X-ray Structure Determination. Crystal Structure Solution

Transcription

1 X-ray Structure Determination Crystal Structure Solution

2 Intro: 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 ). 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. 2

3 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: 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

4 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. Program Use Input Output ABSEN Determination of possible space group(s) by.hkl.see examining systematic absences.sym GENINS Generates instruction file for use by SHELXS Prompted.inx or programs.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 ORTEX Graphical package for viewing structure.ins or.ort or.res (.cif,.fcf).ort,..res.ins 4

5 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 CELL ESDS CELL VOLUME (3) Å3 Write this information in your lab notebook. In crystallography, the cell and esd's are often written (e.g.): (1) (2) (1) (3) 90 Count the non-h atoms in the proposed molecular formula. On the basis that all non-h atoms occupy about 20 Å 3 the molecular formula in this case containing 34 non-h atoms would occupy about 670 Å 3. 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 degrees. 5

6 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. 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): 6

7 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 P2 1 /n a non-standard setting of P2 1 /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 This is a data base of all published structures, so if the frequency is low the space group is less likely. Put P2 1 /n and 1014 into your note book 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

8 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 Select Write.INX and also Add Zerr, Add Space Group SYMM Ops and Add SFAC and UNIT Change the radiation wavelength to (Å this is the currently accepted value for MoKα 1 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 P2 1 /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. 8

9 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 ZERR REM P21/n Monoclinic LATT 1 SYMM 0.5+X,0.5-Y,0.5+Z SFAC C H FE O SN UNIT 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 (actually it will be lower than shown ) It is a guide to the quality of the solution found 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

10 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: 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) 10

11 Examining the.res file using ORTEX has created a new file EX1.INS as follows TITL ex1 CELL ZERR REM P21/n Monoclinic LATT 1 SYMM 0.5+X,0.5-Y,0.5+Z SFAC C H O FE SN UNIT TEMP 20 L.S. 4 BOND FMAP 2 PLAN 20 MOLE 1 FVAR SN FE FE Q Q Q Q Q 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 BOND FMAP 2 PLAN n tells the program to perform n cycles of least squares produces a connectivity list and bond lengths in the.lst file gives a Difference Electron Density synthesis see PLAN 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 U iso 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 U iso becomes very small, this would suggest that a heavier atom is present. 11

12 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 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 FVAR MOLE 1 ANIS 3 SN FE FE Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q Q etc. 12

13 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) Select Use.INS (default) on Dialog

14 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. 14

15 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: Sn = Fe = REM 5-ring #1 C C C C C REM two CO C O C O REM C REM Fe = REM 5-ring #2 C C C C C REM two CO C O C

16 O REM 6-ring 1 C C C C C C REM 6-ring 2 C C C C C C 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. 16

17 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. AFIX command within the instruction file. This then creates an 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 CH 3 H O O 3 C 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 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 17

18 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 = 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 , 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. 18

19 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. Exit ORTEX 19

20 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. 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. Exit ORTEX 20

21 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 The defaults will fill one cell. 21

22 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

23 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 and published online (see 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". 23

24 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) Angstroms and <DHA > 110 deg. D-H d(d-h) d(h..a) <DHA d(d..a) A N1-H1A O2 [ x+1/2, -y, z+1 ] N1-H1B 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 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! 24

25 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! For the same reason, please ask if you need help. 25

26 General Procedure of Structure Solution COLLECT SOME DATA INDEX UNIT CELL COLLECT FULL DATA SET OSCAIL CALCULATE Z DETERMINE SPACE GROUP CREATE.INS FILE DIRECT METHODS SHELXS-97 OR 86 PATTERSON SHELXS-86 OR 97 ORTEX CHECK SPACEGROUP ORTEX SENSIBLE SOLUTION? NO NO SENSIBLE SOLUTION? YES YES LEAST SQUARES REFINEMENT SHELXL-97 CHECK.INS ARE ALL U ISO < 0.12? NO DELETE ATOMS CHECK.INS YES ARE ANY U ISO < 0.01? YES CHECK ATOM TYPE (ORTEX,.LST) NO 26

27 LEAST SQUARES REFINEMENT SHELXL-97 CHECK.LST (DIFFERENCE MAP) CHECK USING ORTEX, SHORTEST DISTANCE LIST IF OK, ADD TO.INS FILE ANY PEAKS > 1? YES REARRANGE ATOMS INTO SENSIBLE ORDER IN.INS NO 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 CHECK BOND LENGTHS, CONNECTIVITY, R-VALUE. CHECK SPACEGROUP, ATOM ASSIGNMENTS, ANY MISTAKES IN.INS IS STRUCTURE CHEMICALLY SENSIBLE? NO YES DRAW DIAGRAMS PREPARE.CIF FILE AND DATA TABLES WRITE DESCRIPTION OF STRUCTURE 27

28 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: Oscail may be downloaded free from site: 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. 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. 28