Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase

The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.     

Exploring the importance of quantum effects in nucleation: the archetypical Ne(n) case

The effect of quantum mechanics (QM) on the details of the nucleation process is explored employing Ne clusters as test cases due to their semi-quantal nature. In particular, we investigate the impact of quantum mechanics on both condensation and dissociation rates in the framework of the microcanonical ensemble. Using both classical trajectories and two semi-quantal approaches (zero point averaged dynamics, ZPAD, and Gaussian-based time dependent Hartree, G-TDH) to model cluster and collision dynamics, we simulate the dissociation and monomer capture for Ne(8) as a function of the cluster internal energy, impact parameter and collision speed. The results for the capture probability P(s)(b) as a function of the impact parameter suggest that classical trajectories always underestimate capture probabilities with respect to ZPAD, albeit at most by 15%-20% in the cases we studied. They also do so in some important situations when using G-TDH. More interestingly, dissociation rates k(diss) are grossly overestimated by classical mechanics, at least by one order of magnitude. We interpret both behaviours as mainly due to the reduced amount of kinetic energy available to a quantum cluster for a chosen total internal energy. We also find that the decrease in monomer dissociation energy due to zero point energy effects plays a key role in defining dissociation rates. In fact, semi-quantal and classical results for k(diss) seem to follow a common "corresponding states" behaviour when the proper definition of internal and dissociation energies are used in a transition state model estimation of the evaporation rate constants.     

Review of structures in low-energy bremsstrahlung: Classical and quantum descriptions

A brief review of recent advances in studying structures in energy dependence of the bremsstrahlung cross sections for low incident electron energies is presented. Examples of structures are given in both classical and quantum formalisms. It is shown that the origin of the structures can be formulated as a lack of contribution to the radiation from electrons with certain angular momenta at certain energies. In quantum mechanics the lack of contribution to the total cross section from certain electron angular momenta is due to zeroes in corresponding dipole matrix elements. In classical mechanics summation over angular momentum is replaced by integration and structures are due to suppressed or enhanced contribution from certain intervals of angular momentum. A survey of the known properties of the matrix elements’ zeroes is given.     

Polarization energies in oligoacene semiconductor crystals

Characterization of the electronically polarized environment and the nuclear relaxation that accompanies charge carriers is fundamental to charge transport in crystalline, polycrystalline, and amorphous organic solids. To study the polarization effects of localized charged carriers, we use quantum/classical QM/MM approaches with charge redistribution and polarizable force field schemes and apply them to crystals of naphthalene through pentacene. We describe the results of a comprehensive investigation of the electronic polarization energies in molecular crystal structures of these oligoacenes and discuss as well the evolution of the nuclear relaxation energies calculated for model oligoacene systems.     

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. Interestingly, our results indicate that the NQM effects in the lipoxygenase reaction are similar in the enzyme and in the reference solution reactions, and thus do not contribute to catalysis. We also reached similar conclusions in studies of other enzymes.     

Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime

The positive charge transfer in DNA is investigated, using the first principle treatment of the electron-vibrational interaction. We show that rearrangements of atoms belonging to base pairs induced by charge transfer are essentially quantum mechanical in nature. Particularly at room temperature, around half of the rearrangements occur via quantum tunneling, while the other half takes place via thermally activated transitions. This effect reduces activation energies for charge transfer between both AT and GC pairs by a factor of two compared to their classical values. These behaviors are described within small polaron theory for the non-adiabatic charge transfer and compared to the experimental data and previous theoretical studies.     

Fewest switches adiabatic surface hopping as applied to vibrational energy relaxation

In this contribution quantum/classical surface hopping methodology is applied to vibrational energy relaxation of a quantum oscillator in a classical heat bath. The model of a linearly damped (harmonic) oscillator is chosen which can be mapped onto the Brownian motion (Caldeira-Leggett) Hamiltonian. In the simulations Tully's fewest switches surface hopping scheme is adopted with inclusion of dephasing in the adiabatic basis using a simple decoherence algorithm. The results are compared to the predictions of a Redfield-type quantum master equation modeling using the classical heat bath force correlation function as input. Thereby a link is established between both types of quantum/classical approaches. Viewed from the latter perspective, surface hopping with dephasing may be interpreted as "on-the-fly" stochastic realization of a quantum/classical Pauli master equation.     

Six-dimensional quantum dynamics of H2 dissociative adsorption on the Pt(211) stepped surface

Results of experimental studies, and theoretical calculations utilizing classical trajectories, have shown that dissociation of H2 on the Pt(211) stepped surface is enhanced at low energies by a molecular trapping mechanism. Because quantum effects can play a large role at the low energies and long lifetimes that characterize molecular trapping, we have undertaken quantum dynamics calculations for this system, the first to treat all molecular degrees of freedom of a gas molecule reacting on a stepped metallic surface. The calculations show that molecular trapping persists in the quantum system, but only at much lower energies than experimentally seen, pointing to possible deficiencies in the potential energy surface. Classical and quasiclassical trajectory calculations on the same potential provide a reasonable picture of reaction overall, but many of the finer details are inaccurate, and certain classical reaction mechanisms are entirely invalid. We conclude that some skepticism should be shown toward any classical study for which long-lived trapping states play a role.     

Thermodynamic integration from classical to quantum mechanics

We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable.     

Classical trajectory study of rotationally inelastic scattering of two HF molecules

Classical trajectory calculations of the partial opacities and integral cross sections for rotationally inelastic collisions of HF—HF were carried out for the j₁ = 0,j₂ = 0 → (11), (02), (22) transitions at initial relative translational energies of 500, 1000, and 8000 cm^?1 and for the (11) → (02) transition at 1000 cm^?1. Three different methods of relating the initial and final quantum rotational levels to classical distributions were used. The results were compared to the quantum calculations of DePristo and Alexander. It was found that the classical method using a random distribution of initial rotational energies was in poor agreement with the quantum results, while the other two methods which assigned definite classical energies to the quantum levels were in good agreement with the quantum results.     

Classical rotational cross sections for H2—HD and HD—HD collisions

Classical trajectory calculations of integral cross sections for rotationally inelastic collisions of HD-para H₂ and HD—HD were carried out for a wide variety of transitions over a wide range of initial relative translational energies. The results of the HD—H₂ calculations were compared with the quantum effective potential calculations of Chu. It was found that the classical method is in reasonably good agreement with the quantum method for the calculation of rotational transitions of HD at the higher initial translational energies, but the classical method is in poor agreement with quantum results for HD excitation at low energies and for H₂ excitations at all energies.     

Path integral calculation of free energies: quantum effects on the melting temperature of neon

The path integral formulation has been combined with several methods to determine free energies of quantum many-body systems, such as adiabatic switching and reversible scaling. These techniques are alternatives to the standard thermodynamic integration method. A quantum Einstein crystal is used as a model to demonstrate the accuracy and reliability of these free energy methods in quantum simulations. Our main interest focuses on the calculation of the melting temperature of Ne at ambient pressure, taking into account quantum effects in the atomic dynamics. The free energy of the solid was calculated by considering a quantum Einstein crystal as reference state, while for the liquid, the reference state was defined by the classical limit of the fluid. Our findings indicate that, while quantum effects in the melting temperature of this system are small, they still amount to about 6% of the melting temperature, and are therefore not negligible. The particle density as well as the melting enthalpy and entropy of the solid and liquid phases at coexistence is compared to results obtained in the classical limit and also to available experimental data.     

Computational Study of Regioselective Synthesis of Triflylpyrazole by Cycloaddition Reaction between Diphenyl Hydrazonoyl Chloride and Phenyl Triflyl Acetylene

The mechanism and regioselectivity of cycloaddition reaction between diphenyl hydrazonoyl chloride and phenyl triflyl acetylene as an electron-deficient dipolarophyl in acetonitrile at room temperature are theoretically investigated using density functional theory and solvent polarized continuum model. Two general mechanism, concerted and stepwise mechanism, have been proposed for this reaction. Each mechanism has two different paths and two possible products. The activation energies of pathways were calculated using quantum mechanical approach and compared with each other. An excellent agreement was observed between the previously reported experimental work and the theoretical approaches for regioselectivity of this reaction.     

Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies

Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute–solvent coupling in a self-consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field-dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.     

Hybrid coupled cluster and molecular dynamics approach: application to the excitation spectrum of cytosine in the native DNA environment

Evolution of the excited state energies of cytosine base in the native DNA environment was investigated using a hybrid coupled cluster and classical molecular dynamics approach. The time averaged excitation energies obtained with the variant of the completely renormalized equation-of-motion with singles, doubles, and non-iterative triples approach that includes a bulk of the correlation effects for excited states, are compared with the analogous calculations in the gas phase. Significant blue shifts for the two lowest singlet excitation energies can be observed as a result of the interaction of the quantum system with the surrounding environment.