Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena

An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Mutual correlation between gas chromatographic retention indices of unsaturated and saturated hydrocarbons found by molecular dynamics

It is shown that gas Chromatographic retention indices for cycloalkenes can be calculated from the corresponding data for cycloalkanes (and vice versa) using computer simulation of intramolecular vibrational and rotational processes by molecular dynamics. For organic compounds structurally related asA → B, the total internal energy differences δE = E(B)-E(A) correlate with the corresponding differences in retention indices δI = I(B)-I(A), and a linear relationship exists δI =aδE + b (a < 0, |ρ| > 0.9). Limitations are found for the use of molecular dynamics for compounds havingn-alkyl radicals with no less than four carbon atoms. In these cases, a simpler model for the evaluation of dynamic molecular parameters should be preferred for the calculation of retention indices of acyclic alkenes and alkanes. The reliability of the retention indices evaluated by the proposed technique is comparable to their interlaboratory reproducibility found using standard nonpolar poly(dimethylsiloxane) stationary phases.     

Computational study of the properties of silicon thin films on graphite

Russian Journal of Physical Chemistry A - The behavior of two thin silicon films on a surface of perfect graphite is studied by means of molecular dynamics. One film is a five-layer section of...     

Evolution of ion induced point defects in silicon

Problems of the dose rate dependence of the defect production by ion beam irradiation are addressed. Damage accumulation effects are studied for sequential and overlapping cascades induced by 1 keV recoils in silicon crystals. The defect generation and evolution is simulated by a molecular dynamics method using the Stillinger–Weber three body potential. It is shown that the damage produced by temporally and spatially overlapping cascades at room temperature can be both smaller and larger than the total damage induced by the individual recoils each starting in perfect crystalline silicon. The different damage levels are related to the characteristics of the defect structure shortly before and after initiating the subsequent cascades.     

Investigation of possible structures of silicon nanotubes via density-functional tight-binding molecular dynamics simulations and ab initio calculations

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

Gas‐Phase Formation of the Disilavinylidene (H2SiSi) Transient

The hitherto elusive disilavinylidene (H₂SiSi) molecule, which is in equilibrium with the mono‐bridged (Si(H)SiH) and di‐bridged (Si(H₂)Si) isomers, was initially formed in the gas‐phase reaction of ground‐state atomic silicon (Si) with silane (SiH₄) under single‐collision conditions in crossed molecular beam experiments. Combined with state‐of‐the‐art electronic structure and statistical calculations, the reaction was found to involve an initial formation of a van der Waals complex in the entrance channel, a submerged barrier to insertion, intersystem crossing (ISC) from the triplet to the singlet manifold, and hydrogen migrations. These studies provide a rare glimpse of silicon chemistry on the molecular level and shed light on the remarkable non‐adiabatic reaction dynamics of silicon, which are quite distinct from those of isovalent carbon systems, providing important insight that reveals an exotic silicon chemistry to form disilavinylidene.     

Selective response of mesoporous silicon to adsorbants with nitro groups

We demonstrate that the electronic structure of mesoporous silicon is affected by adsorption of nitro-based explosive molecules in a compound-selective manner. This selective response is demonstrated by probing the adsorption of two nitro-based molecular explosives (trinitrotoluene and cyclotrimethylenetrinitramine) and a nonexplosive nitro-based aromatic molecule (nitrotoluene) on mesoporous silicon using soft X-ray spectroscopy. The Si atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as evident from the large shifts in emission energy present in the Si L(2,3) X-ray emission spectroscopy (XES) measurements. Furthermore, we find that the energy gap (band gap) of mesoporous silicon changes depending on the adsorbant, as estimated from the Si L(2,3) XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab initio molecular dynamics calculations of model compounds suggest that these changes are due to spontaneous breaking of the nitro groups upon contacting surface Si atoms. This compound-selective change in electronic structure may provide a powerful tool for the detection and identification of trace quantities of airborne explosive molecules.     

Record Atomistic Simulation of Crystalline Silicon: Bridging Microscale Structures and Macroscale Properties

Based on the molecular dynamics software package CovalentMD 2.0, the fastest molecular dynamics simulation for covalent crystalline silicon with bond-order potentials has been implemented on the third highest performance supercomputer “Sunway TaihuLight” in the world (before June 2019), and already obtained 16.0 Pflops (10¹⁵ floating point operation per second) in double precision for the simulation of crystalline silicon, which is recordly high for rigorous atomistic simulation of covalent materials. The simulations used up to 160,768 64-core processors, totally nearly 10.3 million cores, to simulate more than 137 billion silicon atoms, where the parallel efficiency is over 80% on the whole machine. The running performance on a single processor reached 15.1% of its theoretical peak at highest. The longitudinal dimension of the simulated system is far beyond the range with scale-dependent properties, while the lateral dimension significantly exceeds the experimentally measurable range. Our simulation enables virtual experiments on real-world nanostructured materials and devices for predicting macroscale properties and behaviors from microscale structures directly, bringing about many exciting new possibilities in nanotechnology, information technology, electronics and renewable energies, etc. © 2019 Wiley Periodicals, Inc.     

Simulation of silicon clusters from “quantum” Langevin molecular dynamics

We present a simulation method to determine from first principles the structure of low symmetry atomic systems. Our method is based on Langevin molecular dynamics and quantum mechanical interactions derived fromab initio pseudopotential calculations. The molecular dynamics time step with this approach can be one to two orders of magnitude larger than in the Car-Parrinello method, compensating for the time required for self-consistency at each step. Moreover, because the simulation is constrained to reside on the Born-Oppenheimer surface, this method can be used for insulating as well as metallic and charged systems. Application will be made to small silicon clusters.     

Dispersing carbon nanotubes in aqueous solutions by a silicon surfactant: Experimental and molecular dynamics simulation study

The dispersion effect of carbon nanotubes (CNTs) in aqueous solutions by a silicon surfactant (ethoxy modified trisiloxane, named Ag-64) was investigated in detail using experimental method and molecular dynamics simulation. The Si–O–Si chain of silicon surfactant was flexible due to long Si–C bond and it could easily wrap onto the surface of CNTs through hydrophobic and other intermolecular interactions. The hydrophilic part of PEO provided the CNTs dispersed in the aqueous solution and prevented CNTs from aggregating in water through steric stabilization. It was found that Ag-64 could disperse CNTs with different diameters and it was an effective dispersing agent. The results of molecular dynamics simulation indicated that Ag-64 molecules could wrap onto the surface of CNTs leading to steric stabilization so that it could well disperse CNTs, and Van der Waals attraction was the dominating force of Ag-64 adsorbing onto CNTs. Our study may provide experimental and theoretical basis for using silicon surfactants to disperse CNTs, which can open the avenue of new applications for silicon surfactants.     

Molecular Dynamics Simulation of Copper Nanofilm Self-Assembly on Silicon Substrate under Gas-Discharge Plasma Conditions

High Energy Chemistry - Using the molecular dynamics method, the sputtering of a copper target and the subsequent formation of a copper nanofilm on a silicon substrate has been modeled. The process...     

Optical properties of silicon clusters in the presence of water: a first principles theoretical analysis

We investigate the impact of water on the optical absorption of prototypical silicon clusters. Our clusters contain 5 silicon atoms, tetrahedrally coordinated and passivated with either hydrogen or oxygen. We approach this complex problem by assessing the contributions of three factors: chemical reactivity, thermal equilibration, and dielectric screening. We find that the silanone (Si=O) functional group is not chemically stable in the presence of water and exclude this as a source of significant red shift in absorption in aqueous environments. We perform first principles molecular dynamics simulations of the solvation of a chemically stable, oxygenated silicon cluster with explicit water molecules at 300 K. We find a systematic 0.7 eV red shift in the absorption gap of this cluster, which we attribute to thermally induced fluctuations in the molecular structure. Surprisingly, we find no observable screening impact of the solvent, in contrast with consistent blue shifts observed for similarly sized organic molecules in polar solvents. The predicted red shift is expected to be significantly smaller for larger Si quantum dots produced experimentally, guaranteeing that their vacuum optical properties are preserved even in aqueous environments.     

Simulation of self-diffusion on silicon surface using stillinger-weber potential

The self-diffusion of tetrahedrally bonded materials on different surfaces, (100), (110) and (111) is studied by means of molecular dynamics simulation. We use the Stillinger-Weber three-body potential as the only interaction between atoms. The results are compared with experimental measurements and other simulations studies. They indicate that the Stillinger-Weber potential may have to be modified near the surface. Our results indicate that dimer diffusion in silicon may be comparable to single-adatom diffusion.     

Use of polystyrene brushes to investigate the role of interface between substrates and thin homogeneous films

The viscoelastic properties of thin polystyrene (PS) films depend on confinement, as it can modify the molecular dynamics affecting the glass transition. In the recent past, the authors have investigated the region next to the free interface by means of an atomic force microscope suitably modified to monitor the indentation of a tip into a film during a given lapse of time while applying a constant load. Herein, to explore the interface with the substrate, the authors report on experiments in which PS brushes grafted to native silicon oxide were used. It was found that the film wettability on brushes and H‐terminated silicon can be highly improved when compared with native silicon oxide. In addition, the glass transition temperature of thin films increases up to the bulk value in the case of film/brush combinations with high molecular weight or films with high molecular weight on H‐terminated silicon. Data are discussed according to hypotheses such as residual solvent presence, interface free volume, and molecular mechanical coupling. These observations can be of great interest for nanotechnological applications, especially in those instances where one needs to tailor the temperature dependence of viscoelastic properties of thin films. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013, 51, 1149–1156     

Structural and dynamic properties of (SiO2)6 silica nanostructures: a quantum molecular dynamics study

Structural and dynamic properties of the building block of silica nanowires, (SiO2)6, are investigated by Born-Oppenheimer quantum molecular dynamics simulations. Thirteen conformers have been identified, seven of which have not been reported before. The energy component analysis shows that the lower electrostatic interaction differentiates the global minimum from the other structures. We also observe that the maximum hardness principle can be employed to justify the molecular stability for this system. Time profiles of a few density functional reactivity indices exhibit correlations of dynamic fluctuations between HOMO and LUMO and between chemical potential and hardness. Electrophilicity, nucleaofugality, and electrofugality indices are found to change concurrently and significantly, indicating that the nanostructures sampled during the dynamic process are exceedingly reactive and rich in chemistry.     

烯烃分子在氢终止Si(100)-2×1表面的自由基链反应

应用密度泛函理论(DFT)和从头计算分子动力学方法(ab initio MD)研究了不饱和烯烃在氢终止的Si(100)-2×1表面的自由基链反应. 计算表明, 自由基链反应中重要的一步是烷烃链自由基的氢抽提过程, 硅表面上邻近位置(the nearest neighbor, NN)的氢抽提比次邻近位置(the next-nearest neighbor, NNN)的氢抽提有一稍低的能垒. 从头算分子动力学显示, 过渡态的烷烃自由基与氢终止Si(100)-2×1表面上的氢原子能够很容易形成C—H键, 完成一个氢抽提过程, 同时在硅表面产生下一个孤电子, 继续引发链反应.     

Crystal structure prediction using the minima hopping method

A structure prediction method is presented based on the minima hopping method. To escape local minima, moves on the configurational enthalpy surface are performed by variable cell shape molecular dynamics. To optimize the escape steps the initial atomic and cell velocities are aligned to low curvature directions of the current local minimum. The method is applied to both silicon crystals and well-studied binary Lennard-Jones mixtures. For the latter new putative ground state structures are presented. It is shown that a high success rate is achieved and a reliable prediction of unknown ground state structures is possible.     

Impact of Deuteration and Temperature on Furan Ring Dynamics

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.