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: In this article, the enthalpies of reaction have been computed for the conjugate additions of MeSH to six α,β-unsaturated ketones, and substituent effects on the activation energies for the rate-determining step of the thiol addition (reaction of the enone with MeS−) were also computed.
Abstract: CBS-QB3 enthalpies of reaction have been computed for the conjugate additions of MeSH to six α,β-unsaturated ketones. Compared with addition to methyl vinyl ketone, the reaction becomes 1–3 kcal mol–1 less exothermic when an α-Me, β-Me, or β-Ph substituent is present on the C═C bond. The lower exothermicity for the substituted enones occurs because the substituted reactant is stabilized more by hyperconjugation or conjugation than the product is stabilized by branching. Substituent effects on the activation energies for the rate-determining step of the thiol addition (reaction of the enone with MeS–) were also computed. Loss of reactant stabilization, and not steric hindrance, is the main factor responsible for controlling the relative activation energies in the gas phase. The substituent effects are further magnified in solution; in water (simulated by CPCM calculations), the addition of MeS– to an enone is disfavored by 2–6 kcal mol–1 when one or two methyl groups are present on the C═C bond (ΔΔG⧧). The...
82 citations
TL;DR: In this paper, it was shown that peptide release is strongly impaired by mutations of nucleotides within the active site of the Escherichia coli ribosome, in particular by base exchanges at position A2602.
Abstract: Two reactions occur in the ribosome catalytic centre: peptide bond formation and peptide release. Previous modelling has suggested that the hydrolysis reaction during release involves a concerted proton shuttle in the transition state. Kuhlenkoetter et al. have conducted proton inventories of the reaction and find that one hydrogen bond is formed during the rate-limiting step, rather than the three produced during peptide bond formation. They conclude that the peptidyl transferase centre is able to support two different transition states. The active site of the ribosome, the peptidyl transferase centre, catalyses two reactions, namely, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the release-factor-dependent hydrolysis of peptidyl-tRNA. Unlike peptide bond formation, peptide release is strongly impaired by mutations of nucleotides within the active site, in particular by base exchanges at position A2602 (refs 1, 2). The 2′-OH group of A76 of the peptidyl - tRNA substrate seems to have a key role in peptide release3. According to computational analysis4 , the 2′-OH may take part in a concerted ‘proton shuttle’ by which the leaving group is protonated, in analogy to similar current models of peptide bond formation4,5,6. Here we report kinetic solvent isotope effects and proton inventories (reaction rates measured in buffers with increasing content of deuterated water, D2O) of the two reactions catalysed by the active site of the Escherichia coli ribosome. The transition state of the release factor 2 (RF2)-dependent hydrolysis reaction is characterized by the rate-limiting formation of a single strong hydrogen bond. This finding argues against a concerted proton shuttle in the transition state of the hydrolysis reaction. In comparison, the proton inventory for peptide bond formation indicates the rate-limiting formation of three hydrogen bonds with about equal contributions, consistent with a concerted eight-membered proton shuttle in the transition state5. Thus, the ribosome supports different rate-limiting transition states for the two reactions that take place in the peptidyl transferase centre.
82 citations
TL;DR: It is shown that both associative and dissociative transition states have near-zero entropies of activation that are in good agreement with experimental values, and it is believed that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include steric factors determining the configurational volumes during the reaction.
Abstract: Phosphate monoester and anhydride hydrolysis is ubiquitous in biology, being involved in, amongst other things, signal transduction, energy production, and the regulation of protein function. Therefore, this reaction has understandably been the focus of intensive research. Nevertheless, the precise mechanism by which phosphate monoester hydrolysis proceeds remains controversial. Traditionally, it has been assumed and frequently implied that a near-zero activation entropy is indicative of a dissociative pathway. Herein, we examine free-energy surfaces for the hydrolysis of the methyl phosphate dianion and the methyl pyrophosphate trianion in aqueous solution. In both cases, the reaction can proceed through either compact or expansive concerted (A(N)D(N)) transition states, with fairly similar barriers. We have evaluated the activation entropies for each transition state and demonstrate that both associative and dissociative transition states have near-zero entropies of activation that are in good agreement with experimental values. Therefore, we believe that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include (but are not limited to) steric factors determining the configurational volumes available to reactants during the reaction, solvation and desolvation effects that may be associated with charge redistribution upon approaching the transition state and entropy changes associated with intramolecular degrees of freedom as the transition state is approached.
82 citations
TL;DR: This work presents and quantify a technique to identify and characterize local invariances about the transition state of an N-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical molecular dynamics simulation.
Abstract: How a reacting system climbs through a transition state during the course of a reaction has been an intriguing subject for decades. Here we present and quantify a technique to identify and characterize local invariances about the transition state of an N-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical molecular dynamics simulation. We show that at least three distinct energy regimes of dynamical behavior occur in the region of the transition state, distinguished by the extent of their local dynamical invariance and regularity. Isomerization of a six-atom Lennard–Jones cluster illustrates this: up to energies high enough to make the system manifestly chaotic, approximate invariants of motion associated with a reaction coordinate in phase space imply a many-body dividing hypersurface in phase space that is free of recrossings even in a sea of chaos. The method makes it possible to visualize the stable and unstable invariant manifolds leading to and from the transition state, i.e., the reaction path in phase space, and how this regularity turns to chaos with increasing total energy of the system. This, in turn, illuminates a new type of phase space bottleneck in the region of a transition state that emerges as the total energy and mode coupling increase, which keeps a reacting system increasingly trapped in that region.
82 citations
TL;DR: In this paper, a slab model based on periodic density functional theory (DFT) was used to investigate the elementary radical reaction processes of hydrazine decomposition on Ir-based catalysts, and three possible reaction pathways were considered.
82 citations