DASH: a program for crystal structure determination from powder diffraction data

2006 ◽  
Vol 39 (6) ◽  
pp. 910-915 ◽  
Author(s):  
William I. F. David ◽  
Kenneth Shankland ◽  
Jacco van de Streek ◽  
Elna Pidcock ◽  
W. D. Samuel Motherwell ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Global Minimum ◽  
Molecular Structures ◽  
Powder Diffraction Data ◽  
Peak Fitting ◽  
Structure Factors ◽  
Integrated Intensities ◽  
User Friendly

DASHis a user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures. Algorithms for multiple peak fitting, unit-cell indexing and space-group determination are included as part of the program. Molecular models can be read in a number of formats and automatically converted to Z-matrices in which flexible torsion angles are automatically identified. Simulated annealing is used to search for the global minimum in the space that describes the agreement between observed and calculated structure factors. The simulated annealing process is very fast, which in part is due to the use of correlated integrated intensities rather than the full powder pattern. Automatic minimization of the structures obtained by simulated annealing and automatic overlay of solutions assist in assessing the reproducibility of the best solution, and therefore in determining the likelihood that the global minimum has been obtained.

Crystal structure and diffraction data for a polymorph of voglibose (C10H21NO7)

2010 ◽  
Vol 25 (S1) ◽  
pp. S28-S30
Author(s):  
G. Q. Zhang ◽  
G. L. Lv
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Rigid Body ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Molecular Structures ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Crystal And Molecular Structures

X-ray powder diffraction data of voglibose are reported, and its crystal and molecular structures were determined by simulated annealing and rigid-body Rietveld refinement methods. Voglibose was found to be crystallized in triclinic symmetry with space group P-1. The lattice parameters were determined to be a=6.1974(6) Å, b=6.9918(5) Å, c=7.3955(9) Å, α=70.8628(3), β=103.5312(4), γ=94.3867(5)°, V=294.2(2) Å3, and ρcal=1.495 g/cm3. The crystal structure contains isolated C10H21NO7 molecular.

QUALX2.0: a qualitative phase analysis software using the freely available database POW_COD

2015 ◽  
Vol 48 (2) ◽  
pp. 598-603 ◽  
Author(s):  
Angela Altomare ◽  
Nicola Corriero ◽  
Corrado Cuocci ◽  
Aurelia Falcicchio ◽  
Anna Moliterni ◽  
...  
Keyword(s):  
Phase Analysis ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Phase Identification ◽  
Powder Diffraction Data ◽  
Structure Information ◽  
Previous Version ◽  
Experimental Diffraction Pattern ◽  
User Friendly ◽  
Qualitative Phase

QUALX2.0is the new version ofQUALX, a computer program for qualitative phase analysis by powder diffraction data. The previous version ofQUALXwas able to carry out phase identification by querying the PDF-2 commercial database. The main novelty ofQUALX2.0is the possibility of querying also a freely available database, POW_COD. POW_COD has been built up by starting from the structure information contained in the Crystallography Open Database (COD). The latter is a growing collection of diffraction data, freely downloadable from the web, corresponding to inorganic, metal–organic, organic and mineral structures.QUALX2.0retains the main capabilities of the previous version: (a) automatically estimating and subtracting the background; (b) locating the experimental diffraction peaks; (c) searching the database for single-phase pattern(s) best matching to the experimental powder diffraction data; (d) taking into account suitable restraints in the search; (e) performing a semi-quantitative analysis; (f) enabling the change of default choices and strategiesviaa user-friendly graphic interface. The advances ofQUALX2.0with respect toQUALXinclude (i) a wider variety of types of importable ASCII file containing the experimental diffraction pattern and (ii) new search–match options. The program, written in Fortran and C++, runs on PCs under the Windows operating system. The POW_COD database is exported in SQLite3 format.

ExtSym: a program to aid space-group determination from powder diffraction data

2008 ◽  
Vol 41 (6) ◽  
pp. 1177-1181 ◽  
Author(s):  
Anders J. Markvardsen ◽  
Kenneth Shankland ◽  
William I. F. David ◽  
John C. Johnston ◽  
Richard M. Ibberson ◽  
...  
Keyword(s):  
Error Estimates ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
National Laboratory ◽  
Powder Diffraction Data ◽  
Acta Cryst ◽  
Data Set ◽  
Crystal System ◽  
Wide Range ◽  
Integrated Intensities

Once unit-cell dimensions have been determined from a powder diffraction data set and therefore the crystal system is known (e.g.orthorhombic), the method presented by Markvardsen, David, Johnson & Shankland [Acta Cryst.(2001), A57, 47–54] can be used to generate a table ranking the extinction symbols of the given crystal system according to probability. Markvardsenet al.tested a computer program (ExtSym) implementing the method against Pawley refinement outputs generated using theTF12LSprogram [David, Ibberson & Matthewman (1992). Report RAL-92-032. Rutherford Appleton Laboratory, Chilton, Didcot, Oxon, UK]. Here, it is shown thatExtSymcan be used successfully with many well known powder diffraction analysis packages, namelyDASH[David, Shankland, van de Streek, Pidcock, Motherwell & Cole (2006).J. Appl. Cryst.39, 910–915],FullProf[Rodriguez-Carvajal (1993).Physica B,192, 55–69],GSAS[Larson & Von Dreele (1994). Report LAUR 86-748. Los Alamos National Laboratory, New Mexico, USA],PRODD[Wright (2004).Z. Kristallogr.219, 1–11] andTOPAS[Coelho (2003). Bruker AXS GmbH, Karlsruhe, Germany]. In addition, a precise description of the optimal input forExtSymis given to enable other software packages to interface withExtSymand to allow the improvement/modification of existing interfacing scripts.ExtSymtakes as input the powder data in the form of integrated intensities and error estimates for these intensities. The output returned byExtSymis demonstrated to be strongly dependent on the accuracy of these error estimates and the reason for this is explained.ExtSymis tested against a wide range of data sets, confirming the algorithm to be very successful at ranking the published extinction symbol as the most likely.

A benchmark method for global optimization problems in structure determination from powder diffraction data

2010 ◽  
Vol 43 (3) ◽  
pp. 401-406 ◽  
Author(s):  
Kenneth Shankland ◽  
Anders J. Markvardsen ◽  
Christopher Rowlatt ◽  
Norman Shankland ◽  
William I. F. David
Keyword(s):  
Powder Diffraction ◽  
Conjugate Gradient ◽  
Diffraction Data ◽  
Structure Determination ◽  
Global Minimum ◽  
Optimization Problems ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Newton Raphson ◽  
Quasi Newton

Quasi-Newton–Raphson minimization and conjugate gradient minimization have been used to solve the crystal structures of famotidine form B and capsaicin from X-ray powder diffraction data and characterize the χ2agreement surfaces. One million quasi-Newton–Raphson minimizations found the famotidine global minimum with a frequency ofca1 in 5000 and the capsaicin global minimum with a frequency ofca1 in 10 000. These results, which are corroborated by conjugate gradient minimization, demonstrate the existence of numerous pathways from some of the highest points on these χ2agreement surfaces to the respective global minima, which are passable using only downhill moves. This important observation has significant ramifications for the development of improved structure determination algorithms.

Molecular, crystallographic and algorithmic factors in structure determination from powder diffraction data by simulated annealing

2002 ◽  
Vol 35 (4) ◽  
pp. 443-454 ◽  
Author(s):  
Kenneth Shankland ◽  
Lorraine McBride ◽  
William I. F. David ◽  
Norman Shankland ◽  
Gerald Steele
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Solution Process ◽  
Search Space ◽  
Systematic Investigation ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Structure Solution

The crystal structure of famotidine form B has been solved directly from powder diffraction data by the application of simulated annealing. The molecule crystallizes in the monoclinic space groupP21/cwith refined unit-cell dimensionsa = 17.6547 (4),b= 5.2932 (1),c= 18.2590 (3) Å and β = 123.558 (1)° atT= 130 K. The core of this work is a systematic investigation of the influence of algorithmic, crystallographic and molecular factors on the structure solution process. With an appropriate choice of annealing schedule, molecular description and diffraction data range, the overall number of successes in solving the crystal structure is close to 100%. Other factors, including crystallographic search space restrictions and parameter sampling method, have little effect on the structure solution process. The basic principles elucidated here have been factored into the design of theDASHstructure solution program.

Extraction and use of correlated integrated intensities with powder diffraction data

2004 ◽  
Vol 219 (12) ◽  
Author(s):  
Jon P. Wright
Keyword(s):  
Data Quality ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Shape Function ◽  
Peak Shape ◽  
Powder Diffraction Data ◽  
Diffraction Profile ◽  
Peak Overlap ◽  
Integrated Intensities ◽  
Significant Size

AbstractThe transformation of a powder diffraction profile into a set of correlated integrated intensities allows crystallographic calculations to be performed without modelling raw diffractometer counts. By carrying out this transformation it is possible to preserve the information about peak overlap without needing to retain the multitude of experimental details and description of the peak shape function. An implementation is described which allows problems of significant size to be tackled. Least squares refinement, issues of data quality and the generation and importance of free

Crystal and molecular structures of 2-[1-(2-aminoethyl)-2-imidazolidinylidene]-2-nitroacetonitrile (C7H11N5O2) and 2,6-diamino-5-hydroxy-3-nitro-4H-pyrazolo[1,5-a]pyrimidin-7-one monohydrate (C6H6N6O4·H2O) from X-ray, synchrotron and neutron powder diffraction data

1999 ◽  
Vol 55 (4) ◽  
pp. 554-562 ◽  
Author(s):  
V. V. Chernyshev ◽  
A. N. Fitch ◽  
E. J. Sonneveld ◽  
A. I. Kurbakov ◽  
V. A. Makarov ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Neutron Powder Diffraction ◽  
Molecular Structures ◽  
Search Procedure ◽  
Grid Search ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Crystal And Molecular Structures ◽  
Neutron Powder Diffraction Data

The crystal and molecular structures of 2-[1-(2-aminoethyl)-2-imidazolidinylidene]-2-nitroacetonitrile [C7H11N5O2; space group P21/n; Z = 4; a = 7.4889 (8), b = 17.273 (2), c = 7.4073 (8) Å, β = 111.937 (6)°], (I), and 2,6-diamino-5-hydroxy-3-nitro-4H-pyrazolo[1,5-a]pyrimidin-7-one monohydrate [C6H6N6O4·H2O; space group P21/n; Z = 4; a = 17.576 (3), b = 10.900 (2), c = 4.6738 (6) Å, β = 92.867 (8)°], (II), have been determined from X-ray, synchrotron and neutron powder diffraction data using various methods. The structures were originally solved from Guinier photographs with a grid search procedure and the program MRIA using a priori information from NMR and mass spectra on the possible geometry of the molecules. Because the conformation of molecule (I) changed during the bond-restrained Rietveld refinement, solvent water was found in (II) and, moreover, as both Guinier patterns were corrupted by texture, high-resolution texture-free synchrotron data were collected at the BM16 beamline, ESRF, to confirm the original results. Using the set of |F| 2 values derived from the synchrotron patterns after full-pattern decomposition procedures, the structures of (I) and (II) were solved by direct methods via SHELXS96, SIRPOW.92 and POWSIM without any preliminary models of the molecules, and by Patterson search methods via DIRDIF96 and PATSEE with the use of rigid fragments from each of the molecules. The neutron patterns allowed (I) and (II) to be solved using the grid search procedure and correct initial models of the molecules including H atoms. The results obtained from powder patterns measured on different devices demonstrate the high level of reproducibility and reliability of various powder software and equipment, with a certain preference for synchrotron facilities.

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