On the effects of solvent and intermolecular fluctuations in proton transfer reactions

Computational studies on electron and proton transfer in phenol-imidazole-base triads

The electron and proton transfer in phenol-imidazole-base systems (base = NH(2)(-) or OH(-)) were investigated by density-functional theory calculations. In particular, the role of bridge imidazole on the electron and proton transfer was discussed in comparison with the phenol-base systems (base = imidazole, H(2)O, NH(3), OH(-), and NH(2)(-)). In the gas phase phenol-imidazole-base system, the hydrogen bonding between the phenol and the imidazole is classified as short strong hydrogen bonding, whereas that between the imidazole and the base is a conventional hydrogen bonding. The n value in sp(n) hybridization of the oxygen and carbon atoms of the phenolic CO sigma bond was found to be closely related to the CO bond length. From the potential energy surfaces without and with zero point energy correction, it can be concluded that the separated electron and proton transfer mechanism is suitable for the gas-phase phenol-imidazole-base triads, in which the low-barrier hydrogen bond is found and the delocalized phenolic proton can move freely in the single-well potential. For the gas-phase oxidized systems and all of the triads in water solvent, the homogeneous proton-coupled electron transfer mechanism prevails.

Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping

Reliable studies of proton transfer (PT) reactions in solution and in enzymes by combined quantum mechanical/molecular mechanics (QM/MM) approaches with an ab initio description of the quantum region present a major challenge to computational chemists. The main problem is the need for extensive computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. The present work presents a new effective way for performing such calculations by using the frozen density functional (FDFT) approach to generate diabatic surfaces that are used to generate a mapping potential that takes the system from the reactant to the product state. The resulting umbrella sampling/free energy perturbation (US/FEP) mapping is done in full analogy with the approach used in the empirical valence bond (EVB) treatment, moving from the diabatic mapping potential to the adiabatic ground state surface, while an ab initio Hamiltonian is used for the QM part. The present approach provides a particularly effective way for evaluating the free energy associated with both the substrate and the solvent motions. This allows us to obtain a free energy barrier that properly reflects the solute entropy. This advance allows one to obtain ab initio QM/MM (QM(ai)/MM) free energy surfaces for very challenging cases such as the autodissociation of water in water, proton transfer between methanol and water in water, and the effect of Mg2+ ion on such a reaction. We also consider as a benchmark the initial PT reaction in the catalytic cycle of triose phosphate isomerase and obtain excellent results without any adjustable parameters. Our results point out that the present implementation of the FDFT approach provides a very promising approach for evaluating QM(ai)/MM free energy surfaces.

Extended spin-boson model for nonadiabatic hydrogen tunneling in the condensed phase

A nonadiabatic rate expression for hydrogen tunneling reactions in the condensed phase is derived for a model system described by a modified spin-boson Hamiltonian with a tunneling matrix element exponentially dependent on the hydrogen donor-acceptor distance. In this model, the two-level system representing the localized hydrogen vibrational states is linearly coupled to the donor-acceptor vibrational mode and the harmonic bath. The Hamiltonian also includes bilinear coupling between the donor-acceptor mode and the bath oscillators. This coupling provides a mechanism for energy exchange between the two-level system and the bath through the donor-acceptor mode, thereby facilitating convergence of the time integral of the probability flux correlation function for the case of weak coupling between the two-level system and the bath. The dependence of the rate constant on the model parameters and the temperature is analyzed in various regimes. Anomalous behavior of the rate constant is observed in the weak solvation regime for model systems that lack an effective mechanism for energy exchange between the two-level system and the bath. This theoretical formulation is applicable to a wide range of chemical and biological processes, including neutral hydrogen transfer reactions with small solvent reorganization energies.

Further Evidence of an Inverted Region in Proton Transfer within the Benzophenone/Substituted Aniline Contact Radical Ion Pairs; Importance of Vibrational Reorganization Energy

The dynamics of proton transfer within the triplet contact radical ion pair of a variety of substituted benzophenones with N,N-diethylaniline, N,N-dimethyl-p-toluinide, and N,N-diallylaniline are examined in solvents of varying polarity. The correlation of the rate constants with driving force reveal both a normal region and an inverted region providing support for the nonadiabatic nature of proton transfer within these systems. The reorganization of both the solvent and the molecular framework are central in governing the overall reaction dynamics.

Proton-transfer dynamics in the activation of cytochrome P450eryF

Molecular dynamics simulations are combined with quantum chemistry calculations of instantaneous proton-transfer energy profiles to investigate proton-transfer events in the transient pathway of cytochrome P450eryF (6-deoxyerythronolide B hydroxylase; CYP107A1), from the oxyferrous species to the catalytically active ferryl oxygen species (compound I). This reaction is one of the most fundamental unresolved aspects in the mechanism of oxidation that is common to all cytochrome P450s. We find that this process involves an ultrafast proton transfer from the crystallographic water molecule W519 to the distal oxygen bound to the heme group, and a subsequent proton-transfer event from W564 to W519. Both proton-transfer events are found to be endothermic in the oxyferrous state, suggesting that the oxyferrous reduction is mechanistically linked to the proton-transfer dynamics. These findings indicate that the hydrogen bond network, proximate to the O(2)-binding cleft, plays a crucial functional role in the enzymatic activation of P450s. Our results are consistent with the effect of mutations on the enzymatic efficacy.

Protein fluorescence, dynamics and function: exploration of analogy between electronically excited and biocatalytic transition states

With the advent and development of time-resolved spectroscopic techniques and substantial progress in understanding of photophysical and photochemical phenomena, a new goal may be achieved: modeling of biochemical reaction or its elementary step by a photochemical event occurring within the probe, bound to a protein molecule. The probe may be located in a well-determined site of the protein matrix and report on the modulation of the reaction rate by the matrix and by the surrounding solvent, or by interactions in multiprotein complexes and in biomembranes. The advantages of this approach are obvious: in contrast to ordinary biochemical reaction, the excited-state reaction may be started by a short light pulse, and its kinetics may be observed directly with high resolution in time. In addition, if the reaction rate is influenced by the dynamics of the protein matrix, these dynamics may be studied simultaneously with the reaction, by using the same or a similar probe and within the same time range. In this review, the prospects for application of probes exhibiting electron transfer, proton transfer, molecular rotations and isomerizations are presented and discussed. The general problem of photochemical modeling of biochemical reactions is discussed. This modeling may result in deeper understanding of enzyme catalyzed reaction mechanisms.