Literature DB >> 21417248

Explicit versus implicit solvent modeling of Raman optical activity spectra.

Kathrin H Hopmann1, Kenneth Ruud, Magdalena Pecul, Andrzej Kudelski, Martin Dračínský, Petr Bouř.   

Abstract

Raman and Raman optical activity (ROA) spectra of molecules reflect not only molecular structure and conformation but also the dynamics and interactions with the solvent. For polar, biologically relevant molecules in aqueous environment, this often complicates the band assignment and interpretation of the spectra. In the present study, implicit dielectric and explicit solvent models are compared with respect to the influence of the choice of solvent model on the spectral shape. Lactamide and 2-aminopropanol were selected as model compounds, and the Raman and ROA spectra were measured for both enantiomers. Geometries of explicitly solvated clusters were derived from quantum-mechanical calculations, classical (MD), and Car-Parrinello (CPMD) molecular dynamics. The results indicate that although the dielectric model reasonably well reproduces the main spectral features, more faithful intensity profiles, including the inhomogeneous band broadening, are obtained from the explicit MD and CPMD clusters. Additionally, the CPMD clusters are capable of reproducing most spectral features better than the classical dynamics, provided the simulation time is long enough to allow for a complete sampling of the conformational space. The hydrogen-bonded water molecules of the first hydration shell significantly influence the spectral intensities, whereas the effect of loosely attached or distant solvent molecules is minor. In order to average the signal, however, a relatively large number of MD geometries need to be considered, as was also exemplified by simulations of the ROA spectrum of the achiral molecule glycine. An explicit solvent modeling of sizable systems thus requires extensive computations, which became possible only recently due to the development of efficient analytical computational techniques.

Entities:  

Year:  2011        PMID: 21417248     DOI: 10.1021/jp110662w

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  4 in total

1.  Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model.

Authors:  Karen Oda Hjorth Minde Dundas; Maarten T P Beerepoot; Magnus Ringholm; Simen Reine; Radovan Bast; Nanna Holmgaard List; Jacob Kongsted; Kenneth Ruud; Jógvan Magnus Haugaard Olsen
Journal:  J Chem Theory Comput       Date:  2021-05-19       Impact factor: 6.006

2.  Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment.

Authors:  Jakub Kaminský; Valery Andrushchenko; Petr Bouř
Journal:  RSC Adv       Date:  2021-02-23       Impact factor: 3.361

3.  A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides.

Authors:  Karolina Di Remigio Eikås; Maarten T P Beerepoot; Kenneth Ruud
Journal:  J Phys Chem A       Date:  2022-08-05       Impact factor: 2.944

Review 4.  The Clusters-in-a-Liquid Approach for Solvation: New Insights from the Conformer Specific Gas Phase Spectroscopy and Vibrational Optical Activity Spectroscopy.

Authors:  Angelo S Perera; Javix Thomas; Mohammad R Poopari; Yunjie Xu
Journal:  Front Chem       Date:  2016-02-25       Impact factor: 5.221

  4 in total

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