Topic
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.
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TL;DR: This version of KinBot tackles C, H, O and S atom containing species and unimolecular reactions, and automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations.
75 citations
TL;DR: High-level quantum chemical ab initio calculations are employed to locate and characterize global transition states for the peptidyl transferase center and point to feasibility of an eight-membered “double proton shuttle” mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates.
Abstract: Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered "double proton shuttle" mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.
75 citations
TL;DR: Simulation analysis of the calculated energy profile shows that solvent effects due to the protein matrix dramatically alter the intrinsic reactivity of the functional groups involved in the MDH reaction, resulting in energetics similar to that found in aqueous solution.
Abstract: A hybrid numerical method, which employs molecular mechanics to describe the bulk of the solvent-protein matrix and a semiempirical quantum-mechanical treatment for atoms near the reactive site, was utilized to simulate the minimum energy surface and reaction pathway for the interconversion of malate and oxaloacetate catalyzed by the enzyme malate dehydrogenase (MDH) A reaction mechanism for proton and hydride transfers associated with MDH and cofactor nicotinamide adenine dinucleotide (NAD) is deduced from the topology of the calculated energy surface The proposed mechanism consists of (1) a sequential reaction with proton transfer preceding hydride transfer (malate to oxaloacetate direction), (2) the existence of two transition states with energy barriers of approximately 7 and 15 kcal/mol for the proton and hydride transfers, respectively, and (3) reactant (malate) and product (oxaloacetate) states that are nearly isoenergetic Simulation analysis of the calculated energy profile shows that solvent effects due to the protein matrix dramatically alter the intrinsic reactivity of the functional groups involved in the MDH reaction, resulting in energetics similar to that found in aqueous solution An energy decomposition analysis indicates that specific MDH residues (Arg-81, Arg-87, Asn-119, Asp-150, and Arg-153) in the vicinity of the substrate make significant energetic contributions to the stabilization of proton transfer and destabilization of hydride transfer This suggests that these amino acids play an important role in the catalytic properties of MDH
75 citations
TL;DR: This chapter describes the mutarotations of α and β-D-glucose and focuses on the velocity constant k1 + k2, which is important for the formation of ionic intermediates in solvents of low dielectric constant.
Abstract: Publisher Summary This chapter describes the mutarotations of α and β-D-glucose. The mutarotations of all reducing sugars are catalyzed by acids and bases. Differences in the ionization for α and β-D-glucose and possible differences in the transition states for the anomers generally make detailed investigations of the individual velocity constants k1 and k2 desirable. The chapter focuses on the velocity constant k1 + k2. The concerted mechanism is of no significance in the mutarotation of sugars in aqueous solution with the possible exception of reactions catalyzed by the water molecule. However, in solvents of low dielectric constant, the formation of ionic intermediates becomes less favored, and the concerted mechanism can be applied. In the concerted process, both the acid catalyst and the base catalyst take part in the transition state, with addition of a proton at one point in the molecule and with elimination of a proton at another point. However, in a stepwise process, the acid catalyst and the base catalyst act separately.
75 citations
TL;DR: In this paper, the authors analyze midpoint species along the reaction coordinate for hydrogen transfer in the reaction R′−H−M−R−→ R−H+M+R−R+R −H−+M −R′ with Bader's AIM analysis.
75 citations