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Z-matrix template-based substitution approach for enumeration of 3D molecular structures

The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of co...

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Detalles Bibliográficos
Autores principales: Lorpaiboon, Wanutcha, Limpanuparb, Taweetham
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374508/
https://www.ncbi.nlm.nih.gov/pubmed/34430311
http://dx.doi.org/10.1016/j.mex.2021.101416
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author Lorpaiboon, Wanutcha
Limpanuparb, Taweetham
author_facet Lorpaiboon, Wanutcha
Limpanuparb, Taweetham
author_sort Lorpaiboon, Wanutcha
collection PubMed
description The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of compounds of identical formula by quantum chemical methods. This paper provides a comprehensive description of the overall concept followed by a practical tutorial to the approach. • The four steps required for Z-matrix template-based substitution are template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template. • The generated tuples can be used to create chemical identifiers to query compound properties from chemical databases. • All of these steps are demonstrated in this paper by common model compounds and are very straightforward for an undergraduate audience to reproduce. A comparison of the approach in this paper and other options is also discussed.
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spelling pubmed-83745082021-08-23 Z-matrix template-based substitution approach for enumeration of 3D molecular structures Lorpaiboon, Wanutcha Limpanuparb, Taweetham MethodsX Method Article The exhaustive enumeration of 3D chemical structures based on Z-matrix templates has recently been used in the quantum chemical investigation of constitutional isomers, diastereomers and rotamers. This simple yet powerful initial structure generation approach can apply beyond the investigation of compounds of identical formula by quantum chemical methods. This paper provides a comprehensive description of the overall concept followed by a practical tutorial to the approach. • The four steps required for Z-matrix template-based substitution are template construction, generation of tuples for substitution sites, removal of duplicate tuples and substitution on the template. • The generated tuples can be used to create chemical identifiers to query compound properties from chemical databases. • All of these steps are demonstrated in this paper by common model compounds and are very straightforward for an undergraduate audience to reproduce. A comparison of the approach in this paper and other options is also discussed. Elsevier 2021-06-17 /pmc/articles/PMC8374508/ /pubmed/34430311 http://dx.doi.org/10.1016/j.mex.2021.101416 Text en © 2021 The Author(s). Published by Elsevier B.V. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Method Article
Lorpaiboon, Wanutcha
Limpanuparb, Taweetham
Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title_full Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title_fullStr Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title_full_unstemmed Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title_short Z-matrix template-based substitution approach for enumeration of 3D molecular structures
title_sort z-matrix template-based substitution approach for enumeration of 3d molecular structures
topic Method Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374508/
https://www.ncbi.nlm.nih.gov/pubmed/34430311
http://dx.doi.org/10.1016/j.mex.2021.101416
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