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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Peak Profiling of Cimetidine using XFIT

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]
[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]
[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

This example uses example Cimetidine data from the EXPO software

Normally we would want to use Fundamental Parameters peak profiling. But as this is synchrotron data (single wavelength and parallel beam), we should be able to get a way with just using Pseudo-Voight profiling (plus XFIT cannot do Fundamental Parameters profiling on Synchrotron data)

Open up the file and browse the pattern noting the range which gives fairly resolved peaks for profiling. At least 20 peaks are required. Using the File, Details option, set the background to refine with a bit more flexibility (3rd to 5th order).

Selecting Ins/Del Peaks, then PV for Pseudo Voight, click left button on the peaks to profile. Right mouse button to remove a peak. If there are subtle shoulders or humps you are not sure about, ignore them for the moment. Come back to the shoulders if a single Pseudo-Voight peak cannot fit them. Also, if the width of a peak is enlarged compared to its neighbours, this could imply there are really two peaks.

In the following screen dump, we have selected our range.

Peak to profile and fit

For convenience, now fit small sections of the powder pattern. Taking note of any misfits which might indicate there is another peak present. At low angle, these could be due to aberattions caused by sample packing and geometry so be careful. It never hurts to run a standard to check what the default profiles look like, and to check the alignment of the XRD (as well as consider also running an extra sample with an internal standard so the data can be validated against the standards. This type of checking should be considered mandatory, not optional. This can help avoid a lot of un-necessary pain with structure solution.

Fitting small sections of the powder pattern

Note the low angle tail on some of the major peaks in the following screen dump. This could be legitimate peaks or an abberation of the XRD. For the moment, it will be treated as a machine abberation. If the indexing programs give extra "calculated" peaks at these points, it could add extra confidence to the indexing. This also shows why it is important to run standards of known characterstics (NBS/NIST Silicon, annealled Cubic Y2O3) so you can be more confident what is due to the XRD machine, and what is due to the sample.

Fitting the next part of the pattern

When a small peak or shoulder is close to another larger peak (or when there are a group of overlapped peaks), it can be effective to constrain the shapes and widths to be equal. In XFIT, select Ins/Del Peaks, from the Peak Edit Options select Code and you can now graphically link refinement codewords together.

In the following screen image, the shape of two peaks are being linked together by giving them the same name (a letter must be the first character defining the codeword). Just click on the "@" to change it. The same goes with any value on the screen. (this can also be done via the "File Details" menu but this can be quicker for this type of local setting of constraints.

Fitting parts of the pattern with width and shape constraints

Check that the constraints are working and the widths, then the shapes are identical.

Checking constraints are working

Once you are happy with the peak profiling, save the project. Then go into File, Details, then Peaks, Two Theta All Pk Types; and create a text report saving the file as XFIT.TXT ready for importing into the Crysfire powder diffraction indexing suite. To be prompted to save the file, close the TXT Report window. Consider putting the file into a separate subdirectory called crys1. It may be necessary to go back and re-analyse the diffraction data if indexing is not satisfactory, so keeping things in separate subdirectories can limit the risk of "possibly" good results getting overwritten.

Creating a text report of the results ready for importing into Crysfire

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]
[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]
[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]
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