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GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
(American Chemical Society, 2014-02)
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density ...
QM-MM investigation of the reaction products between nitroxyl and O2 in aqueous solution
(Elsevier Science, 2008-09)
By means of combined quantum-classical molecular (QM/MM) dynamics simulations, we investigated the structural properties and the vibrational spectra in aqueous solution of four possible intermediate species of the oxidation ...
Estudo da dinâmica de solvatação de peptídeos por QM/MMStudy of the solvation dynamic of peptides by QM/MM
(Universidade Estadual Paulista (Unesp), 2016)
Docking, qm/mm, and molecular dynamics simulations of the hexose transporter from plasmodium falciparum (pfht)
(Universidade Federal de Minas GeraisBrasilFAR - DEPARTAMENTO DE PRODUTOS FARMACÊUTICOSUFMG, 2016-05)
Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations
(Elsevier B.V., 2015-07-05)
The matrix metalloproteinase family (MMP) constitutes a family of zinc (Zn) proteases that catalyze the breaking of peptide bonds in proteins. These enzymes are very promising drug targets, since they are involved in ...
A silicon laboratory: chemistry without chemicalsUn laboratorio de silicio: química sin reactivos
(Pontificia Universidad Católica del Perú, 2013)
The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step
(Royal Society of Chemistry, 2014-07)
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic ...
Spectroscopy in Complex Environments from QM-MM Simulations
(American Chemical Society, 2018-04)
The applications of multiscale quantum-classical (QM-MM) approaches have shown an extraordinary expansion and diversification in the last couple of decades. A great proportion of these efforts have been devoted to interpreting ...
Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
(American Institute of Physics, 2014-04)
This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics ...