Analyzing the results of a POWDER SOLVE run

We now have to decide, if the crystal structure has indeed been solved in the POWDER SOLVE run. Visually comparing the simulated and experimental powder patterns, it is often obvious whether or not the best crystal structure found by

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-Powder Solve actually matches the true crystal structure. Sometimes, however, it is difficult to make this decision, since moderate intensity differences may be related to an incorrect crystal structure as well as preferred orientation or inaccurate conformations of rigid bodies. In the case of TCHC, the whole carbon ring system has to be defined as a single rigid body, and slight deviations from the true conformation cause significant intensity differences. In order to distinguish between correct and incorrect solutions, it can be helpful to determine close contacts, hydrogen bonding schemes and voids in the crystal structure.

1. Extract the best solution from the POWDER SOLVE output file

1) Select Analysis/Input from the POWDER SOLVE card. Load the file tutorial/TCHC/PS_conf3.trj and choose OVERWRITE. Close the Analysis Input window.

2) Select Analysis/Analyze from the POWDER SOLVE card. In the Analysis Statistics window, change HIGHEST 10 to LOWEST 1 and click on the Search for button. The number of the crystal structure with the lowest Rwp factor is shown in the text window.

3) Select Analysis/Show frames from the POWDER SOLVE card. Change the frame number from 1 to 13 (best solution found). When you press

<ENTER>, the corresponding crystal structure appears in the model window.

To project all symmetry copies of the molecule into the unit cell, choose Crystal Building from the CRYSTAL BUILDER card on the BUILDER 1 stack. Click on UNBUILD CRYSTAL and then on BUILD CRYSTAL.

Close the Crystal Building control panel.

2. Compare the simulated and the experimental powder diffraction pattern Choose Run on the POWDER SOLVE card. In the Powder Solve control panel, set the task to SHOW. Click on RUN to calculate a powder pattern for the current model.

The comparison between the simulated and experimental powder patterns shows some important intensity mismatches, but the overall intensity distribution is correct. Since the number of reflections in the diffraction pattern is significantly higher than the number of degrees of freedom, it is unlikely that the good agreement in the overall intensity distribution is just accidental. We conclude that the current model is probably close to the true crystal structure, but needs further refinement.

In cases without flexible ring systems, successful structure solution typically leads to Rwp factors that differ from the Rwp factor obtained with Powder Fit (over the same angular range) by no more than a factor of two. In the present case, the two values differ by almost a factor of four (24.5 % compared to 6.9 %), but since we were expecting difficulties due to the flexibility of the carbon ring system, we are willing to accept this large relative difference in the Rwp factors.

3. Calculate close contacts

1) Select Simulation Setup/Rigid Bodies from the Powder Solve card. Click on some empty space in the model window to make sure that no atoms are selected. Click on Remove Rigid Bodies in the Rigid Bodies control panel. Choose OK when asked if you want to remove all rigid bodies.

Click on Color Rigid Bodies in the Rigid Bodies control panel.

2) Select Geometry/Close contacts from the Visualizer menu bar. Click on Monitor close-contacts. To examine the close contacts, rotate the model by pressing the right mouse button and dragging the mouse.

There are some close contacts that cannot be attributed to hydrogen bonding, but we do not observe any serious overlap between molecular fragments. The CH3 -NH-CH3 fragment participates in several close contacts that would not be tolerable for a completely refined crystal structure, but that can be accepted at this stage. The O-H..H-C distance of 1.91 Å is clearly too short, but the hydrogen positions where not determined in the structure solution step, and by adjusting the torsion angle of the methyl group it is possible to eliminate this close contact. We conclude that the crystal structure does not have to be rejected because of atomic overlap.

Click on the Turn off close-contact monitoring button and close the Close Contacts panel.

4. Examine hydrogen bonding

Select Build/Edit H-Bonds from the Visualizer menu bar. Click on CALCULATE. Rotate the model to examine the hydrogen bonding pattern.

The hydrogen bonding pattern looks very reasonable. All Hydrogen bonding donors and acceptors participate in hydrogen bonding.

5. Search for voids in the crystal structure

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-Select Geometry/Free Volumes from the Visualizer menu bar. Change the Volume to Calculate from TOTAL to OCCUPIABLE and press CALCULATE. Close the Free Volume panel.

No surfaces should appear in the model window, indicating that there are no significant voids in the crystal structure. Finally, we conclude that the current crystal structure is a very good candidate for the correct crystal structure and save it for further refinement.

Select File/Save Model from the Visualizer menu bar and save the current model.