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      Novel Molecular-Dynamics-Based Protocols for Phase Space Sampling in Complex Systems

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          Abstract

          The adequate exploration of the phase space of a chromophore is a fundamental necessity for the simulation of their optical and photophysical properties, taking into account the effects of vibrational motion and, most importantly, the coupling with a (non-homogeneous) molecular environment. A representative set of conformational snapshots around the Franck-Condon region is also required to perform non-adiabatic molecular dynamics, for instance in the framework of surface hopping. Indeed, in the latter case one needs to prepare a set of initial conditions providing a meaningful and complete statistical base for the subsequent trajectory propagation. In this contribution, we propose two new protocols for molecular dynamics-based phase space sampling, called “local temperature adjustment” and “individual QM/MM-based relaxation.” These protocols are intended for situations in which the popular Wigner distribution sampling procedure is not applicable—as it is the case when anharmonic or nonlinear vibrations are present—and where regular molecular dynamics sampling might suffer from an inaccurate distribution of internal energy or from inaccurate force fields. The new protocols are applied to the case of phase space sampling of [Re(CO) 3(Im)(Phen)] + (im, imidazole; phen, phenanthroline) in aqueous solution, showing the advantages and limitations of regular Wigner and molecular dynamics sampling as well as the strengths of the new protocols.

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          Most cited references54

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          Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg

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            Relativistic regular two‐component Hamiltonians

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              Optimized Slater-type basis sets for the elements 1-118.

              Seven different types of Slater type basis sets for the elements H (Z = 1) up to E118 (Z = 118), ranging from a double zeta valence quality up to a quadruple zeta valence quality, are tested in their performance in neutral atomic and diatomic oxide calculations. The exponents of the Slater type functions are optimized for the use in (scalar relativistic) zeroth-order regular approximated (ZORA) equations. Atomic tests reveal that, on average, the absolute basis set error of 0.03 kcal/mol in the density functional calculation of the valence spinor energies of the neutral atoms with the largest all electron basis set of quadruple zeta quality is lower than the average absolute difference of 0.16 kcal/mol in these valence spinor energies if one compares the results of ZORA equation with those of the fully relativistic Dirac equation. This average absolute basis set error increases to about 1 kcal/mol for the all electron basis sets of triple zeta valence quality, and to approximately 4 kcal/mol for the all electron basis sets of double zeta quality. The molecular tests reveal that, on average, the calculated atomization energies of 118 neutral diatomic oxides MO, where the nuclear charge Z of M ranges from Z = 1-118, with the all electron basis sets of triple zeta quality with two polarization functions added are within 1-2 kcal/mol of the benchmark results with the much larger all electron basis sets, which are of quadruple zeta valence quality with four polarization functions added. The accuracy is reduced to about 4-5 kcal/mol if only one polarization function is used in the triple zeta basis sets, and further reduced to approximately 20 kcal/mol if the all electron basis sets of double zeta quality are used. The inclusion of g-type STOs to the large benchmark basis sets had an effect of less than 1 kcal/mol in the calculation of the atomization energies of the group 2 and group 14 diatomic oxides. The basis sets that are optimized for calculations using the frozen core approximation (frozen core basis sets) have a restricted basis set in the core region compared to the all electron basis sets. On average, the use of these frozen core basis sets give atomic basis set errors that are approximately twice as large as the corresponding all electron basis set errors and molecular atomization energies that are close to the corresponding all electron results. Only if spin-orbit coupling is included in the frozen core calculations larger errors are found, especially for the heavier elements, due to the additional approximation that is made that the basis functions are orthogonalized on scalar relativistic core orbitals. Copyright 2003 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Journal
                Front Chem
                Front Chem
                Front. Chem.
                Frontiers in Chemistry
                Frontiers Media S.A.
                2296-2646
                17 October 2018
                2018
                : 6
                : 495
                Affiliations
                [1] 1Faculty of Chemistry, Institute of Theoretical Chemistry, University of Vienna , Vienna, Austria
                [2] 2Université de Lorraine and CNRS, LPTC UMR 7019 , Nancy, France
                Author notes

                Edited by: Jean-Philip Piquemal, Sorbonne Universités, France

                Reviewed by: Michele Ceotto, Università degli Studi di Milano, Italy; Carles Curutchet, University of Barcelona, Spain

                *Correspondence: Sebastian Mai sebastian.mai@ 123456univie.ac.at

                This article was submitted to Theoretical and Computational Chemistry, a section of the journal Frontiers in Chemistry

                Article
                10.3389/fchem.2018.00495
                6199692
                30386775
                347eeb3b-432d-4e29-85a9-5c089c9df5d7
                Copyright © 2018 Mai, Gattuso, Monari and González.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 31 July 2018
                : 27 September 2018
                Page count
                Figures: 7, Tables: 0, Equations: 3, References: 72, Pages: 14, Words: 11124
                Funding
                Funded by: Austrian Science Fund 10.13039/501100002428
                Award ID: I2883
                Funded by: Agence Nationale de la Recherche 10.13039/501100001665
                Award ID: ANR-15-CE29-0027
                Categories
                Chemistry
                Original Research

                molecular dynamics,phase space sampling,simulation of absorption spectra,initial condition generation,quantum mechanics/molecular mechanics

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