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

Enzymatic decarboxylation of α,β-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 β-methylstyrene (β-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 β-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,β-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,β-unsaturated acids. These results could be used as guidelines for further theoretical and experimental studies on the same and similar systems.

The Grotthuss mechanism for bifunctional proton transfer in poly(benzimidazole)

Poly(benzimidazole) (PBI) has received considerable attention as an effective high-temperature polymer electrolyte membrane for fuel cells. In this work, the Grotthuss mechanism for bifunctional proton transfer in PBI membranes was studied using density functional theory and transition state theory. This study focused on the reaction paths and kinetics for bifunctional proton transfer scenarios in neutral ([PBI]2), single (H+[PBI]2) and double-protonated (H2+[PBI]2) dimers. The theoretical results showed that the energy barriers and strength for H-bonds are sensitive to the local dielectric environment. For [PBI]2 with ε = 1, the uphill potential energy curve is attributed to extraordinarily strong ion-pair H-bonds in the transition structure, regarded as a 'dipolar energy trap'. For ε = 23, the ion-pair charges are partially neutralized, leading to a reduction in the electrostatic attraction in the transition structure. The dipolar energy trap appears to prohibit interconversion between the precursor, transition and proton-transferred structures, which rules out the possibility for [PBI]2 to be involved in the Grotthuss mechanism. For H+[PBI]2 and H2+[PBI]2 with ε = 1, the interconversion involves a low energy barrier, and the increase in the energy barrier for ε = 23 can be attributed to an increase in the strength of the protonated H-bonds in the transition structure: the local dielectric environment enhances the donor-acceptor interaction of the protonated H-bonds. Analysis of the rate constants confirmed that the quantum effect is not negligible for the N-H+ … N H-bond especially at low temperatures. Agreement between the theoretical and experimental data leads to the conclusion that the concerted bifunctional proton transfer in H2+[PBI]2 in a high local dielectric environment is 'the rate-determining scenario'. Therefore, a low local dielectric environment can be one of the required conditions for effective proton conduction in acid-doped PBI membranes. These theoretical results provide insights into the Grotthuss mechanism, which can be used as guidelines for understanding the fundamentals of proton transfers in other bifunctional H-bond systems.

The relationship between charge and molecular dynamics in viscous acid hydrates

Oscillatory shear rheology has been employed to access the structural rearrangements of deeply supercooled sulfuric acid tetrahydrate (SA4H) and phosphoric acid monohydrate, the latter in protonated (PA1H) and deuterated (PA1D) forms. Their viscoelastic responses are analyzed in relation to their previously investigated electric conductivity. The comparison of the also presently reported dielectric response of deuterated sulfuric acid tetrahydrate (SA4D) and that of its protonated analog SA4H reveals an absence of isotope effects for the charge transport in this hydrate. This finding clearly contrasts with the situation known for PA1H and PA1D. Our analyses also demonstrate that the conductivity relaxation profiles of acid hydrides closely resemble those exhibited by classical ionic electrolytes, even though the charge transport in phosphoric acid hydrates is dominated by proton transfer processes. At variance with this dielectric simplicity, the viscoelastic responses of these materials depend on their structural compositions. While SA4H displays a "simple liquid"-like viscoelastic behavior, the mechanical responses of PA1H and PA1D are more complex, revealing relaxation modes, which are faster than their ubiquitous structural rearrangements. Interestingly, the characteristic rates of these fast mechanical relaxations agree well with the characteristic frequencies of the charge rearrangements probed in the dielectric investigations, suggesting appearance of a proton transfer in mechanical relaxation of phosphoric acid hydrates. These findings open the exciting perspective of exploiting shear rheology to access not only the dynamics of the matrix but also that of the charge carriers in highly viscous decoupled conductors.

A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

Mechanisms of photoexcitation and photoionization in small water clusters

The S₀ → S₁ excitation leads to strong polarization and formation of [(H₂O)₂]⁺˙ from which both photoexcited and photoionized products are generated.