Comparison of software for molecular mechanics modeling

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Related publications (16)

What Singles Out the G[8-5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations

Chandan Patel

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalentl ...

Amer Chemical Soc2013

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

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

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

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

Anatole von Lilienfeld

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

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