Search results for "Mechanism"
showing 10 items of 1835 documents
An ab initio study on the mechanism of the F+O3→FO+O2 reaction: comparative reactivity study along the isoelectronic NH2, OH and F radicals series
2004
Abstract The title reaction has been theoretically studied by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At single-reference MP2 and QCISD levels of theory, the potential energy hypersurface (HPES) shows a two-step reaction mechanism through two transition states (TS1 and TS2) and an intermediate (Int). However, the multiconfigurational CASSCF HPES shows a one-step reaction mechanism, as was previously found for the NH2 + O3 and OH + O3 reactions. The results show that the reactivity of the isoelectronic series of NH2, OH, and F radicals increases from the amino radical to the fluorine atom.
Role of the functional group in n-octydimethylsilanes in the synthesis of C8 reversed-phase silica packings for high-performance liquid chromatography
1986
Abstract C8 reversed-phase packings have been sysnthesised by reaction of a 25-nm pore-size high-performance liquid chromatographic silica (10 μm, as(BET) = 297 m2 g-1) with 2,4-lutidine as base and dichloromethane and N,N-dimethylflormamide as solvents, or without solvents and with the following silanes: n-octyldimenthylchlorosilane (C8-Cl), n-octyldimethylhydroxysilane (C8-OH), n-octyldimethylmethoxysilane (C8-OCH3), n-octyldimethylethoxysilane (C8-OC2H5), n-octyldimethyl(dimethylamino) silane [C8-N(CH3)2], n-octyldimethyl(trifluoroacetoxy)silane (C8- OCOCF3), and bis-(n-octyldimethylsiloxane) (C8-O-C8). C8-Cl, C8-OH and C8-OCH3 each form a reactive intermediate with 2,4-lutidine, favouri…
Electroreduction of aliphatic chlorides at silver cathodes in water
2010
The effect of water on the reduction of aliphatic chlorides at silver cathodes was investigated by cyclovoltammetric experiments in acetonitrile, water and their mixture and focused electrolyses in water solutions. The addition of water to acetonitrile gives rise to the formation of new peaks and/or the displacement of pre-existent peaks at dramatically less negative potentials. In a water medium, silver shows a very large electrocatalytic effect towards the reduction of chlorinated aliphatic compounds belonging to the classes of chloromethanes, chloroethanes and chloroethenes, dramatically higher than that observed in aprotic solvents such as dimethylformamide (DMF) or acetonitrile (ACN). …
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…
Biosilica aging: From enzyme-driven gelation via syneresis to chemical/biochemical hardening
2013
Abstract Background The distinguished property of the siliceous sponge spicules is their enzyme (silicatein)-catalyzed biosilica formation. The enzymatically formed, non-structured biosilica product undergoes a molding, syneresis, and hardening process to form the species-specifically shaped, hard structured skeletal spicules. Besides of silicatein, a silicatein-associated protein, silintaphin-2, is assumed to be involved in the process of biosilica formation in vivo. Methods Biosilica has been synthesized enzymatically and determined quantitatively. In addition, the subsequent hardening/aging steps have been followed by spectroscopic and electron microscopic analyses. Results The young spi…
Magnetoelectrochemical modulation of pre-organization processes in a 4,4′-dinitrobiphenyl azacrown macrocyclic lactam
2004
A magnetoelectrochemical effect consisting on the modulation of the reaction rate of pre-organization reactions in a 4,4′-dinitrobiphenyl azacrown lactam is described. The electrochemical response of that compound in DMSO solution at microelectrodes consists in two successive dinitrobiphenyl-centred one-electron transfer processes at −0.9 and −1.6 V vs. AgCl/Ag involving the transition from the dihedral geometry of the neutral starting compound to the planar geometry of the final dianion, resulting in an overall ECE mechanism. In the presence of moderate (0.05–0.2 T) static magnetic fields, the second electron transfer process decreases significantly, the apparent rate constant of the dihed…
Lewis acid induced [4+3] cycloadditions of 2-silyloxyacroleins. Insights on the mechanism from a DFT analysis
2005
The mechanism for the Lewis acid induced [4+3] cycloadditions of 2-(trimethylsilyloxy)acrolein with furan has been examined here through DFT calculations at B3LYP/6-31G* level. The mechanism is a three-step process initialized by the nucleophilic attack of furan to the β-conjugated position of acrolein yielding a zwitterionic intermediate. The key step on the formation of the seven-membered ring is the electrophilic attack of the furan residue to the carbonyl carbon in this intermediate. The endo selectivity experimentally observed is reproduced by the calculations.
Towards an Understanding of the Polar Diels–Alder Reactions of Nitrosoalkenes with Enamines: A Theoretical Study
2006
The polar Diels–Alder reactions of nitrosoalkenes with enamines have been studied using DFT methods at the B3LYP/6-31G* level of theory. These Diels–Alder reactions are characterized by a nucleophilic attack of the enamine at the conjugated position of the nitrosoalkene with concomitant ring-closure. The reactions present a total regioselectivity and a large endo selectivity. The analysis, based on the global electrophilicity of the reagents in the ground state, the natural bond orbital (NBO), and the topological analysis of the electron localization function (ELF) in the endo transition state (TS) and “halfway” along the IRC between the TS and cycloadduct, correctly explain the polar natur…
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…