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  • Biochemistry  (519)
  • Wiley-Blackwell  (519)
  • Copernicus
  • Springer Nature
  • 1985-1989  (519)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985) 
    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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  • 2
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 1-4 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is noticed that inclusion of an electrostatic term in the molecular-mechanical treatment of hydrocarbons would compel the nonbonding parameters of different force fields to become more alike than they are at present. Apart from removing the discontinuity in passing from the calculation of an unfunctionalized parent compound to the calculation of its functionalized derivatives, it is expected that the inclusion would improve results for the hydrocarbons themselves.
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  • 3
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 5-8 
    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 present energy component analysis calculations on alkali atom (Li,Na) hydride (H2O,NH3,H2S) interactions and compare these with corresponding (Li+ … NH3) cation … hydride interactions. In contrast to cation hydride interactions, the neutral atom-hydride interactions are shown to involve considerable contributions from all energy components.
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  • 4
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 28-38 
    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 values of log10 P (partition coefficient, in octanol/water) were calculated for about 200 organic molecules of diverse structures and functionalities. The method involves a simple procedure and appears accurate enough for semiquantitative applications. Further, this method of calculating log10 P values was shown to be successful in providing a better quantitative structure activity relationship (QSAR) than the Hansch-type approach in the study of inhibitory activity of substituted phenols on Bacillus Subtilis spore germination.
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  • 5
    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 computer program SURVIB is described for calculating vibrational anharmonicity constants for polyatomic molecules. The program requires as input a grid of calculated energies in the vicinity of a stationary point. This grid is fit, in a least squares sense, to a polynomial function of the internal coordinates. This analytic representation of the energy surface is employed in a normal mode analysis, and the energy is reexpanded as a polynominal function of the normal mode coordinates (expressed as vectors in the mass-weighted atomic Cartesian coordinate space). The resulting coefficients are used in a second-order perturbation theory analysis to obtain the vibrational anharmonicity constants. Also reported is an application of this program to formaldehyde employing ab initio, RHF, MP2, MP3, and RHF-CI calculations. The spectroscopic constants obtained for H2CO are in good agreement with experimentally derived values recently reported by Reisner.
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  • 6
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 56-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: α↑HF and α↓HF are derived for use in spin polarized Hartree-Fock-Slater programs. They are assumed to depend only on the number of up and down spin electrons in the atom. The calculated eigenvalues show a slight improvement only for carbon, nitrogen, and oxygen.
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  • 7
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy profiles were calculated for τ1, the C—C—C=O torsion, and τ2, the C—C—C—C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, -60), (0, 180), (120, 180), (120, -60), and the maxima (0, 0), (180, 180), and (60, -60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C—H bond trans to a C—C bond (C—Hs) is consistently shorter than a C—H bond (C—Ha) trans to another C—H bond. Specifically, for X—C(α) (= O)—C(β)—C(γ)—C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)—Hs 〈 C(δ)—Ha in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C—H⃛O=C interaction. (2) In the most stable conformers, (0, 60), C(β)—Ha 〈 C(β)—Hs, and C(γ)—Ha 〈 C(γ)—Hs, regardless of X. (3) The average C—C bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)—C(β) 〈 C(β)—C(γ) 〈 C(γ)—C(δ); whereas, when τ1 = 120°, C(α)—C(β) 〈 C(β)—C(γ) 〉 C(γ)—C(δ).
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 76-76 
    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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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 78-78 
    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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  • 10
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 77-77 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 11
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    Journal of Computational Chemistry 6 (1985), S. 88-92 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: If numerical configuration selection procedures are used in MRDCI calculations, the full MRDCI energy may be estimated by adding energy corrections obtained by perturbation theory. Accurate results may then be obtained by including all selected CFs in the zero-order function instead of only the reference CFs.
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  • 12
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    Journal of Computational Chemistry 6 (1985), S. 93-107 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Repulsion and dispersion parameters for alkali-metal halide diatomic molecules were computed by ionic Rittner and truncated Rittner models with radial dependent repulsion terms. Experimental data on the bond energies, the equilibrium interionic distances, and the spectroscopic frequencies were employed for the purpose. The polarizabilities used were also computed from the experimental dipole moments of alkali-metal halides. The potential parameters obtained were compared with parameters from other sources and checked for consistency. The computed potential parameters of alkali-metal halide monomer molecules were used to predict the energetics and geometries for alkali-metal halide dimer molecules. The predicted values are in good agreement with experiment and other calculations indicating the consistency and reliability of the potential employed. Although the magnitude of repulsive and dispersive energy terms varies with potential functions employed, the difference between the two for a molecule is constant. The repulsive term is more sensitive than the attractive term. The uncertainty in the exponential repulsion results in an inaccurate representation of the attractive contribution. Introduction of the radial-dependent repulsion term changes the relative magnitudes of repulsive and dispersive parameters and hence the relative contribution to the total potential with monomers. But this has no significant effect on the energetics and geometries of the dimers.
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  • 13
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    Journal of Computational Chemistry 6 (1985), S. 142-147 
    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 orbitals (LMOs) for several octahedral complexes are presented. Wavefunctions are calculated within the PRDDO approximations and localized by the Boys criterion. Complexes of general formula (NH3)x(CO)6-xM, M = Cr0 or Mn+ and x = 1, 2, or 3 illustrate the general trends for carbonyl complexes. Weak to moderate π-bonding results in three equivalent inner shell LMOs dominantly of metal 3s, 3p and 3d character but highly delocalized to the carbonyls. These three LMOs flank the M-CO bond axis. Other π back-bonding situations result in metal-ligand double bonds which are nonequivalent and have σ-π separability [(NH3)5(py)Mn+] and also equivalent double bonds [(NH3)5(NO)Cr+].
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  • 14
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985) 
    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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  • 15
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    Journal of Computational Chemistry 6 (1985), S. 157-167 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Sets of atom equivalents have been developed which permit the estimation of heats of formation, ΔH°f298(g), from ab initio total energies (3-21G and 6-31G* basis sets). This extends the isodesmic reaction scheme of Pople and the group equivalents of Wiberg. A variety of small inorganic and organic molecules, including fluorocarbons, free radicals, carbocations, and protonated species give excellent agreement with experiment; average errors are less than 1 kcal/mol with unstrained hydrocarbons (both basis sets), and are on the order of 2 kcal/mol for all molecules considered (6-31G*; the 3-21G basis errors, as expected, usually are somewhat higher). The results substantiate Pople's early conclusions that Hartree-Fock theory provides a generally satisfactory description of classical molecules.
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  • 16
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    Journal of Computational Chemistry 6 (1985), S. 173-181 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges obtained with a previously published charge scheme are given for amino acids and peptides. In order to do this, a method of handling charged species with the basic scheme2,3 has been developed. The charges obtained for alkylammonium ions and carboxylate ions with the scheme are presented and compared with CNDO and ab initio values. The calculated experimental dipole moments of the zwitterionic forms of glycine, alanine and β-alanine are then discussed. Finally, the atomic charges obtained for the naturally occurring amino acids are given, both in the form of the N-acetyl-N′-methyl amino acid amides, used as models for the amino acid residues in enzymes, and as the free zwitterionic amino acids. The charges obtained show a good correlation with n. m. r. chemical shifts of both carbon and hydrogen atoms.
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  • 17
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    Journal of Computational Chemistry 6 (1985), S. 189-199 
    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 MO calculations have been performed for neutral and cationic C2H2F2 structures. Olefinic and carbene structures are investigated for the neutral isomers, while olefinic, carbene, and fluoronium-type cations are found. Stability orders and rotational barriers are discussed in terms of orbital and Coulomb interaction. Contrary to previous studies, the higher stability of the geminal isomers is interpreted to be caused by Coulomb attraction.
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  • 18
    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 method of graphically exhibiting detailed information about a three-dimensional electron distribution function f(x,y,z) is described. Contour lines f = constant are drawn on a set of equidistant parallel planes that intersect the distribution, and a perspective view of all contours on all planes is displayed. Representative examples are given.
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  • 19
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    Journal of Computational Chemistry 6 (1985), S. 216-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is described to analyze observed conformations for molecular fragments with more than three torsional degrees of freedom. The method is an adaption of statistical cluster analysis to multidimensional, symmetric, periodic distributions of data points. Application to the molecular fragment M(PPh3)2 with eight torsional degrees of freedom reveals a model of conformational interconversion. The model implies gearing motion of the two PC3 fragments alternating with stepwise inversions of the helicities of the PPh3-propellers.
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  • 20
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    Journal of Computational Chemistry 6 (1985) 
    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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  • 21
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    Journal of Computational Chemistry 6 (1985), S. 148-155 
    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 have carried out a series of molecular mechanics calculations on the alkali ion complexes of valinomycin. For the ions Na+, K+, Rb+, and Cs+ we have found three-fold rotationally symmetric conformations as the lowest energy structures, while for Li+ a markedly asymmetric configuration is preferred. The relative free energies of the complexes show that Li+ is by far the poorest binding partner in solution, followed by Na+, which is in turn far poorer than any of the three larger ions. The binding selectivity derives from the slower variation of the complexation free energy with ionic size than the ionic solvation free energy, so that the ionophore is unable to compete with the solvent for the smaller ions. Our calculated strain energies suggest that valinomycin's failure to form complexes with the smaller ions in solution is due partially to the rigidity of the ionophore structure, which prevents the central cavity from contracting to accommodate them. Certain geometric criteria indicate that K+ provides the best fit to the binding site, although there is some inconsistency between the energetic and geometric criteria of binding ability.
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  • 22
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    Journal of Computational Chemistry 6 (1985), S. 168-172 
    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 protonation energies of alkylated derivatives of NH3 and OH2 are calculated at the Hartree-Fock level with the split-valence 4-31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (∼30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.
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  • 23
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    Journal of Computational Chemistry 6 (1985), S. 182-188 
    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 lowest potential energy surfaces of NO3 have been investigated using CASSCF and contracted CI methods, to determine if NO3 is an intermediate in the oxidation of nitric oxide. This reaction is observed to be termolecular where an intermediate is almost certainly formed. The calculations, which were performed in C2v symmetry, show that the form of NO3 which has a near D3h geometry should not be possible to reach from ground state NO and O2. The energy of this isomer of NO3 is calculated to be 25 kcal/mol higher in energy than separated NO and O2. Furthermore, NO + O2 is separated from NO3 by very high barriers. The C2v constrained barrier is as high as 145 kcal/mol, which makes it very unlikely that NO3 could be formed even along less symmetric pathways. The origin of the barriers are analyzed, and it is shown that a special type of mechanism is involved for the state with the lowest barrier. In this mechanism, which was observed recently also for NiH2, the occupation in each symmetry changes only by one unit in each step of the reaction. The only isomer of NO3 which could be formed is a weak van der Waals complex with a very long bond distance of 6.5 a.u. N2O2 does, however, in this respect seem to be a more likely intermediate with its shorter bond distance of 4.5 a.u. Calculations around the D3h equilibrium further show that 2B2 is the ground state of this isomer of NO3 with 2A2 and 2B1 slightly higher in energy.
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  • 24
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    Journal of Computational Chemistry 6 (1985), S. 200-208 
    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 CGTO integral evaluation, SCF, SCF-gradient, integral transformation, and MR-CI (SD) steps of the COLUMBUS system of programs have been adapted for the CYBER 205. A description is given of our efforts and the partly heavy modifications necessary to exploit the potential of this supercomputer and to avoid its shortcomings. Typical timings are reported, vector and scalar performance are compared.
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  • 25
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    Journal of Computational Chemistry 6 (1985), S. 229-236 
    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 instrument of exploration can be used to develop unrecognized connections among points in a variety of geometric designs. Operational methods are used to derive the relationships, and a new approach to extremum location is demonstrated. The technique is suitable for interpolation problems which arise in experimental design and the treatment of data.
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  • 26
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    Journal of Computational Chemistry 6 (1985), S. 249-255 
    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 direct interconversion of the two C3-symmetric enantiomeric conformations of triethylamine, via C—N bond rotation, has been studied by molecular mechanics (MM2) calculations. The MM2 calculations have been used to characterize the minima (equilibrium geometries) and first-order saddle points (transition states) for this process. For one interconversion, there are five saddle points and six minima. The highest energy saddle point results from the uncoupled rotation of one ethyl group to eclipse the lone pair. Two of the barriers result from coupled rotation of two ethyl groups in close passage.
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  • 27
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    Journal of Computational Chemistry 6 (1985), S. 237-248 
    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 new contracted Gaussian-type orbitals (CGTOs) for molecular calculations have been developed from Li to Ne. The CGTOs are minimal type, i.e. composed of two s-type CGTOs, s1, s2, and one p-type CGTO, p1. They are new family of CGTOs given by Tatewaki and Huzinaga, and others. In the previous works three primitive GTOs are used for s2, which is the main part of the 2s orbital, whereas four primitive GTOs are employed in the present work. The sets generated are [54/5], [64/5], [64/6], [74/6], and [74/7]. In almost all the cases the errors in the 2s and 2p orbital energies are smaller than those of DZ. The resulting 2s orbitals are close to the orbitals of the uncontracted GTO sets, (13/n) and (14/n) of Duijneveldt. It is found that the 2s and 2p orbitals given by [64/6], [74/6], and [74/7] are satisfactorily near to those of Hartree-Fock. The basis sets [54/5], [64/6], and [74/7] are applied to the N2 molecule in the split valence forms of [5211/311], [6211/3111], and [7211/4111]. Adding the d-type polarization functions from one through three, the quality of the basis sets has been examined. All of the three sets show good behavior and the sets augmented with three d-type polarization functions give almost entirely the same results as the very extended basis set.
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  • 28
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    Journal of Computational Chemistry 6 (1985), S. 282-286 
    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 orbital behavior of both the singlet and triplet Rydberg series for 1sns configurations of the He atom has been investigated using one- and two-configuration Hartree-Fock wave functions. The core orbital within the triplet series changes negligibly; however, a contract trend is noticeable as the Rydberg orbital penetrates more into the core region, which is in contrast to that found in the 1s2ns 2S Rydberg series of Li atom. Although some properties of the whole atom can be calculated, the core relaxation of the singlet series can not be drawn without ambiguity because a two-configuration correlated wave function has to be used, and thus the orbital picture is lost.
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  • 29
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    Journal of Computational Chemistry 6 (1985), S. 287-295 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relativistic effective potentials (REP) are now widely used in molecular electronic structure calculations. Tests of these REP are needed to assess their accuracy. This can now be done for AgH and AuH since Lee and McLean have published Dirac-Fock calculations for these molecules. Comparative SCF calculations have been performed for two types of effective potential. Satisfactory agreement between the effective potential results and Dirac-Fock values is found for spectroscopic constants and dipole moments, which supports the use of these potentials for heavy atom containing molecules.
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  • 30
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    Journal of Computational Chemistry 6 (1985) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 31
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    Journal of Computational Chemistry 6 (1985), S. 302-311 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics calculations (MM2) are used to elucidate energies and structures of possible reaction products in olefin metathesis of 2,3-dimethylnorbornadiene. The comparison of experimental and calculational results concerning norbornadiene itself shows excellent agreement both in energy and structure. The predicted isomers of lowest energy in a series of three different reaction products seem highly reliable and will lead to a more precise interpretation of the olefin metathesis reaction and the resulting product distribution. Some sixty different isomers have been considered and structures and energies are given. Nonplanarity of double bonds and van der Waals repulsions of closely related hydrogen atoms in polycyclic cycloolefins are considered in some detail. In order to reduce computing time and efforts in obtaining starting coordinates, a computer program for some dimeric structures was devised, which can combine minimized structures stemming from MM2 calculations.
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  • 32
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    Journal of Computational Chemistry 6 (1985), S. 350-359 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A very efficient algorithm for determining the geometrically feasible binding modes of a flexible ligand molecule at the receptor site is presented. It is based on distance geometry but maintains the requirements of three dimensions. The distance geometry manipulation can superimpose two bodies without explicitly calculating the necessary rigid rotation and translation. The whole conformation space of a flexible molecule can be efficiently examined by considering only a finite number of conformational points. The method is suitable only when the criterion for superposition is some minimum distance limit. It cannot, however, give the exact distance between two points in two different bodies.
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  • 33
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    Journal of Computational Chemistry 6 (1985), S. 343-349 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General expressions for monocenter electron repulsion integrals in a basis of real atomic orbitals are derived in terms of the radial integrals Rabcdk. The final expressions for these integrals can be classified into five main classes which are characterized by the angular part of the real atomic orbitals. For a basis of real s, p, d, and f AO's the total number of monocenter repulsion integrals is 65536, from which 6652 are different from zero. The nonzero integrals can be classified into 430 groups which contain integrals of equal value.
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  • 34
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    Journal of Computational Chemistry 6 (1985), S. 514-519 
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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: Reequilibration processes are often encountered within solids and they have long been described mathematically. However, computation of reequilibration data over entire processes is often difficult. An algorithm has been developed specifically for this purpose. It allows a fast and efficient computation of reequilibration parameters. Anisotropic diffusion can, moreover, be taken into account.
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  • 35
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    Journal of Computational Chemistry 6 (1985), S. 432-436 
    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 real-time docking method using molecular graphics and high-speed calculation of the energy of interaction between a drug and a receptor. A three-dimensional tabulation of the potential is computed prior to the docking experiment, and the total interaction energy is calculated and updated on the display screen in real-time to provide immediate visual feedback to the user as the drug molecule is moved inside the receptor pocket. The “Simplex” method is then used to minimize the energy of interactions after each docking. Using this real-time method, it is now possible to examine rapidly the interactions of a large number of drugs and their analogues with receptor molecules. As an application, the interaction of thyroid hormone and its analogues with prealbumin is considered. The final interaction energies of this very rapid method compare well with those calculated by more orthodox means, while also providing visual feedback on both molecular geometry and energy.
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  • 36
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    Journal of Computational Chemistry 6 (1985), S. 455-461 
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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 thermal limiting high-pressure unimolecular rate constant k∞ represents, operationally, the Laplace transform of the product of microcanonical rate constant for decomposition of molecules having specified energy E [k(E)] and the density of states [N(E)]. By inversion, it is possible to recover k(E)N(E), from which one can obtain the energy dependence of k(E) and the pressure dependence of kuni, the thermal general-pressure unimolecular rate constant. This article examines numerical aspects of three methods of inversion, their reliability and dependence on sampling, i.e., on the number of available experimental data points, by comparing exact k(E) and kuni with those obtained by inversion. It turns out that the method of steepest descents is the best all-round performer.
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  • 37
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    Journal of Computational Chemistry 6 (1985), S. 478-480 
    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 mechanics (MMP2) description of the torsion of a methyl group attached to a conjugated system has been improved by using bond order dependent torsional force constants.
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  • 38
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    Journal of Computational Chemistry 6 (1985), S. 481-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A corrected Born equation, which describes the solute-dipolar solvent interaction by placing the charges of the atoms of the solute at their position in space inside a spherical cavity of the solvent, is used to calculate the solvent effect on three systems: the hydrated OH- ion, the lithiated aziridine, and the lithiated oxirane. It is found that the solvent effect stabilizes the addition of a water molecule to the OH-(H2O)3 system with the additional water acting as a proton donor. It is also found that the lithiation energy of aziridine and oxirane which are found to be 47 and 43 kcal/mol in gas-phase, respectively, decrease to 32 and 23 kcal/mol in water solution.
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  • 39
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    Journal of Computational Chemistry 6 (1985), S. 492-506 
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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 problem of chance correlations in studies of structure - activity relationships using multivariate linear regression techniques is addressed. Random correlations are simulated by scrambling real potency values in data bases consisting of molecules possessing various biological properties. The statistical parameters of these correlations are compared to those obtained using the actual potency/compound data pairs and it is noted that the most noticeable differences are in the magnitude of the F values for the overall regression. Cutoff points for this parameter are suggested, which, when implemented in the recently introduced CASE method that correlates biological activity with substructural descriptors, can serve to weed out effectively the majority of meaningless correlations.
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  • 40
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    Journal of Computational Chemistry 6 (1985), S. 507-513 
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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: SINDO1 calculations were performed to study the reactivity of molecules with a valence number derived from the density matrix. A comparison of valence numbers was made for selected examples of rotation barriers, substituted strained molecules, radical gas phase reactions, and acid-base reactions. Relations between valence, geometry, and energy changes are discussed.
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  • 41
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    Journal of Computational Chemistry 6 (1985), S. 520-532 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for preparing compact orbital and auxiliary basis sets for LCAO-LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3dn-14s1 and 3dn-24s2 configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.
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  • 42
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An iterative algorithm is described for finding topological equivalence, ordering, and canonical numbering of vertexes (atoms) in molecular graphs. Like the Morgan algorithm, it is based on extended connectivities but: (i) the latter are used hierarchically, i. e., the discrimination in the next iteration is carried out only for the vertices having the same extended connectivities (ranks) at the previous iteration; (ii) at equal extended connectivities, additional discrimination is introduced by the ranks of adjacent vertices; (iii) there is no “best name” search; (iv) three levels of complexity of chemical structures are distinguished and handled by different procedures.Two schemes of application of HOC procedures are presented: one directed towards a fast canonical numbering for coding systems, and another one yielding levels of topological equivalence allowing a unique topological representation of the molecule with possible applications to similarity search, structure-activity correlations, etc.
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  • 43
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: A topological code is devised on the basis of the unique topological representation of the molecule described in the preceding two parts of this series.1 By adding to the topological code additional chemical information on atoms and/or bonds, as well as stereochemical information, a chemical and respectively stereochemical code (SHOC) are also constructed. The advantages of the new linear codes are that they are convention-free codes, preserving the symmetry of molecular graph, and easily implemented either manually or by means of computer programs. By concentrating all topological, chemical, and stereochemical information, our code (SHOC) is more compact and more general than the codes based on several separate lists.
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  • 44
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    Journal of Computational Chemistry 6 (1985), S. 581-586 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different schemes are explored for the calculation of the proton transfer process in the hydrogen bonded cation [CH3OH · H · NH3]+. Results from ab-initio calculations with the STO-3G, 3-21G and 4-31G basis sets, are compared in search for an efficient reliable scheme to study the potential energy curves for the proton transfer. The curve constructed from the lowest energies calculated with the frozen optimized geometries of the two possible pairs of proton donor and acceptor fragments, (i.e., CH3OH2+/NH3 and CH3OH/NH4+) is in good agreement with that obtained when all the fragments of the hydrogen bonded complex are completely optimized simultaneously.
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  • 45
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The computer implementation of the HOC procedures presented in Parts I, II and III of this series is based on the module principle. It contains a main program and seventeen subroutines in Fortran IV. The system is able to provide unique atom numbering and code for all kinds of chemical compounds in their tremendous variety of structures.
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  • 46
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    Journal of Computational Chemistry 6 (1985), S. 598-609 
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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 many applications of the distance matrix, D(G), and the Wiener branching index, W(G), in chemistry are briefly outlined. W(G) is defined as one half the sum of all the entries in D(G). A recursion formula is developed enabling W(G) to be evaluated for any molecule whose graph G exists in the form of a tree. This formula, which represents the first general recursion formula for trees of any kind, is valid irrespective of the valence of the vertices of G or of the degree of branching in G. Several closed expressions giving W(G) for special classes of tree molecules are derived from the general formula. One illustrative worked example is also presented. Finally, it is shown how the presence of an arbitrary number of heteroatoms in tree-like molecules can readily be accommodated within our general formula by appropriately weighting the vertices and edges of G.
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  • 47
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    Journal of Computational Chemistry 6 (1985), S. 614-624 
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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 cellular species formed in the hydrolysis of cis-Pt(NH3)2Cl2 (DDP), namely, cis-[Pt(NH3)2XY]n+ (X, Y = Cl-, H2O, OH-; n = 0, 1, 2) have been investigated theoretically using the relativistic and nonrelativistic extended Huckel molecular orbital method. Molecular orbital (MO) results for trans-DDP and its hydrolysis products are also reported for comparison. Transition energies, molar absorption coefficients (∊), and B terms from magnetic circular dichroism (MCD) derived from theory are presented for each of the species studied. The electronic absorption and MCD spectra of all the complexes are predicted to exhibit ligand field transitions arising primarily from excitations between the occupied Pt 5d orbitals and the unoccupied Pt 5d and 6pz orbitals, respectively. The 5d → 6pz transitions are expected to yield intense absorptions in the UV spectral region. Some intensity is generated in the d → d transitions as a result of the low symmetry of these complexes. Correlation of available experimental data with theory allows spectral assignments to be made and predicted. Substituent effects in the cis- and trans-isomeric species are discussed. Finally, the applicability of the EHMO method to these systems is examined.
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  • 48
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    Journal of Computational Chemistry 6 (1985), S. 634-646 
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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 presents a strategy to perform molecular dynamics simulations using parallel processing techniques on a parallel-distributed loosely coupled system consisting of IBM host computers (4341 and 4381) with attached scientific processors (FPS-164). This substantially enhances our ability to perform fast and more realistic large scale many-body trajectory simulations. A powerful extention of the computational range of molecular dynamics the parallel approach offers the opportunity to substantially reduce the simulation time to allow a longer simulation period to study more realistic models and larger systems. It is flexible and uses, for the most part, standard products and straightforward implementation with a broad range of applicability. The implementation of a simulation of water molecules with the inclusion of two- and three-body interactions is discussed. Some considerations in the design and implementation of parallel programs on a loosely coupled system are also presented.
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  • 49
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    Journal of Computational Chemistry 6 (1985), S. 652-655 
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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: We compare calculated total energies for 150 open-chain molecules using ab initio methodology and the PRDDO approximations. The bulk of the errors implicit in the PRDDO approximations are apparently of a one-center nature, i.e., they are due to the number and type of atoms in the molecule, and not the details of the molecular geometry. Atomic correction factors are developed which reduce the errors in the calculated total energy of PRDDO wave functions by a factor of eight relative to the ab initio reference calculations. PRDDO calculations on ring and cage compounds are shown to have additional systematic errors in the total energy.
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    Journal of Computational Chemistry 6 (1985), S. 662-673 
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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: Benzylic anions were studied with the semiempirical MNDO molecular orbital method. Structural changes were analyzed as metal counterions and solvents were allowed to interact with the benzylic carbon. Generally, benzylic carbanions were found to be trigonal planar but became pyramidal or bent when metals were included in the calculation.
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    Journal of Computational Chemistry 7 (1986), S. 13-19 
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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 biological activity of toyocamycin has been examined on the basis of the model developed by Sanyal et al. for the incorporation of nucleoside analogs during transcription. Using the simplified formula of Claverie for intermolecular interactions, computations have been carried out on the pairing energy of toyocamycin base with the complimentary bases as well as on the interaction energy with nucleic acid base pairs. The results are compared with the results of similar computations with nucleic acids. On the basis of the model an attempt has been made to explain the mechanism of the biological action of toyocamycin.
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    Journal of Computational Chemistry 7 (1986), S. 254-254 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 7 (1986), S. 55-57 
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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: Expansion parameters, for use in a 1/R expansion developed at this laboratory for the study of molecular interactions, have been determined for new classes of atoms. Test calculations with these new parameters have yielded very satisfactory results for the glycine zwitterion, in dimer form and solvated, confirming the goodness of the parameters and the appropriateness of the formulation.
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  • 54
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We investigate the intramolecular rearrangement of the P73- ion in which P—P bonds are continuously broken and reestablished resulting in a dynamic structure with all seven phosphorus atoms being chemically equivalent. This leads to 7/3 = 1680 valence tautomers. The P73- ion is a typical fluctuating molecule, distantly related to C10H10 bullvalene. In order to determine the symmetry of the process we first consider the problem of the construction of the rearrangement graph. Initial steps toward this goal are illustrated, and additional characterizations of the graph are derived after its construction by computer. A number of properties of this rather complicated graph having 1680 vertices and 2520 edges are discussed: in particular the occurrence of various cycles, the maximal distance between vertices, the count of neighbors at different distance, and finally its symmetry.
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    Journal of Computational Chemistry 7 (1986), S. 89-89 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 56
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    Journal of Computational Chemistry 7 (1986), S. 93-104 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation of 119 closed- and open-shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data. With proper consideration of failures in specific areas, both methods can be used for the thermodynamics of carbocations containing C, H, N, and O. MINDO/3 predicts unrealistic values for nitrogen containing cations with nitrogen multiple bonds and is not suited for closed-shell cations containing oxygen. Saturated acyclic hydrocarbon radical cations often are computed with abnormally long CC bonds by MNDO. Otherwise, the standard deviation of the two methods is not very different, being in the range of ±13 kcal/mol. MINDO/3 tends to overestimate the cation stabilities, whereas MNDO calculates cations usually too high in energy. Some of the errors which were found in the calculations of the ions are related to the computed values for the parent neutral structures, but others are not.
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    Journal of Computational Chemistry 7 (1986), S. 105-112 
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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: Methods of molecular mechanics were applied to investigate the conformation of the (methyl 2-O-sulfate-4-methyl-α-L-idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms 1C4 and 4C1 and the skew-boat form 2S0(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (3S1, 1S3, and 1S5) were found, yet at least 4 kcal/mol higher than 2S0. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.
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    Journal of Computational Chemistry 7 (1986), S. 140-143 
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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 MNDO parameters for sulfur have been reoptimized. Calculations for a number of sulfur compounds indicate a very significant improvement. Inclusion of d AOs failed to correct the errors for compounds of sulfur in its higher valence states. Since d AOs are not included, the calculations are still confined to compounds of divalent sulfur.
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  • 59
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    Journal of Computational Chemistry 7 (1986), S. 153-157 
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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: Geometrical parameters for pyridine have been calculated using the 6-31G, 6-31G*(5D), 6-31G**(6D), and 6-31G(2 × 6D) basis sets. Comparisons are made with a microwave substitution structure and with results of other ab initio calculations reported in the literature. Particular attention is paid to the influence of polarization functions on the magnitude of the ring angle, 〈C6N1C2, which is analogous to the ipso angle in monosubstituted benzene derivatives.
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    Journal of Computational Chemistry 7 (1986), S. 165-175 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A structural minimization procedure which converges rapidly and restricts the atomic shifts is outlined. It is implemented by adding a harmonic penalty term for the displacements of atomic positions and resetting the reference coordinates with respect to which the constraints are computed during the minimization. The resetting serves to reduce the constraint energy of the minimized structure to negligible levels.
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  • 61
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    Journal of Computational Chemistry 7 (1986), S. 189-200 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational changes in the RNA-protein interaction were studied by calculating the intramolecular interaction energy of a model complex with the use of potential functions. The model complex has hydrogen-bonded water molecules bridging polypeptide NH groups to 2'-hydroxyl groups and sugar ring oxygen atoms. Since the sugar ring is constrained by the bridging water, preliminary calculations with the model compounds, the sugar ring, mononucleoside diphosphates, pCp and pGp, were carried out, and the flexibility and energetics of the sugar ring were compared with the previous results of DNA. The shift of the phase angle of the sugar ring occurred in the complex formation because of the hydrogen bond through the bridging water and the flexibility of the sugar ring. The free energy difference at 298 K is about -74.0 kcal/mol which was obtained from the intramolecular interaction energy difference of -67.5 kcal/mol by adding the conformational entropy change of 21.9 e.u., which in turn was calculated from the evaluation of the determinant of the matrix containing variances and covariances of the internal coordinates.
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  • 62
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    Journal of Computational Chemistry 7 (1986), S. 208-212 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Many authors have contributed expressions for obtaining analytical matrix elements for Morse oscillators. In this work, we discuss the advantages of using these expressions. At the same time, we propose a full numerical method to calculate these matrix elements and we compare, for the I2 system, the different results given by Gallas, Vasan, and Cross, and the variational method.
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  • 63
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    Journal of Computational Chemistry 7 (1986) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 64
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    Journal of Computational Chemistry 7 (1986), S. 417-427 
    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 rearrangement of the 1-methylcyclohexyl cation to the 1,2-dimethylcyclopentyl cation has been studied by MINDO/3 calculations, as an application of the branching mechanism model for cycloalkanes. Possible intermediates and transition states have been characterized by diagonalization of their Hessian matrixes. Two nonequivalent pathways, α and β scissions, are relatively close in energy. The calculated transition states are almost equivalent in energy to those found for cyclohexyl cation. Hence, the energy barriers are higher for the rearrangement of the 1-methyl than for cyclohexyl cation, because the former is less stable than the latter.
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  • 65
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    Journal of Computational Chemistry 7 (1986), S. 457-463 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Time consuming portions in the computation of transport properties of rigid and flexible molecules are the evaluation of subunit hydrodynamic interaction tensors Q and σ, and the procedure for satisfying subunit-subunit distance constraints. Vector algorithms to speed up these parts of the computation are given. Using these algorithms, a vector version of the Ermak-McCammon Brownian dynamics code has been developed on a Cyber-205. To demonstrate the order of speedups that can be achieved, the code was tested on a rigid “trimer” system comprising 24 spherical subunits with a fixed geometry. A speedup of about 14 times for the whole program, and of 45, 6, and 18 times for the computation of Q, σ, and for the procedure to enforce the constraints, respectively, were obtained.
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  • 66
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    Journal of Computational Chemistry 7 (1986), S. 476-481 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown how the refinement of groups of atoms as rigid entities can be implemented in a molecular mechanics program. The method is worked out for the Newton-Raphson scheme and eventually combined with other constraints, including the Eckart conditions. An example is also given.
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  • 67
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: The Generalized Valence Bond [GVB(pp)] multiconfiguration self-consistent field wave function optimization program has undergone substantial revision in migration from serial scalar computers (like IBM and VAX) to the FPS-164, a minisupercomputer. Many of the code optimization strategies applied to the GVB program are portable and applicable to a wide range of scientific application codes. In benchmark calculations, the optimized FPS-164 program, GVB164, is 6.5 times faster than the initial FPS-164 implementation, both programs storing the two-electron integral list on disk. GVB164 runs 30 times faster in wall time (limited by the FPS-164 disk access speed) than a reference version of GVB2P5 on the VAX 11/780. The performance of GVB164 nearly doubles again when all of the two-electron integrals can be stored in main memory.
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  • 68
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    Journal of Computational Chemistry 10 (1989), S. 514-519 
    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 on oxygen for a series of compounds was obtained using Mulliken population, natural population analysis (NPA), integrated projected electron population (IPP) analysis, and Bader's topological density analysis, “integrated Bader populations” (IBP). The orbital-based methods (Mulliken and NPA) predict oxygen charges of about -0.6 whereas the spatial-based methods (IPP and IBP) predict charges of about - 1.2 to - 1.3. The differences are ascribed primarily to the nuclear-centered basis sets used in the orbital methods that minimize local atomic polarization effects. Accordingly, such population analyses should be used for electronic structure considerations only with due circumspection. The IPP method as an approximation to IBP shows gross similarities; small but significant differences vary in a nonsystematic manner and IPP values must also be used with care.
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  • 69
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: An SCF calculation has been performed on C63H113N11O12, a derivative of the immuno-suppressive drug cyclosporin, using a 3-21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential-derived point-charge model based on the force-field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential-derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point-charge models for describing the electrostatic interactions of polypeptides are discussed.
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  • 70
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    Journal of Computational Chemistry 10 (1989), S. 616-627 
    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 present a simple computational method for the evaluation of solute-solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.
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    Journal of Computational Chemistry 10 (1989), S. 648-659 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6-311G(d) triply split valence set with polarization on the resonant atom and 3-21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
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    Journal of Computational Chemistry 10 (1989), S. 635-647 
    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 mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
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    Journal of Computational Chemistry 10 (1989), S. 748-748 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 10 (1989), S. 798-816 
    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 that finds the most probable conformational states of a protein chain is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. The conformation of the entire chain is represented by a sequence of single-residue conformational states; the distinct conformations in this representation are called “chain-states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain-states. The chain-state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α-helices and ∊-strands of excessive length. The probability estimator considers short-range conformational information, medium-range sequence information and some simple long-range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain-state. By selecting the most probable chain-states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition-based importance sampling minimization.
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    Journal of Computational Chemistry 10 (1989), S. 817-831 
    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 that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. Each state corresponds to a rectangular region in the φ, ψ map. The conformation of an entire chain is then represented by a sequence of single-residue conformational states. The distinct “chain-states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly-probable chain-states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance-sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain-states. The importance-sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the φ, ψ map. All values of φ and ψ are allowed, but the less-probable values are sampled less often. To achieve this, the random values of φ and Φ are generated from bivariate gaussian distributions that are determined from known X-ray structures. Separate gaussian distributions are used for proline residues in the α and ∊ states, for glycine residues in the α, ∊, α*, and ∊* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly-generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance-sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain-states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X-ray conformation.
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    Journal of Computational Chemistry 10 (1989), S. 856-860 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are derived for analytical first and second energy derivatives with respect to nuclear coordinates in molecular mechanics force fields employing lone-pair pseudoatoms. These derivatives may further be used for the calculation of normal modes and vibrational frequencies while properly accounting for the presence of pseudoatoms. The equations are applied using the MM2 force field to calculate the vibrational spectrum of methanol to illustrate the applicability of the method. The results are compared to both experiment and a numerical approximation in which small masses are assigned to the lone-pair pseudoatoms.
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    Journal of Computational Chemistry 8 (1987), S. 549-554 
    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 computer-oriented method for the enumeration and generation of physical trees is presented. Physical trees depict acyclic chemical structures, but the term physical is used to stress the process by which the structures are produced.
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    Journal of Computational Chemistry 8 (1987), S. 562-562 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 8 (1987) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 8 (1987), S. 555-561 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero-order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO/2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β-trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between CαH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.
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    Journal of Computational Chemistry 10 (1989), S. 863-868 
    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 steric energy difference (ΔEst) between tertiary carbenium ions (R+) and the corresponding alcohols has been calculated by MM2 for a series of tertiary nonbridgehead substrates and correlated with their rate of solvolytic reactivity. Satisfactory correlation is obtained, except for p-nitrobenzoates of highly congested substrates. The slope and intercept of the correlations remain almost unchanged if bridge-head substrates are included in the plot. However, the quality of the fit is better for bridgehead substrates alone.
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    Journal of Computational Chemistry 10 (1989), S. 753-769 
    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 well-tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree-Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN-(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one-electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree-Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree-Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis-set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
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    Journal of Computational Chemistry 10 (1989), S. 832-849 
    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 geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3-21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
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    Journal of Computational Chemistry 10 (1989), S. 850-855 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β-spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β-spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial -1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
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    Journal of Computational Chemistry 10 (1989), S. 965-974 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A modified scheme of a previously developed concept of atomic valence numbers in molecules is presented. The relation to population analysis is demonstrated. The scheme is suitable for ab initio wave functions with extended basis sets. The procedure involved a combination of symmetric orthogonalization and contraction of the basis set. The method is used for a systematic investigation of a series of compounds with first-row atoms from Li to F. The predicted atomic charges and valence numbers are in line with results from infrared spectroscopy and multipole moment analysis.
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    Journal of Computational Chemistry 8 (1987), S. 651-657 
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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 method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two-dimensional analysis of the conformational interconversion from δ- to λ-[Co(ethane-1,2-diamine) (NH3)4]3+ reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7 kJ mol-1. Substitution at the carbon atoms, variation of the metal-nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol-1 for (N,N,N′,N′-tetramethylethane-1,2-diamine) [(NH3)4]3+.
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  • 87
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
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    Journal of Computational Chemistry 8 (1987), S. 700-717 
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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 present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
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    Journal of Computational Chemistry 8 (1987), S. 718-726 
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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: Stereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.
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    Journal of Computational Chemistry 8 (1987), S. 727-735 
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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 Hartree-Fock instablities of S2N2 are reported and compared with those of S3N3- and S4N42+. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N3-, and S4N42+ are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
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  • 91
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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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  • 92
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To study molecular decomposition pathways it is necessary to use ab initio multireference determinant-configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD-CI (multireference double excitation-configuration interaction technique of Buenker and Peyerimhoff) calculations on the decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
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  • 93
    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 recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first-order, single-step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
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  • 94
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 753-760 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational features of a chiral stationary phase used in column chromatography are discussed. The syn forms invoked in chiral recognition models are consistent with MNDO and MM2 calculations. It is speculated that the inherent flexibility of the syn form makes these phases effective templates for analyte binding.
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  • 95
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 761-771 
    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 electronic structure calculations have been carried out for the He(1S)-Li2 (X̃, 1∑g+) interaction both by the single-configuration SCF and correlated second-order MP2 methods using an extended basis set. From these calculations, an estimate of the isotropic (V0) and first two anisotropic (V2 and V4) terms of the He-Li2 potential surface has been obtained. An assessment of the leading induced-dipole-induced-dipole dispersion energy is presented from the MP2 energies. Where possible, a comparison is made with previous unpublished ab initio calculations by Staemmler and Stahl using the CEPA method.
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  • 96
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 772-777 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force constants for both anomers of glucose are evaluated using CNDO/Force method.
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  • 97
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 778-787 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute-solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
    Additional Material: 8 Ill.
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  • 98
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 788-793 
    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 variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6-31G* and DZ+P, give significantly different results. Use of two d-orbital sets (6-31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d-Orbitals on oxygen are required for consistent electronic structure results, and d-orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈-1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi-polar. The best simple symbolic representation of phosphine oxide is H3P+—0-, rather than H3P=0.
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  • 99
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 810-815 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set expansion and correlation effects on computed hydrogen bond energies of the positive ion complexes AHn · AHn + 1+1, for AHn = NH3, OH2 and FH, have been evaluated. The addition of diffuse functions on nonhydrogen atoms is the single most important enhancement of split-valence plus polarization basis sets for computing hydrogen bond energies. Basis set enhancement effects appear to be additive in these systems. The correlation energy contribution to the stabilization energies of these complexes is significant, with the second order term being the largest term and having a stabilizing effect. The third order term is smaller and of opposite sign, while the fourth order term is smaller yet and stabilizing. As a result, computed MP4 stabilization energies are bracketed by the MP2 and MP3 energies. The overall effect of basis set enhancement is to decrease hydrogen bond energies, whereas the addition of electron correlation increases stabilization energies.
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  • 100
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1025-1039 
    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 advances in computer architecture and software, Newton methods are becoming not only feasible for large-scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second-derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
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