Literature DB >> 33597010

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

Siripreeya Phankingthongkum1, Taweetham Limpanuparb2.   

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.

Entities:  

Keywords:  Chemical education; General chemistry; Molecular graphics software; Molecular model

Mesh:

Year:  2021        PMID: 33597010      PMCID: PMC7887714          DOI: 10.1186/s13104-021-05461-7

Source DB:  PubMed          Journal:  BMC Res Notes        ISSN: 1756-0500


  4 in total

1.  Gabedit--a graphical user interface for computational chemistry softwares.

Authors:  Abdul-Rahman Allouche
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

2.  An idea to explore: Use of augmented reality for teaching three-dimensional biomolecular structures.

Authors:  Celeste N Peterson; Sara Z Tavana; Olukemi P Akinleye; Walter H Johnson; Melanie B Berkmen
Journal:  Biochem Mol Biol Educ       Date:  2020-03-23       Impact factor: 1.160

3.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

Authors:  Marcus D Hanwell; Donald E Curtis; David C Lonie; Tim Vandermeersch; Eva Zurek; Geoffrey R Hutchison
Journal:  J Cheminform       Date:  2012-08-13       Impact factor: 5.514

4.  In silico geometric and energetic data of all possible simple rotamers made of non-metal elements.

Authors:  Taweetham Limpanuparb; Sopanant Datta; Kridtin Chinsukserm; Peerayar Teeraniramitr
Journal:  Data Brief       Date:  2020-03-19
  4 in total
  1 in total

1.  Steric effects vs. electron delocalization: a new look into the stability of diastereomers, conformers and constitutional isomers.

Authors:  Sopanant Datta; Taweetham Limpanuparb
Journal:  RSC Adv       Date:  2021-06-10       Impact factor: 3.361

  1 in total

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