Search results for "molecular dynamics"
showing 10 items of 1075 documents
Determination of the stress distribution at the interface metal-oxide: Numerical and theoretical considerations
2005
In this paper we give a brief presentation of the approaches we have recently developed on the oxidation of metals. Firstly, we present an analytical model based on non-equilibrium thermodynamics to describe the reaction kinetics present during the oxidation of a metal. Secondly, we present the molecular dynamics results obtained with a code specially tailored to study the oxidation and growth of an oxide film of aluminium. Our simulations present an excellent agreement with experimental results.
Numerical Simulations on the Growth of Thin Oxide Films on Aluminum Substrates
2010
We investigated the oxidation of nanocrystalline aluminum surfaces by using variable charge molecular dynamics at 600 K under three oxygen pressures: 1, 10 and 20 atm. The interaction potential was described by the electrostatic plus (Es+) model that allows dynamical charge transfer among atoms. We mainly focused on the effect of the oxygen pressure on the oxidation kinetic, the chemical composition and the microstructure of the oxide films formed. The results show that oxidation kinetics as well as chemical composition and microstructure depend on the applied oxygen pressure. The oxide film thickness tends to a limiting value equal to ~3 nm. Finally, we obtained a partially crystalline oxi…
Molecular dynamics studies of 3D quasicrystals
1993
Abstract The thermodynamic behaviour of monatomic and diatomic models of three-dimensional icosahedral quasicrystals has been studied in NVT and NPT ensembles using molecular dynamics simulations with atoms interacting via Lennard-Jones potentials. We also report on a microcanonical MD simulation of decagonal Al 65 Cu 20 Co 15 quasicrystals where an experimentally determined binary model has been used. To obtain stability in this latter case it is necessary to endow the atoms with effective pair potentials. No transitions to crystalline or amorphous phases were found for diatomic models. Monatomic models, however, display a certain stability only in the low-temperature region. In the range …
Molecular dynamics in low-molar and polymeric ferroelectric liquid crystals
1991
Broadband dielectric spectroscopy covering the frequency range from 10−1 Hz to 109 Hz was employed to study the molecular dynamics in low-molar and polymeric ferrroelectric liquid crystals. At frequencies below 106 Hz the ferroelectric modes, soft and Goldstone mode are observed. In the frequency regime from 106 Hz to 109 Hz a fast relaxation process is found, which is assigned to the hindered rotation of the mesogens around their long molecular axis. It turns out that the molecular dynamics is not principally different between low-molar and polymeric systems.
High-Pressure, High-Temperature Phase Diagram of Calcium Fluoride from Classical Atomistic Simulations
2013
We study the phase diagram of calcium fluoride (CaF2) under pressure using classical molecular dynamics simulations performed with a reliable pairwise interatomic potential of the Born−Mayer−Huggins form. Our results obtained under conditions 0 ≤ P ≲ 20 GPa and 0 ≤ T ≲ 4000 K reveal a rich variety of multiphase boundaries involving different crystal, superionic, and liquid phases, for all of which we provide an accurate parametrization. Interestingly, we predict the existence of three special triple points (i.e., solid−solid−superionic, solid−superionic−superionic, and superionic−superionic−liquid coexisting states) within a narrow and experimentally accessible thermodynamic range of 6 ≤ P …
Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simula…
2019
Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the knowledge about the mechanism of the phosphoryl transfer reaction and the transition state lags behind. In this work, we describe the X-ray crystal structure of the homodimeric Pfk-2 from E. coli, which contains products in one site and reactants in the other, as well as an additional ATP molecule in the inhibitory allosteric site adjacent to the reactants. This complex was previously predicted when studying the kinetic mechanism of ATP inhibit…
Unveiling the reaction mechanism of novel copper N-alkylated tetra-azacyclophanes with outstanding superoxide dismutase activity.
2020
Quantum chemical and multiscale calculations reveal the mechanistic pathway of two superoxide dismutase mimetic N-alkylated tetra-azacyclophane copper complexes with remarkable activity. The arrangement of the binding site afforded by the bulky alkyl substituents and the coordinated water molecule as a proton source play key roles in the reaction mechanism.
Molecular dynamics simulation in aqueous solution of N -methylazetidinone as a model of β -lactam antibiotics
1999
In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having simila…
Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.
2021
We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. Alchemical free energy calculations suggest that positions P3 and P4 could be susceptible to improvement in order to get a larger binding strength. QM/MM simulations unveil the reaction mechanism for covalent inhibition, showing that the nitrile warhead facilitates the recruitment of a water molecule for the proton transfer step.
Structural dynamics in F1ATPase during the first reaction cycle of ATP hydrolysis
1991
Abstract The velocity of ATP hydrolysis, catalyzed by purified F 1 ATPase from Micrococcus luteus , was decelerated on decreasing the temperature. At 13′C one reaction cycle is completed after 20 s. Hydrolysis was triggered upon rapid mixing of the enzyme with ATP. During the first reaction cycle, succeeding structural alterations of the F 1 ATPase were traced by time resolved X-ray scattering. The scattering spectra obtained from consecutive intervals of 1 s, revealed the F 1 ATPase to pass a conformational state exhibiting an expanded (6%) molecular shape. The expanded state was observed between 45% and 65% of the time required to complete the reaction cycle. This pointx out a conformatio…