bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab‐initioMRD–CI calculations on a CNO2 decomposition pathway of nitrobenzene
Authors: Kaufman Joyce J. , Hariharan P. C. , Roszak Szczepan , van Hemert Marc 
Published: January 2005

AbstractTo study molecular decomposition pathways it is necessary to use ab initio multireference determinant–configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD–CI (multireference double excitation–configuration interaction technique of Buenker and Peyerimhoff) calculations on the magnified image decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the magnified image bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of magnified image distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
Characteristics of the Watson‐Crick type hydrogen‐bonded DNA base pairs: An ab initio molecular orbital study
Authors: Aida Misako 
Published: January 2005

AbstractCharacteristics of the Watson‐Crick‐type hydrogen‐bonded base pairs, thymine‐adenine and cytosineguanine, are presented. These were established using an ab initio molecular orbital method. Base–base interactions are revealed to have dominant roles in the structures of nucleic acids and also in their functions. The most stable conformations in Watson‐Crick‐type base pairs are almost in accord with the structure observed in fiber X‐ray diffraction study. Explanations are given of the origin of the sequencedependent local structures which differ from one base pair to the next, as observed in single‐crystal X‐ray analyses. In the case of the thymine‐adenine base pair, it is shown that various geometrical parameters having almost the same stability are available. According to the propeller twist, the instability is not large enough for a base pair to be twisted readily.
Automatic classification of chemical structure databases using a highly parallel array processor
Authors: Rasmussen Edie M. , Downs Geoffrey M. , Willett Peter 
Published: January 2005

AbstractThis article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis‐Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.
Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes
Authors: Hammarström Lars‐Gunnar , Liljefors Tommy , Gasteiger Johann 
Published: January 2005

AbstractThe PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C‐1s core binding energies and 1H‐NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4‐disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.
An algorithm for the location of branching points on reaction paths
Authors: Baker J. , Gill P. M. W. 
Published: January 2005

AbstractA branching point is a point on a reaction path leading from reactants to products (via a transition state) at which it is energetically favorable for the system to break symmetry. Such a point can be defined in terms of normal modes along the reaction path and corresponds to zero curvature (a zero Hessian eigenvalue) along a symmetry‐breaking mode. An effective method for the location of such points is presented and realized in an efficient, practical algorithm designed for use in the ab initio program package Gaussian 82.
Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures, and of electron correlation on relative energies
Authors: Wiberg Kenneth B. , Murcko Mark A. 
Published: January 2005

AbstractThe optimized geometries for the rotamers of propanal, 2‐butanone, isobutyraldehyde, methyl isopropyl ketone, and isobutyric acid obtained using the 3–21G and 6–31G* basis sets are compared, and systematic changes are noted. The relative 6–31G* energies using the 3–21G and 6–31G* geometries are generally the same within 0.1 kcal/mol. The effect of electron correlation on the relative energies is generally small. These and related data show that 6–31G* relative energies obtained using 3–21G geometries are generally satisfactory when studying rotation about CC bonds. However, this is not the case for CO bonds. The calculated relative energies of isomeric compounds are reproduced only with the full MP4 correction for electron correlation.
Hydrogen bonding in MM2
Authors: Allinger Norman L. , Kok Randall A. , Imam Mita R. 
Published: January 2005

AbstractHydrogen bonding is qualitatively accounted for in the early versions of the MM2 program, but not quantitatively. Experimentally, the hydrogen bonds are somewhat shorter and stronger than calculated by MM2. This has been corrected now in MM2(87), by reducing the van der Waals radius of the hydrogen involved in hydrogen bonding for that interaction only, and by increasing the van der Waals' attraction between the hydrogen and the various electronegative atoms to which it can hydrogen bond by about 1–3 kcal/mol, depending on the particular atoms involved. It is now possible to reproduce reasonably well ab initio calculations on simple amides and the methanol dimer, and experimental data on compounds in which a hydroxyl hydrogen is hydrogen bonded to an alcohol, an alkyl chloride, or to a carbon–carbon double bond.
Ab initio studies of the ground‐state potential energy surface of formamide
Authors: Wright Gregory M. , Simmonds Richard J. , Parry David E. 
Published: January 2005

AbstractAb initio calculations employing a standard double‐zeta basis set augmented with various polarization functions have been used to investigate the lowest energy region of the ground‐state potential energy surface of the formamide molecule. Hartree‐Fock calculations with only d polarization functions on the nonhydrogen atoms located two stable minima, that with geometry distorted from planarity having slightly lower energy; only one stable minimum with planar structure is found when p polarization functions on the hydrogens are included. In contrast optimizations, which account approximately for the correlation energy using second‐order Møller‐Plesset perturbation theory consistently favor a single slightly nonplanar minimum energy geometry.
Treatment of symmetry in MO calculations. II. Numerical projection operators for molecular orbitals
Authors: Jaffé H. H. 
Published: January 2005

AbstractThis article describes the numerical application of projection operators to restore the symmetry of molecular orbitals in self‐consistent field (SCF) calculations when the symmetry is lost because of degeneracy or near degeneracy. The application of projection operators is particularly useful in cases of near degeneracies of three or more molecular orbitals, where it is difficult to find an effective algorithm for restoring the symmetry of molecular orbitals by orthonormal transformations.
Development of a program for MCSCF calculations with large basis sets
Authors: Yamamoto Shigeyoshi , Nagashima Umpei , Aoyama Tomoo , Kashiwagi Hiroshi 
Published: January 2005

AbstractA new program named JASON2 for ab initio MCSCF calculations with large basis sets has been developed. In this program, the density‐formulated super‐CI CASSCF method proposed by Roos et al. was adopted in order to overcome difficult problems caused by large basis sets. The sparsity of integrals and vectorization on supercomputers were utilized as much as possible. With JASON2, we performed CASSCF calculations on a Fe–porphine complex with 232 CGTFs (contracted Gaussian‐type functions). Our algorithms and timing data of the above calculations are reported.
Comparison of semiempirical MO methods for open‐shell systems
Authors: Higgins Derek , Thomson Colin , Thiel Walter 
Published: January 2005

AbstractThe use of AM1, MNDO, and MNDOC semiempirical MO methods for calculation of heats of formation and ionization potentials of a series of 38 radicals are described. AM1 and MNDO calculations are reported using both half‐electron (HE) and Unrestricted Hartree Fock (UHF) wavefunctions. Results show the MNDOC method to give lowest overall errors, being slightly better than the HE‐AM1 method. In all cases, the AM1 method shows considerable improvement over MNDO.
Representation of the molecular electrostatic potential by atomic multipole and bond dipole models
Authors: Williams Donald E. 
Published: January 2005

AbstractAb initio wave functions using the 6‐31G** basis set were calculated for a set of 24 organic molecules which included saturated and unsaturated hydrocarbons, fluoro compounds, hydroxyl and ether compounds, carboxylic acids, esters, amines, carbonyl compounds, amides, and N‐methyl amides. The electric potential on a grid within a van der Waals shell around each molecule was calculated directly from the wavefunctions. The electric potential values were modeled by placing multipoles up to quadrupoles at atomic sites. The electric potential was well fitted by a model which included atomic monopoles, dipoles, and quadrupoles. Also, the electric potential was modeled by placing dipoles at bond centers. This bond dipole was either allowed to point in any direction, or was restricted to the bond direction. In general the values shown for the monopoles and the values and directions for the bond dipoles were as expected from considerations of electronegativity and reactivity. For the general bond dipole model in a number of cases the direction of the bond dipole was not parallel to the bond direction. It is suggested that this is an artifact caused by the effects of lone pair electrons or electron delocalization on the model. The restricted bond dipole model fitted the electric potential about as well as the atomic monopole model. Atomic monopole values (net atomic charges) and bond dipole values for various atoms, functional groups, and bonds are discussed. Since bond‐dipole interaction energy has better long‐range convergence than monopole interaction energy, bond dipoles are a useful alternative to atomic monopoles.
Structure and properties of small silicon and aluminum clusters
Authors: Jug Karl , Schluff Hans‐Peter , Kupka Hans , Iffert Rüdiger 
Published: January 2005

AbstractSmall Sin and Aln clusters (n = 3–10) were studied with the semiempirical molecular orbital method (MO) method SINDO1. For each n, various structures were optimized to determine the most stable structure. To obtain good qualitative agreement with available ab initio calculations d orbitals had to be omitted from the basis set. Both silicon and aluminum tend to build three‐dimensional structures rather than two‐ or one‐dimensional structures, except for n = 3 or 4. The structure growth was studied by approaching various sites of stable structures with one or more atoms. It was found that silicon and aluminum exhibit different structure growth, and consequently, different most‐stable structures. Ionization potentials, HOMO‐LUMO energy differences, binding energies per atom, and average atomic valencies are presented.
Application of the higher order finite‐element method to one‐dimensional Schrödinger equation
Authors: Kimura Toshiyasu , Sato Nobuyuki , Iwata Suehiro 
Published: January 2005

AbstractThe accuracy and applicability of the finite‐element method of the higher order interpolation functions to the one‐dimensional Schrödinger equation were examined. When the fifth‐order Lagrange and Hermite interpolation functions were used as the basis functions, practically exact solutions were obtained for all eigenvalues of several model potential energy functions. It was demonstrated that the appropriate analytical integration over the potential energy function within each element is important in the matrix element evaluation. The accuracy of the method was examined for the potential functions with a double minimum, which has a large classically forbidden region. The method was also applied to evaluate the Franck‐Condon factors of the transitions between the 1 1Σ and 2 1Σ states of Na2; the latter state having a double minimum in its potential energy function.
A modular strategy for generating starting conformations and data structures of polynucleotide helices for potential energy calculations
Authors: Schlick Tamar 
Published: January 2005

AbstractWe describe a simple and rapid algorithm for generating data structures and starting coordinates of polynucleotides for potential energy calculations. The algorithm is tailored to investigations in cartesian coordinate, rather than dihedral angle, space. First, instead of a tree structure for molecular design, we set up a helix from a simple list of bonds for the basic DNA subunits (sugar, phosphate, and bases). Second, instead of using successive transformations to obtain a set of coordinates in one reference frame, we apply a simple “matching” routine to patch DNA subunits. Third, we avoid ring closure and geometry optimization by allowing deviations from equilibrium values only for PO3′ bond lengths and O5′PO3′ bond angles at the residue connection sites. A double‐stranded helix is constructed from duplex building blocks (2 hydrogen‐bonded nucleotides) which are in turn built from the basic structural units. Every building block is constructed from two sets of geometric variables: {α, β, γ, χ, P, τmax}, one for each strand. The building blocks are then assembled into a helix by using the 6 rigid body transformations {Δx, Δy, Δz, ΘROLL, ΘTILT, ΘTWIST}. For cartesian space programs, generating starting coordinates by this procedure is particularly useful as an alternative to using actual crystal structure coordinates. After describing the algorithm in detail, we illustrate how it was used to generate model A, B, and Z DNA helices. We conclude by suggesting how the algorithm can be used to pursue a build‐up technique and to set up a wide range of starting conformations in the goal of locating novel helical structures.
Deorthogonalization of atomic originals in the CNDO approach
Authors: Chung‐Phillips Alice 
Published: January 2005

AbstractThe procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO‐3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO‐3G and 6‐31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
First and second derivative matrix elements for the stretching, bending, and torsional energy
Authors: Miller Kenneth J. , Hinde Robert J. , Anderson Janet 
Published: January 2005

AbstractMatrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out‐of‐plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out‐of‐plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space‐fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L‐1‐ and L(L‐1)/2‐independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space‐fixed molecular coordinate system.
Continuum radial dielectric functions for ion and dipole solution systems
Authors: Ehrenson S. 
Published: January 2005

AbstractRadial dielectric constant (permittivity) functions for ionic solute, polar solvent systems of the type obtainable from the Lorentz‐Debye continuum field formulations are reexamined. Major interest is focused on the assumptions underlying these formulations and their expression in limiting field behavior. The analysis is extended to dipolar solutes and the importance of two types of corrections are evaluated. The first draws connections with the concept of the reaction field as employed by Onsager. This correction is shown to be significant as regards range of predicted saturation effects and for dipole moment self‐consistency, for the same type molecule serving as solute and solvent. The second type correction involves the phenomenon of electrostriction whose effects appear much more limited both in range and on the intensity of the fields necessary for its observation. Application of the permittivity functions developed to compute modified Born model hydration energies for a variety of ions is illustrated. Excellent asymptotic approximations for all radial permittivity equations of interest are also presented which should enhance their future utility.
Simple alkyldisilanes: MM2 and ab initio studies of their structures and barriers to rotation
Authors: Profeta Salvatore , Unwalla Rayomand J. , Cartledge Frank K. 
Published: January 2005

AbstractFor a series of simple alkyldisilanes, 3‐21G (*) full gradient geometry optimizations have been performed to yield both structural and conformational energy data which was suitable for calibrating the MM2 force field for disilanes. We have examined several model structures which yielded sufficient information about the rotational potential around the Si–Si bond to enable us to revise and augment those reported by Frierson. These parameters were questioned by us in the course of MM2 studies of 1,2‐disilacyclobutanes. We report new Si–Si torsion parameters as well as pertinent structural data from 3‐21G(*) geometry optimizations and relative conformational energies derived from Møller‐Plesset (MP2/MP3) calculations at the 6‐31(*)/3‐21G(*) level. The new parameters were applied to the 1,2‐dimethyl‐1,2‐disilacyclohexane system and those results are also reported.
Combined bond polarization function basis sets for accurate ab initio calculation of the dissociation energies of AHn molecules (A=LI to F)
Authors: Martin J. M. L. , François J. P. , Gijbels R. 
Published: January 2005

AbstractAn alternative route toward developing basis sets for post‐Hartree‐Fock calculations, the hybrid bond polarization function method, is investigated. Two new basis sets, denoted 6‐31G(d, p)+ B and 6‐31 + G(d,p)+B, are defined for the first‐row hydrides. The dissociation energies of the first‐row hydride species in their respective ground states are computed using full fourth‐order Møller‐Plesset theory, and compared with results obtained with large polarized basis sets containing no bond functions. It is shown that results are competitive even with basis sets as large as 6‐311++G(3df,3pd), while computation times are reduced by a factor of 4 to 20. On empirical grounds, the basis set superposition error should be neglected entirely.
Extrapolation of the time‐step bias in diffusion quantum Monte Carlo by a differential sampling technique
Authors: Garmer David R. 
Published: January 2005

AbstractA new method of eliminating the finite‐time‐step error inherent in diffusion quantum Monte Carlo is presented, utilizing an improved version of the existing differential techniques. An implementation is described and results of several small but representative calculations are discussed. The pertinent computation requirements on these systems were reduced by up to a factor of five by the new algorithm. It is speculated that this method may be easily applied to other quantum Monte Carlo and discretized path integral Monte Carlo techniques having related finite step‐size errors with a possibility of obtaining similar good results.
Optimization of parameters for semiempirical methods I. Method
Authors: Stewart James J. P. 
Published: January 2005

AbstractA new method for obtaining optimized parameters for semiempirical methods has been developed and applied to the modified neglect of diatomic overlap (MNDO) method. The method uses derivatives of calculated values for properties with respect to adjustable parameters to obtain the optimized values of parameters. The large increase in speed is a result of using a simple series expression for calculated values of properties rather than employing full semiempirical calculations. With this optimization procedure, the rate‐determining step for parameterizing elements changes from the mechanics of parameterization to the assembling of experimental reference data.