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      Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution

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          Abstract

          In this Perspective, we outline the essential physicochemical aspects that need to be considered when building a reliable approach to describe absorption properties of solvated systems. In particular, we focus on how to properly model the complexity of the solvation phenomenon, arising from dynamical aspects and specific, strong solute–solvent interactions. To this end, conformational and configurational sampling techniques, such as Molecular Dynamics, have to be coupled to accurate fully atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) methodologies. By exploiting different illustrative applications, we show that an effective reproduction of experimental spectral signals can be achieved by delicately balancing exhaustive sampling, hydrogen bonding, mutual polarization, and nonelectrostatic effects.

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          Comparison of simple potential functions for simulating liquid water

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            Quantum mechanical continuum solvation models.

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              MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

              MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.
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                Author and article information

                Journal
                ACS Phys Chem Au
                ACS Phys Chem Au
                pg
                apcach
                ACS Physical Chemistry Au
                American Chemical Society
                2694-2445
                23 November 2022
                25 January 2023
                : 3
                : 1
                : 1-16
                Affiliations
                Scuola Normale Superiore, Classe di Scienze , Piazza dei Cavalieri 7, 56126Pisa, Italy
                Author notes
                Author information
                https://orcid.org/0000-0002-5430-9228
                https://orcid.org/0000-0002-5637-2853
                https://orcid.org/0000-0002-4872-4505
                Article
                10.1021/acsphyschemau.2c00050
                9881242
                36718266
                7c5bdd19-de8d-4f70-b85a-a5103eea38f7
                © 2022 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 30 September 2022
                : 08 November 2022
                : 08 November 2022
                Funding
                Funded by: H2020 European Research Council, doi 10.13039/100010663;
                Award ID: 818064
                Categories
                Perspective
                Custom metadata
                pg2c00050
                pg2c00050

                aqueous solution,polarization,hydrogen bonding,qm/mm,molecular dynamics

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