Multiconfigurational molecular dynamics with quantum transitions: Multiple proton transfer reactions

Generalized quantum master equations can improve the accuracy of semiclassical predictions of multitime correlation functions

Multitime quantum correlation functions are central objects in physical science, offering a direct link between the experimental observables and the dynamics of an underlying model. While experiments such as 2D spectroscopy and quantum control can now measure such quantities, the accurate simulation of such responses remains computationally expensive and sometimes impossible, depending on the system's complexity. A natural tool to employ is the generalized quantum master equation (GQME), which can offer computational savings by extending reference dynamics at a comparatively trivial cost. However, dynamical methods that can tackle chemical systems with atomistic resolution, such as those in the semiclassical hierarchy, often suffer from poor accuracy, limiting the credence one might lend to their results. By combining work on the accuracy-boosting formulation of semiclassical memory kernels with recent work on the multitime GQME, here we show for the first time that one can exploit a multitime semiclassical GQME to dramatically improve both the accuracy of coarse mean-field Ehrenfest dynamics and obtain orders of magnitude efficiency gains.

Proton transfer kinetics of transition metal hydride complexes and implications for fuel-forming reactions

Proton transfer reactions involving transition metal hydride complexes are prevalent in a number of catalytic fuel-forming reactions, where the proton transfer kinetics to or from the metal center can have significant impacts on the efficiency, selectivity, and stability associated with the catalytic cycle. This review correlates the often slow proton transfer rate constants of transition metal hydride complexes to their electronic and structural descriptors and provides perspective on how to exploit these parameters to control proton transfer kinetics to and from the metal center. A toolbox of techniques for experimental determination of proton transfer rate constants is discussed, and case studies where proton transfer rate constant determination informs fuel-forming reactions are highlighted. Opportunities for extending proton transfer kinetic measurements to additional systems are presented, and the importance of synergizing the thermodynamics and kinetics of proton transfer involving transition metal hydride complexes is emphasized.

The open gate of the K(V)1.2 channel: quantum calculations show the key role of hydration

The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K(+) ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K(+) ~0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating.

Spectral-luminescent properties of 12-oximino derivatives of 8-AZA-D-homogona-12,17a-diones and their concentration dependence

This paper presents the results of the investigation of the spectral-luminescent characteristics of 12-oximino derivative of 8-aza-D-homogona-12,17a-dion, its hydrochloride, and their dependences on the concentration. It has been shown that the form and position of the absorption spectrums of 16,16-dimethyl-12-oximino-8-aza-D-homogona-1,3,5(10),13-tetraene-17a-one in all solvents used are independent of its concentration. At the same time, for its hydrochloride in ethanol and water, a strong dependence of the absorption spectrum on its concentration has been revealed. On the basis of the experimental data it has been concluded that in these solvents dimers of investigated substance, whose bonding force is chelate hydrogen bonds, are formed. The investigation of the luminescence has shown that these substances practically do not fluoresce. Only in ethanol and water we managed to register a very weak luminescence, whose excitation spectrum is close to the absorption spectrum.

New mixed quantumsemiclassical propagation method

The authors developed a new method for calculating the quantum evolution of multidimensional systems, for cases in which the system can be assumed to consist of a quantum subsystem and a bath subsystem of heavier atoms. The method combines two ideas: starting from a simple frozen Gaussian description of the bath subsystem, then calculate quantum corrections to the propagation of the quantum subsystem. This follows from recent work by one of them, showing how one can calculate corrections to approximate evolution schemes, even when the Hamiltonian that corresponds to these approximate schemes is unknown. Then, they take the limit in which the width of the frozen Gaussians approaches zero, which makes the corrections to the evolution of the quantum subsystem depend only on classical bath coordinates. The test calculations they present use low-dimensional systems, in which comparison to exact quantum dynamics is feasible.

Quantum-classical description of the amide I vibrational spectrum of trialanine

A quantum-classical description of the amide I vibrational spectrum of trialanine cation in D2O is given that combines (i) a classical molecular dynamics simulation of the conformational distribution of the system, (ii) comprehensive density functional theory calculations of the conformation-dependent and solvent-induced frequency fluctuations, and (iii) a semiclassical description of the vibrational line shapes which includes nonadiabatic transitions between vibrational eigenstates. Various assumptions that are usually employed in the calculation of condensed-phase vibrational spectra are tested, including the adiabatic, the Franck-Condon, and the second-order cumulant approximations, respectively. All three parts of the theoretical formulation are shown to have a significant impact on the simulated spectrum, suggesting that the interpretation of peptide amide I spectra may require substantial theoretical support.

Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine

A simple approach for numerically exact simulations of nonadiabatic quantum dynamics in multidimensional systems is introduced and applied to the description of the photoabsorption spectroscopy of pyrazine. The propagation scheme generalizes the recently developed matching-pursuit/split-operator-Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] to simulations of nonadiabatic quantum dynamics. The time-evolution operator is applied, as defined by the Trotter expansion to second order accuracy, in dynamically adaptive coherent-state expansions. These representations are obtained by combining the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting computational approach are demonstrated in calculations of time-dependent survival amplitudes and photoabsorption cross sections, using a model Hamiltonian that allows for direct comparisons with benchmark calculations. Simulations in full-dimensional potential energy surfaces involve the propagation of a 24-dimensional wave packet to describe the S(1)S(2) interconversion of pyrazine after S(0)-->S(2) photoexcitation. The reported results show that the generalized MP/SOFT method is a practical and accurate approach to model nonadiabatic reaction dynamics in polyatomic systems.

Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems

A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.

Matching-pursuit∕split-operator Fourier-transform simulations of nonadiabatic quantum dynamics

A rigorous and practical approach for simulations of nonadiabatic quantum dynamics is introduced. The algorithm involves a natural extension of the matching-pursuitsplit-operator Fourier-transform (MPSOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] recently developed for simulations of adiabatic quantum dynamics in multidimensional systems. The MPSOFT propagation scheme, extended to nonadiabatic dynamics, recursively applies the time-evolution operator as defined by the standard perturbation expansion to first-, or second-order, accuracy. The expansion is implemented in dynamically adaptive coherent-state representations, generated by an approach that combines the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting propagation method are demonstrated as applied to the canonical model systems introduced by Tully for testing simulations of dual curve-crossing nonadiabatic dynamics.

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

The nature of the control of water/proton selectivity in biological channels is a problem of a fundamental importance. Most studies of this issue have proposed that an interference with the orientational requirements of the so-called proton wire is the source of selectivity. The elucidation of the structures of aquaporins, which have evolved to prevent proton transfer (PT), provided a clear benchmark for exploring the selectivity problem. Previous simulations of this system have not examined, however, the actual issue of PT, but only considered the much simpler task of the transfer of water molecules. Here we take aquaporin as a benchmark and quantify the origin of the water/proton selectivity in this and related systems. This is done by evaluating in a consistent way the free energy profile for transferring a proton along the channel and relating this profile to the relevant PT rate constants. It is found that the water/proton selectivity is controlled by the change in solvation free energy upon moving the charged proton from water to the channel. The reason for the focus on the elegant concept of the proton wire and the related Grotthuss-type mechanism is also considered. It is concluded that these mechanisms are clearly important in cases with flat free energy surfaces (e.g., in bulk water, in gas phase water chains, and in infinitely long channels). However, in cases of biological channels, the actual PT mechanism is much less important than the energetics of transferring the proton charge from water to different regions in the channels.

Time-dependent quantum methods for large systems

This review focuses on time-dependent methods suitable for simulating the quantum dynamics of processes in large clusters and condensed-phase environments. A number of mean field, quantum-classical, and quantum statistical approximations that avoid the conventional exponential scaling with the number of degrees of freedom are reviewed. In addition, rigorous semiclassical and path integral approaches are described that are feasible in certain physical situations. Select chemical applications illustrating the capabilities of these methods are discussed.

Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2)

A quantum-classical molecular dynamics model (QCMD), applying explicit integration of the time-dependent Schrödinger equation (QD) and Newtonian equations of motion (MD), is presented. The model is capable of describing quantum dynamical processes in complex biomolecular systems. It has been applied in simulations of a multistep catalytic process carried out by phospholipase A(2) in its active site. The process includes quantum-dynamical proton transfer from a water molecule to histidine localized in the active site, followed by a nucleophilic attack of the resulting OH(-) group on a carbonyl carbon atom of a phospholipid substrate, leading to cleavage of an adjacent ester bond. The process has been simulated using a parallel version of the QCMD code. The potential energy function for the active site is computed using an approximate valence bond (AVB) method. The dynamics of the key proton is described either by QD or classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time dependence of the potential energy function in the Schrödinger equation (QCMD/AVB model). Analysis of the simulation results with an Advanced Visualization System revealed a correlated rather than a stepwise picture of the enzymatic process. It is shown that an sp(2)--> sp(3) configurational change at the substrate carbonyl carbon is mostly responsible for triggering the activation process.