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New procedure to obtain Bragg-reflection intensities from FULLPROF suite for powder crystal-structure determination using GEST and PECKCRYST programs

Published online by Cambridge University Press:  29 February 2012

Zhen Jie Feng ,
Yong Lei Zheng ,
Yu Ling Su ,
Biao Shao ,
Ming Tao Li ,
Shi Xun Cao  and
Jin Cang Zhang
Zhen Jie Feng*
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Yong Lei Zheng
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Yu Ling Su
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Biao Shao
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Ming Tao Li
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Shi Xun Cao
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
Jin Cang Zhang
Affiliation:
Department of Physics, Shanghai University, Shanghai, People’s Republic of China
*
a)Author to whom correspondence should be addressed. Electronic mail: fengzhenjie@shu.edu.cn
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Abstract

A useful procedure is described to rapidly obtain Bragg-reflection intensities from the FULLPROF suite, and the Bragg intensities can then be input into the GEST and the PECKCRYST programs for crystal-structure determination of small molecules. An example on using the new procedure for the structure determination from powder diffraction determination of hydrochlorothiazide (C7H8ClN3O4S2) is presented, and the powder-structure results obtained by the PECKCRYST program are in good agreement with previously reported single-crystal results.

Keywords

GESTPECKCRYSTcrystal structureSDPDpowder diffraction
Type
Computer Program
Information
Powder Diffraction , Volume 25 , Issue 4 , December 2010 , pp. 374 - 376
Copyright
Copyright © Cambridge University Press 2010

I. INTRODUCTION

Over the past decade, the technology of structure determination from powder diffraction (SDPD) data has been greatly improved, although not completely routine (David and Shankland, Reference David and Shankland2008). The global optimization methods, i.e., the real-space methods, are widely and successfully used for molecular crystal-structure determination from powder diffraction data (David and Shankland, Reference David and Shankland2008; Harris et al., Reference Harris, Tremayne, Lightfoot and Bruce1994, Reference Harris, Johnston and Kariuki1998, Reference Harris, Johnston, Habershon and Johnson2004; Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002; Engel et al., Reference Engel, Wilke, Kónig, Harris and Leusen1999; Brodski et al., Reference Brodski, Peschar and Schenk2003; Cheung et al., Reference Cheung, Hanson, Habershon and Harris2005; Hanson et al., Reference Hanson, Cheung, Habershon and Harris2005). The main reason that these methods have been so successful in the procedure of SDPD is that the known molecular topology of the materials is used in the methods as far as applicable.

The GEST (Feng and Dong, Reference Feng and Dong2007) and the PECKCRYST (Feng et al., Reference Feng, Dong, Jia, Cao and Zhang2009) programs were developed for structure determination from powder diffraction data by us using genetic algorithm and particle swarm optimization algorithm, respectively. These two programs have been proved to be effective for molecular crystal-structure determination from powder diffraction data. However, we found that the preparation procedure of the input files for GEST or PECKCRYST is complicated that users may become discouraged and give up their efforts to obtain final solutions. If the input files for GEST or PECKCRYST are not prepared correctly, no solution will be obtained. For GEST or PECKCRYST, there are two main input files that need to be prepared. One is a “control” file containing crystal-structure information, known as molecular topology information and control parameters for algorithms. This file can be readily obtained by the recently developed GUI program for GEST and PECKCRYST. The second input file is the Bragg-reflection intensity file (i.e., h k l intensity data). This file can be obtained from the FULLPROF program (Rodriguez-Carvajal, Reference Rodriguez-Carvajal1990) using the Le Bail method (Le Bail et al., Reference Le Bail, Duroy and Fourquet1988). However, the FULLPROF program is complex and may take time for new users to use it effectively.

In this paper, a new procedure for obtaining Bragg-reflection intensities rapidly from the FULLPROF Suite is described. The Bragg intensities can then be used by the GEST or the PECKCRYST program for crystal-structure determination of small molecules.

II. METHOD FOR OBTAINING A BRAGG-REFLECTION INTENSITY FILE

Both the GEST and the PECKCRYST programs based on global optimization methods were developed in the past few years for molecular SDPD. The main difference between them is in the global optimization algorithms used by the programs: the genetic algorithm is used in the GEST program and the particle swarm optimization algorithm is used in the PECKCRYST program. Therefore, the main steps to use these two programs are similar. A friendly GUI program (as shown in Figure 1) was recently developed for GEST and PECKCRYST to help users to rapidly generate a control input file. Before using this GUI program to find the potential structure solution, the Bragg-reflection intensity data file should be obtained using the FULLPROF program. FULLPROF can be downloaded from http://www.ill.eu/sites/fullprof/. The steps for obtaining Bragg-reflection intensity file quickly from the FULLPROF suite are as follows:

  1. 1. Run the “Fullprof_Suite” program, then the “FullProf Suite ToolBar” will be opened.

  2. 2. Click on the “WinPlotr” program from the “FullProf Suite ToolBar.”

  3. 3. Click on “File->Open Pattern File” in the “WinPlotr” program, then, a “Format of data file” window will be opened. Then, select the data format to be used. It can be confusing for the user to determine which data format should be used. An easy way is to use POWDERX program (Dong, Reference Dong1999) to change the data format into “GSAS” or “CPI” format which can be read into the WinPlotr program. The POWDERX program can read “*.xrd” format data which can be made manually. The format of .xrd file opened in notepad is shown below:

    Figure 1. (Color online) The GUI program for GEST and PECKCRYST.

    The first line is the name of the sample and the second line is the total number of the experimental points (Npoints), and it can be calculated according to the following formula:

    Figure 2. (Color online) The output setting, the check box pointed by an arrow must be checked.

    Figure 3. (Color online) Three-dimensional structures of hydrochlorothiazide, C7H8ClN3O4S2: the calculated powder structure (black) and the single-crystal structure (color). The unit cell of the calculated powder structure is displaced slightly along both the a and the c axes.

    Npoints=(StopAngle−StartAngle)/step. Then, the following lines are the experimental points: the first column represents the 2-theta and the second column represents the diffraction intensity.

  4. 4. After the experimental data are read into WinPlotr correctly, click on the menu “Points Selection”-> “Automatic peak search.” In this step, the Bragg-reflection peaks are determined for automatic indexing.

  5. 5. Click on the menu “Points Selection”-> “Save as…” -> “Save as for DICVOL06.” Then, a dialog window “Input parameters for DICVOL” is opened. Input the necessary parameters in this dialog and then click “OK.” After the powder diffraction pattern is indexed, a file called “sample.pcr” is then generated.

  6. 6. “*.pcr” file is the control file for the “Fullprof program.” Click on the “Edpcr” program in the “Fullprof Suite ToolBar” or in the “WinPlotR” tool bar.

  7. 7. In the “Edpcr” program, open the generated “sample.pcr” file. In EdPcr program, click the corresponding buttons to set up the parameter to do profile fitting using the Le Bail method. The important setting is in the “output” button as shown in Figure 2, and the check box pointed by an arrow should be checked. This setting will let the FULLPROF program generate the correct format Bragg-reflection intensity file for GEST or PECKCRYST.

III. EXAMPLE

The crystal structure of hydrochlorothiazide, C7H8ClN3O4S2, was determined using the PECKCRYST program and the procedure described above. The powder diffraction data and data-collection parameters were downloaded from the website http://www.powderdata.info/. Bragg-reflection intensities were obtained using the FULLPROF program. The crystal-structure results obtained by PECKCRYST show that hydrochlorothiazide is monoclinic, with space group P21, unit-cell parameters a=7.389 Å, b=8.494 Å, c=9.991 Å, and β=111.717°. The value of the modified Bragg R factor obtained by the PECKCRYST program is 0.1313 (Feng et al., Reference Feng, Dong, Jia, Cao and Zhang2009). The VESTA software from Momma and Izumi (Reference Momma and Izumi2008) was used to draw the three-dimensional crystal structure determined by SPDP and compared to the structure obtained from a single crystal (Dupont and Dideberg, Reference Dupont and Dideberg1972). As shown in Figure 3, the powder crystal structure does match the single-crystal structure.

ACKNOWLEDGMENTS

This work was supported by the National Natural Science Foundation of China (NSFC) (Grant Nos. 10904088, 50932003, and 10774097) and the Science & Technology Committee of Shanghai Municipality (Grant Nos. 08dj1400202 and 09ZZ95). The authors also thank the late Professor Lachlan M. D. Cranswick for his assistance on preparing this paper.

References

Brodski, V., Peschar, R., and Schenk, H. (2003). “A Monte Carlo approach to crystal structure determination from powder diffraction data,” J. Appl. Crystallogr. JACGAR 36, 239–243.10.1107/S0021889802023208CrossRefGoogle Scholar
Cheung, E. Y., Hanson, A. J., Habershon, S., and Harris, K. D. M. (2005). “Crystal structures from powder X-ray diffraction using genetic algorithms,” Acta Crystallogr., Sect. A: Found. Crystallogr. ACACEQ 61, c114.10.1107/S010876730509519XCrossRefGoogle Scholar
David, W. I. F. and Shankland, K. (2008). “Structure determination from powder diffraction data,” Acta Crystallogr., Sect. A: Found. Crystallogr. ACACEQ 64, 52–64.10.1107/S0108767307064252CrossRefGoogle ScholarPubMed
Dong, C. (1999). “POWDERX: Windows-95-based program for powder X-ray diffraction data processing,” J. Appl. Crystallogr. JACGAR 32, 838.10.1107/S0021889899003039CrossRefGoogle Scholar
Dupont, P. L. and Dideberg, O. (1972). “Structure crystalline de l'hydrochlorothiazide, C7H8ClN3O4S2,” Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. ACBCAR 28, 2340–2347.10.1107/S0567740872006090CrossRefGoogle Scholar
Engel, G. E., Wilke, S., Kónig, O., Harris, K. D. M., and Leusen, F. J. J. (1999). “POWDERSOLVE: A complete package for crystal structure solution from powder diffraction patterns,” J. Appl. Crystallogr. JACGAR 32, 1169–1179.10.1107/S0021889899009930CrossRefGoogle Scholar
Favre-Nicolin, V. and Černý, R. (2002). “FOX, ‘free objects for crystallography’: A modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. JACGAR 35, 734–743.10.1107/S0021889802015236CrossRefGoogle Scholar
Feng, Z. J. and Dong, C. (2007). “GEST: A program for structure determination from powder diffraction data using a genetic algorithm,” J. Appl. Crystallogr. JACGAR 40, 583–588.10.1107/S0021889807008618CrossRefGoogle Scholar
Feng, Z. J., Dong, C., Jia, R. R., Cao, S. X., and Zhang, J. C. (2009). “PECKCRYST: A program for structure determination from powder diffraction data using particle swarm optimization algorithm,” J. Appl. Crystallogr. JACGAR 42, 1189–1193.10.1107/S0021889809034207CrossRefGoogle Scholar
Hanson, A. J., Cheung, E. Y., Habershon, S., and Harris, K. D. M. (2005). “Optimization of genetic algorithm techniques for powder structure solution,” Acta Crystallogr., Sect. A: Found. Crystallogr. ACACEQ 61, c162.10.1107/S0108767305093116CrossRefGoogle Scholar
Harris, K. D. M., Johnston, R. L., and Habershon, S. (2004). Applications of Evolutionary Computation in Chemistry, edited by Johnson, R. L. (Springer, New York), pp. 55–94.CrossRefGoogle Scholar
Harris, K. D. M., Johnston, R. L., and Kariuki, B. M. (1998). “The genetic algorithm: Foundations and applications in structure solution from powder diffraction data,” Acta Crystallogr., Sect. A: Found. Crystallogr. ACACEQ 54, 632–645.10.1107/S0108767398003389CrossRefGoogle Scholar
Harris, K. D. M., Tremayne, M., Lightfoot, P., and Bruce, P. G. (1994). “Crystal structure determination from powder diffraction data by Monte Carlo methods,” J. Am. Chem. Soc. JACSAT 116, 3543–3547.10.1021/ja00087a047CrossRefGoogle Scholar
Le Bail, A., Duroy, H., and Fourquet, J. L. (1988). “Ab-initio structure determination of LiSbWO6 by X-ray powder diffraction,” Mater. Res. Bull. MRBUAC 23, 447–452.10.1016/0025-5408(88)90019-0CrossRefGoogle Scholar
Momma, K. and Izumi, F. (2008). “VESTA: A Three-dimensional visualization system for electronic and structural analysis,” J. Appl. Crystallogr. JACGAR 41, 653–658.10.1107/S0021889808012016CrossRefGoogle Scholar
Rodriguez-Carvajal, J. (1990). “FULLPROF: A program for Rietveld refinement and pattern matching analysis,” Satellite Meeting on Powder Diffraction of the XV Congress of the IUCr, Toulouse, France, p. 127.Google Scholar
Figure 0

Figure 1. (Color online) The GUI program for GEST and PECKCRYST.

Figure 1

Figure 2. (Color online) The output setting, the check box pointed by an arrow must be checked.

Figure 2

Figure 3. (Color online) Three-dimensional structures of hydrochlorothiazide, C7H8ClN3O4S2: the calculated powder structure (black) and the single-crystal structure (color). The unit cell of the calculated powder structure is displaced slightly along both the a and the c axes.