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Relevant bibliographies by topics / Organic crystal-structure prediction (CSP) methods; Blind test

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Academic literature on the topic 'Organic crystal-structure prediction (CSP) methods; Blind test'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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Journal articles on the topic "Organic crystal-structure prediction (CSP) methods; Blind test"

1

Reilly, Anthony M., Richard I. Cooper, Claire S. Adjiman, et al. "Report on the sixth blind test of organic crystal structure prediction methods." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, no. 4 (2016): 439–59. http://dx.doi.org/10.1107/s2052520616007447.

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The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional appr

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2

Bowskill, David H., Isaac J. Sugden, Stefanos Konstantinopoulos, Claire S. Adjiman, and Constantinos C. Pantelides. "Crystal Structure Prediction Methods for Organic Molecules: State of the Art." Annual Review of Chemical and Biomolecular Engineering 12, no. 1 (2021): 593–623. http://dx.doi.org/10.1146/annurev-chembioeng-060718-030256.

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The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them wit

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3

Groom, Colin R., and Anthony M. Reilly. "Sixth blind test of organic crystal-structure prediction methods." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 70, no. 4 (2014): 776–77. http://dx.doi.org/10.1107/s2052520614015923.

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Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.

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4

Lommerse, Jos P. M., W. D. Sam Motherwell, Herman L. Ammon, et al. "A test of crystal structure prediction of small organic molecules." Acta Crystallographica Section B Structural Science 56, no. 4 (2000): 697–714. http://dx.doi.org/10.1107/s0108768100004584.

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A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were cl

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5

Brandenburg, Jan Gerit, and Stefan Grimme. "Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, no. 4 (2016): 502–13. http://dx.doi.org/10.1107/s2052520616007885.

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We analyze the energy landscape of the sixth crystal structure prediction blind test targets with variousfirst principlesandsemi-empiricalquantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko–Scheffler (TS) method, and the density-dependent d

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6

Bardwell, David A., Claire S. Adjiman, Yelena A. Arnautova, et al. "Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test." Acta Crystallographica Section B Structural Science 67, no. 6 (2011): 535–51. http://dx.doi.org/10.1107/s0108768111042868.

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Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CS

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7

Day, Graeme M., Timothy G. Cooper, Aurora J. Cruz-Cabeza, et al. "Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test." Acta Crystallographica Section B Structural Science 65, no. 2 (2009): 107–25. http://dx.doi.org/10.1107/s0108768109004066.

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We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular di

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8

Sugden, Isaac, Claire S. Adjiman, and Constantinos C. Pantelides. "Accurate and efficient representation of intramolecular energy inab initiogeneration of crystal structures. I. Adaptive local approximate models." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 72, no. 6 (2016): 864–74. http://dx.doi.org/10.1107/s2052520616015122.

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The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in theCrystalPredictor II[Habgoodet al.(2015).J. Chem. Theory Comput.11, 1957–1969] program is presented, where the most efficient use of computational effort is ensuredviathe use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule's conformations is initially evaluated

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9

Hoja, Johannes, Hsin-Yu Ko, Marcus A. Neumann, Roberto Car, Robert A. DiStasio, and Alexandre Tkatchenko. "Reliable and practical computational description of molecular crystal polymorphs." Science Advances 5, no. 1 (2019): eaau3338. http://dx.doi.org/10.1126/sciadv.aau3338.

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Reliable prediction of the polymorphic energy landscape of a molecular crystal would yield profound insight into drug development in terms of the existence and likelihood of late-appearing polymorphs. However, the computational prediction of molecular crystal polymorphs is highly challenging due to the high dimensionality of conformational and crystallographic space accompanied by the need for relative free energies to within 1 kJ/mol per molecule. In this study, we combine the most successful crystal structure sampling strategy with the most successful first-principles energy ranking strategy

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10

Mörschel, Philipp, and Martin U. Schmidt. "Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry." Acta Crystallographica Section A Foundations and Advances 71, no. 1 (2015): 26–35. http://dx.doi.org/10.1107/s2053273314018907.

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A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12–15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM

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Dissertations / Theses on the topic "Organic crystal-structure prediction (CSP) methods; Blind test"

1

Day, G. M., T. G. Cooper, A. Cruz-Cabeza, et al. "Significant progress in predicting the crystal structures of small organic molecules ¿ a report on the fourth blind test." International Union of Crystallography, 2009. http://hdl.handle.net/10454/4748.

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no<br>We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecu

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2

Reilly, A. M., R. I. Cooper, C. S. Adjiman, et al. "Report on the sixth blind test of organic crystal-structure prediction methods." 2016. http://hdl.handle.net/10454/8580.

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Yes<br>The sixth blind test of organic crystal-structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal, and a bulky exible molecule. This blind test has seen substantial growth in the number of submissions, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-

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