Classical Molecular Dynamics Calculations Research Articles

5-1 内包原子種がシリコンクラスレート格子熱伝導率に及ぼす影響 : 古典分子動力学法による検討(セッション5:OS1-2 マルチスケール・シミュレーションとナノ計測)

In this study, effects of contained guest atomic species in Si clathrates on the lattice thermal conductivity were studied by using classical molecular dynamics calculations. Their lattice thermal conductivities were calculated from heat current obtained in the calculations, which was called as the Green-Kubo method. As a result, lattice thermal conductivities of type-I Si clathrates, Si_<46>M_8 (M=Na, K, Rb, Cs, Be, Mg, Sr, and Ba), were obtained. The obtained lattice thermal conductivity could be considered as a function of characteristic frequency 1/2(k/m)^<1/2>, where m and k indicate atomic weight of a guest atom and a force constant felt by a guest atom in a Si cage, respectively. Lattice thermal conductivity increases as the characteristic frequency increases in frequency range more than 3THz, even if the atomic weight was artificially changed. On the other hand, in frequency range less than 3THz, lattice thermal conductivity decreases as characteristic frequency increases.

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

When only equilibrium thermodynamics or averages of position-dependent functions in classical molecular dynamics calculations are sought, the choice of the atomic masses in the Hamiltonian becomes irrelevant. Consequently, the masses can be used as free parameters to help improve conformational sampling efficiency in the spirit of Bennett's mass-tensor dynamics (Bennett, C. H. J. Comput. Phys. 1975, 19, 267.). Here we report on the effect of reducing side-chain and solvent masses on the folding behavior of a 9-residue hairpin-forming peptide in solution. A physical motivation for reducing the solvent mass is an effective reduction in solvent viscosity. Side-chain mass scaling is motivated by the idea of solvent potentials of mean force which are employed in select coarse-grained protein models. In the limit of very large mass differences, the mass reduction effectively creates an adiabatic decoupling between solvent, side-chain, and backbone motions, so that both the backbone and side chains move on the instantaneous solvent potential of mean force (PMF) surface, and the backbone additionally moves on the side-chain PMF. Because of the arbitrariness in the choice of masses, this limit only needs to be reached approximately in practice. In particular, we show that a 10-fold reduction in solvent masses and a side-chain mass scale that is intermediate between the scaled solvent and the backbone lead to a quantitative enhancement in conformational sampling.

Investigation of ZPE and temperature effects on the Eley–Rideal recombination of hydrogen atoms on graphene using a multidimensional graphene–H–H potential

We study the Eley–Rideal recombination of H atoms on graphene under the physical conditions of the interstellar medium. Effects of the ZPE motions of the chemisorbed H atom and of the graphene thermal motions are investigated. Classical molecular dynamics calculations undertaken with the multidimensional potential of Bachellerie et al. [Phys. Chem. Chem. Phys. 11 (2009) 2715] are reported. The ZPE effects are the strongest. The closer the collision energy is to the classical reaction threshold the more sizeable the effects. The quantum reaction cross section is also estimated below and above the classical threshold using a capture model.

Evolution of cellular structures duringGe1−xSixsingle-crystal growth by means of a modified phase-field method

We have studied the evolution of cellular structures in Ge 1-x Si x single-crystal growth as a function of process parameters. Because these structures are much larger than those occurring during the solidification of metals, we developed a modified phase-field method, which is able to handle these structure within reasonable computer times using the real material parameters. The model has been tested for computing equilibrium shapes of crystals, dendritic growth, and cellular growth of Ni x Cu 1-x. We also performed classical molecular dynamics calculations in order to compute the diffusion coefficients of Si and Ge in melts of various compositions.

Graphene buffer layer on Si-terminated SiC studied with an empirical interatomic potential

The atomistic structure of the graphene buffer layer on Si-terminated SiC is investigated using a modified version of the environment-dependent interatomic potential. The determination of the equilibrium state by the conjuguate gradients method suffers from a complex multiple-minima energy surface. The initial configuration is therefore modified to set the system in specific valleys of the energy surface. The solution of minimal energy forms a hexagonal pattern composed of stuck regions separated by unbonded rods that release the misfit with the SiC surface. The structure presents the experimental symmetries and a global agreement with an ab initio calculation. It is therefore expected that the interatomic potential could be used in classical molecular dynamics calculations to study the graphene growth.

A desorption mechanism of water following vacuum-ultraviolet irradiation on amorphous solid water at 90 K

Following 157 nm photoexcitation of amorphous solid water and polycrystalline water ice, photodesorbed water molecules (H(2)O and D(2)O), in the ground vibrational state, have been observed using resonance-enhanced multiphoton ionization detection methods. Time-of-flight and rotationally resolved spectra of the photodesorbed water molecules were measured, and the kinetic and internal energy distributions were obtained. The measured energy distributions are in good accord with those predicted by classical molecular dynamics calculations for the kick-out mechanism of a water molecule from the ice surface by a hot hydrogen (deuterium) atom formed by photodissociation of a neighboring water molecule. Desorption of D(2)O following 193 nm photoirradiation of a D(2)O/H(2)S mixed ice was also investigated to provide further direct evidence for the operation of a kick-out mechanism.

Molecular dynamics study ofH2dissociation on H-covered Pd(100)

We employ classical molecular dynamics calculations based on density-functional theory molecule-surface interaction potentials to study H-coverage effects on ${\text{H}}_{2}$ dissociative adsorption on Pd(100). In contrast with one of the basic assumptions of the widely used Langmuir model, we have found that a single isolated H-vacancy is enough to spontaneously dissociate low-energy ${\text{H}}_{2}$ molecules on H-covered Pd(100). We also show that for a given initial coverage (e.g., $\ensuremath{\Theta}=1/2$), the dissociative adsorption probability of low-energy ${\text{H}}_{2}$ molecules can vary by a factor of five depending on the particular arrangement of the H adatoms on the surface.

Enhanced π-π interactions between a C60 fullerene and a buckle bend on a double-walled carbon nanotube

In situ low-voltage aberration corrected transmission electron microscopy (TEM) observations of the dynamic entrapment of a C60 molecule in the saddle of a bent double-walled carbon nanotube is presented. The fullerene interaction is non-covalent, suggesting that enhanced π-π interactions (van der Waals forces) are responsible. Classical molecular dynamics calculations confirm that the increased interaction area associated with a buckle is sufficient to trap a fullerene. Moreover, they show hopping behavior in agreement with our experimental observations. Our findings further our understanding of carbon nanostructure interactions, which are important in the rapidly developing field of low-voltage aberration corrected TEM and nano-carbon device fabrication.

TRANSLATIONAL AND ROTATIONAL ENERGY MEASUREMENTS OF PHOTODESORBED WATER MOLECULES IN THEIR VIBRATIONAL GROUND STATE FROM AMORPHOUS SOLID WATER

For interstellar grains coated with water ice, the most important desorption mechanism at the edge of molecular clouds is photodesorption of water. To reveal details of the photodesorption mechanism, we have measured the translational and rotational energies of H2 O( v = 0) molecules photodesorbed from amorphous solid water and polycrystalline ice following excitation within the first absorption band using a 157 nm laser. The measured translational and rotational temperatures are 1800 K and 300 K, respectively. These energies are in good accord with those predicted by classical molecular dynamics calculations for the “kick-out” of an H2O molecule in the ice by an energetic H atom. The statistical ortho:para ratio of gOPR = 3 is appropriate for the Boltzmann rotational distribution of the H2O molecules.

A DFT and MD Study on the Interaction of Carbon Nano-Materials with Metal Ions

The interaction of manganese (II) ion (Mn2+) with graphene surfaces have been investigated by means of density functional theory (DFT). Also, the molecular dynamics (MD) calculations using molecular mechanics-2 (MM2) potential functions have been applied to the diffusion dynamics of Mn2+ on the graphene surface. Two graphene sheets (n = 19 and 52, where n means numbers of rings in each carbon cluster) were considered as models of graphene surface in the present study. The B3LYP/LANL2MB calculations showed that the Mn2+ ion is located in the ranges 2.28–2.46 Å from the graphene surface. Also, classical MD calculation was applied to diffusion processes of the Mn2+ on the graphene surface (n = 52). The classical MD calculations showed that the Mn2+ ion diffuses from bulk to edge region at 300–600 K and is trapped in the edge region. The nature of the interaction between the Mn2+ ion and the graphene sheet was discussed on the basis of theoretical results.

Interaction of acetonitrile with thin films of solid water

Thin films of water were prepared on Ag at 124 K. Their properties were studied with metastable impact electron spectroscopy, reflection absorption infrared spectroscopy, and temperature programmed desorption. The interaction of acetonitrile (ACN) with these films was studied with the abovementioned techniques. From the absence of any infrared activity in the initial adsorption stage, it is concluded that ACN adsorbs linearly and that the C identical withN axis is aligned parallel to the water surface (as also found on neat Ag). Initially, the interaction with water surface species involves their dangling OD groups. During the completion of the first adlayer the ACN-ACN lateral interaction becomes of importance as well, and the ACN molecules become tilted with respect to the water surface. ACN shows propensity to stay at the surface after surface adsorption even during annealing up to the onset of desorption. The present results for the ACN-water interaction are compared with available classical molecular dynamics calculations providing the orientation profile for ACN on water as well as the ACN bonding properties.

Density functional theory, molecular dynamics, and differential scanning calorimetry study of the RbF–CsF phase diagram

A multiscale modeling approach is developed to compute the phase diagram of the RbF-CsF binary system. The mixing enthalpies of the (Rb,Cs)F solid and liquid solutions are evaluated using density functional theory and classical molecular dynamics calculations, respectively. For the solid solution, 18 different configurations are studied with density functional theory and the surrounded atom model is applied in order to compute the configurational partition function. We also measure the solidus and liquidus equilibria using differential scanning calorimetry. Finally the RbF-CsF phase diagram is constructed using the calculated excess free enthalpies of the solid and liquid solutions and a very good agreement with our experimental data is found.

Modeling Reactive Scattering of F(2P) at a Liquid Squalane Interface: A Hybrid QM/MM Molecular Dynamics Study

To better understand the reactivity of gases with liquid surfaces, experimentalists have recently probed the reactive scattering of atomic fluorine at the surface of liquid squalane (C(30)H(62)). In this paper we further this research by simulating this scattering process at collision energies of 0.5 and 1.0 eV using a hybrid QM/MM molecular dynamics scheme. To model the structure of the liquid surface, classical molecular dynamics calculations were performed utilizing the OPLS-AA force field. During the F + squalane molecular dynamics simulation, QM/MM calculations are performed at every trajectory step by combining the MSINDO semiempirical Hamiltonian with OPLS-AA and using a dynamic partitioning of the atoms in the QM or MM regions via a "seed atom" method. This computational model provides a type of "on-the-fly" direct dynamics applicable to larger scale chemical processes that include the making/breaking of chemical bonds not available in standard force field models. Our results show that H abstraction is the only reactive scattering pathway and that most trajectories result in reactive scattering. Reaction statistics at the squalane surface are discussed, including variation of the results with incident angle and collision energy, and the probability of reaction as a function of carbon atom type, collision depth, and residence time. Product states, including angular distributions and final translational and rovibrational energies, are also considered and found to be significantly affected by the exothermic reaction energy for H abstraction. The vibrational distributions are in good agreement with recent experiments, but the rotational distributions are dominated by a nonthermal component while the experiments, which involve thermal incident energies, show comparable thermal and nonthermal contributions. Results for O + squalane at 1.0 eV, which we also present, show analogous comparisons with experiment, with OH vibrational distributions which are cold and match experiment, while the calculated rotational distributions are dominated by nonthermal behavior.

Ab initio and classical molecular dynamics calculations of the high-pressure melting of Ne

Classical molecular dynamics (CMD) calculations are fast but are heavily dependent on the potential feasibility. On the other hand, first-principles (ab initio) molecular dynamics (AIMD) does not use any empirical knowledge, but can be extremely time consuming. As both techniques have been applied to study melting at extreme conditions, a comparison of the methods is motivated. Furthermore, when melting is studied with MD, the use of coexistent solid and liquid structures (two-phase) in the initial simulation configuration, instead of a only a solid structure (one-phase), can have a significant impact. In this work, comparisons have been made between CMD and AIMD methods applied to one- and two-phase systems for the melting of Ne at high pressure.

Vibrational Predissociation in Hydrogen Bonded Dimers: The Case of (HF)2 and its Isotopomers

We use the dimer (HF???HF) as a model system to understand the dynamics in hydrogen-bonded systems. This particularly simple system has been widely used both in experimental and theoretical studies. Here we focus on the remarkable mode selectivity in vibrational predissociation processes which occur on time scales of picoseconds to nanoseconds. We have performed classical molecular dynamics (MD) calculations on the six-dimensional SO-3 potential energy surface (PES) of (HF)2[1] to estimate absorption spectra and predissociation lifetimes ?PD for various initial vibrational excitations involving HF stretching. Our calculations can qualitatively reproduce the mode selectivity in ?PD observed experimentally: Excitations involving the 'hydrogen-bonded' HF stretching mode give rise to shorter ?PD than those involving the 'free' HF stretching mode. Besides results concerning the HF dimer, this study offers the opportunity to check to what extent classical MD calculations on an accurate and realistic potential are suitable to study dynamical properties in such a molecular system.

Simulation of liquid Rb by the methods of classical and first-principle molecular dynamics and statistical geometrical analysis of the atomic structure models using the Voronoi-Delaunay method

The atomic structures of liquid rubidium were simulated by classical and first-principle Molecular Dynamics methods for a range of temperatures. The pair potentials necessary for the Classical Molecular Dynamics calculations were obtained using diffraction data by the Schommers iterative method. In all cases simulated pair correlation functions and structure factors correctly reproduced the experimental ones. A Delaunay simplex, comprised by four atoms, is the simplest element of the structure. All atomic aggregates in an atomic structure consist of them. The structure factor of the simplicial voids system is additional structural characteristic which allows seeing distinction in structures with almost similar pair correlation functions.

Stable nanoporous alkali halide polymorphs: a first principles bottom-up study

The stability of nanoclusters and nanocluster-based polymorphs of a large range of alkali halides were investigated using state-of-the-art plane wave density functional theory (DFT) calculations. Specifically, the most energetically stable cluster isomers of (MX)12 (M = Li, Na, K, Rb, Cs, X = F, Cl, Br, I) were considered (i.e. the slab and cage) with respect to two bulk polymorphs: rock-salt (rs-MX) and a nanoporous analogue of the zeolite sodalite (SOD-MX). In both cases, these bulk materials can be regarded as being assembled from their respective cluster building block (slab → rs, cage → SOD). For all alkali halides the dense rs-MX phase was found to be more stable than the low-density nanoporous SOD-MX phase. For the (MX)12 clusters, the dense slab cluster isomers were also generally found to be the most stable cluster type except, however, for the LiX series where the cage isomer was energetically preferred. The energy difference between the rs-MX and the SOD-MX bulk polymorphs (per MX unit) was found to follow the same trend as that between the respective (MX)12 slab and cage clusters. Correspondingly, the cage-based SOD-LiX phases were all found to be only marginally metastable with respect to the rs-LiX forms (ΔESOD-rs ≤ 0.05 eV per LiX). From DFT calculations on the low enthalpy landscape of LiF polymorphs, the energy versus volume equations of state of rs-LiF and SOD-LiF were compared with those of a number of other LiF polymorphs showing SOD-LiF to be stable with respect to compression and expansion and very competitive energetically with a number of denser phases. Classical molecular dynamics calculations were also performed to confirm the thermal stability of the SOD-LiF phase, further strengthening our prediction as to the viability of these novel low density nanoporous ionic materials.

Electronic and atomic structure computation of disordered low index surfaces of [formula omitted]-alumina

Electronic and atomic structure of low index polar (0 0 1, 0 1 1, 1 1 1) spinel γ -alumina surfaces have been investigated using a modified large-scale quantum semi-empirical simulations. Atomic structure optimization and electronic structure calculation were done in the direct space on periodic large unit cells in which random distribution of cationic vacancies close to the surface were included. Predicted electronic structures match more accurate ab initio Density Functional Theory (DFT) results on aluminum oxides. We found that the restructured surfaces behave as amorphous-like shapeless planes provided unit cell dimensions are much greater than primitive translations as periodicity constraints are weakened. Aluminum ions vacancies in the surface region are shown to induce a surface atomic disordering even at 0 K, correlated with the appearance of low coordinated ions, as proven experimentally and theoretically with classical Molecular Dynamics (MD) calculation on some aluminum oxide systems. The lowering of the surface charge density is obtained from two distinct mechanisms involving large ion movements. On the oxygen rich plane termination, this results from the formation of O 2 δ− entities. On the aluminum rich plane termination, the same effect is related to a loss of co-ordination number together with a reduction of cationic charge. Furthermore, large-scale simulations allow to statistically quantify specific relaxed surface ion densities for which the Local Density of States (LDOS) is evaluated. Their inferred electronic properties are then compared to available probe molecule adsorption experiments investigated by infrared spectroscopy. We show that surface electronic states are not a simple function of ion coordination. Our large-scale quantum semi-empirical calculation fills the gap between atomic structures predicted by classical MD approach with electronic structure results obtained by DFT on small systems.

Ab initioand classical molecular dynamics of neon melting at high pressure

First-principles and classical molecular dynamics calculations have been performed to study the high-pressure melting curve of Ne. In the low temperature region, simulations with solid and liquid in coexistence (two-phase) with a Lennard-Jones interatomic potential well reproduce experimental findings. As anticipated, there is a melting temperature overestimation when heating a crystal (one-phase) compared to the two-phase results. Furthermore, there is a significant discrepancy comparing the one-phase ab initio curve to previously reported classical predictions: at $150\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$, the calculations in this work show a melting temperature approximately $1000\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ above the estimate based on an exponential-6 potential. However, there is a close match between the one-phase ab initio curve and the classical one-phase results in this work. This could also imply an agreement between a two-phase ab initio and classical two-phase melting curve. Therefore, considering the documented accuracy of the coexistence method, the classical two-phase melting in this work could well indicate the most probable melting behavior. In conjunction with recent theoretical results for Xe, no significant melting slope decrease was observed for Ne in this study.

Electronic structures and hydrogen bond network of ambient water and amorphous ices

We calculate the electronic structure of ambient liquid water (ALW) at 298 K under a pressure of 0.1 MPa using first principle molecular dynamics based on density functional theory. The effect of hydrogen bond (H-bond) on the electronic structure is focused by comparing partial densities of states of low-density amorphous ice (LDA) at 77 K and ALW. The results show that the H-bond number in LDA is larger than that in ALW. More complex H-bond networks of ALW than that of LDA have also been found by classical molecular dynamics calculations.