Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect Is Different for Physiological and Slow Substrates of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures

Conformational switching via an intramolecular H-bond modulates the fluorescence lifetime in a novel coumarin–imidazole conjugate

Achieving synthetic control over light-driven molecular dynamics is essential for designing complex molecule-based devices.

Variational transition state theory: theoretical framework and recent developments

This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications.

Quantum and classical simulations of orotidine monophosphate decarboxylase: support for a direct decarboxylation mechanism

Orotidine 5'-monophosphate (OMP) decarboxylase (ODCase) catalyzes the decarboxylation of OMP to uridine 5'-monophosphate (UMP). Numerous studies of this reaction have suggested a plethora of mechanisms including covalent addition, ylide or carbene formation, and concerted or stepwise protonation. Recent experiments and simulations present strong evidence for a direct decarboxylation mechanism, although direct comparison between experiment and theory is still lacking. In the current work we present hybrid quantum mechanics-molecular mechanics simulations that address the detailed decarboxylation mechanisms for OMP and 5-fluoro-OMP by ODCase. Multidimensional potentials of mean force are computed as functions of structural progress coordinates for the Methanobacterium thermoautotrophicum ODCase reaction: the decarboxylation reaction coordinate, an orbital rehybridization coordinate, and the proton transfer coordinate between Lys72 and the substrate. The computed free energy profiles are in accord with the available experimental data. To facilitate further direct comparison with experiment, we compute the kinetic isotope effects (KIEs) for the enzyme-catalyzed reactions using a mass-perturbation-based path-integral method. The computed KIE provide further support for a direct decarboxylation mechanism. In agreement with experiment, the data suggest a role for Lys72 in stabilizing the transition state in the catalysis of OMP and, to a somewhat lesser extent, in 5-fluoro-OMP.

Computation of kinetic isotope effects for enzymatic reactions

We describe a computational approach, incorporating quantum mechanics into enzyme kinetics modeling with a special emphasis on computation of kinetic isotope effects. Two aspects are highlighted: (1) the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) potential in which the bond forming and breaking processes are modeled by electronic structure theory, and (2) a free energy perturbation method in path integral simulation is used to determine both kinetic isotope effects (KIEs). In this approach, which is called the PI-FEP/UM method, a light (heavy) isotope is mutated into a heavy (light) counterpart in centroid path integral simulations. The method is illustrated in the study of primary and secondary KIEs in two enzyme systems. In the case of nitroalkane oxidase, the enzymatic reaction exhibits enhanced quantum tunneling over that of the uncatalyzed process in water. In the dopa delarboxylase reaction, there appears to be distinguishable primary carbon-13 and secondary deuterium KIEs when the internal proton tautomerism is in the N-protonated or in the O-protonated positions. These examples show that the incorporation of quantum mechanical effects in enzyme kinetics modeling offers an opportunity to accurately and reliably model the mechanisms and free energies of enzymatic reactions.

Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5'-phosphate dependent enzymes L-dopa decarboxylase and alanine racemase

Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the internal proton transfer equilibrium of the external aldimine species in l-dopa decarboxylase, and carbanion stabilization by the enzyme cofactor in the active site of alanine racemase. Solvent effects lower the free energy of the O-protonated PLP tautomer both in aqueous solution and in the active site, resulting a free energy difference of about -1 kcal/mol relative to the N-protonated Schiff base in the enzyme. The external aldimine provides the dominant contribution to lowering the free energy barrier for the spontaneous decarboxylation of l-dopa in water, by a remarkable 16 kcal/mol, while the enzyme l-dopa decarboxylase further lowers the barrier by 8 kcal/mol. Kinetic isotope effects were also determined using a path integral free energy perturbation theory on the primary (13)C and the secondary (2)H substitutions. In the case of alanine racemase, if the pyridine ring is unprotonated as that in the active site, there is destabilizing contribution to the formation of the α-carbanion in the gas phase, although when the pyridine ring is protonated the contribution is stabilizing. In aqueous solution and in alanine racemase, the α-carbanion is stabilized both when the pyridine ring is protonated and unprotonated. The computational studies illustrated in this article show that combined QM/MM simulations can help provide a deeper understanding of the mechanisms of PLP-dependent enzymes. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.

Kinetic isotope effects of L-Dopa decarboxylase

A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.

Critical role of substrate conformational change in the proton transfer process catalyzed by 4-oxalocrotonate tautomerase

4-Oxalocrotonate tautomerase enzyme (4-OT) catalyzes the isomerization of 2-oxo-4-hexenedioate to 2-oxo-3-hexenedioate. The chemical process involves two proton transfers, one from a carbon of the substrate to the nitrogen of Pro1 and another from this nitrogen atom to a different carbon of the substrate. In this paper the isomerization has been studied using the combined quantum mechanical and molecular mechanical method with a dual-level treatment of the quantum subsystem employing the MPW1BK density functional as the higher level. Exploration of the potential energy surface shows that the process is stepwise, with a stable intermediate state corresponding to the deprotonated substrate and a protonated proline. The rate constant of the overall process has been evaluated using ensemble-averaged variational transition state theory, including the quantized vibrational motion of a primary zone of active-site atoms and a transmission coefficient based on an ensemble of optimized reaction coordinates to account for recrossing trajectories and optimized multidimensional tunneling. The two proton-transfer steps have similar free energy barriers, but the transition state associated with the first proton transfer is found to be higher in energy. The calculations show that reaction progress is coupled to a conformational change of the substrate, so it is important that the simulation allows this flexibility. The coupled conformational change is promoted by changes in the electron distribution of the substrate that take place as the proton transfers occur.

Kinetic isotope effects on dehalogenations at an aromatic carbon

In order to interpret the observed isotopic fractionation it is necessaryto understand its relationship with the isotope effect(s) on steps that occur during the conversion of the initial reactant to the final product. We examine this relationship from the biochemical point of view and elaborate on the consequences of the assumptions that it is based on. We illustrate the discrepancies between theoretical and experimental interpretation of kinetic isotope effects on examples of dehalogenation reactions that occur at an aromatic carbon atom. The examples include 4-chlorobenzoyl-CoA dehalogenase-catalyzed conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA, dehaloperoxidase-catalyzed conversion of 2,4,6-trichlorophenol to 2,6-dichloroquinone, and spontaneous hydrolysis of atrazine at pH 12. For this latter reaction we have measured the chlorine kinetic isotope effect and estimated its value theoretically at the DFT level of theory. Results of chlorine kinetic isotope effects suggest that the studied dechlorination reactions proceed in a single step with significant weakening of the carbon-chlorine bond in the transition state.

Site-selective photoinduced electron transfer from alcoholic solvents to the chromophore facilitated by hydrogen bonding: a new fluorescence quenching mechanism

Solute-solvent intermolecular photoinduced electron transfer (ET) reaction was proposed to account for the drastic fluorescence quenching behaviors of oxazine 750 (OX750) chromophore in protic alcoholic solvents. According to our theoretical calculations for the hydrogen-bonded OX750-(alcohol)(n) complexes using the time-dependent density functional theory (TDDFT) method, we demonstrated that the ET reaction takes place from the alcoholic solvents to the chromophore and the intermolecular ET passing through the site-specific intermolecular hydrogen bonds exhibits an unambiguous site selectivity. In our motivated experiments of femtosecond time-resolved stimulated emission pumping fluorescence depletion spectroscopy (FS TR SEP FD), it could be noted that the ultrafast ET reaction takes place as fast as 200 fs. This ultrafast intermolecular photoinduced ET is much faster than the diffusive solvation process, and even significantly faster than the intramolecular vibrational redistribution (IVR) process of the OX750 chromophore. Therefore, the ultrafast intermolecular ET should be coupled with the hydrogen-bonding dynamics occurring in the sub-picosecond time domain. We theoretically demonstrated for the first time that the selected hydrogen bonds are transiently strengthened in the excited states for facilitating the ultrafast solute-solvent intermolecular ET reaction.

Viewpoint: How large is the carbon isotope fractionation of the photorespiratory enzyme glycine decarboxylase?

Despite the intense effort developed over the past 10 years to determine the ¹²C / ¹³C isotope fractionation associated with photorespiration, much uncertainty remains about the amplitude, and even the sign, of the ¹²C / ¹³C isotope fractionation of glycine decarboxylase, the enzyme that produces CO₂ during the photorespiratory cycle. In fact, leaf gas-exchange data have repeatedly indicated that CO₂ evolved by photorespiration is depleted in ¹³C compared with the source material, while glycine decarboxylase has mostly favoured ¹³C in vitro. Here I give theoretical insights on the glycine decarboxylase reaction and show that (i), both photorespiration and glycine decarboxylation must favour the same carbon isotope - the in vitro measurements being probably adulterated by the high sensitivity of the enzyme to assay conditions and the possible reversibility of the reaction in these conditions, and (ii), simplified quantum chemistry considerations as well as comparisons with other pyridoxal 5'-phosphate-dependent decarboxylases indicate that the carbon isotope fractionation favour the ¹²C isotope by ~20‰, a value that is consistent with the value of the photorespiratory fractionation (f) obtained by gas-exchange experiments.

A fragment molecular-orbital–multicomponent molecular-orbital method for analyzing H∕D isotope effects in large molecules

We have developed a fragment molecular orbital (FMO)-multi-component MO (MC_MO) method to analyze isotope effect due to differences between the quantum effects of protons and deuterons for large molecules such as proteins and DNA. The FMO-MC_MO method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously, and can directly express isotope effects, including coupling effects between nuclei and electrons. In our calculations of two polyglycines, which serve as prototypes for biological molecules, by this method, we clearly observed the geometrical relaxation induced by the HD isotope effect in the intramolecular hydrogen bonding portions of the molecules. The HD isotope effect on the interfragment interaction energy, including that of the hydrogen bonding parts, was also demonstrated: the hydrogen bond was weakened by replacement of hydrogen with deuterium. We also developed electrostatic potential approximations for use in the FMO-MC_MO calculations, and the accuracy of the energy differences induced by the isotope effect was independent of the approximation level of the FMO-MC_MO. Our results confirmed that the FMO-MC_MO method is a powerful tool for the detailed analysis of changes in hydrogen bonding and interaction energies induced by the HD isotope effect for large biological molecules.

Modulation of Fragmental Charge Transfer via Hydrogen Bonds. Direct Measurement of Electronic Contributions†

Hydrogen bonds play an important role in an overwhelming variety of fields from biology to surface and supramolecular chemistry. The term "hydrogen bond" refers to a wide range of interactions with various covalent and polar contributions. In particular, hydrogen bonds have an important role in the folding and packing of peptides and nucleic acids. Recent studies also point to the importance of hydrogen bonding in the context of second-shell interactions, in metal binding and selectivity in metalloproteins, and in controlling the dynamics of membrane proteins. In this study, we demonstrate and quantify the modulation of fragmental charge transfer from hydrogen-bonded ligands to a metal center, by employing our recently introduced molecular potentiometer. The molecular details that affect this type of fragmental charge transfer are presented and a path for transferring chemical information is demonstrated. We found that H-bond interactions in the extended positions of axial ligands provide an effective means of modulating the amount of fragmental charge transfer to a metal center, thereby dramatically influencing the electronic properties of the ligand, the binding affinity, and the binding of additional ligands. The magnitude of fragmental charge-transfer modulation induced by a single ligand-solvent H-bond interaction is comparable to those induced by covalent substitution, although H-bond enthalpy is only on the order of several kilojoules per mole. Importantly, we find a significant change in the ligand electronic properties, even for weak C-H...O=C H-bond formation, where the bond enthalpy is substantially lower than for conventional H-bond interactions. The excess fragmental charge transferred to the metal center, deduced from the spectroscopic measurements, correlates well with the computationally determined values. Our findings underscore the importance of second-shell interactions in the active sites of enzymes, beyond the structural and electrostatic importance that is widely recognized today.