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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...

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Autores principales: Koenis, Mark A. J., Visser, Olivier, Visscher, Lucas, Buma, Wybren J., Nicu, Valentin P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
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.
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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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