Free-distribution software for crystal structure determination from powder diffraction (SDPD).
For the 2-ethoxybenzamide exercise during the workshop download: (1) WINPLOTR, (2) MERCURY, (3) McMAILLE, (4) CHEKCELL, (5) ARGUSLAB, (6) winPSSP, (7) EXPO2014, (8) GSAS-II.
Conversion of raw data files into different formats:
PowDLL converter: http://users.uoi.gr/nkourkou/powdll/
Molecular building and molecular geometry optimization:
Arguslab: http://www.arguslab.com/arguslab.com/ArgusLab.html
Used to build from scratch a molecule and optimize its geometry by molecular mechanics and semi-empirical methods. It can also complete and modify molecules downloaded from the Cambridge Structural Database. The results are saved into *.agl files (for Arguslab) an ASCII text Cartesian coordinate files (*.xyz).
Avogadro: https://avogadro.cc/
Data visualization, determination of peak positions, indexing, background estimation, Le Bail and Rietveld fits:
WinPLOTR and FULLPROF:http://www.cdifx.univ-rennes1.fr/winplotr/winplotr.htm
Peak fitting:
Xfit: http://www.ccp14.ac.uk/tutorial/xfit-95/xfit.htm
Used to fit powder diffraction peaks through the fundamental parameters approach, and Pseudo-Voigt and Pearson VII peak shape functions. Peak positions and intensities are obtained in ASCII text files.
Indexing:
McMAILLE: http://www.cristal.org/McMaille/short-manual.html
Right-click on “McMaille-v4.zip” and in the window left-click on “save link as”, and choose the directory for the zip file (e.g., C:/installation_files). Then unzip the file to a chosen folder, e.g. C:/McMaille.
CRYSFIRE: www.ccp14.ac.uk/tutorial/crys/index.html
Space group determination, unit cell evaluation and refinement:
CHEKCELL and CELREF: CCP14 Homepage – Tutorials and Examples – LMGP suite for Windows by Jean Laugier and Bernard Bochu
Used to visualize the fit of peak positions calculated from unit-cell parameters (calculated with indexing software such as McMAILLE, CRYSFIRE, etc) and a *.prn file with experimental peak positions (e.g., written with WinPLOTR). Other uses are the determination of likely space groups and the refinement of unit-cell parameters.
Le Bail, Pawley and Rietveld fits:
EXPGUI & GSAS: https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows
Used for whole pattern decomposition through the Le Bail or Pawley methods as well as for Rietveld refinement. The former results in a reflections file (*.rfl) which can be read by software applying direct-space methods such as WinPSSP. For Rietveld refinements, it is simple to refine small-molecule crystal structures using rigid body geometries or soft bond distance and bond angle restraints and group constraints for isotropic atomic displacement parameters.
GSAS-II: subversion.xray.aps.anl.gov/trac/pyGSAS https://cdifx.univ-rennes1.fr/winplotr/winplotr_frm_downloads.htm
FULLPROF and WinPLOTR: https://cdifx.univ-rennes1.fr/winplotr/winplotr_frm_downloads.htm
Crystal structure solution:
Various free-distribution software packages can be used to solve crystal structures from powders, such as EXPO2014 (direct methods and direct-space methods), and FOX (direct-space methods). WinPSSP (direct-space methods for small-molecule solids) can be used together with WinPLOTR (which includes FULLPROF and the indexing software ITO, TREOR and DICVOL06), CHEKCELL and GSAS.
WinPSSP: http://users.uoi.gr/nkourkou/winpssp/
Used for the location of fragments in the unit cell (e.g., molecules in Cartesian coordinate files composing the asymmetric unit) by direct-space methods using the simulated annealing algorithm.
EXPO2014: http://www.ba.ic.cnr.it/softwareic/expo/expo2014-download/
Used for the determination of atomic coordinates by direct methods and direct-space methods, from laboratory X-ray, synchrotron or neutron powder diffraction data (also for indexing and Rietveld refinement). It works through a semi-automatic procedure requiring minimum user intervention.
FOX: sourceforge.net/projects/objcryst/.
Crystal structure visualization:
Mercury: https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/
Used to visualize molecular and crystal structures from *.cif files and other commonly used formats.
Ortep-3 for Windows: www.chem.gla.ac.uk/~louis/software/ortep/
Calculation of hydrogen positions
CRYSTALS: www.xtl.ox.ac.uk/crystals.1.html
CRYSTALS is a single-crystal diffraction software. We will use it to add Hydrogen atoms to small-molecule organic solids
Crystal structure validation:
PLATON for Windows: www.chem.gla.ac.uk/~louis/software/platon/ . Online: https://checkcif.iucr.org/
Other websites with software are the CCP14 website: http://www.ccp14.ac.uk/
Sincris crystallographic software database: ww1.iucr.org/sincris-top/logiciel/def.html
Armel Le Bail webpage: www.cristal.org/
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