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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 30-35 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A number of cyclobutane derivatives containing one or more double bonds in endo- or exocyclic positions have been studied by the molecular mechanics method within the context of the MM2 force field. Generally speaking, the structures and energies of these compounds are well calculated in cases in which they are known experimentally and are predicted in others. Examples are shown of the use of the moments of inertia of molecules, which are known from microwave studies, in conjunction with molecular mechanics calculations to yield better structures than could be obtained by either method alone. Compounds examined include cyclobutene, methylenecyclobutane, Dewar benzene, and related compounds.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 36-45 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The variable-size simplex optimization method is used to reparametrize the I + A and β parameters of an INDO approximation to the perturbed Hartree-Fock calculation of 13C chemical shifts in hydrocarbons. The absolute shifts for 39 nuclei in a set of molecules containing up to four carbons are reproduced within a standard error of 9.9 ppm for an unconstrained optimization and to a standard error of 10.0 ppm for an optimization constrained to yield gross atomic charges in agreement with double-zeta ab initio calculations.
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  • 3
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A topological model which provides a unifying framework for chemical reactions and molecular structure is proposed. Such basic concepts as overlap, orthogonality, reaction continuity, reaction reversibility, and orbital correspondence are incorporated into the model in a logical fashion. A chemical reaction pathway is regarded as a function that transforms a reactant topological space into its equivalent product space. The unique character usually ascribed to reactants, products, and their wavefunctions is superfluous. The model also allows considerable approximation of the wavefunctions and the reaction pathway without affecting the overall result. A simple orbital mapping technique consistent with the model which traces the transformation of orbitals using intermolecular overlaps of the orbitals is also proposed. The suitability of a given pathway (“allowed” or “forbidden”) can be deduced explicitly without invoking symmetry (or other) rules and without resorting to detailed calculation of reaction energy surfaces. The validity of the mapping procedure has been confirmed by several thermal electrocyclic reactions: the ring-opening isomerizations of substituted cyclopropyl cations, cyclopropyl anion, cyclopropanone, cyclobutene, benzocyclobutene, Dewar benzenes, and 1,3-cyclohexadiene. Orbital mapping with EHT and CNDO/2 MOs correctly predicts the reaction stereochemistry (conrotatory or disrotatory) in every case.
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  • 4
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 46-58 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Current efforts to determine the nature of the interactions that influence protein folding involve, among other things, minimization of an appropriate empirical conformational energy function (ECEPP, Emprical Conformational Energy Program for Peptides) to obtain the native structure. Because of the prohibitive cost of such a massive computational project, either on a conventional large-scale machine at a self-supporting installation or on a dedicated minicomputer, an alternative computer hardware system has been developed to aid in the conformational analysis of proteins. It consists of a Floating Point Systems AP-120B array processor and a Prime 350 minicomputer host. A version of ECEPP has been adapted to run on the AP-120B. The data structures and algorithms chosen for this version reflect the highly unusual parallel architecture of this machine. Benchmark comparisons with BPTI (Bovine Pancreatic Trypsin Inhibitor), a protein of 58 residues and a known structure, have been carried out on this system as well as on an IBM 370/168. They show a significant advantage in speed for the AP-120B/Prime 350 system as well as a substantially lower cost. An energy minimization of BPTI with 154 variable dihedral angles is reported, an effort heretofore prohibited by the computer costs involved.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 6
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 205-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four minimal Gaussian basis sets are generated for the second-row atoms Li through Ne. The first one, MINI-1, consists of a 3-term contraction of primitive Gaussian-type orbitals for 1s, 2s, and 2p atomic orbitals. The convenient shorthand notation would be (3,3) for Li—Be and (3,3/3) for B—Ne. The second one, MINI-2, can be represented by (3,3/4) for B—Ne. In the same way, MINI-3 is described as (4,3) for Li—Be, and MINI-3 and MINI-4 are represented by (4,3/3) and (4,3/4) for B—Ne, respectively. Although the four basis sets are the minimal type, they give the valence shell orbital energies which are close to those of DZ. These four and other sets derived from them are tested for the hetero- and homodiatomic molecules and some organic molecules. They are found to give the orbital energies that agree well with those given by extended calculations. Atomization energies and other spectroscopic constants are also calculated and compared with those of extended calculations. The results clearly indicate that the present basis sets can be used very effectively in the molecular calculations.
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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 240-256 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The optical activity of conjugated dienes is investigated by means of ab initio SCF-CI calculations. The computed electronic spectrum of trans-1,3-butadiene is shown to be in good agreement with the results of more rigorous calculations of the valence transitions and in satisfactory agreement with experiment. The optical rotatory strengths of the lower electronic transitions of twisted 1,3-butadiene as a function of dihedral angle are presented and simulated CD spectra are produced. The N → V1 (π2 → π3*) transition is predicted to have a positive rotational strength for all dihedral angles that correspond to a right-handed twist of the chromophore, in accord with the empirically deduced “diene rule” although for a twist angle of 60°, the rotatory strength is calculated to be almost zero. The role of the orientation of allylic bonds is investigated in the model system 1-butene in which the rotational strength of the π → π* transition as a function of rotation about the 2,3 bond is determined. The effect of allylic bond disposition in dienes on the optical activity of the long-wavelength π2 → π3* transition is simulated by use of the exciton coupling model of Harada and Nakanishi in which two 1-butene molecules with suitable geometries are coupled via interactions of the electric dipole transition moments of their π → π* transitions. The model systems 1,3-butadiene and 1-butene are used to rationalize the apparently anomalous optical activity of (-)-α-phellandrene and (-)-β-phellandrene, both of which should have a diene chromophore with a right-handed twist in their most stable conformers and so should be dextrorotatory. The experimental CD spectrum of α-phellandrene is determined at several temperatures down to -180°C. The observed variation of the apparent rotational strength of the N → V1 transition is in good agreement with that predicted by use of the exciton coupling model.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 189-191 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A MINDO/3 study of homoaromaticity in the 3-cyclobutenyl cation and the Mobius 3-cyclobutenyl anion has been used to evaluate cationic and anionic homoaromaticity quantitatively. π Homodelocalization energies of the two are found equal in isostructural planar comparisons. In planar optimized structures, the homodelocalization energy of the cation is slightly (about 4 kcal) greater than that of the anion, a consequence of the greater 1,3 distance in the latter. Full optimization produces a highly puckered and further stabilized cation, but engenders no change in the Mobius anion. The total stabilization of the cation relative to the anion is 13 kcal, in accord with the generalization that cationic homoaromaticity is more potent than the anionic variety. The fully optimized cation is revealed to actually have a much smaller π homodelocalization energy than the optimized anion, in contrast to the order of overall stabilities. σ-Nonclassical effects, which are stabilizing in the cation but destabilizing in the Mobius anion, provide the rationale for the above.
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  • 9
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The energies of various conformations have been calculated by molecular mechanics for cis and trans isomers of 2,4,7,9-tetraoxabicyclo[4.4.0] decane and 3,5,8,10-tetraoxabicyclo[5.3.0]decane and their methyl derivatives. These molecules are models for reaction products from formaldehyde and the tetrols, pentitols, and hexitols. The conformational equilibria were analyzed for the cis-bicyclo [4.4.0] and cis-bicyclo[5.3.0] systems and compared with available experimental data. The thermodynamic stability of bicyclo[4.4.0] products was found to be higher than that of bicyclo[5.3.0] derivatives in the gas phase in every case studied. Discrepancies with experimental data that exist in a few cases can be ascribed to solvent effects.
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  • 10
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 11
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory is used to examine the effect of substituents on bond lengths in mono- and disubstituted methanes. The relative importance of electrostatic and orbital interaction terms are assessed. The results suggest that for substituents (X) which show powerful σ effects and weak π interactions (e.g., F), the changes in bond length are due primarily to the electrostatic component except in some disubstituted methanes in which case the change in the hyperconjugative ability of the C - X bond is also important. On the other hand, substituents X which show weak σ effects but powerful π interactions (e.g., NH2) affect bond lengths primarily through hyperconjugative interaction of a filled or vacant π-type orbital on X with the adjacent bonds.
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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 334-340 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Equilibrium geometries, force constants, barriers to linearity, charge distributions, dipole moments, and electron spin density of HOO, HOS, HSO, and HSS radicals are calculated by CNDO/2 and INDO methods using respectively the original and some recently introduced scheme of parametrization. Three sets of calculations, namely, CNDO/2(sp), CNDO/2(spd), and INDO, are performed, and the results are compared with the ab initio and experimental values, wherever available. A good agreement is obtained for geometry in the case of CNDO/2 (sp) and INDO calculations. The performance of CNDO/2 (spd) calculations in this regard is quite unreliable. The stretching force constants are considerably overestimated by all the methods, while the bending force constants are in reasonable agreement with the ab initio values. With respect to dipole moments, the CNDO/2 values are in better agreement with the ab initio results than the INDO values. In all the cases, the dipole moment vector directions are in complete disagreement with the ab initio predictions.
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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 358-367 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The localized molecular orbitals (LMOs) of thiophene, furan, and pyrrole are derived from ab initio 4-31G wavefunctions using Boys' criteria for localization. From the transferability point of view, these LMOs are classified as (i) completely different and nontransferable LMOs (these are the lone-pair orbitals on O and N on one hand and those on S on the other hand), (ii) chemically similar lone pairs and inner shells on O and N (of furan and pyrrole, respectively), and (iii) chemically equivalent C—C, C=C, and C—H LMOs in the three heterocycles. The sp3 hybridization of the L core of sulfur, its appreciable polarization, and considerable involvement in bonding in the C—S bond region have been discussed. The present investigation indicates the limitation of the application of semiempirical MO methods to molecules that contain second-row atoms due to both the appreciable core - valence and π-σ interactions involving such atoms. Qualitative investigation of aromaticity and reactivity of the studied heterocycles agrees satisfactorily with experimental observations and shows that conclusions drawn based solely on static factor considerations (charge distribution in the noninteracting molecules) might very well be misleading and such factors determine the ease rather than the final orientation of the substituent.
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 1 (1980), S. 373-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations with full geometry optimization have been carried out on the planar cCc, cTc, tTc, tCt, tTt, and cCt conformers of β-hydroxyacrolein using the 4-21G basis set, and on the cCc and cCt conformers using the 4-31G basis set. The hydrogen-bonded cCc conformer is the most stable and the cCt conformer the least stable, with the other conformers following the above sequence. β-Hydroxy substitution has scarcely any influence on the geometry of the trans-acrolein structure, whereas the geometry of the cis-acrolein structure shows significant changes which depend on whether the O—H group is cis or trans with respect to the CHO group about the C=C bond. The ΔET values for cis → trans isomerization about the C—C bond in cCt and cTc support the hypothesis that these changes in geometry are the result of a destabilizing interaction in cCt and a stabilizing interaction in cTc. The geometry of the hydrogen-bonded structure cCc sets it apart from all the other conformers: it has by far the longest C=C, the longest C=O, the longest O—H, the shortest C—C, and the shortest C—O. Its formation from cCt involves a lengthening of C=C, C=O, and O—H and a shortening of C—C and C—O, indicating a delocalization of charge within the ring. 4-21G calculations have also been made for a distorted cCt structure that has the same bond lengths and angles as the equilibrium cCc structure, and the distortion energy, cCt (equm. geom.) → cCt (distorted geom.), is found to be +13.1 kJ mole-1. Taking the energy of this distorted cCt structure as the baseline, the hydrogen-bonding energy in cCc is found to be  - 80.3 kJ mole-1.
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  • 15
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 87-95 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The carboxylat anion, involved in the structure of numerous compounds of biological interest, participates in a number of intermolecular interactions involving water, cations, and other cellular constituents. A set of ab initio SCF computations have been carried out with an extended polarized basis set on HCOO-, its molecular electrostatic potential, and its interaction with Li+, Na+, K+, and H2O. The results are compared with those of a minimal good quality basis set. An evaluation of the basis set superposition error is made in the two basis as well as that of the contribution of the dispersion energy to the hydration. The analogies and differences in the nucleophilic character of the formate and the phosphate groups are discussed.
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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 73-82 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of the basis set superposition error (BSSE) on the calculated electronic structure of a molecular stacking complex is analyzed with the counterpoise correction method. The complex between para-hydroxyaniline (PHA) and formamidinium cation (FAM) is calculated ab initio with the STO-3G and Whitman-Hornback minimal bases, and with two split valence basis sets: 4-31G and STO-3G(D). When the counterpoise correction is applied, the charge redistribution in the PHA/FAM complex calculated with all four basis sets suggests that the complex is electrostatic in nature and that the main polarization is from the PHA toward FAM. The FAM cation is polarized away from the intermolecular region, thus causing further increase in the electrostatic interaction. This picture is not evident with the STO-3G related bases if the counterpoise correction is not applied. Thus, the BSSE in the charge redistribution is shown to be particularly large in the STO-3G basis and in the diffuse, split valence, STO-3G(D). Both these basis sets suffer from an inappropriate description of the core region. Where there is an improved description of the electron density in the core region, as in the calculations with the energy-optimized Whitman-Hornback basis and with the 4-31G basis, the counterpoise correction has only a very small effect on the charge redistribution. After the counterpoise correction is applied, the two minimal basis sets yield nearly identical charge redistribution results, as do the two split valence bases. It is therefore suggested that basis sets used in the calculation of molecular complexes might be classifiable according to criteria such as the degree of contraction and the quality of the description of angular polarization. This would help in the comparative evaluation of results obtained with different bases since minimal basis sets (or split valence bases) would become directly identifiable as groups yielding qualitatively similar results.
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  • 17
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 18
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 149-156 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry and energy of tetra-tert-butylethylene have been determined by the molecular mechanics method. A twisting of the double bond by 45.5° was found. The ground state of the molecule should be a singlet. The calculated strain energy is higher than those of tri-tert-butylmethane and tetra-iso-propylethylene, but the possibility of synthesis of the compound is not excluded.
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  • 19
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 177-181 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The empirical potential EPEN/2 has been used to establish the structures of isolated hydrogen-bonding ammonia clusters. The most stable forms of the dimer have a linear or near-linear structure. The trimer has a closed structure with zero dipole moment. Two stable tetramer forms were found: one with a closed structure and zero dipole moment in agreement with experimental findings, and one with a pyramidal structure with nonzero dipole moment which may be an artifact of the EPEN/2 potential. The relation of the dimer structures to the limited available experimental information is discussed.
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  • 20
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF-CI calculations on uracil and water-uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C4—O group, while the second is associated with excitation of the C2—O group. In the first n → π* state, hydrogen bonds at O4 are broken, so that the open water-uracil dimer at O4 dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N3—H and a cyclic structure at N3—H and O4 in the ground state, collapses to a different “wobble” dimer at N3—H and O2 in the excited state. The third dimer, a “wobble” dimer at N1—H and O2, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O2 are broken in the second n → π* state, the three water-uracil dimers remain bound. The “wobble” dimer at N1—H and O2 changes to an excited open dimer at N1—H. The “wobble” dimer at N3—H and O4 remains intact, and the open dimer at O4 is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.
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  • 21
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations with a minimal (STO-3G) basis set on a number of sulfur-containing molecules are used to show that Koopmans' theorem and minimal basis calculations may be a simple but adequate way of obtaining inner-shell ionization potentials and chemical shifts of large molecules. The x-ray photoelectron spectrum of (C6H5)2SNSO2C6H4CH3 is discussed with reference to an ab initio SCF minimal basis calculation on the model molecule H2SNSO2H.
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  • 22
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    Journal of Computational Chemistry 2 (1981), S. 225-230 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital (MO) calculations for two series of sulfur-oxygen compounds are reported: the S(IV) system of SO2, H2SO3, HSO3-, and SO32-, and the S(VI) system of SO3, H2SO4, HSO4-, and SO42-. Geometries about the sulfur atoms were optimized using the STO-3G* basis set; energies at these geometries were computed by the STO-3G and 44-31G basis sets both with and without five Gaussian d orbitals on S. The sulfur-oxygen bond lengths and the angles about the central atoms agree fairly well with experiment. The stabilization energy associated with the addition of the d orbitals was found to be a constant amount per bond (ca. 54 and 28 kcal mole-1 in the minimal and extended bases, respectively) in hypervalent compounds. The isomer HSO3- was predicted to be more stable than SO2(OH)-, but the reverse was true for HSO2(OH) compared to SO(OH)2. The deprotonation energies for the acids and the hydration energies for the oxides also were computed and discussed with reference to experimental data.
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  • 23
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    Journal of Computational Chemistry 2 (1981), S. 261-265 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported for H2S, its radical cation, and the H2SSH2+ radical cation. At the MP2/4-31G level the S—S three-electron bond is 2.85 Å long, and has a dissociation energy of 31.2 kcal mole-1. The performance of MNDO semiempirical molecular orbital theory is compared with the ab initio results.
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  • 24
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 251-260 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF and SCF-CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH3, NH2, OH, F, and C2H3 and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C2H3, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.
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  • 25
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    Journal of Computational Chemistry 2 (1981), S. 347-355 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular spin-orbit coupling operator is brought into a simplified form through a convenient choice of origin for the orbital angular momentum operator. The eigenvalue problem of the Hamiltonian that includes the spin-orbit (SOC) operator as a perturbation is solved by means of a linear variational procedure in the basis of the spin-pure molecular eigenstates. Test calculations on benzophenone are presented and the results are compared to experiment. We discuss the minimal size of the spin-pure variational basis needed to achieve stable results as well as the amount of single-excitation configurational mixing needed to describe the spin-pure molecular eigenstates.
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  • 26
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    Journal of Computational Chemistry 2 (1981) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 27
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    Journal of Computational Chemistry 2 (1981), S. 376-383 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical calculations of polymers and solids, especially on an ab initio level, represent a large computational task and therefore necessitate efficient computing methods. This is particularly true for the oscillatory integrals appearing in such calculations. For these integrals efficient integration methods based both on the Chebyshev series and the spline representation of the nonoscillatory part of the integrand are considered; they are found far superior compared with more standard integration rules. In two- and three-dimensional systems, directions with maximum oscillatory behavior can be selected along which these new efficient integration techniques can be used advantageously. The ideas are illustrated by Hückel crystal orbital (HCO) bond orders for the polyacetylene chain and the graphite layer. In the latter example, also, a method for the integration of oscillatory integrands with a singularity is given.
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  • 28
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    Journal of Computational Chemistry 2 (1981), S. 402-409 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Monte Carlo algorithm, capable of simulating numerically the time and space dependence of chemical concentrations in a reacting system, is presented. This method is used to study the phenomenon of trigger waves in the Oregonator model of the Belousov-Zhabotinskii reaction, including the diffusion of species X and Y in one dimension. The results show that a small disturbance in a homogeneous mixture can grow into a chemical (trigger) wave propagating in space at constant velocity. The dependence of this velocity on several factors is studied, namely, initial concentrations, the diffusion of Y, and the stoichiometry of the autocatalytic step of the model. A comparison of the Monte Carlo results with a previous simulation also is discussed.
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  • 29
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    Journal of Computational Chemistry 2 (1981), S. 416-421 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water-water interactions and nonadditivity effects are also significant.
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  • 30
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    Journal of Computational Chemistry 2 (1981), S. 422-432 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations with the STO-3G basis set have been performed to investigate substituent effects on the structures and stabilization energies of water:4-R-pyrimidine complexes, with R including CH3, NH2, OH, F, C2H3, CHO, and CN. Except for the cyclic water:4-aminopyrimidine complex hydrogen bonded at N3, these complexes have open structures stabilized by a nearly linear hydrogen bond formed through a nitrogen lone pair of electrons. When hydrogen bonding occurs at N3, the complexes may have planar or perpendicular conformations depending on the substituent, but when hydrogen bonding occurs at N1, the perpendicular is generally slightly preferred, and there is essentially free rotation of the 4-R-pyrimidine. Primary substituent effects alter the electronic environment at the nitrogens, and tend to make N3 a poorer site for hydrogen bonding than N1, primarily because of a stronger π electron-withdrawing effect at N3. However, the relative stabilities of complexes hydrogen bonded at N1 and N3 are also influenced by secondary substituent effects, which may be significant in stabilizing complexes bonded at N3. Substitutent effects on the structures and stabilization energies of the water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyrimidine complexes are similar to substitutent effects in water:2-R-pyridine and water:4-R-pyridine complexes. Configuration interaction calculations indicate that although absorption of energy by the pyrimidine ring destabilizes the water:4-R-pyrimidine complexes, these may still remain bound in the excited n → π* state. This is in contrast to the fate of open water:2-R-pyridine and water:4-R-pyridine complexes, which dissociate in this state.
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  • 31
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    Journal of Computational Chemistry 2 (1981), S. 460-469 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational behavior of the C-terminal neurotensin pentapeptide, Arg-Pro-Tyr-Ile-Leu OH [NT(9-13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro2-Tyr3) β turn I, an α helix, an extended form, and a (Tyr2-Ile3) β turn III, which are energetically rather close (ΔE 〈 3 kcal/mol). The NT(9-13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.
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  • 32
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Closed-shell SCF calculations on the ground states and direct SCF calculations on the ionized doublet states were carried out for a series of ten-electron hydrides. The correlation of ionization potentials with the degree of protonation and the nuclear charge has been studied for hole states derived from excitation out of both the core and valence molecular orbitals. Calculated proton affinities of the ground states and hole states derived from a given symmetry orbital show a similar trend to that of the ionization potentials.
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  • 33
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    Journal of Computational Chemistry 2 (1981), S. 446-459 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article an algorithm to generate self-avoiding chains fitting a predefined lattice is described. The lattice has to fulfill some mild conditions but can be one, two, or many dimensional. The chains are random in the sense that they are calculated in such a way that every chain fitting the lattice has the same chance to be constructed.
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  • 34
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    Journal of Computational Chemistry 2 (1981), S. 478-482 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The sequential simplex optimization algorithm has been translated into non-Euclidean space. A study of the algorithm in this space suggests that the path of convergence of the simplex depends on the properties of the space so that different convergence paths can be obtained even with the same starting points. The path of convergence approaches the path observed in Euclidean space as the metric constant of the hyperbolic space increases.
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  • 35
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    Journal of Computational Chemistry 3 (1982), S. 154-164 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is outlined which allows an estimation of molecular energies both for a finite basis set including polarization functions and for the Hartree-Fock limit. It is shown that the orbital error of a given minimal basis is covered to a certain relatively constant percentage by an augmented basis set calculation. Thus an improvement factor Qav can be determined by analyzing the corresponding results of small molecules where reasonable estimates of HF limit energies can be taken from the literature. For a combination of Pople's STO-3G and 6-31G* basis sets Qav turns out to be 0.955.
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  • 36
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    Journal of Computational Chemistry 3 (1982), S. 208-213 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation calculated by MINDO/3 are reported for 42 carbocations for which experimental heats of formation have been published. Errors associated with these calculations can be large, with an overall range of ±13 kcal/mol. Correction of systematic errors in the MINDO/3 calculations by means of hydrocarbon models and isodesmic relationships results in a reduction in the range of errors to ±8 kcal/mol. Comparison with experimental heats of reaction of hydride transfer equilibria minimizes experimental errors and gives an average absolute error of 2 kcal/mol with a range of ±3 kcal/mol.
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  • 37
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    Journal of Computational Chemistry 3 (1982), S. 227-228 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Most quantum chemists regard semiempirical methods as ephemeral and computationally cost efficient. For this reason, an article dealing with computational efficiency of semiempirical methods is probably very unfashionable. However, experience at a big computer installation, shared by ab-initio and semiempirical quantum chemists shows that the second group actually consumes more computer time than the first. Obviously, the greater size of the molecules in semiempirical calculations outweighs the inherent efficiency of these methods. The present article describes a simple method for accelerating SCF-type semiempirical methods.
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  • 38
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    Journal of Computational Chemistry 3 (1982), S. 95-111 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Linear mechanisms of catalytic and noncatalytic chemical reactions which are theoretically feasible have been classified and coded using a detailed procedure for the unique numbering of cycles, edges, and vertices in the kinetic graphs. The following classification criteria are used in a hierarchical order: number of cycles and vertices, mutual connectivity of the cycles, manner of linking any pair of cycles, number of elements linking two cycles, mutual position of two cycles joined to a third one, orientation of edges, and presence of pendant vertices. All the types and classes of mechanisms are presented for reactions having up to five and four routes, respectively.
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  • 39
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    Journal of Computational Chemistry 3 (1982), S. 127-129 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: An improved method for obtaining a few eigenvalues and eigenvectors of the symmetric matrix system is presented: \documentclass{article}\pagestyle{empty}\begin{document}$$(A - \lambda S)c = 0$$\end{document} where S ≠ I. The method allows us to handle larger systems more easily than any other known to the author. It requires the inversion of S, and N3 step, but thereafter each eigenvector and eigenvalue is obtained in a length of time proportional to N2. The relation of this method to the MOR and MMOR methods developed recently for handling the case, S = I, is discussed.
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  • 40
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The ionization potentials of iron pentacarbonyl (1), ethylene-iron tetracarbonyl (2), cobalt tetracarbonylhydride (3), and nickel tetracarbonyl (4) have been calculated using a Green's function perturbation method based on the INDO approximation. It is shown that the deviations from Koopmans' theorem are largest in the Co complex, while the smallest reorganization energies of strongly localized MOs with predominant metal 3d character are found in the Fe carbonyls 1 and 2. The calculated Koopmans' defects are analyzed by an investigation of the relaxation terms of the self-energy part and are compared with previous INDO results for Cr, Mn, and Fe tricarbonyl derivatives. Additionally, orbital energies, bond indices, and net charges for the ground states of 1-4 are calculated and compared with experimental data.
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  • 41
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    Journal of Computational Chemistry 3 (1982), S. 185-190 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Nonempirical molecular orbital studies on a series of isomeric octyn-1-ols indicated that the anomalous stability of the alkoxide of 3-octyn-1-ol isomer is probably related to stereochemical and polarization properties of the molecule. The calculations correlated with the experimental observation that the least stable isomer should be the terminal alkyne, 7-octyn-1-ol.
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    Journal of Computational Chemistry 3 (1982), S. 178-184 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry and energy of some bornanylidene, fenchylidene, and bifluorenylidene derivatives have been determined by the molecular mechanics method. Low twisting of the double bond was found for the compounds of the first two series. The difficulties found in the synthesis of 2-di-tert-butylmethylenefenchane can be related to a remarkable strain energy which is only slightly lower than that of tetra-tert-butylethylene. A twisted conformation is the preferred one in bifluorenylidene and its 1,1′-dimethyl derivative (E isomer) in agreement with experimental data. Conformational inversion and E-Z interconversion paths are discussed for the latter compound and theoretical results are compared with dynamic NMR data.
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  • 43
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    Journal of Computational Chemistry 3 (1982), S. 372-380 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Spin-orbit and dispersion energy contributions to the energy curves of XeF are examined. A rapid variation in the spin-orbit coupling with internuclear separation is found for both the ground and excited states. This result can explain the experimentally observed ordering of the ionic excited states when the spin-orbit perturbation couples 2σ and 2π energy curves obtained by both all-electron and effective core potential (ECP) calculations at the first-order configuration interaction (FOCI) level of accuracy. Damped dispersion energy contributions to the ground-state energy curve are shown to be comparable to the charge transfer contribution. The energy curve for XeF is in reasonable agreement with experimental results and a calculation of the analogous XeCl curve confirms the qualitative correctness of the calculation. The energy curves and transition moments were then applied to two problems related to the efficiency of the XeF laser. Photodissociation of the X state provides a means of removing a bottlenecked vibrational level but a calculation of the radiative transition probability between the X and A states finds the cross section is too small to yield rates competitive with collisional deactivation. The bottlenecked state may also be removed by electron dissociative attachment but the calculated energy curves for the X states of XeF and XeF- do not cross at a low energy indicating a small cross section.
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  • 44
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    Journal of Computational Chemistry 3 (1982), S. 445-450 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparison is made of MNDO and MINDO/3 calculations for saturated silicon-containing molecules, and with experimental values, for heats of formation, molecular geometries, charge distributions, and ionization potentials. Except for bond angles, it is found that with the published parameter values the MINDO/3 program gives more reliable results than MNDO. For unsaturated molecules, a comparison of bond lengths and stabilities of Si multiple bonds as given by the two programs and ab initio methods is made, and large discrepancies between predicted structures are pointed out. Some reasons for the dicrepancies are discussed.
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    Journal of Computational Chemistry 3 (1982), S. 468-470 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The dication C2H22+ has been investigated by ab initio molecular orbital theory. It is found to have a linear (D∞h), structure with a triplet (3σ-g) ground state. Deprotonation to C2H+ is exothermic by 9.8 kcal/mol, but this process is hindered by a large barrier of 65 kcal/mol.
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    Journal of Computational Chemistry 3 (1982), S. 265-268 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicit functional forms for both the two-electron Coulomb integral, (aa∣bb), and the one-center core-orbital integrals, ZA-1 (aa∣ZA), are derived which permit the penetration integrals to be fully derived and calculated. With these forms the 3Σu+ of the H2 molecule is unstable. These forms are generalized so that they are suitable for optimizing semiempirical predictions of experimental one-electron properties.
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    Journal of Computational Chemistry 3 (1982), S. 274-274 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 3 (1982), S. 605-605 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 1-8 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF calculations of the equilibrium geometries have been carried out on nine possible isomers of MH2N2, where M = C or Si, and compared with the results of MNDO calculations. The results for the carbon compounds are in good agreement with available experimental data, but in the case of the silicon compounds, the molecules are predicted to be unstable with respect to decomposition to SiH2 and N2. The inclusion of electron correlation at the MP3 level does not alter the order of the relative stabilities, although the importance of the correlation contribution varies substantially between the different isomers.
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    Journal of Computational Chemistry 4 (1983), S. 23-32 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer-oriented algorithm is developed for enumerating and generating all rigorously planar benzenoid hydrocarbons. An additional algorithm is also developed for identification and enumeration of carcinogenic bay regions. The results are reported for undisrupted benzenoid structures up to ten fused rings. The reported numbers of isomeric benzenoids do not agree with the results in the literature, because other authors included in their considerations some polyhexes which are not strictly planar structures (e.g., helicenes) or which represent rings of hexagons (e.g., circulenes). The reported results for enumeration of bay regions fully agree with those of Balasubramanian et al.
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  • 53
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    Journal of Computational Chemistry 4 (1983), S. 58-67 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A low-cost microcomputer and package of assembly language routines has been developed to emulate the structure and performance of a large analog computer. The advantages of the analog computer, as implemented in this scheme, include (1) a significant reduction in the programming effort involved in modeling complex dynamic systems and (2) the control of the simulation and model parameters in a completely interactive and flexible manner. The symbolic nomenclature and schematic representations involving devices, such as integrators, comparators, multipliers, and function generators, offers a powerful alternative to the more conventional numerical methods, that is, to provide very simply the solutions to large systems of differential equations. This approach invariably leads the user to a more thorough understanding of the dynamic character of the system. The technique is illustrated using a chemical kinetics example involving the simulation of laser-induced fluorescence. The results of this work have provided an assessment of a systematic error that occurs when using induced resonance fluorescence to measure OH concentrations in the troposphere of the earth.
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    Journal of Computational Chemistry 4 (1983), S. 104-109 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Approximate minimum energy reaction paths have been calculated for two thioketone-enethiol tautomeric systems using an ab initio SCF-MO method. The calculations indicate nearly equal stabil ties of the isolated tautomers in both systems and an energy barrier of ca. 85 kcal/mol for their interconversion. This barrier is expected to be significantly lower in solution as a result of solvent-solute interactions.
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    Journal of Computational Chemistry 4 (1983), S. 114-122 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 molecular mechanics force field, as modified for halogens, is able to predict the structures, dipole moments, and energies of the isomers of benzene hexachloride. For benzene tetrachloride and naphthalene tetrachloride the field exaggerates the stability of conformers with axial chlorine, but gives satisfactory results if the field is modified to allow for interaction between electronegative substituents and the π electrons.
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    Journal of Computational Chemistry 4 (1983), S. 124-124 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 57
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    Journal of Computational Chemistry 4 (1983), S. 127-135 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A relativistic effective core potential (REP) has been generated for the uranium atom and used in self-consistent-field calculations of the A states of UH, UF, and their ions. Energy curves were calculated at the base configuration level which ensures the dissociating atoms are described by Hartree-Fock wavefunctions. The electronic bonding of these molecules is found to be similar to that of comparable alkaline-earth hydrides and fluorides. The uranium 6p, 6d, and 5f orbitals retain their atomic character but the orbitals extend into the bonding region and are distorted by overlap repulsion and electrostatic effects. Nonetheless, the atomic energetic coupling determines that low energy states will have the maximum spin multiplicity and maximum orbital angular momentum projection consonant with the charge-transfer bonding.
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    Journal of Computational Chemistry 4 (1983), S. 154-157 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Following an earlier proposal to evaluate electron repulsion integrals over Gaussian basis functions by a numerical quadrature based on a set of orthogonal polynomials (Rys polynomials), \documentclass{article}\pagestyle{empty}\begin{document} $$ (\eta \eta \parallel \eta \eta) = 2(\rho/\pi)^{1/2} \sum\limits_{\alpha = 1, N} I_x(u_{\alpha})I_{y}(u_{\alpha}) I_z(u_{\alpha})W_{\alpha} $$ \end{document} a computational procedure is outlined for efficient evaluation of the two-dimensional integrals Ix, Iy, and Iz. Compact recurrence formulas for the integrals make the method particularly fitted to handle high-angular-momentum basis functions. The technique has been implemented in the HONDO molecular orbital program.
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    Journal of Computational Chemistry 4 (1983), S. 175-180 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: CNDO/Force and compliance constant methods were applied to define general quadratic potential functions for F2CO and HCOF. A satisfactory set of compliants was obtained by suitably scaling down the stretching and stretch-stretch elements of the initial force constant matrix, evaluated by the CNDO/force approach, followed by fitting the compliants to available experimental data.
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    Journal of Computational Chemistry 4 (1983), S. 218-225 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of the determination of the vibration-rotation eigenvalue in diatomic molecules is considered. An eigenvalue equation totally independent from the eigenfunction is written for any potential, analytical or numerical. This equation uses uniquely the vibration-rotation canonical functions; its resolution is reduced to that of a simple and classical numerical problem. Examples of numerical applications for analytical (Morse) and numerical potentials are presented. It is shown that the vibrational eigenvalues deduced from the eigenvalue equation are within 10-6 cm-1 of the exact values. Comparison with conventional methods are presented and discussed.
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  • 61
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Symmetry methods employed in the ab initio polyatomic program HONDO are extended to the coupled perturbed Hartree-Fock (CPHF) formalism, a key step in the analytical computation of energy first derivatives for configuration interaction (CI) wavefunctions, and energy second derivatives for Hartree-Fock (HF) wavefunctions. One possible computational strategy is to construct Fock-like matrices for each nuclear coordinate in which the one- and two-electron integrals of the usual Fock matrix are replaced by the integral first derivatives. “Skeleton” matrices are constructed from the unique blocks of electron-repulsion integral derivatives. The correct matrices are generated by applying a symmetrization operator. The analysis is valid for many wavefunctions, including closed- or open-shell spin-restricted and spin-unrestricted HF wavefunctions. To illustrate the method, we compare the computer time required for setting up the coupled perturbed HF equations for eclipsed ethane using D3h symmetry point group and various subgroups of D3h. Computational times are roughly inversely proportional to the order of the point group.
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    Journal of Computational Chemistry 4 (1983), S. 449-460 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As a model reaction for peptide and bond formation, the SN2 reactions between glycine and ammonia have been studied with and without amine catalysis: \documentclass{article}\pagestyle{empty}\begin{document}$${\rm NH}_3 + {\rm NH}_2 {\rm CH}_2 {\rm COOH} + ({\rm NH}_3 ) \to {\rm NH}_2 {\rm CH}_2 {\rm CONH}_2 + {\rm H}_2 {\rm O} + ({\rm NH}_3 )$$\end{document} using ab initio molecular-orbital methods. For each of the catalyzed and uncatalyzed reactions, two reaction mechanisms have been examined: a two-step and a concerted mechanism. The stationary points of each reaction, including intermediate and transition states, have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of the reaction. The calculations demonstrate that a second ammonia molecule catalyzes amide bond formation, and that the two-step mechanism is more favorable than the concerted one for the catalyzed reaction, while for the uncatalyzed reaction both mechanisms are competitive.
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  • 63
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Basis-set balance parameters, defined in terms of various projections of an abstract force vector in the space spanned by the logarithms of orbital exponents, are evaluated for a sample of 100 Gaussian basis sets. These basis sets are taken from a random Gaussian distribution of bases, centered on the best energy, fully variational uniform quality (UQ) atomic orbital (AO) basis sets. With each basis geometry optimization has been carried out for model molecule dimethyl sulfoxide, the wavefunction of which molecule is exceptionally sensitive to basis-set errors. Correlations between the balance of basis sets and calculated molecular properties are analyzed.
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  • 64
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    Journal of Computational Chemistry 4 (1983), S. 513-523 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory has been used to probe the effect of the substituent X on the structures, strain energies, stabilization energies, inversion barriers, and proton affinities of carbanions CH3CX CH3- and cis-C3H4X-, where X = H, F, CN, and NC. All geometries have been optimized with a 3-21G basis set, and the parent anions (X = H) were also optimized with the same basis set with a diffuse function added (i.e. the 3-21 + G basis set). The anions, with the exception of the α-cyanoisopropyl anion, are pyramidal. The out-of-plane angle, α, for the pyramidal anions decreases in the order F 〉 H ≈ NC 〉 CN, and the barriers to inversion follow the same order with the cyclopropyl anions consistently having higher barriers than the isopropyl anions. The substituents strongly stabilize the anions with the stabilization energy following the order CN 〉 NC 〉 F. The cyano group slightly reduces the strain energy of cyclopropane, but the isocyano and fluoro substituents are weakly and strongly destabilizing, respectively. The pyramidal cyclopropyl anions are less strained than the cyclopropanes except when the substituent is a cyano group where the strain energies are reversed but are very similar. The planar anions all have higher strain energies than the cyclopropanes.
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    Journal of Computational Chemistry 4 (1983), S. 552-555 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A very simple yet effective device for reducing the number of self-consistent-field (SCF) cycles in central finite-difference calculations of molecular properties is presented. The efficiency of this is demonstrated by MINDO/2 calculations of the force constants of a variety of molecules. The device consists of using information about the wavefunction at two values of a perturbation parameter to provide an estimate of the wavefunction at a third. This estimate is then used as an initial guess in an SCF procedure. The underlying theory is discussed and applications to other problems are suggested.
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    Journal of Computational Chemistry 4 (1983), S. 567-577 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio computation procedure to obtain electronic transition wave numbers in solution is presented and discussed. The continuum description of the bulk solvent is adopted, and solute-solvent interaction is reduced to a closed-form interaction operator added to the solute Hamiltonian. The resulting Schrödinger equations are solved variationally. No limitations are imposed on the shape of the solvent cavity or on the level of accuracy of the ab initio procedure.
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    Journal of Computational Chemistry 4 (1983), S. 605-605 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 594-604 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PA) of 80 neutral bases were calculated using the semiempirical molecular orbital procedure MNDO. These were compared with the corresponding experimental and, where available, ab initio STO-3G and 4-31G data. For the 12 bases studied which led to ions which were not hyperconjugatively stabilized, the mean absolute error between the calculated and experimental values was 7.2 kcal mol-1. However, a plot of these data revealed a clear tendency of MNDO to underestimate the PAs of the more basic molecules. Where hyperconjugative stabilization of the ion was possible, the calculated PAS were underestimated by a further 7-10 kcal mol-1 for each attached alkyl group. Calculated and observed methyl-and ethyl-cation affinities were compared for 18 bases with qualitatively similar results.
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    Notes: Ab initio crystal orbital calculations have been performed on regular polyethylene chains applying basis sets of minimal and double-zeta quality. Relative stabilities of periodic all-trans, all-gauche, and alternating trans-gauche conformers have been evaluated, including extensive geometry optimization. Potential curves for a simultaneous rotation around C—C single bonds from the all-trans to the all-gauche conformation have been computed applying the rigid-rotor approximation, the flexible-rotor approximation, and an additional reoptimization of C—C distances. A rigid-rotor potential curve from the all-trans to the alternating trans-gauche conformation has been computed as well. Results obtained are compared with ab initio calculations on butane and pentane and with semiempirical and empirical force-field studies on polyethylene.
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    Journal of Computational Chemistry 5 (1984), S. 64-71 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The degrees of conformational freedom of poly L-D β-helical chain are analyzed consistent with the helical parameters of gramicidin A structure. From conformational energy calculations, “helical librations” that can be sustained by this structure are described and the energy of libration as a function of the cavity size is presented. Two different modes of conformational change are identified corresponding to librations of all L-D-peptide units or all D-L-peptide units while retaining the helical parameters. Such helical librations are considered relative to conformational perturbations due to the presence of an ion in the channel.
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    Journal of Computational Chemistry 4 (1983), S. 410-418 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical calculations with the semiempirical molecular orbital (MO) method SINDO1 were performed on excited states of the following five- and six-membered heterocycles containing nitrogen: imidazol, pyrazol, pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine. The geometries and adiabatic excitation energies of T1, S1, S2 were calculated. We also present charges, bond orders, and dipole moments. Consequences of these results for UV spectroscopic data are discussed.
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    Journal of Computational Chemistry 4 (1983) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 4 (1983), S. 461-469 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy calculations are presented for the head-to-head dimerized β helices for Gramicidin A transmembrane channel structures. The calculations take into account both left- and right-handed β helices, and various side-chain conformations. The energetics of the dimerization is studied by considering various docking geometries. It is concluded from these vacuum-energy calculations that the lowest energy conformation for the channel dimer is that comprised of left-handed β helices.
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    Journal of Computational Chemistry 4 (1983), S. 488-493 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: UMNDO reaction path calculations for trapping of the ethylene-cation radical with ground state oxygen suggest that formation of a dioxetane radical cation proceeds through the intermediacy of a peroxycation radical. The predicted enthalpy of activation (ΔH
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    Journal of Computational Chemistry 4 (1983), S. 506-512 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General guidelines for development of small but efficient basis sets for intermolecular interaction calculations have been proposed and tested for simple model systems. It has been demonstrated that the use of overlap matched atomic orbitals (OMAO) leads to significant improvement in the first-order exchange and electrostatic penetration contributions. Basis sets assuring proper charge distribution lead to a better description of the electrostatic multipole component. The ab-initio effective-core-model potential technique permits a considerable reduction of basis size while having little effect on the selfconsistent field (SCF) interaction energy if basis-set superposition error is corrected properly.
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    Journal of Computational Chemistry 4 (1983), S. 524-541 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical calculations of the geometric, energetic, electronic, and vibrational features of a transition structure for gas-phase water-formaldehyde addition (FW1
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    Journal of Computational Chemistry 5 (1984), S. 197-199 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Group equivalents which are useful for converting energies derived from ab initio calculations into enthalpies of formation have been obtained. They allow ΔHf to be estimated from 6-31G* energies with an uncertainty on the order of ±2 kcal/mol.
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    Journal of Computational Chemistry 5 (1984), S. 207-215 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effect of different exponents, Slater, Burns, Clementi, and Best Limited Molecular Orbital (BLMO) on the approximate one-electron property expectation values from minimum basis-set calculations is reported for Roothaan-Hartree-Fock (RHF), neglect of diatomic differential overlap (NDDO), and maximum overlap method (MOM) calculations on FH, CO, and LiH.
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    Journal of Computational Chemistry 5 (1984), S. 225-229 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Changes of electronic charge distribution following the lowest singlet n-π* transitions of benzaldehyde, benzamide, benzoic acid, the phthalaldehydes, pyridine, and the diazines have been examined using the CNDO-S/CI method. A Singlet n-π* transition is found as a general rule to direct electronic charges to the para position of the atom in the ring that carries the lone pair or to which the substituent carrying the lone pair is attached.
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    Journal of Computational Chemistry 5 (1984), S. 261-262 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 5 (1984), S. 241-247 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
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    Journal of Computational Chemistry 5 (1984), S. 272-279 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Various algorithms for evaluating nonbonded interactions in molecular dynamics (MD) simulations of macromolecular systems are considered, and a combination of two techniques using a space grid for finding neighbor atoms is proposed. The application of grid search techniques to nonrectangular periodic systems is discussed. Finally, the computing time required by different algorithms is compared on a Cray-1 vector processing computer as well as on a CDC Cyber 170/760 sequential computer. Neighbor list techniques turn out to be faster than the grid search techniques for the systems considered here. However, storage requirements may exclude the use of neighbor list techniques for large systems. Finally, MD of complex macromolecular systems turned out to be about 4-14 times faster on a Cray-1 than on a Cyber 170/760.
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    Journal of Computational Chemistry 5 (1984), S. 280-287 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program is described which evaluates the second-order Møller-Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two-dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree-Fock. Some numerical results and timings are presented.
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    Journal of Computational Chemistry 5 (1984), S. 299-306 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanical calculations for hetero-substituted hydrocarbons present certain difficulties that are not encountered in dealing with hydrocarbons. Ways are proposed to overcome such difficulties, sometimes by two-step or iterative computation. The following topics are considered: fitting the force field by using data from studies in solution; ways to estimate atomic charges or, alternatively, bond moments; ways to account for field effects upon atomic charges and bond moments.
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    Notes: It is shown that a Lagrange multiplier method to constrain one or several internal coordinates, or averages and combinations of these, is easily implemented in a molecular mechanics computer program that uses Newton-Raphson (NR) minimization. Results are given for constraints on nonbonded distances and torsion angles. When a potential energy surface is to be explored, it is much better to constrain the average of three torsion angles around a bond than to constrain a single torsion angle. Certain conversions can only be achieved when averages of torsion angles around different bonds are constrained. Combinations of constraints have been applied to evaluate differences between calculated and observed geometries and to obtain transition states for relatively large molecules from results for smaller molecules at relatively low costs. The efficieny of the combination of the Lagrange multiplier method and NR minimization in terms of computing time can be rated as good.
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    Journal of Computational Chemistry 5 (1984), S. 343-348 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical calculations by the combined empirical force-field (EFF)-extended Hückel molecular orbital (EHMO) approach confirm that octalene and benzo-|c|-octalene present π-bond fixation with a common single bond between the cyclooctatetraene and cyclooctatriene fragments, whereas the structure of dibenzo-|c, j|-octalene is characterized by a central double bond. The dynamic behavior of these compounds is discussed and the interconversion energy barriers are calculated; the inversion of the cyclooctatriene ring is faster than that of the cyclooctatetraene ring in octalene, but it is slower in benzo-|c|-octalene.
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  • 87
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    Journal of Computational Chemistry 5 (1984), S. 349-352 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas fully exploiting the periodicity symmetry of the electron density of polymers are deduced. They are shown to lead to efficient algorithms for the evaluation of Coulomb and exchange interactions in those systems.
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  • 88
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    Journal of Computational Chemistry 5 (1984), S. 363-373 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized monopole expansions for the subunits of the nucleic acids are developed by a reparametrizatio of the Hückel-Del Re procedure designed to reproduce closely the electrostatic properties obtained with precise overlap multipole expansions. It is shown that satisfactory values of both potential and field may be obtained for different DNA conformations and for a transfer RNA. The charge redistribution occuring between the subunits upon forming the nucleic acids is also investigated by ab initio calculations and accounted for in developing the new parametrization.
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  • 89
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    Journal of Computational Chemistry 5 (1984), S. 381-386 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The nitrogen protonation energies of the imino bases HN=CHR, where R is H, CH3, NH2, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree-Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree-Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree-Fock nitrogen protonation energies of the imino bases HN=CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O=CHR.
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  • 90
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    Journal of Computational Chemistry 5 (1984), S. 395-410 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry and energy of 2-aza-1,3-butadiene and 2,3-diaza-1,3-butadiene have been calculated using the 6-31G* basis set as a function of the CNCC and CNNC dihedral angles, respectively. With the 2-aza derivative potential minima are located at 0° (trans) and at about 130° for a gauche structure approximately 9.5 kJ mol-1 less stable than the trans. Potential maxima are at about 75° giving a gauche barrier height of approximately 19 kJ mol-1 relative to the trans structure, and at 180° (cis) giving a barrier height of approximately 14.5 kJ mol-1 relative to the 130° gauche structure. With the 2,3-diaza derivative the gauche barrier has disappeared and there are a series of gauche structures in the region 70°-100° of almost equal energy 12.5-15 kJ mol-1 less stable than the trans. In addition the cis barrier is much greater, nearly 70 kJ mol-1 relative to the trans structure. Inclusion of electron correlation, accounting for about 50% of the correlation energy, produces no significant changes in the shape of the potential energy curves. There are systematic and progressive changes in almost all the geometrical parameters as the =CH— groups in butadiene are replaced by =N—. The outward tilt and compression within the methylene groups show adverse steric interactions to be operative in the cis structures. The values of Vnn indicate that gauche structures of both the 2-aza and the 2,3-diaza derivatives near the cis structure are more compact (as with butadiene), and gauche structures of the 2-aza derivative near the trans structure are less compact (as with butadiene). Originating in the changes in bond lengths and bond angles, rotation-independent nuclear-nuclear interactions again play an important role.
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  • 91
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    Journal of Computational Chemistry 5 (1984), S. 441-450 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A number of force fields of the molecular mechanics type have been tested for their ability to represent as an energy minimum, the observed crystal structure for three cyclic hexapeptides, cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), and cyclo-(-D-Ala-D-Ala-Gly-Gly-Gly-Gly-). The most effective force field tested was that recently proposed by Kollman and co-workers, notwithstanding its use of “united” atoms for CH, CH2, and CH3 groups. Fields proposed by Levitt, and adaptations of that of Scheraga and co-workers, were also effective. Force fields in which hydrogens bonded to electronegative atoms were not specified explicitly were less accurate in representation.
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  • 92
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    Journal of Computational Chemistry 5 (1984), S. 576-580 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Accurate vibration-rotation eigenvalues EvJ are sought for very high levels (up to dissociation) of a diatomic potential. The method used is the recent “eigenvalue equation” method [Kobeissi et al., J. Comput. Chem., 4, 218 (1983)] which dissociates the determination of the eigenvalue from that of the eigenfunction. A new mathematical formulation for any numerical potential is presented, which reduces the problem to the use of a single recurrent formula. A numerical application to the model potential used by Cashion [J. Chem. Phys., 39, 1872 (1963)], up to v = 23, gives results equal to the exact eigenvalues to approximately 10-14 cm-1. Another application to the model potential used by Johnson [J. Chem. Phys., 67, 4086 (1977)], up to v = 60, gives similar results.
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  • 93
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    Journal of Computational Chemistry 5 (1984), S. 535-547 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio self-consistent-field (SCF) algorithm taking into account all the features of the one-dimensional translational periodicity and the helical symmetry is presented. This algorithm includes the long-range correction to the Coulomb potential and is designed to calculate the band structure of periodic one-dimensional polymers (planar or helical). Its efficiency in terms of computing time and numerical accuracy is tested via applications on a (LiH)n chain, polyethylene, and four conformers of polypropylene.
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  • 94
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    Journal of Computational Chemistry 5 (1984), S. 598-605 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO molecular orbital calculations have been employed to investigate limited reaction pathways and potential energy surfaces for a series of SN2 reactions. Model calculations for X- + CH3X (X = H, F, OH, OCH3, and CN) indicate that the MNDO method gives qualitative agreement with ab initio studies except for the hydride-CH4 exchange. Studies involving alkylation of pyridine (Menschutkin reaction) were also carried out. For the reaction of pyridine with CH3Cl, which involves charge separation, our MNDO studies (which do not include solvation effects) do not produce a characteristic SN2 pathway. For the reaction of pyridine with trimethyloxonium cation [(CH3)3O+] as the alkylating agent, a well defined SN2 reaction pathway was obtained; this reaction involves charge transfer. A potential energy surface for the pyridine-trimethyloxonium cation reaction shows the presence of a saddle point transition state that resembles starting materials, in agreement with the Hammond postulate for this exothermic reaction.
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  • 95
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The vertex numbering obtained by application of the HOC algorithm can be converted into two sequences of numbers: If each vertex starting with vertex 1 is only counted once, the sums of numberings of adjacent vertices form sequence Si (i = 1-N), while the sums of Si values form sequence Mi (i = 1-N). These two sequences can be used for (i) two new topological indices, M and N, the latter being of extremely low degeneracy, and the former correlating with boiling points of alkanes; (ii) a criterion based on sequence Si for ordering graphs which possess the same number N of vertices; and (iii) a quantitative measure, also based on sequence Si, for appreciating the similarity or dissimilarity of pairs of graphs. Comparisons with other topological indices, ordering criteria, and similarity measures for graphs show that the newly devised procedures compare favorably with those known previously.
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  • 96
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    Journal of Computational Chemistry 5 (1984), S. 640-649 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The core potentials for atoms of atomic numer 1-18 fitted to ion spectra by Chang, Habitz, Pittel, and Schwarz have been extended to the molecular case in a Gaussian lobe basis by using a six-Gaussian (6G-POT) representation for the exponential factors of the atomic core potentials. In a (9s/5p/1d) basis the 6G-POT one-electron energies, dipole moments, and Mulliken charges are improved over a one-Gaussian potential form for HF, NH3, and H2O; BeO also yields good agreement within 2.6% of the experimental bond length. For HCl, the core potential shows larger errors in the dipole moment (7%) and one-electron eigenvalues (2%), but a 75% saving in computer time is realized for HCl compared with only about 35% for first-row systems using the 6G-POT core potentials. Analytical expressions are given to extend the 6G-POT method up to s, p, d, f, and g valence shells.
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  • 97
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    Journal of Computational Chemistry 5 (1984), S. 612-628 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab inito molecular orbital calculations of the phosphorus- and sulfur-containing series PH2X, PH3X+, SHX, and SH2X+ (X = H, CH3, NH2, OH, F) have been carried out over a range of Gaussian basis sets and the results (optimized geometrical structures, relative energies, and electron distributions) critically compared. As in first-row molecules there are large discrepancies between substituent interaction energies at different basis set levels, particularly in electron-rich molecules; use of basis sets lower than the supplemented 6-31G basis incurs the risk of obtaining substituent stabilizations with large errors, including the wrong sign. Only a small part of the discrepancies is accounted for by structural differences between the optimized geometries. Supplementation of low level basis sets by d functions frequently leads to exaggerated stabilization energies for π-donor substituents. Poor performance also results from the use of split valence basis sets in which the valence shell electron density is too heavily concentrated in diffuse component of the valence shell functions, again likely to occur in electron-rich molecules. Isodesmic reaction energies are much less sensitive to basis set variation, but d function supplementation is necessary to achieve reliable results, suggesting a marginal valence role for d functions, not merely polarization of the bonding density. Optimized molecular geometries are relatively insensitive to basis set and electron population analysis data, for better-than-minimal bases, are uniform to an unexpected degree.
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  • 98
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    Journal of Computational Chemistry 5 (1984), S. 571-575 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Classical conformational analysis was applied to the study of the variation of heats of formation (HOF) and geometrical parameters of small-ring propellanes. As expected, the calculated HOF is the smallest for [4,4,4] propellane I and the largest for [2,2,2]propellane X. In spite of the different trends exhibited by the strain energy components, the calculated HOF values may be reproduced within a simple additivity scheme. The calculated bridgehead-bridgehead bond length is the longest for [2,2,2]propellane (1.655 Å), lowers with increasing molecular size, and is equal to 1.558 Å for [4,4,4]propellane. In agreement with experimental findings the latter value is significantly larger than the standard value of 1.54 Å typical for unstrained hydrocarbons. Other calculated geometrical parameters as well as HOF values cannot be compared with experimental and/or theoretical results since there is a lack of reliable experimental data. Surprisingly, [2,2,2]propellane was found to be more flexible than the less strained bicyclo[2,2,2]octane.
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  • 99
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    Journal of Computational Chemistry 2 (1981), S. 20-29 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital structures and energies of B2F4, B2Cl4, N2O4, and C2O42- have been calculated for both perpendicular D2d and planar D2h rotamers. The experimental trend toward greater preference for the D2d forms in going from B2F4 to B2Cl4 is reproduced. N2O4 favors the planar conformation, although the rotation barrier is overestimated at the theoretical levels used. The oxalate dianion is calculated to be more stable in the D2d conformation; the experimental planar arrangement in the solid may be due to crystal packing forces. The preferences for one conformation over another are small; analysis indicates that different effects may predominate in each case: π stabilization for B2F4, hyperconjugation for B2Cl4, lone-pair interactions for N2O4, and electrostatic repulsions for C2O42-.
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  • 100
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Means by which the Onsager theory of dielectrics may be modified in a general way to include important structurally nonspecific electrical effects exercised at or near the cavity boundary are developed and discussed. In essence they rely upon extraction of limiting numerical solutions of the Laplace equation potentials for multiple shells approximating regions of smoothly varying permittivity surrounding the dipole-containing cavity. The results of several such modifications, which usefully retain the original reaction and cavity field forms, are applied to evaluate the dielectric constants of polar solvents acting as support media for mean-space-charge attenuation of intracavity electrical interactions, and in correlation of isolated molecule and condensed phase properties of formally nonassociated solvents. For the most part such predictions and correlations are found to be improved by a wide variety of physically reasonable continuity functions. Where they are not, more rational patterns of deviations consistent with possible modes of intramolecular charge transfer and weak intermolecular association in formally nonassociated liquids are detected. Some limited comparisons with particle- and structure-dependent theories, e.g., the mean spherical model and discrete lattice formulations, also suggest that the present permittivity modifications can effectively simulate important short-range nonspecific liquid ordering effects. Various factors relating to possible adaption of the limit procedures developed to other inhomogeneous dielectric medium calculations are also briefly outlined.
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