Kinetics and thermodynamics of enzymatic decarboxylation of α,ß-unsaturated acid: a theoretical study.

Enzymatic decarboxylation of α,ß-unsaturated acid through ferulic acid decarboxylase (FDC1) has been of interest because this reaction has been anticipated to be a promising, environmentally friendly industrial process for producing styrene and its derivatives from natural resources. Because the local dielectric constant at the active site is not exactly known, enzymatic decarboxylation to generate ß-methylstyrene (ß-MeSt) was studied under two extreme conditions (ε = 1 and 78 in the gas phase and aqueous solution, respectively) using the B3LYP/DZP method and transition state theory (TST). The model molecular clusters consisted of an α-methylcinnamate (Cin) substrate, a prenylated flavin mononucleotide (PrFMN) cofactor and all relevant residues of FDC1. Analysis of the equilibrium structures showed that the FDC1 backbone does not play the most important role in the decarboxylation process. The potential energy profiles confirmed that the increase in the polarity of the solvent could lead to significant changes in the energy barriers, especially for the transition states that involve proton transfer. Analysis of the rate constants confirmed the low/no quantum mechanical tunneling effect in the studied temperature range and that inclusion of the fluctuation of the local dielectric environment in the mechanistic model was essential. Because the computed rate constants are not compatible with the time resolution of the stopped-flow spectrophotometric experiment, the direct route for generating ß-MeSt after CO2 elimination (acid catalyst (2)) is unlikely to be utilized, thereby confirming that indirect cycloelimination in a low local dielectric environment is the rate determining step. The thermodynamic results showed that the elementary reactions that involve charge (proton) transfer are affected by solvent polarity, thereby leading to the conclusion that overall, the enzymatic decarboxylation of α,ß-unsaturated acid is thermodynamically controlled at high ε. The entropy changes due to the generation of molecules in the active site appeared more pronounced than that due to only covalent bond breaking/formation or structural reorientation. This work examined in detail for the first time the scenarios in each elementary reaction and provided insight into the effect of the fluctuations in the local dielectric environment on the enzymatic decarboxylation of α,ß-unsaturated acids. These results could be used as guidelines for further theoretical and experimental studies on the same and similar systems.

The mechanism of excited state proton dissociation in microhydrated hydroxylamine clusters.

The dynamics and mechanism of excited-state proton dissociation and transfer in microhydrated hydroxylamine clusters are studied using NH2OH(H2O)n (n = 1-4) as model systems and the DFT/B3LYP/aug-cc-pVDZ and TD-DFT/B3LYP/aug-cc-pVDZ methods as model calculations. This investigation is based on the Förster acidity scheme and emphasizes the photoacid dissociation in the ground (S0) and lowest singlet-excited states (S1) and the interplay between the photo and thermal excitations. The quantum chemical results suggest that the intermediate complexes are formed only in the S1 state in a low local-dielectric environment (e.g., ε = 1) and that upon the S0→ S1 transition, the photon energy excites mostly NH2OH, which leads to a homolytic cleavage of the O-H bond and to dynamically stable charge-separated Rydberg-like H-bond complexes (e.g., NH2O˙-H3O(+)˙). The potential energy surfaces for proton displacement in the smallest Rydberg-like H-bond complex support the intersection of the S0 and S1 states in low local-dielectric environments, whereas in a high local-dielectric environment (e.g., ε = 78), these two states are completely separated. Based on the static results, a photoacid-dissociation mechanism that involves Rydberg-like H-bond complex formation, an H-bond chain extension and fluctuations in the local-dielectric environment is proposed. NVT-BOMD simulations confirm the static results and show that the dynamic behavior of the dissociating proton in the S1 state is not different from that of the protonated H-bond systems in the ground state, which consists of the oscillatory shuttling and structural diffusion motions. These findings allow our theoretical methods, which have been used successfully in protonated H-bond systems in the ground state, to be applied in the study of the photoacid-dissociation processes. The current theoretical study suggests effective steps as well as guidelines for the investigation of the dynamics of the photoacid-dissociation and transfer processes in the Förster acidity scheme, provided that the exciting photon does not lead to a significant change in the structure of the intermediate complex in the excited state.

Proton transfer reactions and dynamics of sulfonic acid group in Nafion®.

Proton transfer reactions and dynamics of the hydrophilic group (-SO(3)H) in Nafion® were studied at low hydration levels using the complexes formed from CF(3)SO(3)H, H(3)O(+) and nH(2)O, 1 ≤n≤ 3, as model systems. The equilibrium structures obtained from DFT calculations suggested at least two structural diffusion pathways at the -SO(3)H group namely, the "pass-through" and "pass-by" mechanisms. The former involves the protonation and deprotonation at the -SO(3)H group, whereas the latter the proton transfer in the adjacent Zundel complex. Analyses of the asymmetric O-H stretching frequencies (ν(OH)) of the hydrogen bond (H-bond) protons showed the threshold frequencies (ν(OH*)) of proton transfer in the range of 1700 to 2200 cm(-1). Born-Oppenheimer Molecular Dynamics (BOMD) simulations at 350 K anticipated slightly lower threshold frequencies (ν(A)(OH*,MD)), with two characteristic asymmetric O-H stretching frequencies being the spectral signatures of proton transfer in the H-bond complexes. The lower frequency (ν(A)(OH,MD))) is associated with the oscillatory shuttling motion and the higher frequency (ν(B)(OH,MD))) the structural diffusion motion. Comparison of the present results with BOMD simulations on protonated water clusters indicated that the -SO(3)H group facilitates proton transfer by reducing the vibrational energy for the interconversion between the two dynamic states (Δν), resulting in a higher population of the H-bonds with the structural diffusion motion. One could therefore conclude that the -SO(3)H groups in Nafion® act as active binding sites which provide appropriate structural, energetic and dynamic conditions for effective structural diffusion processes in a proton exchange membrane fuel cell (PEMFC). The present results suggested for the first time a possibility to discuss the tendency of proton transfer in H-bond using Δν(BA)(OH,MD)) and provided theoretical bases and guidelines for the investigations of proton transfer reactions in theory and experiment.

Proton transfer reactions and dynamics in protonated water clusters.

Proton transfer reactions and dynamics were theoretically studied using the hydrogen-bond (H-bond) complexes formed from H(3)O(+) and nH(2)O, n = 1-4, as model systems. The investigations began with searching for characteristics of transferring protons in the gas phase and continuum aqueous solution using DFT method at the B3LYP/TZVP level, followed by Born-Oppenheimer molecular dynamics (BOMD) simulations at 350 K. B3LYP/TZVP calculations revealed the threshold asymmetric O-H stretching frequencies (ν(OH)*) for the proton transfers in the Zundel complex (H(5)O) in the gas phase and continuum aqueous solution at 1984 and 1881 cm(-1), respectively. BOMD simulations suggested lower threshold frequencies (ν(OH,MD)* = 1917 and 1736 cm(-1), respectively), with two characteristic ν(OH,MD) being the IR spectral signatures of the transferring protons. The low-frequency band could be associated with the "oscillatory shuttling motion" and the high-frequency band with the "structural diffusion motion". These can be regarded as the spectroscopic evidences of the formations of the shared-proton structure (O···H(+)···O) and the H(3)O(+)-H(2)O contact structure (O-H(+)···O), respectively. Since the quasi-dynamic equilibrium between the Zundel and Eigen complexes was suggested to be the rate-determining step, in order to achieve an "ideal" maximum efficiency of proton transfer, a concerted reaction pathway should be taken. The most effective interconversion between the two proton states, the shared-proton structure and the H(3)O(+)-H(2)O contact structure, can be reflected from comparable intensities of the oscillatory shuttling and structural diffusion bands. The present results iterated the previous conclusions that static proton transfer potentials cannot provide complete description of the structural diffusion process and it is essential to incorporate thermal energy fluctuations and dynamics in the model calculations.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.