[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]
(This Webpage Page in No Frames Mode)

CCP14

Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

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

Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs

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

Now assuming you have an acceptable peak profile list, it is time to try and index the powder diffraction pattern.

As possibly repeated elsewhere, for organics, it can be best to scope the range of possible results by running ALL the indexing programs (ito, treor, treor, taup, kohl, lzon and fjzn). In this example, this might seem quite contrived as the result is quite obvious (we already know the true answer), but in most cases, being to lax on scoping the possible range of solutions could put you in a world of pain!

For example, on standard laboratory instruments where alignment and sample preparation are of high quality, you might still be lucky to get Figure Of Merits greater than 10 on large cell organics.

As per the Crysfire tutorials, run XF2CRYS to convert the XFIT.TXT file into a Crysfire *.CDT file. (The wavelength in this case is 1.52904 Angstrom)

For brevity of this tutorial (though you can be running Chekcell concurrently with Crysfire), run All 7 elligible programs (ito, treor, treor, taup, kohl, lzon and fjzn). Whem prompted, a rule of thumb is to use around 25 peaks, but everyone has their favourite values when these is an excess of peaks to choose from)

Running Crysfire

In this example, it is obvious which is the "most likely" cell but in a larger cell, you may have a number of different cells with close FOM's such that closer examination will be necessary. Le Bail whole profile fitting might help you and at worse case, you may have to try to solve the structure using the different cells to see which gives the most reasonable answer.

A few things to look out for include doubling and halving of cell volumes as an indicator of possible "true" cells. 

20  456.0    1279.51   1.00 P ITO12/log    15Apr00 01:27:31    141  10.3918  18.8147   6.8230  90.000 106.437  90.000  100.661    28.249   233.503      .000    86.762      .000  crys = crys
20  453.4    1279.650  1.00 P DICVOL91/log 15Apr00 01:34:20 Mon__1  10.3922  18.8153   6.8233  90.000 106.437  90.000  100.653    28.247   233.483      .000    86.756      .000  crys = crys
20  446.48   1279.638  1.00 P LZONv6.22g   15Apr00 01:42:02  70001  10.3922  18.8152   6.8233  90.000 106.437  90.000  100.6535   28.2476  233.4844     .0000   86.7544     .0000 crys = crys
20  446.48   1279.638  1.00 P LZONv6.22g   15Apr00 01:42:02  20001  10.3922  18.8152   6.8233  90.000 106.437  90.000  100.6535   28.2476  233.4844     .0000   86.7544     .0000 crys = crys
20  446.47   1279.638  1.00 P FJZNv6.21a   15Apr00 01:38:30    121  10.3922  18.8152   6.8233  90.000 106.437  90.000  100.6535   28.2476  233.4844     .0000   86.7543     .0000 crys = crys
20  446.29   1279.638  1.00 P FJZNv6.21a   15Apr00 01:38:30    123  10.3922  18.8152   6.8233  90.000 106.437  90.000  100.6535   28.2476  233.4843     .0000   86.7543     .0000 crys = crys
20  426.0    1279.679  1.00 P DICVOL91/log 15Apr00 01:34:20 Mon__2  10.6969  18.8157   6.8233  90.000 111.281  90.000  100.653    28.246   247.374      .000   114.540      .000  crys = crys
20  420.11   2559.286  2.00 B KOHLv6.20h   15Apr00 01:36:56      8  19.9573  18.8153   6.8232  90.000  92.705  90.000   25.1633   28.2473  215.2714     .0000    6.9472     .0000 crys = crys
20  167.52   5118.269  4.00 B KOHLv6.20h   15Apr00 01:36:56     10  20.7853  18.8140  13.6460  90.000 106.435  90.000   25.1607   28.2514   58.3749     .0000   21.6859     .0000 crys = crys
20  162      1279.753  1.00 P TREOR90/log  15Apr00 01:34:54 Mon__1  10.3921  18.8173   6.8232  90.000 106.438  90.000  100.6558   28.2413  233.4924     .0000   86.7631     .0000 crys = crys
20  138.4    2559.74   2.00 P ITO12/log    15Apr00 01:27:31    666  13.6490  18.8158  10.3917  90.000 106.433  90.000   58.348    28.246   100.659      .000    43.361      .000  crys = crys
20  138.2    2559.74   2.00 P ITO12/log    15Apr00 01:27:31    667  13.6490  18.8158  10.3917  90.000 106.433  90.000   58.348    28.246   100.659      .000    43.361      .000  crys = crys
20  107.29   2559.415  2.00 P LZONv6.22g   15Apr00 01:42:02  30001  13.6492  18.8144  10.3910  90.000 106.433  90.000   58.3464   28.2501  100.6730     .0000   43.3638     .0000 crys = crys
20   81.65   7679.006  6.00 B KOHLv6.20h   15Apr00 01:36:56     16  20.4708  18.8150  19.9594  90.000  92.698  90.000   23.9163   28.2483   25.1575     .0000    2.3090     .0000 crys = crys

Now run Chekcell and we can graphically go through this mass of results. When prompted, the wavelength used for the peak positions is 1.52904 Angstrom

Running Chekcell

Performing a spacegroup assignment using the Best Group option in Chekcell suggests that P 21/A could be the best spacegroup.

Thus the result is:

  • Cell type: Monoclinic
  • Cell constants: 10.392 18.815 6.823 90.00 106.44 90.00
  • Volume: 1279.50
  • Spacegroup: P 21/A

This automatica spacegroup assignment should only be used as a guide and the other spacegroups manually browsed through to see the differences in observed and calculated lines.

Spacegroup Assignment using Chekcell

Also note, as per the peak profiling page, that those low angle shoulders are most likely due to something weird in the XRD geometry and sample preparation.

Looking closely at the background

The cell also calculates a HKL at a peak we missed in the peak profiling. (minor confidence booster)

Looking closely at the background

The conditions used for assigning the spacegroup are viewable as well if you wish.

Spacegroup Conditions within Chekcell

[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]
[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]
(This Webpage Page in No Frames Mode)
If you have any queries or comments, please feel free to contact the CCP14