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  • Biochemistry  (145)
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  • 1980-1984  (145)
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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 58-62 
    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 simple and very rapid method for the calculation of electrostatic isopotential maps is proposed. The potential is composed of transferable bond fragments. According to chemical evidence, σ-, lone-pair, and π-bond contributions are considered. The computational work is proportional to the first power of the number of bond orbitals; therefore very large systems, such as enzymes or DNA, can be handled also. Transferability of bond orbital characteristics such as polarity, s character, and orientation is discussed. Though the absolute value of the potential is overestimated, trends obtained with STO-3G calculations are reflected correctly.
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  • 2
    Electronic Resource
    Electronic Resource
    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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  • 3
    Electronic Resource
    Electronic Resource
    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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  • 4
    Electronic Resource
    Electronic Resource
    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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  • 5
    Electronic Resource
    Electronic Resource
    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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  • 6
    Electronic Resource
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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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  • 7
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 244-250 
    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 set of programs has been developed to calculate molecular spin-orbit interaction with Gaussian-type wavefunctions in connection with the popular GAUSSIAN 76 program. The spin-orbit contributions to the fine structure of O2 (X3∑g-), NH (X3∑-), and CH2 (X3B1) are evaluated with the standard STO-3G and 6-31G basis sets; for NH the influence of bond functions added to the latter basis set is also investigated. The results are compared to values previously obtained with other types of basis sets.
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 273-277 
    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 semianalytic method is presented for computing the concentration distribution in enzyme-substrate fast reaction systems. By means of this method, not only can much computation work be saved but a semianalytic expression for the concentration distribution will be obtained. This expression is very useful for analysis and discussion of the kinetic characteristics of this kind of reaction system.
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  • 9
    Electronic Resource
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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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  • 10
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 12
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 15
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    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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  • 16
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 40-46 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several deficiencies and potential sources of error in the torsion angle driving method, the approach employed most frequently for the simulation of conformational interconversions, have been studied. A general explanation of the observed effects is given in terms of the energy surface and of the effects brought about by “side valleys.” Several examples of molecular mechanics calculations of conformational interconversions, among them the cyclohexane ring inversion, illustrate the problems.
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  • 17
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    Journal of Computational Chemistry 3 (1982), S. 62-68 
    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 molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(=NH)NH2], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine =NH is preferred over the -NH2 site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN=CN cis and trans isomers, respectively, while all the stable HC(NH2)2+ and HC(NH)2- species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C - N single-bond rotation in HC(=NH)NH3+, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN=CN isomers, respectively.
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  • 18
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    Journal of Computational Chemistry 3 (1982), S. 112-116 
    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 the H2SSH· and H2SCl· radicals and for the H2SClH+· radical cation. The two neutral species are found to be very weakly bound van der Waals' complexes, whereas the H2SClH+· radical cation is bound by 11.9 kcal mol-1 at MP2/4-31G. The importance of charge in σ* radicals is discussed.
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  • 19
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    Journal of Computational Chemistry 3 (1982), S. 117-124 
    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 blend of Haselgrove's method and the biased selection method for evaluating multidimensional integrals was tested. The results were mixed. The error estimate varied from being proportional to 1/N when N was less than ca. 60,000 to being proportional to 1/√N when N was greater than 60,000. Also, for N greater than 60,000, the error estimate was one-half the error estimate given by biased selection alone. These numbers should be compared with the 10,000 points used to find an optimum set of Haselgrove's parameters. It is reasonable to expect that if 100,000 points were used in the optimization of Haselgrove's parameters that the above results would be found with 60,000 replaced by 600,000.
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  • 20
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    Journal of Computational Chemistry 3 (1982), S. 130-134 
    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 axial Gaussian lobe orbital (AGLO) representations of 3d and 4f orbitals proposed by LeRouzo and Silvi have been angularly optimized to ensure spherical symmetry of filled 3d and 4f shells. The functions have been tested on the hydrogen atom in the presence of high quality s and p basis sets and found to provide excellent minimal Gaussian representations of polarization functions. Exact orbital degeneracy is not obtained within each shell, however. Tabulated values are given to allow arbitrary scaling of the 3d and 4f lobe mimic orbitals.
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  • 21
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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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  • 22
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    Journal of Computational Chemistry 3 (1982), S. 208-213 
    ISSN: 0192-8651
    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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  • 23
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    Journal of Computational Chemistry 3 (1982), S. 227-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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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  • 24
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    Journal of Computational Chemistry 3 (1982), S. 260-264 
    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 steps in a nonconventional algorithm for self-consistent field calculations are outlined, and calculations on cumulenes are given to demonstrate the convergence properties of the method. The approach is essentially open ended and is likely to be cost effective on computer systems with minimal core.
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  • 25
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    Journal of Computational Chemistry 3 (1982), S. 273-273 
    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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  • 26
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    Journal of Computational Chemistry 3 (1982), S. 445-450 
    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 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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  • 27
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    Journal of Computational Chemistry 3 (1982), S. 468-470 
    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 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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  • 28
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    Journal of Computational Chemistry 3 (1982), S. 477-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Neutral, protonated, and deprotonated formamide isomers were studied at the 3-21G SCF level with complete geometry optimization. Ten stable structures, ten first-order saddle points, and three second-order saddle points (conformational maxima) are reported. [Total energies are reported in hartrees (1 hartree = 627.51 kcal/mol = 2625.5 kJ/mol) and energy differences are reported in kJ/mol (1 kJ/mol = 0.239 kcal/mol).] Rotational barriers and proton affinities are discussed and compared to isoelectronic amidine species.
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  • 29
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 495-506 
    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 structures of the methyl and silyl amines and phosphines and their ions have been calculated using ab-initio SCF theory and the 3-21G basis set. The computed structures give excellent agreement with the available experiment data without the inclusion of d functions, with the exception of (SiH3)2N- and the isoelectronic molecules (SiH3)2O and (SiH3)2C2- where d functions are essential. The observed trends in computed basicities and acidities are reproduced by the calculations.
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  • 30
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    Journal of Computational Chemistry 3 (1982), S. 548-551 
    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 conversion of the cyclobutene cation radical to the 1,3-butadiene cation radical has been studied using MINDO/3 and ab initio SCF MO methods. Not only smooth electrocyclic but also stepwise, non-electrocyclic routes were considered. Both calculational methods agree that the preferred reaction path is a novel nonelectrocyclic one proceeding through an intermediate “cyclopropylcarbinyl cation radical.” The quantitative agreement in the activation parameters calculated by the two methods is excellent. The proposed intermediate also provides an attractive explanation for the mass spectrometric fragmentation patterns of the cyclobutene and butadiene cation radicals.
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  • 31
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    Journal of Computational Chemistry 2 (1981), S. 1-6 
    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 barriers on the MINDO/3 reaction paths for π and σ approaches to concerted cycloaddition of methylene to s-cis-1,3-butadiene are analyzed by a new energy decomposition scheme and compared to the results of published extended Hückel calculations. The relatively small (6 kcal) preference for the σ approach is essentially based on next-nearest-neighbor (1,3) resonance interactions, which are stabilizing in the σ but destabilizing in the π approach. Both routes are characterized by large distortion energies (mainly disrotation at the diene termini in the case of the π approach) and nonbonded repulsions. The excessive magnitude of both of these effects ultimately derives from the weak pericyclic binding which prevails at initial diene geometries, especially the pericyclic topology involving the methylene LUMO. Although previous work has emphasized the contribution of closed-shell repulsions to the barrier, no such effect is explicitly included in MINDO. The closed-shell repulsions to which the extended Hückel barrier has been solely attributed are shown to involve next-nearest-neighbor (antiaromatic) resonance interactions.
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  • 32
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    Journal of Computational Chemistry 2 (1981), S. 14-19 
    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, has been used to establish the structures of isolated hydrogen-bonded clusters in methanol. The most stable configuration of the dimer is found to have a trans near-linear form, whereas the most stable forms of the trimer and tetramer are cyclic. Charge interactions in the tetramer make it the most stable, in terms of energy per hydrogen bond, of these three species. These results are in conformity with various types of experiment. Other species of dimer, trimer, and tetramer, corresponding to local energy minima, have also been identified.
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  • 33
    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 C=O bond length and fC=O,C=O, the corresponding harmonic stretching force constant, are calculated ab initio using the 4-31G basis set (augmented by polarization functions on the sulfur and chlorine) with full geometry optimization for the monosubstituted carbonyl compounds RCHO, where R = H, CHO, CH=CH2, CO2H, CH=CHOH, OH, OC(=O)OH, OOH, S—H, Li, F, Cl, and NH2. Straight-line relationships are found in plots of ln[fC=O,C=O] vs. ln[rC=O] for the series of compounds in which carbon atoms and oxygen atoms are bonded directly to the carbonyl carbon, in accordance with the empirical expression f = C′/rn. The slopes and intercepts give n = 7.62 and 6.47, C′ = 62.6 and 48.6, for the lines with carbon and oxygen as the atom bonded directly to the carbonyl carbon, respectively. The point for formaldehyde lies very close to the C line, whereas the points for SH, Li, F, Cl, and NH2 lie closer to the O line.
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  • 34
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    Journal of Computational Chemistry 2 (1981), S. 161-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters for sulfoxides used in force field MM1 were modified to be incorporated into force field MM2. The conformations of ten alkyl sulfoxides were then calculated using MM2 with these new parameters. The alkyl groups used were methyl, ethyl, isopropyl, and t-butyl. It was found that of the many possible conformations for these compounds, only one or two stable conformers exist, and that the number of these conformers agrees with the number of reported S—O stretching frequencies in almost every case. No apparent correlation between the vibration frequency and the molecular structure was found.
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  • 35
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    Journal of Computational Chemistry 2 (1981), S. 182-187 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Harmonic force fields have been calculated for the planar hydrogen-bonded ring conformer of β-hydroxyacrolein, cCc, which is the most stable, and the chain conformer, cCt, generated by 180° rotation of O—H about the C—O bond axis. The equilibrium structure obtained using the 4-31 G basis set with full geometry optimization was employed in each case. Selected force constants for the bonds directly concerned in the formation of the ring from the chain structure, and the increments in going from the one to the other, are compared with the values for the corresponding conformers of performic and formic acids. As the ring size increases from four in trans-formic acid, to five in cis-cis-performic acid and to six in the cCc conformer of β-hydroxyacrolein there is a successive increase in the mechanical strength of the hydrogen-bridging unit. The energy changes for the chain → ring conversion do not follow this progression: performic acid is out of order. But, since a force constant is a localized bond property, whereas the energy changes are determined not only by interactions specific to the hydrogendonor and hydrogen-acceptor groups but also by interactions involving more distant parts of the molecule, the force constants for the bonds directly concerned in the formation of the hydrogen bridge provide a less ambiguous basis for comparing the strength of the intramolecular hydrogen bonding.
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  • 36
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    Journal of Computational Chemistry 2 (1981), S. 188-199 
    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 the structural, energetic, and electronic properties of mixed water-uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N1—H and O2, N3—H and O2, and N3—H and O4. Open structures form at O4, N1—H, and N3—H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N1—H and the cyclic one at N1—H and O2. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N3—H and a cyclic structure at N3—H and O4. The third cyclic structure at N3—H and O2 collapses to the “wobble” dimer at N3—H and O4. The two “wobble” dimers are significantly more stable than the open dimer formed at O4, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N1—H than N3—H, owing to a more favorable molecular dipole moment alignment when association occurs through H1. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water-uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.
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  • 37
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    Journal of Computational Chemistry 2 (1981), S. 287-303 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a computer program we have been developing to build models of molecules and calculate their interactions using empirical energy approaches. The program is sufficiently flexible and general to allow modeling of small molecules, as well as polymers. As an illustration, we present applications of the program to study the conformation of actinomycin D. In particular, we study the rotational isomerism about the D-Val-, L-Pro, and L-Pro-Sar amide bonds as well as comparing the energy and structure of the Sobell model and the x-ray structure of actinomycin D.
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  • 38
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    Journal of Computational Chemistry 2 (1981), S. 304-323 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials and Mulliken net atomic charges were calculated from STO-3G, 6-31G, and 6-31G** SCF-MO wavefunctions for hydrogen fluoride, water, ammonia, methane, acetylene, ethylene, carbon dioxide, formaldehyde, methanol, formamide, formic acid, acetonitrile, diborane, and carbonate ion. In each case optimized net atomic charges (potential-derived charges) were also obtained by fitting the electrostatic potentials calculated directly from the wavefunctions in a shell enveloping the molecules outside of their van der Waals surfaces. The electrostatic potentials calculated from the potential-derived charge distributions were then compared with the defined quantum mechanical electrostatic potentials and with the electrostatic potentials of the Mulliken charge distributions.
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  • 39
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    Journal of Computational Chemistry 2 (1981), S. 356-360 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: At high levels of ab initio theory (6-31G*//4-31G), the most stable C4H42+ isomer is indicated to be the nonplanar cyclobutadiene dication (1a); the planar form, 1b, is indicated to be 7.5 kcal/mol less stable. The second most stable C4H42+ isomer, the methylenecyclopropene dication, is indicated to prefer the perpendicular (2a) over the planar (2b) arrangement by 7 kcal/mol. The “anti van't Hoff” cyclo-(HB)2C=CH2 system (4), isoelectronic with 2, also prefers the perpendicular conformation (4a), and retains the C=C double bond. The linear butatriene dication (3) is the least stable C4H42+ species investigated. The perpendicular (D2d) arrangement (3a), permitting double allyl cationlike conjugation, is preferred over the planar D2h form (3b) by 26 kcal/mol. The heat of formation of the most stable form of C4H42+, 1a, is estimated to be 623-640 kcal/mol. This species should be thermodynamically stable toward dissociation into smaller charged fragments.
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  • 40
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New estimates of Hartree-Fock limit energies (ERHF) for selected AH and AHn hydrides, diatomic and linear polyatomic molecules have been made utilizing ESCF values recently reported in the literature for HF, N2, CO, NH3, and CH4 which are very close to the respective limits. These new values have been used to investigate the applicability of Ermler and Kern's procedure for estimating ERHF: i.e., a factor f is first evaluated from data for reference molecules, where f = ERHF/ESCF, which is then used with ESCF values for other molecules to obtain their ERHF values. f has been evaluated for three groups of reference molecules—HF, H2O, NH3, CH4, N2, and CO; CH4, C2H2, C2H4, and C2H6; and C2H2, HCN, and N2—utilizing ESCF data in the literature for many Gaussian-type orbital (GTO) basis sets together with some new values calculated at the (9,5,1) to (13,8,2) levels. Trends in the variation of f within each group of reference molecules from one basis set to another, and the trends in f from one group of reference molecules to another, are discussed in detail. To minimize the influence of these effects in an ERHF estimate it is recommended that the f value should be derived from reference molecules which possess a similar combination of structural features, i.e., bonded hydrogen, single, double, or triple bonds, and the number of lone-pair electrons. Further calculations show that an f value based on data for closed-shell molecules is not applicable to open-shell species.
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  • 41
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    Journal of Computational Chemistry 2 (1981), S. 53-57 
    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 charge distributions along the CH bonds of methane, ethylene, and acetylene have been obtained by numerical integration of 6-31G** wavefunctions. Several criteria for assigning electron populations to carbon and hydrogen lead to negative charge on H for methane and ethylene and a positive charge on H for acetylene. These results are contrasted with the charges derived from the μCHeff obtained from infrared intensity measurements. The difference between the results from infrared intensities and from the electron density calculations has been shown to result from incomplete orbital following in the molecular deformation and the creation of a “bent-bond” moment. Its magnitude has been estimated.
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  • 42
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    Journal of Computational Chemistry 2 (1981), S. 83-86 
    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 modified integral package for evaluation of two-electron integrals over Gaussian basis functions is described. Modifications are implemented in the MOLECULE program system and are especially suited for the study of large molecules and molecular complexes.
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  • 43
    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 Gaussian-type basis sets for molecular calculations are usually prepared by an atomic SCF program in which spherical coordinates are used. On the other hand, many molecular SCF and CI programs are written by using the Cartesian coordinates and as a result six-membered d-type functions (x2, y2, z2, xy, yz, zx)e-γr2 are often used. They contain one additional 3s function which does not exist in the atomic calculation. Therefore, we shall have an incorrect, deeper molecular binding energy, unless we readjust the atomic total energy by adding the 3s orbital to the original basis set. Some examples are shown in the case of Cu2 molecule, where we have found that the correction is quite appreciable, which was overlooked in previous work.
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  • 44
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    Journal of Computational Chemistry 2 (1981), S. 108-125 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Compact contracted Gaussian basis sets introduced in the preceding article are tested for ab initio molecular calculations on molecules containing third-row atoms (Na through Cl). It is found that the effect of splitting valence orbitals is essential for these molecules and addition of polarization functions to split basis sets can yield computed geometries, spectroscopic constants, and atomization energies in close agreement with the result of near Hartree-Fock calculations.
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  • 45
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    Journal of Computational Chemistry 2 (1981), S. 157-160 
    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 new method is presented for the calculation of partition coefficients of solutes in water lipid systems. Log P values are calculated based on the charge densities of the atoms as determined by quantum mechanical methods. In this article, the results have been obtained from charge densities calculated by two methods: MINDO/3 and Hückel-type calculation based primarily on topology. Results are favorably compared with those obtained by fragment analysis.
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  • 46
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    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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  • 47
    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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  • 48
    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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  • 49
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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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  • 50
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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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  • 51
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    Journal of Computational Chemistry 2 (1981), S. 266-272 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Significant improvements in calculational efficiency and capability with the self-consistent electron pairs (SCEP) method has resulted from several new computational developments. A new procedure for constructing the important internal Coulomb and exchange operators has substantially reduced the preiteration time. A general scheme for utilizing molecular symmetry has been used to advantage in reducing the number of pair functions and external operators that must be found explicitly at each iteration. A projection operator tool has been implemented and found to be quite effective at minimizing the number of iterations required at some point on a potential energy surface when an SCEP wavefunction exists for some nearby point. These and other improvements in the program construction have yielded sizable reductions in time for some representative test cases, including water and a potential energy curve for formaldehyde. The new SCEP program also performs low-order perturbation theory treatments and coupled electron pair approximation (CEPA) calculations using the same operator approach. The usefulness of the approach is demonstrated by very large scale calculations on the stability of the two interstellar glycine conformers. These calculations involve the variational treatment of 82,205 symmetry-adapted singly and doubly substituted configurations involving 225 internal electron pairs.
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  • 52
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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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  • 53
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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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  • 54
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    Journal of Computational Chemistry 3 (1982) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 55
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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: Orbital mapping analysis based on CNDO/2 molecular orbitals has been used to survey the thermal ring-opening isomerizations of cyclobutenes and benzocyclobutenes. Isoelectronic substitutions within the molecular framework of cyclobutene (e.g., CH2 replaced by CH-, OH+, NH, NH2+) result in ground-state orbital correlations via both conrotatory and disrotatory pathways in several cases, in contrast to the parent hydrocarbon conrotatory stereochemistry. The results substantiate the heteroatom effects previously revealed by orbital mapping for the disrotatory thermal isomerizations of isoelectronic Dewar benzenes. Qualitative patterns, such as nodal shifts in the butadiene π orbital, are discussed in relation to the mapping correlations. The isoelectronic benzocyclobutenes give ground-state orbital correlations via conrotatory pathways only, which suggests that delocalization may reduce the heteroatom perturbation.
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  • 56
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    Journal of Computational Chemistry 3 (1982), S. 471-476 
    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 distance geometry approach to conformational calculation has been shown to be very effective at producing large molecular structures satisfying many given, long-range constraints on the interatomic distances. I now present a significant extension of the method that handles strictly geometric constraints as well as before while also locating conformers of very low energy. The main feature of the algorithm is a projection of the molecule from a low energy conformation in a high dimensional space to three dimensions in such a way as to perturb the energy as little as possible. Tests of the method on very small systems with simple energy functions completely explored by independent means show that the global minimum of energy is sometimes attained. In every case the final energy is very low, and geometric constraints are completely satisfied.
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  • 57
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    Journal of Computational Chemistry 3 (1982), S. 486-494 
    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 MNDO-UHF method has been applied to a large number of organic and inorganic radical species. The obtained results demonstrate that thermodynamical data as well as their equilibrium structures are in reasonable agreement with experimental findings.
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  • 58
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The O—H bond length and the quadratic, cubic, and quartic stretching force constants, calculated ab initio using the unscaled 4-31G basis set with full geometry optimization, are reported for 30 planar conformers of ten molecules contaning either the C—OH, N—OH, or O—OH group. The data are analyzed in terms of the general form of Clark's equation, and the power functions and exponential functions proposed by Herschbach and Laurie. In the case of the quadratic constants, significant trends are found in the values of the parameters depending on whether the O—H group is bonded to carbon, nitrogen, or oxygen, and whether it is non-hydrogen-bonded or involved in intramolecular hydrogen bond formation in four-, five-, or six-membered rings. Using data for diatomic molecules, O—H, and C—H bonds, and the C=O and C—C bonds in planar monosubstituted carbonyl compounds, the parameter dij in the power function equation for quadratic constants, which can be regarded as the distance of closest approach of the two nuclei, is shown to increase progressively along the series (i) diatomic molecule; (ii) similar bond in a polyatomic environment with one of the two atoms covalently bonded to a neighboring atom; (iii) as in (ii) but with the second atom hydrogen bonded; and (iv) with both atoms covalently bonded to neighboring atoms.
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  • 59
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    Journal of Computational Chemistry 3 (1982), S. 556-560 
    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 improved version of the direct inversion in the iterative subspace algorithm is developed. The method is significantly more efficient than the previous version, and is applicable to intrinsically divergent or slowly convergent cases. Comparisons indicate that the method is superior to the recently proposed quadratically convergent (QC-SCF) method of Bacskay.
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  • 60
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    Journal of Computational Chemistry 3 (1982), S. 571-579 
    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 electronic states and barriers to internal rotation in allene (1a), 1-silaallene (2a), and 2-silaallene (3a) are investigated computationally using ab-initio molecular orbital methods. Planar geometries with two-, three-, and four-π-electron configurations have been considered as possible transition states (1b-3d). Structures have been optimized at the Hartree-Fock level with a small split valence basis set (3-21G) and higher level calculations with basis sets of split valence (6-31G) and split valence plus polarization function (6-31G*) quality include correlation energy estimates from Møller-Plesset second-and third-order perturbation theory. The electronic barrier to internal rotation in allene is estimated near 53 kcal/mol whereas the corresponding barriers in 1-silaallene and 2-silaallene are considerably smaller, ca. 35 and 20 kcal/mol, respectively. The transition states are predicted to possess bent geometries in all three molecules with open-shell singlet, three-π-electron configurations in 1 and 2 (1c, 2c) but a closed-shell singlet, two-π-electron configuration in 3 (3d).
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  • 61
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    Journal of Computational Chemistry 3 (1982), S. 603-603 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 62
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Ab initio molecular orbital calculations are reported for complexes of hydroxide and methoxide anions with water and methanol. The basis set dependence of the results is carefully considered for HO- ⃛ H2O. 4-31G and 6-31G* calculations yield similar geometrical predictions; however, the 6-31G* basis set is superior for computing dissociation energies. Further extension to the 6-31G** level provides little change. The dissociation energies for the complexes range from 25 to 37 kcal/mole with hydroxide ion and methanol acting as the strongest base and acid. The difference in gas phase acidities of water and methanol is halved by the introduction of one solvent molecule.
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  • 63
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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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  • 64
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    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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    Journal of Computational Chemistry 2 (1981), S. 363-367 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF Hartree-Fock calculations are used to predict properties of the guanidinium fragment present in tetrodotoxin and saxitoxin, toxins known to block the sodium channels of the nerve cell membrane. The results, in terms of net atomic charges and geometries, are compared to similar calculation results obtained for the Na+-H2O complex.
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    Journal of Computational Chemistry 2 (1981), S. 384-391 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: With a view of using data on solutions and liquids for parameter fitting in molecular mechanical force fields, Abraham's theory of solvation is incorporated in the force field procedure. Geometries and bond moments are estimated internally, partial account being taken of bond-bond induction, and used to calculate the intramolecular electrostatic energy, dipole moment, and the dipole and quadrupole terms in the solvation energy. Three dielectric constants are used, one for the solute in the vapor, one for the solution, and one for the intramolecular space through which dipole-dipole interactions take place. Examples are given, including such where computation differs with measurement, to illustrate the performance of the scheme.
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    Journal of Computational Chemistry 2 (1981), S. 414-415 
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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 energy hypersurface for the system Li(H2O)4+-F(H2O)4- is investigated using the polarization model. A possible mechanism for the production of HF in this solution droplet is observed.
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    Journal of Computational Chemistry 2 (1981), S. 433-445 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parametrization of MNDO for aluminum and comparisons of calculated molecular properties with experimental values indicate the general usefulness of MNDO to study aluminum-containing compounds. Although results are not as good as for molecules containing only C, H, N, and O, they are nevertheless accurate enough to be useful, especially when predictive biases noted in this article are considered. Inclusion of the d orbital in the MNDO scheme may improve the aluminum results. Results for boron-containing molecules not previously reported are also reported in this article.
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    Journal of Computational Chemistry 3 (1982) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 70
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Ab initio molecular orbital theory with the STO-3G basis set is used to examine both charge and energy interactions in a series of meta- and para-substituted phenylborate anions and toluenes. Comparison of the results is made with data for substituted anilinium cations. It is concluded that whereas NH3+ is a powerful σ acceptor, with essentially no π interaction, BH3- is primarily a π donor, and, to a slight extent only, a π donor. CH3 is indicated to be both a weak σ and π donor. Energies of interaction of BH3- and NH3+ with a series of substituents are an order of magnitude larger than corresponding values for CH3. Interaction energies for BH3- are of opposite sign to those for NH3+. The results may be understood qualitatively using perturbation molecular orbital (PMO) theory.
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    Journal of Computational Chemistry 3 (1982), S. 23-27 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The reaction between atomic oxygen and carbon disulfide is predicted to lead to at least two primary products, which are the dithiiranone (1) and the oxathiirane-thione (2) and/or the carbon disulfide S-oxide (4). The possible intramolecular equilibria 1 ⇄ 2, 1 ⇄ 3, 2 ⇄ 4, and 2 ⇄ 5 as well as the fragmentations of the possible intermediates 1-5 have been studied theoretically within the semiempirical CNDO/B framework as conceivable ground-state reactions. On the basis of MO correlations and potential energy changes along the reaction paths, supplementary with previously reported experimental data, the single molecular transformations and the eventual product formations are discussed.
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    Journal of Computational Chemistry 3 (1982), S. 28-36 
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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 topological resonance energy (TRE) model was introduced independently by the Zagreb Group (in 1975) and by Aihara (in 1976). Several practical obstacles arise in the computation of TRE. Ways to surmount them are pointed out. Descriptions of algorithms, optimizations, and the efficient computer program are presented. Possible numerical instability is discussed.
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  • 73
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    Notes: The molecular structures of tricyclohexane, norbornane, quadricyclane, and cubane were completely refined by standard ab initio force relaxation on the 4-21G level. The results can be used as a basis to interpret some contradictory experimental reports found in the literature and to establish some hitherto unobserved structural trends involving the C—C and C—H bond distances of the cases studied. Group Delta;E values for C—(H)3(C), C—(H)2(C)2, and C—(H)(C)3 (Benson's notation) derived from the total energies of the completely relaxed 4-21G geometries of a number of unstrained hydrocarbons are also listed. The values are used to estimate the strain energies of the systems studied and of the optimized 4-21G geometries of cyclopropane, cyclobutane, cyclohexane, and bicyclo (2.1.0)pentane. Cooperative effects in the strain energies are discussed.
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    Journal of Computational Chemistry 3 (1982), S. 75-88 
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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: This article develops computer programs for computer generation of nuclear spin species and nuclear spin statistical weights of rovibronic levels. The programs developed here generate nuclear spin species and statistical weights from the group structures known as generalized character cycle indices (GCCIs) which are computed easily from the character table of the PI group of the molecule under consideration. Procedures are illustrated with examples.
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    Journal of Computational Chemistry 3 (1982) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 3 (1982), S. 135-139 
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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: It is well known that if the formation of hydrocarbons during Fischer-Tropsch synthesis occurs via the condensation polymerization mechanism, there is little hope for selectivity enhancement in the desired range of products. Recent data on low surface area model catalysts, where readsorption is unlikely, have shown that at low conversions, the product distribution obeys the condensation polymerization mechanism and the distribution of products is shifted to lower-molecular-weight hydrocarbons. We have used a computer simulation of the growth of hydrocarbon chains to obtain a picture of the catalyst surface under synthesis conditions. Such an approach could prove useful in distinguishing between various theoretical models. We have applied the simulation to compare the changes in selectivity when readsorption occurs and when it does not. The dynamic behavior of the reacting system which is obtained from the computer results has shown that selectivity to lower-molecular-weight hydrocarbons is a stronger function of the extent of reaction than the incorporation of readsorption into the chain growth mechanism.
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  • 77
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Bond correlation energies ∊(XY) have been derived by partitioning second-order Rayleigh-Schrödinger-Møller-Plesset (RSMP) correlation energies. Values of ∊(XY) depend on the type of bonding between atoms X and Y. They can be considered as comprising correlation energies of bond, lone, and inner-shell electron pairs of the group XY. Once a set of appropriate increments ∊(XY) has been obtained, it is possible to estimate unknown RSMP energies of larger molecules. This concept also can be used when estimating total correlation energies E(CORR). For this purpose e(XY) values have been derived from known E(CORR) energies of small molecules. It is shown that ∣∊(XY)∣ increments increase linearly with the number n of electron pairs of the group XY. The function ∊(n) becomes zero for n = 1/2 (one uncorrelated electron) and passes through -0.042 for n = 1, which is approximately the correlation energy of the bonding electron pair of H2 or a 1s inner-shell pair. With the aid of estimated E(CORR) and HF limit energies, Schrödinger energies and theoretical heats of formation of relatively large molecules are obtained.
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    Journal of Computational Chemistry 3 (1982), S. 191-207 
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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: It is shown that even the CPMET approximation for the contributions of fourfold excitations can be replaced by a more sophisticated method. Furthermore, an approximation is presented for the contributions of threefold excitations which are neglected in CPMET. Finally, it is described how the advantages of different CEPA methods can be united in a single CEPA scheme (called CEPA-U). The various approximations are discussed in terms of Slater determinants, and it is shown how the relatively large amount of details can be handled with the help of computer programs, i.e., how knowledge engineering can be successfully applied here.
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    Journal of Computational Chemistry 3 (1982), S. 229-233 
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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: Fifty-one structures have been calculated by the MINDO/3 method to evaluate the errors introduced by branching and by the presence of the heteroatom. The structures are evaluated by comparisons which reveal that the calculated ΔHf values reflect a bias because of the presence of the heteroatom. With two carbons or more in a chain attached to a heteroatom group, a linear relationship exists which makes possible the calculation of reasonably accurate ΔHf values for unbranched alcohols, primary or secondary amines, ethers, thioethers, thiols, and alkyl chlorides. Branching errors do not seem to be linearly related among the systems. Some errors in calculations of geometries are also discussed.
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    Journal of Computational Chemistry 3 (1982), S. 234-250 
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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: Theoretical HF/6-31G* (Hartree-Fock, 6-31G* basis set) and MP2/6-31G* (second-order Møller-Plesset, 6-31G* basis set) vibrational frequencies based on complete quadratic force fields have been obtained for a set of 36 one- and two-heavy-atom molecules comprising first-row elements for which experimental spectroscopic data are available. Frequencies calculated at the HF/6-31G* level are an average of 12.6% higher than experimental values. Partial treatment of electron correlation via the perturbation method of Møller and Plesset, terminated at second order, leads to a significant reduction in this error, although theoretical MP2/6-31G* frequencies are still larger than the experimental quantities by 7.3%. Part of the difference may be traced to the restriction of quadratic force fields, as comparison with experimental harmonic frequencies shows deviations of only 9.5% and 4.7% for the two levels, respectively. The calculated frequencies are used in conjunction with the corresponding theoretical equilibrium structures to obtain absolute molecular entropies, which may in turn be used to yield entropies of reaction. These latter quantities are generally in good accord with entropies derived using experimental structures and frequencies.
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    Journal of Computational Chemistry 3 (1982), S. 273-273 
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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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    Notes: The molecular structure of the stretched form of n-nonane, as a typical long-chain hydrocarbon, was refined by geometrically unconstrained ab initio force relaxation on the 4-21G level. The C—C bonds and C—H bond distances in the interior of the hydrocarbon chain are found to be longer (by about 0.001 Å and 0.002 Å, respectively) than those near the end of the chain. Similarly, interior C—C—C bond angles are 0.4° larger than the terminal angles. The variation of structural parameters with distance from the molecular ends levels off after the second carbon atom, and the geometry of methylene is practically constant from C3 on. However, if one end of the system is perturbed by moving the inplane methyl hydrogen away from equilibrium, the resulting destabilizing electronic effects are transmitted through the C—C bond distance chain in such a way that significant perturbations are still experienced at C5. Molecular mechanics (MM2) gives a structure in which the small changes in bond lengths and angles with chain location are well reproduced.
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    Journal of Computational Chemistry 3 (1982), S. 305-316 
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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 formalism developed in the preceding article is used in a normal coordinate analysis of the pyrimidine base cytosine. The results of both planar and nonplanar vibrations are reported. The model yields 66 frequencies with an average error of about 6.5 cm-1 (ca. 0.5%). The vibrational modes are compared with experimental data and discussed in terms of potential energy distributions and Cartesian displacements. Two isolated low-frequency (near 200 cm-1) out-of-plane modes are predicted in the vicinity of where two such modes are believed to occur. In addition, the model has taken into account the observed coalescence of the torsional and wagging modes of the amino group upon deuteration of the amino group. Recent data from sulfur-substituted cytosine (2-thiocytosine) were useful in making assignments.
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    Journal of Computational Chemistry 3 (1982), S. 329-334 
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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 coefficients of a 1/R expansion (containing long-range electrostatic interaction, medium-range electrostatic-induced dipole attraction, short-range dispersive attraction, and very short overlap interaction terms) have been determined, within a semiempirical approach, from the results of a priori calculations. The formulation has been applied to the study of the stable conformations of benzene complexes.
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    Journal of Computational Chemistry 3 (1982), S. 354-362 
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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 experimental IR and Raman spectra of ethylene oxide have been reinvestigated with particular attention to the intensities. The absolute IR intensities have been measured for the gaseous state. The spectra have been simulated by using a normal coordinate analysis coupled with a CNDO determination of the intensities. The intensity calculation using polarization functions appears to be more reliable than the standard version. Furthermore, the force field has been extended for ethylene sulfide.
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  • 86
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    Journal of Computational Chemistry 3 (1982), S. 385-399 
    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 principles and structure of an LCAO-MO ab-initio computer program which recalculates all two-electron integrals needed in each SCF iteration are formulated and discussed. This approach - termed “direct SCF” - is found to be particularly efficient for calculations on very large systems, and also for calcuations on small and medium-sized molecules with modern minicomputers. The time requirements for a number of sample calculations are listed, and the distribution of two-electron integrals according to magnitude is investigated for model systems.
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  • 87
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    Journal of Computational Chemistry 3 (1982), S. 417-420 
    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 force field has been used to calculate the strain energies of a representative series of bridgehead alkenes, and the results compared to similar previous calculations using the MM1 force field. The new results roughly parallel the old ones, although the strain energy of a given compound is normally higher with MM2 than MM1. These differences are largely negated, however, when the OS (olefinic strain) value is considered.
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  • 88
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: With the purpose of deciphering conformational inversion processes of typical mobile bicyclic molecules, torsional energy surfaces near the enantiomers of bicyclo[4.2.1]nonan-9-one (1) and bicyclo-[4.2.2]decane (2) were prepared using molecular mechanics with an improved two-bond drive technique. Inversion of 1 takes place most favorably via a Cs transition state with the tetramethylene chain over the ethano bridge [1B, ΔH± 6.1 (calculated) vs. 6.8 (observed) kcal/mol]. An alternative pathway involving a Cs local energy minimum (1C), in which the tetramethylene chain is bent over the carbonyl, has a barrier 2.4 kcal higher than 1B. The global energy minimum conformation of 2 has boat-chair cyclooctane and twist-boat cyclohexane rings (BCTB), and enantiomerizes into its mirror image (BCTB') via three intermediates: TCTB, CB, and TCTB'. The highest point in the proposed pathway, a saddlepoint CB, is calculated to lie 8.0 kcal/mol above BCTB (observed ΔH± 7.8 kcal/mol). The advantage of the two-parametric over the one-parametric torsional energy surface is discussed.
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  • 89
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Existing schemes for evaluation of the characteristic polynomial of a graph suffer from limited practicality. Their application to large molecules inordinately increases the amount of labor. Here a procedure is outlined which is useful even for large molecules. It is based on a not widely known property of the collection of characteristic polynomials for Ulam's subgraphs, which, when added, give the derivative of the characteristic polynomial of the initial graph. The characteristic polynomials for Ulam's subgraphs are, as a rule, easier to derive due to the presence of many pending bonds in graphs of chemical interest. The last step requires an integration of a polynomial (which is a straightforward step) and determining the constant of integration, which represents the determinant of the adjacency matrix. The available methods for determing the additive constant (the determinant) are combinatorially much simpler than the initial task of finding all of the coefficients of the characteristic polynomial. The approach is illustrated on selected benzenoid hydrocarbons, nonbenzenoid, and nonalternant systems. Construction of the characteristic polynomials can be accelerated by considering auxiliary fragments and irreducible subgraphs separately and combining them in the final expression. Many auxiliary fragments allow their characteristic polynomials to be expressed in a closed form using recursive relations. The results for complex molecules can thus be written in a relatively compact form. Finally, the derivative of the characteristic polynomial, expressed in terms of selected auxiliary functions and irreducible components, can be integrated directly to give the result in terms of contributions signifying various fragments rather than as an explicit function of x.
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  • 90
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    Journal of Computational Chemistry 3 (1982), S. 451-467 
    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 application of the self-consistent field (SCF) local-impurity formalism to quasi-one-dimensional systems is discussed. We describe a general procedure for an accurate numerical determination of the Green's function matrix elements of the unperturbed system. An application to a local impurity in a model chain with two orbitals per unit cell is reported. The changes in the charge-bond-order matrix and in local and total density of states due to the impurity are discussed with special emphasis on the changes at the critical points (van Hove singularities) at the band edges. The Green's matrix approach is used to reexamine long-range Friedel oscillations caused by an impurity in a strictly one-dimensional metal. The extent of the long-range tail of the perturbed charge density is in an inverse relation to the localization length of the impurity state: the stronger the perturbation the more localized is the bound state and the more extended are the oscillations in the charge distribution. The results for the model chain with two orbitals per unit cell indicate that the impurity-induced change in charge distribution may be locally screened by redistribution of the population of the on-site orbitals, therefore damping possible oscillations and leading to a faster decay than in strictly one-dimensional systems.
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  • 91
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    Journal of Computational Chemistry 3 (1982), S. 507-511 
    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 inadequate description of molecular systems involving lone pairs by the original PCILO method is analyzed on some examples. A modified PCILO version for the lone-pair description is proposed. The success of this method is represented in the same examples.
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  • 92
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    Journal of Computational Chemistry 3 (1982), 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: Localized molecular orbital (LMO) energies obtained from the canonical molecular orbital (CMO) energies and unitary transformation or from the matrix of the Fock operator and the LMOs are described. The results for water and ethylene are given, and compared with earlier work of Wilhite and Whitten.
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  • 93
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    Journal of Computational Chemistry 3 (1982), S. 525-547 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute-solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN/2 potential for methane-water interactions) and 124 water molecules (using the MCY potential for water-water interactions). Again, the convergence of solute-solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN/2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.
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  • 94
    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 studies were conducted on quantitative aspects of π-nonbonded, σ-σ*, n-σ*, and throughbond interactions in R1CH2(CH2)N-1 CH2 R2, where R1 and R2 are H and/or nonbonding AO, n, and N = 2, 3, and 4. Geometrical preferences were found to depend both on π-nonbonding and bond-antibonding interactions, the latter being more important. Level orderings and energy splittings involved in the through-bond interactions of diradicals can be qualitatively predicted by examining the signs of the overlap between the n orbitals and a common vicinal σ* bond orbital, using simple orbital patterns and paying special attention to the “backside” tails of bond orbitals.
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  • 95
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    Journal of Computational Chemistry 3 (1982), S. 588-592 
    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 analysis has been made of the applicability of various sets of nonbonded interaction potential parameters which do not consider hydrogen atoms explicitly, to represent molecular packing interactions in crystals of ferrous porphyrin complexes, which are models for deoxyhemoglobin. Ordered regions of the structures are well described, but disordered solvent or ligands cause difficulty.
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  • 96
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    Journal of Computational Chemistry 3 (1982), S. 593-602 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF-MO-LCAO ab-initio computations were carried out for the four tautomers 2-pyridone, 2-hydroxypyridine, 3-pyridone, and 3-hydroxypyridine interacting with a water molecule placed at different positions and orientations around each of them. The computed interaction energies were fitted by an analytical potential consisting of a 6-12 Lennard-Jones term plus a Coulombic one. The root-mean-square deviation of the fit is 2.5 kJ/mol. We report isoenergy contour maps for some important cross sections and obtain a qualitative trend of the solvation entropy, in agreement with available experimental data. The obtained potentials were used for Monte Carlo simulation of four clusters consisting of a tautomer molecule as solute and 50 water molecules, at 300 K. The problem of the transferability of fitting constants is also examined.
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  • 97
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    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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  • 98
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    Journal of Computational Chemistry 2 (1981), S. 12-13 
    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 CN stretching frequencies in amides have been predicted satisfactorily by the CNDO/2 method. The large variation in ΔE is explained on the basis of extent of resonance in amides.
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  • 99
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    Journal of Computational Chemistry 2 (1981), S. 38-40 
    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 first calculation of a molecule, N2, by the SCF-Xα-SW method using the theoretically derived parameter αta is reported.
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  • 100
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    Journal of Computational Chemistry 2 (1981), S. 368-375 
    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 approximate analytic expression is derived, based on a novel model for the reactive-diffusive processes in a electrochemiluminescence (ecl) experiment. The physical system treated is one in which ecl is produced by stepping the voltage of a planar electrode to the diffusion-limited reduction value for an emitter species in the presence of a bulk oxidant precursor (9,10-DPA with benzoyl peroxide). The unknown rate constants are determined by a least-squares curve-fitting computer code. The model, though crude, provides an excellent fit to the ecl intensity versus time data, including the rise portion of the curve.
    Additional Material: 2 Ill.
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