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Aims
To become familiar with the general process involved in solving crystal structures and hence methods for
solving the phase problem
Objectives
It is possible to solve crystal structures using a black box approach, and in some senses this tutorial
guides you through the problem in this manner. However, at points in the tutorial you will be guided to
relevant reading and it is important that you read this background so that you can get the most out of this
practical. The information that you will get in the accompanying lectures will of course be important,
and we hope that the combination of the two together will give you a fuller view of X-ray structure
determination.
2
We will be using a freeware package OSCAIL for this practical, because it provides a cohesive Windows
interface for a number of crystallographic packages. Embedded within this is one of the most widely
used solution packages, SHELX.
There is a lot of academic freeware available for crystallography; much available over the web from:
http://www.iucr.org/sincris-top/logiciel/
This makes it very easy for anyone in academia to provide themselves with a range of quality software.
The authors of this free software are rewarded by being cited in many publications if you perform a
cited reference search in Web of Science on G. Sheldrick you will get some idea!
It would be useful for you to remind yourself of the following (from 3rd year solid state)
The seven crystal systems
Bravais lattices
Systematic Absences
Symmetry
3
Procedure for practical
This manual contains a worked example of a structure solution. There is a lot of information contained
within the tutorial, so you will work through this at your own pace. It will also describe how to produce
the final data tables and diagrams for your final report.
It is important to try to understand the procedures involved, and their importance. Each student will be
working on the same example at this stage, so feel free to discuss and help one another. Although this is a
worked example, it is a real data set so any problems you encounter will be realistic.
The worked example does not, however, describe a rote procedure for structure solution it will just give
you the general idea. A flow chart is provided at the end which gives an idea of the stages involved.
In the second stage of the practical, you will be given further data sets, together with the information that
the synthetic chemist would normally provide. It is up to you to solve the structure, and provide
appropriate data tables and diagrams which will be included in your report, but do ask for guidance.
Please keep detailed notes of your strategy in a notebook as you proceed.
Introduction to Oscail
Oscail is a Graphical User Interface for Windows which combines a number of crystallographic programs
within one front. A list of the programs you are likely to use, and their input/output files is given
below.
4
A worked example EX1
STEP 1
The first stage is to check the unit cell and hence determine the number of molecules (or number of
formula units) in the unit cell.
Start Oscail.
Use Change Jobname to insert EX1 and use Change Directory to point Oscail at the directory
containing EX1.TXT and EX1.HKL
The status line should show ex1 and the Directory you are using..Oscail can't cope with directory names
with spaces (e.g. "My Documents") so choose appropriately.
Note that the crystal system is Monoclinic with a beta angle of 105.93 degrees.
5
STEP 2
The next stage is to determine the space group. The space group is a representation of the symmetry of
the crystal structure. There are 230 possible space groups, but it can be determined by examining the
systematic absences in the reflections. You should remember that systematic absences, e.g. h+k+l = 2n,
give information on the Bravais lattice of the unit cell. Other absences give us information on the
symmetry elements (e.g. mirror planes, rotation axes) within the structure. See the copy of International
Tables for X-ray Crystallography which summarises the space groups.
Open up ex1.hkl in, e.g. notepad. You will see that this is a list of h,k,l followed by a measurement of
intensity, and the error in the intensity. Scrolling down you will see that some intensities are very high,
others almost zero. There is usually a "pattern" to the zero intensity reflections - these give an indication
of the symmetry. It is a big job to examine these by eye so we will use the computer.
In this case the unit cell is Monoclinic, so select Monoclinic as the Crystal System (default)
6
Examine the table. What is going on here is that each possible systematic absence is listed on the left
hand side, each of which relates to a certain symmetry element. The number of reflections for each case
is listed, and if the systematic absences are occurring (i.e. if by Cut 3 the number is zero) the symmetry
element is passed to the right hand side. (see International Tables for X-ray Crystallography)
From this, the possible space groups are given.
In this case, the Space Group is clearly P21/n a non-standard setting of P21/c No. 14.
It can be selected using the number 1014 or by typing in P21/n when asked.
The Space Group frequency information indicates that this is the most common Space Group that was on
the Cambridge Data Base at the end of 1997. This is a data base of all published structures, so if the
frequency is low the space group is less likely.
Put P21/n and 1014 into your note book. 1014 means space group number 14 in a non-standard setting.
Choosing a space group is not always a simple matter but in this case it is uniquely determined by
systematic absences. The most important absence is h0l h+l=2n+1.
Sometimes ABSEN will not give a space group. In this case you may have to look at the systematic
absences yourself, and perhaps use a fairly low symmetry space group to start with. Once you have
solved the structure, you may then be able to spot higher symmetry.
The opposite case is when ABSEN returns several spacegroups. There are a number of ways of
proceeding:
1) Choose the spacegroup with the highest "frequency"
2) Choose the spacegroup with the highest symmetry. If this fails, move to lower symmetry.
3) Choose the spacegroup with the lowest symmetry - then if appropriate, change to higher symmetry
later.
There is really no consensus on which is best!
7
STEP 3
In this section we will prepare an instruction file for the program SHELXS the structure solution part of
SHELX. For this all we need to know is the spacegroup, an approximate chemical formula, plus the
unit cell, errors on the unit cell, and a value of Z. Any slight mistake in these values is not usually
critical, unless the chemist has not synthesised the correct compound (or the crystallographer has selected
an atypical crystal!)
You are now ready to generate the input Files for SHELXS.
Select Run Job and GENINS
From Add SFAC and UNIT, insert the Molecular formula as given in section 1 (the 1 after Sn is
required) C27 H20 Fe2 O4 Sn1
This is the conventional order: always C first, H second, then the rest in alphabetical order.
More information is now written to the screen including the mean atomic volume per non-H atom, which
at 17.8 is not too bad and close enough to the 20 that was suggested in STEP 1.
8
When you return to Oscail, select EDIT and EDIT .INX to look at the file which you have created it
should look as follows:
TITL ex1
CELL 0.71073 14.0650 11.7470 15.2140 90.000 105.930 90.000
ZERR 4 0.0010 0.0020 0.0030 0.000 0.010 0.00
REM 1014 4 4 P21/n Monoclinic
LATT 1
SYMM 0.5+X,0.5-Y,0.5+Z
SFAC C H FE O SN
UNIT 108 80 8 16 4
TEMP 20
TREF 200
HKLF 4
END
Most lines should now be self-explanatory. The LATT 1 tells the program that the spacegroup is
Primitive and centrosymmetric. SYMM describes the space group. SFAC tells the program which atoms
are present so that it can use the appropriate scattering factors. TREF 200 is a command for Direct
Methods the equivalent for Patterson is simply PATT. 200 is the number of phase permutations to be
used for Direct Methods - this can be increased if no suitable solution is found. HKLF 4 tells the program
the format for the data. Most of these lines or cards will be retained throughout the process. Now close
this editing program.
In Oscail, select Run Job and SHELXS-97
SHELXS-97 will now use Direct Methods to try to solve the structure.
"Review Screen Output?" - this allows you to slowly go through the output from the process, and note
down important details. Click YES to go back through, then NO when you've finished.
The best Combined Figure Of Merit (CFOM) is 0.0575. (actually it will be lower than shown 0.0259)
It is a guide to the quality of the solution found.
0.0575 is satisfactory. It is difficult to generalize but the following may be useful
a CFOM of >0.18 is unlikely to be correct
a CFOM of <.08 is o.k.
a CFOM of <0.01 could indicate trouble.
But no problems here - the peak search found 3 heavy atoms and labelled them as one Sn and two Fe with
about 30 other atoms.
You can also examine the SHELXS output in detail when you return to Oscail using Edit.LST
9
STEP 4
The structure may be essentially solved at this stage, but there is quite a way to go yet. First we want
to examine the structure so far.
What you do at this stage depends on your experience; it would be normal to delete rubbish and to start to
refine 'good' atoms , but new users should do the following:
You should see a five-membered ring and a six-membered ring within the mess. You can label atoms
with the fourth button along.
We know that the CFOM was o.k., and there is some kind of structure there.
This together with some more 'good atoms' is enough for SHELXL-97/2. the structure refinement
program.
Exit ORTEX
Note: We have solved the structure using Direct Methods. Patterson methods are usually used when
there is a particularly heavy atom in this case it would seem that Patterson would be appropriate since
Sn is present. However, if you try Patterson (go back to INX and replace TREF 200 with PATT), it gives
very little solution. It can often be a case of trial and error, so bear this in mind if you get rubbish.
SHELXS-86 is often better for Patterson methods, but it suffers from not knowing all of the periodic
table! It knows about: H, B, C, N, O, F, NA, AL, SI, P, S, CL, K, CR, MN, FE, CO, NI, CU, AS, SE,
BR, MO, RU, AG, SN, SB, I, OS, PT, AU and HG
For any other atom, you have to use the closest atom in the periodic table as a substitute.
(If you have tried PATT, then go back and repeat with TREF 200 again)
10
Examining the .RES file using ORTEX has created a new file EX1.INS as follows
TITL ex1
CELL 0.71069 14.0650 11.7470 15.2140 90.000 105.930 90.000
ZERR 4 0.0010 0.0020 0.0030 0.000 0.010 0.00
REM 1014 4 4 P21/n Monoclinic
LATT 1
SYMM 0.5+X,0.5-Y,0.5+Z
SFAC C H O FE SN
UNIT 27 20 4 2 1
TEMP 20
L.S. 4
BOND
FMAP 2
PLAN 20
MOLE 1
FVAR
SN1 5 0.2251 0.7310 0.0140 11.000000 0.05
FE2 4 0.3415 0.5947 0.1183 11.000000 0.05
FE3 4 0.1771 0.6657 -0.1492 11.000000 0.05
Q1 1 0.3255 0.7314 -0.0569 11.000000 0.05 92.84
Q2 1 0.1063 0.5967 -0.0888 11.000000 0.05 90.35
Q3 1 0.3499 0.8619 0.1135 11.000000 0.05 82.81
Q4 1 0.1853 0.8761 -0.1544 11.000000 0.05 75.20
Q5 1 0.2824 0.6634 0.1933 11.000000 0.05 73.52
etc.
This now becomes our instruction file. You can see the the first section is the same as before. The four
commands in the middle are as follows:
These will now be retained for the rest of the procedure. Always check that they are present - sometimes
changing things in Ortex can cause them to go missing!!
Each atom is, at this stage, listed with the following info:
ATOM NAME ORDER IN SFAC LIST x y z Site occupancy Uiso (peak height)
The non-metal atoms are all called Q at this stage and treated as carbon atoms. This will be changed
shortly.
You should remember that what the program is looking for is electron density. The higher the electron
density, the heavier the atom on the site.
Thus, if the Uiso becomes very large (see below), this would indicate that the electron density is smeared
out and thus either a lighter atom is present or there is no atom there at all.
Similarly, if Uiso becomes very small, this would suggest that a heavier atom is present.
11
STEP 5
Refinement is carried out by a least squares procedure, and is a misnomer in that it can be used for
much of the expansion of the structure. This is because of a powerful technique known as difference
Fourier (see Giacovazzo, p367)
Having obtained a solution in STEP 4 the idea behind refining at this stage is that real atoms will refine to
give reasonable thermal parameters (or displacement parameters) and rubbish will give poor thermal
parameters. All atoms other than the Sn and Fe atoms are given the atom type number of carbon (1) at this
stage.
Select Edit.INS
The displacement parameter (DP Uiso)) is in the last column and the 'atoms' with parameters greater
than 0.10 are probably just rubbish (this depends on the temperature at which the data were recorded).
Thus, delete the lines with atoms with Uiso>0.1
Put ANIS 3 before Sn1. ANIS 3 will allow the three metal atoms to refine anisotropically (as ellipsoids).
This will remove 'ghost peaks' which tend to appear around heavy atoms when refined isotropically (as
spheres).
The same thing could be achieved with the command ANIS $Sn $Fe
The MOLE instructions are not required so delete them. These are only useful if there are separate
unconnected molecules.
WGHT 0.100000
FVAR 0.13637
MOLE 1
ANIS 3
SN1 5 0.226249 0.267577 00.016342 11.00000 0.03291
FE2 4 0.346042 0.406012 00.121607 11.00000 0.03795
FE3 4 0.178050 0.335470 -0.150092 11.00000 0.04625
Q1 1 0.324649 0.2998930 -0.033997 11.00000 0.39306
Q2 1 0.024962 0.4256730 -0.157574 11.00000 0.17959
Q3 1 0.358723 0.0867860 00.094139 11.00000 0.29454
Q4 1 0.161066 0.1129700 -0.205832 11.00000 0.32711
Q5 1 0.326852 0.2983050 00.232021 11.00000 0.43936
Q6 1 0.285237 0.0971800 00.034347 11.00000 0.03731
Q7 1 0.139994 0.1960100 -0.174997 11.00000 0.06230
Q8 1 0.504608 0.3021610 00.063233 11.00000 0.04464
Q9 1 0.326816 0.0329210 00.113064 11.00000 0.43280
Q10 1 0.296678 0.304419 -0.153253 11.00000 0.05835
Q11 1 0.189732 0.510961 -0.161369 11.00000 0.05828
Q12 1 0.089445 0.240542 00.057026 11.00000 0.03657
Q13 1 0.244192 0.536331 00.060608 11.00000 0.03715
Q14 1 0.161799 0.116853 00.016950 11.00000 0.37455
Q15 1 0.259947 0.535667 00.159385 11.00000 0.04944
Q16 1 0.351887 0.250176 00.271245 11.00000 0.04657
Q17 1 0.375769 0.288576 -0.160103 11.00000 0.05671
Q18 1 0.141003 0.531732 -0.009313 11.00000 0.04511
Q19 1 0.131593 0.488191 -0.098591 11.00000 0.05230
Q20 1 0.439979 0.337379 00.087887 11.00000 0.04919
etc.
12
Save the file and exit PFE.
You should, at this stage, examine the structure using ORTEX to see your new structure.
Select Run Job and ORTEX (default)
You will see that the structure is now clearer and less messy, but there are atoms missing. We need to
find them.
The wR2 value will now drop further. Note also the values of R1 and R(int). R1 is the non-weighted R-
value. R(int) is a measure of the quality of the raw data in relation to the space group and should be
<0.15. If it is very high, either the data quality is not great or you have selected the wrong space group.
What we are hoping to do here is looking for the missing atoms from the structure. The program
allows us to look at the difference Fourier listing and add in any range of high peaks (which may
correspond to atoms)
13
The first 16 peaks in the Difference Fourier are now listed.
The last column is the peak height. Your file will be slightly different, but the first 4 peaks are all close to
4 then there is a clear drop in intensity. Insert the number of large peaks (4) into Dialog 10 and OK.
A 'stick' picture of the molecule now appears on the screen.
If you rotate the molecule you will see that all looks reasonable.
14
To rename the atoms, firstly rotate the structure until you can see all of the atoms clearly.
Select Edit on the ORTEX (stick) Menu.
You need to be careful. In Edit atoms are selected with the mouse
and the atom's name is shown on the bottom left. When an atom is
selected three actions are possible.
2. Press (or C on the keyboard) and you can change an atoms name.
The way you number things is up to you but there are obvious things to do, like numbering in order round
rings, etc.
The Carbon atoms are last and sorted in numerical order. Check that all atoms have Unique Names.
Duplicate names will cause SHELXL to fail. If you have made a mistake and have 2 C13s
say then just change one of them to C53 for the moment.
Another thing to do is to sort the atoms in the editor. This makes things clearer for you. So, put all the
atoms of a ring together, with the iron atom to which they are connected, etc. Use cut and paste. This is
tedious, but in larger structures it can make things clearer. Use REM cards to add in comments for
yourself.
An example would be:
15
O4 3 0.35221 0.74654 0.27005 11.0 0.05
REM 6-ring 1
C12 1 0.28321 0.90329 0.03351 11.0 0.05
C13 1 0.34364 0.94584 -0.01845 11.0 0.05
C14 1 0.38817 1.05871 -0.00356 11.0 0.05
C15 1 0.36536 1.12503 0.06960 11.0 0.05
C16 1 0.30527 1.08418 0.11507 11.0 0.05
C17 1 0.26316 0.97301 0.10125 11.0 0.05
REM 6-ring 2
C18 1 0.09035 0.75582 0.05788 11.0 0.05
C19 1 0.08409 0.70607 0.14321 11.0 0.05
C20 1 -0.00122 0.72627 0.17459 11.0 0.05
C21 1 -0.06929 0.80421 0.13042 11.0 0.05
C22 1 -0.05925 0.85886 0.04346 11.0 0.05
C23 1 0.02050 0.83360 0.01560 11.0 0.05
HKLF 4
END
Now go to EDIT.LST and scroll down this file. You will shortly come across the connectivity list, as
follows:
This can often be helpful in problematic and/or large structures where it is difficult to get a good picture
from ORTEX. You can follow the connectivity (a bit like a logic puzzle) and work out which atom is
which. Here we have been able to achieve this using ORTEX but be aware of this useful listing.
It is also useful if the connectivity breaks in ORTEX often symmetry related atoms are found, and it
makes sense to move these so that a sensible molecule is found. This will be explained when needed.
16
STEP 6
In this case, we will be locating the hydrogen atoms geometrically, so we will use this order. Sometimes
H atoms (e.g. for water molecules) have to be found from the difference list, and this would be done as
stage c). It is important to locate as many H atoms as we can, since this can provide us with important
information on hydrogen bonding within our structure.
H atoms are very light (!) and can be very difficult to locate in a difference map, particularly if heavy
atoms are present. Therefore, we use the fact that for many cases we KNOW where the H atoms should
be geometrically and refine them using a riding model (i.e. the hydrogen rides on the appropriate C
position). In "light" structures with good data, we can find the H atoms and refine them like any other
atoms...but here we will use geometry.
To add hydrogen atoms geometrically the SHELX HFIX command can be used. This then creates an
AFIX command within the instruction file.
The precise command to be used can be complex, but there are a couple of useful cases:
H
H H H
H H H H
CH3
H3C O O
H H H H
H H
H
Aromatic HFIX 43 Chain HFIX 23 Hydroxyl HFIX 147
Thus, use Edit.INS and put in the following four lines after FMAP 2
HFIX 43 C2 C3 C4 C5 C8 C9 C10 C11
HFIX 43 C13 C14 C15 C16 C17 C19 C20 C21 C22 C23
HFIX 23 C6
ANIS
(You could also use e.g. HFIX 23 1.3 C6, where the -1.3 asks for the H to have a thermal paramater 30%
greater than its C)
ANIS will allow all non-H to refine anisotropically. This can be done together with the H atoms, or
separately. However, it must be done at some stage for a decent refinement.
Change L.S. 4 to e.g. L.S. 8 so that more refinement cycles are performed. Save and close the file.
17
answer Yes to Overwrite .INS ?
EX1 should now be close to fully refined, i.e. all shifts, all shifts/esd etc should be zero by the end of the
refinement.
The final refinement procedure to follow is to examine the .INS file. There is a parameter called WGHT
at the top of the file. At this stage it will be = 0.10000. Near the bottom of the file (above the difference
map) is another WGHT value. Copy this and replace the first value with the new value. Keep the
reiterations until WGHT is the same at the top and the bottom of the .INS file.
(by my reckoning this should end up as being around 0.0548, but dont take my word for it!)
In some cases there will be hydrogen bonding in the structure. If you are not sure, then you can put the
command HTAB into the .INS file. Any strong H-bonding found will be listed in the .LST file, just
above the difference map at the bottom of the file. See the section "Other Useful Information" for more
details.
There are more sophisticated methods of finding all the H-bonding in the structure - ask if you would like
information.
18
STEP 7
We need good pictures so that we can get an idea of the structure this will help us when we are writing a
description of the structure. This stage can often take longer than solving the structure, but then if you
cant describe it whats the point of solving it?!!! We will use ORTEX, but there are many, many
packages which can be used (e.g. ORTEP, PLATON, STRUPLO, ATOMS.)
Select Hardcopy and print directly on your printer or write HPGL or WMF for insertion into Word.
Exit ORTEX
19
STEP 8
Inter Molecular Contacts You may miss this section out if you wish.
There are no expected inter molecular H-bonds in this case. It is possible to check for C-H...O
interactions (which are currently popular) as follows:
Since the contacts would only be from oxygen it is only necessary to search around these atoms.
If you are going to do this then edit the .INS file so that all the O atoms are consecutive and sequential.
This is a pain which is why it is a good idea to save a backup of your .INS file before you do it.
The contact distances are shown on the right - the O...C distances less than 3.4 are shown and some would
merit further investigation.
This is really just for information, however. Normal bond lengths are given near the foot of the .LST
file.
Exit ORTEX
20
STEP 9
Building the Crystal Lattice
21
Sometimes this can give you a useful picture of the orientation of molecules within the crystal. It is worth
rotating this picture around for a while to try to find the best view. Once you have found this, print out a
hard copy.
22
STEP 10
Tables of Data for Your Report
The CIF (or Crystallographic Information File) is a summary file of your refinement. It can be used to
check if your refinement has any major problems using a process called CHECKCIF. We will not use
this here, but this will be demonstrated if required.
Crystallography is a highly computer-oriented subject, and it seems appropriate that it is one of the first
areas in which publications are transmitted by e-mail and published online (see www.iucr.org and the
electronic publications section Crystal Structure Communications you can also examine CIFs online
here too). This has helped speed up publication of results it can take less than 2 weeks, as opposed to 6
months to 1 year (or longer!) for regular publications.
Select Add Standard etc. (default) and insert Insert the correct items and click OK
the Compound Name (code) and click OK
Edit the tables to select a small number of the important bondlengths and angles and print these for your
report.
"Important bond lengths" - a nicely ambiguous term! In general, if there are metals in your structure, then
the interesting bond lengths are all those to the metal. In small organic molecules, all bond-lengths are
"interesting".
23
Other Useful Commands
Any of these should actually be done before ACTA is added to the command file.
1. Hydrogen Bonds
These are sometimes present and are important when describing how the molecule connects. To search
for normal H-bonds, insert the command
HTAB
in the instruction section of the .ins file. Run SHELXL-97, then inspect the .lst file. Near the bottom of
the file, before the difference list, there may be a short list which would look something like:
Hydrogen bonds with H..A < r(A) + 2.000 Angstroms and <DHA > 110 deg.
This tells you that N1 is hydrogen bonded to O2 and O1. The O2 and O1 are not in the same molecule as
N1 (or each other), but in molecules related by symmetry (shown in the square brackets). To finish this
off, you convert these into HTAB commands in the .INS file. The above example would translate as
follows:
The EQIV commands tell the program which symmetry elements you are using, and gives them each a
number. In some cases no symmetry will appear in square brackets. In this case you do not need an
EQIV command since the bond is INTRA-molecular.
Some molecules are handed (or chiral). This can only be determined by X-ray diffraction if there are
heavy atoms present. Chiral molecules must have a non-centrosymmetric spacegroup, and is signalled in
the .lst file by the FLACK parameter, which should be 0 if the structure is correct and 1 if it is inverted
(i.e. wrong chirality). If it is 1, then the command
MOVE 1 1 1 1
In cases where there are no heavy atoms (>O) and the structure is non-centrosymmetric, you should use
the command
MERG 3
This merges equivalent reflections so that no attempt it made to derive the chirality.
In rare cases, crystals are racemic (i.e. contain a mix of handedness). In these cases we use other
commands to refine the Flack parameter and so to determine the proportion of both forms. Hopefully we
will not encounter such crystals within this practical!
24
Section 2 Solving your own structure.
Normally in a research lab, crystals (of varying quality) will be provided to the crystallographer, who will
select and mount the crystals on the diffractometer, collect the data and solve the structure. Modern data
collected takes from a couple of hours upwards, solving the structure is (often) relatively trivial
producing diagrams, data tables and writing the papers takes a lot longer!
It is good procedure to request that the synthetic chemist provides the expected molecular formula in
diagrammatic form and also the list of ingredients as some unexpected features may appear in the
structure.
Crystals are generally of the order of 0.5mm or less. These have to be mounted on a small glass fibre, not
a job to be tackled after a night out! Anyone who would like practise in this is welcome to try it out. It is
important to pick a representative crystal, since is often tempting to pick a big, shiny crystal which is
unlike the others this is likely to be a recrystallised solvent and NOT the material of interest.
You will be given some structures of your own to solve. These are ranked as easy, medium and
difficult, so you'll start with an easy one.
All the information that you need is contained on the sheet you will be given - unit cell, likely
composition etc. The hkl file is on the floppy disk. The name of this file should be used for your
new structure refinement - e.g. if you find your data file is called
JS091.hkl
then use JS091 as the root. In other words, everywhere you see "EX1" in the example, use
JS091.
You should use the flow chart below as a guide, together with the worked example - but use your
common sense to decide new course of action that you may need to take, as compared with the
example. No two structure solutions are the same!
25
General Procedure of Structure Solution
CALCULATE Z
DETERMINE SPACE GROUP
CREATE .INS FILE
ORTEX ORTEX
CHECK
SPACEGROUP
YES YES
CHECK .INS
DELETE ATOMS
ARE ALL U ISO < 0.12? NO
YES
CHECK .INS
NO
26
LEAST SQUARES REFINEMENT
SHELXL-97
NO
REARRANGE ATOMS INTO
SENSIBLE ORDER IN .INS
CHECK .LST
(DIFFERENCE MAP)
REFINE WGHT
CHECK H-BONDING WITH HTAB
IS STRUCTURE
CHEMICALLY SENSIBLE? NO
YES
DRAW DIAGRAMS
PREPARE .CIF FILE AND DATA TABLES
WRITE DESCRIPTION OF STRUCTURE
27
This tutorial was originally written by P. McArdle, NUI, Galway
Expanded and adapted for use by the University of Aberdeen by J. M. S. Skakle
In these practicals students learn how to solve and refine crystal structures using SHELXS and
SHELXL and how to examine a crystal lattice with ORTEX. The software operates under
Win98, Win95 or NT-4. One Worked Tutorial and a number of data sets are provided.
The system should only be used by academic staff who are registered SHELX users. If you are
not a registered SHELX user then it is easy to be one if you fill the form available from.
http://shelx.uni-ac.gwdg.de/SHELX
There is one worked example EX1 and a number of other examples to pick from. Each one
contains details on the composition and data collection.
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