Method for the computational comparison of crystal structures

Willighagen, Egon; Wehrens, Ron; Verwer, P.; Gelder, René de; Buydens, L.M.C.

doi:10.1107/s0108768104028344

Cited by 45 publications

(33 citation statements)

References 16 publications

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“…7, and remains a good match if the sample size is increased to 30 molecules. This type of conflict between a good visual match and non-agreement of the space group of the MGAC match and the experiment crystal structure was previously mentioned for the case of GAHPIO and is also discussed below for the case of CBMZPN and exemplify the issues encountered when comparing crystal structures 65. No match was found for the BANGOM02 polymorph.…”

Section: Resultsmentioning

confidence: 91%

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

et al. 2009

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This paper describes the application of our distributed computing framework for crystal structure prediction (CSP), Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC) to predict the crystal structure of flexible molecules using the General Amber Force Field (GAFF) and the CHARMM program. The MGAC distributed computing framework which includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling crystal structures using a distributed parallel genetic algorithm, local energy minimization of the structures followed by the classifying, sorting and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.

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Section: Resultsmentioning

confidence: 91%

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

et al. 2009

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“…Other methods developed for crystal structures have been developed too, for example, using a radial distribution functions [56], which capture the packing of organic crystal structures. Such approaches have been used to cluster crystal structures [57] and compare properties [58].…”

Section: A Categorization Of Descriptorsmentioning

confidence: 99%

A Survey of Quantitative Descriptions of Molecular Structure

Guha

Willighagen²

2012

Current Topics in Medicinal Chemistry

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Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, across a molecular surface. In this article we first present a broad categorization of descriptors and then describe applications and toolkits that can be employed to evaluate them. We highlight a number of issues surrounding molecular descriptor calculations such as versioning and reproducibility and describe how some toolkits have attempted to address these problems.

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“…The works of Willighagen and Oganov combine radial distribution functions with ion-specific information such as charge state or neutron scattering length to describe crystal structure. 5,6 De Gelder derives his similarity function using weighted cross correlations of the powder diffraction pattern, 7 while Rupp et al have used a matrix representation of structure based upon the Coulomb interaction between ions.…”

Section: Introductionmentioning

confidence: 99%

Proposed definition of crystal substructure and substructural similarity

2014

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There is a clear need for a practical and mathematically rigorous description of local structure in inorganic compounds so that structures and chemistries can be easily compared across large data sets. A new method for decomposing crystal structures into substructures is given, and a similarity function between those substructures is defined. The similarity function is based upon both geometric and chemical similarity. This construction allows for large-scale data mining of substructural properties, and the analysis of substructures and void spaces within crystal structures. The method is validated via the prediction of Li ion intercalation sites for the oxides. Tested on databases of known Li-ion containing oxides, the method reproduces all Li-ion sites in an oxide with a maximum of 4 incorrect guesses 80% of the time.

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Method for the computational comparison of crystal structures

Cited by 45 publications

References 16 publications

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

A Survey of Quantitative Descriptions of Molecular Structure

Proposed definition of crystal substructure and substructural similarity

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