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High Throughput Profiling of Molecular Shapes in Crystals
Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfac...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764928/ https://www.ncbi.nlm.nih.gov/pubmed/26908351 http://dx.doi.org/10.1038/srep22204 |
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author | Spackman, Peter R. Thomas, Sajesh P. Jayatilaka, Dylan |
author_facet | Spackman, Peter R. Thomas, Sajesh P. Jayatilaka, Dylan |
author_sort | Spackman, Peter R. |
collection | PubMed |
description | Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. |
format | Online Article Text |
id | pubmed-4764928 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-47649282016-03-02 High Throughput Profiling of Molecular Shapes in Crystals Spackman, Peter R. Thomas, Sajesh P. Jayatilaka, Dylan Sci Rep Article Molecular shape is important in both crystallisation and supramolecular assembly, yet its role is not completely understood. We present a computationally efficient scheme to describe and classify the molecular shapes in crystals. The method involves rotation invariant description of Hirshfeld surfaces in terms of of spherical harmonic functions. Hirshfeld surfaces represent the boundaries of a molecule in the crystalline environment, and are widely used to visualise and interpret crystalline interactions. The spherical harmonic description of molecular shapes are compared and classified by means of principal component analysis and cluster analysis. When applied to a series of metals, the method results in a clear classification based on their lattice type. When applied to around 300 crystal structures comprising of series of substituted benzenes, naphthalenes and phenylbenzamide it shows the capacity to classify structures based on chemical scaffolds, chemical isosterism, and conformational similarity. The computational efficiency of the method is demonstrated with an application to over 14 thousand crystal structures. High throughput screening of molecular shapes and interaction surfaces in the Cambridge Structural Database (CSD) using this method has direct applications in drug discovery, supramolecular chemistry and materials design. Nature Publishing Group 2016-02-24 /pmc/articles/PMC4764928/ /pubmed/26908351 http://dx.doi.org/10.1038/srep22204 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Spackman, Peter R. Thomas, Sajesh P. Jayatilaka, Dylan High Throughput Profiling of Molecular Shapes in Crystals |
title | High Throughput Profiling of Molecular Shapes in Crystals |
title_full | High Throughput Profiling of Molecular Shapes in Crystals |
title_fullStr | High Throughput Profiling of Molecular Shapes in Crystals |
title_full_unstemmed | High Throughput Profiling of Molecular Shapes in Crystals |
title_short | High Throughput Profiling of Molecular Shapes in Crystals |
title_sort | high throughput profiling of molecular shapes in crystals |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764928/ https://www.ncbi.nlm.nih.gov/pubmed/26908351 http://dx.doi.org/10.1038/srep22204 |
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