Search results for "Transition State"
showing 10 items of 85 documents
A simple model for barrier frequencies for enzymatic reactions.
2010
We present a simple model to rationalize the effects of environment on the reaction barrier frequencies derived from free energy profiles. These frequencies are relevant in deviations of a rate constant from its transition state theory value and in determining which environmental dynamics participate in the reaction. In particular, this simple model can be used to understand the changes in the reaction barrier frequencies of an enzymatic catalyzed reaction and the corresponding uncatalyzed process in aqueous solution, a change which has implications for dynamical environmental effects on the enzymatic reaction. Two possible cases are analyzed, in which the polarity (charge separation/locali…
Application of SQMFF Vibrational Calculations to Transition States: DFT and ab Initio Study of the Kinetics of Methyl Azide and Ethyl Azide Thermoly…
1998
DFT including nonlocal corrections and ab initio calculations at MP2 and MP4 levels of theory have been performed in order to provide information concerning the mechanism of the rate limiting step of the thermal decomposition of methyl azide and ethyl azide. The chemically interesting points of the ground-state potential energy surface have been fully optimized, and a detailed normal-mode analysis for the reagents and the transition states is presented. The well-established scaled quantum mechanical force field method has been used to obtain reliable vibrational frequencies for these molecular structures. The force fields of transition states have been modified by using the scale factors co…
A theory ofnonverticaltriplet energy transfer in terms of accurate potential energy surfaces: The transfer reaction from π,π* triplet donors to 1,3,5…
2004
Triplet energy transfer (TET) from aromatic donors to 1,3,5,7-cyclooctatetraene (COT) is an extreme case of "nonvertical" behavior, where the transfer rate for low-energy donors is considerably faster than that predicted for a thermally activated (Arrhenius) process. To explain the anomalous TET of COT and other molecules, a new theoretical model based on transition state theory for nonadiabatic processes is proposed here, which makes use of the adiabatic potential energy surfaces (PES) of reactants and products, as computed from high-level quantum mechanical methods, and a nonadiabatic transfer rate constant. It is shown that the rate of transfer depends on a geometrical distortion paramet…
Ab Initio Study of the Mechanism and Thermochemistry of the Atmospheric Reaction NO + O3 → NO2 + O2
2002
The atmospheric reaction between NO and ozone has been investigated using ab initio methods. The structures of all reactants, products, intermediates, and transition states of reaction 1 have been optimized and characterized at the UMP2(full) level of theory. The 6-31G(d), 6-311G(d), and 6-311G(df) basis sets have also been used to calibrate the effect of the basis set functions on the optimized structures and energies of all stationary points. Finally, we have reoptimized at the UMP4(SDQ, full)/6-31G(d) and 6-311G(d) levels. The energetics of the reaction has been studied more accurately within the G2 and G2(MP2) schemes. Also, QCISD(T)/6-311G(d) single-point calculations have been perform…
1,3-Dipolar cycloadditions of electrophilically activated benzonitrile N-oxides. Polar cycloaddition versus oxime formation.
2006
The reactions of electrophilically activated benzonitrile N-oxides (BNOs) toward 3-methylenephthalimidines (MPIs) have been studied using density functional theory (DFT) at the B3LYP/6-31G* level. For these reactions, two different channels allowing the formation of the [3 + 2] cycloadducts and two isomeric (E)- and (Z)-oximes have been characterized. The 1,3-dipolar cycloadditions take place along concerted but highly asynchronous transition states, while formation of the oximes is achieved through a stepwise mechanism involving zwitterionic intermediates. Both reactions are initiated by the nucleophilic attack of the methylene carbon of the MPIs to the carbon atom of the electrophilically…
Nucleation pathway and kinetics of phase-separating active Brownian particles
2016
Suspensions of purely repulsive but self-propelled Brownian particles might undergo phase separation, a phenomenon that strongly resembles the phase separation of passive particles with attractions. Here we employ computer simulations to study the nucleation kinetics and the microscopic pathway active Brownian disks take in two dimensions when quenched from the homogeneous suspension to propulsion speeds beyond the binodal. We find the same qualitative behavior for the nucleation rate as a function of density as for a passive suspension undergoing liquid-vapor separation, suggesting that the scenario of an effective free energy also extends to the kinetics of phase separation. We study the …
Rate Theory for Electrocatalytic Systems: Fixed Potential Formulation for General, Electron Transfer, and Proton-Coupled Electron Transfer Reactions
2019
Atomistic modeling of electrocatalytic reactions is most naturally conducted within the grand canonical ensemble (GCE) which enables fixed chemical potential calculations. While GCE has been widely adopted for modeling electrochemical and electrocatalytic thermodynamics, the electrochemical reaction rate theory within GCE is lacking. Molecular and condensed phase rate theories are formulated within microcanonical and canonical ensembles, respectively, but electrocatalytic systems described within the GCE require extension of the conventionally used rate theories for computation reaction rates at fixed electrode potentials. In this work, rate theories from (micro) canonical ensemble are gene…
Unified Rate Theory of Electrochemistry and Electrocatalysis: Fixed Potential Formulation for General, Electron Transfer, and Proton-Coupled Electron…
2019
Atomistic modeling of electrocatalytic reactions is most naturally conducted within the grand canonical ensemble (GCE) which enables fixed chemical potential calculations. While GCE has been widely adopted for modeling electrochemical and electrocatalytic thermodynamics, the electrochemical reaction rate theory within GCE is lacking. Molecular and condensed phase rate theories are formulated within microcanonical and canonical ensembles, respectively, but electrocatalytic systems described within the GCE require extension of the conventionally used rate theories for computation reaction rates at fixed electrode potentials. In this work, rate theories from (micro)canonical ensemble are gener…
Enzymatic effects on reactant and transition states. The case of chalcone isomerase.
2007
Chalcone isomerase catalyzes the transformation of chalcone to naringerin as a part of flavonoid biosynthetic pathways. The global reaction takes place through a conformational change of the substrate followed by chemical reaction, being thus an excellent example to analyze current theories about enzyme catalysis. We here present a detailed theoretical study of the enzymatic action on the conformational pre-equilibria and on the chemical steps for two different substrates of this enzyme. Free-energy profiles are obtained in terms of potentials of mean force using hybrid quantum mechanics/molecular mechanics potentials. The role of the enzyme becomes clear when compared to the counterpart eq…
Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
2015
Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…