X-ray Structure Determination
Much of what you will have learned about crystal structures so far has been fairly abstract and far removed from what is actually done in research labs. Crystal structure solution is a vast area of interest (see, for example, the journal Acta Cryst. and also the web pages of the IUCr - International Union of Crystallography - at www.iucr.org ). We need to know about crystal structures for a variety of reasons, including:
1) Understanding how atoms and ions interact and bond
2) Correlating the structure with physical properties, e.g. magnetism, conduction 3) Making calculations based on the structure – e.g. band structure
This practical is thus designed to delve more deeply into crystal structure solution – and the best way to do that is to do it for yourself!
Aims
To become familiar with the general process involved in solving crystal structures and hence methods for solving the phase problem
Objectives
By the end of this practical you should:
• Be able to calculate Z (number of molecules) for any given structure
• Understand how systematic absences are used to determine possible space groups
• Be familiar with simple instructions within the crystal structure solution/refinement packages SHELXS and SHELXL
• Know the difference between Patterson and Direct Methods and how these “solve” the phase problem • Be able to solve a (straightforward!) structure
In this experiment you will learn about the following:
• the unit cell, its contents and their relationship to the molecular formula. • how to deduce the Space Group for the system.
• how to generate input for and use SHELXS to solve the structure by Direct and Patterson methods. • how to examine the "Solution" using ORTEX. ( or by using the .INS file )
• how to use SHELXL and ORTEX to interactively build up the structure. • how to get pictures of the molecule or structure.
• how to search for lattice contacts using ORTEX. • how to build the crystal lattice
• how to generate data for your report
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.
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
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.
Program Use Input Output
ABSEN Determination of possible space group(s) by examining systematic absences
.hkl .see
.sym GENINS Generates instruction file for use by SHELXS
programs
Prompted .inx or .ins SHELXS (86 or 97) Structure solution by Patterson or Direct Methods .inx or .ins
.hkl
.res .lst
SHELXL-97 Structure refinement .ins
.hkl
.res or .ins .lst (.cif, .fcf) ORTEX Graphical package for viewing structure .ins or .ort or
.res
.ort, . .res .ins
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.
The information you need is as follows: Molecular formula C27 H20 O4 Fe2 Sn1
UNIT CELL 14.0650 11.7470 15.2140 90.000 105.930 90.000 CELL ESDS 0.00100 0.00200 0.00300 0.00000 0.01000 0.00000 CELL VOLUME 2417.2(3) Å3
Write this information in your lab notebook.
In crystallography, the cell and esd's are often written (e.g.): 14.065(1) 90
11.747(2) 105.93(1) 15.214(3) 90
Count the non-H atoms in the proposed molecular formula.
On the basis that all non-H atoms occupy about 20 Å3 the molecular formula in this case containing 34 non-H atoms would occupy about 670 Å3. This divides into 2417 (CELL VOLUME) 3.6 times. Thus Z the number of molecules in the UNIT CELL will be about 4. (The possibilities for Z are limited by the space group, however - we will guide you on likely values for each example.
(In general, it is the C,N, and O atoms that occupy the large space – metals are much smaller) Note that the crystal system is Monoclinic with a beta angle of 105.93 degrees.
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.
Space Group possibilities can be examined using the program ABSEN.
Determination of the correct space group is one of the most important steps in determining a crystal structure.
Select Run Job and ABSEN
In this case the unit cell is Monoclinic, so select Monoclinic as the Crystal System (default) The following table is produced (next page):
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.
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
Select Write .INX and also Add Zerr, Add Space Group SYMM Ops and Add SFAC and UNIT
Change the radiation wavelength to 0.71073 (Å – this is the currently accepted value for MoKα1
radiation). You will notice the choice of Direct Methods or Patterson – leave this on DM in the first instance – we will come to this later (see
e.g. Clegg, Crystal Structure determination)
If you wish, add a comment line to the files - this may be useful in the future.
Insert the UNIT CELL dimensions - a b c alpha beta gamma from your notes
(EX1.TXT). Use the down cursor to move down then click on OK.
On Dialog 13 Enter ZERR, set Z to 4 (as calculated previously) and the ESDs (estimated standard deviations) to the values in EX1.TXT
From the Add Symm Ops default, select by Number on Dialog 11
Insert 1014 (the number of P21/n) on Dialog 10 (JMSS note: not all space groups are accessible with
the program and so sometimes we must use International Tables for X-ray Crystallography to “code up” the space group)
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.
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.
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:
Select Run Job and ORTEX (default) If asked Use Existing .ORT ? answer NO to Use Defaults ? answer YES
If Dialog 30 appears with .INS or .RES ? select .RES
What now appears on the screen may look like a mess but rotate and spin the structure around For y Rotation use the left/right cursor keys, the up/down keys for z and shift + left/right keys for x 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)
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:
L.S. n tells the program to perform n cycles of least squares
BOND produces a “connectivity list” and bond lengths in the .LST file FMAP 2 gives a “Difference Electron Density” synthesis – see PLAN
PLAN n produces a list of the n strongest peaks in the difference Fourier map
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.
The site occupancy has 10 added to it to prevent it from refining.
Uiso is the isotropic displacement parameter (sometimes misleadingly referred to as “thermal parameter) and gives a measure of how much the atom “moves” from its site. At this stage it is isotropic and unrefined (giving a circle of displacement)
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.
“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 Run Job and SHELXL-97/2.
Notice that the wR2 is dropping through the cycles. This is one of the measures of the quality of the refinement (see Clegg, Crystal Structure Determination, p42-43)
At the end of the refinement, answer Yes to Overwrite .INS ? 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….
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)
answer No to Use existing ex1.ORT ?
answer Yes to Use Defaults ? and use the INS file.
You will see that the structure is now clearer and less “messy”, but there are atoms missing. We need to find them.
Exit from ORTEX.
Select Run Job and SHELXL-97/2
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. answer Yes to Overwrite .INS ?
Select Run Job and ORTEX (default) answer No to Use existing ex1.ORT ? answer No to Use Defaults ?
answer YES to Use Covalent Radii for Bonds ? On Dialog 2 Check Add Diff Map Qs and OK.
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)
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. It is now necessary to name all the atoms with reasonable names.
Number the Carbons from C1 up to C27 and the four Oxygens from O1 - O4. The oxygens are on the CO groups attached to the Fe atoms.
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.
1. Click a blank area of the screen to clear the selector.
2. Press (or C on the keyboard) and you can change an atoms name. 3. Press (or D on keyboard) to delete an atom.
Change (rename) all of the atoms and then
Select Update (this will overwrite the old .INS file) Select the Default options.
The way you number things is up to you but there are obvious things to do, like numbering in order round rings, etc.
The result of the ORTEX operations are now written to EX1.INS
Open up this file using EDIT.INS and examine it. You will notice that it has changed our 4 essential commands (L.S. 4, FMAP 2, PLAN 20, BOND) – change these back (p11). Also, if there is no command END at the end of the file, add this in.
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:
Sn1 5 0.22626 0.73239 0.01644 11.0 0.03648 0.02348 = 0.03467 0.00102 0.01039 0.00027 Fe1 4 0.17780 0.66479 -0.15002 11.0 0.05383 0.03735 = 0.03711 -0.00257 0.01091 0.00131 REM 5-ring #1 C1 1 0.13024 0.51651 -0.10141 11.0 0.05 C2 1 0.04320 0.57750 -0.15440 11.0 0.05 C3 1 0.05620 0.58740 -0.23500 11.0 0.05 C4 1 0.13610 0.53340 -0.24790 11.0 0.05 C5 1 0.18268 0.48964 -0.16858 11.0 0.05 REM two CO C24 1 0.13839 0.80317 -0.17941 11.0 0.05 O1 3 0.11863 0.89584 -0.19520 11.0 0.05 C25 1 0.29921 0.69617 -0.15269 11.0 0.05 O2 3 0.37819 0.70852 -0.15970 11.0 0.05 REM C6 1 0.14077 0.46713 -0.00602 11.0 0.05 REM Fe2 4 0.34607 0.59369 0.12161 11.0 0.03351 0.02912 = 0.04321 0.00436 0.00710 0.00426 REM 5-ring #2 C7 1 0.24261 0.46242 0.06103 11.0 0.05 C8 1 0.33825 0.44443 0.04475 11.0 0.05 C9 1 0.40808 0.43346 0.13086 11.0 0.05 C10 1 0.36534 0.44463 0.20446 11.0 0.05 C11 1 0.25923 0.46260 0.15815 11.0 0.05 REM two CO C26 1 0.43875 0.66369 0.08776 11.0 0.05 O3 3 0.50681 0.70004 0.06556 11.0 0.05 C27 1 0.34939 0.69060 0.21262 11.0 0.05
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
Close and save this .INS file.
Select Run Job and SHELXL-97/2.
The wR2 factor will now decrease again, since now you are using the correct atoms.
If the maximum and minimum peaks in the Difference map (at the foot of the output) are not greater than 1.0 (absolute value) then you have found and refined all of the non-H atoms. There are reasons, however, why this may not always be the case…
Now go to EDIT.LST and scroll down this file. You will shortly come across the connectivity list, as follows:
Covalent radii and connectivity table for ex1 Sn1 - C12 C18 Fe2 Fe1 Fe1 - C24 C25 C4 C2 C5 C3 C1 Sn1 C1 - C5 C6 C2 Fe1 C2 - C3 C1 Fe1 C3 - C4 C2 Fe1 C4 - C3 C5 Fe1 C5 - C1 C4 Fe1 C24 - O1 Fe1 O1 - C24 C25 - O2 Fe1 O2 - C25 C6 - C1 C7 Fe2 - C26 C27 C9 C8 C11 C7 C10 Sn1 C7 - C11 C8 C6 Fe2 C8 - C9 C7 Fe2 C9 - C8 C10 Fe2 C10 - C9 C11 Fe2 C11 - C7 C10 Fe2 C26 - O3 Fe2 O3 - C26 C27 - O4 Fe2 O4 - C27 C12 - C17 C13 Sn1 C13 - C12 C14 C14 - C15 C13 C15 - C16 C14 C16 - C15 C17 C17 - C12 C16 C18 - C23 C19 Sn1 C19 - C18 C20 C20 - C21 C19 C21 - C20 C22 C22 - C21 C23 C23 - C18 C22
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.
STEP 6
If we are fairly happy with the structure at this stage, we can a) Add hydrogen atoms
b) Refine all non-H anisotropically
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:
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.
Select Run Job and SHELXL-97/2 H H H H H H O O H C H3 CH3 H H H H H H H H
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 don’t take my word for it!)
Examine the structure using all the defaults in ORTEX
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.
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 can’t describe it what’s 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 Run Job and ORTEX answer No to Use existing ex1.ORT ? answer Yes to Use Defaults ?
Select Use .INS (default) on Dialog 30. Rotate the structure to get a good view. Select Atom then Ellipsoids
POS.L can be used to position atom labels.
Select Hardcopy and print directly on your printer or write HPGL or WMF for insertion into Word.
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.
Select Run Job and ORTEX
answer Yes to Use existing ex1.ORT ?
Select Atom and Pac/Con
Select Search for Contacts (default)
Insert O1 and O4 (case does not matter) as the atom range and set the max Contact distance to 3.4 and OK
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.
STEP 9
Building the Crystal Lattice
Select Run Job and ORTEX answer No to Use existing ex1.ORT ? answer No to Use defaults ?
Check Add Unit Cell on Dialog 2 and default
on other Dialogs Select Atom and Pac/Con
Select Lattice Pack and OK
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.
STEP 10
Tables of Data for Your Report
Add the command ACTA to the .INS file after FMAP 2
and run SHELXL-97/2 again. This will generate .CIF and .FCF files.
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.
From Oscail select Run Job and CIFTAB
Select Add Standard etc. (default) and insert the Compound Name (code) and click OK
Insert the correct items and click OK
When dialog 3 returns select Crystal/Atom Tables and OK A .TEX file is now written.
Click EXIT and OK
Start WORD and open this file.
Select Table 1 – highlight the actual table - and use Convert Text to Table to format the (comma delimited) table, and similarly for the further tables in the document.
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".
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. D-H d(D-H) d(H..A) <DHA d(D..A) A
N1-H1A 0.774 2.348 174.63 3.119 O2 [ x+1/2, -y, z+1 ] N1-H1B 0.811 2.555 143.04 3.240 O1 [ x+1/2, y+1/2, z+1/2 ]
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:
EQIV $1 X+0.5, -Y, Z+1 EQIV $2 X+0.5, Y+0.5, Z+0.5 HTAB N1 O2_$1
HTAB N2 O1_$2
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.
2. Chirality and the MERG command
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
will invert the structure.
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!
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.
Data collecting involves
a) confirming the material is crystalline b) determining the unit cell
c) collecting data through a large section of reciprocal space
Your own structures
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!
General Procedure of Structure Solution
COLLECT SOME DATA – INDEX UNIT CELL COLLECT FULL DATA SET
CALCULATE Z DETERMINE SPACE GROUP
CREATE .INS FILE
DIRECT METHODS
SHELXS-97 OR 86 SHELXS-86 OR 97 PATTERSON
SENSIBLE SOLUTION? NO NO
YES YES
CHECK SPACEGROUP
ORTEX
LEAST SQUARES REFINEMENT SHELXL-97
CHECK .INS
ARE ALL UISO < 0.12?
SENSIBLE SOLUTION?
ORTEX
NO DELETE ATOMS
YES CHECK .INS
ARE ANY UISO < 0.01? YES CHECK ATOM TYPE
(ORTEX, .LST)
NO
ANY PEAKS > 1 ?
NO
YES
CHECK USING ORTEX, SHORTEST DISTANCE LIST – IF OK, ADD TO .INS FILE
LEAST SQUARES REFINEMENT SHELXL-97
CHECK .LST
(DIFFERENCE MAP)
REFINE U ANIS, ADD RIDING H ATOMS SHELXL-97
CHECK .LST
(DIFFERENCE MAP)
LOOK FOR ANY NON-RIDING H ADD TO .INS AND REFINE
“REFINE” WGHT CHECK H-BONDING WITH HTAB
IS STRUCTURE CHEMICALLY SENSIBLE?
YES
CHECK BOND LENGTHS, CONNECTIVITY, R-VALUE. NO CHECK SPACEGROUP, ATOM ASSIGNMENTS, ANY MISTAKES IN .INS DRAW DIAGRAMS
PREPARE .CIF FILE AND DATA TABLES WRITE DESCRIPTION OF STRUCTURE
REARRANGE ATOMS INTO SENSIBLE ORDER IN .INS
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
Crystallography Centre, NUI, Galway
This data remains the property of NUI,Galway its use is FREE to
ACADEMIC users. Commercial users must obtain permission for its use.
From site: http://www.nuiGalway.ie/cryst/xlearn/xlearn.htm
Oscail may be downloaded free from site: http://www.nuiGalway.ie/cryst/
This will be a later version than that used for this tutorial, but the essential features are the same.
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
Inorganic Chemistry, NUI, Galway
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.
