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.

Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

Abstract: Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts. Previous work with Escherichia coli alkaline phosphatase (AP), however, suggests that this enzyme catalyzes the hydrolysis of phosphate monoesters through a loose, dissociative transition state, similar to that in solution. AP also exhibits catalytic promiscuity, with a low level of phosphodiesterase activity, despite the tighter, more associative transition state for phosphate diester hydrolysis in solution. Because AP is evolutionarily optimized for phosphate monoester hydrolysis, it is possible that the active site environment alters the transition state for diester hydrolysis to be looser in its bonding to the incoming and outgoing groups. To test this possibility, we have measured the nonenzymatic and AP-catalyzed rate of reaction for a series of substituted methyl phenyl phosphate diesters. The values of beta(lg) and additional data suggest that the transition state for AP-catalyzed phosphate diester hydrolysis is indistinguishable from that in solution. Instead of altering transition state structure, AP catalyzes phosphoryl transfer reactions by recognizing and stabilizing transition states similar to those in aqueous solution. The AP active site therefore has the ability to recognize different transition states, a property that could assist in the evolutionary optimization of promiscuous activities.

Classical transition state theory: A lower bound to the reaction probability

Abstract: We derive a rigorous lower bound to the microcanonical reaction probability in classical collinear atom–diatom collisions. This lower bound complements the upper bound provided by transition state theory, and the information needed to calculate the bound is acquired automatically in the search for the periodic orbit dividing surfaces that are possible transition states for the reaction. Numerical calculations for F+H2 and H+Cl2 over a wide energy range show that the lower bound provides the best available estimate of the reaction probability, short of a full dynamical calculation.

Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms

Abstract: A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantum mechanical/molecular mechanical simulations. The model, designated AM1/d-PhoT, is parametrized for H, O, and P atoms to reproduce high-level density-functional results from a recently constructed database of quantum calculations for RNA catalysis (http://theory.chem.umn.edu/Database/QCRNA), including geometries and relative energies of minima, transition states and reactive intermediates, dipole moments, proton affinities, and other relevant properties. The model is tested in the gas phase and in solution using a QM/MM potential. The results indicate that the method provides significantly higher accuracy than MNDO/ d, AM1, and PM3 methods and, for the transphosphorylation reactions, is in close agreement with the density-functional calculations at the B3LYP/6-311++G(3df,2p) level with a reduction in computational cost of 3-4 orders of magnitude. The model is expected to have considerable impact on the application of semiempirical QM/MM methods to transphosphorylation reactions in solution, enzymes, and ribozymes and to ultimately facilitate the design of improved next- generation multiscale quantum models.

Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States. Ab Initio Evidence

Abstract: Ab initio molecular orbital calculations reveal enhanced hydrogen bonding of a water molecule to the transition states for the Diels-Alder reactions of cyclopentadiene with methyl vinyl ketone (MVK) and acrylonitrile. The optimal interaction energies are found to be 1.5-2.0 kcal/mol more favorable for hydrogen bonding to the oxygen or nitrogen in the transition states than for the dienophiles. This support the assertion from a prior simulation study that the observed rate accelerations for Diels-Alder reactions in aqueous solution arise from this hydrogen-bonding effect in addition to a relatively constant hydrophobic term

Reaction surface Hamiltonian for the dynamics of reactions in polyatomic systems

Abstract: The reaction path description of chemical reactions has difficulty if there are regions where the reaction path is sharply curved, as is typically the case, e.g., in light atom (e.g., H,D) transfer reactions. It is shown here how this can be overcome by introducing two reaction coordinate‐like degrees of freedom, i.e., two coordinates, r1 and r2, that are allowed to undergo arbitrarily large amplitude motion (LAM). Rather than a reaction path and a reaction coordinate measuring distance along it, the picture is now that of a reaction surface with two reaction‐like coordinates (r1,r2) which specify position on the surface. The reaction surface is defined by minimizing the potential energy of the polyatomic system for fixed values of r1 and r2, and an algorithm for using ab initio quantum chemistry methods to do this is described. The remaining (3N−8) internal degrees of freedom are characterized as local harmonic motion orthogonal to the reaction surface; these local normal modes are defined by diagonalizi...