A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software

OBJECTIVE: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. RESULTS: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, vis...

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Autores principales: Phankingthongkum, Siripreeya, Limpanuparb, Taweetham
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Research Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7887714/
https://www.ncbi.nlm.nih.gov/pubmed/33597010
http://dx.doi.org/10.1186/s13104-021-05461-7
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author Phankingthongkum, Siripreeya
Limpanuparb, Taweetham
author_facet Phankingthongkum, Siripreeya
Limpanuparb, Taweetham
author_sort Phankingthongkum, Siripreeya
collection PubMed
description OBJECTIVE: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. RESULTS: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets.
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spelling pubmed-78877142021-02-17 A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software Phankingthongkum, Siripreeya Limpanuparb, Taweetham BMC Res Notes Research Note OBJECTIVE: The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented. RESULTS: Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D structures with bond-line structures. These topics are typically covered in general chemistry for first-year undergraduate students. Detailed step-by-step procedures are provided for all tasks for both programs so that instructors and students can adopt one of the two programs in their teaching and learning as an alternative to molecular model sets. BioMed Central 2021-02-17 /pmc/articles/PMC7887714/ /pubmed/33597010 http://dx.doi.org/10.1186/s13104-021-05461-7 Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Note
Phankingthongkum, Siripreeya
Limpanuparb, Taweetham
A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title_full A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title_fullStr A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title_full_unstemmed A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title_short A virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
title_sort virtual alternative to molecular model sets: a beginners’ guide to constructing and visualizing molecules in open-source molecular graphics software
topic Research Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7887714/
https://www.ncbi.nlm.nih.gov/pubmed/33597010
http://dx.doi.org/10.1186/s13104-021-05461-7
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