Harriott Nowell & Kenneth Shankland ISIS Facility
Rutherford Appleton Laboratory Chilton, Didcot
Oxon OX11 0QX United Kingdom
Introduction
The object of this tutorial is to guide you through the structure solution of chlorpropamide (I). It assumes that you are already familiar with DASH and in particular with Tutorial 1. The stages in this tutorial correspond exactly to the stages in Tutorial 1, so it is always possible to refer back to Tutorial 1 at any time for a more detailed description. In it, you will learn how to (a) handle structures that are more flexible than hydrochlorothiazide, (b) solve a structure from a low resolution data set, and (c) see one of the potential pitfalls of global optimisation i.e. local minima.
Cl
S N N O O
O
H H
(I) Data
The data set “cp.xye” is synchrotron X-ray diffraction data collected on BM16 at the European Synchrotron Radiation Facility, λ = 0.800077Å.
Stage 1: Reading the data
Open DASH and select the directory in which the chlorpropamide data resides.
Select the ‘View data / determine peak positions’ option, then select the “cp.xye”
data file using the ‘Browse’ button.
1Copyright CCLRC / CCDC
142 -Stage 2: Examining the data
The data spans -4 to 22° 2θ. Why are there two theta values less than zero? Of course, there is no reason that data should not be collected on both sides of the beam stop! In this particular case, it is a function of the multiple crystal-analyser detector used on station BM16. This data adds nothing to the structure solution process and so it is necessary to edit the data file and remove points with 2θ values less than zero. Since there are no Bragg peaks apparent in the positive 2θ data until approximately 3.4° 2θ, it is possible to reduce the data further still.
Here we will use data in the range 2°-22° 2θ. To make life simple, we’ve provided a file, “cp_2.xye” that contains this range and is ready to use. If you want to see the procedure for creating it, see the short section at the end of the tutorial.
Reopen DASH, remembering to select the directory in which the chlorpropamide data resides, select the ‘View data / determine peak positions’ option, then select the “cp_2.xye” data file using the ‘Browse’ button. Note that this data set was collected quickly at the end of a day’s beamtime, and so only extends to 22° 2θ. Hence the data set extends to a resolution of only ~2Å.
Stage 3. Fitting the peaks to determine the exact peak positions
Select the first twenty peaks using the method described in Tutorial 1, Stage 3.
Here is a guide to the positions (° 2θ) of the first twenty peaks:
3.4383 6.1080 6.8792 8.5344 8.9466
9.4316 9.9800 10.1033 10.2499 10.3269
10.7041 11.1635 11.3767 11.5027 12.2579
12.3053 13.3092 13.4047 13.5143 13.5696
Stage 4. Indexing
Copy the twenty peak positions from DASH, using the ‘Peak positions’ option in the ‘View’ menu, and paste into a file with the correct format for your favourite autoindexing program, such as Dicvol.
Your indexing program may reveal a number of possible unit cells. The unit cell with the highest figures of merit should be orthorhombic with volume ~1266A3. Dicvol, for example, returns an orthorhombic cell with a = 26.66826Å, b = 9.08435Å, c = 5.22571Å and volume = 1265.999Å3 with figures of merit M(20)=107.1 and F(20)=506.6
Closer inspection of the other unit cells that are suggested by the indexing program will reveal that many of them are slight monoclinic distortions of the above unit cell, with almost identical volumes and lattice parameters and β ≈ 90°.
Other suggestions generally have much lower figures of merit and can be ruled out immediately.
Considering that the orthorhombic unit cell has the best figures of merit, and that it is usually best to try the simplest option first, we will go ahead to the next stage assuming an orthorhombic unit cell, with the lattice parameters given above.
Stage 5. Stop and think
Does the cell make sense? In this case we estimate the molecular volume to be
~290Å3, from the fact that there are 17 non-Hydrogen atoms in the molecule.
Therefore, given the unit cell volume of ~1266Å3 we know from this very rough approximation that the cell is most likely to accommodate 4 molecules. At this point, your knowledge of space group frequencies should suggest to you that P212121 is a strong possibility.
Stage 6. Checking the cell and determining the space group
Reopen DASH and select the ‘Preparation for Pawley refinement’ option. Enter the lattice constants, the space group P222 will automatically be selected. Go to the next step of the wizard and select the “cp_2.xye” file, synchrotron radiation and enter 0.800077Å for the wavelength.
Close the wizard and ensure that the tick marks generally correspond to peaks in the diffraction pattern. The presence of some excess tick marks indicates probable systematic absences, this means that a space group of higher symmetry might be more appropriate. Go to ‘Crystal symmetry’ in the ‘View’ menu and scroll through some of the possible space groups. You will see that some of the space groups can be ruled out immediately; for example, face centred and body centred lattices leave some peaks unaccounted for. Many of the primitive lattice space groups appear likely from the tick mark positions. In this situation, where more than one possible space group exists, it is logical to begin with the most frequently occurring space group (a table of frequency of occurrence of space groups is given in the DASH manual). In this case, the most frequently occurring orthorhombic space group is P212121, so select this (number 19), confirm visually that it matches the data and click on OK.
144 -Stage 7. Extracting intensities
Choose 7 isolated peaks from across the pattern. Fit these peaks using the method described in Tutorial 1 Stage 7, then carry out the Pawley refinement. The initial 3 cycles of least squares refinement only involve the terms corresponding to the background and to the individual reflection intensities, accept these three cycles.
The next 5 cycles of least squares refinement involve the terms describing background, intensities, unit cell and zero point. These refinement details will be suggested automatically by DASH.
When these cycles are complete check the difference line; this should be almost flat by this point. The final Pawley χ2 should be between about 3 and 4.
Accept this Pawley fit and save it as “cp.sdi”.
Stage 8 : Molecule construction
Construct a 3D molecular description of the molecule using your favourite modelling software and save it in PDB, MOL or MOL2 format. This can be done, for example, by importing an ISIS/Draw sketch into WebLab ViewerLite.
For further details, see Tutorial 1 Stage 8. Save this as cp.pdb, cp.mol or cp.mol2.
Stage 9 : Setting up the Structure Solution Run
• Reopen DASH and select the 'Simulated Annealing Structure Solution' option.
• Select the “cp.sdi” file
• Press the Import button and select cp.pdb, cp.mol or cp.mol2 (the file that you created in Stage 8); a Z-matrix file called cp.zmatrix will be generated automatically.
• Read in the cp.zmatrix file.
Note that as Z = 4 for P212121, it follows that Z′ = 1 because we know from Stage 5 that the cell is most likely to accommodate 4 molecules. Therefore, only one Z-matrix needs to be read in.
At this point, DASH will confirm that there are 13 variable parameters. These parameters are listed when you click on ‘Next’. There are 3 parameters describing the positional coordinates, 4 describing the molecular orientation within the unit cell and 6 variable torsion angles. All ‘v’ (short for vary) boxes are ticked by default, indicating that all 13 parameters are allowed to vary during the structure solution. Click ‘Next’, then ‘Solve’, then the ‘Play’ button to begin
the simulated annealing. NB: Keen chemists should resist the urge to restrict the torsional rotations pertaining to the two bonds around the carbonyl group! The uses of, and advantages of, restricted rotations in relation to this urea type linkage are discussed in Tutorial 3.
Stage 10 : Monitoring structure solution progress
The progress of the structure solution can be followed by monitoring the profile χ2
and the difference plot. Remember that the Simplex button (‘fast forward’
button) can be pressed at any time to accelerate the search in the vicinity of the current minimum.
Once a profile χ2 of approximately 10 or less is reached, you can be sure that a very good structure has been found, as this value is only ~3 times the Pawley χ2 value. Finalise the solution by pressing the Simplex button and accepting the answer.
If your final profile χ2 is a bit higher than 10, you are clearly close and perhaps only a single atom at the end of the chain is slightly misplaced. Take a close look at the output structure and read the section below.
Stage 11 : Examining the output structure
View the molecule and the unit cell using the .pdb file that has been created by DASH. The structure should be chemically reasonable in terms of molecular conformation and intermolecular distances. The potential for H-bonding is obvious.
Unrefined DASH solution with profile χ2 < 10. Note the potential for hydrogen bonding between the symmetry related molecules.
146
-However, it is entirely possible that you have obtained a structure solution with a χ2 value close to, but not less than 10. Is it correct? Consider the output structure below, taken from a solution with a final profile χ2 of approximately 10.7.
Spot the difference – an unrefined DASH solution with profile χ2 = 10.7.
In this case, it is a structure that differs only slightly from the corrrect structure, giving rise to a local minimum with a profile χ2 slightly higher than that of the correct crystal structure.
The subtle differences become clearer when both initial structures are overlaid with a molecule of chlorpropamide detemined from a single crystal experiment .
Unrefined DASH solution with χ2< 10 (stick), overlaid upon a single crystal solution (cylinder). The agreement is excellent.
Unrefined DASH solution with χ2> 10 (stick), overlaid upon a single crystal solution (cylinder). The agreement is still good and the differences could be overcome in a Rietveld refinement, but nevertheless, you can do better.
Stage 12 : Take home message
Global optimisation processes may locate local minima, particularly if (a) the molecule under study is highly flexible (b) Z′ > 1 or (c) the data are of limited resolution. Looking at the above example of a false minimum, it is clear that superficially, it can look chemically plausible. This is hardly surprising, as it lies at a point on the χ2 hypersurface very close to the global minimum of the crystal structure. Accordingly, it is always prudent to run a structure solution multiple times (with different random numbers of course…) to ensure that a consistent minimum has been reached.
Troubleshooting
Please ask any of the demonstrators for help if you run into problems with DASH.
WebLab ViewerLite Version 3.20 (12/8/98) is Copyright 1998 Molecular Simulations Inc.
DICVOL91: LOUER, D. & LOUER, M. (1972). J. APPL. CRYST. 5, 271-275.
BOULTIF, A. & LOUER, D. (1991). J. APPL. CRYST. 24, 987-993
148 -Procedure for editing a data file
First, create a copy of the “cp.xye” file. Open this copy in an ASCII file editor, such as Wordpad, delete the data between –4 and 1.998° 2θ and save the file as
“cp_2.xye”. Remember that column 1 in the data file corresponds to the 2θ value, column 2 to the diffracted intensity and column 3 to the estimated standard deviation of the intensity.