Search results for "molecular dynamic"

The Coordination of Uranyl in Water: A Combined Quantum Chemical and Molecular Simulation Study

2005

The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell…

Interpretation of the Ni K-edge EXAFS in nanocrystalline nickel oxide using molecular dynamics simulations

2011

Abstract Analysis of atomic structure at the nanoscale is a challenging task, complicated by relaxation phenomena and thermal disorder. In this work, the x-ray absorption spectroscopy at the Ni K-edge was used to address this problem in nanocrystalline NiO (nano-NiO) at 300 K. The analysis of the first two coordination shells using conventional two-shell single-scattering approximation allowed us to determine the expansion of the average lattice but contraction of the Ni―O bonds in the first coordination shell in nano-NiO in comparison with the bulk nickel oxide. The EXAFS signal generated within the first six coordination shells (up to ~ 6.5 A) was successfully interpreted using classical …

Reversible isomerization of metal nanoclusters induced by intermolecular interaction

2021

Most inorganic nanoparticles are directly surface-terminated (and -stabilized) by protecting ligands, which could greatly affect the atomic packing and physical/chemical properties of their inorganic cores. Here, we show that the intermolecular interactions between the adsorbed molecules and surface ligands can also affect the core structure of inorganic nanoparticles. Through the coupling/decoupling of cationic surfactants (cetyltrimethylammonium cations, CTA+) and anionic surface ligands (para-mercaptobenzoic acid, p-MBA) in the aqueous phase, we have achieved a reversible transformation between two isomers of [Au25(p-MBA)18]− nanoclusters. The interconversion process between the two isom…

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

2019

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …

Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations

2017

This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s444. The resource allocation within the PSI share at CSCS and on the PSI compute cluster Merlin4 is also acknowledged. D. B. is grateful for a fellowship within the Sciex-NMS programme. A. K. was supported by Latvian Science Council Grant no. 187/2012.

Radiation from multi-GeV electrons and positrons in periodically bent silicon crystal

2014

A periodically bent Si crystal is shown to efficiently serve for producing highly monochromatic radiation in a gamma-ray energy spectral range. A short-period small-amplitude bending yields narrow undulator-type spectral peaks in radiation from multi-GeV electrons and positrons channeling through the crystal. Benchmark theoretical results on the undulator are obtained by simulations of the channeling with a full atomistic approach to the projectile-crystal interactions over the macroscopic propagation distances. The simulations are facilitated by employing the MBN Explorer package for molecular dynamics calculations on the meso-, bio- and nano-scales. The radiation from the ultra-relativist…

A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS

2019

Abstract The effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate, HEThDP, on the enzyme-substrate interactions and their consequences on the biosynthesis of R-phenylacetylcarbinol, R-PAC, by the acetohydroxy acid synthase, AHAS, is addressed by molecular dynamics simulations. It is found that the form of HEThDP, which favors the formation of R-PAC, is that having the 4-aminopyrimidine ring with the N1′ atom protonated and the N4′ atom as aminopyrimidinium ion. Under this form both active sites of AHAS have the ability to perform the catalysis, unlike that observed for the other possible protonation states of N1′ and N4′ atoms.

Self-assembly of colloidal micelles in microfluidic channels.

2016

The self-assembly of amphiphilic Janus colloids in microfluidic channels is studied using hybrid molecular dynamics simulations with fully resolved hydrodynamic interactions incorporated through the multi-particle collision dynamics algorithm. The simulations are conducted at a density and temperature where the Janus particles spontaneously self-assemble into spherical micelles to minimize the interface between the solvophobic caps and the surrounding solvent. In confined systems, this contact area can also be reduced by aggregation at the channel walls. Indeed, a sizable fraction of free particles and small clusters with three and four members are found at the walls when the microfluidic c…

2021

The binding of natural ligands and synthetic drugs to the P2Y12 receptor is of great interest because of its crucial role in platelets activation and the therapy of arterial thrombosis. Up to now, all computational studies of P2Y12 concentrated on the available crystal structures, while the role of intrinsic protein dynamics and the membrane environment in the functioning of P2Y12 was not clear. In this work, we performed all-atom molecular dynamics simulations of the full-length P2Y12 receptor in three different membrane environments and in two possible conformations derived from available crystal structures. The binding of ticagrelor, its two major metabolites, adenosine diphosphate (ADP)…

Exploring kainate receptor pharmacology using molecular dynamics simulations.

2010

Ionotropic glutamate receptors (iGluRs) are enticing targets for pharmaceutical research; however, the search for selective ligands is a laborious experimental process. Here we introduce a purely computational procedure as an approach to evaluate ligand–iGluR pharmacology. The ligands are docked into the closed ligand-binding domain and during the molecular dynamics (MD) simulation the bi-lobed interface either opens (partial agonist/antagonist) or stays closed (agonist) according to the properties of the ligand. The procedure is tested with closely related set of analogs of the marine toxin dysiherbaine bound to GluK1 kainate receptor. The modeling is set against the abundant binding data …