ReX: a computer program for structural analysis using powder diffraction data

2009 ◽  
Vol 42 (3) ◽  
pp. 538-539 ◽  
Author(s):  
Mauro Bortolotti ◽  
Luca Lutterotti ◽  
Ivan Lonardelli
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Nonlinear Least Squares ◽  
Geometric Constraints ◽  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Structure Solution ◽  
Definition Of

Multi-platform software has been developed for the analysis of powder diffraction data, with particular focus on structure solution. The program provides a Rietveld optimization engine, with the possibility of refining parameters describing both the sample and the instrument model. Geometric constraints such as rigid fragments and torsion angles can be defined for the atomic structure, to reduce the number of degrees of freedom of the model. An innovative hierarchical description of the asymmetric unit has been adopted, which allows, in principle, the definition of arbitrarily complex geometric relationships. Additionally, global optimization algorithms may be used in place of the standard nonlinear least squares, when particularly challenging problems are being faced.

scholarly journals Crystal structure solution of an elusive polymorph of Dibenzylsquaramide

2013 ◽  
Vol 28 (S2) ◽  
pp. S470-S480 ◽  
Author(s):  
Anna Portell ◽  
Xavier Alcobé ◽  
Latévi M. Lawson Daku ◽  
Radovan Černý ◽  
Rafel Prohens
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Features ◽  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
X Ray ◽  
The Third ◽  
Group Assignment ◽  
Structure Solution

The crystal structure of the third polymorph of dibenzylsquaramide (Portell, A. et al., 2009), (fig. 1) has been determined from laboratory X-ray powder diffraction data by means of direct space methods using the computing program FOX. (Favre-Nicolin and Černý, 2002) The structure resolution has not been straightforward due to several difficulties on the indexing process and in the space group assignment. The asymmetric unit contains two different conformers, which has implied an additional difficulty during the Rietveld (Rietveld, 1969) refinement. All these issues together with particular structural features of disquaramides are discussed.

scholarly journals Solving molecular crystal structures from laboratory X-ray powder diffraction data withDASH: the state of the art and challenges

2005 ◽  
Vol 38 (2) ◽  
pp. 249-259 ◽  
Author(s):  
Alastair J. Florence ◽  
Norman Shankland ◽  
Kenneth Shankland ◽  
William I. F. David ◽  
Elna Pidcock ◽  
...  
Keyword(s):  
Global Optimization ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Search Space ◽  
Powder Diffraction Data ◽  
Multi Centre Study ◽  
X Ray ◽  
Structure Solution

The crystal structures of 35 molecular compounds have been redetermined from laboratory monochromatic capillary transmission X-ray powder diffraction data using the simulated-annealing approach embodied within theDASHstructure solution package. The compounds represent industrially relevant areas (pharmaceuticals; metal coordination compounds; nonlinear optical materials; dyes) in which the research groups in this multi-centre study are active. The molecules were specifically selected to form a series within which the degree of structural complexity (i.e. degrees of freedom in the global optimization) increased systematically, the degrees of freedom increasing with increasing number of optimizable torsion angles in the structural model and with the inclusion of positional disorder or multiple fragments (counterions; crystallization solvent;Z′ > 1). At the lower end of the complexity scale, the structure was solved with excellent reproducibility and high accuracy. At the opposite end of the scale, the more complex search space offered a significant challenge to the global optimization procedure and it was demonstrated that the inclusion of modal torsional constraints, derived from the Cambridge Structural Database, offered significant benefits in terms of increasing the frequency of successful structure solution by restricting the magnitude of the search space in the global optimization.

scholarly journals Breaking the structure complexity limits for powder based structure solution

2014 ◽  
Vol 70 (a1) ◽  
pp. C1789-C1789
Author(s):  
Michal Hušák
Keyword(s):  
Simulated Annealing ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Heavy Atom ◽  
Computational Time ◽  
Correct Result ◽  
Powder Diffraction Data ◽  
Theoretical Limit ◽  
Torsion Angles ◽  
Structure Solution

There exist theoretical predictions trying to determine how much complex crystal structure can be solved from perfect powder diffraction data [1]. The theoretical limit for perfect synchrotron data is about 300 DOF (degree of freedom) while one of the current record solves only 42 DOF problem simplified by heavy atom presence [2]. We have tried to determine a realistic DOF limit based on perfect simulated powder diffraction data. For the simulation we have chosen structures from CSD with 1 single peptide molecule in asymmetric unit cell, 2-8 amino acids, 10-39 DOF. The parameters of the simulated powder diffractogram used were close to typical perfect measurement on ID31 of ESRF - wavelength 0.5 Å, range 0.5°-15°, step 0.002°, FWHM 0.01°. The structure solution tests were done by SA (simulated annealing) in DASH 3.2 software [3]. To speed up the computation we have used parallel processing obtained by MDASH extension. Influence of Mogul CSD based torsion angles bias on the calculation effectiveness was investigated as well. The results demonstrate the required number of SA steps depends exponentially on the problems DOF. This requires for problems close to 30 DOF about 10E+10 SA steps and years of single CPU computational time. The Mogul based bias can significantly help for compounds like peptides - e.g. for simulation based on compound CSD code AHAREH (4 peptides, DOF 24) the Mogul based calculation gives 50 times more often correct result than non-restricted SA run. We believe the 40 DOF structures can be solved routinely on 16-32 CPU clusters from perfect data not influenced by preferred orientation when the Mogul CSD torsion angles bias will be used. Without developing a more efficient algorithm than SA solution we do not see a way how to get really close to the 300 DOF theoretical limit. Acknowledgement: This work was supported by the Grant Agency of Czech Republic, Grant No. 106/14/03636S. Fig. caption: Dependence of required simulated annealing steps required to get one solution on DOF and the use of Mogul based bias.

scholarly journals PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction data

2010 ◽  
Vol 43 (2) ◽  
pp. 370-376 ◽  
Author(s):  
Silvina Pagola ◽  
Peter W. Stephens
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Space Structure ◽  
Molecular Solids ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Structure Solution

This work describes the computer programPSSP(powder structure solution program) for the crystal structure solution of molecular solids from X-ray powder diffraction data. This direct-space structure solution program uses the simulated annealing global optimization algorithm to minimize the difference between integrated intensities calculated from trial models and those extracted in a Le Bail fit of the experimental pattern, using a cost function for dealing with peak overlap through defined intensity correlation coefficients, computationally faster to calculate thanRwp. The methodology outlined is applicable to organic solids composed of moderately complex rigid and flexible molecules, using diffraction data up to relatively low resolution.PSSPperformance tests using 11 molecular solids with six to 20 degrees of freedom are analyzed.

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
Sign in / Sign up

Export Citation Format

Share Document