Search results for "molecular dynamics"
showing 10 items of 1075 documents
Adsorption dynamics of molecular nitrogen at an Fe(111) surface.
2017
We present an extensive theoretical study of N adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states. Our QCT calculations confirm that there are activated and nonactivated paths …
Inverse Conformational Selection in Lipid–Protein Binding
2021
International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups excha…
Three-dimensional solvation structure of ethanol on carbonate minerals
2020
Calcite and magnesite are important mineral constituents of the earth’s crust. In aqueous environments, these carbonates typically expose their most stable cleavage plane, the (10.4) surface. It is known that these surfaces interact with a large variety of organic molecules, which can result in surface restructuring. This process is decisive for the formation of biominerals. With the development of 3D atomic force microscopy (AFM) it is now possible to image solid–liquid interfaces with unprecedented molecular resolution. However, the majority of 3D AFM studies have been focused on the arrangement of water at carbonate surfaces. Here, we present an analysis of the assembly of ethanol – an o…
A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice
2020
We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1lp.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cybp.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1lp.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dyna…
Equilibrium properties of the reaction H2⇌ 2H by classical molecular dynamics simulations
2013
We have developed a classical molecular dynamics model for the hydrogen dissociation reaction, containing two- and three-particle potentials derived by Kohen, Tully and Stillinger. Two fluid densities were investigated for a wide range of temperatures, and 11 fluid densities were considered for one temperature. We report the temperature range where the degree of reaction is significant, and also where a stable molecule dominates the population in the energy landscape. The three-particle potential, which is essential for the reaction model and seldom studied, together with the two-particle interaction lead to a large effective excluded volume diameter of the molecules in the molecular fluid.…
Muscimol hydration and vibrational spectroscopy – The impact of explicit and implicit water
2022
The presented study focuses on the interaction of the well-known neurotoxin muscimol with water. Two approaches for the water solvent are applied – the explicit and the implicit. The muscimol-water clusters were obtained by the molecular dynamics simulations and the first solvation shell was kept for further studies. Implicit water was mimicked via the polarized continuum model (PCM). All three tautomeric forms of the free muscimol molecule are considered in the calculations. The combined theoretical and experimental vibrational IR and Raman studies determined the stability of the prevailing zwitterion form in water. We proved that water molecules in the first solvation shell are crucial fo…
On new efficient algorithms for PIMC and PIMD
2002
Abstract The properties of various algorithms, estimators, and high-temperature density matrix (HTDM) decompositions relevant for path integral simulations are discussed. It is shown that Fourier accelerated path integral molecular dynamics (PIMD) completely eliminates slowing down with increasing Trotter number P . A new primitive estimator of the kinetic energy for use in PIMD simulations is found to behave less pathologically than the original virial estimator. In particular, its variance does not increase significantly with P . Two non-primitive HTDM decompositions are compared as well: one decomposition used in the Takahashi Imada algorithm and another one based on an effective propaga…
Oleochemical carbonates: A comprehensive characterization of an emerging class of organic compounds
2022
Dialkyl carbonates (DAC) with short-medium alkyl length - oleochemical carbonates – are attracting attention because of their appealing properties, including low viscosity, flammability, toxicity, environ- mental impact and wide range of applications: lubricants, personal care, fuel additives etc. However, not much is known concerning their chemical physical properties and, more importantly, on the nature of microscopic correlations that eventually determine bulk performances. In view of this paucity, we pre- sent a large exploration of a series of chemical physical properties of a set of DACs ranging from dimethyl up to didodecyl carbonate. This study extends previously determined database…
The molecular dynamics of thermoreversible networks as studied by broadband dielectric spectroscopy
1995
Polybutadienes modified by a small number of 4-phenyl-1,2,4-triazoline-3,5-dione form thermoreversible networks via hydrogen bonding between the polar stickers. The molecular dynamics of systems with different contents of polar stickers are investigated by broadband dielectric spectroscopy in the frequency regime of 10−1–109 Hz. Unmodified polybutadiene shows two relaxation processes, the α-relaxation which is correlated to the dynamic glass transition of the polybutadiene, and a β-relaxation corresponding to a local relaxation of polybutadiene segments. In the polar functionalized systems, besides these two relaxations, an additional relaxation process (called α*) is observed, which occurs…
trans-4-Bromo-ONN-azoxybenzene at 100 K.
2004
The crystal structure of the alpha isomer of trans-4-bromoazoxybenzene [systematic name: trans-1-(bromophenyl)-2-phenyldiazene 2-oxide], C(12)H(9)BrN(2)O, has been determined by X-ray diffraction. The geometries of the two molecules in the asymmetric unit are slightly different and are within approximately 0.02 A for bond lengths, approximately 2 degrees for angles and approximately 3 degrees for torsion angles. The azoxy bridges in both molecules have the typical geometry observed for trans-azoxybenzenes. The crystal network contains two types of planar molecules arranged in columns. The torsion angles along the Ar-N bonds are only 7 (2) degrees, on either side of the azoxy group.