Hostname: page-component-cd9895bd7-p9bg8 Total loading time: 0 Render date: 2024-12-17T03:52:20.441Z Has data issue: false hasContentIssue false

Combined powder X-ray diffraction data and quantum-chemical calculations in EXPO2014

Published online by Cambridge University Press:  21 February 2017

Angela Altomare
Affiliation:
Institute of Crystallography (IC), National Research Council, Bari, Italy
Fulvio Ciriaco
Affiliation:
Department of Chemistry, University of Bari, Italy
Corrado Cuocci*
Affiliation:
Institute of Crystallography (IC), National Research Council, Bari, Italy
Aurelia Falcicchio
Affiliation:
Institute of Crystallography (IC), National Research Council, Bari, Italy
Flavio Fanelli
Affiliation:
Institute of Crystallography (IC), National Research Council, Bari, Italy Department of Pharmacy – Drug Science, University of Bari, Italy
*
a)Author to whom correspondence should be addressed. Electronic mail: [email protected]

Abstract

This paper describes new features implemented in the EXPO2014 software and aimed at assisting crystallographers in the use of quantum-chemistry calculations in combination with experimental powder diffraction data. The implemented tools are useful in particular in two important steps of the process of crystal structure determination from powder diffraction data: (1) preparing accurate structural model suitable for crystal structure determination by real-space methods; (2) validating structure determination. The combination of experimental/quantum-chemical methods in EXPO2014 is now managed easily thanks to the following capabilities: (a) converting crystallographic data in input files and reading molecular geometry from output files of a wide variety of computational chemistry packages (GAMESS-US, NWChem, Gaussian, CRYSTAL, ABINIT, QUANTUM ESPRESSO); (b) optimizing the geometry of a molecule using Open Babel's force fields; (c) a graphical interface to run semi-empirical quantum calculation by MOPAC (Molecular Orbital PACkage); (d) producing input file for dispersion-corrected density functional theory.

Type
Technical Articles
Copyright
Copyright © International Centre for Diffraction Data 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R., Corriero, N., and Falcicchio, A. (2013). “EXPO2013: a kit of tools for phasing crystal structures from powder data,” J. Appl. Crystallogr. 46, 12311235.CrossRefGoogle Scholar
Belsky, A., Hellenbrandt, M., Karen, V. L., and Luksch, P. (2002). “New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design,” Acta Crystallogr. B 58, 364369.Google Scholar
Bergmann, J., Le Bail, A., Shirley, R., and Zlokazov, V. (2004). “Renewed interest in powder diffraction data indexing,” Z. Kristallogr. 219, 783790.Google Scholar
CPMD (1990). http://www.cpmd.org/, Copyright IBM Corp 1990–2015, Copyright MPI für Festkörperforschung Stuttgart 1997–2001.Google Scholar
David, W. I. F., Shankland, K., McCusker, L. B., and Baerlocher, Ch. (2002). Structure Determination from Powder Diffraction Data (Oxford University Press, New York). IUCr Monograph on Crystallography 13.Google Scholar
Dinnebier, R. E. and Billinge, S. J. L. (2008). Powder Diffraction: Theory and Practice (RCS Publishing, Cambridge).CrossRefGoogle Scholar
Dovesi, R., Orlando, R., Erba, A., Zicovich-Wilson, C. M., Civalleri, B., Casassa, S., Maschio, L., Ferrabone, M., De La Pierre, M., D'Arco, P., Noel, Y., Causa, M., Rerat, M., and Kirtman, B. (2014). “CRYSTAL14: a program for the ab initio investigation of crystalline solids,” Int. J. Quantum Chem. 114, 12871317.CrossRefGoogle Scholar
Faber, J. and Fawcett, T. (2002). “The Powder Diffraction File: present and future,” Acta Crystllogr. B 58, 333337.Google ScholarPubMed
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Keith, T., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, O., Foresman, J. B., Ortiz, J. V., Cioslowski, J., and Fox, D. J. (2013). Gaussian 09, Revision D.01 (Computer Software), Gaussian, Inc., Wallingford, CT, United States.Google Scholar
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococcioni, M., Dabo, I., Dal Corso, A., Fabris, S., Fratesi, G., de Gironcoli, S., Gebauer, R., Gerstmann, U., Gougoussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Scandolo, S., Sclauzero, G., Seitsonen, A. P., Smogunov, A., Umari, P., and Wentzcovitch, R. M. (2009). “QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials,” J. Phys.: Condens. Matter. 21, 395502395520.Google Scholar
Gonze, X., Amadon, B., Anglade, P. M., Beuken, J.-M., Bottin, F., Boulanger, P., Bruneval, F., Caliste, D., Caracas, R., Cote, M., Deutsch, T., Genovese, L., Ghosez, Ph., Giantomassi, M., Goedecker, S., Hamann, D., Hermet, P., Jollet, F., Jomard, G., Leroux, S., Mancini, M., Mazevet, S., Oliveira, M. J. T., Onida, G., Pouillon, Y., Rangel, T., Rignanese, G.-M., Sangalli, D., Shaltaf, R., Torrent, M., Verstraete, M. J., Zérah, G., and Zwanziger, J. W. (2009). “ABINIT : first-principles approach to material and nanosystem properties,” Comput. Phys. Commun. 180, 25822615.Google Scholar
Grazulis, S., Chateigner, D., Downs, R. T., Yokochi, A. F. T., Quiros, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P., and Le Bail, A. (2009). “Crystallography Open Database – an open-access collection of crystal structures,” J. Appl. Crystallogr. 42, 726729.CrossRefGoogle ScholarPubMed
Grimme, S., Antony, J., Ehrlich, S., and Krieg, H. (2010). “A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu,” J. Chem. Phys. 132, 154104154119.CrossRefGoogle ScholarPubMed
Groom, C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016). “The Cambridge Structural Database,” Acta Crystallogr. B 72, 171179.CrossRefGoogle ScholarPubMed
Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94,” J. Comput. Chem. 17, 490519.3.0.CO;2-P>CrossRefGoogle Scholar
Hehre, W. J., Ditchfield, R., and Pople, J. A. (1972). “Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type basis sets for use in molecular orbital studies of organic molecules,” J. Chem. Phys. 56, 22572261.Google Scholar
Kohn, W. (1999). “Nobel lecture: electronic structure of matter-wave functions and density functionals,” Rev. Mod. Phys. 71, 12531266.Google Scholar
Kresse, G. and Hafner, J. (1993). “Ab initio molecular dynamics for liquid metals,” Phys. Rev. B 47, 558561.CrossRefGoogle ScholarPubMed
MOPAC2016 (2016). James J. P. Stewart, Stewart Computational Chemistry (Colorado, CO, USA, Springs). http://OpenMOPAC.net.Google Scholar
Naelapää, K., van de Streek, J., Rantanen, J., and Bond, A. D. (2012). “Complementing high-throughput X-ray powder diffraction data with quantum-chemical calculations: application to piroxicam form III,” J. Pharm. Sci. 101, 42144219.CrossRefGoogle ScholarPubMed
O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., and Hutchison, G. R. (2011). “Open Babel: an open chemical toolbox,” J. Cheminf. 3, 33.CrossRefGoogle ScholarPubMed
Perdew, J. P. and Wang, Y. (1992). “Accurate and simple analytic representation of the electron-gas correlation energy,” Phys. Rev. B 45, 1324413249.CrossRefGoogle ScholarPubMed
Perdew, J. P., Burke, K., and Ernzerhof, M. (1996). “Generalized Gradient approximation Made simple,” Phys. Rev. Lett. 77, 38653868.CrossRefGoogle ScholarPubMed
Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, V. A. III, and Skiff, W. M. (1992). “UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations,” J. Am. Chem. Soc. 114, 1002410035.Google Scholar
Stephens, P., Devlin, F., Chabalowski, C., and Frisch, M. (1994). “Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields,” J. Phys. Chem. 98, 1162311627.CrossRefGoogle Scholar
Sholl, D. S. and Steckel, J. A. (2009). Density Functional Theory: A Practical Introduction (John Wiley & Sons, Inc., Hoboken).Google Scholar
Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M., and Montgomery, J. A. (1993). “General atomic and molecular electronic structure system,” J. Comput. Chem. 14, 13471363.CrossRefGoogle Scholar
Smrcok, L., Mach, P., and Le Bail, A. (2013). “Decafluorocyclohex-1-ene at 4.2 K – crystal structure and theoretical analysis of weak interactions,” Acta Crystallogr. B 69, 395404.Google Scholar
Tkatchenko, A. and Scheffler, M. (2009). “Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data,” Phys. Rev. Lett. 102, 7300573008.CrossRefGoogle Scholar
Valiev, M., Bylaska, E. J., Govind, N., Kowalski, K., Straatsma, T. P., van Dam, H. J. J., Wang, D., Nieplocha, J., Apra, E., Windus, T. L., and de Jong, W. A. (2010). “NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations,” Comput. Phys. Commun. 181, 14771489.CrossRefGoogle Scholar
van de Streek, J. and Neumann, M. A. (2010). “Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations,” Acta Crystallogr. B 66, 544558.CrossRefGoogle ScholarPubMed
Villars, P., Berndt, M., Brandenburg, K., Cenzual, K., Daams, J., Hulliger, F., Massalski, T., Okamoto, H., Osaki, K., Prince, A., Putz, H., and Iwata, S. (2004). “The PAULING FILE, Binaries Edition,” J. Alloys Compd. 367, 293297.CrossRefGoogle Scholar