Concept

Comparison of software for molecular mechanics modeling

Publications associées (33)

First-Principles Modeling of the Adsorption Geometry and Electronic Structure of Ru(II) Dyes on Extended TiO2 Substrates for Dye-Sensitized Solar Cell Applications

Michael Graetzel, Mohammad Khaja Nazeeruddin, Filippo de Angelis

We report a systematic density functional theory (DFT) computational investigation of Ru(II) sensitizer/TiO2 systems relevant to dye-sensitized solar cells (DSSCs). Focusing on the prototypical N719 and the recently introduced YE05 sensitizers, and conside ...

American Chemical Society2010

Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism

Matteo Dal Peraro

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme is implicated in replication initiation and DNA topology ...

2008

Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis

Ivano Tavernelli

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization ...

2008

Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: Application to the intramolecular hydrogen transfer in pentadiene

Jiri Vanicek

The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in e ...

2007

Coexistence of one- and two-dimensional supramolecular assemblies of terephthalic acid on Pd(111) due to self-limiting deprotonation

Klaus Kern, Harald Brune, Marta Canas Ventura, Sylvain Clair

The adsorption of terephthalic acid [C6H4(COOH)(2), TPA] on a Pd(111) surface has been investigated by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure spectroscopy under ultrahig ...

2006

Atom centered potentials for the description and the design of chemical compounds within density functional theory

Within the Born-Oppenheimer picture of the electronic Schrödinger equation the external potential due to the nuclei influences the resulting expectation values during the self consistent field procedure. In this thesis, the optimization and the benefit of ...

EPFL2005

Ab initio molecular dynamics simulation of redox reactions of transition metal ions in aqueous solution and proteins

Ivano Tavernelli

Redox potentials measure the free energy required to transfer a mol. species (ion) between two states of different total charge. In soln. a major contribution to the redox potential is the hydration free energy difference of the ion in the two oxidn. state ...

2005

The conformational behavior of novel glycosidase inhibitors with substituted azepan structures: An NMR and modeling study

Pierre Vogel, Eliazar Rodriguez Garcia

The conformational analysis of a series of configurational isomers of 2-(hydroxymethyl)azepan-3,4,5,6-tetrols 1-4 has been carried out. H-1 NMR spectroscopic data, especially vicinal J couplings and nuclear Overhauser enhancements (NOE), assisted by molecu ...

2004

Evidence for the Blue 10p S62+ Dication in Solutions of S8(AsF6)2: A Computational Study Including Solvation Energies

The energetics of dissocn. reactions of S82+ into stoichiometric mixts. of Sn+, n = 2-7, and Sm2+, m = 3, 4, 6, 10, were investigated by the B3PW91 method [6-311+G(3df)//6-311+G*] in the gas phase and in soln., with solvation energies calcd. using the SCIP ...

2004

Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations

Ursula Röthlisberger

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/mol. mechanics Car-Parrinello study of key steps of the enzymic reaction for a representative ...

2003

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