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In this study, a molecular dynamics (MD) study has been performed on composition and temperature dependences of mechanical properties of CdTe[Formula: see text]Se[Formula: see text] ([Formula: see text], 0.50 and 0.75) nanowires with a diameter of 6.93 nm. The simulation results show that CdTe[Formula: see text]Se[Formula: see text] nanowire seems to be more ductile, whereas CdTe[Formula: see text]Se[Formula: see text] nanowire seems to be more brittle at 1 K. Moreover, the temperature and composition exert significant effects on the mechanical properties of CdTeSe nanowires under stretching. We conclude that the dominancy of Se atoms yields a higher stability and strength at the lower temperature of 1 K, whilst it is the same for the nanowires with both higher Te and Se contents at the higher temperature of 300 K. The radial distribution functions (RDFs) have also been calculated for the CdTeSe nanowires based on the pair separation distance at 1 and 300 K.

International audience; An analytical interatomic bond order potential for the Be–O system is presented. The potential is fitted and compared to a large database of bulk BeO and point defect properties obtained using density functional theory. Its main applications include simulations of plasma-surface interactions involving oxygen or oxide layers on beryllium, as well as simulations of BeO nanotubes and nanosheets. We apply the potential in a study of oxygen irradiation of Be surfaces, and observe the early stages of an oxide layer forming on the Be surface. Predicted thermal and elastic properties of BeO nanotubes and nanosheets are simulated and compared with published ab initio data.

WOS: 000441595000011 In this study, the geometrical, thermal, and energetic properties of zinc-blende CdTe1-xSex (x = 0.25, 0.50, and 0.75) nanoparticles were investigated using the bond order potential based on the modern classical molecular dynamics (MD) method. All MD simulations were performed using LAMMPS. Some physical properties were investigated, such as compositional variations of Cd, Te, and Se atoms; order parameter; radial distribution function; coordination number; potential energy; and heat capacity (Cv). The simulation results were compared with the available experimental results. The obtained results revealed that an increase in the composition of Se atoms can provide contributions to stability, which is desirable to increase the efficiency of solar cells. Ahi Evran University Scientific Research Projects Coordination UnitAhi Evran University [TBY.C1.17.001] This work was supported by the Ahi Evran University Scientific Research Projects Coordination Unit ( Project Number: TBY.C1.17.001). The numerical calculations reported in this paper were partially performed at the TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources).

We use molecular dynamics simulation to study the mechanisms of plasticity during cutting of monocrystalline and polycrystalline silicon. Three scenarios are considered: (i) cutting a single crystal silicon workpiece with a single crystal diamond tool, (ii) cutting a polysilicon workpiece with a single crystal diamond tool, and (iii) cutting a single crystal silicon workpiece with a polycrystalline diamond tool. A long-range analytical bond order potential is used in the simulations, providing a more accurate picture of the atomic-scale mechanisms of brittle fracture, ductile plasticity, and structural changes in silicon. The MD simulation results show a unique phenomenon of brittle cracking typically inclined at an angle of 45° to 55° to the cut surface, leading to the formation of periodic arrays of nanogrooves in monocrystalline silicon, which is a new insight into previously published results. Furthermore, during cutting, silicon is found to undergo solid-state directional amorphisation without prior Si-I to Si-II (beta tin) transformation, which is in direct contrast to many previously published MD studies on this topic. Our simulations also predict that the propensity for amorphisation is significantly higher in single crystal silicon than in polysilicon, signifying that grain boundaries eases the material removal process.

Nanometric cutting of single crystal silicon on different crystal orientations and at a wide range of temperatures (300–1500 K) was studied through molecular dynamics (MD) simulations using two sorts of interatomic potentials, an analytical bond order potential (ABOP) and a modified version of Tersoff potential, so as to explore the cutting chip characteristics and chip formation mechanisms. Smaller released thermal energy and larger values of chip ratio (ratio of the uncut chip thickness to the cut chip thickness) as well as shear plane angle were obtained when cutting was performed at higher temperatures or on the (1 1 1) crystal plane, implying an enhancement in machinability of silicon. Nonetheless, the subsurface deformation depth was observed to become deeper under the aforementioned conditions. Further analysis revealed a higher number of atoms in the chip when cutting was implemented on the (1 1 0) crystal plane, attributable to the lower position of the stagnation region which triggered less ploughing action of the tool on the silicon substrate. Regardless of temperature of the substrate the minimum chip velocity angle was found while cutting the (1 1 1) crystal plane of silicon substrate whereas the maximum chip velocity angle appeared on the (1 1 0) surface. A discrepancy between the two potential functions in predicting the chip velocity angle was observed at high temperature of 1500 K, resulting from the overestimated phase instability and entirely molten temperatures of silicon by the ABOP function. Another key observation was that the resultant force exerted by the rake face of the tool on the chip was found to decrease by 24% when cutting the (1 1 1) surface at 1173 K compared to that at room temperature. Besides, smaller resultant force, friction coefficient at the tool/chip interface and chip temperature was witnessed on the (1 1 1) crystal plane, as opposed to the other orientations.

Hexagonal diamond is the harder and stiffer alternative of traditional cubic diamond for today’s technology. Although several theoretical attempts have been performed to understand the ground-state elastic properties of hexagonal diamond, little is known about the high-pressure elastic properties of this key material. Unlike previous theoretical methods, we report the application of second-generation reactive bond order potential for the first time to elaborate the pressure-dependent properties of hexagonal diamond in conjunction with geometry optimization calculations up to 500 GPa. Pressure dependency of density, five independent elastic constants, bulk, shear and Young moduli, Poisson ratio, elastic wave velocities, anisotropy parameter, Kleinman parameter, and stability conditions of hexagonal diamond were evaluated. Overall, considered properties of hexagonal diamond display evident increments under pressure, and their ground-state values are in reasonable agreement with available theoretical data. © 2015, Springer-Verlag Berlin Heidelberg.

A general recursion method for tight-binding molecular dynamics simulations is described in terms of a bond-order potential based on the Lanczos basis. The simple recursive algorithm for calculating the band energy and the forces is intrinsically linear in the scaling of the computational efforts for large systems and very suitable for parallel computation. As a test of this method, constant energy molecular dynamics simulations are performed for carbon materials. The conserved total energy indicates that the forces are of good quality.

C c –C c and C a –C b bonds in C 70 have dominant characteristics of double bonds, whereas the remaining six other types of bonds are single bonds with contributions from π-electron density. ‘Single’ bonds can act as active sites in chemical reactions which would typically require a multiple bond, such as addition of an ozone molecule, due to the fact that all adjacent bonds can serve as an efficient source of π-electron density. Thus any alteration in the electron density distribution following functionalization has far-reaching impact. We note that formation of the most stable ozonide isomer causes the smallest total perturbation in the electron density of the parent fullerene and C–C bond evolution correlates well with the shape of the minimum energy path for the ozone ring opening reaction on the fullerene surface. Finally, we observe that the O–O bond in C 70 O 3 is protocovalent, and as such resembles the O–O bond in H 2 O 2 .

Macroscopic tribometry is linked to classical atomistic simulations in order to improve understanding of the nanoscale interfacial processes during sliding of hydrogenated DLC (a-C:H) against a metal (W) in dry and lubricated conditions. Experimentally, using an online tribometer, wear and roughness measurements are performed after each sliding cycle, which are then correlated with the frictional resistance. Ex situ analysis is also performed on the worn surfaces (i.e. plates and counterfaces) using X-ray photoelectron spectroscopy, Auger electron spectroscopy and cross-sectional transmission electron microscopy imaging of the near-surface region. Then, in order to elucidate the atomistic level processes that contribute to the observed microstructural evolution in the experiments, classical molecular dynamics are performed, employing a bond order potential for the tungsten–carbon–hydrogen system. Macroscopic tribometry shows that dry sliding of a-C:H against W results in higher frictional resistance and significantly more material transfer compared with lubricated conditions. Similarly, the molecular dynamic simulations exhibit higher average shear stresses and clear material transfer for dry conditions compared with simulations with hexadecane as a lubricant. In the lubricated simulations, the lower shear stress and the absence of a material transfer are attributed to hexadecane monolayers that are partially tethered to the a-C:H surface and significantly reduce adhesion and mechanical mixing between the sliding partners.

International audience; We show herein how mechanical forces at macro or micro scales may affect the biological response at the nanoscale. The reason resides in the intimate link between chemistry and mechanics at the molecular level. These interactions occur under dynamic conditions such as the shear stress induced by flowing blood or the intracellular tension. Thus, resisting removal by mechanical forces, e.g., shear stresses, is a general property of cells provided by cellular adhesion. Using classical models issued from theoretical physics, we review the force regulation phenomena of the single bond. However, to understand the force regulation of cellular adhesion sites, we need to consider the collective behavior of receptor-ligand bonds. We discuss the applicability of single bond theories to describe collective bond behavior. Depending on bond configuration, e.g., presently "parallel" and "zipper", the number of bonds and dissociation forces variably affect the kinetics of multiple bonds. We reveal a marked efficiency of the collective organization to stabilize multiple bonds by sharply increasing bond lifetime compared to single bond. These theoretical predictions are then compared to experimental results of the literature concerning the kinetic parameters of bonds measured by atomic force microscopy and by shear flow. These comparisons reveal that the force-control of bonds strongly depends on whether the force distribution on multiple bonds is homogeneous, e.g., in AFM experiments, or heterogeneous, e.g., in shear flow experiments. This reinforces the need of calculating the stress/strain fields exerted on living tissues or cells at various scales and certainly down to the molecular scale.

In this paper a new interatomic potential based on the Kieffer force field and designed to perform molecular dynamics (MD) simulations of carbon deposition on silicon surfaces is implemented. This potential is a third-order reactive force field that includes a dynamic charge transfer and allows for the formation and breaking of bonds. The parameters for Si‐C and C‐C interactions are optimized using a genetic algorithm. The quality of the potential is tested on its ability to model silicon carbide and diamond physical properties as well as the formation energies of point defects. Furthermore, MD simulations of carbon deposition on reconstructed (100) silicon surfaces are carried out and compared to similar simulations using a Tersoff-like bond order potential. Simulations with both potentials produce similar results showing the ability to extend the use of the Kieffer potential to deposition studies. The investigation reveals the presence of a channelling effect when depositing the carbon at 45 incidence angle. This effect is due to channels running in directions symmetrically equivalent to the (110) direction. The channelling is observed to a lesser extent for carbon atoms with 30 and 60 incidence angles relative to the surface normal. On a pristine silicon surface, sticking coefficients were found to vary between 100 and 73%, depending on deposition conditions. (Some figures may appear in colour only in the online journal)

CdTe has been a special semiconductor for constructing the lowest-cost solar cells, and the CdTe-based Cd${}_{1\ensuremath{-}x}$Zn${}_{x}$Te alloy has been the leading semiconductor for radiation detection applications. The performance currently achieved for the materials, however, is still far below theoretical expectations. This is because the property-limiting nanoscale defects that are easily formed during the growth of CdTe crystals are difficult to explore in experiments. Here, we demonstrate the capability of a bond-order potential-based molecular dynamics method for predicting the crystalline growth of CdTe films during vapor deposition simulations. Such a method may begin to enable defects generated during vapor deposition of CdTe crystals to be accurately explored.

Coulson’s bond order is a chemically intuitive quantity that measures the difference in the occupation of bonding and anti-bonding orbitals. Both empirical and rigorously derived bond order expressions have evolved in the course of time and proven very useful for atomistic modeling of materials. The latest generation of empirical formulations has recently been augmented by screening-function approaches. Using friction and wear of diamond and diamond-like carbon as examples, we demonstrate that such a screened bond order scheme allows for a faithful description of dynamical bond-breaking processes in materials far from equilibrium. The rigorous bond order expansions are obtained by systematic coarse-graining of the tight binding approximation and form a bridge between the electronic structure and the atomistic modeling hierarchies. They have enabled bottom-up derivations of bond order potentials for covalently bonded semiconductors, transition metals, and multicomponent intermetallics. The recently developed magnetic bond order potential gives a correct description of both directional covalent bonds and magnetic interactions in iron and is able to correctly predict the stability of bulk Fe polymorphs as well as the intricate properties of dislocation cores. The bond order schemes hence represent a family of reliable and powerful models that can be applied in large-scale simulations of complex processes involving fracture, wear, and plasticity.

It is shown that Kekule structures do not realistically predict the behavior of p-electron properties of those polycyclic hydrocarbons that have many fixed double bonds. This is caused by the fact that such molecules would be destabilized by delocalization. We analyze a group of polycyclic hydrocarbons with a large number of fixed bonds, whose geometry was determined by means of an unrestricted symmetry-broken UB3LYP/6-311G(d, p) DFT method. We put forward a new concept, the unpaired bond order, and show that it is well correlated with bond lengths, but poorly correlated with Pauling bond orders. Hence, in this way we provide a simple test of the validity of the Pauling-bond-order concept for the molecule being considered.

A fundamental challenge in engineering biologically inspired materials and systems is the identification of molecular structures that define fundamental building blocks. Here, we report a systematic study of the effect of the energy of chemical bonds on the mechanical properties of molecular structures, specifically, their strength and robustness. By considering a simple model system of an assembly of bonds in a cluster, we demonstrate that weak bonding, as found for example in H-bonds, results in a highly cooperative behaviour where clusters of bonds operate synergistically to form relatively strong molecular clusters. The cooperative effect of bonding results in an enhanced robustness since the drop of strength owing to the loss of a bond in a larger cluster only results in a marginal reduction of the strength. Strong bonding, as found in covalent interactions such as disulphide bonds or in the backbone of proteins, results in a larger mechanical strength. However, the ability for bonds to interact cooperatively is lost, and, as a result, the overall robustness is lower since the mechanical strength hinges on individual bonds rather than a cluster of bonds. The systematic analysis presented here provides general insight into the interplay of bond energy, robustness and other geometric parameters such as bond spacing. We conclude our analysis with a correlation of structural data of natural protein structures, which confirms the conclusions derived from our study.

A new bond multiplicity measure based on the Wiberg-type bond covalency index and the atomic charge from population analysis is presented. Heuristically derived formulas allow one to evaluate the character of the chemical bond, especially its ionicity degree. Numerical results at RHF/ROHF theory level demonstrate that full multiplicities of typical chemical bonds are close to formal orders and their basis set dependence is inconsiderable, especially for highly polarized chemical bonds.

Nanocoatings have the potential to improve the surface properties of various materials. They are of extreme importance for surfaces in sliding contact such as highly stressed engine parts. Here, nanocoatings have to be optimized with respect to low friction properties and a high wear resistance to enhance the energetic and environmental efficiency. An important example are diamond-like carbon (DLC) films, which exhibit high mechanical stability depending on their deposition process. We present an introduction to this field of tribology by giving a short overview on DLC films, on the influence of lubricants from a theoretical point of view and in a broader sense, on basic principles of modeling tribological processes with molecular dynamic methods.

Effective interatomic potentials are frequently utilized for large-scale simulations of materials. In this work, we generate an effective interatomic potential, with Niobium as an example, using the force-matching method derived from a material database which is created by the first-principle molecular dynamics. It is found that the potentials constructed in the present work are more transferable than other existing potential models. We further discuss how the first-principles material database should be organized for generation of additional potential.

We present a detailed analysis of the structure of liquid carbon near the freezing line. The results are obtained by molecular simulation using a recently developed state-of-the-art bond order potential. We find that along the melting line the liquid is predominantly threefold coordinated up to pressures far beyond the liquid–graphite–diamond triple point. We find no sign of a first-order liquid–liquid phase transition when, at 10 500 K and ~300 GPa, the local structure of the liquid along the melting line changes dominant coordination from three- to fourfold.

Recently proposed communication theory treatment of the chemical bond is outlined. The molecular systems in atomic resolution are interpreted as “communication” systems in which “signals” of the electron allocations to constituent atoms are propagated from the molecular input (source), e.g., the atomic promolecule reference, to the molecular output (receiver) via a network defined by the conditional two-electron probabilities. The electron delocalization accompanying the bond formation is responsible for the noise affecting the flow of information throughout the system. The conditional entropy and mutual information descriptors of such molecular communication channels are identified as overall measures of the covalent and ionic components of the system chemical bonds, and a distinction between the electron-sharing and coordination (donor–acceptor) bonds is investigated. These entropy/information descriptors of the chemical bond are illustrated in the two-electron, two-orbital model. This analysis covers the orbital and spin channels for the singlet (bonding) and triplet (nonbonding) states. The overall bond-order conservation in the model and the competition between the bond ionicity and covalency is stressed. The model polyatomic systems discussed include the π bonds in butadiene and benzene in the Huckel theory approximation. The predictions from the communication theory approach compare favorably with the chemical intuitive values and bond orders from other orbital approaches, e.g., the quadratic index of Wiberg and the two-electron multiplicities of the difference approach. The Hirshfeld partition of molecular electron density is briefly summarized and the average entropies of the local stockholder communication channel it generates are proposed as alternative information descriptors of the chemical bonds in molecules.

A new semi-empirical force field has been developed to describe hydrogen-bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for the hydrogen bond potential were optimized to best fit crystallographic data from a number of protein structures. Refinement of medium-resolution structures with this additional restraint leads to improved structure, reducing both the free R-factor and over-fitting. However, the improvement is seen only when stringent hydrogen bond selection criteria are used. These findings highlight common misconceptions about hydrogen bonding in proteins, and provide explanations for why the explicit hydrogen bonding terms of some popular force field sets are often best switched off.

A recent analytic expression for the $\ensuremath{\sigma}$ bond order of $\mathrm{sp}$-valent systems with open structures is generalized to close-packed structures. This requires the retention of both the four-member ring contribution and the second-order embedding-type terms which arise naturally within the tight-binding formalism of bond-order potential theory. This relatively simple analytic expression for the $\ensuremath{\sigma}$ bond order of $\mathrm{sp}$-valent systems with half-full shells is shown to predict excellent bond orders over a wide range of coordination from the open graphitic and diamond lattices through simple cubic to the close-packed face-centered-cubic structures. The critical importance of the ring term on the structural stability of close-packed systems is demonstrated.

The LAGROBO functional representation of the atom-diatom interaction has been extended to the case of three different atom reactive systems having two open product channels and an atom in an electronically excited state. The analytic formulation of the LAGROBO model is given and its application to the construction of the potential energy surface of the Li+FH and O(1D)+HCl reactions are discussed. Reactive properties calculated on these surfaces using quasiclassical methods are compared with experimental findings.

The purpose of this paper is to study the model [4 + 4] photocycloaddition of butadiene + butadiene by using direct dynamics calculationswith no geometric constraintsto describe motion along excited-state reaction paths and subsequent decay to the ground state. We use the molecular mechanics−valence bond (MMVB) potential, which is calibrated against previous CASSCF calculations for this system (Bearpark, M. J.; Deumal, M.; Robb, M. A.; Vreven, T.; Yamamoto, N.; Olivucci, M.; Bernardi, F. J. Am. Chem. Soc. 1997, 119, 709−718). Our dynamics calculations show that efficient nonradiative decay of butadiene + butadiene in the presence of two different S1/S0 conical intersections can account for the formation of many products. The major product predicted by MMVB is consistent with the limited experimental data available.

The advantage of mapping calculated potential energy values onto the space of the bond order coordinates is discussed with special concern for the possibility of designing functional representations of the interaction. A rotating model defined in the bond order space is proposed.

Tungsten has been chosen as the divertor armour material in ITER and is the main candidate material for plasma-facing components for future fusion reactors. Interaction of plasma components with the material leads to degradation of the performance and thus the lifetime of the in-vessel components. On top of that special attention is drawn to tritium retention in the reactors vessel from a safety point of view, since tritium is radioactive material. In order to gain better understanding of the mechanisms driving accumulation of plasma components in the material and subsequent degradation of the material, atomistic simulations are employed. The focus of this work is on so-called self trapping of H and He atoms or, in other words, Frenkel pair formation in bulk tungsten in the presence of H and He atoms. Two versions of a model embedded atom interatomic potential and a bond order potential were tested by comparing it with ab initio data regarding the binding properties of pure He and He-H-Vacancy clusters and energetics of Frenkel pair formation. As a result of Molecular Dynamics simulations at nite temperature, the values of critical H concentration needed for the generation of a Frenkel pair in the presence of He clusters wereobtained. The results show that the critical H concentration decreases with thsize of He cluster present in the simulation cell and thus, Frenkel pair formation by H is facilitated in the presence of He clusters in the material. Keywords: tungsten, plasma facing material, hydrogen retention, helium, molecular dynamics.

The tensile strength of single-walled carbon nanotubes (CNT) is examined using a continuum-atomistic (CA) approach. The strength is identified with the onset of the CNT instability in tension. The focus of this study is on the effects of multi-body atomic interactions. Multiscale simulations of nanostructures usually make use of two- and/or three-body interatomic potentials. The three-body potentials describe the changes of angles between the adjacent bonds – bond bending. We propose an alternative and simple way to approximately account for the multi-body interactions. We preserve the pair structure of the potentials and consider the multi-body interaction by splitting the changing bond length into two terms. The first term corresponds to the self-similar deformation of the lattice, which does not lead to bond bending. The second term corresponds to the distortional deformation of the lattice, which does lead to bond bending. Such a split of the bond length is accomplished by means of the spherical–deviatoric decomposition of the Green strain tensor. After the split, the continuum-atomistic potential can be written as a function of two bond lengths corresponding to the bond stretching and bending independently. We apply an example exponential continuum-atomistic potential with the split bond length to the study of tension instability of the armchair and zigzag CNTs. The results of the study are compared with those obtained by Zhang et al. (2004. J. Mech. Phys. Solids 52, 977–998) who studied tension instability of carbon nanotubes by using the Tersoff–Brenner three-body potential, and with recent experimental results on the tensile failure of single walled carbon nanotubes.

We present a method for studying mechanochemical bond breaking (i.e. induced by the external mechanical force) by means of Molecular Dynamics simulations. The method is based on application of artificial force acting in desired direction particular atoms, which is known as the Steered Molecular Dynamics method. We have applied SMD formalism to the DFT Molecular Dynamics, opposite to classical force-field potential in original SMD method. We have applied this method to the example system consisting of silver cation coordinated by two imidazole rings in order to study the bond breaking phenomenon under the external force. Moreover, the method allowed us to evaluate the force necessary to break the bond and observe different phenomena accompanying the bond rupture such as stretching of the bond and changes in potential energy surface. Evaluated breaking force gives the results which are in good agreement with experimental value. We intend to use the method for other systems that we investigate experimentally in our group. Keywords: mechanochemistry; COGEF; Molecular Dynamics; artificial force; bond rupture