Tight-binding Molecular Dynamics Simulations Research Articles

Divide-and-Conquer-Type Density-Functional Tight-Binding Simulations of Hydroxide Ion Diffusion in Bulk Water.

The diffusion of the hydroxide ion in bulk water was examined by linear-scaling divide-and-conquer density-functional tight-binding molecular dynamics (DC-DFTB-MD) simulations using three different-sized unit cells that contained 522, 1050, and 4999 water molecules as well as one hydroxide ion. The repulsive potential for the oxygen-oxygen pair was improved by iterative Boltzmann inversion, which adjusted the radial distribution function of DFTB-MD simulations to that of the reference density functional theory-MD one. The calculated diffusion coefficients and the Arrhenius diffusion barrier were in good agreement with experimental results. The results of the hydroxide ion coordination number distribution and potential of mean force analyses supported a dynamical hypercoordination diffusion mechanism.

Point defects in turbostratic stacked bilayer graphene.

The special properties of graphene can be largely influenced by point defects in the lattice. However, TEM studies of topological defects in few-layered graphene have rarely been reported. In this work, the two simplest forms of point defects monovacancy and divacancy in twisted bilayer graphene are characterized using aberration-corrected transmission electron microscopy (AC-TEM) at 80 kV. A convenient approach by using a negative mask in the fast Fourier transform (FFT) has been applied to separate the image signal of the two graphene layers. In the study combined with density functional theory (DFT) calculations and tight-binding molecular dynamics simulations, the analysis of the defect structure and movement shows the stability and migration behavior of both defects. DFT calculations indicate that the migration of monovacancy in bilayer graphene needs to overcome a higher energy barrier.

Theoretical Investigation of Molecular and Electronic Structures of Buckminsterfullerene-Silicon Quantum Dot Systems.

Density functional theory (DFT) and density functional tight binding (DFTB) molecular dynamics (DFTB/MD) simulations of embedding and relaxation of buckminsterfullerene C60 molecules chemisorbed on (001) and (111) surfaces and inside bulk silicon lattice were performed. DFT calculations of chemisorbed fullerenes on both surfaces show that the C60 molecule deformation was very small and the C60 binding energies were roughly ∼4 eV. The charge analysis shows that the C60 molecule charges on (001) and (111) surfaces were between -2 and -3.5 electrons, respectively, that correlates well with the number of C-Si bonds linking the fullerene molecule and the silicon surface. DFT calculations of the C60 molecule inside bulk silicon confirm that the C60 molecule remains stable with the deformation energy values of between 11 and 15 eV for geometries with different C60 configurations. The formation of some C-Si bonds causes local silicon amorphization and corresponding electronic charge uptake on the embedded fullerene cages. Charge analysis confirms that a single C60 molecule can accept up to 20 excessive electrons that can be used in practice, wherein the main charge contribution is located on the fullerene's carbon atoms bonded to silicon atoms. These DFT calculations correlate well with DFTB/MD simulations of the embedding process. In this process, the C60 molecule was placed on the top of the Si(111) surface, and it was further exposed by a stream of silicon dimers, resulting in subsequent overgrowth by silicon.

Self-organised formation of nanotubes from graphene ribbons. A molecular dynamics study

The conditions for self-organised formations of carbon nanotubes from two parallel graphene ribbons were studied in a density functional adjusted tight binding molecular dynamics simulation. We have found that the seemingly trivial process is significantly limited by the thermal motion of the carbon atoms. There are further difficulties as well, primarily the unfavourable position of the atoms at the edges of the zigzag graphene ribbons. In repeated molecular dynamics runs we analysed the conditions of perfect coalescences, the influence of the substrate and the impact of the zigzag graphene ribbon positions. We have obtained that contrary to the abovementioned unfavourable conditions perfect nanotube production can be obtained using substrates. As the positioning of the substrate can be made with piezoelectric devices, this can significantly help the experimental realisation of the nanotube formation as well.

In Situ Atomic Level Dynamics of Heterogeneous Nucleation and Growth of Graphene from Inorganic Nanoparticle Seeds.

An in situ heating holder inside an aberration-corrected transmission electron microscope (AC-TEM) is used to investigate the real-time atomic level dynamics associated with heterogeneous nucleation and growth of graphene from Au nanoparticle seeds. Heating monolayer graphene to an elevated temperature of 800 °C removes the majority of amorphous carbon adsorbates and leaves a clean surface. The aggregation of Au impurity atoms into nanoparticle clusters that are bound to the surface of monolayer graphene causes nucleation of secondary graphene layers from carbon feedstock present within the microscope chamber. This enables the in situ study of heterogeneous nucleation and growth of graphene at the atomic level. We show that the growth mechanism consists of alternating C cluster attachment and indentation filling to maintain a uniform growth front of lowest energy. Back-folding of the graphene growth front is observed, followed by a process that involves flipping back and attaching to the surrounding region. We show how the highly polycrystalline graphene seed evolves with time into a higher order crystalline structure using a combination of AC-TEM and tight-binding molecular dynamics (TBMD) simulations. This helps understand the detailed lowest-energy step-by-step pathways associated with grain boundaries (GB) migration and crystallization processes. We find the motion of the GB is discontinuous and mediated by both bond rotation and atom evaporation, supported by density functional theory calculations and TBMD. These results provide insights into the formation of crystalline seed domains that are generated during bottom-up graphene synthesis.

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...

Fragmentation network of doubly charged methionine: Interpretation using graph theory.

The fragmentation of doubly charged gas-phase methionine (HO2CCH(NH2)CH2CH2SCH3) is systematically studied using the self-consistent charge density functional tight-binding molecular dynamics (MD) simulation method. We applied graph theory to analyze the large number of the calculated MD trajectories, which appears to be a highly effective and convenient means of extracting versatile information from the large data. The present theoretical results strongly concur with the earlier studied experimental ones. Essentially, the dication dissociates into acidic group CO2H and basic group C4NSH10. The former may carry a single or no charge and stays intact in most cases, whereas the latter may hold either a single or a double charge and tends to dissociate into smaller fragments. The decay of the basic group is observed to follow the Arrhenius law. The dissociation pathways to CO2H and C4NSH10 and subsequent fragmentations are also supported by ab initio calculations.

Structural features and thermal properties of W/Cu compounds using tight-binding potential calculations

We present an orthogonal tight-binding (TB) potential model for W/Cu binary systems. This model can reasonably predict the electronic structures, elastic properties, and thermodynamics properties of W/Cu systems. Furthermore, by performing the TB Monte Carlo simulations and the TB molecular dynamics simulations, we find that (1) the W(110) surface in the fusion reactor exhibits pre-melting behaviors, (2) W and Cu atoms in a W/Cu binary system prefer to form single element domains, and (3) the interface between a W domain and a Cu domain degrades the transport property of the heat in a W/Cu system significantly.

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.

Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma.

We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C-C and Si-Si bonds are generated. Finally, we conclude that our TB-QCMD etching simulator is effective for designing the optimal conditions for etching processes in which chemical reactions play a significant role.

High kinetic stability of hypercubane: Tight-binding molecular dynamics study

Using tight-binding molecular dynamics simulations we study thermal stability of the hypothetical hydrocarbon hypercube or tesseract which is called hypercubane over the wide temperature range T=1000⿿2000K. We find that hypercubane (in the case of its synthesis) will show high kinetic stability and its lifetime at room temperature will reach ⿼1014s. The molecular dynamics data obtained is confirmed by means of the additional PBE/6-311G(d,p) density functional calculations. Unique channel and final products of the hypercubane decay are also determined.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Topological and Energetic Conditions for Lithographic Production of Carbon Nanotubes from Graphene

Density Functional Based Tight-Binding (DFTB) molecular dynamics (MD) simulations were performed for producing carbon nanotubes from graphene nanoribbons. The constant temperature simulations were controlled with the help of Nosé-Hoover thermostat. In our systematic study we obtained critical curvature energies and determined topological conditions for nanotube production from two parallel graphene nanoribbons. We obtained linear relationship between the curvature energy and the square of the curvature.

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

Tight-Binding Quantum Chemical Molecular Dynamics Simulations of Mechanisms of SiO2 Etching Processes for CF2 and CF3 Radicals

The plasma etching of SiO2 by CF2 and CF3 radicals is investigated by using our etching simulator based on tight-binding quantum chemical molecular dynamics method. During etching simulations, C–F and Si–O bonds dissociate and C–O and Si–F bonds are generated. Moreover, CO, CO2, COF, and COF2 molecules form, which is consistent with previous experimental studies. We also examine the dependence of the etching mechanism of CF2 and CF3 radicals on the kinetic energy of irradiation. At a low kinetic energy of 10 eV, a CF2 radical dissociates more Si–O bonds than a CF3 radical does. This is because the high chemical reactivity of the CF2 diradical accelerates the etching process. At a high kinetic energy of 150 eV, a CF3 radical dissociates more Si–O bonds than a CF2 radical does. This is because a CF3 radical generates a greater number of reactive F atoms than a CF2 radical does and thus forms more Si–F bonds. Thus, we conclude that our etching simulator modeled the different SiO2 etching mechanisms of CF2 an...

Critical interpretation of CH- and OH- stretching regions for infrared spectra of methanol clusters (CH₃OH)n (n = 2-5) using self-consistent-charge density functional tight-binding molecular dynamics simulations.

Vibrational infrared (IR) spectra of gas-phase O-H⋅⋅⋅O methanol clusters up to pentamer are simulated using self-consistent-charge density functional tight-binding method using two distinct methodologies: standard normal mode analysis and Fourier transform of the dipole time-correlation function. The twofold simulations aim at the direct critical assignment of the C-H stretching region of the recently recorded experimental spectra [H.-L. Han, C. Camacho, H. A. Witek, and Y.-P. Lee, J. Chem. Phys. 134, 144309 (2011)]. Both approaches confirm the previous assignment (ibid.) of the C-H stretching bands based on the B3LYP/ANO1 harmonic frequencies, showing that ν3, ν9, and ν2 C-H stretching modes of the proton-accepting (PA) and proton-donating (PD) methanol monomers experience only small splittings upon the cluster formation. This finding is in sharp discord with the assignment based on anharmonic B3LYP/VPT2/ANO1 vibrational frequencies (ibid.), suggesting that some procedural faults, likely related to the breakdown of the perturbational vibrational treatment, led the anharmonic calculations astray. The IR spectra based on the Fourier transform of the dipole time-correlation function include new, previously unaccounted for physical factors such as non-zero temperature of the system and large amplitude motions of the clusters. The elevation of temperature results in a considerable non-homogeneous broadening of the observed IR signals, while the presence of large-amplitude motions (methyl group rotations and PA-PD flipping), somewhat surprisingly, does not introduce any new features in the spectrum.

Tight-binding quantum chemical molecular dynamics simulations of the low friction mechanism of fluorine-terminated diamond-like carbon films

The super-low friction mechanism of fluorine-terminated diamond-like carbon (F-terminated DLC) is investigated by using our tight-binding quantum molecular dynamics code and compared with that of hydrogen-terminated DLC (H-terminated DLC). Under a contact pressure of 1 GPa, F- and H-terminated DLC show smooth sliding and low friction coefficients of 0.07 and 0.04, respectively. The ion radius of fluorine is larger than that of hydrogen, which leads to the larger asperity of the F-terminated DLC surface. Thus, the friction coefficient of F-terminated DLC is slightly larger than that of H-terminated DLC. We also perform friction simulations under contact pressures of 3 and 7 GPa. Under a contact pressure of 3 GPa, the friction coefficients are 0.09 and 0.13 for F- and H-terminated DLC, respectively. F-terminated DLC shows the same friction behavior as seen under a contact pressure of 1 GPa, whereas the C–C bond formation reaction is observed at the interface of H-terminated DLC under a contact pressure of 3 GPa, leading to a slightly higher friction coefficient than when under a contact pressure of 1 GPa. Thus, under a contact pressure of 3 GPa, F- and H-terminated DLC show different friction behaviors. Furthermore, under a high contact pressure of 7 GPa, bond formation and dissociation are observed at the friction interface in F- and H-terminated DLC. C–C bond formation is observed more frequently in H-terminated DLC than in F-terminated DLC, and the lifetime of C–C bonds in H-terminated DLC is much longer. At this higher pressure, H-terminated DLC shows a high friction coefficient of 0.42 due to strong C–C bonds at the friction surface, whereas F-terminated DLC shows a low friction coefficient of 0.08. The strong repulsive interaction at the interface of F-terminated DLC that arises from the large negative charge and ion size of fluorine maintains the distance between DLC films under a high contact pressure. This prevents strong C–C bond formation at the friction surface, which results in the low friction properties of F-terminated DLC. We suggest that the friction properties of DLC films under a high contact pressure are improved by F termination.

Nanosecond quantum molecular dynamics simulations of the lithium superionic conductorLi4−xGe1−xPxS4

The microscopic origin of high conductivity at room temperatures in lithium superionic conductors has remained a fundamental unsolved problem, although the recent discovery of ${\mathrm{Li}}_{10}$${\mathrm{GeP}}_{2}$${\mathrm{S}}_{12}$ was a great step toward the application of solid electrolytes. We achieve long-time (2-ns) tight-binding molecular dynamics simulations of ${\mathrm{Li}}_{4\ensuremath{-}x}$${\mathrm{Ge}}_{1\ensuremath{-}x}$${\mathrm{P}}_{x}$${\mathrm{S}}_{4}$ and observe the diffusion process where lithium atoms collectively hop into neighboring lithium sites by kicking the lithium atoms occupying these sites out. Furthermore, it is found that excess lithium atoms or doped lithium vacancies trigger a new diffusion process and drastically reduce the activation energy. We discuss the dynamic properties of lithium atoms in these materials, such as the diffusion constant, the activation energy, and the diffusion path.

Tight-binding Molecular Dynamics Simulation of the Endohedral Complex C4H4@C60

Tight-binding molecular dynamics simulations were carried out to analyze the thermal stability of the tetrahedrane molecule inside the [60]fullerene cage over the temperature range T = 400 − 800 K. The temperature dependence of the endohedral complex lifetime to the moment of tetrahedrane decay was obtained from the numerical experiment. The height of the minimum energy barrier preventing the decomposition of the encapsulated tetrahedrane molecule was found to be similar for the isolated one. Possible channels and final products of its decomposition were also studied.

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.