Transition state

About: Transition state is a research topic. Over the lifetime, 4978 publications have been published within this topic receiving 117965 citations. The topic is also known as: transition state of elementary reaction.

A theoretical study on the catalysis of Cu-exchanged zeolite for the decomposition of nitric oxide

Abstract: The catalysis of Cu-exchanged zeolite for the direct decomposition of nitric oxide was investigated by hybrid density functional theory (B3LYP) using a molecular model of the active site. For reactions of two NO molecules over a Cu ion bound to the zeolite model (ZCu), the structures and energies of adsorption complexes and transition states were examined and compared with those of the corresponding reactions over an isolated Cu+ and Cu atom and also reactions of free NO. The ZCu shows an enhanced catalytic activity compared with the isolated Cu+. The ZCu and adsorbed molecules interact strongly in the transition state structures through π(d–p) bonding. Theory also suggests that the Cu atom has the potential to be a highly active catalyst for the NO decomposition reaction.

Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase

Abstract: The reaction mechanism of arylmalonate decarboxylase is investigated using density functional theory calculations. This enzyme catalyzes the asymmetric decarboxylation of prochiral disubstituted malonic acids to yield the corresponding enantiopure carboxylic acids. The quantum chemical cluster approach is employed, and two different models of the active site are designed: a small one to study the mechanism and characterize the stationary points and a large one to study the enantioselectivity. The reactions of both α-methyl-α-phenylmalonate and α-methyl-α-vinylmalonate are considered, and different substrate binding modes are assessed. The calculations overall give strong support to the suggested mechanism in which decarboxylation of the substrate first takes place, followed by a stereoselective protonation by a cysteine residue. The enediolate intermediate and the transition states are stabilized by a number of hydrogen bonds that make up the dioxyanion hole, resulting in feasible energy barriers. It is f...

Deeper Insight into the Factors Controlling H2 Activation by Geminal Aminoborane-Based Frustrated Lewis Pairs.

Abstract: H2 activation mediated by geminal aminoborane-based frustrated Lewis pairs (FLPs; R2 N-CH2 -BR'2 ) has been computationally explored within the density functional theory framework. It is found that the activation barrier of this process as well as the geometry of the corresponding transition states strongly depend on the nature of the substituents directly attached either to the acidic or the basic centers of the FLPs. The physical factors controlling the whole activation path are quantitatively described in detail by means of the activation strain model of reactivity combined with the energy decomposition analysis method. This methodology suggests a highly orbital-controlled mechanism where the degree of charge transfer cooperativity between the most important donor-acceptor orbital interactions, namely LP(N)→σ*(H2 ) and σ(H2 )→pπ (B), along the reaction coordinate constitutes a suitable indicator of the reaction barrier.

Ab initio calculations on the mechanisms of hydrocarbon conversion in zeolites: Skeletal isomerisation and olefin chemisorption

Abstract: Quantum chemical calculations on zeolite-catalysed hydrocarbon conversion mechanisms have been carried out. The one-step skeletal isomerisation (methyl shift) and the olefin chemisorption reactions have been considered. The results obtained indicate that the product distribution of both reactions are determined by the activation energies rather than by the reaction heats. The shift of an existing branch is calculated to be significantly (by about 10 kcal/mol) easier than branch formation in n-alkanes in agreement with the experimental data. Only a small difference is found between n-butane and n-pentane isomerisation, which contrasts with experiment and suggests that at least one of these reactions does not proceed via a one-step methyl shift. Calculations show also that alkyl groups larger than methyl may be shifted.

Amidases Have a Hydrogen Bond that Facilitates Nitrogen Inversion, but Esterases Have Not

Abstract: Enzymes are powerful biocatalysts that provide rate accelerations of up to 1019 fold compared to the corresponding uncatalyzed reaction in solution. The origin of the remarkable performance displayed by enzymes has fascinated and puzzled researchers for over a hundred years. It is clear that the catalytic effect is a consequence of the higher degree of transition state stabilization for the enzyme catalyzed reaction compared to the corresponding uncatalyzed reaction. It is still not well understood exactly how this transition state stabilization occurs and the relative importance of various catalytic effects are discussed. Catalytic effects involving electrostatics, near attack conformers, dynamic effects and an economy in atomic motion are discussed in this thesis. The importance of electrostatic effects is corroborated in this thesis. A single hydrogen bond in transition state constitutes an important difference between amidases and esterases. A hydrogen bond in transition state is found in all sixteen analyzed amidases representing ten different reaction mechanisms and eleven different folding families. The hydrogen bond is shown to be either substrate assisted or enzyme assisted. The role of this hydrogen bond is to assist nitrogen inversion in amidases. Esterases lack this interaction in transition state and therefore they are very poor catalysts in the hydrolysis of amides. Electrostatic interactions are found to facilitate proton transfer that enhances the rate of lipase catalyzed N-acylation of amino alcohols. In this thesis electrostatic effects in the substrate are shown to be important for the lipase catalyzed transacylation of acrylates The α,β-double bond present in acrylates introduce electronic effects that has the consequence of restricting the conformational freedom of the substrate in its ground state to two flat conformations, s-cis and s-trans. It is shown that acrylates form near attack conformers (NACs) from their ground state s-cis/s-trans planar conformations. The ability of the enzyme to accommodate such apparent s-cis/s-trans substrate conformations dictates the probability to form productive transition states and thus the reaction rate. Dynamic effects are important in enzymes. In this thesis it is found that a point mutation increases the flexibility of a neighbouring residue in Candida antarctica lipase B. This allows the mutated enzyme to explore conformations not accessible for the wild-type enzyme. The dynamics has the effect to decrease steric interactions in transition state with concomitant rate increase for the transacylation of methyl methacrylate. In this thesis an economy of atomic motion during enzyme catalysis is observed. Nitrogen inversion in amidases constitutes an interesting example. A rotation as part of the reaction mechanism for amide bond hydrolysis would involve much more motion.