Tight-binding Molecular Dynamics Research Articles

A Molecular Dynamics Study of the Rotational Dynamics and Polymerization of C60 in C60-Cubane Crystals

AbstractRecently, heteromolecular crystals of fullerene C60 and cubane (C8H8) have been synthesized. For some temperatures the C60 molecules are free to rotate whereas cubanes behave like a static bearing in a so-called rotor-stator phases. In this work we report classical and tight-binding molecular dynamics simulations in order to investigate the rotor-stator dynamics and polymerization processes. Our results show that, for 200 K and 400 K, cubane molecules remain basically fixed, presenting only thermal vibrations within the timescale of our simulations, while C60 fullerenes show rotational motions. Fullerenes perform “free” rotational motions at short times (< 1 ps), small amplitude hindered rotational motions (librations) at intermediate times, and rotational diffusive dynamics at long times (> 10 ps). Random copolymerization among cubanes and fullerenes were observed when temperature is increased, leading to the formation of a disordered structure.

Formation of a five-seven pair couple defect in double-walled carbon nanotubes under bending deformation

Simulations of double-walled carbon nanotubes under bending deformation using the tight-binding molecular dynamics method were carried out. Five- and seven-membered ring pair defects were formed after emission of several atoms from the tube structure. These defect pair couples have different structures corresponding to the number of emitted atoms and stabilize the resulting nanotubes. Our results imply that the defect pair couples represent one of the potential origins of the experimentally observed plastic deformations that have been shown to occur in double-walled carbon nanotubes. The various defects obtained by the simulations are discussed in relation to other defect types.

Growth ofsp−sp2nanostructures in a carbon plasma

The growth of sp and ${\mathrm{sp}}^{2}$ nanostructures in a carbon plasma is simulated by tight-binding molecular dynamics. The simulations are arranged so as to mimic the cluster formation conditions typical of a pulsed microplasma cluster source which is used to grow nanostructured $\mathrm{sp}\text{\ensuremath{-}}{\mathrm{sp}}^{2}$ carbon films [L. Ravagnan et al., Phys. Rev. Lett. 98, 216103 (2007)]. The formation of linear, ring, and fullerenelike objects in the carbon plasma is found to proceed through a very long multistep process. Therefore, tight-binding simulations of unprecedented duration have been performed by exploiting the disconnected topology of the simulated carbon plasma which made it possible to implement a computationally efficient divide-and-diagonalize procedure. Present simulations prove that topologically different structures can be formed in experiments, depending on the plasma temperature and density. A thorough characterization of the observed structures as well as their evolution (caused both by thermal annealing and by cluster ripening) is provided.

The atomic charge distribution in glasses obtained by terahertz spectroscopy

It is demonstrated that the width of the uncorrelated atomic charge distribution can beextracted from the frequency dependence of the coupling coefficient for far-infrared absorptionmeasured experimentally by a time-domain terahertz spectroscopy technique. This value forAs2S3 glass isfound to be 0.12 (e). A density functional theory-based tight-binding molecular dynamics model ofAs2S3 glass qualitatively supports these findings.

Formation of carbon nanotube semiconductor-metal intramolecular junctions by self-assembly of vacancy defects

Atomistic processes of carbon nanotube semiconductor-metal intramolecular junction formation are investigated by tight-binding molecular dynamics simulations and first-principles total energy calculations. We show that the junctions can be formed by reconstruction of vacancy clusters through a series of generalized Stone-Wales transformations [Chem. Phys. Lett. 128, 501 (1986)]. Our simulations suggest a mechanism for synthesis of carbon nanotube semiconductor-metal intramolecular junctions with specific locations and controlled sizes and show the possibility of application to nanoelectronic devices. Our simulations study also provides a microscopic explanation to the superplastic deformation in single-wall carbon nanotubes.

Energetically competitive growth patterns of silicon clusters: Quasi-one-dimensional clusters versus diamond-like clusters

Silicon clusters with a diamond-like core and energetically competitive non-diamond clusters were studied using the nonconventional tight-binding molecular dynamics simulation method. Non-diamond clusters were constructed according to a quasi-one-dimensional pentagon-based regular growth pattern. A nontrivial competition between surface and core reconstructions in the clusters, in order to reach energetically favorable atomic arrangements, was observed. This prevents unlimited growth via the one-dimensional pattern. Starting from ${\mathrm{Si}}_{43}$, there was substantial deviation from the stacked pentagon motif, and for ${\mathrm{Si}}_{61}$, one end of these clusters became almost two-dimensional. Clusters with a diamond-like core were subjected to substantial reconstruction. These were energetically unfavorable relative to non-diamond clusters for the sizes considered ($\ensuremath{\leqslant}71$ atoms). The importance of capped pentagon motifs in the surface reconstruction for energetically competitive nanometer-size diamond-like clusters was demonstrated. A lower bound of 115 atoms for the transition from non-diamond structure to diamond-like structure is estimated by extrapolation of the present results.

Energetics and electronic structure of armchair nanotubes with topological linedefects

We study the electronic structure and energetics of carbon nanotubes with topological linedefects consisting of fused pentagons and octagon rings by means of first-principlescalculation in density functional theory and tight-binding molecular dynamics simulations.The tubes with the topological line defects are found to exhibit magnetic ordering wherepolarized electron spins are localized around the topological defect and ferromagneticallyaligned along the defect. Our analyses of the electronic energy band and spin densitydistributions reveal that this ferromagnetic spin ordering is associated with the edge statesthat are inherent in the graphite ribbon with zigzag edges. The tight-bindingmolecular dynamics simulations show that the nanotubes with the topologicalline defects are thermally stable up to temperature of 3000 K and disrupted over4000 K.

Tight-binding molecular dynamics study of the role of defects on carbon nanotube moduli and failure

We performed tight-binding molecular dynamics on single-walled carbon nanotubes with and without a variety of defects to study their effect on the nanotube modulus and failure through bond rupture. For a pristine (5,5) nanotube, Young's modulus was calculated to be approximately 1.1 TPa, and brittle rupture occurred at a strain of 17% under quasistatic loading. The predicted modulus is consistent with values from experimentally derived thermal vibration and pull test measurements. The defects studied consist of moving or removing one or two carbon atoms, and correspond to a 1.4% defect density. The occurrence of a Stone-Wales defect does not significantly affect Young's modulus, but failure occurs at 15% strain. The occurrence of a pair of separated vacancy defects lowers Young's modulus by approximately 160 GPa and the critical or rupture strain to 13%. These defects apparently act independently, since one of these defects alone was independently determined to lower Young's modulus by approximately 90 GPa, also with a critical strain of 13%. When the pair of vacancy defects adjacent, however, Young's modulus is lowered by only approximately 100 GPa, but with a lower critical strain of 11%. In all cases, there is noticeable strain softening, for instance, leading to an approximately 250 GPa drop in the apparent secant modulus at 10% strain. When a chiral (10,5) nanotube with a vacancy defect was subjected to tensile strain, failure occurred through a continuous spiral-tearing mechanism that maintained a high level of stress (2.5 GPa) even as the nanotube unraveled. Since the statistical likelihood of defects occurring near each other increases with nanotube length, these studies may have important implications for interpreting the experimental distribution of moduli and critical strains.

Structure and Dynamics of Angiotensin (1-7) Vasoactive Peptide in Aqueous Solution at the Density-Functional Based Tight-Binding Level

Summary: Structure and dynamics of heptapeptide Angiotensin (1-7) in aqueous solution have been investigated by means of density-functional based tight-binding molecular dynamics simulations. Solvent-solute interactions have been studied using a hybrid QM/MM method. The backbone of the heptapeptide remains relatively rigid in aqueous solution compared to gas phase. The solvent acts as a cushion, preventing the free motion of the molecule. Tyrosine is the residue which presents the smallest flexibility and the largest number of water molecules in its first solvation shell. This is in good agreement with the previously published NMR results. The intra– and intermolecular hydrogen bridges have been quantified and analyzed in terms of conformation and stability.

Local order in undercooled liquid metals: A tight binding molecular dynamics approach

We use constant (zero) pressure molecular dynamics based on a semi-empirical tight binding model to simulate the structures of liquid Ni, Cu, Pd and Au in the stable and undercooled states. We compare our data with the available experiments (neutron scattering for Ni, EXAFS for Pd). We analyze the structure in terms of Voronoi polyhedra and use the neighbors defined by this analysis to perform a Common Neighbors Analysis. We show that a small but significant difference in the number of bonds with five common neighbors exists between undercooled Ni and the other elements. We question the possible experimental observation of such a difference and its relevance to the issue of the existence of an icosahedral short range order in the liquid.

Atomic and electronic structure of crystalline–amorphous carbon interfaces

Interfaces of diamond with amorphous carbon (a-C) are investigated using tight-binding molecular dynamics simulations. Such interfaces are found to be stable, with a-C atoms covalently bonded to the diamond surfaces. The atomic and electronic structure of the a-C region is consistent with previous results on pure a-C and does not depend critically on the diamond face exposed. However, surface properties influence the relative stability of interfaces with high density a-C. In this case, the interfacial region is small and very dense homogeneous a-C grows on diamond. At lower densities, carbon atoms nucleate on diamond surfaces and create an intermediate region between diamond and a-C. The shape of diamond crystals embedded in a-C is predicted using the Wulff construction with appropriately defined energies for surfaces with overlayer material. These predictions are verified by empirical potential simulations of nanodiamond inclusions in a-C matrix. The electronic density of states and the dielectric function, calculated for our samples containing a-C/diamond interfaces, show that optoelectronic properties of these composite materials are dominated by a-C.

Structural correlations in light irradiated Ge 36Se 64 amorphous films—Radial distribution function study

The effect of laser irradiation on the electronic structure of amorphous Ge 36Se 64 films has been detected by studying the variation of the bond length ( r) and the coordination number C N. The total distribution function T( r) of the as deposited film is characterized by the first coordination sphere corresponding to the superposition of the correlation Ge–Se and Se–Se situated at 2.53 Å. The average estimated C N is 2.519. The second peak ascribed to the correlation Se–Se lies at 3.85 Å showing good agreement with other published data. After irradiation, the first peak of T( r) shows a considerable shift towards a small r and a reduction of C N. On the contrary, the second neighbor data shows a slight increase of r and a great increment of C N value (5.11 before irradiation against 6.59 after irradiation). Study of the variation of both r and C N values induced by subsequent annealing of the film is also given. The relative concentrations of the Ge Ge, Ge Se and Se Se bonds, as well as, the number of the GeSe 4 tetrahedral per atom are calculated using the continuous random network (CRN) and the chemically order continuous random network (COCRN) models. These calculations argue the presence of Ge 2(Se 1/2) 6 ethane like unit in addition to Ge(Se 4) 1/2 even with the COCRN model. The formation of dynamical bonds during irradiation of the film under study is suggested. Correlation to volume changes during illumination studied by tight binding molecular dynamics computer simulation has been also considered.

Thermal stability of metallic single-walled carbon nanotubes: anO(N) tight-binding molecular dynamics simulation study

Order(N)tight-binding molecular dynamics (TBMD) simulations are performed to investigate the thermal stabilityof (10,10) metallic single-walled carbon nanotubes (SWCNTs). Periodic boundary conditions (PBCs)are applied in the axial direction. The velocity Verlet algorithm along with the canonicalensemble molecular dynamics (NVT) is used to simulate the tubes at the targetedtemperatures. The effects of slow and rapid temperature increases on the physicalcharacteristics, structural stability and the energetics of the tube are investigated andcompared. Simulations are carried out starting from room temperature and thetemperature is raised in steps of 300 K. The stability of the simulated metallic SWCNT isexamined at each step before it is heated to higher temperatures. The first indication ofstructural deformation is observed at 600 K. For higher heat treatments the deformationsare more pronounced and the bond-breaking temperature is reached around 2500 K.Gradual (slow) heating and thermal equilibrium (fast heating) methods give the value ofradial thermal expansion coefficient in the temperature range between 300 and 600 K as0.31 × 10−5 and 0.089 × 10−5 K−1, respectively. After 600 K, both methods give the same value of0.089 × 10−5 K−1. The ratio of the total energy per atom with respect to temperature is found to be3 × 10−4 eV K−1.

Temperature dependence of the tensile properties of single-walled carbon nanotubes:O(N)tight-binding molecular-dynamics simulations

This paper examines the effect of temperature on the structural stability and mechanical properties of 20-layered (10,10) single-walled carbon nanotubes (SWCNTs) under tensile loading using an $\mathrm{O}(N)$ tight-binding molecular-dynamics simulation method. We observed that (10,10) tube can sustain its structural stability for the strain values of 0.23 in elongation and 0.06 in compression at $300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Bond-breaking strain value decreases with increasing temperature under stretching but not under compression. The elastic limit, Young's modulus, tensile strength, and Poisson ratio are calculated as 0.10, $0.395\phantom{\rule{0.3em}{0ex}}\mathrm{TPa}$, $83.23\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$, and 0.285, respectively, at $300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. In the temperature range from $300\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}900\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, Young's modulus and the tensile strengths decrease with increasing temperature while the Poisson ratio increases. At higher temperatures, Young's modulus starts to increase while the Poisson ratio and tensile strength decrease. In the temperature range from $1200\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}1800\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the SWCNT is already deformed and softened. Applying strain on these deformed and softened SWCNTs does not follow the same pattern as in the temperature range of $300\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}900\phantom{\rule{0.3em}{0ex}}\mathrm{K}$.

Structural and electronic properties of the fullerene isomers ofSi38: A systematic theoretical study

A systematic study of the structural and electronic properties of the 17 Si38 fullerene cage isomers, which are constructed by making all possible permutations among their pentagons and hexagons, is presented. For the full optimization of these structures, a tight-binding molecular-dynamics method is firstly applied, and the resulting structures were further optimized with two more accurate but more time-consuming methods, namely, the generalized tight-binding molecular dynamics and a density-functional theory calculation at the B3LYP level. In addition, the Si20 fullerene cage, optimized with the same methods, is also presented for comparison. The results of all these methods are in good agreement with each other, and they all predict the same isomer as the energetically most stable structure among these 17 isomers. In all the fullerene isomers, half of the atoms are nearly coplanar with their three neighbors, and half lie on sharp corners of the polyhedral cage, coinciding with a distinction between half of the atoms adopting an sp 2 -like hybridization and the other half using essentially pure p orbitals in their bonding to nearest neighbors.

Structural and electronic properties of V, Nb and Ta nanoclusters by tight-binding molecular dynamics simulations

We present tight-binding molecular dynamics (TBMD) calculations on V, Nb and Ta nanoclusters with N = 15, 65, 175 and 369 atoms. We found that rhombic dodecahedra are energetically favoured over rhombic hexahedra and icosahedra, with V forming the most compact cluster with the gyration radius increasing with the cluster size. In addition, from the calculated electronic density of states we found that the cluster size plays an important role in the HOMO–LUMO gap and that an increase in cluster size results in enhancement of the electronic density around the Fermi level. Furthermore, we found that the small clusters ( N = 15, 65) exhibit energy gap that persists even at 900 K. These findings originate from charge transfer occurring between the inner and outer cluster atoms; interestingly, we found that in the small N = 15, 65 clusters electronic charge accumulates at each surface site at the expense of the inner cluster atoms, while in the larger clusters, N = 175 and 369, charge is gathered on the central particles of the cluster, suggesting different sub-surface character of the clusters. These findings are in agreement with available experimental and theoretical data and promise to offer important information for creating nanostructured materials with improved properties suitable for multiple technological applications.

Modelling of photoinduced changes in chalcogenide glasses: a-Se and a-As2Se3

The microscopic processes in chalcogenide glasses caused by illumination have been investigated using tight-binding molecular dynamics computer simulation. After the photon absorption we have treated the excited electron and hole independently. We found covalent bond breaking in amorphous networks with photo-induced excited electrons, whereas excited holes contribute to the formation of inter-chain bonds. We also observed a correlated macroscopic volume change of the amorphous sample. The interplay between photo-induced bond breaking and inter-chain bond formation leads to either volume expansion or shrinkage. Our results provide a new and universal description, which can explain simultaneously the photo-induced volume expansion and shrinkage. The model is supported by the results of recent measurements carried out by Y. Ikeda and K. Shimakawa.

Structure and Dynamics of β-Cyclodextrin in Aqueous Solution at the Density-Functional Tight Binding Level

Structure and dynamics of beta-cyclodextrin (beta-CyD), a prototype host for inclusion compounds of biological interest, is investigated by means of density-functional based tight-binding molecular dynamics (MD) simulations. The computational protocol is benchmarked against available experimental data and first-principles calculations. Solvent-solute interactions, including the diffusion into and dwell time of the solvent in the cavity of beta-CyD, are studied with a hybrid QM/MM method. Comparison of MD simulations of beta-CyD in the gas phase and in water shows that the solvent reduces the flexibility of the structure framework, while the terminal hydroxyl groups become more flexible and are embedded in a network of hydrogen bonds. Our 160 ps MD simulations, provide enough sampling to discuss the dynamics of the water inside the cavity. The dwell time of the encapsulated water molecule has a wide distribution with a peak at 70 fs. Surprisingly, despite only the 17% difference between the "top" and "bottom" opening area of the beta-CyD cone, 64% of the water molecules enter the cavity through the slightly bigger "bottom" aperture.

Development of Constraint Algorithm for the Number of Electrons in Molecular Orbitals Consisting Mainly 4 f Atomic Orbitals of Rare-Earth Elements and Its Introduction to Tight-Binding Quantum Chemical Molecular Dynamics Method

Our original tight-binding quantum chemical molecular dynamics code, “Colors”, has been successfully applied to the theoretical investigation of complex materials including rare-earth elements, e.g., metal catalysts supported on a CeO2 surface. To expand our code so as to obtain a good convergence for the electronic structure of a calculation system including a rare-earth element, we developed a novel algorithm to provide a constraint condition for the number of electrons occupying the selected molecular orbitals that mainly consist of 4 f atomic orbitals of the rare-earth element. This novel algorithm was introduced in Colors. Using Colors, we succeeded in obtaining the classified electronic configurations of the 4 f atomic orbitals of Ce4+ and reduced Ce ions in a CeO2 bulk model with one oxygen defect, which makes it difficult to obtain a good convergence using a conventional first-principles quantum chemical calculation code.

Theoretical Study on the Electronic and Electrical Properties of p-Type Transparent Conducting Metal Oxides

Transparent conducting oxides (TCOs) continue to be in high demand because of their immediate applications. In addition to good quality n-type TCOs, there is increasing demand for good p-type TCOs. In the present study, we reported a theoretical study on the electronic and electrical properties for p-type TCO, Zn-doped In2O3 (IZO). The geometries of IZO were optimized using the density functional theory (DFT). Based on these optimized structures, the density of states, frontier molecular orbital contours, and electrical conductivity of IZO were calculated by combining the tight-binding quantum chemical molecular dynamics program, “Colors” and Monte Carlo method. The calculated band gap by “Colors” at G point is 2.87 eV, which is in good agreement with experimental value. In density of states of IZO, a shallow acceptor-type impurity level associate with Zn doping was observed above the top of the valence band. The frontier orbital analysis shows that the acceptor-type impurity level consists of O 2p and Zn 3d. On the other hand, the electrical conductivity and carrier mobility of IZO were evaluated. Comparing the electrical conductivity of IZO with that of its parent material In2O3, it was found that the electrical conductivity increased significantly when Zn-dopant was introduced to In2O3. The higher electrical conductivity of IZO was considered to be attributed to impurity state and therefore the p-type conductivity.