Semi-empirical Potential Energy Functions Research Articles

Free surfaces and multilayer interfaces in the GaAs/AlAs system

Semiempirical potential energy functions have been utilized for a variety of calculations in the Ga-Al-As system: (1) surface energies have been calculated for several orientations of GaAs; (2) ledge energies for the GaAs(00 1 ) (As terminated) surface show long range interaction effects with the ledge energy increasing with spacing; (3) GaAs(001)/AlAs(001) superlattices have been simulated for a range of interlayer spacings with the excess interfacial energy per interlayer increasing from 5 erg/cm 2 at an interlayer spacing of 1 molecular layer (5.8 Å) to 50 erg/cm 2 at an interlayer spacing of 18 molecular layers (103.8 Å).

Computer simulation of thin amorphous Si films on crystalline Si substrates

Using a semiempirical potential energy function for Si, thin amorphous films of Si have been simulated on crystalline Si by a partial melting and subsequent quenching process. After relaxation at 450 K., the dominant structural feature was a dense free surface skin with a void layer underneath for both c-Si(100) and c-Si(111) substrates and for film thicknesses up to 16 A. Tetrahedral coordination was maintained throughout the amorphous region and structural differences were noted in the α-Si/c-Si interface region for the two orientations considered.

Long-range ledge-ledge interactions on Si(111) surfaces: I. No kinks or surface point defects

Surface ledges of the [211̄] and [2̄11] type on the Si(111) surface provide a dilational contribution to the strongly compressive surface stress tensor. Computer calculations using a semiempirical potential energy function show (a) monatomic ledge-ledge interaction even at spacings of 50 Å, (b) strong reconstruction on some ledge orientations and negligible changes on others leading to ledge energies in the range 0.01–0.22 eV/atom compared to a face energy of 0.38 eV/atom, and (c) that the surface stress tensor dominates the relaxation around ledges.

Surface Stress Tensor Mediation of the Ledge Nucleation/Growth Process with the Surface Reconstruction Process in GaAs

ABSTRACTA new GaAs semiempirical potential energy function which utilizes both two-body and three-body contributions has been used to evaluate the surface energy and surface stress tensor for the (111) and (001)(As-terminated) surfaces as well as for ledges on the (001) surface. Both surface and ledge reconstruction patterns appear to be driven by stress tensor considerations and a long range ledge-ledge interaction arises via the stress tensor. The impact of this finding on two dimensional cluster formation and nucleation at the growing surface is very substantial.

A Structural Analysis of Thin Amorphous Silicon Films

AbstractUsing a semiempirical potential energy function for Si, thin amorphous films of Si have been simulated on crystalline Si by a partial melting and subsequent quenching process. After relaxation at 450°K, the dominant structural feature was a dense free surface skin with a void layer underneath for both c-Si(100) and c-Si(111) substrates and for film thicknesses up to 16Å. Tetrahedral coordination was maintained throughout the amorphous region and structural differences were noted in the α-Si/c-Si interface region for the two orientations considered.

The effect of surface stress on the reconstruction of the Si(111) surface

Abstract Stress tensors and their influence on the reconstruction of Si(111) surfaces were calculated using a “statics” computer simulation technique based on a semi-empirical potential energy function. Analyses were aimed at investigating long-range stress interactions on ideal and defective Si(111) surfaces. Calculations indicate that the perfect Si(111) surface is under a large compressive stress. Formation of ledges and surface vacancies, in particular, were found to reduce this compressive stress.

The effect of surface stress on the reconstruction of the Si(111) surface

Stress tensors and their influence on the reconstruction of Si(111) surfaces were calculated using a “statics” computer simulation technique based on a semi-empirical potential energy function. Analyses were aimed at investigating long-range stress interactions on ideal and defective Si(111) surfaces. Calculations indicate that the perfect Si(111) surface is under a large compressive stress. Formation of ledges and surface vacancies, in particular, were found to reduce this compressive stress.

Site selectivity of alkaline earth metal cations in zeolite A

Application of a semiempirical potential energy function to calculation of the site selectivity of alkaline earth metal cations in zeolites NaA and KA is described. Twenty-seven unit cells were adopted as a model compound. J. E. Huheey's [ J. Phys. Chem. 69, 3285 (1965)] electronegativity equalization method was used to calculate the net charge of framework. Although Mg 2+ and Ca 2+ ions show site I selectivity, Ba 2+ ion is distributed over two sites. To study zero-coordinated cations, X-ray data were used for Ca 6A, Sr 6A, and KA. The greater tendency of K + ion to occupy eight-ring sites is discussed in terms of site selectivities of the divalent cations.

Adsorption, potential maps and diffusion of Si, C, and SiC on A Si(111) surface

Using semi-empirical potential energy functions, both the adsorption configurations and binding energies for carbon on silicon surfaces have been determined and the activation energy for surface diffusion evaluated. Simulation of Si, C and SiC diffusion on a Si(111) surface shows Si to be the most mobile, C to be slightly less mobile and SiC to be quite immobile.

Reconstruction and energetics for surfaces of silicon, diamond and β-SiC

A semi-empirical potential energy function comprising two- and three-body interactions was employed in association with a Monte Carlo procedure to calculate the energies and structures for Si(100), Si(111), C diamond(100), C diamond(111) and various index planes of β-SiC surfaces. Calculated results for adatom and vacancy free surfaces, were found to be in fair agreement with experiments.

Theoretical study of ionic selectivities and adsorption of water in zeolite A

The site selectivity of alkali metal ions in the dehydrated and hydrated zeolite A is discussed by using the semiempirical potential energy functions. The net charges of framework atoms are calculated by the electronegativity equalization method. In the dehydrated zeolite A, the calculated solvation heats of gaseous cations by dehydrated and hydrated zeolite A frameworks agree semiquantitatively with the experimental data. The symmetry of cation positions and size of cations explain the site selectivity. When the dehydrated zeolite A is hydrated, the first four water molecules are bound to the cations on sites II and III, with the binding energy of −25.9 and −28.5 kcal mol −1 respectively. The site selectivity of sodium ions in the hydrated zeolite A is shown to be site(I)>site(II)>site(III).

Origins of life: Conformational energy calculations on primitive tRNA nestling an amino acid

We report conformational energy calculations on our proposal of a molecular interaction theory for the origin of the nucleic acid-directed, adaptor-mediated synthesis of proteins that links the phenomena of chemical and biological evolution. A particular conformation of a pentanucleotide turns out to be a double-sided template for a primitive decoding system. It is able to neatly nestle an amino acid via hydrogen bonds, and this complex is found to be an energetically favourable conformation. The total potential energy of the complex is calculated using semi-empirical potential energy functions. A local-minimum conformation is obtained and its features are reported. The template conformation of the pentanucleotide is found to have an energy value far lower than a regular helical conformation. When the amino acid is nestled in the cleft of the template-conformation through specific hydrogen bonds, the energy is further lowered. A D-amino acid nestled into the PIT (Primitive tRNA) is found to be less stable than its L counterpart, as revealed by energy calculations.

Configurational characteristics of the polysulfides, . Dipole moments and gauche effects in poly (1,3‐dithiocane)

AbstractSeveral earlier studies of poly(alkylene sulfides) have not yielded evidence for a sulfur gauche effect, in contrast to the large attractive gauche effect found particularly in the lower members of the poly(alkylene oxides). In this study the dipole moments at 25°C and the corresponding temperature coefficient of poly(1,3‐dithiocane)Structure based name: poly(thiomethylonethiopentamethylene). [SCH2S(CH2)5]x are calculated in the rotational isomeric‐state approximation, and the results compared to the values determined by experiment. In the calculations the energy Eσ′ = [Eg± − Et] associated with S. . .CH2 interactions in the SCH2SCH2 segment is adjusted to attain agreement between theory and experiment. The results indicate that an extra stabilization energy of ca. 0,9 kcal . mol−1 must be added to these gauche states relative to the trans state (beyond that determined by conformational energy calculations based on semiempirical potential energy functions). This provides the first evidence of a large attractive sulfur gauche effect in the polysulfides, about equal in magnitude to that found for the analogous poly(methylene oxide).

Configurational chracteristics of the polysulfides, 3. Dipole moments of poly(trimethylene sulfide) and comparisons between some polysulfides and the corresponding polyoxides

AbstractConformational energy calculations indicate that poly(trimethylene sulfide) (P3MS) approximates the idealized freely‐rotating chain in that gauche‐trans energy differences in this molecule are very small. This occurs because the relatively long SC bond tends to relieve congestion within the P3MS chain. The bonds in poly(trimethylene oxide) (P3MO) are much more constrained to a particular rotational state because the OC bond is shorter than the SC one, and in this sense P3MO is considerably less flexible. In this study the dipole moments 〈μ2〉0 of P3MS are measured as a function of temperature, and the results analyzed in terms of the rotational isomeric‐state theory. Using conformational energies derived from semiempirical potential energy functions, a three‐rotational‐state model gave values of the dipole moment in good agreement with experiment. Theoretical and experimental values of the temperature coefficient of 〈μ2〉0 were in disagreement, however, and a five‐rotational‐state model based on that adopted by Flory in a similar study of polymethylene failed to remove this discrepancy. Some statistical properties are tabulated for the n‐alkylene polysulfides studied to date and for structurally related polyoxides. In these types of molecules, strong preferences for pairs of gauche states in CH2SCH2SCH2 and CH2 OCH2OCH2 sequences give rise to unusually small values of the dipole moment.

Configurational characteristics of the polysulfides, 1. Dipole moments of poly(pentamethylene sulfide)

AbstractPoly(pentamethylene sulfide)Structure‐based name: poly(thiopentamethylene). (P5MS) [S(CH2)5]x was prepared by the condensation polymerization of nearly equimolar amounts of pentamethylene dibromide and the sodium salt of 1,5‐pentanedithiol. Selective precipitations were used to obtain a fraction of the polymer, and dielectric constant measurements on solutions of it in benzene were used to obtain dipole moments over the range 20–60°C. Rotational isomeric state calculations based on conformational energies obtained from semiempirical potential energy functions gave results in fair agreement with experiment. Since extensive previous studies on a number of polyoxides have demonstrated the difficulty in calculating the energy of the O…CH2 interactions, the energy of the corresponding S…CH2 interactions in P5MS was adjusted to obtain better agreement between theory and experiment.

Conformational analysis and conductivity via dopant intercalation model for PPS and PPO (Polyphenylene sulfide and oxide)

Abstract Semi-empirical potential energy functions in conjunction with quantum mechanical methods were used to characterize the intrachain interactions and conformational aspects of the processable polymers PPS and PPO. The purpose of this study was to elucidate the structural aspects of the dopant-polymer interaction and mechanism of electrical conduction subsequent to doping of these materials. These polymers, upon doping, can reach high levels of conductivity in spite of the fact that the crystalline conformation of the chains is non-planar and little conjugation along the chains is expected due to the presence of the chalcogenide atom. Chain flexibility and rearrangement upon doping will be discussed. Calculations have indicated that the rotations about C-X (X=O, S) bonds and stretching of the ⟨C-X-C angle can facilitate the intercalation of a dopant moiety in a manner that conduction can occur via an interchain mechanism. A dopant intercalation model will be presented and its consequences on conducti...

Crystalline-State Configurations of Alkylene Sulfide Polymers

Semi-empirical potential energy functions were used to calculate the conformational energies of several alkylene sulfide polymers of structure [S(CH2)y]. The polymers chosen were those for which crystalline-state configurations were known, specifically those having y=1,2,3, and 5, respectively. The configurations of minimum conformational energy were generally found to correspond to the crystalline-state configurations. The only exceptions occurred for conformational-energy differences close to zero, which is to be expected since in these cases even small differences in intermolecular packing energies could obviously play an important role. Some preliminary comments are also made on the here-to-fore unstudied polysulfides corresponding to y=4, 6, and higher. Comparisons with the corresponding polyoxides [O(CH2)y] help elucidate the effect of the size of the hetero-atom X (S or O), its effective charge, the C–X bond length, and the C–X–C bond angle. The most important difference between the polysulfides and polyoxides appears to be the fact that the C–S bond is considerably longer than the C–O bond.

Studies of the dimensions of oligopeptides by singlet-singlet energy, transfer and theoretical calculations. I. Influence of glycine on the dimensions of tetrapeptides.

The efficiency of energy transfer between a fluorescent donor, L-tyrosine, and a fluorescent acceptor, L-tryptophan, has been determined in R'-L-Trp-L-Ala-L-Tyr-R", R-L-Trp-L-Ala-L-Ala-L-Tyr-R", and R'-L-Trp-Gly-L-Ala-L-Tyr-R" in ethanol solution. The protecting groups R' and R" were respectively tert-butyloxycarbonyl and methyl ester. A conformational theoretical analysis of molecules studied has been performed in parallel on the basis of semiempirical conformational potential energy function. In the theoretical models all the side chains have been represented by a methyl group. From the distribution of distances between chromophores obtained theoretically, transfer efficiencies have been computed assuming a random orientation of the chromophores (k-2 equals 2/3). The comparison of calculated efficiencies with the values determined experimentally for the same value of k-2 has been used as a check for the theoretical model. Both experimental and theoretical studies have been shown that the glycyl residue procudes a reduction of dimensions when it replaces in a tetrapeptide a residue with a beta-carbon atom such as the L-alanyl residue. However, only a qualitative agreement between experimental and theoretical values of the efficiencies has been obtained.

Comparative study of the semiempirical three-parameter potential energy functions for diatomic molecules

A comparative study is made of four three-parameter semiempirical potential energy functions for 32 electronic states of diatomic molecules and their ions:n2:X1gS g + ,B3πg,A3 gSu,C3u,B′3 gSu.a1 πg, a′gS u − ,Ω1δuN 2 + :X2 gS g gS +A2 π,C2 gS u + ,B2 gS u + CO:X1gS+,a3 π, a′3 gSu,e3 gS−,d3gD1,A1π CO+:X2gS+,A2 π,B2gS+ O2:X3gS g − ,B3 gSu,c1 gS u − ,b1gS g s ,a1 δg,c3 δu O 2 + :X2πg,A2 πg, a1 πg,b4 gS g − A program for numerically integrating the radial Schrodinger equation by the Cooley method is worked out. Certain additional units are introduced to conserve computer time. The resulting vibrational levels are compared with the experimental levels for all the electronic states studied. It is concluded on the basis of this analysis that it is not possible to describe equally well all the electronic states of various molecules on the basis of any single three-parameter potential function. A method for choosing a potential function for describing some particular electronic state of a diatomic molecule is proposed.

Isotactic poly(p-fluorostyrene): Conformation and molecular packing analysis

Abstract The chain conformation and molecular packing of isotactic poly(p-fluorostyrene) have been examined using calculations made with semiempirical potential energy functions. Isolated chain conformational energies indicate no difference in conformation for the fluoropolymer from the conformation for isotactic polystyrene. The energy for packing poly(p-fluorostyrene) chains into a crystalline array as 31 or 41 helices was also compared with the energies for packing polystyrene in both of these helical forms. While not being the lowest energy mode of packing for poly(p-fluorostyrene), the packing of 41-helices does yield a local energy minimum. Such packing of 41 helical polystrene chains is considerably less energetically feasible. The results indicate the causes for the experimentally observed difference in the crystalline conformations of the two isotactic polymers as being due to intermolecular influences.