Search results for "molecular dynamics"
showing 10 items of 1075 documents
Vibrational Sum Frequency Generation Spectroscopy of the Water Liquid–Vapor Interface from Density Functional Theory-Based Molecular Dynamics Simulat…
2013
International audience; The vibrational sum frequency generation (VSFG) spectrum of the water liquid-vapor (LV) interface is calculated using density functional theory-based molecular dynamics simulations. The real and imaginary parts of the spectrum are in good agreement with the experimental data, and we provide an assignment of the SFG bands according to the dipole orientation of the interfacial water molecules. We use an instantaneous definition of the surface, which is more adapted to the study of interfacial phenomena than the Gibbs dividing surface. By calculating the vibrational (infrared, Raman) properties for interfaces of varying thickness, we show that the bulk spectra signature…
Dithiametacyclophane mit Dreifachbindungen
1994
Dithiametacyclophanes with Triple Bonds Schemes 1 and 2 show the syntheses of dithia[8]metacyclo-phanes 4a-d and tetrathia[m.n]metacyclophanes 9, 10 by cyclization reactions applying the cesium effect. All these cyclophanes contain C—C triple bonds which influence the molecular dynamics; especially the halogen substituents in 4b-d obstruct the topomerization.
MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions
2013
Filamins (FLN) are large dimeric proteins that cross-link actin and work as important scaffolds in human cells. FLNs consist of an N-terminal actin-binding domain followed by 24 immunoglobulin-like domains (FLN1-24). FLN domains are divided into four subgroups based on their amino acid sequences. One of these subgroups, including domains 4, 9, 12, 17, 19, 21, and 23, shares a similar ligand-binding site between the β strands C and D. Several proteins, such as integrins β2 and β7, glycoprotein Ibα (GPIbα), and migfilin, have been shown to bind to this site. Here, we computationally estimated the binding free energies of filamin A (FLNa) subunits with bound peptides using the molecular mechan…
Tracking Ca
2019
We characterize thus-far elusive domain rearrangements of a calcium-transporting ATPase in the native membrane.
Mesoscopic organization in ionic liquids.
2017
We discuss some published results and provide new observations concerning the high level of structural complexity that lies behind the nanoscale correlations in ionic liquids (ILs) and their mixtures with molecular liquids. It turns out that this organization is a consequence of the hierarchical construction on both spatial (from ångström to several nanometer) and temporal (from fraction of picosecond to hundreds of nanosecond) scales, which requires joint use of experimental and computational tools. © 2017, Springer International Publishing Switzerland.
Mesoscopic structural organization in triphilic room temperature ionic liquids
2013
Room temperature ionic liquids are one of the most exciting classes of materials in the last decade. The interest for these low melting, ionic compounds stems from both their technological impact and the stimulating plethora of structural and dynamic peculiarities in the mesoscopic space-time scales. It is nowadays well-established that they are characterised by an enhanced degree of mesoscopic order originating from their inherent amphiphilicity. In this contribution we highlight the existence of a further degree of mesoscopic complexity when dealing with RTILs bearing a medium length fluorous tail: such triphilic materials (they simultaneously contain polar, hydrophobic and fluorophilic m…
A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates…
2011
Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alky…
Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**
2021
Abstract We present the results of classical and QM/MM simulations for the inhibition of SARS‐CoV‐2 3CL protease by a hydroxymethylketone inhibitor, PF‐00835231. In the noncovalent complex the carbonyl oxygen atom of the warhead is placed in the oxyanion hole formed by residues 143 to 145, while P1–P3 groups are accommodated in the active site with interactions similar to those observed for the peptide substrate. According to alchemical free energy calculations, the P1′ hydroxymethyl group also contributes to the binding free energy. Covalent inhibition of the enzyme is triggered by the proton transfer from Cys145 to His41. This step is followed by the nucleophilic attack of the Sγ atom on …
Frictional Forces between Strongly Compressed, Nonentangled Polymer Brushes: Molecular Dynamics Simulations and Scaling Theory
2010
By means of molecular dynamics simulations and scaling theory we study the response of opposing polymer brushes to constant shear motion under good solvent conditions. Model systems that contain explicit solvent molecules (Lennard-Jones dimers) are compared to solvent-free systems while varying of the distance between the grafted layers and their molecular parameters, chain length and grafting density. Our study reveals a power-law dependence of macroscopic transport properties on the Weissenberg number, W, beyond linear response. For instance, we find that the kinetic friction constant scales as μ ∼ W0.57 for large values of W. We develop a scaling theory that describes our data and previo…
A variable charge molecular dynamics study of the initial stage of nickel oxidation
2010
Abstract The oxidation of nickel single crystals is investigated by using variable charge molecular dynamics. The simulations are performed on three nickel low-index surfaces ((1 0 0), (1 1 0) and (1 1 1)) at temperatures between 300 K and 950 K. The results show that the shape of the oxidation kinetics is independent of the crystallographic orientation and the temperature under the present conditions. The oxide thin film grows according to an island growth mode, this initial stage of oxidation can be divided in three steps: (i) the dissociative chemisorption step (ii) the oxide island nucleation and (iii) the lateral growth of the island. The first step is slowdown/speedup by the surface o…