Search results for "THERMODYNAMICS"
showing 10 items of 2774 documents
Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.
2014
M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex where the target adenine is flipped out into the active site. Key protein–DNA interactions established by the target adenine in the active site are described in detail. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. According to our free energy calculations the reaction takes…
Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.
2010
We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism. In the first case, we found associative transition-state (TS) structures, while in the enzyme TS structures have dissoc…
Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods
2015
The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylamino acids, with N-succinyl-R-phenylglycine being the best substrate. We investigated the molecular mechanisms for both reactions exploring the potential energy surface. Then, molecular dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues wi…
Calculation of the rate constants for hydrogen abstraction reactions by Hydroperoxyl radical from Methanol, and the investigation of stability of CH3…
2020
Abstract Master equation (ME) with Lennard-Jones potential utilized to simulate the collision between CH3OH and HO2 radical in the presence of bath gas. The reaction mechanism explored through the lowest doublet potential energy surface at CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory that is barrierless and forms shallow energized intermediate at the entrance channel. The investigation of the fractional population showed that lifetime of CH3OH.HO2 intermediate (INT*) is fairly short due to its shallow depth, and at the low temperature, most reaction takes place by re-dissociation back to reactants and also when the pressure is high enough, the INT* is thermalized and comes into eq…
Copper(II)-Binding Induces a Unique Polyproline Type II Helical Structure within the Ion-Binding Segment in the Intrinsically Disordered F-Domain of …
2019
Reproduction of the dominant vector of Zika and dengue diseases, Aedes aegypti mosquito, is controlled by an active heterodimer complex composed of the 20-hydroxyecdysone receptor (EcR) and ultraspiracle protein. Although A. aegypti EcR shares the structural and functional organization with other nuclear receptors, its C-terminus has an additional long F domain (AaFEcR). Recently, we showed that the full length AaFEcR is intrinsically disordered with the ability to specifically bind divalent metal ions. Here, we describe the details of the exhaustive structural and thermodynamic properties of Zn2+- and Cu2+-complexes with the AaFEcR domain, based on peptide models of its two putative metal …
Disequilibrium melt distribution during static recrystallisation
2004
Melt migration and segregation, and the rheology of partially molten rocks in the upper mantle and lower crust, strongly depend on the grain-scale distribution of the melt. Current theory for monomineralic aggregates predicts a perfectly regular melt framework, but high-temperature experiments with rock-forming minerals + melt show considerable deviations from this predicted geometry. Disequilibrium features, such as fully wetted grain boundaries and large melt patches, have been described; these were mainly attributed to surface-energy anisotropy of the minerals. We present static analogue experiments with norcamphor + ethanol that allow continuous in situ observation of the evolving liqui…
Influence of PVP/VA copolymer composition on drug–polymer solubility
2015
In this study, the influence of copolymer composition on drug-polymer solubility was investigated. The solubility of the model drug celecoxib (CCX) in various polyvinylpyrrolidone/vinyl acetate (PVP/VA) copolymer compositions (70/30, 60/40, 50/50 and 30/70 w/w) and the pure homopolymers polyvinylpyrrolidone (PVP) and polyvinyl acetate (PVA) was predicted at 25 °C using a thermal analysis method based on the recrystallization of a supersaturated amorphous dispersion (recrystallization method). These solubilities were compared with a prediction based on the solubility of CCX in the liquid monomeric precursors of PVP/VA, N-vinylpyrrolidone (NVP) and vinyl acetate (VA), using the Flory-Huggins …
Influence of oxygen vacancies on the photorefractive effect in barium titanate single crystals
1990
Abstract In this work the influence of the vacancies concentration in pure BaTiO3 single crystals is studied. It is shown that the oxidation and the reduction do not change the electrooptic coefficients. The reduction modifies the nature of the majority carriers. An evaluation of the trap density N is done.
Relaxation of certain integral functionals depending on strain and chemical composition
2012
We provide a relaxation result in $BV \times L^q$, $1\leq q < +\infty$ as a first step towards the analysis of thermochemical equilibria.
First-principles modelling of complex perovskite (Ba1-xSrx)(Co1-yFey)O3-δ for solid oxide fuel cell and gas separation membrane applications
2010
The results of the first principles spin-polarized DFT calculations of the atomic and electronic structure of a complex perovskite (Ba1-xSrx)(Co1-yFey)O3-δ (BSCF) used as a cathode material for solid oxide fuel cells (SOFC) and gas separation membranes are presented and discussed. The formation energies of oxygen vacancies are found to be considerably smaller than in other magnetic perovskites, e.g. (La,Sr)MnO3, which explains the experimentally observed strong deviation of this material from stoichiometry. The presence of oxygen vacancies induces a local charge redistribution, associated with the local lattice perturbation, and expansion of the equilibrium volume, in line with the experime…