Reactive Empirical Bond Order Potential Research Articles

Atomistic simulations of nanoindentation on the basal plane of crystalline molybdenum disulfide (MoS2)

In the present work, nanoindentation on the basal surface of a crystalline molybdenum disulfide (MoS2) thin film is investigated by molecular statics (MS) calculations. A previously parameterized interatomic potential combining the reactive empirical bond-order and Lennard-Jones potentials is implemented into the LAMMPS molecular simulation package and refined for improved prediction of the mechanical properties of MoS2 at athermal conditions. Nanoindentation simulations are performed using three indenter sizes with specific focus on the incipient plastic deformation event within the MoS2single crystal. MS calculations show that a local phase transformation occurs beneath the indenter at plastic yield without the presence of broken Mo–S bonds. The structural characteristics of the phase transformation are captured using a slip vector analysis. The nanoindentation simulations provide insight into the mechanical response of MoS2 during contact deformation characteristic of both synthesis and application for better design of MoS2 nanoparticle lubricants.

The atomic scale structure of nanographene platelets studied by X-ray diffraction, high-resolution transmission electron microscopy and molecular dynamics

The atomic structure of commercially available nanographene platelets has been studied by high energy X-ray diffraction, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy and molecular dynamics simulations using the reactive empirical bond order potential. Atomic models of the structure have been constructed and then relaxed using the molecular dynamics method and the model based simulations are compared with the experimental data both in reciprocal and real space. All model relaxations and the X-ray diffraction experiments have been carried out at 300K. The proposed models consisting of about 2500 carbon atoms arranged within four graphitic layers with a diameter of 46Å, reproduced correctly all features of the experimental data. The atomic arrangement within an individual layer can be described in terms of the paracrystalline ordering, in which lattice distortions propagate proportionally to the square root of interatomic distances. The paracrystalline structure was simulated by introducing the topological point defects such as the Stone–Thrower–Wales defects, single- and double-vacancies, randomly distributed in the network. Such defects lead to curvature of individual layers and this effect was also analyzed. The generated models are related to the observations by high-resolution transmission electron microscopy.

Thermal Vibrations of Single-Layered Graphene Sheets by Molecular Dynamics

Dynamics problems in the thermal vibration of single-layered graphene sheets (SLGSs) are investigated using molecular dynamics (MD) method based on the Brenner's second-generation reactive empirical bond order (REBO) potential. The in plane stiffness and Poisson ratio of SLGSs are calculated by stretching SLGSs. The effective thickness of SLGSs is obtained by MD simulations for the thermal vibration of SLGSs through the natural frequency. The natural frequencies for SLGSs of different sizes with initial stress in different temperatures are calculated through MD. The thin plate theory can predict the MD results very well in a certain range of strain. For the nonlinear relation between stress and strain when the strain is very large, the deviation between the MD results and plate theory becomes larger when the strain increases. The difference between the plate theory and the MD results becomes more and more obvious, when the size of graphene sheet is very small.

Reactive Bond-Order Potential for Si-, C-, and H-Containing Materials

A new bond-order potential for modeling systems containing silicon, carbon, and hydrogen, such as organosilicon molecules (CxSiyHz), solid silicon, solid carbon, and alloys of silicon and carbon, is presented. This reactive potential utilizes the formalism of the second-generation reactive empirical bond-order potential (REBO) [Brenner et al. J. Phys.: Condens. Matter 2002, 14, 783] for hydrocarbons and the REBO parameters for silicon [Schall, Gao, Harrison. Phys. Rev. B 2008, 77, 115209]. Modifications to the hydrocarbon REBO potential were made to improve the description of three-atom type systems. The widespread use of Brenner’s REBO potential, its ability to model a wide range of hydrocarbon materials, and the existence of parameters for several atom types are some of the motivating factors for obtaining this Si–C–H (2B-SiCH) parametrization. The usefulness and flexibility of this potential is demonstrated by examining the properties of organosilicon molecules, the bulk, surface, and defect properties of SiC, and the properties of amorphous silicon carbide.

Formation and Classification of Amorphous Carbon by Molecular Dynamics Simulation

By using molecular dynamics simulation, the formation mechanisms of amorphous carbon in a particular sp3-rich structure were researched. The problem that reactive empirical bond order potential cannot represent amorphous carbon properly was resolved in the transition process from graphite to diamond by a high pressure and the deposition of amorphous carbon thin films. Moreover, a new potential model, which is based on the electron distribution simplified as a point charge, was developed by using the downfolding method. As a result, the molecular dynamics simulation with the new potential could demonstrate the transition from graphite to diamond at the pressure of 15 GPa, which agrees with an experimental report and the deposition of sp3-rich amorphous carbon.

Mechanical behavior of MoS2 nanotubes under compression, tension, and torsion from molecular dynamics simulations

The mechanical behavior of different types of single-walled and double-walled MoS2 nanotubes when subjected to external compressive, tensile, and torsional loading is investigated using classical molecular dynamics simulations. The forces on the atoms are determined using a reactive empirical bond-order potential parameterized for Mo-S systems. The simulations report on the elastic properties of the different MoS2 nanotube systems as well as the interrelationships between the buckling behavior and the structural parameters of the nanotubes, such as length, diameter, chirality, and number of walls. The simulations predict that the most important factor influencing mechanical response is the number of walls present and, to a lesser extent, the diameters of the nanotubes, with the other structural parameters predicted to have little effect on the results over the range investigated. These findings are consistent with reported density functional theory calculations and experimental data for WS2 and MoS2 nanotubes.

Graphene-like structure of activated anthracites

The structure of a series of activated carbons prepared from anthracite by chemical activation has been studied using wide-angle x-ray scattering, molecular dynamics and Raman spectroscopy. The BET surface areas of the investigated samples are in the range 1500–3430 m2 g−1 and the average pore sizes vary from 0.75 to 1.35 nm. The diffraction measurements were carried out to a maximum value of the scattering vector Kmax = 22 Å−1. The obtained diffraction data have been converted to a real space representation in the form of the pair correlation function. The structure of the studied samples consists of one or two graphite-like layers, stacked without spatial correlations. The size of the ordered layer region is approximately 24 Å. The atomic arrangement within an individual layer has been described in terms of paracrystalline ordering, in which lattice distortions are propagated proportionally to the square root of inter-atomic distances. The paracrystalline structure has been simulated by introducing the Stone–Thrower–Wales, mono-vacancy and di-vacancy defects, randomly distributed in the network. These defects lead to the formation of a defected network with the presence of non-hexagonal rings in which distortion of the structure extends outside of a defect region. Computer generated structural models have been relaxed at room temperature using the reactive empirical bond order potential for intra-layer interactions and the Lennard-Jones potential for inter-layer interactions. For such generated models the structure factors and the pair correlation functions were computed. A good agreement between the simulation results and the experimental data in both reciprocal and real space provides evidence for the correctness of the proposed models. The Raman data support the validity of these models. Porosity of the activated anthracites is discussed in relation to their defective structure.

Influence of Intertube Additional Atoms on Sliding Behaviors of Double-Walled Carbon Nanotube

The effects of intertube additional atoms on the sliding behaviors of double-walled carbon nanotubes (DWCNTs) are investigated using molecular dynamics (MD) simulation method. The interaction between carbon atoms is modeled using the second-generation reactive empirical bond-order potential coupled with the Lennard—Jones potential. The simulations indicate that intertube additional atoms of DWCNT can significantly enhance the load transfer between neighboring tubes of DWCNT. The improvement in load transfer is guaranteed by the addition of intertube atoms which are covalently bonded to the inner and outer tubes of DWCNT. The results also show that the sliding behaviors of DWCNT are strongly dependent of additional atom numbers. The results presented here demonstrate that the superior mechanical properties of DWCNT can be realized by controlling intertube coupling. The general conclusions derived from this work may be of importance in devising high-performance CNT composites.

Modified reactive empirical bond-order potential for heterogeneous bonding environments

An improvement to the AIREBO potential for hydrocarbons is presented in which contributions to the bond order are determined by the local bonding environment around the bond, rather than the average of the environments around the two constituent atoms. This bond-centric approach decreases the errors by ~80% in the fullerene-type systems for which the original approach leads to the most severe errors. With the newly developed and parameterized method, energy errors are less than 0.7 eV for a collection of hydrocarbon molecules not used in the fitting. This modified AIREBO potential is expected to be more useful not only for the molecular hydrocarbons and fullerene isomers studied here, but also for the full range of carbon and hydrocarbon systems to which the AIREBO potential has been applied.

Adsorption of colloid nanoparticles on carbon nanotubes studied by means of molecular dynamics simulations

In this work we deal with interactions of colloid nanoparticles with carbon nanotubes across water and some organic solvents. The aim of this work is to track the range of dispersion interactions between these two species as functions of their structure, local geometry, role of solvents applied, etc. The studies are based on molecular dynamics simulations and the structure of carbon nanotubes (single and multi-walled) are described according to Adaptive Intermolecular Reactive Empirical Bond Order potential while interaction of colloid nanoparticles with other components of the system involves the Hamaker potential. Thus, we are able to study energetic effects related to position of nanoparticles on nanotubes surfaces, nanotubes flexibility and effects related to chemical nature of solvents used. We found that single walled nanotubes interact stronger at sidewalls while multi-walled on tips. Metallic nanoparticles lead to deformation of the nanotubes structures and reveal huge energy of dispersion interactions, comparable to chemical bonds energy. Silica covered metallic nanoparticles interact weakly and their behavior on the nanotubes surfaces can be additionally affected by their charges when water is considered as solvent. We found that in that case the diffusion of silica covered nanoparticles is anomalous and obeys the sub-diffusion mechanism in crowded systems. We also found that preferential location of nanoparticles on nanotubes tips is difficult to realize by controlling only physical conditions under which the system is considered.

Assessment of the resonance frequency of cantilever carbon nanocones using molecular dynamics simulation

The resonance frequencies of cantilever carbon nanocones (CNCs) up to 4 nm in height are determined using molecular dynamics simulation based on adaptive intermolecular reactive empirical bond order potential. The frequency content of the free vibrations of CNCs under a lateral initial excitation at the tip is analyzed using fast Fourier transformation, and the resonance frequencies are obtained. The results are reported for various samples to investigate the dependency of the resonance frequency to the geometrical parameters and temperature of CNCs.

Hyperthermal Atomic Oxygen and Argon Modification of Polymer Surfaces Investigated by Molecular Dynamics Simulations

The deposition of reactive and unreactive particles on polymer surfaces at hyperthermal incident energies is investigated using classical molecular dynamics simulations. The forces are calculated with the second-generation reactive empirical bond-order potential with modified parameters for C,H,O interactions. Three prototypical polymers, polyethylene (PE), polypropylene (PP) and polystyrene (PS), are modified by atomic oxygen and argon that are deposited with kinetic energies of 25, 50 and 100 eV. The non-reactive argon is predicted to primarily break carbon–carbon bonds and remove hydrogen as a secondary process, while the reactive oxygen is more efficient at removing hydrogen during new bond formation with the polymer. The PE and PP are found to have similar responses to hyperthermal argon and oxygen deposition, while PS is found to be the most susceptible to oxygen modification.

Molecular dynamics simulation of energetic hydrogen isotopes bombarding the crystalline graphite(001)

Molecular dynamics simulation is applied to the investigation of the isotopic effects during a hydrogen isotope atom bombarding the crystalline graphite containing four graphene sheets. Both Brenner's reactive empirical bond order potential and Ito's interlayer intermolecular potential are adopted to represent `àBAB" stacking of graphite. The simulation results reveal that the mass of the incident species has a big influence on the absorption on and the reflection from the upside graphite surface, the peaks of which shift toward higher end side of incident energy as the mass increases. The absorption coefficient of the incident tritium is large, compared with that of the incident either hydrogen or deuterium. To penetrate the four- sheet graphite at some striking locations, deuterium and tritium need more kinetic energy. It is found that both the mass and the incident energy of the incident species affect the energy transfer to background substrate. These results would be important for understanding the tritium retention occurring in fusion devices.

Self-Assembly of Graphene Nanoribbons with Unsaturated Edges

ABSTRACTWe studied the self-assembly mechanisms of Graphene Nanoribbon (GNR) with unsaturated edges and demonstrated the ability of GNR to self-assemble into novel stable structures. We proposed three mechanisms which dictate the self-assembly evolution of GNR with unsaturated edges. Using the Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO) potential, we performed molecular dynamics simulations on initially-planar GNRs with unsaturated edges. The simulation results showed that the self-assembly mechanisms and final conformations of the GNRs correlate well with the proposed GNR self-assembly mechanisms. Furthermore, the simulations also showed the ability of a narrow GNR to self-assemble into various nanostructures, such as tapered graphene nano-rings and graphene nanoscrolls with an embedded nanotube.

Mechanisms of Ion-Beam Modification of Terthiophene Oligomers from Atomistic Simulations

Ion-beam deposition on organic surfaces is a common approach to induce surface modification. Here, the difference in argon and polyatomic thiophene hyperthermal deposition on terthiophene oligomers is explored in classical molecular dynamics simulations. The forces on the atoms are determined using the second-generation reactive empirical bond order potential for hydrocarbons that is modified to include sulfur. Details of the potential fit and parametrization are provided. The simulations predict that the thiophene induces fracture of the terthiophene rings while largely retaining the chemical structure of terthiophene. Conversely, argon is predicted to alter the number of carbons within the terthiophene during modification.

Reaction between graphene and hydrogen under oblique injection

The reaction between a graphene sheet and an incident hydrogen atom was clarified through a classical molecular dynamics simulation based on the modified Brenner’s reactive empirical bond order potential under the NVE condition, in which the number of particles (N), volume (V), and total energy (E) are conserved. The energy dependence of three types of reaction (i.e., adsorption, reflection, and penetration) for the oblique injection of a hydrogen atom into a graphene sheet was investigated. The reaction depends on the energy and two angular parameters, namely, the polar angle θ and the azimuthal angle φ of the incident hydrogen atom. The reflection and adsorption rates were found to strongly depend on θ. This dependence is caused by the three-dimensional structure of small potential barriers that cover adsorption sites (i.e., a local minimum point of the potential energy). The θ dependence of the penetration rates was observed. The penetration rates are proportional to cos2θ. The φ dependence of the penetration rates was also observed when θ is large.

A deformation–fluctuation hybrid method for fast evaluation of elastic constants with many-body potentials

A universal, fast deformation–fluctuation hybrid approach with the merits of both the direct and fluctuation methods for evaluation of elastic constants is proposed. Deformation is shown to provide an inherent connection between the latter two methods. Based on this finding, the hybrid method utilizes group perturbation of atoms by means of six homogeneous deformations for fast evaluation of the Born term in the stress fluctuation method. The hybrid method is tested with three typical and widely used many-body potentials, i.e., for crystalline silicon with a Stillinger–Weber potential, for crystalline copper with second nearest-neighbor modified embedded-atom method and for diamond with a second-generation reactive empirical bond order potential. The calculated elastic constants agree well with either the theoretical or experimental results for all three cases. The hybrid method is especially valuable for complicated many-body potentials for which the analytical second derivative of the energy is challenging or impractical to obtain.

Transformation of nano-diamonds to carbon nano-onions studied by X-ray diffraction and molecular dynamics

The transformation of ultra-dispersed diamond nanoparticles of about 50 Å in diameter into carbon nano-onions has been studied by high-energy X-ray diffraction and molecular dynamics simulations using the reactive empirical bond order potential. Structural models have been constructed for pristine nano-diamonds and nano-diamonds annealed at 1673 K, 1973 K and 2273 K. These models have been relaxed using the molecular dynamics method and the model based structure factors and the pair correlation functions are compared with the experimental data. All model relaxations and the X-ray diffraction experiments have been carried out at 300 K. Two starting models consisting of 5460 atoms with a single diamond core and an amorphous-like outer shell and for a twinned diamond core and a similar amorphous outer shell containing in total about 13,500 atoms reproduced correctly features of the experimental data. The atomic models of two intermediate and final fully graphitized structures, consisting of the same numbers of atoms and containing the series of defected icosahedral fullerenes describe satisfactorily the atomic arrangements for the samples annealed at 1673 K, 1973 K and 2273 K. The generated models of the nano-diamonds and the nano-onions are related to the previous observations by high-resolution transmission electron microscopy.

Properties on the edge: graphene edge energies, edge stresses, edge warping, and the Wulff shape of graphene flakes

It has been shown that the broken bonds of an unreconstructed graphene edge generate compressive edge stresses leading to edge warping. Here, we investigate edge energies and edge stresses of graphene nanoribbons with arbitrary orientations from armchair to zigzag, considering both flat and warped edge shapes in the presence and absence of hydrogen. We use the second generation reactive empirical bond order potential to calculate the edge energies and stresses for clean and hydrogenated edges. Using these energies, we perform a Wulff construction to determine the equilibrium shapes of flat graphene flakes as a function of hydrogen chemical potential. While edge stresses for clean, flat edges are compressive, they become tensile if allowed to warp. Conversely, we find that edge energies change little (∼1%) with edge warping. Hydrogenation of the edges virtually eliminates both the edge energy and edge stresses. For warped edges an approximately linear relationship is found between amplitudes and wavelengths. The equilibrium shape of a graphene flake is determined by the value of the hydrogen chemical potential. For very small (and large) values of it the flakes have a nearly hexagonal (dodecagon) shape with zigzag oriented edges, while for intermediate values graphene flakes are found with complex shapes.

Methane in carbon nanotube: molecular dynamics simulation

The behaviour of methane molecules inside carbon nanotubes at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by a rigid set of five interaction centres localized on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamic properties of confined molecules are considered. The simulation results show the decreases of the diffusion coefficient of methane molecules with density. At higher densities diffusion coefficient values are almost independent of molecular shape, but at low densities one observes faster motion of the super-atom molecule than that for the tetrahedral model of the molecule. For loadings of methane considered here the nanotube flexibility, introduced by the reactive empirical bond order (REBO) potential for interactions between carbon atoms of nanotube, does not have an effect on diffusivity of methane molecules, and its impact on the molecular structure is weak. It is found that methane molecules in the vicinity of the nanotube wall show tripod orientation with respect to the nanotube surface.