Quantum Molecular Dynamics Method Research Articles

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer.

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Ab Initio Nonadiabatic Quantum Molecular Dynamics.

The Born-Oppenheimer approximation underlies much of chemical simulation and provides the framework defining the potential energy surfaces that are used for much of our pictorial understanding of chemical phenomena. However, this approximation breaks down when the dynamics of molecules in excited electronic states are considered. Describing dynamics when the Born-Oppenheimer approximation breaks down requires a quantum mechanical description of the nuclei. Chemical reaction dynamics on excited electronic states is critical for many applications in renewable energy, chemical synthesis, and bioimaging. Furthermore, it is necessary in order to connect with many ultrafast pump-probe spectroscopic experiments. In this review, we provide an overview of methods that can describe nonadiabatic dynamics, with emphasis on those that are able to simultaneously address the quantum mechanics of both electrons and nuclei. Such ab initio quantum molecular dynamics methods solve the electronic Schrödinger equation alongside the nuclear dynamics and thereby avoid the need for precalculation of potential energy surfaces and nonadiabatic coupling matrix elements. Two main families of methods are commonly employed to simulate nonadiabatic dynamics in molecules: full quantum dynamics, such as the multiconfigurational time-dependent Hartree method, and classical trajectory-based approaches, such as trajectory surface hopping. In this review, we describe a third class of methods that is intermediate between the two: Gaussian basis set expansions built around trajectories.

Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.

The fluorescent non-natural 4-aminophthalimide (4AP) base, when paired to the complementary 2,4-diaminopyrimidine (DAP) nucleobase, is accommodated in a B-DNA duplex being efficiently recognized and incorporated by DNA polymerases. To complement the experimental studies and rationalize the impact of the above non-natural bases on the structure, stability and dynamics of nucleic acid structures, we performed quantum mechanics (QM) calculations along with classical molecular dynamics (MD) simulations. QM calculations were initially focused on the geometry and energetics of the 4AP:DAP non-natural pair and of H-bonded base pairs between 4AP and all the natural bases in their classical Watson-Crick geometries. The QM calculations indicate that the 4AP:DAP pair, despite the fact that it can form 3 H-bonds in a classic Watson-Crick geometry, has a stability comparable to the A:T pair. Then, we extended the study to reverse Watson-Crick geometries, characteristic of parallel strands. MD simulations were carried out on two 13-mer DNA duplexes, featuring a central 4AP:DAP or A:T pair, respectively. No major structural deformation of the duplex was observed during the MD simulation. Snapshots from the MD simulations were subjected to QM calculations to investigate the 4AP:DAP interaction energy when embedded into a duplex structure, and to investigate the impact of the two non-natural bases on the stacking interactions with adjacent bases in the DNA duplex. We found a slight increase in stacking interactions involving the 4AP:DAP pair, counterbalanced by a moderate decrease in H-bonding interactions of the 4AP:DAP and of the adjacent base pairs in the duplex. The results of our study are in agreement with experimental data and complement them by providing an insight into which factors contribute positively and which factors contribute negatively to the structural compatibility of the fluorescent 4AP:DAP pair with a B-DNA structure.

Investigation of melting at the uranium γ phase by quantum and classical molecular dynamics methods

Melting at the high-temperature uranium γ phase at pressures up to 0.8 TPa and temperatures up to 2 × 104 K is studied using quantum and classical molecular dynamics methods. The position of the equilibrium melting curve is estimated based on quantum calculations according to the Lindemann criterion. An interatomic-interaction potential is developed for classical molecular dynamics simulation of the properties of uranium in the γ phase and liquid state. The melting curve is calculated using the modified Z method. The curve is in agreement with the known experimental data at pressures below 0.1 TPa and the found estimate. The calculated melting curve is also compared with the Simon–Glatzel equation theoretical model.

Explicit inclusion of electronic correlation effects in molecular dynamics

We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for the inhomogeneity inherent in the process of quantum molecular dynamics (MD) simulation. We also propose an efficient algorithm based on the second-moment approximation to the electronic density of states for the search of the optimal variation parameters, from which the effective renormalized interatomic MD potentials are fully determined. By considering a minimal one-correlated-orbital Anderson many-particle model based on tight-binding hopping integrals, this fast GA-MD method is benchmarked with that using exact diagonalization to solve the GA variational parameters. In the infinite damping limit, the efficiency and accuracy are illustrated. This novel method will open up an unprecedented opportunity enabling large-scale quantum MD simulations of strongly correlated electronic materials.

Theoretical Study of the Heterolytic σ Bond Cleavage on the Ge═O Bond of Germanone. An Insight into the Driving Force from Both Electronic and Dynamical Aspects.

The mechanism of the σ bond cleavage of H2O, NH3, Me2C═O, H2, CH4, BH3, and SiH4 on the Ge═O bond of germanone is examined by means of both quantum mechanical (QM) and molecular dynamics (MD) methods. The QM calculations show that the σ bonds of all the substrates are heterolytically broken on the very largely polarized Ge═O bond. Before the σ bond cleavage, the substrate at first approach the Ge═O germanium in the cases of H2O, Me2C═O, and NH3, and in contrast, the Ge═O oxygen in the cases of H2, CH4, BH3, and SiH4. For the cases of H2O, NH3, and Me2C═O, a cluster in which the substrate coordinates to the Ge exists before the σ bond cleavage, and this coordination of the substrate plays an important role on the heterolytic σ bond cleavage. The QM-MD simulations are also conducted for the case of H2O, and they show that the kinetic energy of the H2O-coordinated cluster especially concentrates on the coordinated H2O oxygen to strongly oscillate the coordinate bond between the H2O oxygen and the Ge. This oscillation further enlarges just before the O-H σ bond cleavage, and the kinetic energy of this oscillation would be transmitted to the normal mode of the O-H bond breaking. Thus, the coordination and the vibration of the H2O oxygen was thought to be an important driving force of the heterolytic cleavage of the O-H σ bond in both electronic and dynamical aspects.

Calculating the melting curves by the thermodynamic data matching method: Platinum-group refractory metals (Ru, Os, and Ir)

A technique for reconstructing thermal properties, including the melting curve, of refractory metals based on the use of experimental data on caloric properties available up to the melting point and some regularities of the Debye–Gruneisen theory has been proposed. The calculation result is the consistent system of high-temperature thermal data, including the thermal expansion coefficient, solid-phase density, and volume jump upon melting. This technique was tried-out on refractory platinum-group metals based on experimental data on the enthalpy of the metals and confirmed by consistency with a thermodynamic calculation using shock-wave experiments and results obtained by the quantum molecular dynamics method.

Theoretical study of the chemical reactions by the combination of quantum mechanical and molecular dynamics methods

Theoretical study of the chemical reactions by the combination of quantum mechanical and molecular dynamics methods

Acid activation mechanism of the influenza A M2 proton channel

The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel responsible for the acidification of the influenza virus interior, an important step in the viral lifecycle. Four histidine residues (His37) in the center of the channel act as a pH sensor and proton selectivity filter. Despite intense study, the pH-dependent activation mechanism of the AM2 channel has to date not been completely understood at a molecular level. Herein we have used multiscale computer simulations to characterize (with explicit proton transport free energy profiles and their associated calculated conductances) the activation mechanism of AM2. All proton transfer steps involved in proton diffusion through the channel, including the protonation/deprotonation of His37, are explicitly considered using classical, quantum, and reactive molecular dynamics methods. The asymmetry of the proton transport free energy profile under high-pH conditions qualitatively explains the rectification behavior of AM2 (i.e., why the inward proton flux is allowed when the pH is low in viral exterior and high in viral interior, but outward proton flux is prohibited when the pH gradient is reversed). Also, in agreement with electrophysiological results, our simulations indicate that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain; the four transmembrane helices flanking the channel lumen alone seem to determine the proton conduction mechanism.

Quantum Mechanical and Molecular Dynamics Studies of the Reaction Mechanism of the Nucleophilic Substitution at the Si Atom.

The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans.

First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm3 and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atom model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κQMD) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ)QMD] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ∼20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.

Study of the equation of states for deuterium, helium, and their mixture

Equation of states for deuterium, helium, and their mixture is studied by using the quantum molecular dynamics (QMD) method. We calculate the equation of states for helium with density from 0.32 to 5 g/cm3 at temperature from 1000 to 50000 K. Results are compared with the chemical model (CM), at T less than 10000 K, and QMD is in good agreement with the CM. The shock Hugoniot curves are also calculated, and the results are in good agreement with the gas-gun experiment. The mechanism of the metal-insulator transition for helium is studied by computing its pair distribution function and density of states. The equation of states (EOS) for deuterium with density from 0.19 to 0.84 g/cm3 at temperatures from 20 to 50000 K is computed. For deuterium molecule the degree of dissociation is calculated, and the effect of the molecular vibration is accounted for using the EOS model. Theoretical Hugoniot states are also calculated and compared with the results of experiments and other theories; the maximum compressibility of hydrogen is about 4.9, and deuterium 4.4; these agree with the results of most experiments and theories. Due to the zero point motion of atoms being not taken into account, the theoretical results at low temperatures are smaller than those of experiments. The deuterium-helium mixture is studied, and its 293 points of equation of states for various xHe with densities from 0.19 to 0.84 g/cm3 at temperatures from 100 to 50000 K are calculated. The linear mixing approximation (LMA) is checked, and the maximum of the volume distinction is about 7%; the results indicate that LMA is a cursory approximation.

Quantum molecular dynamics simulation of hydrogen diffusion in zirconium hydride

The behavior of hydrogen in zirconium hydride in the high-temperature range has been investigated using the quantum molecular dynamics method. The δ phases of compositions ZrH1.75 and ZrH2 and the liquid phase are considered. The self-diffusion coefficients of hydrogen are calculated as a function of the temperature in the range from 1000 to 6000 K. For the ZrH1.75 and ZrH2 hydrides, the obtained values are close to each other. At temperatures of 1000–2000 K, the hydrogen diffusion is determined not only by the mobility of hydrogen atoms but also by the transition from the energetically favorable tetrahedral positions into the excited state. The obtained values of the diffusion coefficients in the temperature range of 1000–1200 K are in good agreement with the experimental data.

Properties of warm dense polystyrene plasmas along the principal Hugoniot.

Polystyrene (CH) is often chosen as the ablator material for inertial confinement fusion (ICF) targets. Its static, dynamical, and optical properties in warm, dense conditions (due to shock compression) are important for ICF designs. Using the first-principles quantum molecular dynamics (QMD) method, we have investigated the equation of state (EOS) and optical reflectivity of shock-compressed CH up to an unprecedentedly high pressure of 62 Mbar along the principal Hugoniot. The QMD results are compared with existing experimental measurements as well as the SESAME EOS model. Although the Hugoniot pressure and/or temperature from QMD calculations agrees with experiments and the SESAME EOS model at low pressures below 10 Mbar, we have identified for the first time a stiffer behavior of shocked CH at higher pressures (>10 Mbar). Such a stiffer behavior of warm, dense CH can affect the ablation pressure (shock strength), shock coalescence dynamics, and nonuniformity growth in ICF implosions. In addition, we corrected the mistake made in literature for calculating the reflectivity of shocked CH and obtained good agreements with experimental measurements, which should lend credence to future opacity calculations in a first-principles fashion.

Quantum molecular dynamics simulation of shock-wave experiments in aluminum

We present quantum molecular dynamics calculations of principal, porous, and double shock Hugoniots, release isentropes, and sound velocity behind the shock front for aluminum. A comprehensive analysis of available shock-wave data is performed; the agreement and discrepancies of simulation results with measurements are discussed. Special attention is paid to the melting region of aluminum along the principal Hugoniot; the boundaries of the melting zone are estimated using the self-diffusion coefficient. Also, we make a comparison with a high-quality multiphase equation of state for aluminum. Independent semiempirical and first-principle models are very close to each other in caloric variables (pressure, density, particle velocity, etc.) but the equation of state gives higher temperature on the principal Hugoniot and release isentropes than ab initio calculations. Thus, the quantum molecular dynamics method can be used for calibration of semiempirical equations of state in case of lack of experimental data.

First-principles thermal conductivity of warm-dense deuterium plasmas for inertial confinement fusion applications.

Thermal conductivity (κ) of both the ablator materials and deuterium-tritium (DT) fuel plays an important role in understanding and designing inertial confinement fusion (ICF) implosions. The extensively used Spitzer model for thermal conduction in ideal plasmas breaks down for high-density, low-temperature shells that are compressed by shocks and spherical convergence in imploding targets. A variety of thermal-conductivity models have been proposed for ICF hydrodynamic simulations of such coupled and degenerate plasmas. The accuracy of these κ models for DT plasmas has recently been tested against first-principles calculations using the quantum molecular-dynamics (QMD) method; although mainly for high densities (ρ > 100 g/cm3), large discrepancies in κ have been identified for the peak-compression conditions in ICF. To cover the wide range of density-temperature conditions undergone by ICF imploding fuel shells, we have performed QMD calculations of κ for a variety of deuterium densities of ρ = 1.0 to 673.518 g/cm3, at temperatures varying from T = 5 × 103 K to T = 8 × 106 K. The resulting κQMD of deuterium is fitted with a polynomial function of the coupling and degeneracy parameters Γ and θ, which can then be used in hydrodynamic simulation codes. Compared with the "hybrid" Spitzer-Lee-More model currently adopted in our hydrocode lilac, the hydrosimulations using the fitted κQMD have shown up to ∼20% variations in predicting target performance for different ICF implosions on OMEGA and direct-drive-ignition designs for the National Ignition Facility (NIF). The lower the adiabat of an imploding shell, the more variations in predicting target performance using κQMD. Moreover, the use of κQMD also modifies the shock conditions and the density-temperature profiles of the imploding shell at early implosion stage, which predominantly affects the final target performance. This is in contrast to the previous speculation that κQMD changes mainly the inside ablation process during the hot-spot formation of an ICF implosion.

Quantum Trajectory-Electronic Structure Approach for Exploring Nuclear Effects in the Dynamics of Nanomaterials.

A massively parallel, direct quantum molecular dynamics method is described. The method combines a quantum trajectory (QT) representation of the nuclear wave function discretized into an ensemble of trajectories with an electronic structure (ES) description of electrons, namely using the density functional tight binding (DFTB) theory. Quantum nuclear effects are included into the dynamics of the nuclei via quantum corrections to the classical forces. To reduce computational cost and increase numerical accuracy, the quantum corrections to dynamics resulting from localization of the nuclear wave function are computed approximately and included into selected degrees of freedom representing light particles where the quantum effects are expected to be the most pronounced. A massively parallel implementation, based on the message passing interface allows for efficient simulations of ensembles of thousands of trajectories at once. The QTES-DFTB dynamics approach is employed to study the role of quantum nuclear effects on the interaction of hydrogen with a model graphene sheet, revealing that neglect of nuclear effects can lead to an overestimation of adsorption.

G143 粒子表面衝突時の電子へのエネルギー伝達に関する量子分子動力学的研究(OS-7:マイクロ・ナノ熱工学(4))

In the present study the quantum molecular dynamics method was applied to an energy transfer problem to an electron during a particle surface collision process in order to elucidate how the energy of the particle collision transfers to the emitted electrons and to develop the applicable simulation method for such small energy transfer phenomena. The effects of the collision energy on the energy transfer to an electron were investigated by the non-adiabatic quantum molecular dynamics method when a xenon molecule was collided with the surface so as to elucidate the predominant factor of the energy transfer to the emitted electron.

Ab Initio Simulation of Complex Dielectric Function for Dense Aluminum Plasma

AbstractWe present calculations of frequency‐dependent complex dielectric function of dense aluminum plasma by quantum molecular dynamics method for temperatures up to 20 kK. Analysis shows that the dependencies for real and imaginary parts can be interpolated by the Drude formula with two effective parameters: the mean charge of ions and the effective frequency of collisions. The rise of these parameters with temperature deviates from simple theoretical predictions (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Pressure and Electrical Resistivity Measurements on Hot Expanded Metals: Comparisons with Quantum Molecular Dynamics Simulations and Average‐Atom Approaches

AbstractWe present experimental results on pressures and resistivities of expanded nickel and titanium at respective densities of 0.1 g/cm3 and 0.2 g/cm3, and in a range of temperature of 1‐3 eV that corresponds to the warm dense matter (WDM) regime. These data are used to benchmark different theoretical approaches. A comparison is presented between fully 3‐dimensional quantum molecular dynamics (QMD) methods, based on density functional theory, with average‐atom (AA) methods, that are essentially one dimensional. AA methods are used to identify interband transitions and photoionization thresholds. In this regime the evaluation of the thermodynamic properties as well as electrical properties is difficult due to the concurrence of density and thermal effects which directly drive the metal‐non‐metal transition. QMD simulations are also helpful to give a precise estimation of the temperature of experiments which is not directly accessible [1] (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)