Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics

Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.     

Microwave ionization of highly excited hydrogen atoms

Within a 1-dimensional model we calculate quantum mechanically the probability to ionize a highly excited hydrogen atom by a monochromatic microwave field. Based on a detailed analysis of the ionization process we developed a computational scheme as well as a simple physical framework which are presented and discussed. Our calculations are in good agreement with the experimental results. We show that the experimentally measured ionization thresholds are due to a sharp transition between two localization regimes and that recently measured structures below the classical chaos border are due to unresolved clusters of Floquet pseudo crossings. We propose an experimental method by which one could measure the distance and distribution of crossing Floquet eigenvalues.     

Mechanism of chemical reactions in the active site of aspartate N-acetyltransferase NAT8L revealed by molecular modeling

The results of a computational study of the synthesis of a key brain metabolite, N-acetyl-l-aspartate, catalyzed by aspartate N-acetyltransferase, encoded by the NAT8L gene, are reported. The reaction Gibbs energy profiles were computed using molecular dynamics simulations with interaction potentials estimated on-the-fly by the quantum mechanics/molecular mechanics QM(PBE0/6-31G**)/MM(CHARMM) approach. The revealed reaction mechanism includes four elementary steps with corresponding activation energies not exceeding 14 kcal mol^?1     

Control of nonadiabatic dissociation dynamics with the use of laser-induced wave packet interferences

Based on wave packet interferences induced by a stationary laser field, a simple way of controlling nonadiabatic dissociation dynamics is proposed. We treat a simple two-state model of diatomic molecules. In this model, there exist two dissociative potential energy curves which cross and are strongly coupled at an internuclear distance, and thus dissociations into one channel are predominant. We propose a control scheme to selectively dissociate a molecule into any favorite channel by choosing the laser frequency and intensity appropriately. The semiclassical estimation of desirable laser parameters can be performed easily by regarding the dissociation processes as nonadiabatic transitions between the Floquet states. The agreement between the semiclassical estimation and the quantum wave packet calculation is found to be satisfactory in the high frequency region (> or =1000 cm(-1)) where the Floquet state picture is valid. In the low frequency region (<1000 cm(-1)), on the other hand, there are discrepancies between them due to the invalidity of the Floquet picture and the dissociation probability is sensitive to the laser phase. This control scheme is applied to the predissociation dynamics of NaI, NaI-->Na+I.     

Bohmian mechanics with complex action: a new trajectory-based formulation of quantum mechanics

In recent years there has been a resurgence of interest in Bohmian mechanics as a numerical tool because of its local dynamics, which suggest the possibility of significant computational advantages for the simulation of large quantum systems. However, closer inspection of the Bohmian formulation reveals that the nonlocality of quantum mechanics has not disappeared-it has simply been swept under the rug into the quantum force. In this paper we present a new formulation of Bohmian mechanics in which the quantum action, S, is taken to be complex. This leads to a single equation for complex S, and ultimately complex x and p but there is a reward for this complexification-a significantly higher degree of localization. The quantum force in the new approach vanishes for Gaussian wave packet dynamics, and its effect on barrier tunneling processes is orders of magnitude lower than that of the classical force. In fact, the current method is shown to be a rigorous extension of generalized Gaussian wave packet dynamics to give exact quantum mechanics. We demonstrate tunneling probabilities that are in virtually perfect agreement with the exact quantum mechanics down to 10(-7) calculated from strictly localized quantum trajectories that do not communicate with their neighbors. The new formulation may have significant implications for fundamental quantum mechanics, ranging from the interpretation of non-locality to measures of quantum complexity.     

Elucidating collision induced dissociation products and reaction mechanisms of protonated uracil by coupling chemical dynamics simulations with tandem mass spectrometry experiments

In this study we have coupled mixed quantum‐classical (quantum mechanics/molecular mechanics) direct chemical dynamics simulations with electrospray ionization/tandem mass spectrometry experiments in order to achieve a deeper understanding of the fragmentation mechanisms occurring during the collision induced dissociation of gaseous protonated uracil. Using this approach, we were able to successfully characterize the fragmentation pathways corresponding to ammonia loss (m/z 96), water loss (m/z 95) and cyanic or isocyanic acid loss (m/z 70). Furthermore, we also performed experiments with isotopic labeling completing the fragmentation picture. Remarkably, fragmentation mechanisms obtained from chemical dynamics simulations are consistent with those deduced from isotopic labeling. Copyright © 2015 John Wiley & Sons, Ltd.     

Photodissociation Exploration for Near-Visible UV Absorption of Molecular Bromine

The photodissociation of Br2 was investigated within the near-visible UV absorption band. Based on thepotential curves for the ground and low-lying excited states, the optical cross-sections for the discrete transitions of C1Πu, B3Π+0u, A3Π1u <—X1Σ+g and their total energy absorption spectrum are derived, and the quantum yield of (Br+Br*) channel are determined correspondingly. The one-dimensional Landau-Zener model is used to evaluate the behavior of curve crossing during photodissociation. The results indicate that the influence of nonadiabatic mechanism, which may be caused by the electronic-vibrational interplay between the B and C states, is negligibly small for the (Br+Br*) channel. From the Landau-Zener modeling of the observed product recoil parameter fi(Br+Br), the best-fit value of the coupling matrix element or coupling strength between the diabatic B and C state potentials is obtained.     

Non-adiabatic molecular dynamics with quantum solvent effects

Three novel approaches extending quantum-classical non-adiabatic (NA) molecular dynamics (MD) to include quantum effects of solvent environments are described. In a standard NA-MD the solute subsystem is treated quantum mechanically, while the larger solvent part of a system is treated classically. The three novel approaches presented here are based on the Bohmian formulation of quantum mechanics, the stochastic Schrödinger equation for the evolution of open quantum systems and the quantized Hamilton dynamics generalization of classical mechanics. The approaches extend the standard NA-MD to incorporate the following quantum effects of the solvent. (1) Branching, i.e. the ability of solvent quantum wave packets to split and follow asymptotically diverging trajectories correlated with different quantum states of the solute. (2) Decoherence, i.e. loss of quantum interference within the solute subsystem induced by the diverging solvent trajectories. (3) Zero point energy that contributes to NA coupling and must be preserved during the energy exchange between solvent and solute degrees of freedom. The Bohmian quantum-classical mechanics, stochastic mean-field and quantized mean-field approximations incorporate the quantum solvent effects into the standard quantum-classical NA-MD in a straightforward and efficient way that can be easily applied to quantum dynamics of condensed phase chemical systems.     

Two-color resonant multiphoton ionization study of CO. The rotational energy transfer behavior of CO A1 Πstate

Two-color resonant multiphoton ionization provides a novel technique, complementary to LIF, for studying state-to-state molecular relaxation dynamics. A set of formulae applicable to two-color pulsed laser ionization experiments has been derived to evaluate the rotational energy transfer probability for CO(A)-CO(X)collision pairs. The magnitude of this probability is on the order of 1/10 for rotational quantum jump ΔJ = ±1 and diminishes with increasing ΔJ. For the same > J(<±3), a transition with e/f symmetry conservation is always more probable than that with an e/f change.     

Electronic properties of liquid ammonia: a sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH3)n; n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05+/-0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng et al., J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74+/-0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16+/-0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V 0=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates.