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一种分子模型集的虚拟替代品:在开源分子图形软件中构建和可视化分子的初学者指南。

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

机构信息

Science Division, Mahidol University International College, Mahidol University, Salaya, Phutthamonthon, Nakhon Pathom, 73170, Thailand.

出版信息

BMC Res Notes. 2021 Feb 17;14(1):66. doi: 10.1186/s13104-021-05461-7.

DOI:10.1186/s13104-021-05461-7
PMID:33597010
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7887714/
Abstract

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.

摘要

目的

介绍一种将分子图形软件作为入门级化学学习者的分子模型集的简单且免费替代品的应用。

结果

基于 Avogadro 或 IQmol,我们为学生提出了四组任务,构建基本分子几何形状、可视化轨道和密度、预测分子极性以及将 3D 结构与键线结构匹配。这些主题通常在为一年级本科生开设的普通化学课程中涵盖。为两个程序的所有任务都提供了详细的逐步操作步骤,以便教师和学生可以在教学中采用这两个程序之一作为分子模型集的替代方案。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/989e/7890864/5a21891ed0bc/13104_2021_5461_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/989e/7890864/5a21891ed0bc/13104_2021_5461_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/989e/7890864/5a21891ed0bc/13104_2021_5461_Fig1_HTML.jpg

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本文引用的文献

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J Chem Educ. 2020 Oct 13;97(10):3872-3876. doi: 10.1021/acs.jchemed.0c00579. Epub 2020 Aug 25.
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geometric and energetic data of all possible simple rotamers made of non-metal elements.由非金属元素构成的所有可能简单旋转异构体的几何和能量数据。
Data Brief. 2020 Mar 19;30:105442. doi: 10.1016/j.dib.2020.105442. eCollection 2020 Jun.
3
An idea to explore: Use of augmented reality for teaching three-dimensional biomolecular structures.
一个值得探索的想法:使用增强现实技术教授三维生物分子结构。
Biochem Mol Biol Educ. 2020 May;48(3):276-282. doi: 10.1002/bmb.21341. Epub 2020 Mar 23.
4
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.阿伏伽德罗:一个先进的语义化学编辑器、可视化和分析平台。
J Cheminform. 2012 Aug 13;4(1):17. doi: 10.1186/1758-2946-4-17.
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Gabedit--a graphical user interface for computational chemistry softwares.Gabedit--用于计算化学软件的图形用户界面。
J Comput Chem. 2011 Jan 15;32(1):174-82. doi: 10.1002/jcc.21600.