Indexing, profile fitting and space group selection

A. Indexing

B. Profile fitting

C. Selecting space groups for structure solution Part 2: Conformer analysis

A. Sketching the tetracycline ion

B. Optimizing the tetracycline ion with the COMPASS force field

C. Searching low-energy conformers by Dynamics/Simulated Annealing D. Optimizing low energy conformations with MOPAC

Part 3: Structure solution

A. Setting up a POWDER SOLVE run

B. Analyzing the results of a POWDER SOLVE run Part 4: Structure refinement

Part 1: Indexing, profile fitting and space group selection

A. Indexing

1. Loading the powder pattern

If Cerius² is not already running, open a UNIX window, go to the directory

‘tutorial’ and type in cerius2 followed by <ENTER>.

To load the powder diffraction pattern, find the POWDER INDEXING card on the POWDER SOLVE stack and click on Experimental Data to bring up the 1-D Experimental Data control panel. Set the data file format to XY-GRAPH.

The powder diffraction data can be found under tutorial/TCHC/tetracycline_hydrochloride_xrd.grf. Load the data and close the 1-D Experimental Data control panel.

2. Generating a peak list and setting the wavelength

We will use the Automatic Peak Search tool to generate the peak list.

100

-Click on Peak Positions on the POWDER INDEXING card to bring up the Peaks panel. In the Peaks panel, click on Preferences to open the Automatic Peak Search panel. Choose SAVITZKY-GOLAY as the peak detection method. Change the low amplitude cutoff to 5 %. Click on RUN to start the peak search.

Now we have to make sure that all peaks are correctly placed and that no peaks have been missed in the low angle part of the diffraction pattern. Therefore, we have to magnify the diffraction pattern until we see the statistical noise. Then scan over the diffraction pattern horizontally, looking at only a small number of diffraction peaks at a time. In this particular case, no modification of the automatically generated peak list should be necessary.

To magnify the diffraction pattern, move the mouse horizontally and vertically while pressing SHIFT and the middle mouse button. To scan over the diffraction pattern, move the mouse while pressing the middle mouse button only.

Finally, we have to set the wavelength. The experimental data has been measured at a synchrotron radiation source at a wavelength of 0.692 Å.

In the Peaks panel, click in the wavelength input field and change the wavelength to 0.692 Å.

3. Indexing the powder pattern

We will first try to index the powder pattern with TREOR90.

Click on Run on the Powder Indexing card to bring up the Run Indexing panel. In the Run Indexing panel, click on the Run TREOR90 button to start TREOR90. By default, all seven crystal systems are searched to find the unit cell. TREOR90 will not be able to find the unit cell, and a window with the message 'Sorry - cell parameters were not found' will open. Click in that window with the left mouse button to close it.

Now we will try to index the powder pattern with DICVOL91. By default, the search is only carried out for crystal systems of high symmetry, and we first have to change the preferences to look for orthorhombic, monoclinic and triclinic space groups as well.

In the Run Indexing panel, click on Preferences next to DICVOL91. In the DICVOL91 Preferences panel, enable the search for orthorhombic, monoclinic and triclinic cells. Close the DICVOL91 Preferences panel and click on the RUN DICVOL91 button to start DICVOL91. The calculation may take several minutes.

We will now examine the DICVOL91 results and create a model with an empty unit cell that corresponds to the best solution found.

Click on the Analysis button that is related to DICVOL91 to bring up the DICVOL91 Analysis panel. This panel shows a list of solutions ranked according to their agreement with the peak positions in the peak list. The best solution is highlighted, and the corresponding cell parameters are shown.

Click on Create empty unit cell from solution and close the DICVOL91 Analysis panel.

B. Profile fitting

To make sure that the result of the indexing procedure is in agreement with the experimental powder pattern and to prepare the structure solution step, we will now run through the profile fitting procedure.

Select the POWDER FIT card from the POWDER SOLVE stack and click on Run to open the Powder Fit panel.

Before we start refining the profile, we have to set the wavelength again.

In the Powder Fit panel, click on Radiation to open the Radiation panel.

Change the radiation source from COPPER to SYNCHROTRON and set wavelength (1) to 0.692 Å. Close the Radiation panel.

In the profile fitting procedure, we will determine background parameters, profile parameters, peak intensities, cell parameters and the zero point shift of the diffractogram. A modified Pawley algorithm is used to provide a high degree of stability, and it is usually possible to refine all parameters simultaneously.

102

-1) In the Powder Fit panel, click on Range to bring up the Profile Range panel. Set the upper limit of the profile range to 20º. Cutting of the high angle part of the powder pattern helps to reduce calculation times. Close the Profile Range panel.

2) In the Powder Fit panel, click on Profiles to bring up the Peak Profile Refinement panel. Change the constant peak width w from 0.02º to 0.002º.

The default value of 0.02º is too large for powder data measured with synchrotron radiation. Switch on the refinement of all profile parameters.

Close the Peak Profile panel.

3) In the Powder Fit panel, click on Cell to bring up the Cell Parameter Refinement panel. Switch on the refinement of the cell parameters a, b and c. Close the Cell Parameter Refinement panel.

4) In the Powder Fit panel, click on Background to open the Background Refinement panel. Switch on the refinement of the zero parameter. The refinement of the background parameters is switched on by default

5) The refinement of all peak intensities is switched on by default. Click on RUN in the Powder Fit panel to refine all parameters simultaneously.

Continue refining all parameters simultaneously by clicking on the RUN button until the Rwp parameter does not improve any further. The Rwp

parameter is shown in the graphs window and in the text window.

Now we have to compare the simulated and experimental powder patterns under high magnification in order to check if all experimental peaks are well described by the simulated profile.

Magnify the powder pattern and scan over it as described in section A of this tutorial.

There should be no significant mismatch between the simulated and calculated powder pattern. We have successfully determined the unit cell of TCHC.

When this tutorial was written, an Rwp parameter of 6.35% was obtained at this point. The unit cell is orthorhombic, with a=15.7325 Å, b=12.8523 Å and c=10.9799 Å.

C. Selecting space groups for structure solution

Certain space groups appear more frequently than others. According to the Cambridge Crystallographic Database, about 76 % of all organic and organometallic compounds crystallize in only 5 space groups and about 90% of all organic and organometallic crystal structures are covered by the 17 most frequent space groups [5]. In general, many space groups can be discarded based on chirality, density considerations or systematic absences. It is common practice to start with the most frequent possible space group in the structure solution step. If the crystal structure can not be solved in this space group, one has to work down the list of possible space groups in the order of decreasing probability.

The most frequent orthorhombic space group is P 21 21 21. A convenient way to investigate the effect of systematic absences is to repeat the profile fitting procedure in this space group.

Select the CRYSTAL BUILDER card from the BUILDERS 1 stack, click on Symmetry and choose Space Groups from the pull down menu. Enter 'P 21 21 21' in the Space Group input field of the Space Groups panel.

Click on RUN in the Powder Fit panel.

A Rwp factor of 6.38% should be obtained at this point, compared to 6.36% in space group P 1. Symmetry allowed reflections are indicated by green tick marks in the graphs window. In P 1, three reflections of very small or no intensity occur below 4º, while they are symmetry-forbidden in P 21 21 21. The difference of the experimental and the simulated powder pattern shown in the graphs window does not reveal any missing peaks of significant intensity in P 21 21 21. It can thus be concluded that the space group P 21 21 21 is in agreement with the experimental powder diffraction pattern. In part 3 of this tutorial, we will see that the crystal structure of TCHC can indeed be solved in P 21 21 21.

Finally, we save the result of the first part of this tutorial for later use.

In the Visualizer control panel, change the model name from ‘index’ to

‘PF_P212121’

Select File/Save Model from the Visualizer menu bar to open the Save Model panel. Enter ‘PF_P212121’ in the input field situated below the file browser and press SAVE to save the unit cell and the outcome of the profile fitting procedure.

104