On the classical behavior, coherent and incoherent contributions to scattering of atoms from a surface

In this work we calculate the coherent and incoherent contributions to the diffraction probability of atoms scattered by a surface. We are interested in exploring the relative importance of each of these contributions, and compare them with results obtained from molecular dynamics calculations. To achieve this goal, we employed a method developed by Heller that consists of writing the incident plane wave as a sum of Gaussian wave packets, propagating them independently by using the time dependent Schrödinger equation, and constructing the scattered wave function by adding coherently the scattered packets. For the system studied, the molecular dynamics results show the largest intensity in the specular region and also display a classical rainbow structure. On the other hand, the quantum results exhibit diffraction features, with the coherent contribution accounting for most of the total intensity probability.     

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.     

Sequences of ultrafast non-resonant multiphoton transitions in a three-electronic level molecule

Non-resonant multiphoton transitions between three electronic states of a molecular system are studied. Based on a projection operator formalism which is formulated in the framework of the so-called time-local as well as the time-nonlocal approach, time-dependent Schrödinger equations are obtained, which include effective couplings to the laser field. For both procedures a slowly varying amplitude approximation can be invoked. The resulting time-local equations are solved in a much more efficient way than the original effective Schrödinger equations. The validity of these approximations is verified numerically for a two-photon process. Furthermore, the effective Schrödinger equations are specified to sequences of two-photon and three-photon transitions. The derived equations are applied to a molecular system consisting of three electronic states with Morse-type potential energy curves. Using different laser pulse scenarios the conditions are discussed under which a sequence of two-photon and three-photon transitions can take place.     

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car–Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion—the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.     

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase

Nuclear quantum mechanical effects have been examined for the proton transfer reaction catalyzed by triosephosphate isomerase, with the normal mode centroid path integral molecular dynamics based on the potential energy surface from the recently developed reaction path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were treated quantum mechanically, while all other atoms were dealt classical mechanically. The quantum mechanical activation free energy and the primary kinetic isotope effects were examined. Because of the quantum mechanical effects in the proton transfer, the activation free energy was reduced by 2.3 kcal/mol in comparison with the classical one, which accelerates the rate of proton transfer by a factor of 47.5. The primary kinetic isotope effects of kH/kD and kH/kT were estimated to be 4.65 and 9.97, respectively, which are in agreement with the experimental value of 4+/-0.3 and 9. The corresponding Swain-Schadd exponent was predicted to be 3.01, less than the semiclassical limit value of 3.34, indicating that the quantum mechanical effects mainly arise from quantum vibrational motion rather than tunneling. The reaction path potential, in conjunction with the normal mode centroid molecular dynamics, is shown to be an efficient computational tool for investigating the quantum effects on enzymatic reactions involving proton transfer.     

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath

A hybrid quantum/classical molecular dynamics approach is applied to a proton transfer reaction represented by a symmetric double well system coupled to a dissipative bath. In this approach, the proton is treated quantum mechanically and all bath modes are treated classically. The transition state theory rate constant is obtained from the potential of mean force, which is generated along a collective reaction coordinate with umbrella sampling techniques. The transmission coefficient, which accounts for dynamical recrossings of the dividing surface, is calculated with a reactive flux approach combined with the molecular dynamics with quantum transitions surface hopping method. The hybrid quantum/classical results agree well with numerically exact results in the spatial-diffusion-controlled regime, which is most relevant for proton transfer in proteins. This hybrid quantum/classical approach has already been shown to be computationally practical for studying proton transfer in large biological systems. These results have important implications for future applications to hydrogen transfer reactions in solution and proteins.     

Hybrid classical quantum force field for modeling very large molecules

A coherent computational scheme on a very large molecule in which the subsystem that undergoes the most important electronic changes is treated by a semiempirical quantum chemical method, though the rest of the molecule is described by a classical force field, has been proposed recently. The continuity between the two subsystems is obtained by a strictly localized bond orbital, which is assumed to have transferable properties determined on model molecules. The computation of the forces acting on the atoms is now operating, giving rise to a hybrid classical quantum force field (CQFF ) which allows full energy minimization and modeling chemical changes in large biomolecules. As an illustrative example, we study the short hydrogen bonds and the proton-exchange process in the histidine-aspartic acid system of the catalytic triad of human neutrophil elastase. The CQFF approach reproduces the crystallographic data quite well, in opposition to a classical force field. The method also offers the possibility of switching off the electrostatic interaction between the quantum and the classical subsystems, allowing us to analyze the various components of the perturbation exerted by the macromolecule in the reactive part. Molecular dynamics confirm a fast proton exchange between the three possible energy wells. The method appears to be quite powerful and applicable to other cases of chemical interest such as surface reactivity of nonmetallic solids. © 1996 John Wiley & Sons, Inc.     

Simulating quantum dynamics in classical environments

Methods for simulating the dynamics of composite systems, where part of the system is treated quantum mechanically and its environment is treated classically, are discussed. Such quantum–classical systems arise in many physical contexts where certain degrees of freedom have an essential quantum character while the other degrees of freedom to which they are coupled may be treated classically to a good approximation. The dynamics of these composite systems are governed by a quantum–classical Liouville equation for either the density matrix or the dynamical variables which are operators in the Hilbert space of the quantum subsystem and functions of the classical phase space variables of the classical environment. Solutions of the evolution equations may be formulated in terms of surface-hopping dynamics involving ensembles of trajectory segments interspersed with quantum transitions. The surface-hopping schemes incorporate quantum coherence and account for energy exchanges between the quantum and classical degrees of freedom. Various simulation algorithms are discussed and illustrated with calculations on simple spin-boson models but the methods described here are applicable to realistic many-body environments.     

Intermolecular Interactions and Spectroscopic Signatures of the Hydrogen-Bonded System—n-Octanol in Experimental and Theoretical Studies

n-Octanol is the object of experimental and theoretical study of spectroscopic signatures and intermolecular interactions. The FTIR measurements were carried out at 293 K for n-octanol and its deuterated form. Special attention was paid to the vibrational features associated with the O-H stretching and the isotope effect. Density Functional Theory (DFT) in its classical formulations was applied to develop static models describing intermolecular hydrogen bond (HB) and isotope effect in the gas phase and using solvent reaction field reproduced by Polarizable Continuum Model (PCM). The Atoms in Molecules (AIM) theory enabled electronic structure and molecular topology study. The Symmetry-Adapted Perturbation Theory (SAPT) was used for energy decomposition in the dimers of n-octanol. Finally, time-evolution methods, namely classical molecular dynamics (MD) and Car-Parrinello Molecular Dynamics (CPMD) were employed to shed light onto dynamical nature of liquid n-octanol with emphasis put on metric and vibrational features. As a reference, CPMD gas phase results were applied. Nuclear quantum effects were included using Path Integral Molecular Dynamics (PIMD) and a posteriori method by solving vibrational Schrödinger equation. The latter applied procedure allowed to study the deuterium isotope effect.     

Exact supersymmetric solution of Schrödinger equation for central confining potentials by using the Nikiforov–Uvarov method

We present the exact supersymmetric solution of Schrödinger equation with the Morse, Pöschl–Teller and Hulthén potentials by using the Nikiforov–Uvarov method. Eigenfunctions and corresponding energy eigenvalues are calculated for the first six excited states. Results are in good agreement with the ones obtained before.     

Density dynamics in some quantum systems

The quantum domain behavior of classical nonintegrable systems is well‐understood by the implementation of quantum fluid dynamics and quantum theory of motion. These approaches properly explain the quantum analogs of the classical Kolmogorov–Arnold–Moser type transitions from regular to chaotic domain in different anharmonic oscillators. Field‐induced tunneling and chaotic ionization in Rydberg atoms are also analyzed with the help of these theories. Quantum fluid density functional theory may be used to understand different time‐dependent processes like ion‐atom/molecule collisions, atom‐field interactions, and so forth. Regioselectivity as well as confined atomic/molecular systems and their reactivity dynamics have also been explained. © 2013 Wiley Periodicals, Inc.     

Semi-classical generalized Langevin equation for equilibrium and nonequilibrium molecular dynamics simulation

Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matter in different phases. Normally, the atomic dynamics are described by classical equations of motion and the effect of the environment is taken into account through the fluctuating and frictional forces. Generally, the nuclear quantum effects and their coupling to other degrees of freedom are difficult to include in an efficient way. This could be a serious limitation on its application to the study of dynamical properties of materials made from light elements, in the presence of external driving electrical or thermal fields. One example of such system is single molecule dynamics on metal surface, an important system that has received intense study in surface science. In this review, we summarize recent effort in extending the Langevin MD to include nuclear quantum effect and their coupling to flowing electrical current. We discuss its applications in the study of adsorbate dynamics on metal surface, current-induced dynamics in molecular junctions, and quantum thermal transport between different reservoirs.     

Long-range energy transfer and ionization in extended quantum systems driven by ultrashort spatially shaped laser pulses

The processes of ionization and energy transfer in a quantum system composed of two distant H atoms with an initial internuclear separation of 100 atomic units (5.29 nm) have been studied by the numerical solution of the time-dependent Schr?dinger equation beyond the Born-Oppenheimer approximation. Thereby it has been assumed that only one of the two H atoms was excited by temporally and spatially shaped laser pulses at various laser carrier frequencies. The quantum dynamics of the extended H-H system, which was taken to be initially either in an unentangled or an entangled ground state, has been explored within a linear three-dimensional model, including the two z coordinates of the electrons and the internuclear distance R. An efficient energy transfer from the laser-excited H atom (atom A) to the other H atom (atom B) and the ionization of the latter have been found. It has been shown that the physical mechanisms of the energy transfer as well as of the ionization of atom B are the Coulomb attraction of the laser driven electron of atom A by the proton of atom B and a short-range Coulomb repulsion of the two electrons when their wave functions strongly overlap in the domain of atom B.