Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo Expo2014 Crystal structures solution by powder diffraction data PDF generated September 17, 2021 by Kalin's PDF Creation Station WordPress plugin 1 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo Table Of Contents EXPO2014 documentation ...................................................... 3 General information ........................................................... 5 EXPO2014 installation ......................................................... 8 Tutorials .................................................................. 15 Preparing input file .......................................................... 25 Commands of EXPO2014 ...................................................... 28 Preparation of data .......................................................... 31 Indexing .................................................................. 40 Space group determination ..................................................... 53 Structure solution by Direct Methods (DM) .......................................... 58 The steps of structure solution by DM ............................................. 70 Extraction of the integrated intensities ............................................. 71 Normalization of the integrated intensities .......................................... 77 Structure invariants estimate .................................................... 81 Phasing by tangent formula ..................................................... 84 Fourier map calculation and crystal structure optimization .............................. 88 Structure solution by direct space methods .......................................... 97 Parallelism in Expo2014 for structure solution by direct space method ...................... 119 Rietveld Refinement ......................................................... 123 Crystal Structure Visualization ................................................. 130 EXPO2014 commands ....................................................... 131 How to .................................................................. 134 File ..................................................................... 135 Modify .................................................................. 139 Select ................................................................... 140 View .................................................................... 141 Tools .................................................................... 145 Geometry Optimization ...................................................... 146 Bond Valence Sum .......................................................... 154 Info .................................................................... 157 Appendix A: Average volume of the atoms ......................................... 167 Appendix B: Extinction symbols and corresponding space groups ......................... 170 2 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo EXPO2014 documentation http://www.ba.ic.cnr.it/softwareic/expo/ EXPO2014 [A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, N. Corriero and A. Falcicchio, (2013). J. Appl. Cryst. 46, 1231-1235], the latest version of EXPO2009 [A. Altomare, M. Camalli, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, (2009). J. Appl. Cryst. 42, 1197-1202.] is able to perform all the steps of the structure solution process by powder diffraction data: indexing, space group determination, estimation of the reflection integrated intensities, structure solution by Direct Methods or/and by direct space/hybrid approaches, model refinement by Rietveld technique. Authors A. Altomare*, C. Cuocci*, C. Giacovazzo*, A. Moliterni*, R. Rizzi*, N. Corriero* and A. Falcicchio* *Institute of Crystallography-CNR, via Amendola 122/o 70126 Bari, Italy [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] Contact For questions, problems and suggestions, please, visit http://www.ba.ic.cnr.it/softwareic/expo/contact-us/ 3 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo We kindly ask you to fill the survey. Main Reference If EXPO2014 is used in the solution process of a structure, whose results are published in a scientific paper, please, include the following reference: A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, N. Corriero and A. Falcicchio, (2013). J. Appl. Cryst. 46, 1231-1235. _______________________________________________ 4 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo General information http://www.ba.ic.cnr.it/softwareic/expo/general-information/ EXPO2014 is able to perform all the steps of the structure solution process by powder diffraction data: indexing, space group determination, estimation of the reflection integrated intensities, structure solution by Direct Methods or/and by direct space/hybrid approaches, model refinement by Rietveld technique. The program has been designed to: require a minimal information as input; work automatically; reduce the user intervention and facilitate the interaction by means of a user-friendly graphic interface. Program specification X-ray, synchrotron or neutron diffraction data can be used. There are no limits on the number of counts in the pattern. The background of system EXPO2014 is the updated version of EXPO2009. Its main steps are (please, select each topic for more details): Indexing An automatic peak search routine generates a list of “d” values corresponding to the experimental diffraction peaks. The values are processed for providing the cell parameters. Space Group Determination A statistical analysis of the experimental diffraction intensities compatible with the identified crystal system is performed. This step is able to provide a list of all the possible extinction symbols ranked according to calculated probability values. For each extinction symbol, the corresponding list of compatible space groups (one or more than one) is supplied via graphic interface. Structure Solution Structure solution can be carried out by adopting one of the two alternative following approaches: Direct Methods for phasing the reflections. The electron density map is calculated and then optimized. Direct Space methods for generating trial structure models (compatible with the expected molecular geometry) and selecting that one providing the best agreement with the experimental data. 5 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo Rietveld Refinement The structure model is refined by the Rietveld method. Each procedure of EXPO2014 can be activated by using a specified command or directive in the input file, or by selecting a specific graphic option. The information about commands, directives and graphic options are contained in this manual. EXPO2014 creates the following files (in the work directory): – a direct access file to preserve data and results (name.bin); – an ascii file containing the Miller indices (hkl) and the experimental structure factor moduli of the generated reflections (name.hkl); – an ascii file which stores diffraction peak positions if the indexing process has been carried out (name.pea); – an output file containing information about all the steps of the structure determination process (name.out). Other files associated to the application of particular strategies can be also generated by EXPO2014. Authors A. Altomare*, C. Cuocci*, C. Giacovazzo*, A. Moliterni*, R. Rizzi*, N. Corriero* and A. Falcicchio* *Institute of Crystallography-CNR, via Amendola 122/o 70126 Bari, Italy [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] Contact For questions, problems and suggestions, please, visit http://www.ba.ic.cnr.it/softwareic/expo/contact-us/ We kindly ask you to fill the survey. Acknowledgements The authors are indebted to Giovanni Luca Cascarano and Mariarosaria Mallamo for their help in the development of the graphic environment. 6 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo Main References If EXPO2014 is used in the solution process of a structure, whose results are published in a scientific paper, please, include the following reference: A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, N. Corriero and A. Falcicchio, (2013). J. Appl. Cryst. 46, 1231-1235 . _______________________________________________ 7 / 177 Expo2014 - 09-17-2021 Crystal structures solution by powder diffraction data - http://www.ba.ic.cnr.it/softwareic/expo EXPO2014 installation http://www.ba.ic.cnr.it/softwareic/expo/expo2014-installation/ Hardware and software environment EXPO2014 is built utilizing OpenGL for three-dimensional molecular visualization and GTK for the graphic user interface. All binary packages are pre-compiled by using the Intel Fortran Composer XE 2013 and the GNU C++ compiler. Expo2014 runs on the most popular operating systems: Windows, Apple’s