the phase relatlonship between the scattered waves
is then destroyed.
When deductive methods fo r determinlnq structure are applied, the miasing
phase lnformation can be measured and an image obtained by oomputing a n inverse
Fourler transform o
Deductive methods can nearly alvaya be appl Led to diffraction
patterns from single crystals .
Often, hovever, trial-and-error methods have te be
used to determine structures.
Electromagnetlc lense s are used to focua the electrons in an electron microacope.
Bi ther an electr on dlffraction pattern or an !mage can be recorded from
M object .
The Lmage contains the phase i nformatlo n vhich ls lost vhen the d1ffract i on patte rn Ls r ecorded.
It also allows very small obj ects to be poiiltioned
in the electron beam so that diffraction experiments can be carrled out vith much
smaller specimens t han la possible with X- rays.

~ctually the crystallite had to be carefully oriented to ensure that its


c-axi s pointed in the incident beam direction.
This orientation was a chieved by
tilting t ha atage about t...-o axes which were mutual ly perpendicular both to each
other and to the directio n of the incident beam.
If the object 18 reorientad , by
tilting the s t age , a d l fferent projecti on appears i n the imAge.
By recordlnq
microqraphs of objecta at a variety of orientations it i8 posaible to gain an idea
o f thelr three-dimensional structures.

The abi 11ty to form an image qives electron diffraction an advantage over
X-ray diffract i on. It ia o ften sicpler to appreciate certain kinds of information
about an object from its diffraction patter n than from an imAge eg. information
ccncerni ng periodicity - wltness the relatlonsh1p bet~een the intenaity distrl butlon of the diffraction pattern and the autocorrelation function in Section
111 . 3.
The corresponding i mage . vhic:h CM be formed when electrons are used, provides e valuable c he c:~ on the LnterpretatLon of the diffraction pattern.
It also
provides a source of phaae in formation.
When the diffraction pattern i8 recorded
all phase l nformation is lost since the photographic film detects I( ~) - as in Sec tion 111.2.
The microscope can be considered te perform an inverse Fourier transfo~ en F(~) to synthesise en image of t he object.
Reverslng the process by
Fourier transformation yie lds F(21 ~ich conveys t h a phase informaticn lost when
the diffracti on pattern vas recordad.
But note that the simpla Born approximati on

>< OOCS '"

l53

Bibliography
3. Chapter 1

H. Semat , "Introduction to Atomic and Nuclear Physics W , 4th ed., Chapman and
Hall , Landon (1962)
Host books on atomLc physics cover the material in Chapte r r.
Sernat qives a particularly simple and readabla account with referances te sources of further information.
4. Chapter II

Bibliography

D.C. Champeney , ~Fourier Transfo~ and their Physical Applicat ions",


Acadernic Press, London ( 197 3)
Tha most useful accoune of Fourier transforms for supplementing this book the
appendLces are a useful source of proofs .
R.

Br&cewell, "The Fourier Transform and itB


Landon (l965J

App lications~ ,

McGraw-Hill.

l . Introduct1.on

Similar to the book by Champeney but with emphasis on applications in e 1ectrical


engineering.

Thls biblioqraphy 18 lntended to indicate a few sources ef further information especlally those which 1 have faund particularly useful myself .
lt 15 not lntended

G.N. Watson, "A Treatlse on the Theory o f Sessel Functions" , 2nd ed .


Cambridge Univeraity Press , Cambr idge (1966 )

te be comprehensive 1n some s8cticns 1 have been very selective because so many


book~

are ava ilable.

As far as possible 1 have recommended books which glve a

brcad coverage of each topie - these books usually g ive references te che original
literature.
Review arttcles and research papers are included only where 1 consider
that they are especially useful.

A detailed account of Sessel functions - useful as a reference book.


G. Harburn, C.A. Taylor and T . R . Welberry, "Atl as of Optical Transforms",
Bell , !.ondon (1975)
Uses optical diffraction to illustrate many of the properties oE Fourier traDsforms
which are either statad or derived analytically in this b?ok.

2 . General
R. W. Jan;es, '''The Optici!ll Principies of the Dlffraction ef X-Rays", Bell,
London ( 1 954 )

M. Xerker, "The SCattering of Light a nd other Electromagnetic Radio.tion",

The best single source 01 lnformation en the underlying physics af X-rey dLff r ac tion
Lt la hardly concerned a t a11 vith appl ications.
An excellent reference book gin~e
the ~aterial is covered in considerab le depth.

A very detailed account DE exact and R.D.G. theorles of light scattering.


The
foruulae usually apply to unr ationa1ised units; bu t sometimes formulae appropriate
to SI units creep in without comment.

A.

Guinier. "X-Ray Diffraction in Crystals. Imperfect Crystals and Amorphous


Bodies~, Freeman, London (1966)

A use fuI sour~e DE inforcation on X-ray diffraction theory; its approach i9 more
rigorous than that adopted here and more topics are covered.

B. O. CUl l ity , "Eleme nts of X-Ray OiEfractlon " . 2nd ed., Addison-Wesley,
1.oOOon (1978)
Detalled accounts oE many applicat i ons oE K-ray diffraction - partlcularly the prac tical aspects.
Bragg ' s law 19 the startlng point Eren whlch the theory i s derived;
there 1s no mention of Fourier transforms.
"Internationa l Table's for X-Ray Cry sUli l lography". lCynoc h Press , Birmingham
(l969- 74)
The four volumes of this book have a misleadinq title - only the first is exclusively c oncerned with diffraction by crysUlils.
They are a mine oE useful inEormatlon on atonie scatterLng factor s , seattering by dilute solution s of colloidal
particles, diffr actLon 9~etry, Lorentz f actor s e t c.

l52

Academic Press , London (1969 )

Ii . C. van de HUlst. "Light Scattering by Small Particles ", Chapman and Hall.
London (1957)
Covers rather less material than Kerker but pro vides more e xplanation.
Exact
theories are included - the "amall" in the title only implies that the qeomet ric
optlcs approach i 5 excluded .
G. I!!. Bacon, "Neutron Diffraction", 2nd ed., Cl arendon Pres5 , OXford (1962)
A reasonably detailed. yat readable, account of ne utron dlffraction.
El ectron difEraction and microscopy are covered in Section 14.
S. Chaptar nI
The material in this chapter is covered in mDst books on K-ray crystalloqraphy -

sea S.ction 12.

155

Bibl iography

Bibliography

154
6. Olapter IV

The books by James (SecUen 2) and Randall (section 8 ) are uselul 80urces of further inlormation on diffraetion by liquida and amorphous 8OlLds.

C.A. TayLor and H. Lipson , Optical Transforcs : Their Preparation and Appllcation
te X-Ray Diffraction Problems", Bell, Lcndon (1964 )

10. Chapter VIII

Glves an account of the methods used to s~late X-cay diffraction ~th light .
More resulta froD thLa technique are glven 1n the boo:k by Ha rburn e t al.
(Sec t1on 4).

H. Lipson and C.A. Taylor ,. "Four ier Transforms and X- Ray Diffractian-, Bel l .

London (1958)
The results ol Sectiona VI II.2 and VIII . 3 are derived for the case of a perfect
three-dimensional crystal.

Further LnfOrlB5tion on dLffraction qeometry appears 1n Vol . II cf the "Inte:rnatlonal


Tables for X-Ray CrYlltallography" (Sect ion 2 ) .

other tepies are eovered in the books by James and Guinier - see Seetion 2.

7. Chapeer V

11. Chapter IX

B.r. Bleanel' and S. Sle aney, "El ectricity llnd Magnetlslll" , 2nd ed . ,

A . (luq, F . B .C . Crick And H. W. Wyelroff. "Diffr act i on by Hel ical Structures

Clarendon Press, Oxford (1965)

ti,

Aeta Crysta11ographica , 11 , 199- 213 (1 958)

Gives a use fuI account cf the intensity of electromagnetLc waves useful for making
the simpLe approach adopted in this book more rlgorous.

brief out complete account of the t heory of diffraction by helices.

P-G . de Gennes, The Physics of Liquid Crystals" , Clarendon Press, Oxford


The material in thLs chapter 15 covered in cost books on X-ray crystallography
(Section 12 ) and in the book by James (Section 2) .
8.

(1974)

Gives a cleAr description of the various kinds of liquid crystAls and a detailed
account of their preperties.

Chapt.er VI
12 . Chapter

J.T. Randa11 , "The Diffraetion of X-Rays and Electrona by Amorphous Solids,


Liquids a~ Gases ", ChApman and F..all, Lenden (1934 )
A clear account of the methods used to obtain diffraction patterns from gases and
the formu1a e used to interpret them .
O. Kratky and l. Pil z, "Reeent Advances and Applicationa ol 01ffuae X-Ray Small

Angle Scatter ing en Blopolymers in Oilute SOlutiona" , QUarterly Review8 el


Biephys i es, ,2.1 481 - 537 (1972)
Gives a simple aeoount ef the experimental methods used to measure the intensity
of X-raya seattered by aolutiens of mac ro~lecules and colloidal partieles, as well
as the theery used te interpret the results .
A good aource ef references to the
original literature .
The book by James (Section 2) is an especially useful source ef further information.
9. Chapter VII

R. Bosemann, "Parac rysta1s ln Bi oJXIlymers and Synthetie Polymers


Endeavour, E, 99-105 (19731

M
,

A simple acoount of t he paracrystal t heory of X-ray diffraetion by non-crysta11ine


systems.
C.A. Croxton. -lntroduction to Liquid State Physics, Wiley, Lendon (1975 )
A comprehenslbl e account of recent theories of the liquid atate - including theor i ea of the interferenc. function.

J. Pickworth Glusker and K. N. Trueblood , "Crystal Structure Analysis : A Primer " ,


OXford Univer s ity Press, London (19721
simple account af the principIes and methads invol ved ln d e termdning the struc tures of mo l eculea i n single crystals.
Includes an extensive bibliography which
should be cansul ted for details af other books on X-ray crysta l lo;raphy - the bibliography is not so reliable far diffraction by less ordered syatems.

woolfson. "An Introduction to X- Ray Crystallography", Cambridge University


Press , Cambridge (1970)

M.M.

Similar in scope to the Ix>ok by Pickworth G1usker and Trueb100d but 1es$ elementary.
Gives excellent accounts ef many aspects of the principIes af X- ray crys tallography - experimental methods a r e a lso included.
T .L. B1ul'l de11 and t..N. Jahnaon , "Protein Crystallography", Academic Press,
London (197 61
An account of the specialised techniques used to determine the structures of
globular pretein molecules in single crystals.

W. L. Bra99, -The Crystalline Sta te", Bel1 , Lendan (1966)


A survey of erystallography, firs t published in 1933 . whlch has subsequent ly been
reprinted.
13. Chapter XI
H. Lip.on and B. Steeple, "Interpretation ol X-Ray Powder Di ftrAceien Patterns,
Macml11an, Lenden (1970)

Bibliography

l5.

A very complete and reedable Account of the applications oE X-ray diffraction by


crystal line powders.
S. Arnott , "Fiber Diffraction Analysis oE Blopolym.e r Mclecules" , Transactions c E
the Ame rican Crystlllloqrllph!c Assoclation, 2.r 31-56 ,(1973)

Gives a brie f AOCOunt cE d iffraction by crystalline fibre s and an up-to-date


account

oE

~ethods

uged te r ef ine atructural codel..

Inc lude s detall a

oE d if frac-

tion by tne d lfferent k i nds cE "staelstlcal" c:rystal structures tbat can adse .
Unfortunately lt 15 published in a ra ther inaccesaible joucnal .
14 . O\6p ter XII

Index

S.G. Llpson and H. Lipson , "Optical Physics " , Carrbridge Unlversity Pre ss .
cambridge 0.966 )
The mest u seful optles text te 8uppl ell'.ent th!s book.

I n c ludes detalled accounts

oi rraunho fer diffractio n and 1t5 relationship be image formation .


C.J. Ta y Lor and B.R. Pul Lan , ~Compute% and Optical Proceasi ng o f pictures" , ln
"Non-Destructi ve Testi.ng ", R.S. Sharpe M., Vol.II , pp 65-87, Academic Pre s5 ,
London (1973 )
Descri bes the fornation o f 1.aages and holO' the properti es e f the Fourier tra nsforn
can be expl oited to analyse them.
0.1'. ParSCIns (Ed . ) , "Shert Wavelength Micro scopy", Allna1 s of the New York. Academy

o f Sciences , 306 , 1-339 (1978)


A col1ection o f papers descri b ing some recen t advance s i n e1ectron and X-ra y
rn lcroscopy

A .1'1. Cilauert (Ed. ) , "PracticaL Nethods in E1ectro n Mic ro 9Cepy" , North-Holland,


AIIstardal:l (1 972)
At prese nt there are three volumes o f th1s book - IIIOr e are planned .
So f a r they
deal ~ ith the principIe s o f e 1e ctron cicroscopy , the oper a tion of the microscope,
speciaen preparat i on, electro n diffraction a nd some of the methods wh ich can be
u sad to a nalyee electron micrographs.
J.!'!. Cowle y, "DifErtletion Phys i cs", North-Holltlnd, Ams terdam (1975)
netaile~ aeeount oE d i fEr a ct10n physics whieh is particultl rly strong on e l ectron
diEtraction, ineluding etl l c ulation when the simple Born approximation i9 inadequate.

Abbe theo ry 142- 1 4 5


Aberra tions oE an e 1ect ron lens 14 7
Abse nce o f diEf raction spots Erem a
crystal 1 32
Absence o f layer lines 1 10 , 132
AbsoLute intensity measurements
eEfect o f fundamental a:mstan ts 8-9
eEfect of loss oE scatter at lO\</'
Q values 21
for crystals 130
problems in measurinq 53
see a150 Absorption of X- rays ,
Loren tz cor rection , Polari satial
facto r , Scale factor
Absorpti on of X-raya 47
correction Eor in X-ray
ery5ta11ography l30
Absorptioo edge 4 7-49
expl oitation tor f11ters 2 , 4 7
A1phtl-helix 107-109, 136
Amorphous solids
diff r ac tio n geoJretry 3 3
interEerence function 67-70
X-uy diffraction by 64 - 73
Anisotropie temperature factor l30
An n u1us , Fourier transform of l OO
Anoll:lalous scattering 4 5- 50
as means of de te rmininq
chlrali t y 30, So
e f fect en rotation pattern of
a c rys t al 128
ARtl - parallel chains
i n nel!latic o r ganisatio n 112
in two-start helix 110
Applicatlons o X- ray diff ractlon 1, 17
see also Amorphous sol id , Crystal ,
Crystalline fibre, C:rysl;all lne

powder , Gas, Li quid , Liqu1d c ryscal .


MoLecular helix, Polymer, SoLution
Arrangement of ool ecules see Molecula r
arrangement
l\.s YlIJIIetrlc unlt 131
Atom , Fourie r trans f orm of 40-42
Atonde reso lutlon 145-14 7
Atomic scattering Eacto r 40 - 42
corre ct1an f o r anomalous
scatte ring 49-50
in Four ier transforo of
crystal 123
molecul a r helix 109
IlIOlecul e 42
Auto-correlation f~ctioo 18-19 , 150
relatlooship t o i mage f ormation 144
Bem al chart 83
Eo r rotation paetero o f a crystal 126
Besse1 functlc:n 12 , 98-99
in Fourier trans f ol'1ll of
annulus 100
continuous helix 98-100
cylindrically symmetric Eunctio ll 12
disc 114
discootinuc us helix 104
Bom approxiroation 16 , ISO
Bragg reflection
abge n ce caused by syllllIEt:ry 1 32
t o r focusing X-ray s
J
f o r prod.ucing non o c h roma t ic X- rays 3
nomenclature 125
Bragg' s law 81 , 125
Bremsstrehl\mg 2
Calcium oxalate , ~cro c rystalline
deposits 135

l57

l ndex

158
Cartilaqe, X- ray di f f r action
fro m 6 7 , 1 1 3
Ce n t.re of syrunetry 22
centrosyll'ltetry see Centre of syllUlletry
Charac teristic radiation 2
OI.elll1cal analysis 1, 1 7

of c rystall i ne powders

134-135

Chirali ty

abili t y te determine i n crystal 128


aete nU.na t i o:l
by anolllalous scatterLng 30 . SO
f or molecula r helix 140
effece en nematic o J::qanisation a s
of molecular structure 4 3
of helix 106
Choleste ric liquid crystal
Cholesterol 1.15
Coaxial he lices 1 10

1 15

Coherence
cl in cident X-raya 18
of seattered X-rays S
see also )[-~y laser
Collagen . as exanple of o riented
polymer 114
CollimaHo n 2 . 146-147
ef f ect o f n cn-pin- hole
CO!llton effect 5

62

Contlnuous helix 94-100


gene rat10n of diseon tinuc us
h e lix Ero ra 101
convolutLon

12-13

decoovo lutiCl1

63

generation o f
crystal structure by ll9-120
diso r dered crystal by 88
Fou rier transfortll. o E d1scootinuous
helix by

102

helLx by 94 ~95
molecula.r hell x by 107
on e~d i mension a1 crystal by
76 - 77
rela ~ian5hlp te cross -corre1 ation
18
representing s~aring o f
dif f ratt ion pattem 6 2
Cross-cor:rel ation f unction la
re latiooship t o c a 1Vo1ution 18
Crys t al
de t.e rtrin atiCX1 e E
ch l ral ity in 50
IXIlecu1ar structure ln 1, 1 29-131
disorde red 87- 89
for f ocus i ng x-rays 3
identlflcation af unknown 1 , 1 7
Lnperfect 87-66 , 89 , 130
monoch r o mato r 3
mos aL c 89-90
ooe- dimensicnal 76- 93
s yame t ry 131- 133
three- d lnens ional 119 - 133

see a 1so Crystalline fibre, Crystall1ne powder , Cubic c rystal , Liquld


c ry s t al , Orthorhombic crysta1 ,
OscLllatit;n pattern , Pre cesslon
pattern, Rctation pattern, S tatis tica1 crysta1 structure, TetragCC1al
crysta 1, Trlclinlc c rysta1
Crysta111ne flbre 134, 13-13 7
Crysta111ne powde r 134 - 135
Crystallography 119-133
CubL c crystal 132
Cyl l nd r lcal averaqing 112-115
o f di ffraction d.a:.a frQ m a
crys t alline fibre 136 - 137,
139 - 140
CyUnd ri cal s ymmetr
Fouri e r transform of a functi on wi th
w1th 12
o f di f fr action fro~ a
con tin \,lo u s hclix 98, 100
neeatic L1 3-1 14
Dark-fieLd mi e rosoopy 145
Deccnvolutl on 63
Depth a f field 14 5
of e 1ect ron mic ros cope 149
Detector geometr 33- 35
for a one-dirmnsiona1 cryst a1 83
for a three-dlmensianal cryst~l
126 , 128-129
DiffractLon
e1ectrCZ'l see El ectr on diffraction j
scatterLn g
Fraunho fer 143
geome try fo l:.': a
c ry s t a1 125-12 9
crystllll.ine fi bre l38
c rysta1line powder 135
n e ma tl c 113
one -dimen sion crysta1 00-64, 90-92
syste~ with spherica1 symmetry
31- 33
1.1ght see Light diffraction j
s caruring
neu t ron ~ Ne ut r on diffractlon l
scatte rL ng
X- ray see X- Ray diff r actionl
s catterinq
Diffuse intensity, from a
disordered c r.ystal 88-89
Direct co r rellltion function 73
Dire ct methods 20-22
appli ed te a
crys t a1 129
ideal solution 56- 57
one-dicensi on c rys t a1 86
Disc , Fourier transfonl o f 114

159

I ndex
01 soontin uous he1ix 10 1-106
gene r lltion of a oolecu1ar
he1i x from 107
Disorc1e r ed crystal 87-89
see a1so "'.osaic sprea d, Occupancy o f
a 1 a ttice site , Paracrystal
Dl sorde red phase
mixed with -ordered phase ea
s ee a1so Amorphous sol id , Disordercd
c rysta1 , Gas, Gel, Li quid ,
Liqu i d crystaL, One - d icens i on al
crystal, Soli d , Solution
~A, AlS eKamp1e o f a tlO'O-sta r t he1 i x
110
COt p rodu c to pI:Ope rties o f 00
Elastic scattering
of e 1ectI:Ons and neutrons l4-16
of X-rays 5
E1ectron
X- r ay emissiCll from accelerated 3, 5
X-ra y scatter:lng by an
asse lltlly of e 1ectro n s 7- 8
a 1ectran in an a t o e 40-4 2 , 45 ~50
s ingle e 1ectron 3- 5, 45-47
Electron density
aete rmination in a
crystal 129
one-dimensional crysta l
86-87
Electron diffraction/seatte ring 14-16 ,
142 , 146 , 147-151
by a gas 53
b y a mica crys talli t e 150
E1e c tron lens 1 4 7
abe rr a tions o f 14 7
E lectron microscope 15 , 145 -146 ,
147- 15l
E lect ron micrograph of mica I SO
En zyme, X- ray di ffra ction from
a crystal of 128
Equlltor 81
Equa t o ri a1 interferen ee fun ction 114
Ewald sphe rc 31-33
applied to
depth o He1d 14 5 , 149
di ffr acti on f r OIll a
crys tal 125 , 126 , 128
c rystalline fibre 135
c rys talline powde r 135
helix 100 , 102
mosaic crysta 1 90
nel'llat ic 113
one-di mensional c rystal 81
s ystem with spheriea 1 symmetry 33
tilted ane-dimen s ional
c rysta1 84 , 91
Lonmtz cor rection 9 0- 92

Fibra
crystal.llne 1.34, 136-140
ln appl1cab l 1 ity of Guinier ' s
1aw to 57
with nematic organisation 1 10-112
Fl1 te r, for producing monoc hromatic
X- rays 2 ,47
Fl sh fin-ray, X-ray diffractlon by 11 7
Focusinq o f X-rays
by Bragg reflection 3
by tot a l l nte rnal reflection 2-3
Peurier inversion see Invers e
Fourier transfOrn
FOurier transform
def1nit.lon 10
effect of
frequency of v ari a tion ln
t rans foroed fLf1ction 45
n o15e 56
i nve rsl on t,heo rem 10

o, '"

annu1 \,ls l OO
atom <;0-42
cent rosynre tric fun ction 22
continuous helix 94-100
c rys tal 12]
cylindri ca11y syIllllEtri c f lrletLon 12
di s e 114
dlsoon t inuous he1ix 102-106
d l sorered crysta1 87- 8 8
itr)e rfect 1attice 87-88
lat tiee 11 9 -12 3
IlO lecu1ar heHx 106-1 10
mo1ecule 42 - 45
o n e - dimensional crysta1 76-80
o n e - dimens ion al 1attice 76 - 80
projection ]9 , 85, 145
s phere 43
s p he rlcally sy!!llletric func t lon II
projection properties ]9 . 85 , 145
prop ertles 10-13
sectioos of 39 , 85, 145
Fractional un i t cell coordinates 121
e f feet of symmetry on 131
F r aun h o f e r diffraction 142-143
Frequency of variation in a funct i on,
ef f ect o n its Four ier transfo rm <l5
Friedel ' s 1aw 29

G.,
di ff r actioo geometr
ideal ~ l deal gas

33

Gel
inappli cability of Guinier' s 1aw
o r lente d 110- l 12
Glasses see ~rphous solids

57

'. radiatlon
radiation

Guinier ' S l ~ 57-62


Qrlnier plot. 60
Raed sphere mode L for l1quids
Heavy atoe method

l n d ex

lndex

160

74

20

relatlonship to real space


reflnement 27
Hellcal no lecule see Molecular helix
Hel1cal s ynxetry o~rl ented polyooer
mol ecules l36
in c ry s t alline fibre s 140
Helice s , coaxial 110
Helix

a lpha see Alpha-hel ix


contlnu~ see Continuo us helix
disconti n uous see Dlscon t inuous
hel1x
i ntegral see Integral helix
mol ecular See M:Jlecular hel1x
non-inteqral
see Non- in tegral helix
tvo-sta rt see 'I"./o-sta rt helix
Ideal g a s
deduc tion o f QOlecular struct ure
in 56- 58
de fini tion 51
diffra ctLcn o E e l ectrons by 53

diffract1.on oE X-rays by 51-57


I deal sol u Uon
deduc tion o f ro l eeular struct u re
in 56- 62
defl n i tion 51
diffr scticn o E X-rays by 5 1-63
l dentification of lJIIknOlo'J'l substances

see ChelJical anys is


Ima ge furma Uon 142 - l45
In:perfec t c ~s t al 87 - 88, 89 ; 130
Inpe rfect Lattiee 88
lnperfe c t orientation 89
in c rystall1ne fib res 13 7
lndexing a diffraction pattern from a
erystal (rota1:.LO'I patternl 127
erystalline fibre l37
one - dirnensittl al erystal 81
I nte9 ra1 h elix 101
lnterferen ce fun ction f o r an
amorpho u s soli d o r liquid 67-72
molecular he l Lx 10 7
ne matlc 11 3- 114
OIle-dimensiona1 e rys tal 78
lnte rmalecu.lar p o ten t l,al flonetion 73
lnverse Fourier t r aJlsforrn 10
re1ationship to i oage
f o rmat i on 14 4, 14 7 , ISO
scale fac to r in 10
I solllOqtlous replaceoent 20

L~<

2, 48
2, 47

18

Lattice
inperfect 88
occupml cy o f si ':.es 140
ooe - dimen s ion al 76
r eciprocal 121 - 129
th r ee-di oensiona1 1 19-1 21
Laye r lLne
absence caused b y symn:etry llO , 1 32
OOfini1:.1on 81
fo r a
continuous helix 94
discontinuo us he1! x 102-104
intensi t y 85-86
Lens
electron 147
X-ray 146
Ligh t diffraction/scatte ring 1 3- 14, 16
.!IS step i n image formation 142 - 14 3
for simu lating X-ray diff raction 37- 39
Liquid
diffrac t ion geo~try 33
hard sphere mode1 o E 74
interference fune t ion 67- 72
X- ray diffractiO'l by 64-75
Li quid erysta1
choiesteric 115
nematic n O-115
smectic 115-117
twi sted n emat ic 1 15
Lo ren tz eorrection
fer a ene - dimensional crysta1 90- 92
for a threQ-dillJimsiona1 c rystal 1 30
:Lc:Y..'- ang1e X-ra y diffraction
definition 40
for dete r mining 10w resoll.1tion
structure 4 3
from ideal gases and 501 uti OO5 54
meridional pat te ms fo r onedimen sional c rystals 86
Low reso1utioo see Re solution
Macrotoolecules 1n sol ution 54 -5 6
Matrix representat10n of a
symrnet ry element 131
Meri d1an 81
in t e nsity distributLCC'I a10ng 85- 86
re lationship t.o preferred
o rient.!lti on ll3- 114
Mica

e l ectron di ff rac tion pattern of


e 1ectron !Id.croqr aph of 149

150

Micrcscope , theory of 142-14 7


see also oark- fi elc. microscopy ,
Electron mi croscopy , X-ray
tderoscopy
Mirrar image see Chiral ity
Mixture s o f disordered 4.'ld
o r dered pha.ses 60
Molecular arrange~n t
chi rality o f 28
determLn a t ion 40
as aiQl of studies on liquida arld
alllOrphous solids 65
in amorph ous solids and
liquids 72 - 73
in crysta11in e fibres 140
in liquid crystals ~ Liquid crystal
Molecul ar he1ix 10 7-110
in crystalline fibres 1 36 , 140
in ne mati c ll 5
Molecular shape
determin a t.ion 43- 4 5
in i deal sol ution 54 , 56-6 2
eff ect on radil.1s of gyrat ion 61
see also MOl ecul a r str ucture
MOlecular 5tr ucture
at low reso l ut ioo 43-45
chi rality o f 28
de t ermination 1, 40
i n crys tals 119, 129-131
i n i deal gases an d solutions 56- 58
i'k>lecu 1e
Fo urier t ran sfo rm o f 42 -45
helic al 107- 110
scatterlng of X- rays by 42-45
at 10w re 50lut i on 43-45
Mbnochromat i c X-ray s , -)
M:lnochromator
exp l oi t i l'l9 Bragg reflection
polarisa. t ion by 5
MOsaie spread 69- 90
a pplica.tion to di ff r ac t i on by a
crysta11ine fibra 137
e rystalline powde r 13 4-1)5
distlnction f rom t wisted nematic 115
relatJonship t o Lorentz
correetion 90-91
Neroatic o r ganisatioo 110 -11 5
tvi s t ed 115
Neutron diffraction jsca t te ri ng 14 - 16 ,
145 - 146
atomic scatterlng f ac t o r f or 42
Noise
e ffect on Fou rie r t r ansfo rro 56
Non-integral h e lix 104
Occupancy of a l at t ioe site

140

161

ene- dimension al c rystal 76 -9 3


One - dillll!nsi onal 1attice 76
Optical diffraction !!!. Light
diff r action /scat terlng
Orde re d phase
m1xed with disordere d phase SO
see also Crystal , Crysta lline fibre,
c rystAll1ne powde r, Liquid e rystal
Orien tatio n
inpe r fect 139
in
crystallLne Ubre 1 3'7 -1 39
gel 112
nem.!ltic 110-115
smectic 11 5 -11 7
pre ferred 1 , 17
unialCi a1 112
Oriented gel 112
Oriented polymers
in c rys t a.lli ne fibre s 137-140
nematic organisation of 110-115
Ornste i n- Zemike eq uat i on 73
Ortho rhDnlbic crys t al 125 - 128 , 132
OScillatioo pat tem o f a c ryst.a l 12 8
Packing fraction 70-72
Pack ing of mol ecules see /4::l1e c ular
pack ing
Pa r acrys t al
wl th disorder of the first kind 89
with disorder of the secmd kind 6 4
Pa r affin 'o/ax , X-ray diffraction f r OID 34
Paralle 1 chaln s
in coaxial helices 110
in re1a tien 1:.0 nell.atic organisat ion
112
P .!Itterson function 18-19
app1ie ation in the
he .!l\')' .!Itom wethod 20
isomorpho us replaceroent method 20
tria. l-and-e rro r wethod 24
spheri ca11y s yrornetri c 56
P a u l ing and COrey model fo r the
al pha- helix 109
Prcus- Yevic)c approximatioo 74
Phase deterllnation
direct aEthods 20-22
effect of
cent rosycme try 22
coheren t source 18
for a
c ry s tal 129
c rystallin e fib re 139
ideal. gas 56
ideal aol ution 56- 58
ene-dimensional c rysta1 86
h eavy atoro method 20, 27

Index

162

i somorphous r eplacecent cethod


relo.ticrJship te l mage fOrllation

20
147

trial-mld-err or a:ethods 24
Phase problelll 17-18
sol ut i oo of see Phase dete rndnation
Phase transltio"S'; s ymmetry changes
accoli.pany!n g 6 4
Polaris ation
by a mcnoclu ::oClAtor
correct:lon e f diffraction data
for 9, 1 30
e f 8cattered X- rays 4
o f X-raya frol:! synch rotrons .md

sto raqe r ings 5


scatterin g o
polarl sed X- ray s
3-4
un pol arised X-raya 4
Polarisatlon fac to r 5
ter crystals L):)
Poly- L- a lanine, as eltMllle of a
hellcal ~Lecule 109 . 136 , 140
Polyuers
helical molecules oE 107- 110
h e lLcal syltllletry ef 136

in c rys talllne libres 1 36- 1 39


preferred orientation of 1, 17, 113
see ;,lso Orientad p o lyrne ['S
Positron. in synchrotrClns and
stor~ rlngs
5
Potenti al fu'lct.icn see Intermol ecular
poten tl al function
Powder motilad L34-135
Powder pattem 1 35
Precess i on pattern ei a crystal 128
Prefrred orientat 1on 1, 17 , 113
Probli.n s, determination oE 1lO1ecular
structure by X-rey
crystellography 129
see also Alp h a he1i)( , En::yme
['roton. . scatt e r ing oE X- rays by 4
Q- s p ace
concept of 31- 3 3
e Efect oE vari ation in real
spare on 4 5
ceasurement of 33 -35
refineoe nt oE structu ral
mode1s i n 27, 1 31
\Dli ts oE 35
Quan t.1,lIII tlleory
neg1ect of 1- 2
of anomalous sc"tterinq 45
of sc:attar1nq by Al\
atom 40-41
e lectron 5

Iodex

Radial distribution function


definition 68
t.heories for liquid s 73-75
t~o-di mensional

ll~

Radi\l.s of q)'ration 60-62


Rayleiqh- I)ebye-Gans theory 14
as an eX4lIl1e oE tl'.e Boro
approxLmation 16
Ray1eiqh scattering 14
R.O.G. theory see Ray1eigh - Debye-Gans
theory
Re ciproca! lattic:e 121-129
Reciproca1 latt i ee llJ'.its 35
Reciproc"l spac:e 35 see also
Q-space
Refinement of s tructural mode1s 2 4
advan tages of Q- s p ace
re ofinelU'lnt 27 , 131
fu r crystals 130-131
for c:rystalline fibres 140
relatlonship of real s:ac:e refinement
te heavy atorn method 27
Reflection of X- ray a aee Bragq
reflectial, TotaITnternal
refle ction
Resolutlon 24-27 , 43- 45
atomc 145- 147
effect oE wa ve1ength 145
effec:t on
applieatioos 40
ehirality 28
10w reso1ution molecular
structure 43 -4 5
of a microscope 144-145
o f diffraction patterns Erorn a
crystal 129
crysta11ine Eibra 137- 139
Rotation als of sy~try 110, 131
matri x repn:-sentation of 131-132
Ro tation pattern of a c ry stal 125 - 128
re 1ationship to crystalline fibre
pattem 137
Rubber , X-ray diffraction Erom 66 , 1 38
Scale factor
a r isinq frcm not ma.\ng absolute
intensity measurements 53
i n Fourier inversioo 10
5catteri ng
an omalous see an o nao1 0 us seatterinq

of
eleetrcns see Electron diffractionJ
seatte r i ng
light see Ught diffractionl
scatteri n g
neutrons see Nel.1trCXI di ffractionl
scatteri'9
)(-rays ~ x-rays , scattered

Short- r anqe o rder 70


Siuu l ation o f X- ray diffraction
with l1qht 37- 39
Serew axis of syll!lfletry 1 31
in a erysta1line :ibre 136
Shapes oof IDOlec:ules see Holi.~cula r shape
Sc:earing 62-6 3
Smeetie organisation 115-111
50ft x- r ays 146
Soluti on
applicatioo oE synchr otron
radiati on 62
diff r ac tion qeometry for a 33
ideal see Ideal sol ution
inapplicabi lity o f Guinier ' s law
when conoentrated 58
of w.aerorr.olecu les 54-56
removal of smea r inq from
diffraction pattem 62-63
Space qroup 132
Sphere, Fourier transform of 4]
Spheriea1 everaginq o f diffra ction
data f roro
amorphous solids and liquids
33 , 52, 65
erysta.lline powders 137
g ases and solutials 33 , 52
Spherica l symmetry
diffraction geometry for
systems wi th ]3
Fou ri e r transforID of funetion with 11
measurlng diffraction p"ttem from
system wi th 35
of an atom and atcn.ic scattc ring
factor 40- 41
Patterson f\:lleticn with 56
Statistical crystal struct ure 139 , 1 40
Statistical o tests 87
Storage rin9 5
Structure factor
for an art:J:lrphous solid or liqui Cl 6 7
for a crystal 123
see a l so Interference function
Structures oE m01ecules see
Molecular structur e
SyQDEltry
causing absence o f
di ffraetion spots froID a
cryst.al 132-133
laye r Unes 110, 132
changes aecol!panying phase
transi tions 64
sea aiso Asymmetrie uni t , cent re oE
s ymme try , cylindrleal symmetry,
Meli eal sy1lll!letry , Rotlltion axis ,
Serew axis , Spaoe qroup, Spherical
symme try , SYlJlllle t ry eletllent

163

SyllllOe tI)' element 131


see ,,150 Centre of sylllJ:letI)' ,
Rotatlon axis, Serew axis
Synchrot ron 5
as X-ray sou r oe Eor investiqat.inq
solutlon s 62
Syst.emat ie ebsence 1 32
Temperature fact o r, f or a e rystal 130
Tetragonal c ryst a1 127, 1 32
'ltIermal vibrations in ocryst als 89, 1 30
'ltIree- dimensional crysta1 119-133
Three- dimensional lattice 1 19 -1 21
Tiltinq
effeet on me ri dional diEfraction
pattem. 84
of erystalline f i bres 139
'Iotal eorre l ation flriction 73
'Iotal i n temal reflectial , for
focus in q X-rays 2-3
T rial- and-e r ror !lIethod of phase
determ1nation 2 4
app l1 cation o f 11ght diffraction
37- 39
app11eatio n to
<!IIDO rphous so 11 as an d l1q uids
72- 73
c rystalline fi bre s 1 39-140
ideal gases 53
s t a t us of resulta 147
Tric11n 1e eryatal 122-12 3 . 125
Trlrication erren Ln Fouder
tran sfomation 24- 28
effect en
refinernen t 27
struct\l ra dete rrnin ation fo r
amorphous solids and liquids 72
gases 56
one':" dimensiOllal crystals 86-87
in microscC9Y 145
'l'Wisted n emat1 c 115
TWo-stll.rt h elix 110
Uniaxi al orientation 112
Unit cell 119
determination of e l cctron
density in 129 - 131
for crystalline fibre 136, 140
s ymrnetry of contents 131
Uni t cell coo r dinates 121
Vectors , properties of dot produc:t

80

Water
interference funetion for 69
radi al distribution funetion o E 69
X-ray diEf r act..Lon pattern of 66

164

[ ndel!:

Wavelenqth
effect en res o lution

L45

oE C! le ct raJs 15, 1 47
oE neuerons 15
cE X-raya
Lncident 2

scattered 3 , S
Wax , X-ray diffr actia1~il~t'J'I .Qf
W1ener-Khintchine thfKl;reil' 19 . --"
X-Ray crystallography
X- Ray l aser lB
X-Ray lens 146
X- Ray Illl.croscc:pe 1-46

34

1 19-13)
..

X- Raya

emission of

by acceleratinq Ch,rges 3 ;~."


from synchrotron s an~ "!;tt"orage
r i n gs 5
i nc1de n t en a spec1l!1en
cohe rence of 18

r ubber

stretched 136
UIlstretched 66
water 66

oollimation o 2 . 146 - 147


focuslng c f 2- 3
lJlOIloc:hromatisatlon a E

wave length 0 1'

2-3 , 47

reflect:ed see Bragg re fl ectlon ,


Tot al i n te rn a l reflection
sctlit t ered

absolut e i n tenslty cE aee


Absolut e in tens! ty lt2~re me n ts
anollal ous scat te r lnq see
An omal ous scatte r i ng- by

asse!lbly o f electrons

7- 8

lltOlIl 40-42, 45-50


electr cm ) - 5 , 45-46
IlIOlecule 42 - 45
al l o'" Q v alues 43- 45
protarl 4
s p he re 4 )-4 5

coherence aE

CODJItcfi effect Ln
polarlsatico oE .c:
quant U!ll theor)' of ~ Quantum
U1 eor)'
wa ve 1engt:h o f
3, 4
see also lC- R;ey diffrac Uon l

scattering
50ft 146
X- Ray d iEf r action/scattering
representatico b y a Fourier
t rans f orm 7-10
from M
amorphous soli d 0 1:" l1qui a 64-73
crystal 1 19 - 133
crystalline Ubre 1]6-1 40

___

caaTP~.

c rystalline powder 134-135


fibre (\oiith nematic orgBllisation)
llO-1l5
gla5s 64-73
hel1x 94- 110
ideal gas o r solution 51-59
Uquid crysta l 110-117
ene-dimensional c rystal 76 - 9 3
geometry of 31- )9
re1ati onship te microsco?y 142- 151
simulation of ~ith light 37-39
see also Low-ang1e lC- r ay diff r action
X-Ray diffraction pattezn of
a crysta1 of an enzyme 128
a fish fin - ray 117
ca1cium oxa1ate mi c r ocrysta1s 135
carti1aqe 67
a lesion in 113
paraffin wax 34

,."TV.C - S P

RllU.lOTE(~ ."

fig. IV.) .

X-Ray diffraction pattern of paraffin wax .

fig . VII . l .

X-Ray diffraction pattern of water


(taken by 0 . 5 . Hickey) .

~i9.

VII . 2 .

X-Ray diffraction pattern of rubber (unstretched) .

Piq. VII . J .

X-Ray dlffraction pattern of normal human


costal cartllaqe .

F1g. IX.l) .

X- Ray d1ffraction pattern from a lesion in


ag1n9 human costal cart1lage .

F1q . IX . 16 .

X-Ray d1ffract1on pattern from a fish fin-ray o

Fiq. x.B.

X-Rey diffraction pattern of a crystAl ot the


enzyrne 6-pholphoqluconate dehydroqenase , extrac ted fro m Iheep l i ver, obtained by the preceslion
Qethod (taxen by Dr. M.J. Adama ) .

Fig. XI.l .

X-Ray diffraction pattern of a micr o-crystalline deposit in abone marrow biopsy: the
positions of the ringa and their relativa 1ntensities showed that the mlcro-crystal a consisted of calci~ oxalate.

Fi g . XI . J .

X-Ray diffraction patte r n of str etched rubber;


the e-a xis was tilted slightly f r om the pe r pendicular to the inc i dent X- ray beam (taken by
K.E. Davies) .

~ig.

XII.4.

Electr on microqraph of a mica crystallite.


The bar represents a dlstance of 10 ~m
(taken by S.M.W . Grundy).

~ig.

XII.5.

Electr on dlffractlon pattern of a part of the


mica crystalllte shown in ~i9. XII.4 (taken
by S .M.W. Grundy).