Tutorials

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Tutorial 1 - Crystal structure determination of  Cimetidine compound


The first tutorial is supplied for carrying out the full pathway of the ab-initio structure solution process (from indexing up to the structure solution) in case of cimetidine.



The only required information by  EXPO2014 is the diffraction data and the chemical formula (C10H16N6S4).

The examples directory contains the necessary files:


To access to examples directory:


and select the file cime.exp.


The content of file cime.exp is here reported


%structure cime

%job cimetidine (C10H16N6S) -- Synchrotron data

%initialize

%data

pattern cime.pow

wavelength 1.52904

synchrotron

%ntreor

%continue


It contains the minimal required information (name of data file, wavelength and type of radiation used to collect the data if different from X-rays) and commands for the ab-initio structure solution. This file can be visualized and eventually modified by the 'Edit' button.




More information about the creation of input file can be found in the section Preparing input file.

Clicking on OK the powder diffraction data will be displayed.



Selecting Next, an automatic peak search procedure will be applied and the d-values corresponding to the selected experimental peaks will be automatically supplied to the indexing procedure. At the end of this process  EXPO2014 will provide the indexing results by graphic interface:



Click on OK to accept the selected plausible cell parameters and to move to the next step: the space group determination.



The space group determination step, as well as Direct Methods, requires the unit cell content information. It can be easily derived by taking into account the structure formula and the cell volume (Vcell) provided by the window above or by the output file of  EXPO2014.

The cell content is given by Z multiplied by the structure formula. You can calculate Z as the ratio between Vcell and the molecular volume (Vmol): Z = Vcell/Vmol.
Vmol can be calculated by one of the two following alternative ways:

  1. Using the 18 Å3 rule: counting all the non-hydrogen atoms in the chemical formula and multiplying this number by 18 Å3;
  2. Using the following approximate atomic volumes: 14 Å3 for C, 12 Å3 for N, 11 Å3 for O, 5 Å3 for H, 26 Å3 for Cl, 25 Å3 for S.

In case of cimetidine compound, the chemical formula is C10H16N6S4 and the cell volume is 1280 Å3. If the fist criterion is applied, the molecular volume is given by: Vmol = 20 x 18 = 360 Å3.

The corresponding Z value is: Z = Vcell/Vmol = 1280/360 = 3.55, that can be approximated to 4. So 4 molecules of cimetidine are in the unit cell and the unit cell content to be supplied to  EXPO2014 by graphic interface is(C10H16N6S)4 or C40H64N24S4



Click on OK in order to perform the space group determination and then on Next button to go on continuously. At the end of the procedure a list of the Extinction Groups, compatible with the lattice symmetry and ranked according to a probability value, is given:







the most plausibile  Extinction Group P 1 21/a 1 is automatically selected and by clicking on OK the space group P 21/a, corresponding to this extinction group, will be chosen.


After the determination of the space group, EXPO2014 starts with the extraction step which is carried out in the selected space group. Click on Next button continuously. At the end of the process a list of integrated intensity values, extracted from the experimental powder pattern, is obtained and automatically supplied to Direct Methods for structure solution.  

The final result will be visualized on JAV Molecular Viewer.



Some errors in the assignment of carbon or nitrogen atomic species can be easily recognized and corrected by using the option 'Modify' from JAV menu.


Tutorial 2 - Crystal structure solution of 2-Mercaptobenzoic acid compound



The aim of this example is to guide the user in case of failure of a default run of EXPO2014.


Open  EXPO2014 by double click on Expo2014 icon.

Click on File > Load Examples

Select the input file 'merca.exp'.



%Structure merca

%Initialize

%Job 2-Mercaptobenzoic acid

%Data

Cell       7.885  5.976   14.949  90.0  100.48  90

SpaceGroup p 21/c

Content    C 28 O 8 S 4 H 24

Pattern    merca.xy

Wavelength 1.54056

%continue


In this example it is assumed that the cell and space group have been already determined and the unit cell content corresponds to 4 molecule of C7H6O2S.


Click on Next button to go on continuously.

The final structure model provided by  EXPO2014 could not correspond to the correct crystal structure of 2-Mercaptobenzoic acid. This can occur when the most plausible set of phases, provided by Direct Methods, is unreliable.

In a default run of  EXPO2014, Direct Methods generate several phasing trials; 20 of them are stored and ranked according to decreasing values of a suitable combined figure of merit (CFOM). The largest CFOM set of phases is automatically selected for structure solution. In case of failure, all the rest of stored phasing trials should be explored in order to find the solution.

This can be automatically performed by graphic interface:

a) Selecting from the top-level menu  Solve and then Explore Trials

b) Clicking on the Select all new trials button

c) Clicking on GO


At the end of the procedure,  EXPO2014 will rank the phasing trials (and the corresponding structure models) according to the increasing RF  agreement factor values.  


The best solution (corresponding to the lowest RF value) will be selected and displayed.


More information about the strategies to apply when Direct Methods fail are described in the next section of this manual.


Tutorial 3 - Crystal structure solution of paracetamol compound by direct space methods


The purpose of this tutorial is to guide the user through the crystal structure solution by direct space methods of paracetamol (form I polymorph) compound.




Open  EXPO2014, select  Load Examples and load the input file 'paracetamol.exp'.

Clicking on Next button, the file paracetamol.mol, containing a 3D molecular description of paracetamol, will be loaded and displayed and the following window will appear:



Select Execute; the Simulated Annealing procedure will be applied performing 10 runs whose corresponding final structure models can be explored by the button Solutions



References

Cimetidine - Cernik, R.J., Cheetham, A.K., Prout, C.K., Watkin, D.J., Wilkinson, A.P., Willis, B.T.M. (1991). J. Appl. Cryst. 24, 222-226.


2-Mercaptobenzoic acid - Florence, A. J., Shankland, N., Shankland, K., David, W. I. F, Pidcock, E., Xu, X., Johnston, A., Kennedy, A. R., Cox, P. J., Evans, J. S. O., Steele, G., Cosgrove, S. D. & Frampton, C. S. (2005). J. Appl. Cryst. 38, 249-259.


Paracetamol (form I polymorph) - Florence, A. J., Shankland, N., Shankland, K., David, W. I. F, Pidcock, E., Xu, X., Johnston, A., Kennedy, A. R., Cox, P. J., Evans, J. S. O., Steele, G., Cosgrove, S. D. & Frampton, C. S. (2005). J. Appl. Cryst. 38, 249-259.


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