Density-functional Tight-binding Molecular Dynamics Simulations Research Articles

Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations.

The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.

Annihilation dynamics of a dislocation pair in graphene: Density-functional tight-binding molecular dynamics simulations and first principles study

The time evolution of a dislocation pair in graphene is investigated by performing subnanosecond-scale molecular dynamics simulations based on the density-functional tight-binding method. The simulations show the self-healing behavior of the graphene lattice, resulting in complete annihilation of dislocations, that is, the formation of the pristine graphene structure. To understand the mechanism of the structural developments, first principles calculations are performed for the principal dislocation structures observed in the density-functional tight-binding/molecular dynamics simulations. We reveal the characteristic bonding states in the area around the dislocation structures by bond analyses based on the Wiberg bond index and crystal orbital Hamilton population approaches. The unusual local bonding states mainly originate from geometrical features of the out-of-plane deformation of the dislocation structures. The annihilation processes of dislocations in graphene are discussed in relation to the local bonding states of the dislocation structures.

Artificial neural network correction for density-functional tight-binding molecular dynamics simulations

Abstract

Density-Functional Tight-Binding Molecular Dynamics Simulations of Excess Proton Diffusion in Ice Ih, Ice Ic, Ice III, and Melted Ice VI Phases.

The structural, dynamical, and energetic properties of the excess proton in ice were studied using density-functional tight-binding molecular dynamics simulations. The ice systems investigated herein consisted of low-density hexagonal and cubic crystalline variants (ice Ih and Ic) and high-density structures (ice III and melted ice VI). Analysis of the temperature dependence of radial distribution function and bond order parameters served to characterize the distribution and configuration of hundreds of water molecules in a unit cell. We confirmed that ice Ih and Ic possess higher hexagonal symmetries than ice III and melted ice VI. The estimated Grotthuss shuttling diffusion coefficients in ice were larger than that of liquid water, indicating a slower proton diffusion process in high-density structures than in low-density systems. The energy barriers calculated on the basis of the Arrhenius plot of diffusion coefficients were in reasonable agreement with experimental measurement for ice Ih. Furthermore, the energy barriers for high-density structures were several times larger than those of low-density systems. The simulation results were likely related to the suppression of proton transfer in disordered water configurations, in particular, ice with low hexagonal symmetry.

Divide-and-Conquer Density-Functional Tight-Binding Molecular Dynamics Study on the Formation of Carbamate Ions during CO2 Chemical Absorption in Aqueous Amine Solution

Abstract Divide-and-conquer-type density-functional tight-binding molecular dynamics simulations of the CO2 absorption process in monoethanolamine (MEA) solution have been performed for systems containing thousands of atoms. The formation of carbamate anions has been widely investigated for neutral systems via ab initio molecular dynamics simulations, yet the present study is aimed at identifying the role of hydroxide ions in acid-base equilibrium. The structural and electronic analyses reveal that the hydroxide ion approaches, via Grotthuss-type shuttling, the zwitterionic intermediates and abstracts a proton from the nitrogen atom of MEA. We also estimated the fraction of reacted CO2 and carbamate formed at different initial CO2 concentrations that confirm a high absorbed CO2 concentration decreases the fraction of MEA(C) formed due to the abundance of MEA(Z) in the solution.

Temperature-dependent BN cluster formation dynamics from a boron cluster: Density-functional tight-binding molecular dynamics simulations

The time-evolution dynamics of a boron nitride (BN) cluster from an amorphous B cluster is simulated by quantum chemical molecular dynamics based on the density-functional tight-binding method. In the simulations, N atoms are sequentially supplied around the B cluster in conjunction with the arc-melting BN fullerene synthesis from B-rich compounds. The simulations are performed at 1000, 1500, 2000, 2500, and 3000K, and we run 30 trajectories for 200ps at each temperature. At low temperature (1000K), the BN clusters tend to form stuffed cage structures, characterized by internal BN branched units. As the temperature increases, the proportion of stuffed cage structures decreases, whereas that of cage-like structure increases. At intermediate temperatures (2000 and 2500K), most of the BN clusters develop into hollow structures, exhibiting a strong cage forming preference. At 3000K, the BN clusters tend to form sparse branched chain structures, without forming cage-like structures. Mobility analysis of the cluster atoms at all the temperatures reveals that the transition from a liquid-like state to a solid-like state occurs at 2000 and 2500K, whereas the cluster remains in a solid-like state at 1000K and a liquid-like state at 3000K. The N2 dissociation reactions from the BN cluster proceed through various N2 unit formation processes in the BN cluster. We describe details of the representative N2 unit formation processes classified by the bonding of the cluster N atoms.

Early Decay Mechanism of Shocked ε-CL-20: A Molecular Dynamics Simulation Study

e-2,4,6,8,10,12-Hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) is currently the most powerful explosive commercially available. Nevertheless, the early decay events of shocked e-CL-20 still remain unclear. We perform quantum based self-consistent charge density-functional tight-binding molecular dynamics simulations, in combination with the multiscale shock simulation technique, to reveal the events with four specified shock velocities (Us) of 8 to 11 km/s. We find that the temperature and pressure increases and that the volume reduction is enhanced with increasing shock strength. The ring opening is observed to trigger molecular decay at all four shock conditions; while the sufficient NO2 fission is observed at Us = 8 and 9 km/s, and strongly inhibited at Us = 10 and 11 km/s. Moreover, the evolution of main chemical species, such as active intermediates, stable products, and clusters, is strongly dependent on the shock strength. NO2 and H are dominant in the primary intermediates, responsible for w...

Contrasting mechanisms for CO2 absorption and regeneration processes in aqueous amine solutions: Insights from density-functional tight-binding molecular dynamics simulations

CO2 chemical absorption and regeneration processes in aqueous amine solutions were investigated using density-functional tight-binding molecular dynamics simulations. Extensive analyses of the structural, electronic, and dynamical properties of 100 independent trajectories supported the contrasting mechanisms in the absorption and regeneration processes. In the CO2 absorption process, bicarbonate formed where the hydroxyl anion migrated through the hydrogen-bond network of water molecules, namely, by a Grotthuss-type mechanism. On the other hand, direct proton transfer from the protonated amine to the hydroxyl group of bicarbonate, which is called the ion-pair mechanism, was the key step to the release of CO2.

分割統治型密度汎関数強束縛分子動力学 (DC-DFTB-MD)法の最近の展開

分割統治型密度汎関数強束縛分子動力学 (DC-DFTB-MD)法の最近の展開

Self-consistent-charge density-functional tight-binding molecular dynamics simulations of amorphous TiO2 growth

Molecular dynamics simulations based on self-consistent-charge density-functional tight-binding (SCC-DFTB) energies indicate that upon a single molecular TiO2 impact onto the amorphous TiO2 surface the resulting structure becomes more disordered as demonstrated by calculated pair distribution functions from corresponding trajectories. The obtained results agree well with previous ones using classical modeling and may serve as a benchmark for further development and validation of new forms of empirical potentials.

Collision-induced fusion of twoC60fullerenes: Quantum chemical molecular dynamics simulations

We characterize the collision-induced fusion reaction of buckminsterfullerenes by means of direct self-consistent-charge density-functional tight-binding molecular dynamics simulations. In agreement with experimental data, we find that the highest probability of fusion is for collisions with incident energy range of 120--140 eV. In this energy region, fusion occurs by way of the formation of hot, vibrationally excited peanut-shaped structures within 1 ps. These nanopeanuts further undergo relaxation to short carbon nanotubes and are cooling by evaporation of short carbon chains during the next 200 ps. The size of the fusion product after the evaporation agrees well with the average size of carbon clusters experimentally detected after collisions on the microsecond time scale. The average number of $s{p}^{3}$ carbons in our simulations is in an excellent correlation with experimental cross sections.

Single-walled carbon nanotube growth from a cap fragment on an iron nanoparticle: Density-functional tight-binding molecular dynamics simulations

Growth of a single-walled carbon nanotube (SWNT) from a corannulene cap fragment on an iron cluster is demonstrated using density-functional tight-binding molecular dynamics simulations of laser synthesis. In order to explore multiple reaction pathways for the cap fragment to evolve into tubular form on the iron surface, reaction dynamics between the metal-bound cap fragment and gas-phase carbon atoms were investigated. It is found that rapid growth of the cap fragment can take place when carbon atoms are supplied in the vicinity of the cap fragment. In this reaction process, a high-density supply of add atoms leads also to rearrangements of existing $s{p}^{2}$-carbon-cap structures involving the formation of pentagons and heptagons as long-lived defects, while short-lived four- and eight-membered rings and short polyyne chains appear during the dynamics as important intermediate structures, facilitating growth.

Density-functional tight-binding molecular dynamics simulations of SWCNT growth by surface carbon diffusion on an iron cluster

Iron-catalyzed SWCNT growth by carbon diffusion starting from a carbon cap has been demonstrated in density-functional tight-binding molecular dynamics simulations. A C 40 (5,5) SWCNT cap attached to an Fe 38 cluster was employed as initial model system. After 40 carbon atoms were supplied onto the iron surface for 20 ps, dynamics were continued for 160 ps without supply of further carbon feedstock. Growth of the SWCNT sidewall is mainly due to surface-diffusion of short carbon chains, and to a lesser degree due to sub-surface diffusion. Newly created rings consist only of pentagons and hexagons, while heptagons are infrequent and short-lived, which seems to be caused by the slower, more ordered sidewall growth due to the diffusion process.

Investigation of Possible Structures of Silicon Nanotubes via Density-Functional Tight-Binding Molecular Dynamics Simulations and ab Initio Calculations

We show, computationally, that single-walled silicon nanotubes (SiNTs) can adopt a number of distorted tubular structures, representing respective local energy minima, depending on the theory used and the initial models adopted. In particular, "gearlike" structures containing alternating sp(3)-like and sp(2)-like silicon local configurations have been found to be the dominant structural form for SiNTs via density-functional tight-binding molecular dynamics simulations (followed by geometrical optimization using Hartree-Fock or density function theory) at moderate temperatures (below 100 K). The gearlike structures of SiNTs deviate considerably from, and are energetically more stable than, the smooth-walled tubes (the silicon analogues of single-walled carbon nanotubes). They are, however, energetically less favorable than the "string-bean-like" SiNT structures previously derived from semiempirical molecular orbital calculations. The energetics and the structures of gearlike SiNTs are shown to depend primarily on the diameter of the tube, irrespective of the type (zigzag, armchair, or chiral). In contrast, the energy gap is very sensitive to both the diameter and the type of the nanotube.

The structure and stability of Si60 and Ge60 cages: a computational study.

Structural studies of fullerene-like Si(60) and Ge(60) cages using ab initio methods were augmented by density functional tight-binding molecular dynamics (DFTB-MD) simulations of finite temperature effects. Neither the perfect I(h) symmetry nor the distorted T(h) structures are true minima. The energies of both are high relative to distorted, lower symmetry minima, C(i) and T, respectively, which still preserve C(60)-type connectivity. Both Si(60) and Ge(60) favor C(i) symmetry cages in which Si and Ge vertexes exhibit either near-trigonal or pyramidal geometries. These structural variations imply significant reactivity differences between different positions. The small magnetic shielding effects (NICS) indicate that aromaticity is not important in these systems. The inorganic fullerene cages have lower stabilities compared with their carbon analogs. Si(60) is stable towards spontaneous disintegration up to 700 K according to DFTB-MD simulations, and thus has potential for experimental observation. In contrast, Ge(60) preserves its cage structure only up to 200 K.

Study of the misfit dislocations in semiconductor heterostructures by density functional TB molecular dynamics and path probability methods

The atomic and electronic structures of semiconductor heterostructures are studied using the density-functional tight-binding molecular dynamics simulations. Atomic structures of misfit dislocations both edge type 1/2 〈110〉 (001) and 60° dislocations in the semiconductor heterostructures, like Ge/Si(001), InAs/GaAs and InP/GaAs(001) systems are studied by using order of N [O(N)] calculational method. The path probability method in the statistical physics is used to study the influence of the interface disorder on the atomistic properties of the semiconductor heterostructures. It is shown that the compositional intermixing influences quite significantly on the electronic and thermodynamic properties of semiconductor heterostructures, especially on the critical layer thickness hc for the generation of misfit dislocations.