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GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra
[Image: see text] As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI i...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2019
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988127/ https://www.ncbi.nlm.nih.gov/pubmed/31830414 http://dx.doi.org/10.1021/acs.jcim.9b00956 |
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author | Koenis, Mark A. J. Visser, Olivier Visscher, Lucas Buma, Wybren J. Nicu, Valentin P. |
author_facet | Koenis, Mark A. J. Visser, Olivier Visscher, Lucas Buma, Wybren J. Nicu, Valentin P. |
author_sort | Koenis, Mark A. J. |
collection | PubMed |
description | [Image: see text] As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments. |
format | Online Article Text |
id | pubmed-6988127 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-69881272020-01-30 GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra Koenis, Mark A. J. Visser, Olivier Visscher, Lucas Buma, Wybren J. Nicu, Valentin P. J Chem Inf Model [Image: see text] As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments. American Chemical Society 2019-12-12 2020-01-27 /pmc/articles/PMC6988127/ /pubmed/31830414 http://dx.doi.org/10.1021/acs.jcim.9b00956 Text en Copyright © 2019 American Chemical Society This is an open access article published under a Creative Commons Non-Commercial No Derivative Works (CC-BY-NC-ND) Attribution License (http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html) , which permits copying and redistribution of the article, and creation of adaptations, all for non-commercial purposes. |
spellingShingle | Koenis, Mark A. J. Visser, Olivier Visscher, Lucas Buma, Wybren J. Nicu, Valentin P. GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra |
title | GUI Implementation of VCDtools, A Program to Analyze
Computed Vibrational Circular Dichroism Spectra |
title_full | GUI Implementation of VCDtools, A Program to Analyze
Computed Vibrational Circular Dichroism Spectra |
title_fullStr | GUI Implementation of VCDtools, A Program to Analyze
Computed Vibrational Circular Dichroism Spectra |
title_full_unstemmed | GUI Implementation of VCDtools, A Program to Analyze
Computed Vibrational Circular Dichroism Spectra |
title_short | GUI Implementation of VCDtools, A Program to Analyze
Computed Vibrational Circular Dichroism Spectra |
title_sort | gui implementation of vcdtools, a program to analyze
computed vibrational circular dichroism spectra |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988127/ https://www.ncbi.nlm.nih.gov/pubmed/31830414 http://dx.doi.org/10.1021/acs.jcim.9b00956 |
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