Fundamental Developments in Direct-Space Techniques for Structure Solution from Powder Diffraction Data

2004 ◽  
Vol 443-444 ◽  
pp. 11-22
Author(s):  
Scott Habershon ◽  
David Albesa-Jové ◽  
Eugene Y. Cheung ◽  
Giles W. Turner ◽  
Roy L. Johnston ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Investigation ◽  
Powder Diffraction Data ◽  
Single Crystal Diffraction ◽  
R Factor ◽  
Structure Solution

Solids that can be prepared only as microcrystalline powders are not suitable for structural investigation using single crystal diffraction techniques, and it is necessary instead to carry out structure determination using powder diffraction data. In this paper, we focus on a direct-space strategy for solving crystal structures directly from powder diffraction data in which a hypersurface based on the powder profile R-factor Rwp is searched using a Genetic Algorithm, and we highlight some recent fundamental developments relating to this methodology.

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

2019 ◽  
Vol 234 (4) ◽  
pp. 257-268 ◽  
Author(s):  
Carina Schlesinger ◽  
Michael Bolte ◽  
Martin U. Schmidt
Keyword(s):  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Real Space ◽  
Powder Diffraction Data ◽  
The Real ◽  
Pharmaceutical Salts ◽  
Structure Solution ◽  
Space Method

Abstract Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

FIDDLE. Simultaneous Indexing and Structure Solution from Powder Diffraction Data using a Genetic Algorithm and Correlation Functions

2019 ◽  
Author(s):  
Carmen Guguta ◽  
Jan M.M. Smits ◽  
Rene de Gelder
Keyword(s):  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Correlation Functions ◽  
Cross Correlation ◽  
Simultaneous Optimization ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Matching Technique

A method for the determination of crystal structures from powder diffraction data is presented that circumvents the difficulties associated with separate indexing. For the simultaneous optimization of the parameters that describe a crystal structure a genetic algorithm is used together with a pattern matching technique based on auto and cross correlation functions.<br>

Gaining insights into the evolutionary behaviour in genetic algorithm calculations, with applications in structure solution from powder diffraction data

2002 ◽  
Vol 353 (3-4) ◽  
pp. 185-194 ◽  
Author(s):  
Scott Habershon ◽  
Kenneth D.M. Harris ◽  
Roy L. Johnston ◽  
Giles W. Turner ◽  
Jennifer M. Johnston
Keyword(s):  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
Structure Solution

scholarly journals Structure determination from powder diffraction data

2007 ◽  
Vol 64 (1) ◽  
pp. 52-64 ◽  
Author(s):  
W. I. F. David ◽  
K. Shankland
Keyword(s):  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Optimization Methods ◽  
Protein Crystal ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Combined Use ◽  
Complementary Techniques

Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

Crystal structure determination from powder diffraction data by the application of a genetic algorithm

1997 ◽  
Vol 212 (8) ◽  
Author(s):  
K. Shankland ◽  
W. I. F. David ◽  
T. Csoka
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Full Advantage ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Structure Determination ◽  
Powder Diffraction Data ◽  
Flexible Molecules

AbstractA genetic algorithm (GA) based method for solving crystal structures directly from powder diffraction data has been developed. The method is based around fitting the diffraction data generated from trial structures against the measured diffraction data and has the ability to handle flexible molecules and multiple fragments. It is computationally highly efficient and takes full advantage of the implicit parallelism of the GA. The method is illustrated with the solutions of three crystal structures of varying complexity.

scholarly journals Structure determination from X-ray powder diffraction data at low resolution

2014 ◽  
Vol 70 (a1) ◽  
pp. C143-C143
Author(s):  
Hongliang Xu
Keyword(s):  
Single Crystal ◽  
Diffraction Pattern ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Direct Methods ◽  
Atomic Resolution ◽  
Powder Diffraction Data ◽  
Low Resolution

Knowledge of the structural arrangement of atoms in solids is necessary to facilitate the study of their properties. The best and most detailed structural information is obtained when the diffraction pattern of a single crystal a few tenths of a millimeter in each dimension is analyzed, but growing high-quality crystals of this size is often difficult, sometimes impossible. However, many crystallization experiments that do not yield single crystals do yield showers of randomly oriented micro-crystals that can be exposed to X-rays simultaneously to produce a powder diffraction pattern. Direct Methods routinely solve crystal structures when single-crystal diffraction data are available at atomic resolution (1.0-1.2Å), but fail to determine micro-crystal structures due to reflections overlapping and low-resolution powder diffraction data. By artificially and intelligently extending the measured data to atomic resolution, we have successfully solved structures having low-resolution diffraction data that were hard to solve by other direct-method based computation procedures. The newly developed method, Powder Shake-and-Bake, is implemented in a computer program PowSnB. PowSnB can be incorporated into the state-of-the-art software package EXPO that includes powder data reduction, structure determination and structure refinement. The new combination could have potential to solve structures that have never been solved before by direct-methods approach.

Determination of the [Pt(NH3)5Cl]Br3 crystal structure from X-ray powder diffraction data using multi-population genetic algorithm

2017 ◽  
Vol 32 (S1) ◽  
pp. S110-S117 ◽  
Author(s):  
A. N. Zaloga ◽  
I. S. Yakimov ◽  
P. S. Dubinin
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Population Genetic ◽  
Powder Diffraction Data ◽  
Distribution Maps ◽  
Structure Solution ◽  
Population Genetic Algorithm

The paper describes an approach for automated crystal structure solution from powder diffraction data using the multi-population genetic algorithm (MPGA). The advantage of using co-evolution with the best individual exchange, compared with the using of the evolution with a single genetic algorithm without interpopulation exchange, is shown. As an example, the paper describes the use of MPGA for solving the [Pt(NH3)5Cl]Br3 crystal structure, having the tetragonal I41/a space group [a = 17.2587(5) Å, c = 15.1164(3) Å, Z = 16, unit-cell volume V = 4502.61(10) Å3]. The MPGA convergence charts and the atomic positions distribution maps of the MPGA populations are given. The description of the final structure solution is also shown.

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