Cargando…
Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method
The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10144652/ https://www.ncbi.nlm.nih.gov/pubmed/37110825 http://dx.doi.org/10.3390/molecules28083591 |
_version_ | 1785034150008324096 |
---|---|
author | Aschi, Massimiliano Palombi, Laura Amadei, Andrea |
author_facet | Aschi, Massimiliano Palombi, Laura Amadei, Andrea |
author_sort | Aschi, Massimiliano |
collection | PubMed |
description | The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic–molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds). |
format | Online Article Text |
id | pubmed-10144652 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-101446522023-04-29 Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method Aschi, Massimiliano Palombi, Laura Amadei, Andrea Molecules Article The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic–molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds). MDPI 2023-04-20 /pmc/articles/PMC10144652/ /pubmed/37110825 http://dx.doi.org/10.3390/molecules28083591 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Aschi, Massimiliano Palombi, Laura Amadei, Andrea Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title | Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title_full | Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title_fullStr | Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title_full_unstemmed | Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title_short | Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method |
title_sort | theoretical–computational modeling of cd spectra of aqueous monosaccharides by means of molecular dynamics simulations and perturbed matrix method |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10144652/ https://www.ncbi.nlm.nih.gov/pubmed/37110825 http://dx.doi.org/10.3390/molecules28083591 |
work_keys_str_mv | AT aschimassimiliano theoreticalcomputationalmodelingofcdspectraofaqueousmonosaccharidesbymeansofmoleculardynamicssimulationsandperturbedmatrixmethod AT palombilaura theoreticalcomputationalmodelingofcdspectraofaqueousmonosaccharidesbymeansofmoleculardynamicssimulationsandperturbedmatrixmethod AT amadeiandrea theoreticalcomputationalmodelingofcdspectraofaqueousmonosaccharidesbymeansofmoleculardynamicssimulationsandperturbedmatrixmethod |