The time correlation function (tcf) formulas for rate constants κ derived via the stable states picture (SSP) of chemical reactions are applied to a wide variety (a–d) gas and solution phase reaction models. (a) For bimolecular reactions, we show that flux tcf governing corresponds standard numerical trajectory calculation methods. Alternate which focus on saddle point surfaces, thus increasing computational efficiency. Advantages SSP discussed. (b) unimolecular simple results found in both...

Despite long study, a molecular picture of the mechanism water reorientation is still lacking. Using numerical simulations, we find support for pathway in which rotating molecule breaks hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form H-bond undercoordinated second-shell neighbor. The cleavage and occur concertedly not successively as usually considered. This involves large-amplitude angular jumps, rather than commonly accepted sequence small diffusive steps,...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCurrent status of transition-state theoryDonald G. Truhlar, William L. Hase, and James T. HynesCite this: J. Phys. Chem. 1983, 87, 15, 2664–2682Publication Date (Print):July 1, 1983Publication History Published online1 May 2002Published inissue 1 July 1983https://pubs.acs.org/doi/10.1021/j100238a003https://doi.org/10.1021/j100238a003research-articleACS PublicationsRequest reuse permissionsArticle Views3280Altmetric-Citations745LEARN ABOUT THESE...

Many highly proliferative cells generate almost all ATP via glycolysis despite abundant O2 and a normal complement of fully functional mitochondria, circumstance known as the Crabtree effect. Such anaerobically poised are resistant to xenobiotics that impair mitochondrial function, such inhibitors rotenone, antimycin, oligomycin, compounds like carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), uncouple respiratory electron transfer system from phosphorylation. These also toxicity...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTime-dependent fluorescence solvent shifts, dielectric friction, and nonequilibrium solvation in polar solventsG. Van der Zwan James T. HynesCite this: J. Phys. Chem. 1985, 89, 20, 4181–4188Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/j100266a008https://doi.org/10.1021/j100266a008research-articleACS PublicationsRequest reuse...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOuter-sphere electron-transfer reactions and frequency-dependent frictionJames T. HynesCite this: J. Phys. Chem. 1986, 90, 16, 3701–3706Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/j100407a044https://doi.org/10.1021/j100407a044research-articleACS PublicationsRequest reuse permissionsArticle Views1008Altmetric-Citations462LEARN ABOUT THESE...

The results of a molecular dynamics (MD) computer simulation are presented for the solvation an ion pair instanteously produced from neutral pair, in model polar aprotic solvent. These time-dependent fluorescence analyzed theoretically to examine validity several linear response theory approaches, as well various theoretical descriptions (e.g., Langevin equation) solvent per se. It is found that these dominated short times by simple inertial Gaussian behavior, feature which absent many...

We detail and considerably extend the analysis recently presented in Science 2006, 311, 832- 835 of molecular mechanism water reorientation based on dynamics simulations analytic framework extended jump model (EJM). The is shown to occur through large-amplitude angular jumps due exchange hydrogen (H)-bond acceptors, with a minor contribution from diffusive H-bond frame between these exchanges. robust character this respect different models discussed. fully characterize events, including...

Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution have already been profoundly affected by the application existing ...Read More

A theoretical model is presented for the vibrational dynamics of highly excited CH and CD overtones in benzene perdeuterobenzene. The origin, path, time scale overtone relaxation are described. critical near resonant interaction responsible energy flow from an CH(D) oscillator to ring a Fermi resonance coupling, identified by Sibert, Reinhardt, Hynes [Chem. Phys. Lett. 92, 455 (1982)]. Quantum spectra calculated both independent dependent perspectives good qualitative agreement found with...

The dynamics of water molecules next to hydrophobic solutes is investigated, specifically addressing the recent controversy raised by first time-resolved observations, which concluded that some are immobilized groups, in strong contrast previous NMR conclusions. Through molecular simulations and an analytic jump reorientation model, we identify mechanism a solute provide evidence no solutes. Their moderate rotational slowdown compared bulk (e.g., factor less than 2 at low concentration)...

The reorientation of a water molecule is important for host phenomena, ranging over—in an only partial listing—the key dynamic hydrogen-bond network restructuring itself, aqueous solution chemical reaction mechanisms and rates, ion transport in membranes, protein folding, enzymatic activity. This review focuses on related dynamics pure water, solutes with hydrophobic, hydrophilic, amphiphilic character, from tetra-methylurea to halide ions amino acids. Attention given the application theory,...

Molecular dynamics simulations are used to examine two key aspects of recent ultrafast infrared experiments on liquid water dynamics. It is found that the relation between OH stretch frequency and length hydrogen bond in which involved, currently assumed be one-to-one, instead characterized by considerable dispersion time scale interpreted terms a stochastic modulation surrounding solvent highly frictionally damped system shown governed bond-breaking -making dynamics, whereas motion an...

It is shown how a dynamical theory for proton transfer rates in solution can be implemented molecular-dynamics simulation model reaction system. The the nonadiabatic limit, which occurs via quantum tunneling of proton. importance coupling to solvent and an intramolecular vibration illustrated, results are successfully compared with analytic rate-constant expressions several limiting regimes.

Molecular dynamics (MD) simulations of the model SN2 reaction Cl−+CH3Cl→ClCH3+Cl− in water, and variants thereof, are presented. The resulting transmission coefficients κ, that measure deviations rates from transition state theory (TST) rate predictions due to solvent-induced recrossings, used assess validity generalized Langevin equation (GLE)-based Grote–Hynes (GH) theory. GH found agree with MD results within error bars calculations for each 12 cases examined. This agreement extends...

Molecular dynamics are computed for a model SN2 reaction Cl−+CH3Cl→ClCH3+Cl− in water and found to be strongly dependent on the instantaneous local configuration of solvent at transition state barrier. There significant deviations from simple picture passage over free energy barrier coordinate, thus, marked departure theory occurs form recrossings. Factors controlling discussed, and, particular, rate change atomic charge distribution along coordinate is have major effect dynamics. A frozen...

The acid ionization of HCl in water is examined via a combination electronic structure calculations with ab initio molecular orbital methods and Monte Carlo computer simulations. following key features are taken into account the modeling: polarization solute reaction system by solvent, quantum character proton nuclear motion, solvent fluctuation reorganization along effects on potential, Grotthuss mechanism aqueous transfer. found to involve following: first, nearly activationless motion...

Water molecule rotational dynamics within a chloride anion's first hydration shell are investigated through simulations. In contrast to recent suggestions that the ion's is rigid during water's reorientation, we find labile sphere, consistent with previous assessments of as weak structure breaker. The nondiffusive reorientation mechanism found involves hydrogen-bond partner switch large amplitude angular jump and departure from shell. An analytic extended model accounts for simulation...

Molecular Dynamics simulations are used to examine several key aspects of recent ultrafast infrared experiments on liquid water dynamics in an amplified and extended version a communication [J. Phys. Chem. A 2002, 106, 11993]. It is found that the relation between OH stretch frequency length hydrogen bond which involved characterized by considerable dispersion. This dispersion, part related varying OHO angle bond, precludes one-to-one correspondence length. Further, it time scale currently...

Sum frequency generation (SFG) spectroscopy is a powerful experimental technique to probe surface structures. This paper presents new theoretical mode of nonempirical analysis SFG spectra for interfacial structures, which considerably generalizes our previous effort (Chem. Phys. 2000, 258, 371), involved several empirical elements. The method based on time correlation function the frequency-dependent hyperpolarizability, can be straightforwardly evaluated via molecular dynamics simulations...

The rate constant k for condensed phase chemical reactions is found when a saddle point normal mode analysis holds and the dynamic solvent forces are of generalized Langevin type. If reactive nonreactive modes uncoupled, deviation from its transition state value ktst governed by nonadiabatic friction on mode. In more typical case where coupled k/ktst an effective which completely accounts intramode coupling. Some simple illustrations coupling effects given.

A Landau−Zener curve crossing formulation is developed for proton transfer rate constants over the range of coupling. This approach spans weak coupling regime, where a nonadiabatic tunneling, to strong at reaction transition state motion quantized vibration lying above barrier in coordinate. The theory requires that there solute surrounding polar solvent and includes influence vibrational heavy particles between which transfers. Analytic formulas are given various limits strength frequency...