Direct chemical dynamics simulations: coupling of classical and quasiclassical trajectories with electronic structure theory

Paranjothy, Manikandan; Sun, Rui; Zhuang, Yu; Hase, William L.

doi:10.1002/wcms.1132

Cited by 101 publications

(121 citation statements)

References 119 publications

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“…For obtaining branching ratios, MD simulations are required. Such a MD simulation can be performed efficiently starting either from TSs with a proper initial condition sampling at TS or from reactant regions using a collective coordinate approach such as meta‐dynamics …”

Section: Bifurcationmentioning

confidence: 99%

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Maeda

Harabuchi

Ôno

et al. 2014

Int J of Quantum Chemistry

350

280

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The intrinsic reaction coordinate (IRC) approach has been used extensively in quantum chemical analysis and prediction of the mechanism of chemical reactions. The IRC gives a unique connection from a given transition structure to local minima of the reactant and product sides. This allows for easy understanding of complicated multistep mechanisms as a set of simple elementary reaction steps. In this article, three topics concerning the IRC approach are discussed. In the first topic, the first ab initio study of the IRC and a recent development of an IRC calculation algorithm for enzyme reactions are introduced. In the second topic, cases are presented in which dynamical trajectories bifurcate and corresponding IRC connections can be inaccurate. In the third topic, a recent development of an automated reaction path search method and its application to systematic construction of IRC networks are described. Finally, combining these three topics, future perspectives are discussed.

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Section: Bifurcationmentioning

confidence: 99%

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Maeda

Harabuchi

Ôno

et al. 2014

Int J of Quantum Chemistry

350

280

View full text Add to dashboard Cite

show abstract

“…The strategy that we follow is to use the Born-Oppenheimer molecular dynamics (BOMD) 20,21 approach to visualize the reaction in a box, our "nanoreactor" in the spirit of Ref. 22 , whereby the system explores the potential energy surface at a specified temperature, simulated by a Nosé-Hoover thermalizing bath 23 .…”

Section: Table Of Contents (Toc)mentioning

confidence: 99%

Stereodynamical Origin of Anti-Arrhenius Kinetics: Negative Activation Energy and Roaming for a Four-Atom Reaction

Coutinho

Silva

Oliveira

et al. 2015

J. Phys. Chem. Lett.

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The OH + HBr → H2O + Br reaction, prototypical of halogen-atom liberating processes relevant to mechanisms for atmospheric ozone destruction, attracted frequent attention of experimental chemical kinetics: the nature of the unusual reactivity drop from low to high temperatures eluded a variety of theoretical efforts, ranking this one among the most studied four-atom reactions. Here, inspired by oriented molecular-beams experiments, we develop a first-principles stereodynamical approach. Thermalized sets of trajectories, evolving on a multidimensional potential energy surface quantum mechanically generated on-the-fly, provide a map of most visited regions at each temperature. Visualizations of rearrangements of bonds along trajectories and of the role of specific angles of reactants' mutual approach elucidate the mechanistic change from the low kinetic energy regime (where incident reactants reorient to find the propitious alignment leading to reaction) to high temperature (where speed hinders adjustment of directionality and roaming delays reactivity).

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“…Trajectory calculations on the underlying potential energy surface (PES) represent the straightforward way to obtain directly reaction rates 19 . Unfortunately these calculations require high computational costs and only for systems of few atoms can be done efficiently.…”

Section: Introductionmentioning

confidence: 99%

Divided Saddle Theory: A New Idea for Rate Constant Calculation

Daru

Stirling

2014

J. Chem. Theory Comput.

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We present a theory of rare events and derive an algorithm to obtain rates from postprocessing the numerical data of a free energy calculation and the corresponding committor analysis. The formalism is based on the division of the saddle region of the free energy profile of the rare event into two adjacent segments called Saddle Domains. The method is built on sampling the dynamics within these regions: auxiliary rate constants are defined for the Saddle Domains and the absolute forward and backward rates are obtained by proper reweighting. We call our approach Divided Saddle Theory (DST). An important advantage of our approach is that it requires only standard computational techniques which are available in most molecular dynamics codes. We demonstrate the potential of DST numerically on two examples: rearrangement of alanine-dipeptide (CH3CO-Ala-NHCH3) conformers and the intramolecular Cope reaction of the fluxional barbaralane molecule.

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Direct chemical dynamics simulations: coupling of classical and quasiclassical trajectories with electronic structure theory

Cited by 101 publications

References 119 publications

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Stereodynamical Origin of Anti-Arrhenius Kinetics: Negative Activation Energy and Roaming for a Four-Atom Reaction

Divided Saddle Theory: A New Idea for Rate Constant Calculation

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