Literature DB >> 17552801

Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: application to a Mannich base in solid state and in vacuum.

Aneta Jezierska1, Jarosław J Panek, Aleksander Koll, Janez Mavri.   

Abstract

Car-Parrinello molecular dynamics (CPMD) study was performed for an anharmonic system-an intramolecularly hydrogen bonded Mannich-base-type compound, 4,5-dimethyl-2(N,N-dimethylaminemethyl)phenol, to investigate the vibrational spectrum associated with the O-H stretching. Calculations were carried out for the solid state and for an isolated molecule. The classical CPMD simulation was performed and then the proton potential snapshots were extracted from the trajectory. The vibrational Schrodinger equation for the snapshots was solved numerically, and the (O-H) envelope was calculated as a superposition of the 0-->1 transitions. The potential of mean force for the proton stretching mode was calculated from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling, nuclear quantum effects, and effects of the environment. Perspectives for application of the presented methodology in the computational support of biocatalysis are given in the study.

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Year:  2007        PMID: 17552801     DOI: 10.1063/1.2736692

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  5 in total

1.  Theoretical description of hydrogen bonding in oxalic acid dimer and trimer based on the combined extended-transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV).

Authors:  Mariusz P Mitoraj; Rafał Kurczab; Marek Boczar; Artur Michalak
Journal:  J Mol Model       Date:  2010-05-28       Impact factor: 1.810

2.  The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer.

Authors:  Linus O Johannissen; Nigel S Scrutton; Michael J Sutcliffe
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

3.  Hydrogen bridges of polycyclic aromatic systems with O-H···O bonds--a gas-phase vs. solid-state Car-Parrinello study.

Authors:  Jarosław J Panek; Aneta Jezierska
Journal:  J Mol Model       Date:  2015-01-24       Impact factor: 1.810

4.  Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car-Parrinello Molecular Dynamics and Electronic Structure Inspection.

Authors:  Jarosław J Panek; Joanna Zasada; Bartłomiej M Szyja; Beata Kizior; Aneta Jezierska
Journal:  Int J Mol Sci       Date:  2021-05-14       Impact factor: 5.923

5.  Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines.

Authors:  Agata Martyniak; Jarosław Panek; Aneta Jezierska-Mazzarello; Aleksander Filarowski
Journal:  J Comput Aided Mol Des       Date:  2012-09-07       Impact factor: 3.686

  5 in total

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