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Concept

Comparison of software for molecular mechanics modeling

Publications associées (16)

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano Andres Abriata

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, m ...

2020

ONETEP plus TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory

Cédric Weber, Edward Baxter Linscott

We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlate ...

2020

Bimolecular charge transfer reactions at and through the liquid-liquid interface

Grégoire Clément Gschwend

Interfaces are ubiquitous in Nature. Among them, soft interfaces are essential constituents of biological tissues. Indeed, many electrochemical reactions and phenomena take place at these interfaces. In this respect, ITIES are an interesting model to study ...

EPFL2019

Using PyMOL as a platform for computational drug design

Shuguang Yuan

PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing ...

Wiley2017

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Ursula Röthlisberger, Jiri Vanicek, Swarnendu Bhattacharyya, Sergey Antipov

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quant ...

2017

Multipole moments for embedding potentials: Exploring different atomic allocation algorithms

Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of ...

Wiley-Blackwell2016

Adsorption Thermodynamics and Intrinsic Activation Parameters for Monomolecular Cracking of n-Alkanes on Bronsted Acid Sites in Zeolites

Berend Smit

Experimental' measurements of the rate coefficient (k(app)) and apparent enthalpies and entropies of activation (Delta H-app arid Delta S-app) for alkane cracking catalyzed by acidic zeolites can be used to characterize the effects of zeolite structure and ...

American Chemical Society2015

QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS

Changru Ma

We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simu ...

Elsevier Science Bv2015

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

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

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, 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

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