First-principles Molecular Dynamics Calculations Research Articles

Structure and Properties of Dense Silica Glass

The O K-edge x-ray Raman scattering (XRS), Brillouin scattering and diffraction studies on silica glass at high pressure have been elucidated in a unified manner using model structures obtained from First-Principles molecular dynamics calculations. This study provides a comprehensive understanding on how the structure is related to the physical and electronic properties. The origin of the “two peak” pattern in the XRS is found to be the result of increased packing of oxygen near the Si and is not a specific sign for sixfold coordination. The compression mechanism involving the presence of 5- and 6-fold coordinated silicon is confirmed. A slight increase in the silicon-oxygen coordination higher than six was found to accompany the increase in the acoustic wave velocity near 140 GPa.

Comparative first-principles study of TiN/SiNx/TiN interfaces

Using first-principles quantum molecular dynamics (QMD) calculations, heterostructures consisting of one monolayer of interfacial Si${}_{x}$N${}_{y}$ inserted between several monolayers of thick slabs of B1(NaCl)-TiN (001) and (111) were investigated in the temperature range of 0 to 1400 K. For the interpretation of the interfacial structures, samples of amorphous SiN and Si${}_{3}$N${}_{4}$ were also generated. The temperature-dependent QMD calculations in combination with subsequent variable-cell structural relaxation revealed that the TiN(001)/B1-SiN/TiN(001) interface exists as a pseudomorphic B1-SiN layer only at 0 K. At finite temperature, this heterostructure transforms into distorted octahedral SiN${}_{6}$ and tetrahedral SiN${}_{4}$ units aligned along the ${110}$ directions. At 300 K, the aggregates of the SiN${}_{x}$ units are close to a disordered, essentially amorphous SiN. After heating to 1400 K and subsequent relaxation at 300 K, the interfacial layer corresponds to a strongly distorted Si${}_{3}$N${}_{4}$-like structure. The B1-SiN, Si${}_{3}$N${}_{4}$-like SiN, and Si${}_{3}$N${}_{4}$-like Si${}_{2}$N${}_{3}$ interfaces between the TiN(111) slabs are stable in the whole temperature range considered here. The B1-SiN interfaces are unstable with respect to a formation of Si-vacancies at finite temperatures. An estimate of interfacial formation energies showed that the most favorable configurations of the (111) interfaces are silicon atoms tetrahedrally coordinated to nitrogen. The most stable (001) B1-derived heterostructure with Si${}_{0.75}$N interface consists of both tetrahedrally and octahedrally coordinated silicon atoms. A comparison with the results obtained by earlier ``static'' ab initio calculations at 0 K shows the great advantage of the QMD calculations, which accounts for the effects of thermal activation of structural reconstructions.

Large amplitude fluxional behaviour of elemental calcium under high pressure

Experimental evidences are presented showing unusually large and highly anisotropic vibrations in the “simple cubic” (SC) unit cell adopted by calcium over a broad pressure ranging from 30–90 GPa and at temperature as low as 40 K. X-ray diffraction patterns show a preferential broadening of the (110) Bragg reflection indicating that the atomic displacements are not isotropic but restricted to the [110] plane. The unusual observation can be rationalized invoking a simple chemical perspective. As the result of pressure-induced s → d transition, Ca atoms situated in the octahedral environment of the simple cubic structure are subjected to Jahn-Teller distortions. First-principles molecular dynamics calculations confirm this suggestion and show that the distortion is of dynamical nature as the cubic unit cell undergoes large amplitude tetragonal fluctuations. The present results show that, even under extreme compression, the atomic configuration is highly fluxional as it constantly changes.

J056032 第一原理分子動力学法を用いた高分子電解質膜の劣化シミュレーション

To clarify the degradation mechanism of proton exchange membrane (PEM) in a polymer electrolyte fuel cell (PEFC), we studied the degradation process of Nafion widely used as PEM by the first-principles molecular dynamics (FPMD) method. FPMD calculations were carried out using our "Violet" program, based on density functional theory (DFT) with B3LYP exchange-correlation functional and 6-31G (d) basis sets. We successfully clarified the dynamics of the reactions in which the main chain end was decomposed by OH radicals. Moreover, it was revealed that the reaction pass differs whether there are water molecules or not in the reaction system. In order to elucidate the difference, we calculated activation energies in these reactions by DFT method. The activation energy of the reaction with water molecules is lower than that of without a water molecule. Therefore, we conclude that water molecules work as a catalyst in the degradation reaction.

Structural, elastic, vibrational and electronic properties of amorphous Al2O3 from ab initio calculations

First-principles molecular dynamics calculations of the structural, elastic, vibrational and electronic properties of amorphous Al2O3, in a system consisting of a supercell of 80 atoms, are reported. A detailed analysis of the interatomic correlations allows us to conclude that the short-range order is mainly composed of AlO4 tetrahedra, but, in contrast with previous results, also an important number of AlO6 octahedra and AlO5 units are present. The vibrational density of states presents two frequency bands, related to bond-bending and bond-stretching modes. It also shows other recognizable features present in similar amorphous oxides. We also present the calculation of elastic properties (bulk modulus and shear modulus). The calculated electronic structure of the material, including total and partial electronic density of states, charge distribution, electron localization function and the ionicity for each species, gives evidence of correlation between the ionicity and the coordination for each Al atom.

First-Principles Study on the Mechanisms for H2 Formation in Ammonia Borane at Ambient and High Pressure

First-principles molecular dynamics calculations were performed to investigate the mechanism on thermal decomposition of H2 of ammonia borane (NH3BH3) at ambient and high pressure. Under atmospheric pressure, one H2 molecule was released through an intramolecular reaction of a single NH3BH3. Nudged elastic band calculations show that the activation barrier for the decomposition in the crystalline environment is reduced by almost 1/3 from the gas phase value. When the system is heated under pressure two H2 were liberated. The reaction follows an intermolecular pathway involving the concerted interaction of three NH3BH3. The results demonstrate the importance and practical significance of pressure on increasing the evolution of H2 from NH3BH3.

Interacting Lewis-X Carbohydrates in Condensed Phase: A First-Principles Molecular Dynamics Study

We performed first-principles molecular dynamics calculations at finite temperature, to study the interacting conformations of Lewis-X (LeX) trisaccharides in the crystalline phase. The calculated cell parameters and detailed atomic structure of the LeX molecule compare well to the experimental data obtained by X-ray diffraction. We identify and characterize the hydrogen-bond network, responsible for the mutual interaction of the LeX pairs, whereas we find the intramolecular conformation and stability to be mainly assured by dispersion forces. The relative contributions to the crystallization energy of the hydrogen bonds and of the dispersion forces are defined and quantified. From this study, candidate configurations for the fully hydrated, in vivo structures of homotypic LeX-LeX interactions at cell surfaces can be proposed. We discuss how these configurations could also be relevant for the adhesion and self-assembly of nanostructures.

Dissociation of O2 Molecules on Strained Pb(111) Surfaces

By performing first-principles molecular dynamics calculations, we systematically simulate the adsorption behavior of oxygen molecules on the clean and strained Pb(111) surfaces. The obtained molecular adsorption precursor state, and the activated dissociation process for oxygen molecules on the clean Pb surface are in good agreements with our previous static calculations, and perfectly explains previous experimental observations [Proc. Natl. Acad. Sci. U.S.A. 104, 9204 (2007)]. In addition, we also study the influences of surface strain on the dissociation behaviors of O2 molecules. It is found that on the compressed Pb(111) surfaces with a strain value of larger than 0.02, O2 molecules will not dissociate at all. And on the stretched Pb(111) surfaces, O2 molecules become easier to approach, and the adsorption energy of the dissociated oxygen atoms is larger than that on the clean Pb surface.

First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase

We report first-principles molecular dynamics calculations based on density functional theory performed on the entrance part of the D-path pathway in bovine cytochrome c oxidase. Our models, which are extracted from the fully reduced and oxidized X-ray structures, include His503 as a protonatable site. We find that the protonated His503 with the deprotonated Asp91 [H503–N δ1H + and D91–C γOO γ] are more energetically favorable than other protonation states, [H503–N δ1 and D91–C γOOH], with an energy difference of about − 5 kcal/mol in reduced case, while the [H503–N δ1H+ and D91–C γOO −] state is energetically unstable, about + 3 kcal/mol higher in energy in the oxidized case. The local interaction of His503 with the surrounding polar residues is necessary and sufficient for determining the energetics. The redox-coupled rotation of His503 is found to change the energetics of the protonation states. We also find that this rotation is coupled with the proton transfer from His503 and Asp91, which leads to the transition between the two different protonation states. This study suggests that His503 is involved in the proton supply to the D-path as a proton acceptor and that the redox-controlled proton-transfer-coupled rotation of His503 is a key process for an effective proton supply to the D-path from water bulk. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.

First-Principles Molecular-Dynamics Calculations on Chemical Reactions and Atomic Structures Induced by H Radical Impinging onto Si(001)2 × 1:H Surface

Chemical reactions between hydrogen terminated Si(001)2 x 1 surface and impinging H radical are investigated by means of first-principles molecular-dynamics simulations. Reaction probabilities of abstraction of surface terminating H atom with H2 formation, adsorption onto Si surface and reflection of impinging H atom are analyzed with respect to the kinetic energy of incident H radical. The probabilities of abstraction and adsorption turn out to be ranging from 0.81 to 0.58 and from 0.19 to 0.42, respectively, while that of reflection almost zero. As initial kinetic energy of the impinging atom increases, the reaction probability of abstraction decreases and that of absorption increases. Metastable H-absorbed atomic configurations are also derived by optimizing the structures obtained in the impinging dynamics calculations. They are candidates of the so-called reservoir site which is a key to understand the unity hydrogen coverage observed after an exposure to gaseous H atom ambient despite existing residual vacant sites due to abstraction.

Surface reconstruction of ultrathin silicon nanosheets

Si nanosheets are a promising candidate material for nanoscale devices but a thorough understanding of their surface properties is still lacking. Here we find, using first-principles molecular-dynamics calculations, a new surface structure specific to a double-layer Si nanosheet. The new surface structure, which can be labeled as Si(1 1 1)-2 × 2 in the same fashion as the bulk Si surface, is formed during surface reconstruction at finite temperature. The reconstructed nanosheet surface consists of highly distorted tetrahedra as on the Si(1 1 1)-2 × 1 surface, but its electronic band structure is markedly different from that of Si(1 1 1)-2 × 1. The vibrational properties of the reconstructed Si nanosheet are also found to reflect the distortion in the tetrahedral order.

A computational study of ultrafast acid dissociation and acid–base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation

We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa∼0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ∼50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ∼1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 Å can take place on a sub-picosecond timescale.

Structural and optical properties of liquid CO2 for pressures up to 1 TPa

We report on the use of first-principles molecular dynamics calculations to examine properties of liquid carbon dioxide in the pressure-temperature range of 0-1 TPa and 200-100 000 K. The computed equations of state points are used to predict a series of shock Hugoniots with initial starting conditions that are relevant to existing and ongoing shock-wave experiments. A comparison with published measurements up to 70 GPa shows excellent agreement. We find that the liquid undergoes a gradual phase transition along the Hugoniot and have characterized this transition based on changes in bonding and structural properties as well as the conductivity and reflectivity of the fluid.

Pressure-Induced Intermolecular Interactions in Crystalline Silane-Hydrogen

The structure and dynamics of a recently discovered solid silane-hydrogen complex under high pressure are elucidated with first-principles molecular dynamics calculations. A structure with orientationally disordered silane and hydrogen with their centers of mass arranged in a distinctive manner are found. Natural bond orbital analysis reveals that perturbative donor-acceptor interactions between the two molecular species are enhanced by pressure. The experimentally observed anticorrelated pressure-frequency dependency is a consequence of these novel interactions. Moreover, the experimentally observed multiple Raman peaks of H2 can be explained by temporal changes in the environment due to deviations of the lattice parameters from the ideal cubic lattice.

First-Principles Characterization of Amorphous Phases of MB12H12, M = Mg, Ca

Complex borohydrides have been studied as candidate materials for vehicular hydrogen storage. In particular, M(BH4)2, where M = Mg or Ca, has received considerable attention because of its high gravimetric capacity for H2. Experimental observations indicate an initial decomposition reaction: 6M(BH4)2 → 5MH2 + MB12H12 + 13H2, where the MB12H12 species are amorphous. We use first-principles density functional theory to study the structural and energetic properties of MB12H12. The purpose of these calculations is to investigate why these materials form amorphous structures. We have identified two possible reasons for MB12H12 adopting apparently amorphous rather than crystalline structures. First, our calculations reveal a large number of structurally distinct polymorphs having near-degenerate energies. We simulate an X-ray diffraction (XRD) pattern for each polymorph and compute the Boltzmann-averaged XRD patterns for MgB12H12 and CaB12H12. These average patterns appear to be amorphous, having very broad peaks. Therefore, we predict that the amorphous MB12H12 materials observed experimentally may be an intimate mixture of a very large number of structurally distinct crystallites. Second, our first-principles molecular dynamics calculations indicate that cations are highly mobile near room temperature; analysis of cation radial distribution functions gives liquid-like rather than solid-like features that could also result in an experimental observation of an amorphous XRD pattern near room temperature.

Crystal structure and elastic properties of ZrB compared with ZrB 2: A first-principles study

The existences of potential crystal structures of ZrB and ZrB 2 are studied by means of first-principles molecular dynamics calculations. The face-centered cubic ZrB (space group Fm-3 m, No. 225) with lattice constant a = 4.900 Å and hexagonal ZrB 2 (space group P6/mmm, No. 191) with a = 3.170 Å and c = 3.544 Å have been proved to be both mechanically and dynamically stable. The optimized lattice parameters for both ZrB and ZrB 2 agree with both the experimental data and previous theoretical calculations. Basic elastic properties of ZrB compared with ZrB 2 using the first-principles calculations are investigated. The bulk moduli 160.6 and 229.1 GPa, shear moduli 102.7 and 210.5 GPa, Young’s moduli 253.9 and 483.5 GPa, and Poisson ratios 0.2365 and 0.1483, are obtained for ZrB and ZrB 2, respectively. Density of state has been explored to discuss the difference of electronic structure between ZrB and ZrB 2. The reasons of lower Young’s moduli of ZrB compared with that of ZrB 2 are discussed as well.

Impact of strain on the surface properties of transition metal carbide films: First-principles study

The effect of in-plane lattice strain on the atomic and electronic properties of low-index transition metal (M=Ti, Nb, and Ta) carbide surfaces is studied by first-principles molecular dynamics calculations using a pseudopotential plane-wave technique. The most stable cubic rock-salt phase is considered for carbides. The first-principle study of various [(001), (110), and metal-terminated (111)] carbide surfaces reveals that both compressive and tensile strains strongly affect surface relaxation and electronic properties (work function values and band structures). The most stable (001) carbide surfaces exhibit rumpling between transition metal and carbon atoms in the topmost surface layers, which depends on the applied strain. The work function (WF) for the metal-terminated (111) surfaces varies monotonically, rather strongly depending on the applied strain (the range of variation reaches about 1 eV), while the WF for the (001) surface varies nonmonotonically with a much smaller resulting variation over the wide range of the applied strains. Surface energy calculations show that surface stability is also governed by the applied strain.

Structures of the icosahedral clusters in Ni–Nb–Zr–H glassy alloys determined by first-principles molecular dynamics calculation and XAFS measurements

To elucidate the hydrogen localization sites in the atomic clusters of Ni–Nb–Zr–H glassy alloys exhibiting room-temperature Coulomb oscillation, we investigated the effect of hydrogen on the electronic state of the elements forming the glassy alloys, as well as the coordinating position of the hydrogen atoms, by X-ray absorption fine structure (XAFS) analysis, referencing theoretical simulation results. The XANES (X-ray absorption near edge structure) part of the XAFS spectra for each (Ni, Zr and Nb) K-edge of (Ni 0.36Nb 0.24Zr 0.40) 89H 11 shows clear multiple scattering effects caused by charged hydrogen atoms. The distorted Ni 5Zr 5Nb 3 cluster with the maximum size of 0.55 nm is characterized by five Ni atoms constituting half a pentahedron and an opposite pentahedral Zr–Nb assembly. For the hydrogen localization sites, the first-principles calculations show that there are two Zr–Zr–Nb–Nb, four Zr–Zr–Zr–Nb, two Zr–Zr–Nb–Ni and two Zr–Zr–Zr–Ni tetrahedrons, in the order of stability.

First-principles studies of liquid lithium under pressure

Effects of compression on the structural and electronic properties of liquid lithium areinvestigated with first-principles molecular dynamics calculations. Within a largepressure range up to 60 GPa, along isotherms from 600 to 1000 K, several structuraltransformations were found. The liquid structures at high pressure are foundto be not sensitive to the temperature within this range. It is shown that theradial distribution functions broadly resemble the corresponding solid phases,particularly at low pressures. The evolution of the electronic structure under pressurealso shows a remarkable similarity to the underlying solid. However, detailedanalyses of the temporal liquid inherent structures show that the instantaneousshort-range order may differ significantly from the underlying known solid phase.

Concerted Hydrogen-Bond Dynamics in the Transport Mechanism of the Hydrated Proton: A First-Principles Molecular Dynamics Study

First-principles molecular dynamics calculations performed in a fully converged basis set are used to reveal new details about the mechanism of the anomalous proton-transport process in water, a fundamental question dating back over 200 years. By separating actual structural diffusion from simple rattling events, wherein a proton shuttles forth and back in a hydrogen bond, it is found that the former are driven by a concerted mechanism in which hydronium begins to accept a hydrogen bond from a donor water molecule while the proton-receiving water molecule simultaneously loses one of its acceptor hydrogen bonds. The kinetics of the process are found to be in good agreement with recent experiments.