A QM/MM study on the catalytic mechanism of pyruvate decarboxylase

Pyruvate decarboxylase (PDC) is a typical thiamin diphosphate (ThDP)-dependent enzyme with widespread applications in industry. Though studies regarding the reaction mechanism of PDC have been reported, they are mainly focused on the formation of ThDP ylide and some elementary steps in the catalytic cycle, studies about the whole catalytic cycle of PDC are still not completed. In these previous studies, a major controversy is whether the key active residues (Glu473, Glu50′, Asp27′, His113′, His114′) are protonated or ionized during the reaction. To explore the catalytic mechanism and the role of key residues in the active site, three whole-enzyme models were considered, and the combined QM/MM calculations on the nonoxidative decarboxylation of pyruvate to acetaldehyde catalyzed by PDC were performed. According to our computational results, the fundamental reaction pathways, the complete energy profiles of the whole catalytic cycle, and the specific role of key residues in the common steps were obtained. It is also found that the same residue with different protonation states will lead to different reaction pathways and energy profiles. The mechanism derived from the model in which the residues (Glu473, Glu50′, Asp27′, His113′, His114′) are in their protonated states is most consistent with experimental observations. Therefore, extreme care must be taken when assigning the protonation states in the mechanism study. Because the experimental determination of protonation state is currently difficult, the combined QM/MM method provides an indirect means for determining the active-site protonation state.     

Computational study toward understanding the photodissociation mechanism of sarin

The potential energy surface for sarin (C₄H₁₀FO₂P) dissociation into (CH₃)₂CHO+PO(F)(CH₃), CH₃+(CH₃)₂CHOPO(F), and F+(CH₃)₂CHOPO(CH₃) in the T₁ and S₁ states were investigated at the complete‐active‐space self‐consistent field (CASSCF) with the 6‐31G** and aug‐cc‐PVDZ basis sets. The different reaction pathways are characterized on the basis of the computed potential energy surface and surface crossing point, the time‐dependent density functional theory (TD‐DFT) was used to calculate the vertical energies based on the CAS(8,7)/6‐31G** optimized excited structures, which may provide some new insights into the mechanism of the ultraviolet photo‐degradation of sarin molecules. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study toward understanding ultrafast internal conversion of excited 9H-adenine

The CASPT2/CASSCF method with the 6-311G basis set and an active space up to (14, 11) was used to explore the ultrafast internal conversion mechanism for excited 9H-adenine. Three minima, two transition states, and seven conical intersections were obtained to build up the two deactivation pathways for the internal conversion mechanism. Special efforts were made to explore the excited-state potential energy surfaces near the Franck-Condon region and determine the various barriers in the processes of deactivation. The barrier required from the 1pipi (1La) state to deactivate nonradiatively is found to be lower than that required from the 1pipi (1Lb) state. On 250 nm excitation, the 1pipi (1La) state is populated, and the transition from 1pipi (1La) to the lowest 1npi state involves very low barriers, which may account for the observed short (<50 fs) lifetime of the 1pipi excited state. The deactivation of the lowest 1npi state is required to overcome a barrier of 3.15 kcal/mol, which should be responsible for the 750 fs lifetime of the npi excited state. On 267 nm excitation, the vibrationally active 1pipi (1Lb) state is populated. Excitation at 277 nm prepares the 1pipi (1Lb) state without much excessive vibrational energy, which may be responsible for the observed >2 ps lifetime.     

The electrochemical investigation of the catalytic power of pyruvate decarboxylase and its coenzyme

The change in the energy barriers for the heterogeneous reduction of pyruvate decarboxylase (PDC) relative to its coenzyme, thiamin pyrophosphate (ThPP), was determined experimentally using square wave voltammetry (SWV) to be 5.3 kcal/mol. These results are in agreement with those of reaction rate acceleration provided by thiamin-dependent decarboxylases relative to their coenzyme as determined kinetically based on the pK(a) suppression by the enzyme environment.     

Theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase

The reaction pathway of deformylation catalyzed by E. coli peptide deformylase (PDF) has been investigated by the density functional theory method of PBE1PBE on a small model and by a two-layer ONIOM method on a realistic protein model. The deformylation proceeds in sequential steps involving nucleophilic addition of metal-coordinated water/hydroxide to the carbonyl carbon of the formyl group, proton transfer, and cleavage of the C-N bond. The first step is rate-determining for the deformylation, which occurs through a pentacoordinated metal center. The estimated activation energies with the ONIOM method are about 23.0, 15.0, and 14.9 kcal/mol for Zn-, Ni-, and Fe-PDFs, respectively. These calculated barriers are in close agreement with experimental observations. Our results demonstrate that the preference for metal coordination geometry exerts a significant influence on the catalytic activity of PDFs by affecting the activation of the carbonyl group of the substrate, the deprotonation of the metal-coordinated water, and the stabilization of the transition state. This preference for coordination geometry is mainly determined by the ligand environment and the intrinsic electronic structures of the metal center in the active site of the PDFs.     

Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate

The determination of pyruvate formate lyase crystallographic structure brought new insights to its mechanism of reaction and presented the possibility of a direct attack to the substrate from cysteine 418 as opposed to the previously expected cysteine 419. An inhibition study performed by Knappe and co-workers, using substrate-analogue methacrylate, confirms that cysteine 418 is most likely to add directly to pyruvate, since an inhibition product has been found as a substituent in this residue. The work presented here consists of a study of the inhibition mechanism of pyruvate formate lyase by methacrylate, using density functional theory with the hybrid B3LYP functional. We were able to determine all pertinent structures, confirm the proposed experimental mechanism, and add important detail to the energy profile associated with the mechanism of inhibition. Additionally, the obtained results provide the energy values for both the chemical reaction and the stereochemical reorganization necessary in order for the thiol-methacrylate adduct to come within reactional reach of Cys419.     

Theoretical studies toward understanding the excited state dynamics of a bichromophoric molecule

By means of the time-dependent density functional theory, the authors study the torsional dynamics of the lowest singlet electronic excited state (S1) of a bichromophoric molecule, 2-(9-anthryl)-1H-imidazo [4,5-f]-phenanthroline (AIP). The intramolecular dynamical relaxation process, the S1 potential energy surface, and the vibrationally resolved electronic absorption and fluorescence spectra are estimated. The results reveal that the strong electron-nuclear coupling leads to a dynamic structural distortion in S1 state so that the mirror-image symmetry of absorption and fluorescence spectra of AIP breaks down. The torsional motion between the donor and acceptor moieties in AIP favors the intramolecular electronic energy transfer process. The transfer rate is dominated by the relaxation time along S1 low-frequency torsional motion.     

The catalytic power of pyruvate decarboxylase. A stochastic model for the molecular evolution of enzymes.

Pyruvate decarboxylase (PDC) catalyzes the decarboxylation of pyruvate anion by a factor of around 10(12), compared with the non-enzymic decarboxylation by thiamine, under standard state conditions of 1 mM pyruvate and thiamine diphosphate (TDP), pH 6.2. Free-energy diagrams constructed on the basis of earlier measurements for the enzymic and non-enzymic reactions give some information on catalysis by PDC. PDC stabilizes the reactant state preceding TDP addition to pyruvate by 76 kJ mol-1 and the transition state for the addition by 83 kJ mol-1. PDC stabilizes the reactant state preceding decarboxylation (presumably alpha-lactyl-TDP) by 27 kJ mol-1 and the transition state for decarboxylation by 68 kJ mol-1. In addition, the free-energy diagrams reveal a leveling of reactant-state free energies in the enzymic reaction compared with the non-enzymic reaction, in that the former are nearly equal to each other. The enzyme-bound transition-state energies are similarly leveled. The energetic leveling of reactant states has been noted by Albery, Knowles and their coworkers in many enzymic reactions and termed 'matched internal thermodynamics.' They showed that the result would arise naturally (and inevitably) in the 'evolution to perfection' of enzymes, when the evolutionary process was treated by a deterministic model. The critical assumption of this model was the validity of a Marcus-type or Br?nsted-type linear free-energy relationship between rate and equilibrium constants for reactions occurring wholly within enzyme complexes. Here a completely stochastic simulation of molecular evolution, with no deterministic assumptions, is shown to reproduce both 'matched internal thermodynamics' and the 'matched internal kinetics' or leveling of transition-state energies noted here. The Albery-Knowles result is thus more general than might have been supposed.     

An ab initio study toward understanding the mechanistic photochemistry of acetamide

The potential energy surfaces for CH(3)CONH(2) dissociation into CH(3) + CONH(2), CH(3)CO + NH(2), CH(3)CN + H(2)O, and CH(3)NH(2) + CO in the ground and lowest triplet states have been mapped with DFT, MP2, and CASSCF methods with the cc-pVDZ and cc-pVTZ basis sets, while the S(1) potential energy surfaces for these reactions were determined by the CASSCF/cc-pVDZ optimizations followed by CASSCF/MRSDCI single-point calculations. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. A comparison of the reactivity among HCONH(2), CH(3)CONH(2), and CH(3)CONHCH(3) has been made, which provides some new insights into the mechanism of the ultraviolet photodissociation of small amides.     

Theoretical studies of the mechanism of catalytic hydrogen production by a cobaloxime

Our theoretical studies of the standard reduction potentials of the molecular complex [Co(II)(dmgBF(2))(2)](0) (dmgBF(2) = difluoro-boryldimethylglyoximate) in acetonitrile solution shed light on its electrocatalytic mechanism for hydrogen production. Three such mechanisms have been proposed, all proceeding through the formation of Co(III)H. Our results indicate that the mechanism involving a Co(II)H intermediate is the most likely.     

Theoretical study of the phosphotriesterase reaction mechanism

Phosphotriesterase (PTE) is a binuclear zinc enzyme that catalyzes the hydrolysis of extremely toxic organophosphate triesters. In the present work, we have investigated the reaction mechanism of PTE using the hybrid density functional theory method B3LYP. We present a potential energy surface for the reaction and provide characterization of the transition states and intermediates. We used the high resolution crystal structure to construct a model of the active site of PTE, containing the two zinc ions and their first shell ligands. The calculations provide strong support to an associative mechanism for the hydrolysis of phosphotriesters by PTE. No protonation of the leaving group was found to be necessary. In particular, the calculations demonstrate that the nucleophilicity of the bridging hydroxide is sufficient to be utilized in the hydrolysis reaction, a feature that is of importance for a number of other di-zinc enzymes.     

Theoretical study of catalytic effects in micellar solutions

The catalytic effect of charged micelles as manifested through the increased collision frequency between the counterions of an electrolyte in the presence of such micelles is explored by the Monte Carlo simulation technique and various theoretical approaches. The micelles and ions are pictured as charged hard spheres embedded in a dielectric continuum with the properties of water at 298 K with the charge on micelles varying from zero to z(m) = 50 negative elementary charges. Analytical theories such as (i) the symmetric Poisson-Boltzmann theory, (ii) the modified Poisson-Boltzmann theory, and (iii) the hypernetted-chain integral equation are applied and tested against the Monte Carlo data for micellar ions (m) with up to 50 negative charges in aqueous solution with monovalent counterions (c; z(c) = +1) and co-ions (co; z(co) = -1). The results for the counterion-counterion pair correlation function at contact, g(cc)(sigma(cc)), are calculated in a micellar concentration range from c(m) = 5 x 10(-)(6) to 0.1 mol/dm(3) with an added +1:-1 electrolyte concentration of 0.005 mol/dm(3) (for most cases), and for various model parameters. Our computations indicate that even a small concentration of a highly charged polyelectrolyte added to a +1:-1 electrolyte solution strongly increases the probability of finding two counterions in contact. This result is in agreement with experimental data. For low charge on the micelles (z(m) below -8), all the theories are in qualitative agreement with the new computer simulations. For highly charged micelles, the theories either fail to converge (the hypernetted-chain theory) or, alternatively, yield poor agreement with computer data (the symmetric Poisson-Boltzmann and modified Poisson-Boltzmann theories). The nonlinear Poisson-Boltzmann cell model results yield reasonably good agreement with computer simulations for this system.     

苯并噻二唑醇解反应机理的理论研究

苯并噻二唑（BTH）是新型植保制剂。预防对象包括白粉病、锈病、霜霉病等阻引。 为更好地了解BTH的环境行为，本文研究了BTH醇解反应机理及反应的动力学。     

Theoretical study of catalytic dinitrogen reduction under mild conditions

Density functional theory results on key steps of Schrock's catalytic cycle are presented. The quantum chemical modeling of the dinitrogen-reducing reaction steps is conducted without simplifying the bulky HIPT [HIPT = 3,5-(2,4,6-iPr(3)C(6)H(2))(2)C(6)H(3)] substituents at the triamidoamine ligand.     

Theoretical study of hydrolysis mechanism of khellin

This paper describes khellin hydrolysis mechanism using semiemperical PM3 implemented in Gaussian 03 package. The calculations show that in the presence of an acidic media, an enolate molecular ion leads directly to ω-acetokhellinone while in the basic media it leads to khellinone.     

A theoretical study of the catalytic mechanism of formate dehydrogenase

A theoretical study of the hydride transfer between formate anion and nicotinamide adenine dinucleotide (NAD(+)) catalyzed by the enzyme formate dehydrogenase (FDH) has been carried out by a combination of two hybrid quantum mechanics/molecular mechanics techniques: statistical simulation methods and internal energy minimizations. Free energy profiles, obtained for the reaction in the enzyme active site and in solution, allow obtaining a comparative analysis of the behavior of both condensed media. Moreover, calculations of the reaction in aqueous media can be used to probe the dramatic differences between reactants state in the enzyme active site and in solution. The results suggest that the enzyme compresses the substrate and the cofactor into a conformation close to the transition structure by means of favorable interactions with the amino acid residues of the active site, thus facilitating the relative orientation of donor and acceptor atoms to favor the hydride transfer. Moreover, a permanent field created by the protein reduces the work required to reach the transition state (TS) with a concomitant polarization of the cofactor that would favor the hydride transfer. In contrast, in water the TS is destabilized with respect to the reactant species because the polarity of the solute diminishes as the reaction proceeds, and consequently the reaction field, which is created as a response to the change in the solute polarity, is also decreased. Therefore protein structure is responsible of both effects; substrate preorganization and TS stabilization thus diminishing the activation barrier. Because of the electrostatic features of the catalyzed reaction, both media preferentially stabilize the ground-state, thus explaining the small rate constant enhancement of this enzyme, but FDH does so to a much lower extent than aqueous solution. Finally, a good agreement between experimental and theoretical kinetic isotope effects is found, thus giving some credit to our results.     

Theoretical study on second hyperpolarizabilities of phenylacetylene dendrimer: toward an understanding of structure-property relation in NLO responses of fractal antenna dendrimers

This contribution explores the relation between molecular second hyperpolarizabilities (gamma) and molecular architecture in phenylacetylene dendrimers using the semiempirical molecular orbital method, that is, INDO/S method. The orientationally averaged gamma of a large-size phenylacetylene dendrimer, which is composed of 24 units of phenylacetylenes and is referred to as D25, is found to be about 50 times as large as that of the diphenylacetylene monomer. In contrast, the gamma(s)() value of D25 is found to be about 6 times as small as that of the para-substituted phenylacetylene oligomer (L25) composed of 24 units of phenylacetylenes. To investigate the structure-property relation in gamma for D25 and L25, we examine the spatial contributions of electrons to gamma values using gamma density analysis. The present analysis reveals that the dominant contributions of electrons to gamma of D25 are localized in the linear-leg regions parallel to the applied electric field and the contributions are also well segmented at the meta-connected points (benzene rings), while the spatial distribution of the gamma density of L25 is extended over the whole region of the chain, and the dominant contribution stems from the both-end regions. It is found for D25 that the magnitude of contributions to gamma in the internal region is more enhanced than that in the outer region. We further found that the magnitudes of contributions in internal linear-leg regions of D25 are somewhat larger than those of the same-size isolated linear-leg molecules. This suggests that the slightly remaining pi-conjugations via the meta-branching points still enhance the contributions to gamma localized in the linear-leg regions. These features of spatial contributions to gamma of D25 are found to originate in the fractal architecture, in which pi-conjugation lengths in the linear-leg region increase on going from the periphery to the core. Finally, fractal antenna dendrimers are expected to be promising novel nonlinear optical (NLO) substances with a controllability of the magnitude and spatial contribution of the third-order NLO properties.