Relatell
Ttdes o Jnterest
Book.
ASHBY
Dislocatlon ModeUlng of Physical Systems
BATA
Advances In Uquld Crystal Research and Apphcations (2 Vals )
CARTER
Preface
HOPKINS
The Mechanlcs of Solids
KRISHNAN el 01
ThermaJ Expanslon of Crystals
PAMPUN
CrystaI Growth 2nd edition
TANNER
Xray 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 Xray 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 Xray 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 Xrays by isolated a toms a nd molecules .
In s~
aequent chapters the ~ay9 l n whlch interference oodifies the pattern oE scattered
Xrays, 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 Xrey d i ffrac t ion pattern .
The final chapt ar demonstrates t hat tha lnterpretation of Xray dlf f r act i on pattern s i5 s imply an application o E physical opt ics.
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 Xr ay dlf fractian
patterns, thelr backg r ound s are likely to be very dlf fe r ent.
The technique o f
Xray 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 postgraduate 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 Xray 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.
BiBLI"TEL'.\
_ _______________________________________. _
L~
. ~
~(L~O~~
~~
_ I
Preface
SI units are used throughout .
Units can cause confusion when comparing f ormulaa fer the intensity of Xraya 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 WoodheadGalloway 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
1.2
1.3
1.'
1.5
1.5
CHAPrER Il
,
L
3
4
5
6
ILl
II . 2
IL 3
II .4
ILS
Ir.6
Ir . 7
CHAPTER III
Introduction
XRay beanas
Polar ised Xray s
Unpol a rised Xrays
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
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
54
54
Int.roduction
Ccn t inuous helix
Discontinuous he l ix
1obl ecu1ar helix
Ne matic organisation
SmecUc organisation
SUl!lIIlary
THREEDlMENSIONAL CRYS'IALS
x.l
x.2
X. 3
4J
45
33
37
CHAPTER VIII
31
31
OfAPTER VII
Int:roduction
EloIald sphere
Qspace
5illlu1ation by oplica! diffraction
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
XRay 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.
known 9Ubstances.
XRaya are scattered by the eIectrons in matter; t his chapter deaI s with these
aepects of Xra y seattering by an electron which f oem t he foun dation f or the &naIysl. of Xray 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
>
>
"'Zw
>Z
Fig. r. 2 .
rS4 PM
Fig. 1.1 .
good agreeme nt wi t h quantum mechanics and , more importantly , experimental obser vati ons.
1.2 . X Ray beams
In this book the Xray 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 Xrays produced by a t ypical generator , with a copper anode , as a function o f wavelength.
XRays 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 Xrays
with a s heet o f a suitaole metal foil  nickel in the case oE Xrays 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 pioholes which ,
typical ly, have a diaceter of around 100 ~m.
Details of the appara tus used for Xray 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
xrays usi ng e ither of two different methods.
One expl oits the total internal
r eflection o f Xrays i n air at suitable sur f acesl t he glancing ang le at a glass surt ace f or copper 1<0. Xrays 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 Xrays 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 Xra 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 zaxla and the ya xis i5 defined so as
te form a right  hand ed Cartesian coordlnate system.
The apparent azrbiguity in the
defl n ition of the zaxis (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 zaxis
with the same fr equency as the electric vector of the i ncioent Xray beam conse quent l y it acts a s a source of Xrays 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 zaxis) , 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 1019 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 Xr 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 Xraya 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
makes an a ngle 'z with the zaxis ~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 Xray diffr<!lction ana1yA conventi onal Xray . generator produces unpolarised Xrays 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 Xrays, also produce plane polarised radia t ion ; the Xrays 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 Xrays 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 Xrays , 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 Xraya
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 Xray bearn.
lbeae scattered
Xrays 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
Xrays 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 xrays
lf the incident Xray 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 nonpolarised.
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,
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 )
beam i6 scattered by several e lectrons, ther e i s a de f inite phase relationship bet ween the scattered waves ; Compton scattered Xr 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 Xraya 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 Xray 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 Xray 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
CHAPTER
[J
11.1. Introductlon
If Xray 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 Xraya coneerns the distribution of electrons since it is the electrons
in aattar which acatter Xrays.
50 far only scatterLng by a single electron has
been considered.
When an assembly of electrons scatters Xrays , i nterferenee
effects are llkely to occur .
lt is the se lnterference effects which lead to the
features of the diffraction pattern.
1[. 2.
&
2.
is defined by
~)
( H. l)
~ .2.
Now lf there were only a single electron a t P the vave scattered by the
vol~
XRay Diffraction
INCIDENT
8EAM
SCATTEA:EO
6EAM
Flg . II.l.
Scattering by
<'.lo
body.
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 Xrays 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
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 
(Il .4 )
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
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 Xray 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
F ( ~)
sin a
XRay 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
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.
"'"
02
Fig . 11 . 3 .
lE equation 11.6 defines F(g) as the Fourier tcansform of p{:) , then the
~n
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
dQ
(11. 7)
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
threedimenslonal 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~
A cos o + i A sin a
but here F(Q) i5 real so that
A sin a
0=
X Ray Diffraction
12
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 nonzero only at a
.. t of polnts.
Figure 11.5 ShOW8 a twodimensi 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
Jo'"
(1I.9)
Jo . ln equation 11.9, ls the zeroorder 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 
mo
( _ 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(!.) ..
J
s
(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 Xray 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 Xrays, 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 Xray 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
Xraya .
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]
dr
( II . 13J
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
XRay Di ffracti on
14
 no)
(II.14 )
).  h! (mv)
(Il . 15 )
whe re now v is the roo cmean 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:.
F(~)
v(!..) exp
(L
!:2.)
dr
(I I.181
16
XRay Diffraction
a dtfferent aet of constants has to be used f er Xrays , 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
RaylelghDebyeGana 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
no
11. 7. 5lUlmary
I nter feren ce effects occur bet"'een Xrays 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 Xray 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 Xray 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 theposi tions o f mol ecule8 .
XRay 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
XRay DiffractLon
p (!:.)
!oR.'
dQ
f,
(III.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
tvedimensional 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 Xray wiI:!Ive scattered in the directien speclfied by
.Q. .... hich c an .be obtained.
Hence the phases of the scattered Xrays are lost IoI'hen
a diffraction pattern i8 recorded .
This loss of phase information constitutes the
socalled "pha8e problem " of Xray 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
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 Xray 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 .
P(!.l)
"(~ + ~l)
dE..l
iIII.2)
P(!..)
f
,
I (Q) ex.p (  i
!: ~) d~
(III.4)
d2.
[eqn,II.5)
The final line is a property of the inverse transform of F(2)F (~) known as the
WienerKhintchine 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 electrondense 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 Xray 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 Xray 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.
over a range of Q
l.
2.
Calculate
3.
4.
P(~)
from
I(~l
2.
5.
6.
Calculate
7.
8.
F(~l
TABLH UI.2.
IncrelDent 2,.
2.
10.
lf
11 .
12.
1 11. 1.
repl acement~
I ( ~)
1..
2.
3.
4.
5.
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.
using equation
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
9.
21
F O (R.) .. F (Q.)
F H (SlJ
B.
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~===:~~
.. j
(i
r Q) dr
"
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.>
..
XRay 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
(111.5)
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~~~Lf,.0~~~~15
Q(""'t ) ~
(r)
cos
(1:: Q) de
(IlI.6)
Fl g. III . 2 .
An
10
o
05
Figure II1 . 2 shov,s the onedimensional 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 Qaxis 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
Fi9. r ll.3.
~ oooa
.e
23
24
25
The problelll wit h all deductiva l3ethods of solving the ?hase problem 15 that
[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.
02
20
15
 o
10
0'5
' 5
20
r~
Pi g. III.4 .
Square peak.
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
15
10
05
50  4 O 3 0
20
3 0
4 0
Q~
The an.wer to this que.tion wll1 be illustrated by a si~ple oned ~nsional &xaaple .
Piq. III.5.
50
2.
XRay Diffraction
27
o
0.
C'
~
Q.. 0"
02
20
 15
10
 05
0 5
'0
'5
20
r~
FiC}. 111 . 6 .
QoS
:
~C>6
'"
0.4
<>2.
2<>
+s
FiC}. 111.7.
o.,
Qos
zo
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
'0
C~;;,.A
os
e
o
B
1 0
r5
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.)
exp ( i
!.: 2.)
dr
( III. 7)
.. F" (2.)
by a
thls
Fig.
p(r)
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 Xray 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 squareplanar structures are
both achiral ie. they ~e identical te their mirror images.
Thus the structure
can be solved Wl4llIbiguously.
However each subunit consists of a pol ymer chain
wound lnto some specific threedimensional 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
y* (2.) e:xp ( i
~ R)
The result
dI(
(eqn.llI.71
1",, ""
f.
<
exp
(i
!.:~')
dQ.'
,,,..  '"
"'p(!.)
[eqn . l1I.ll
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 upsidedown 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  anderror.
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 rialande 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 (.!.)
XRays 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 Xrays 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 Qspac: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 Qspace  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 onedimensi 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
XRay Diffraction
32
Diffraction Geometry
33
I(~)
and
F{~).
that I (~) 15 capable of existing throughout the whole of this same Q space . Thus
there ls a distribution of intensity which exists in Qspace , 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 Qspace .
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 Qspace.
But ,
as we shall see , not all of Qspace 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 Xrays 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 NTo_t~Io...::"l\<i?:_~~O'
BEAM
Fig . IV . l.
Ewald sphere.
I NCIDE.NT
&EAM
';oj~~'F_.;.,c17J_j
.
O'
IV. 3. Qspace
"\PIIERLC,',L
SUR~ACE
1llROUGII
POlNT5 IN Q SPACE "'ITH
THE 5AME VALUE Of g
EWALO 5P'ilERE
Fig. IV.2.
Diffraction
geo~etry
for a sphericallyaveraged
scatterer.
35
Diffract i on Geometry
34
FILM
,/
C
SPECIMEN
INCIDENT BEAM
Fig . I V. S .
F1q. IV.).
C'(lINDER AX l5
~oJ<::::::b':"""""
INCt DENT
8EA""
Flg. lV.4.
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
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 )
lf R 19 t he dis
(IV .1)
UElIX AXIS
( x !R) J
R can
(IV . 2)
INCI DENT
DIRE CT JON
froa a
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 Qspace .
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
Qspace 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
Sspace or nspace) .
 >"l, >JI
SEA ""
pattern.
Flg. IV. 7.
~~TECTOR
XRay Oiffraction
39
39
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.
Fig. IV.9.
~ical
4l
CHAPTER V
V.l. Introduction
The wavelengths of Xrays are of the arder of the distances between ato~s i n
molecules ego copper Kn Xrays have A ~ 154 pro and the carbontocarbon single bond
15 also around 154 pm long .
Thus, if data are col1ected to sufflciently high Q
values, an Xray diffraction experiment can provide information on the arrangernent
of atoms in molecules.
XRay 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
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 Xray 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
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 XRay 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 Xray dlEEraction patterns when a
chiral structure is to be distlngulshed from 1ts mirror image.
(V.l)
'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)
"
f (Q) '"
(Qr l :jr
ev. )
>u(:;> er '"
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 Xray diffracti on data
from a suitab le systec .
V.4. Mo l @cules at l o ..... resolution
F(Ql ..
F (~)
.,
fj (Q) exp
(i
~.2)
43
4n r 2 " si ne (Qr) d r
'" (x )
Thi s integral
(V .S )
jo ,
FeQ )
., n t(Qa }
(V.6 )
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 Xrays scattered in the sama direction by different parts of
the sphere.
As this simple model fer the molecular transform ignores the fact
EUS
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 Xrays 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 Qspace
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.
os .
,o
"  ... .. ..
',5
2 0
o
Fig . v.3.
(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 )
XRay
46
D i ff ~action
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
w~
z = (e/m) Ee exp (1 w t)
2 
t )/(W~
 w
+ i k w)
(V . 91
The r esult
(V .IO)
\5
(V . l l )
2
2
2
Cw J (w _ w + i
k wl
O plotted against
lncident Xrays 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 Xray 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)
The i ntens ity oE the Xraya 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
.how.
4.
~Ray
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 Xray 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 socalled ~Kedqe" i9 the close5t to
the X ray wa vele nqths used for diffraction experiments.
Also A.o , for the Kedge,
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
~
]J ,
iJ
;;:
49
DiffractioD
::1
o.z.
00,3
WA,VE~GTW
Fiq. V.S.
004
J\o_l49pm
Absorp~lon
( f'I"')+
NIC.KEL
l54pm
Flq. V.5.
Filtering copper
WAVELf.NGTM :JIoo
fe lO} .,
Xrays with nickel.
f{Q}
(V.15]
XRay 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.
f eo)
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 .
V.7 . SUlUDary
The resultant Xray 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 Xrays 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
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 Xr 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 Xrays 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 Xrays scattered, i n t he same directlo n, by diffe rent parts
ot the same solute molecule.
8ecause interference between Xrays 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
KRay 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
(VIol)
k
~here
L L
fj ( Q) fk(Q) exp
(i
!1k Q)
('11.2)
bet~een
LE
N {
f~(Q}
+ 2
L
>
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
(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
54
XRay Diffraction
'OOr~
55
___
'or""';::::                WATER
10
10
15
05
.20
Flq. VI.l.
10
1 5
20
0 r~~~~~~
Q (.",1) iI>
PROTE IN
Fl g. VI .2.
l1ne)
(VI. 4)
., 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)
roolecules do not interfer e with those scattered by othe r solute or solvent moleeul es .
Cle~rly intarference with Xrays seattered by other solute molecule s wl1 1
be neqligible lf the salute ls suffl ciently dilute.
But how can interferenee
wlth Krays 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
XRay Diffraction
57
falls off fair l y r a pidly, in the region of Qspace 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 Xrays 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""
(Qr)
dQ
(VI. 7)
o+~5~~,O~~~~15~c
20
Q 4
Fig. vr.3.
__
scale )
XHay Diffraction
58
59
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 enedimensional .
I
AlU'
+ 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
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 .
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)
'"
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

(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)
NF
[eqn . VI.5]
[2)
2 2
NP v exp (1(0) exp (
Q2G~)
, ,)
Q
G
(eqn. V1.17]
(VI.18)
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
2
+ G
p
q
(3 / 5) 1: a
Sph ere
Radlus a
Ellipsold
Semiaxes a, a and ya
Long , thin r ed
Length l
Random coil
Meansquare endtoend
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>
el
61
X Ray Oiffrac ti on
60
distance
{ (2 + / ) / S}I:! a
.l/121:!
~) ~/6~
(eqo. VI. 19 ]
leqos. VI . IO a nd VI . 15 1
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
> 
c:;1
(VI. 22)
>  G /3
~u l ae
a,...
10
'H
~.
~+
oz
1(0) ., M,2
0 '5
10
2.0
15
Q,(nm I )
.
Fiq . VI . 5 .
62
T {D(~)}  T {I( ~)
T (I(~)
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 Xrays 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 Xray beam as possible.
Synchrotrons are increasingly
beinq used as intense Xxa y sources for investigating solutions but the more traditional approach is to use an Xray beam with a large cross  sect iona l area .
Haw does i nc r easing t he crosssectional 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 crosssectional a r ea o f the X ray beam is a lso i ncreased.
Thus, although
the Xray i ntensity per uni t a rea i s l imited , the total lntensity can be increased
by using a bellO with a larger crossseetional 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 pinhole coll ~~te d Xray beam meets t he detector at a paint  but a beam
with a larger cr o sssectional 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(~)}
vh1ch is simply
(VI. 25)
VI . 8. Summary
In an i deal gas lnterfe r enee betwee n Xrays 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 Xray bell.lll of larqe cross sectional area may be used, in stead of a p inhole 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.
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 Xray diffraction patterns from both liquida and amorphous solid5.
XRay 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
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
64
L L::
j
(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 Qspace , 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
66
Fig. VI I . 3 .
67
lf tne gas consists of N identical molecules, this equation can be simplif ied ta
Fi g. VII .l .
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.
sine (Qt"k )
(VIL3)
69
68
The secand line f0 1 10...5 froro the f i rst since N and (N  1) are essentially the
'"
Sr /V } g(r)
s (Q)
1 + no
2
411 r g(r ) sine (Qr) dr
02
(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
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
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.
X Ray Diffraction
70
1 (Q)
NF
l O.
5(Q) '" 1 + no
(VII.6)
4n
{g(t)  1)
'l'"
(Q1S (Q )
sine (Qr) d r
'"
~41ues
~,
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)
Fig. VII.6.
ro
12.
o.~_
20
"
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.
"
Fig. VIL7.
lICDOS
14
XRay Diffraction
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
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?
72
(r)  1
(l/no)
(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 Qspace 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 Qspace 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 trialanaerror.
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
XRay 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)
(  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
XRay Diffraction
TABLE VII.l.
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
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. longrange attractive
termo
Long range forces do not appear to contribute much to the structures of
most liquids  although for water, longrange 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 .
77
e  AXIS
CHAPTER VIII
.....
.. ...
Onedimensional Crystals
VIII.l. Introductian
A crystal i s a salid with a regularly repetitive structure.
As in any solid ,
interference wi ll oceur between Xrays 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
lAYE Il
76
Onedimensional crystal .
Figure VII I.I shows a sehematic example of a onedimensional 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 threedimenslonal 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 eaxis 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.
,.
XRay Diffractton
"
'(2) .,
L:
exp {l
!..:12.1
(VIlI . l)
jl
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
vector~.
'(2)
+ exp
30
i z.o
G
~
(O
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 Xrays scattered by the crystal can now be calculat ed.
4"
Q.C _ _
,in (Ns 21 2 )
., eKp
Since
~ IIJ
.,
(VII!.J )
where PCR'
sin
(~.212)/sin
(~.g2 )
4n
1T
Q.C _
(VIII.4(
N = 50
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 Qspaee;
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.
X Ray Diffraction
80
CA ( S
1
1.1
,,<L '
,:::
onedimenslonal
I+   ~
~::.
 .
"'",
Fig. VI I I.4.
The
(, AXI S
"
E WAl D 5PHERE
81
,.,
2 ~c
'!.
BEAM
\ 2 ., O

"
But
Fi; . VI II . 5 .
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 nanzero anl y on these planes, lt follo,",5 from equa t i on
VII I.4 , ehat I( ~) too is nonzero only an them .
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
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 Xraye ls incident at rlght angles ta the e  axis of a onedimensional 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 nonze r a only o n a set of planes ,
sp&ced 2~/c apart in Qspace , 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 ea xis, and therefore perpendic ular ta the equator, i5 called t he "mer1dian" .
In Fi g. VIII.5 t he e  axis of Qspaee i5 de finad to be paral l el to the eaxis
of real space, naturally 1t passes through O the or i gin of Qapa.ce .
The planes
on which I (2.1 is nonzero are perpendicular te the eaxis and, therefore , te t he
t axis .
The t th plane of Qspace crosses the caxis at a dls t ance
(VIII.61
82
TABLE VIl I. l .
83
(t . C) coor dLnates tor a fla t film Ferpen dLcular te t he lncident X ray beam .
E""'''LD
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 nonzera.
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 taxis.
{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 Qspa ce on a flat fil~.
OOnsiderable trigo nometric manipulati on is required to relate the components in Qspaee to those on the film  see Volume 11 oE
the "International Tables for XRay 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 nonzero 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 Qspace uslng equation IV.2: t hey can then be equated with t oE equation
VIII. 6 in order to determine c.
10
10
15
XRay Diffraction
8'
85
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 nonzera 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 onedimens 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.
can be c alculat ed
fr~
~axls.
01. ,

",here
(1;/2)/(2,./),)
(VI II. 7)
(V I n.S )
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 eaxis.
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 Caxl 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 onedimensional 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 onedimensional crystal being amp l ified a l ong certain p l anes of
Qspace 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 eaxis .
'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)
86
XRBy DiffTBction
OoeDimensional Crystals
tal, 15 given by
F
(tl 
1 p [ Z) exp
(2'1111z) dZ
(VIII.ll)
Note chat point s 410ng the eaxis , where P (2) 18 nonzero , 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 eax is and on the plane vi th l _ O.
lf e 19 large , the eaxis appears on the meridiano
Since I(~) decreases rapidly ,
in lntensity, off the eaxis , 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 eaxis direction , p(Z) ,
can be deduced from a l owangle 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:
Q 2Tillc
E'{tl exp ( 21'Tiiz)
p(Z) 
(V IIL 12 )
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
,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 Xrays 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 Qspace 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
(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 Xray
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, onediDIen s lonal cryatal.
Let the
rootmean 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
XRay DiCfraction
B.
e AXIS
ef the speeimen .
No more energy ls absorbed: Xrays 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
onedimensional crystal .
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 eaxLs 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 onedimensional example of mosaic spread  a lthough i n the onedimensional 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 caxis 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 Xrays scattered by different crystallites are negl i gLble.
A priori we might have considered a naed f or
both intra and intercrystal11te ~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 rerystallit 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 intererystal lnterference function wi ll have settled
to a val ue of unity for the region of Qspace i n whi ch i ntraerystallite Lnterference effeets are observed"
Since intercrystallite 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 Qspace.
For a per fect onedimensional crystal the distribution oE
tLlts ls inf1n itely narrov ie. there is a unique e  axis as in Fiq . VII I . l.
lf the
eaxis 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 Qspace 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 Qspace 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.
X Ray Diffrac t i on
90
SURFACE DEFlNED
BY 9 VECTORS
eECTION OF
E'W'ALD
:;;<1.
91
SPH ER
CURVE O N
WH ICH SURFACO:S
INTERSECT
"
o'
Suppose a vector
2.
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 Qsp4ce, 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 Qspace . this lntensity ls actual1y spread over a vol~ e f
Qspace  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
ospace , over Wh1ch the lntensity assoclated w1th the peint P is distributed,
'2
XRay Diffraction
intersects the surface over an area which subtends a solid angla 01 Q at O, the
'3
e of
Q6B
Thus the v o lum4! eLement in Qspace which pa sses through the surface of the Ewald
sphere 15 given by
6V .. (2'11/;\. ) 2 60 Q6B
cos (1jl/21
(VIII. L7)
~)
and VIII.17
(VIII. L8)
'!'he rotatlon allow5 the 1oO'hole volume of Qspaee, 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
(VIII.20)
since the Fourler transform, F(21 , multiplied by its eomplex conjugate, gives the
total i nten sity over thLs volume of Qspaee.
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 Xray wavelength.
The Lorent... factor ceon be calculated from Q
by usinq equation [[.4 whieh relates' te Q.
95
HELlX MIS
1
CHAPTER IX
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 onedlmensional
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 cnedimensional 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 oned 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.
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 onedimenslonal 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 onedimensi onal crysta l , its Fourier
transforn i s nonz 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 Xray 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
XRay Diffraction
96
(: .. (0
F igure
IX. 2 defines the Carteslan (x ,y,z) and cylindrical polar (r,e ,z l coordlnates which
can be usad to describe
2 + S2) "
en to a plane perpendicular to the hel1x axis (the zaxls ) 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 Qspace delinad by the vector~.
The ~axis of real space and the taxls oE
Qspace are defined to be p5rallel as ln Fig. VIII.6~ the direetion ol an Xray
beam, which la incldent at rlght angles to the helix axis, could be taken to de fine
the directlona ol the xaxis and the aaxis.
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 aaxis is parallel to the xaxi s, the ;  axis ls parallel
to the zaxls and, consequently, the Saxis 15 parallel to the yaxis, lt lellows,
from equatLons IX.l and IX.2, that
(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
~l
2w.tz/p} d z
(IX.6)
Now that the Fourier transferm 1s nonzero 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 Qspace aneS are perpendicular to the zaxla 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 nedimenslonal 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
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
XRay Diffraction
9.
we now make the substitutlons
x
*' 
and
~r
2wZ 
'JI
2 ..
n =7
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
n=6

n =5
/"',
where JnlX ) 18 the n th arder Bessel function of the fir st kind, definea in equation 11.9.
n =4
/'.
sinee
exp (iln/2)  coa Ctw/21 + i sin (tn/21
whlch has the same value as 1 i
n =3
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)
n=1
!\ ~
(IX.S)
ThU8
On eaeh plane aE Qspace 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
cA
10
Fiq. IX.3.
20
+
99
100
..
____....... S
CA
1
2
OA
__ .
~._~=
~._
4ft
A.
.,AA . .,
o
1
2
3
AA.
.4
eA
Fl q. IX.4.
l (C,!) for
t _
4ft
*.
~
As
CA
101
continuous helix.
Figure IX.4 shows the intensity, I (( , el , in 4 section of Qspace which contalns the eaxis.
The threedimensional 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 nonzero ..... hen X equals zero . Phys ically the diffraction pattern must have nonzero 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
zaxls.
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.
, ,.
/
XRay 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,
20/p
'f
? E
INTECRAL
NON INTEGRAL
F'lg. n.1.
XRay
104
Dif f ~a ctio n
105
n " l ... 4m
0, 1, 2 
TABLE IX . l.
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 
l.
(f  Nm) It
'"'
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 nonintegral 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
XRay Diffrac ti on
106
1,,
7
4
3
2
O
1
2
3
4
~
,
7
6
INTEGRAL
Fiq. IX . a.
,,
2ft/<.
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 subunits.
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 subuni 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
NCHINTEGRAL
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 Qspace; therefore, a discontlnuous helix only yields nonzero intensity a10n9 t h i s axis at lnterval s of 2T/q in
Qspace .
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 Qspace , 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 nonintegral helix ) .
SO far
ve have ignored the hand of the helix.
Either helix in Fig. IX. 7 could b e rightor 1efthanded, 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 subun i t s , then a subunit 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
Jn( ~ r)
(r) exp { i
(IX . l2 )
n ( rp + n/2) }
n
x
Jn(~r ) exp {
n(~ +
nn)}
cj
+ 2I1 t /N
rj
j
0j + 2 (2nt/ N),
cj
ej +
J (211t /N) ,
Zj +q
Zj + 2q
Zj
+ 3q
l 06
109
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 ahelix 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 ohelix ,
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 Xra y diffraction pattern.
Fiq. IX.9.
Poly L~lanine.
By
would be
F ((, v , l) .. !(Q)
(Er) exp i
(IX . 13)
n(1/I + ,,/2)
TABLE IX . 2.
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)
(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 onedimens 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 zaxis .
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
+ lr/2) ... 2T l
z / c}
( I X.14 )
110
XRay Diffraction
"'FOLO AXIS
2FOIJ) AXIS
*e
f
Fig. IX.LO.
Fig. [K. Il .
Nematic organlsation .
AA 4ssembly of u
l el" chains, ",here both point in the same di rection , o r socalled "anti  par./lllcl "
chains, like ctlA. which po1nt in diEfe r ent directions .
IE the constituent chains
of a ustart hel1x are pa.u.llel (as opposed to antiparallell, they may be r elated
by a ufold 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 ustart
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 Qspaee, as a result of
symmetry in real space . is a eornmon feature in Kray diffraetion by crystals  and
onedimens i ona l erystals are no exception .
In particular iE the parallel chains
o f a u start helix are rel ated by a ufold 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 Qspaee.
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.
111
112
113
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 Xray d iffrac tien pattern wilI no 10nger be spherically averaged.
In ~y systecs the l ong axes of the r odshaped ~olecu l e5 Are reasonably perallel but the molecules have random r otat lons about these axes.
Furthernore there
need be no r egular sidetasid e spacings between molecules le. although they are
oriented , their urangenent la not c rysta lllne .
Then t he structure projected on
A polymer chain, 11ke polyL 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 odshaped IIIOlecules "'hich a r e oriented,
pointinq rando~y up and down, with no regular sidetoside 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 zaxi s and the taxis i5 parallel to it in Q space.
A
(~.l
f r~
>
( rX.1S l
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)
XRay Diffrac t i on
114
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 twodimensiona l in s t e ad of threedlmensi 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 Qspace ~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
116
XRay Di f fr act i on
117
i
+x
Fig . 1)(.16.
Fig. IK.14.
chapter .
Figure 1X. 16 ShOW8 the Xray d i ffra c tion pattern froro a system vhich reseobIes Fig. 1X.15 in having a l arered structure but no regular Sidete  side arrangement of molecu l es .
apart in Q space.
e  AXIS
1111
IIIII 1
111 1
F iq . 1X . 1 5 .
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 Qspaee, perpendicular to the ineident Xray beam, and so the intensity
distribution along the eaxis 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 Qspaee, 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 onedimensional crystal .
I X. ?
SlJIDI[Iary
118
XRay 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 Qspace , 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 Xray beam for a point on the ~ ax is to
appear on a diffractlon pattern .
CHAPTER X
Threedlmenslonal Crystals
X.l . Introduction
A true cryatal has a atructure which is repetitive in three dicensiona.
Extan.ion ol the theory ef diifraction by onedimen.ional cryatala into three
dimen.iona ia all that is required to underatand the diffraction patterna froe
cryatala  i n princip1e .
I n practice Xray crystallography involve. speciali.ed
tachniques and haa aome of ita own jargon .
Tbie specialisation ha. ari.an because
Xray 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 Xray cryste1logrephy has ateracted far more attention than any other
application ef Xrey 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 Xray diffraction data froc enree dimensional crystals .
lt ie only intended to ~ive a sketchy account of Xray
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 Xray 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 threedimenaiona l l attice o f
peints_
The figure actually demonstrates the propert ies o f a tvodimensional
crystal  the bebaviour in a third dimension ia ioplied by that in the other two.
This simple approach to explaininq the properties of threedimensional 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 threedimena ia"lal lattice ia Oefined by three vector s , a , b and c. aa shown
in F'ig. x.2.
In the onedimenllional can of Section VIII . 2 , thelattiCe 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
ThreeOimensional 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 )
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.
!! >
.. . ,.
1'1; . X.3.
121
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
ThreeDimensional CrYltall
(Il,I)
el
~.
when rlq.
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
Qapace , O'.
Figure X.4 ahowa a twodl~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 
w.
(2, ')
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
onedimensi onal lattlce, ol effeetively infinlte extent , all have th a~ h.lght.
eon.equently the value of the Fourier tran.fora of a threedimensional 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
nonzaro .
Note tlu.t
Icb* + t~*
 ( Ih!,*
..
kb* ...
(x . 6 )
where the 8\lJ11C4tion haa to be t aken over all the atana ln a unit cell.
Now the
Fourier traoeform i, only nonzero at those pointa in Qllpace 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
ThreeOimensional eryatals
XRay 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
Fig. x.5.
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 Xray heam.
The cylindrical polar coordinates (~,*,') of a peint in
Qapace 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 Qspace 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 "caxis". Accordin; to Section II.4 F(h) and, therefore, I(h) are rotated abcut the paraUel
eaxia of Qspace.
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 Qspace
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 SPIlERE
a,ob,oc
(I6y90"
eAXIS
Flg. K.6.
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 caxis so that lts Fourier transform ia rota tea
&bout the parallel eaxis.
For an orthorhombic cell c la parallel te c le. it is
coincldent with the !;axia.
The eaxis 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.
l.IOGRAPRY Section 2) .
.1
12 T
(1' l O.'
."
ao
0. 1. 0
0,1,1
0. 1.1
l Ioz;
Fiq. X.7.
"
,,~
lo.l
o.u
1.2.2
0,0,0
10..,0 ",O
2.0 1. 2.0
~""
cU,i
2,0.1
Ql.l
2.0.1
,lO
(lCIO)
c*  2:1 / c
 le'"
~ .. l~t Ql '
~.l
2rr/e
b*  2rr/ b
127
XRay 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
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 Xray 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 erialanderror.
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
".
IhreeDimensional Cry8tall
"8
tOQ
.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 .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 Qap&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 Qapace, 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
Xray wavelengtha qenerally used in diffraction experimenta.
Prota1n cryatal. are
u.ually imperfece, in the sena. deacribed in the onedi 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 Xray 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
XRay
130
D i ff ~ act ioD
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 XRay Crystalloqrapr,y".
Fina11y , if very aocurate r esulta are requlred, 4n absorptlon oorrectlon must be
applled.
This correction recoqniaes thAt Xray 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,)
h.'!:I
131
0'1
.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 riqhthanded 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
ufold .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 2fold
rotaclon axi. a. an .xaepla .
If th. j eh atom in a un1t cel l ha . fraccional unit
c.llooordinat (X" Yj, Zj ) ' a 2tol 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
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 baxe . 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
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 ceaeof P (h) the aummatlon 01
which la
o
1
O
133
I h reeDimensional Crystala
~j
 1
Actually no other comblnation of values for a , S and y is compatible w1th the only
aymmatry alemants of the unlt call be1ng three, nonparallel 2fold rotation axes .
Then the unit cell must haye autually perpendicular edgea Le . its shape ia orthorhombic ( a~c ) , tetragonal ( a~c ) or cubic (abc ) .
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 utold 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.16nead 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 Qspa 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.
135
CHAPTER XI
XI.l. Introductlon
Flg. XI.l.
The a1m of thia chapter le te d.scribe the Xray 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.
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 microeryatals 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 threedimensional 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
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 Qspace 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 Qspa 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
XRay Diffraction
136
137
Fiq. XI.2.
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 eaxes.
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
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 eaxis, 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 eaxis, 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 eaxis 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
XRay Diffracdon
De
139
tion pattern.
Flq. Xl. 3.
the eaxis vas tilted s lightly from the perpendicular to the lncident Kray beam (takan by
:l.E. DAvles).
Flq. XI. 4.
Fiq. XI.5.
140
XRay 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 talanine 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 trialanderror 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 1eftbanded
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 ghthanded 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 rialenderror 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 .
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 Qspace, 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 caxes are defined by the axes ef the helLcal polymer chains.
Crystallites have randam rotation~ about their caxes ; 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
EYEPlfCf 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 Xray 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 Xrey d iEfract l o n analysis.
~rmation
",'"
'"
",
,,'
,,',,'
":",
"
X
S'
Fig. XII . l.
~I
, ,~
"" ,
,"
,"
,"
,","
"
'.:
Or.JECT
~
) CO"DE"~ER LE~
\
1,
,5OUIICE
( VIRTUAl.)
I~GE
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 Xray 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 Qspace 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.
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 eyepiece
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.
This .ame extent of Qapace 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 darkfield"
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 darkfield microscope.
Figure III . e
ahowa that the darkfield 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 darkfield 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 Qspace
which lie s en tbis spherical surfa ce is used te syntheaise an 1maqe of the ob'ect.
It aplane sectlen of Qapace, 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 Qspaee 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 Xrays (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
146
DI "AALTI OH PLANE
={j~~::==================================~I~to DIAMETER
"AM
..
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.
141
,.6
X Ray Diffraction
Re l ationshi p t o Hi c r oacopy
PROJEC.YOR LENS
O&JEC.TlVE LENS
Fig . XI I .4.
Fig. XI I.S.
OBJEGT
CONDENSER LEN5
SOURCE
Fig . XI I. 3.
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 eyepiece 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.
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
X Hay Dffraction
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 Qspace , 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
151
The abi 11ty to form an image qives electron diffraction an advantage over
Xray 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
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
App lications~ ,
McGrawHill.
l . Introduct1.on
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
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.
2 . General
R. W. Jan;es, '''The Optici!ll Principies of the Dlffraction ef XRays", Bell,
London ( 1 954 )
The best single source 01 lnformation en the underlying physics af Xrey 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.
A use fuI sour~e DE inforcation on Xray diffraction theory; its approach i9 more
rigorous than that adopted here and more topics are covered.
B. O. CUl l ity , "Eleme nts of XRay OiEfractlon " . 2nd ed., AddisonWesley,
1.oOOon (1978)
Detalled accounts oE many applicat i ons oE Kray 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 XRay 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
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 Kray crystalloqraphy 
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 XRay Diffraction Problems", Bell, Lcndon (1964 )
Glves an account of the methods used to s~late Xcay 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
threedimensional crystal.
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 . ,
ti,
Gives a use fuI account cf the intensity of electromagnetLc waves useful for making
the simpLe approach adopted in this book more rlgorous.
(1974)
Gives a cleAr description of the various kinds of liquid crystAls and a detailed
account of their preperties.
Chapt.er VI
12 . Chapter
M
,
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.
Bibliography
l5.
oE
~ethods
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.
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
134135
Chirali ty
1 15
Coherence
cl in cident Xraya 18
of seattered Xrays S
see also )[~y laser
Collagen . as exanple of o riented
polymer 114
CollimaHo n 2 . 146147
ef f ect o f n cnpin hole
CO!llton effect 5
62
1213
decoovo lutiCl1
63
generation o f
crystal structure by ll9120
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
Crosscor: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 29131
disorde red 87 89
for f ocus i ng xrays 3
identlflcation af unknown 1 , 1 7
Lnperfect 8766 , 89 , 130
monoch r o mato r 3
mos aL c 8990
ooe dimensicnal 76 93
s yame t ry 131 133
three d lnens ional 119  133
159
I ndex
01 soontin uous he1ix 10 1106
gene r lltion of a oolecu1ar
he1i x from 107
Disorc1e r ed crystal 8789
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'Osta 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 l416
of Xrays 5
E1ectron
X r ay emissiCll from accelerated 3, 5
Xra y scatter:lng by an
asse lltlly of e 1ectro n s 7 8
a 1ectran in an a t o e 404 2 , 45 ~50
s ingle e 1ectron 3 5, 4547
Electron density
aete rmination in a
crystal 129
onedimensional crysta l
8687
Electron diffraction/seatte ring 1416 ,
142 , 146 , 147151
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 3133
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
onedi mensional c rystal 81
s ystem with spheriea 1 symmetry 33
tilted anedimen s ional
c rysta1 84 , 91
Lonmtz cor rection 9 0 92
Fibra
crystal.llne 1.34, 136140
ln appl1cab l 1 ity of Guinier ' s
1aw to 57
with nematic organisation 1 10112
Fl1 te r, for producing monoc hromatic
X rays 2 ,47
Fl sh finray, Xray diffractlon by 11 7
Focusinq o f Xrays
by Bragg reflection 3
by tot a l l nte rnal reflection 23
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 <;042
cent rosynre tric fun ction 22
continuous helix 94100
c rys tal 12]
cylindri ca11y syIllllEtri c f lrletLon 12
di s e 114
dlsoon t inuous he1ix 102106
d l sorered crysta1 87 8 8
itr)e rfect 1attice 8788
lat tiee 11 9 12 3
IlO lecu1ar heHx 1061 10
mo1ecule 42  45
o n e  dimensional crysta1 7680
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 1013
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 142143
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
l n d ex
lndex
160
74
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 eedi oensiona1 1 191 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 102104
intensi t y 8586
Lens
electron 147
Xray 146
Ligh t diffraction/scatte ring 1 3 14, 16
.!IS step i n image formation 142  14 3
for simu lating Xray 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 6475
Li quid erysta1
choiesteric 115
nematic n O115
smectic 115117
twi sted n emat ic 1 15
Lo ren tz eorrection
fer a ene  dimensional crysta1 90 92
for a threQdillJimsiona1 c rystal 1 30
:Lc:Y..' ang1e Xra 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
150
140
161
Index
162
20
147
trialmlderr or a:ethods 24
Phase problelll 1718
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 Xraya frol:! synch rotrons .md
Iodex
ll~
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 ~ xrays , scattered
163
80
Water
interference funetion for 69
radi al distribution funetion o E 69
Xray 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 Xraya
Lncident 2
scattered 3 , S
Wax , Xray diffr actia1~il~t'J'I .Qf
W1enerKhintchine thfKl;reil' 19 . "
XRay crystallography
X Ray l aser lB
XRay lens 146
X Ray Illl.croscc:pe 146
34
1 1913)
..
X Raya
emission of
r ubber
stretched 136
UIlstretched 66
water 66
23 , 47
asse!lbly o f electrons
7 8
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 710
from M
amorphous soli d 0 1:" l1qui a 6473
crystal 1 19  133
crystalline Ubre 1]61 40
___
caaTP~.
,."TV.C  S P
RllU.lOTE(~ ."
fig. IV.) .
fig . VII . l .
~i9.
VII . 2 .
Piq. VII . J .
F1g. IX.l) .
F1q . IX . 16 .
Fiq. x.B.
Fig. XI.l .
XRay diffraction pattern of a micr ocrystalline deposit in abone marrow biopsy: the
positions of the ringa and their relativa 1ntensities showed that the mlcrocrystal a consisted of calci~ oxalate.
Fi g . XI . J .
~ig.
XII.4.
~ig.
XII.5.
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