Semi-empirical Potential Energy Functions Research Articles

Molecular dynamics study of surface nucleation and growth mechanism in Cu-based CuPtPd ternary alloy system

This study report that a classical molecular dynamics (MD) simulation method has been performed to investigate the nucleation and growth mechanism from amorphous matrix of Cu-based CuPtPd ternary alloy system with different Pt and Pd addition at nano-scale. The Embedded Atom Method (EAM) utilizing the Sutton-Chen (SC) version is used to calculate interatomic interactions as a semi-empirical potential energy function. The crystallization stages have been examined by using computational method at different annealing temperatures using Johnson-Mehl-Avrami-Kolmogorov (JMAK) equations. The structural developments of systems are analysed with radial distribution function (RDF). Crystallized fractions (x) against annealing time have been calculated from the crystal-type bonded pairs based on Honeycutt-Andersen (HA) cluster analysis index. It is found that an increase in annealing temperature of systems plays important role for crystallization. In addition, the surface nucleation and one-dimensional growth are favourable for low Cu compositions in the CuPtPd system at low annealing temperatures. These findings shed new light on understanding the crystallization kinetics of CuPtPd system by using computer simulation method.

Investigation of the Effect of Pressure and Cooling Rate on the Local Order for Cu and Ni Metallic Systems: A Molecular Dynamics Simulation

In this study, the orientational order of two important transition metals, nickel and copper, are simulated by using a molecular dynamics (MD) simulation with a semi-empirical potential energy function based on the embedded atom model for systems. The local order of atomic structures is investigated by using bond order parameters at slow and fast cooling rates during the crystallization process. In addition, the radial distribution function (RDF) is calculated to determine the structural properties of the systems. All these physical parameters are analysed under 0 and 5 GPa pressures.

The integral-differential and integral approach for the estimation of the classical Lennard-Jones and Biswas-Hamann potentials

Many well-known semiempirical potential energy functions have been used to construct potential energy curves from the physical or chemical properties of atoms. In this study, we identify the Lennard-Jones and Biswas-Hamann potential parameters and use these to calculate and reconstruct potential energy curves using experimental datasets of gold atom. Two different approaches are studied in detail. The Lennard-Jones potential yielded complex conjugate eigenvalues for both approaches. Numerical estimates proved the considered approaches gives better approximations as constructed and reconstructed potential energy curves were almost graphically indistinguishable.

The integral-differential and integral approach for the estimation of the classical Lennard-Jones and Biswas-Hamann potentials

Many well-known semiempirical potential energy functions have been used to construct potential energy curves from the physical or chemical properties of atoms. In this study, we identify the Lennard-Jones and Biswas-Hamann potential parameters and use these to calculate and reconstruct potential energy curves using experimental datasets of gold atom. Two different approaches are studied in detail. The Lennard-Jones potential yielded complex conjugate eigenvalues for both approaches. Numerical estimates proved the considered approaches gives better approximations as constructed and reconstructed potential energy curves were almost graphically indistinguishable.

Ab initio MP2 and density functional theory computational study of AcAlaNH2 peptide hydration: a bottom-up approach.

AcAlaNH2 ⋅ n H2O (n=1-13) complexes have been proposed as models to account for water solvent effects on the molecular properties of N-acetyl-L-alanine amide. Ab initio computations are planned to evaluate peptide-water interactions and to provide a means for approximating relative effects of the short-range many-body interactions arising in real solution without introducing any external parameters intended to quantify empirical or semiempirical potential-energy functions. The present bottom-up approach reveals the formation of compact ring clusters of water molecules strongly bonded to peptidic polar groups throughout hydrogen bonds. The explicit coordination of water molecules around the peptide renders the fully extended (FE) and polyproline II (PPII) conformers more stable with respect to the 310 helix or γ turn. The alternance of donor and acceptor groups on both sides of the FE and PPII conformers allows for synergy and extensive H-bonding.

Organic Heterojunctions for Photovoltaic Applications: C60 Growth on Pentacene

AbstractUsing atomic-scale Molecular Dynamics (MD) and energy minimization techniques in conjunction with semi-empirical MM3 potential energy functions, we consider the adsorption of a C60 molecule on a series of hypothetical pentacene structures that vary only in the tilt of the angle that the short axis of the pentacene molecules makes with the underlying surface (the long axis lying essentially flat, as on a metal substrate). Important relationships were discovered between the angle adopted by the short axis of pentacene on the surface, φ1, and the adsorption and diffusion characteristics of C60. Static energy calculations show that there is a transition of the deepest energy minima from between the pentacene rows at low values of φ1 to within the rows at high values of φ1, where φ1 is the angle the pentacene short axis makes with the surface. MD confirms this trend by the predominant residence locations at the extreme φ1 values. Furthermore, MD results suggest that the C60 traverses the pentacene surface in the east-west direction for lower φ1 values (φ1 ≤ 40°) and in the north-south direction for higher φ1 values (φ1 ≥ 70°). Taking both static and dynamic results together, the most favorable tilt angles for mono-directional nanowire growth should occur between 70° and 80° off-normal.

An Iterative Global Optimization Algorithm for Potential Energy Minimization

In this paper we propose an algorithm for the minimization of potential energy functions. The new algorithm is based on the differential evolution algorithm of Storn and Price (Journal of Global Optimization, vol. 11, pp. 341--359, 1997). The algorithm is tested on two different potential energy functions. The first function is the Lennard Jones energy function and the second function is the many-body potential energy function of Tersoff (Physics Review B, vol. 37, pp. 6991--7000, 1988; vol. 38, pp. 9902--9905, 1988). The first problem is a pair potential and the second problem is a semi-empirical many-body potential energy function considered for silicon-silicon atomic interactions. The minimum binding energies of up to 30 atoms are reported.

Structure-based conformational preferences of amino acids.

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for alpha-helices and beta-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion.

Dynamics of collision-induced desorption: Ar–Xe/Pt(111)

We have performed a detailed study of collision-induced desorption (CID) of Xe from Pt(111) by hyperthermal Ar atoms striking the surface. The study combines extensive molecular beam experiments with detailed molecular dynamics calculations in an effort to quantify fully and to understand in detail the dynamics of this model system. The calculations employ accurate semi-empirical potential energy functions for all relevant interatomic interactions. We have characterized the CID process with respect to incidence energy, Ei, angle, θi, and substrate surface temperature, Ts, for both the isolated adsorbate and the Xe/Pt(111) monolayer. The generally good agreement of the calculated results such as the desorption yield and desorbate energy and angular distributions with the experimental measurements demonstrates that the calculations capture the most important aspects of the CID processes.

Kinetic Monte Carlo studies of early surface morphology in diamond film growth by chemical vapor deposition of methyl radical.

We present results of off-lattice kinetic Monte Carlo simulations of early stages of low-pressure diamond film growth from a C[111] substrate via methyl radical and hydrogen vapor deposition. Interactions are governed by a semiempirical interatomic potential energy function. Rates for surface chemisorption and desorption of hydrogen and chemisorption of methyl radical that have been calculated by Raff and co-workers are used to assign real time to the Monte Carlo steps. The rate-determining step is the deposition or attempted deposition of methyl radical. Between ${\mathrm{CH}}_{3}$ surface events, the surface is relaxed by standard Monte Carlo methods. During the relaxation process C-C bonds may form and break, and surface diffusion occurs. We study the rate of formation of pair bonds and larger clusters of chemisorbed carbon over a 20-ms simulation, during which the initial surface becomes covered and small diamond ledges begin to form. This rate of growth is in accord with observed rates for diamond film growth from methyl radical. \textcopyright{} 1996 The American Physical Society.

Coupling between localized C-H oscillators obtained from semi-empirical two-dimensional potential energy functions

This contribution presents a theoretical approach based on computations of two electronically coupled CH oscillators located in ortho-, meta- and para-position, respectively. The two-dimensional potential energy surfaces built up by chosen pair of local oscillators were calculated by semi-empirical quantum chemical calculations. Relevant coupling was found out in the case of ortho-positioned oscillators. The vibrational eigenvalues were obtained from a two-dimensional Hamilton operator using a variational setup.

A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: Solvation effects on the conformational equilibrium of dimethoxyethane

Solvent effects on the conformational equilibria of dimethoxyethane (DME, CH3–O–CH2–CH2–O–CH3) have been studied using molecular dynamics simulation with a combined molecular mechanical and semiempirical quantum mechanical potential energy function. The potential of mean force around the central O–C–C–O dihedral angle of DME in water was determined using umbrella sampling, with the DME molecule treated by the modified intermediate neglect of diatomic differential overlap (MNDO) method and water molecules described using the extended simple point charge model. This potential of mean force shows the same bias as the gas phase potential energy surface calculated by MNDO: the heights of the barriers are underestimated and the stability of the gauche conformation with respect to the trans conformation is overestimated. However, the calculated stabilization of the gauche state by solvation is in good agreement with experimental results, suggesting a quite reasonable description of this system by the combined potential energy function. The solute–water atom pair distributions and the averaged percentage of solute–water hydrogen bonding does not change much when the central dihedral angle changes, but in the gauche conformation one water hydrogen can be hydrogen bonded with the two solute oxygen atoms simultaneously. The interactions between DME and its explicit water environment favor the gauche over the trans conformation much more than predicted by the reaction field model, although the overall relative stabilities predicted by the latter model are not so biased due to compensation of errors. The trans conformation of the outer C–O–C–C dihedral angles is most favored during the simulations, which is qualitatively different from the reaction field prediction that the trans–gauche+–gauche− would be the most stable conformer in solution.

Configuration‐dependent properties of polyoxyethylene chains in the third‐order interaction approximation

AbstractConformational energies of polyoxyethylene chains in the third‐order interaction approximation are calculated using a semiempirical potential energy function in the usual manner. Configuration‐dependent properties of POE in the third‐order are also calculated, and more close to the experimental data.

Fundamental aspects of film nucleation and growth in chemical vapor deposition

The importance of surface reconstruction plus the generation of stress and electric fields at expanding islands during film formation are extremely important considerations for both surface cluster formation and ledge movement kinetics in the overall film deposition process. Using computer simulations and semi-empirical potential energy functions for Si and GaAs, both long-range field effects and cluster excess energy effects are demonstrated. Using a continuum approach with a ledge energy that depends on cluster radius, great differences relative to the classical nucleation picture are found. For vicinal surface orientations, an equation for film growth velocity is developed which incorporates gas phase transport, surface transport, ledge collection efficiency, ledge attachment kinetics and excess energy storage due to deposition stress and adsorbate trapping. The paper first treats the case of Si film formation from SiH 4 in H 2 with only SiH 2 forming in the adlayer. It then extends the treatment to deal with other Si intermediates formed in the adlayer which then desorb into the gas phase. Finally, the treatment is extended to consider SiN x film formation from SiH 4 + NH 3 in H 2.

The role of ledges in stress tensor-mediated surface processes for Si and GaAs

Calculation results of terrace and ledge reconstruction-induced surface stress tensors, using semiempirical potential energy functions for Si, GaAs, GaAs/Al, and GaAs/Si, are reviewed. Long-range (∼50 to 100 A) interaction effects between ledges and between interfaces are pre sented. Two-dimensional homogeneous and heterogeneous nucleation effects are also presented, showing that Actatom cluster populations are strongly influenced by these reconstruction events. The consequences of these reconstruction-induced surface fields on γ plots, ledge motion kinetic laws, surface Actatom transport, and solute partitioning at ledges are discussed. The numerical results were generated largelyvia Monte Carlo calculations and thus neglect entropy effects.

Fundamental aspects of film nucleation and growth

At real surfaces, atomic reconstruction generates a surface stress tensor that influences all subsequent surfaces processes like roughening, cluster formation, nucleation, adsorption layer characteristics, and layer flow kinetics. Here, computer simulation results using semiempirical potential energy functions for the Si–Ga–As and Al–Ga–As systems are used to illustrate some important long-range effects on ledge/ledge interaction and cluster excess energy that would not have been anticipated using the conventional dangling bond viewpoint. New insight has also been added to adsorption layer isotherm considerations and an equation for crystal growth velocity, which incorporates gas phase transport, surface transport, ledge attachment kinetics, plus ledge trapping of adsorbate species, is given.

Simulation of GaAs cluster formation on GaAs(001̄), AlAs(001̄), Si(001), and As1/Si(001) surfaces

Recently developed semiempirical potential energy functions for the Ga–As–Si and Ga–As–Al systems have been applied here to determine the excess formation energy for GaAs clusters on GaAs(001̄), AlAs(001̄), Si(001), and one atomic layer As-covered Si(001) substrates as a function of cluster size and cluster shape by the Monte Carlo technique. Pyramidal type ledges on the GaAs clusters are found to be the favored ledge for the first three layers while an inverted-pyramidal type ledge is also favored in certain cases for the As1/Si(001) substrate. Cluster formation at ledges is compared with cluster formation on a flat terrace for the Si(001) and the As1/Si(001) substrates.

Conformational studies of N‐acetyl‐N′‐methylamide derivatives of α‐aminobutyric acid, norvaline, and valine. II. Conformational energy calculations and comparison with experimental results

AbstractConformational analyses on a series of dipeptides CH3—C*O—NH—CH(R)—C*O—HN—CH3 with side chains such as R = CH2CH3, CH2CH2CH3, and CH(CH3)2 are described. Calculations were carried out by using semiempirical potential energy functions of Brant et al. The results were compared with those reported by Vásquez et al. and Chuman et al., who employed the ECEPP program in their analyses. The averages of the vicinal coupling constant J and the side‐chain conformer fractions p(χ1) and p(χ2)′ were estimated therefrom for preferred conformations. The characteristic features of the experimental observations derived from the 1H‐nmr measurements are reasonably well reproduced by these calculations.

Theoretical studies on alpha-helix--DNA interactions.

The interaction energies between (Ala)10 and alpha-helix fragment and different nucleotide sequences in right-handed B-form have been optimized using semi-empirical potential energy functions. The energies are calculated for two different orientations of the alpha-helix, viz., when the alpha-helix axis taken in the N----C direction is (i) parallel and (ii) antiparallel to the 5'-3' ascending strand of DNA, proximal to it. When both the DNA molecule as well as the alpha-helix are treated as rigid molecules it is found that a polyalanine alpha-helix has slightly more favourable contacts when it is in the proximity of a four nucleotide sequence of 5'-(N-A-T-N)-3' type, where N is either a purine or a pyrimidine. However, when the two interacting molecules are allowed to undergo local structural variations then the interaction energy appears to be independent of the base sequence confirming the non-specific nature of these interactions.

Computer simulation of ledge formation and ledge interaction for the silicon (111) free surface

Both strip and triangular clusters, composed of <2 11 > ledges, have been simulated on the Si (111) surface. The long range ledge-ledge interaction and the surface stress tensor distribution have been evaluated for these two pill-box geometries using a semi-empirical potential energy function that incorporates both two-body and three-body contributions. The consequences of the ledge-ledge interaction on two-dimensional nucleation for Si (111) has been evaluated as a function of Si adatom supersaturation and shown to differ significantly from conventional theory where such interaction is neglected.