Ab Initio QM/MM Studies of the Phosphoryl Transfer Reaction Catalyzed by PEP Mutase Suggest a Dissociative Metaphosphate Transition State

2008 ◽  
Vol 112 (13) ◽  
pp. 4102-4108 ◽  
Author(s):  
Dingguo Xu ◽  
Hua Guo
Keyword(s):  
Transition State ◽  
Ab Initio ◽  
Transfer Reaction ◽  
Phosphoryl Transfer ◽  
Pep Mutase

The Transition State of the Phosphoryl-Transfer Reaction Catalyzed by the Lambda Ser/Thr Protein Phosphatase

1999 ◽  
Vol 121 (27) ◽  
pp. 6382-6390 ◽  
Author(s):  
Richard H. Hoff ◽  
Pamela Mertz ◽  
Frank Rusnak ◽  
Alvan C. Hengge
Keyword(s):  
Transition State ◽  
Protein Phosphatase ◽  
Transfer Reaction ◽  
Phosphoryl Transfer

The mechanism and kinetics of the HCO + HONO → HCHO + NO2 reaction — A DFT study

2007 ◽  
Vol 85 (7-8) ◽  
pp. 453-460
Author(s):  
Xiaomin Sun ◽  
Zhengting Cai ◽  
Dachang Feng ◽  
Wenshang Bian ◽  
Qing'an Qiao ◽  
...  
Keyword(s):  
Transition State ◽  
Ab Initio ◽  
Density Function ◽  
Rate Constants ◽  
Transition State Theory ◽  
Transfer Reaction ◽  
Function Theory ◽  
State Theory ◽  
Density Function Theory ◽  
Variational Transition State Theory

The hydrogen-transfer reaction of HCO + HNO2 → HCHO + NO2 has been studied using both the density function theory (DFT) and high-level ab initio method. Three complete reaction paths have been located for the transfer reaction. Geometry optimization and frequency calculation have been performed at the B3LYP/6-311++G** level. QCISD(T) and G3B3 methods have been used to verify the single-point energy. On the basis of the ab initio data, the rate constants have been deduced over a temperature range of 300–3000 K using the transition-state theory and canonical variational transition-state theory with small-curvature tunneling effect. The calculated rate constants have been compared with the previous reported values.Key words: density function theory, reaction mechanism, variational transition-state theory, rate constant.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Nitro–Nitrite Isomerization and Transition State Switching in the Dissociation of Ionized Nitromethane: A Threshold Photoelectron–Photoion Coincidence Spectroscopy Study

2009 ◽  
Vol 15 (2) ◽  
pp. 157-166 ◽  
Author(s):  
Brandon Ferrier ◽  
Anne-Marie Boulanger ◽  
David M.P. Holland ◽  
David A. Shaw ◽  
Paul M. Mayer
Keyword(s):  
Transition State ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Bond Cleavage ◽  
Cleavage Reaction ◽  
Nitrite Ion ◽  
Methyl Nitrite ◽  
Bond Cleavage Reaction ◽  
Entropy Of Activation ◽  
Lower Entropy

Threshold photoelectron–photoion coincidence (TPEPICO) spectroscopy has been employed to investigate the competition between bond cleavage and rearrangement reactions in the dissociation of ionized nitromethane, 1. Modeling TPEPICO breakdown diagrams with a combination of RRKM theory and ab initio calculations at the G3 level of theory allowed the derivation of the activation energy for the isomerisation of 1 to ionized methyl nitrite, 2, 82 kJ mol−1. In addition, evidence was found for a transition state switch in the bond cleavage reaction in 1 leading to CH3• + NO2+. As internal energy increases, the effective transition state for this reaction becomes tighter (i.e. is characterized by a lower entropy of activation, Δ‡S). Fitted thresholds for NO+ and CH2OHO+ ions, originating from the isomeric methyl nitrite ion, are consistent with G3 level ab initio calculations.

Structure and activity of phosphoglycerate mutase

1981 ◽  
Vol 293 (1063) ◽  
pp. 121-130 ◽  
Keyword(s):  
Active Site ◽  
Transfer Reaction ◽  
Chemical Kinetic ◽  
Phosphoglycerate Mutase ◽  
Phosphoryl Transfer ◽  
X Ray ◽  
Histidine Residues ◽  
Ping Pong ◽  
Available Information ◽  
Structure And Activity

The structure of yeast phosphoglycerate mutase determined by X-ray crystallographic and amino acid sequence studies has been interpreted in terms of the chemical, kinetic and mechanistic observations made on this enzyme. There are two histidine residues at the active site, with imidazole groups almost parallel to each other and approximately 0.4 nm apart, positioned close to the 2 and 3 positions of the substrate. The simplest interpretation of the available information suggests that a ping-pong type mechanism operates in which at least one of these histidine residues participates in the phosphoryl transfer reaction. The flexible C-terminal region also plays an important role in the enzymic reaction.

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