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The article explains the various mechanisms that are involved in the concerted proton-electron transfer (CPET) taking place during the homogeneous reduction of dioxygen to water. The CPET is shown to significantly decreases with decrease in the endergonicity of ET.

The synthesis, properties and the stability of the various intermolecular and enol tautomers of the Watson-Crick base pair models are discussed. These compounds are shown to be dynamically metastable.

Density functional theory QM/MM studies were carried out on the deacetylation reaction catalyzed by histone-deacetylase-like-protein (HDLP) in order to characterize the catalytic mechanism for histone-deacetylase (HDACs). The calculations were based on the pseudobond ab initio QM/MM approach, which was successfully employed in the study of several enzymes and were carried out with modified versions of the Gaussian03 and TINKER programs.

A finite temperature ab inito molecular dynamics (AIMD) study is undertaken using forces obtained 'on the fly' from electronic structure calculations to investigate the addition product distribution as well as the underlying mechanistic aspects of the reaction. The method highlights the predominance of a stepwise zwitterionic mechanism governing addition product formation on the Si(100)-2 X 1 surface.

The mechanism of the reaction pathway of the [4 + 2] Diels-Alder adduct formation on Si(100)-2x1 surface is described. The ab initio molecular dynamics (AIMD) study shows that forces are generated 'on the fly' from electronic structure calculations.

Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage. [ABSTRACT FROM AUTHOR]

Understanding the chemical reaction mechanisms governing how small organic molecules attach to semiconductor surfaces can lead to new strategies for creating specific surface patterns such as single adduct monolayers. In this study, room-temperature ab initio molecular dynamics simulations of one and two 1 ,3-cyclohexadiene (CHD) molecule(s) reacting with the Si(1 OO)-2 xl surface reveal that adducts form via a carbocation-mediated two-step mechanism. Dimer flipping can either promote or prevent bond formation depending on how the CHD approaches. CHDs often travel past several Si dimers before finding the proper local environment. The resulting intermediate can persist for more than 4 ps, allowing the second bond to form with any adjacent Si dimer. The additional reactive site accounts for a large portion of the discrepancy between the predicted thermodynamic and observed experimental product distribution. Surface adducts protect a 5.6 Å region, direct unbound CHD exploration, and can cause adjacent dimers to flip. [ABSTRACT FROM AUTHOR]

Concerted proton-electron transfer (CPET) is documented for the homogeneous reduction of O2 to HO2 in water by the one-electron-reduced heteropolytungstate anion, α-PW12O404- (11e). At 0.01-0.3 M H+, O2 reduction occurs via outer-sphere electron transfer followed by proton transfer (ETPT, with rate constant kET). Between 0.30 and 1.9 M H+, rates increase linearly with [H+] due to a parallel CPET pathway in which H+ is now a reactant: (l/2)kobs = kET + kCPET[H+] (kET = 1.2 M-1 s-1; kCPET = 0.8 M-2 s-1). Control experiments rule out preassociation between H+ and 11e. Analysis of plausible rate expressions shows that the first-order dependence on [H+] is uniquely consistent with multisite CPET, and a deuterium kinetic isotope effect of 1.7 is observed. Reductions of O2 by α-SiW12O405- confirm theoretical predictions that CPET decreases in significance as ET becomes less endergonic. Marcus analysis, including the temperature dependence of ΔG°, gives reorganization energies, λET = 41.5 kcal mol-1 and λCPET = 52.4 kcal mol-1. At 1.5 M H+, ∼75% of the (11e,O2) encounter pairs form within 6 Å of H+ ions. This value (6 ± 1 Å) is the "reaction distance" for proton diffusion and probably close to that for CPET. Even so, the 70-200 Ps lifetimes of the (11e,O2) pairs provide additional time for H+ to diffuse closer to O2. CPET is first-order in [H+] because ke for "cage escape" from (11e,O2) pairs is much larger than kCPET, such that the rate expression for CPET becomes -(1/2)d[11e]/dt= (kd/ke)/kCPET[11e][O2][H+], where kd is the rate constant for (11e,O2) pair formation. Overall, the findings suggest that the emergence of CPET, with hydronium ion as the proton donor, may prove a general feature of sufficiently endergonic reductions of dioxygen by otherwise "outer-sphere" complexes (or electrode reactions) at sufficiently low pH values in water. [ABSTRACT FROM AUTHOR]