Mechanisms of photoisomerization of the prenylated flavin mononucleotide cofactor: a theoretical study.

The enzymatic decarboxylation of α,ß-unsaturated acids using the ferulic acid decarboxylase (Fdc1) enzyme and prenylated flavin mononucleotide (prFMN) cofactor is a potential, environmentally friendly reaction for the biosynthesis of styrene and its derivatives. However, experiments showed that the enzyme activity of Fdc1 depends on the ring structure of prFMN, namely, the iminium and ketimine forms, and the loss of enzyme activity results from prFMNim → prFMNket photoisomerization. To obtain insight into this photochemical process and to improve the enzyme efficiency of Fdc1, two proposed photoisomerization mechanisms with different proton sources for the acid-base reaction were studied herein using theoretical methods. The potential energy surfaces calculated using the density functional theory method with the Becke, 3-parameter, and Lee-Yang-Parr hybrid functionals and DZP basis set (DFT/B3LYP/DZP) and TD-DFT/B3LYP/DZP methods confirmed that the light-dependent reaction occurs in the rate-determining proton transfer process and that the mechanism involving intermolecular proton transfer between prFMNim and Glu282 (external base) is energetically more favorable than that involving intramolecular proton transfer in prFMNim (internal base). The thermodynamic results obtained from the transition state theory method suggested that the exothermic relaxation energy in the photo-to-thermal process can promote the spontaneous formation of a high-energy-barrier transition state, and an effective enzymatic decarboxylation could be achieved by slowing down the formation of the undesirable thermodynamically favorable product (prFMNket). Because the rate constant for formation of the high-energy-barrier transition state varies exponentially over the temperature range of 273-298 K, and experimental results have shown that incubating Fdc1 on ice results in a complete loss of enzyme activity, it is recommended to perform the decarboxylation reaction at 285 K to strike a balance between minimizing enzyme stability loss at 273 K and mitigating the effects of UV irradiation. The computational strategy and fundamental insights obtained in this study could serve as guidelines for future theoretical and experimental investigations on the same and similar photochemical systems.

Photoluminescence mechanisms of BF2-formazanate dye sensitizers: a theoretical study.

Photodynamic therapy (PDT) is an alternative, minimally invasive treatment for human diseases such as cancer. PDT uses a photosensitizer to transfer photon energy directly to cellular 3O2 to generate 1O2 (Type II), the toxicity of which leads to cancer cell death. In this work, the photoluminescence mechanisms of a BF2-formazanate dye sensitizer (BF2-FORM) and its iodinated derivative (BF2-FORM-D) were studied using complementary theoretical approaches; the photoluminescence pathways in the S1 and T1 states were studied using density functional theory (DFT) and time-dependent (TD)-DFT methods, the kinetic and thermodynamic properties of the pathways using the transition state theory (TST), and the time evolution and dynamics of key processes using non-adiabatic microcanonical molecular dynamics simulations with surface-hopping dynamics (NVE-MDSH). Evaluation of the potential energy surfaces (PESs) in terms of the rotations of the phenyl rings suggested a pathway for the S1 → S0 transition for the perpendicular structure, whereas two pathways were anticipated for the T1 → S0 transition, namely, [T1 → S0]1 occurring immediately after the S1/T1 intersystem crossing (ISC) and [T1 → S0]2 occurring after the S1/T1 ISC and T1 equilibrium structure relaxation, with the T1 → S0 energy gap being comparable to the energy required for 3O2 → 1O2. The PESs also showed that because of the heavy-atom effect, BF2-FORM-D possessed a significantly smaller S1/T1 energy gap than BF2-FORM. The TST results revealed that at room temperature, BF2-FORM-D was thermodynamically more favorable than the parent molecule. Analysis of the NVE-MDSH results suggested that the librational motions of the phenyl rings play an important role in the internal conversion (IC) and ISC, and the S1/T1 ISC and T1 → S0 transitions could be enhanced by varying the irradiation wavelength and controlling the temperature. These findings can be used as guidelines to improve and/or design photosensitizers for PDT.

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 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.

Photolytic mechanisms of hydroxylamine.

The photodissociation of small molecules has been extensively studied because of the increase in environmental problems related to the atmosphere of the Earth. In this work, the photodissociation mechanisms of hydroxylamine (NH2OH) as a model molecule in its lowest singlet-excited (S1) state were systematically studied using the complete active space second-order perturbation theory (CASPT2) and transition state theory (TST). In particular, this study focused on nonradiative relaxation processes that convert the S0 → S1 excited-state molecule to its products in their respective electronic ground states. The potential energy curves obtained from relaxed scans suggest that O-H dissociation is the preferred process in the S1 state. For the N-O and N-H dissociation pathways, thermally excited precursors were hypothesized to form in the S0 state to circumvent O-H dissociation. Thus, S0 → S1 vertical excitations lead to transition structures in the S1 state, which fragment to their respective electronic-ground-state products. The thermodynamic and kinetic results confirmed the precursor hypothesis, showing that the exothermic energy caused by the formation of HNO and H2 is sufficient to generate such precursors in the S0 state. Additionally, the TST confirmed that unimolecular isomerization-dissociation is a two-step process that generates products effectively by direct photolysis of the corresponding covalent bonds. In particular, the process consists of O-H bond dissociation, followed by spontaneous isomerization and formation of H2 in its electronic ground state, resulting in the high quantum yield observed in the UV absorption experiments in the preferential formation of HNO and H2. The configuration interaction coefficients of the characteristic structures on the potential energy curves revealed considerable changes in the multiconfigurational character of the wavefunctions, especially for the transition structures. These are characterized by the development of Rydberg orbitals, being produced at the intersection of the S0 and S1 states. The present study highlights the effects of thermal selectivity and the multiconfigurational character of the wavefunctions on photodissociation. Because detailed information on the photolytic mechanisms of isolated NH2OH is limited both theoretically and experimentally, these results provide fundamental insight into unimolecular photodissociation, posing ground for future studies on related systems.