Quantum tunneling effect in entanglement dynamics

Quantum tunneling effect in entanglement dynamics between two coupled particles with separable Gaussian initial state is investigated using entangled trajectory molecular dynamics method in terms of the reduced‐density linear entropy. It has been presented through showing distinguish contribution of single trajectory to linear entropy between classical trajectory and entangled trajectory with same initial state. We find that quantum tunneling effect makes single trajectory's contribution remarkably decrease under quantum dynamics compared to classical dynamics. The nonlocality of quantum entanglement is presented, and the energy transfer between two coupled particles through quantum correlations and classical ones is also discussed in the end. © 2015 Wiley Periodicals, Inc.     

Quantum tautomerization in porphycene and its isotopomers: Path-integral molecular dynamics simulations

Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T = 300 K mainly occurs via a so-called concerted mechanism through the D_2h second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism.     

Nuclear quantum effects at aqueous metal interfaces captured by molecular dynamics simulations

In this review, we summarize the recent development in modeling nuclear quantum effects at aqueous metal interfaces. First, we review the nuclear quantum effects on the water-metal interface at ultrahigh vacuum. Then, we illustrate the nuclear quantum effects at the potential of zero charge conditions. At last, we give some outlook for the perspective work in modeling the nuclear quantum effects at electrochemical interfaces and some practical simulation strategies.     

Quantum bits with polyacetylene

The dynamics of a polyacetylene single chain as a system for possible physical implementations of quantum bits is determined. This novel proposition is studied by varying intensity and duration of application of an electric field as well as the intensity, number, and position in the polymer chain of impurity molecules. The behavior of soliton pairs, whose associated energy levels form the quantum bit, is analyzed. The chain is modeled by a modified Pariser-Parr-Pople Hamiltonian extended to include the effects of an external electric field and the parameters of the impurity molecules. The effect of the variation of the field and impurities on the separation of the energy levels associated with soliton pairs is analyzed by numerical integration of the equations of motion. Two different approaches for controlling the separation of levels are presented, and their features compared. First, the use of changes in the electric field to control the distance (and ultimately coupling) between two solitons moving freely on the chain or captured by the potential generated by the impurity molecules. Second, the change in the intensity of the impurities alone, with no application of an external field. We have found that the effect of the use of the field on the separation of levels is much smaller than the one obtained by changes in the parameters of the impurity molecules, which eventually led us to achieve quantum bit behavior in a polyacetylene chain. The influence of the field and impurity parameters in the energy levels is determined, as well as their role in the coupling of the two solitons on the chain. Critical values for distance between solitons, intensity of field, and impurities that determine whether a pair of solitons can work as a quantum bit are obtained.     

Nonadiabatic relaxation dynamics of water anion cluster and its isotope effects by ring‐polymer molecular dynamics simulation

We have applied a recently developed hybrid quantum ring‐polymer molecular dynamics method to the nonadiabatic p → s relaxation dynamics in water anion clusters to understand the isotope effects observed in previous experiments. The average relaxation times for (H₂O)₅₀^? and (D₂O)₅₀^? were calculated at 120 and 207 fs, respectively, and are comparable to the experimental results. Therefore, we conclude that nuclear quantum effects play an essential role in understanding the observed isotope effects for water anion cluster nonadiabatic dynamics. The nonadiabatic relaxation mechanisms are also discussed in detail. © 2014 Wiley Periodicals, Inc.     

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.     

Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions

Ab initio and molecular mechanics studies of LiPF₆ and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li⁺/PF₆^? complexes obtained from quantum chemistry revealed a preference for C_3V symmetry structures for Li⁺–P separations under 2.8 Å, C_2V symmetry for Li⁺–P in the range of 2.8–3.3 Å and C_4V symmetry for Li⁺–P separations larger than 3.3 Å. Electron correlation effects were found to make an insignificant contribution to binding in the Li⁺/PF₆^? complex. By contrast, analogous studies of PF₆^?/PF₆^? and PF₆^?/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF₆ melts was parameterized to reproduce the geometries and energies of Li⁺/PF₆^?, PF₆^?/PF₆^?, PF₆^?/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF₆ melts were performed to validate this quantum chemistry‐based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF₆ solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001     

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.     

The IR spectrum of supercritical water: Combined molecular dynamics/quantum mechanics strategy and force field for cluster sampling

Supercritical water was analyzed recently as a gas of small clusters of waters linked to each other by intermolecular hydrogen‐bonds, but unexpected “linear” conformations of clusters are required to reproduce the infra‐red (IR) spectra of the supercritical state. Aiming at a better understanding of clusters in supercritical water, this work presents a strategy combining classical molecular dynamics to explore the potential energy landscape of water clusters with quantum mechanical calculation of their IR spectra. For this purpose, we have developed an accurate and flexible force field of water based on the TIP5P 5‐site model. Water dimers and trimers obtained with this improved force field compare well with the quantum mechanically optimized clusters. Exploration by simulated annealing of the potential energy surface of the classical force field reveals a new trimer conformation whose IR response determined from quantum calculations could play a role in the IR spectra of supercritical water. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers

Conventional molecular dynamics simulations of macromolecules require long computational times because the most interesting motions are very slow compared to the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is, with bond lengths, bond angles, and torsions as independent variables, gives a theoretical possibility of eliminating all uninteresting fast degrees of freedom from the system. This article presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived that are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations of a 56 residue globular protein. For the first time it was possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is, with fixed bond lengths, bond angles, and rigid aromatic groups, the characteristic step size is 4 fs, which is 2 times higher than with fixed bond lengths only. The step size can be increased up to 11 fs when rotation of hydrogen atoms is suppressed. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1354–1364, 1997     

Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion–repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 38–50, 1998     

OOPSE: an object-oriented parallel simulation engine for molecular dynamics

OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.     

Molecular dynamics method in studies of molecular film growth processes

This review is an attempt to analyze some of the experimental problems arising in the course of growth of orientated molecular films using metal monophthalocyanine (MPc) films as an example and to demonstrate the possibilities of molecular dynamics simulation of these processes for solving experimental problems. Examples of theoretical simulation of adsorption processes are given; formation of a molecular monolayer is considered for copper phthalocyanine films as an example.     

Quantum manifestations of classical trajectories in molecular systems

Quantum chaos, understood as the effect of the underlying classical dynamics on the stationary quantum properties in classically chaotic systems, is examined in two molecular floppy systems. Realistic models of two degrees of freedom for HO₂ and HCN/HNC are considered. The structure of the classical phase space is studied using Poincaré surfaces of section and the dynamical characteristics of the corresponding wave functions analyzed also in phase space with the aid of Husimi functions. Some wave functions show strong localization along periodic orbits. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Investigation of chiral recognition by molecular micelles with molecular dynamics simulations

Molecular dynamics simulations were used to characterize the binding of the chiral drugs chlorthalidone and lorazepam to the molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The project’s goal was to characterize the nature of chiral recognition in capillary electrophoresis separations that use molecular micelles as the chiral selector. The shapes and charge distributions of the chiral molecules investigated, their orientations within the molecular micelle chiral binding pockets, and the formation of stereoselective intermolecular hydrogen bonds with the molecular micelle were all found to play key roles in determining where and how lorazepam and chlorthalidone enantiomers interacted with the molecular micelle.     

Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH₃, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 977–988, 1998     

Quantum nonadiabatic dynamics of hydrogen exchange reactions

In continuation of our earlier effort to understand the nonadiabatic coupling effects in the prototypical H + H₂ exchange reaction [Jayachander Rao et al. Chem. Phys. 333 (2007) 135], we present here further quantum dynamical investigations on its isotopic variants. The present work also corrects a technical scaling error occurred in our previous studies on the H + HD reaction. Initial state-selected total reaction cross sections and Boltzmann averaged thermal rate constants are calculated with the aid of a time-dependent wave packet approach employing the double many body expansion potential energy surfaces of the system. The theoretical results are compared with the experimental and other theoretical data whenever available. The results re-establish our earlier conclusion, on a more general perspective, that the electronic nonadiabatic effects are negligible on the important quantum dynamical observables of these reactive systems reported here.     

New faster CHARMM molecular dynamics engine

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. © 2013 Wiley Periodicals, Inc.