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  • 1
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Closed-shell SCF calculations on the ground states and direct SCF calculations on the ionized doublet states were carried out for a series of ten-electron hydrides. The correlation of ionization potentials with the degree of protonation and the nuclear charge has been studied for hole states derived from excitation out of both the core and valence molecular orbitals. Calculated proton affinities of the ground states and hole states derived from a given symmetry orbital show a similar trend to that of the ionization potentials.
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  • 2
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 40-46 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several deficiencies and potential sources of error in the torsion angle driving method, the approach employed most frequently for the simulation of conformational interconversions, have been studied. A general explanation of the observed effects is given in terms of the energy surface and of the effects brought about by “side valleys.” Several examples of molecular mechanics calculations of conformational interconversions, among them the cyclohexane ring inversion, illustrate the problems.
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  • 3
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 62-68 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF molecular orbital calculations have been performed to ascertain the conformational preferences of protonated, neutral, and deprotonated amidine [HC(=NH)NH2], using the 3-21G split valence basis set. The states of eight stable species, eight transition states, and four higher-order saddle points have been determined by complete geometry optimization utilizing analytic energy gradient techniques. Protonation at the amidine =NH is preferred over the -NH2 site by 37.1 kcal/mol. Neutral amidine has rotational barriers of 9.6 and 11.7 kcal/mol for the HN=CN cis and trans isomers, respectively, while all the stable HC(NH2)2+ and HC(NH)2- species possess torsional barriers larger than 23 kcal/mol. There is, however, essentially free C - N single-bond rotation in HC(=NH)NH3+, the calculated barriers being 0.7 and 1.8 kcal/mol for the cis and trans HN=CN isomers, respectively.
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  • 4
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    Journal of Computational Chemistry 3 (1982), S. 112-116 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital calculations are reported for the H2SSH· and H2SCl· radicals and for the H2SClH+· radical cation. The two neutral species are found to be very weakly bound van der Waals' complexes, whereas the H2SClH+· radical cation is bound by 11.9 kcal mol-1 at MP2/4-31G. The importance of charge in σ* radicals is discussed.
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  • 5
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    Journal of Computational Chemistry 3 (1982), S. 117-124 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A blend of Haselgrove's method and the biased selection method for evaluating multidimensional integrals was tested. The results were mixed. The error estimate varied from being proportional to 1/N when N was less than ca. 60,000 to being proportional to 1/√N when N was greater than 60,000. Also, for N greater than 60,000, the error estimate was one-half the error estimate given by biased selection alone. These numbers should be compared with the 10,000 points used to find an optimum set of Haselgrove's parameters. It is reasonable to expect that if 100,000 points were used in the optimization of Haselgrove's parameters that the above results would be found with 60,000 replaced by 600,000.
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  • 6
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    Journal of Computational Chemistry 3 (1982), S. 130-134 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The axial Gaussian lobe orbital (AGLO) representations of 3d and 4f orbitals proposed by LeRouzo and Silvi have been angularly optimized to ensure spherical symmetry of filled 3d and 4f shells. The functions have been tested on the hydrogen atom in the presence of high quality s and p basis sets and found to provide excellent minimal Gaussian representations of polarization functions. Exact orbital degeneracy is not obtained within each shell, however. Tabulated values are given to allow arbitrary scaling of the 3d and 4f lobe mimic orbitals.
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  • 7
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    Journal of Computational Chemistry 3 (1982), S. 154-164 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is outlined which allows an estimation of molecular energies both for a finite basis set including polarization functions and for the Hartree-Fock limit. It is shown that the orbital error of a given minimal basis is covered to a certain relatively constant percentage by an augmented basis set calculation. Thus an improvement factor Qav can be determined by analyzing the corresponding results of small molecules where reasonable estimates of HF limit energies can be taken from the literature. For a combination of Pople's STO-3G and 6-31G* basis sets Qav turns out to be 0.955.
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  • 8
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    Journal of Computational Chemistry 3 (1982), S. 208-213 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation calculated by MINDO/3 are reported for 42 carbocations for which experimental heats of formation have been published. Errors associated with these calculations can be large, with an overall range of ±13 kcal/mol. Correction of systematic errors in the MINDO/3 calculations by means of hydrocarbon models and isodesmic relationships results in a reduction in the range of errors to ±8 kcal/mol. Comparison with experimental heats of reaction of hydride transfer equilibria minimizes experimental errors and gives an average absolute error of 2 kcal/mol with a range of ±3 kcal/mol.
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  • 9
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    Journal of Computational Chemistry 3 (1982), S. 227-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Most quantum chemists regard semiempirical methods as ephemeral and computationally cost efficient. For this reason, an article dealing with computational efficiency of semiempirical methods is probably very unfashionable. However, experience at a big computer installation, shared by ab-initio and semiempirical quantum chemists shows that the second group actually consumes more computer time than the first. Obviously, the greater size of the molecules in semiempirical calculations outweighs the inherent efficiency of these methods. The present article describes a simple method for accelerating SCF-type semiempirical methods.
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  • 10
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    Journal of Computational Chemistry 3 (1982), S. 260-264 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The steps in a nonconventional algorithm for self-consistent field calculations are outlined, and calculations on cumulenes are given to demonstrate the convergence properties of the method. The approach is essentially open ended and is likely to be cost effective on computer systems with minimal core.
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  • 11
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    Journal of Computational Chemistry 3 (1982), S. 273-273 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 12
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    Journal of Computational Chemistry 3 (1982), S. 445-450 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparison is made of MNDO and MINDO/3 calculations for saturated silicon-containing molecules, and with experimental values, for heats of formation, molecular geometries, charge distributions, and ionization potentials. Except for bond angles, it is found that with the published parameter values the MINDO/3 program gives more reliable results than MNDO. For unsaturated molecules, a comparison of bond lengths and stabilities of Si multiple bonds as given by the two programs and ab initio methods is made, and large discrepancies between predicted structures are pointed out. Some reasons for the dicrepancies are discussed.
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  • 13
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    Journal of Computational Chemistry 3 (1982), S. 468-470 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The dication C2H22+ has been investigated by ab initio molecular orbital theory. It is found to have a linear (D∞h), structure with a triplet (3σ-g) ground state. Deprotonation to C2H+ is exothermic by 9.8 kcal/mol, but this process is hindered by a large barrier of 65 kcal/mol.
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  • 14
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    Journal of Computational Chemistry 3 (1982), S. 477-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Neutral, protonated, and deprotonated formamide isomers were studied at the 3-21G SCF level with complete geometry optimization. Ten stable structures, ten first-order saddle points, and three second-order saddle points (conformational maxima) are reported. [Total energies are reported in hartrees (1 hartree = 627.51 kcal/mol = 2625.5 kJ/mol) and energy differences are reported in kJ/mol (1 kJ/mol = 0.239 kcal/mol).] Rotational barriers and proton affinities are discussed and compared to isoelectronic amidine species.
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  • 15
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    Journal of Computational Chemistry 3 (1982), S. 495-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures of the methyl and silyl amines and phosphines and their ions have been calculated using ab-initio SCF theory and the 3-21G basis set. The computed structures give excellent agreement with the available experiment data without the inclusion of d functions, with the exception of (SiH3)2N- and the isoelectronic molecules (SiH3)2O and (SiH3)2C2- where d functions are essential. The observed trends in computed basicities and acidities are reproduced by the calculations.
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  • 16
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    Journal of Computational Chemistry 3 (1982), S. 548-551 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conversion of the cyclobutene cation radical to the 1,3-butadiene cation radical has been studied using MINDO/3 and ab initio SCF MO methods. Not only smooth electrocyclic but also stepwise, non-electrocyclic routes were considered. Both calculational methods agree that the preferred reaction path is a novel nonelectrocyclic one proceeding through an intermediate “cyclopropylcarbinyl cation radical.” The quantitative agreement in the activation parameters calculated by the two methods is excellent. The proposed intermediate also provides an attractive explanation for the mass spectrometric fragmentation patterns of the cyclobutene and butadiene cation radicals.
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  • 17
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    Journal of Computational Chemistry 13 (1992), S. 478-491 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extensive conformational analysis of 3′-azido-3′-deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine - furan, furan - azide, furan - methylene, and methylene - hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2—;HO), which until recently has not been mentioned in the literature, is observed in a few low-energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6—;OH and H6—Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OH—Ofur, which also has not been mentioned for AZT in the literature until recently). The AM1-optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
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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: The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5 — C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H—H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
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  • 19
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    Journal of Computational Chemistry 13 (1992), S. 585-594 
    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 derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial \cos \phi }}\frac{{\partial \cos \phi }}{{\partial x}} $$\end{document} where φ is a bond or torsion angle, E(φ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, -1/sin φ, when φ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, φ°, other than 0 or π, such as in E(φ) = κ[1 + cos(nφ - phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial x}} $$\end{document} This form still possesses singularities for the bond angle forces since the last factor is undefined when φ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.
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  • 20
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    Journal of Computational Chemistry 13 (1992), S. 622-632 
    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 monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
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  • 21
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    Journal of Computational Chemistry 13 (1992) 
    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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  • 22
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    Journal of Computational Chemistry 13 (1992), S. 722-729 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio study of 3-chloro-, 3-hydroxy-, 3-mercapto-, and 3-amino-propanenitrile and 4-chloro-bu- tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
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  • 23
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    Journal of Computational Chemistry 13 (1992), S. 772-791 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
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  • 24
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    Journal of Computational Chemistry 13 (1992), S. 842-850 
    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 electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO-3G, 3-21G, and 6-31G* basis set ab initio and MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo-p-dioxins. The main topological features as well as the absoltue and relative minima location obtained from ab initio calculations are independent from the choice of the basis set. MNDO calculations are in good agreement with the ab initio ones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods with ab initio for any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core-valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wiley & Sons, Inc.
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  • 25
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    Journal of Computational Chemistry 13 (1992), S. 874-882 
    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 numerical method for solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(φ) and potential energy V(φ) are expressed as functions of the torsional angle φ. Molecular examples include ethane, chloroethane, and 1,2-dichloroethane for which I(φ) and V(φ) have been derived from the HF/6-31G* optimized geometries and energies at φ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm-1 of the experimental values. Approximations for the off-diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 912-918 
    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 electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH3X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the 1JCC (ortho-ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH3X molecules considered are also studied. It is suggested that in a molecule PX, rP/R where rP is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 565-569 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium-sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.
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  • 28
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    Journal of Computational Chemistry 13 (1992), S. 595-601 
    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 two-component Kramers' restricted Hartree-Fock method (KRHF) has been developed for the polyatomic molecules with closed shell configurations. The present KRHF program utilizes the relativistic effective core potentials with spin-orbit operators at the Hartree-Fock (HF) level and produces molecular spinors obeying the double group symmetry. The KRHF program enables the variational calculation of spin-orbit interactions at the HF level. KRHF calculations have been performed for the HX, X2, XY(X, Y = I, Br), and CH3I molecules. It is demonstrated that the orbital energies from KRHF calculations are useful for the interpretation of spin-orbit splittings in photoelectron spectra. In all molecules studied, bond lengths are only slightly expanded, harmonic vibrational frequencies are reduced, and bond energies are significantly decreased by the spin-orbit interactions.
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  • 29
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    Journal of Computational Chemistry 13 (1992), S. 614-621 
    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 computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV-vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
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  • 30
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    Journal of Computational Chemistry 13 (1992), S. 651-656 
    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 polynomial path is introduced for the calculation of liquid state free energies. The well-characterized SPC, TIP4P, and MCY water models were used to demonstrate its efficiency, as well as its range of applicability in conjunction with Monte Carlo computer simulations using thermodynamic integration based on Gaussian quadratures. The technique employed is compared with the slow-growth method (another variant of thermodynamic integration), the perturbation method, and the use of the grand-canonical ensemble.
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    Journal of Computational Chemistry 13 (1992), S. 675-680 
    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 free energy gradient or Hessian of a molecule interacting with a liquid represented by a dielectric continuum is derived in the self-consistent reaction field formalism. An ellipsoidal approximation of the cavity is proposed with an algorithm to automatically define the ellipsoid from the nuclear coordinates of the atoms. With this approximation, geometry optimization of the solvated molecule becomes very fast. This method has been implemented in some standard ab initio or semiempirical computational codes. As a first test of the method, full geometry optimization of formamide in a high dielectric constant medium reveals that the CPU time needed for one optimization cycle is less than 3% longer for a solvated species than for the corresponding free molecule.
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    Journal of Computational Chemistry 13 (1992), S. 718-721 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry of acryloyl fluoride was optimized completely at the RHF/6-31G* level of theory at 10 points on the theoretical potential energy curve for internal rotation. The energies obtained were used to determine a six term cosine expansion of the torsional potential energy function. This function was then refined using the experimental torsional transition frequencies in the s-trans and s-cis wells in conjunction with the geometrical parameters optimized at the RHF/6-31G* level. The effective potential function obtained is compared with previous results. The necessity of accounting for relaxation of the geometry upon internal rotation is stressed. © 1992 by John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 13 (1992), S. 768-771 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite-difference Poisson-Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge-solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 793-798 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simulation data from an off-lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end-to-end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 838-841 
    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 bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters from ab initio 6-31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 830-837 
    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 semi-empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more-or-less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley & Sons, Inc.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X-ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SEring(MNDO) ≍ 32.9 kcal/mol] almost compensates the resonance energy (Eresonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔHr ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1089-1097 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1119-1124 
    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 particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two- and three-dimensional system. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1170-1170 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 13 (1992), S. 1216-1233 
    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 distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum-energy conformers using a method of classification that partitions φψ space. The MC-generated configurations are compared with those generated from high-temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low-energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of φ - ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 13 (1992), S. 1-11 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET-enkephalin using MSEED to compute the solvent-accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent-accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.
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    Journal of Computational Chemistry 13 (1992), S. 57-65 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The application of molecular mechanics methods for the study of structures has become a standard approach to conformational analysis. The MM2 force field has been extended to include imines. In general, a diverse group of aliphatic and aromatic imine structures can now be treated. The rotational energy profiles and barriers to N-substituted imines about the Csp2—Csp2 single bonds adjacent to C=N functional group were calculated via ab initio MO theory. Information obtained from the quantum mechanical calculations at the 3-21G, 6-31G*, and MP4/6-31G* //6-31G* levels was used both to study the phenomena involved and to parameterize MM2. The syn-anti isomerization was also studied, and the mechanistic pathways have been evaluated. In cases where the comparison with experimental data can be made, the agreements are good.
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    Journal of Computational Chemistry 13 (1992), S. 93-101 
    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 recently extended SINDO1 method is used to study geometries, electronic structures, and chemical bonding of transition metal organometallic compounds. The optimized distances and angles between metal atoms and organic ligands are in fair agreement with experimental data and are comparable to ab initio results. The comparison of orbital energies between the current method and ab initio methods shows that the method can give a correct description of electronic structure and bonding patterns of organometallic compounds. The method is also used to calculate atomic and bond valence, which are defined in terms of appropriate combinations of first-order density matrix elements for molecules. The valence indices provide a straightforward and easy-to-interpret way to analyze the magnitude of metal-carbon and metal-metal bonds.
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    Journal of Computational Chemistry 13 (1992), S. 135-141 
    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 preliminary study of the capability of the finite difference and finite element methods (FDM, FEM) to evaluate eigenvalues of one-, two-, and three-dimensional self-adjoint operators is reported with reference to applications dealing with the description of vibrational levels. Results of harmonic oscillator model potentials and ab initio PES for the water molecule are obtained by using the FDM. In spite of the large matrices used, low accuracy, nonvariational results are found. A different method, based on FEM and normal coordinates, is therefore proposed. Two nearly harmonic cases are studied and it is shown that variational results with higher accuracy can be obtained with a moderate cost. The vibrational levels of the water molecule are also calculated in order to compare the results with those of the FDM treatment.
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    Journal of Computational Chemistry 13 (1992), S. 160-164 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain, parallel approach to direct Hartree-Fock calculations is presented and discussed. The suggested scheme allows for a near asymptotic speedup involving a very low parallelization overhead without compromising the vector performance of vector-parallel architectures. A shared-memory MIMD implementation, for which very high speeds of computation have been achieved, is discussed in detail.
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    Journal of Computational Chemistry 13 (1992), S. 187-198 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article we report a newly developed direct CI program and its preliminary applications. This program is based mainly on the relationship between direct and exchange type loops and the rederivation of the external loop shapes.
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    Journal of Computational Chemistry 13 (1992), S. 199-213 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute-solvent coupling in a self-consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field-dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.
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    Journal of Computational Chemistry 13 (1992), S. 257-267 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: PEFF is a new computer program designed to assist in the development of empirical force fields used in molecular mechanics calculations. Its main features are: constrained and unconstrained energy minimization available with four different techniques, rigid group refinement, crystal lattice summations, calculation of normal modes, thermodynamic functions and crystallographic temperature factors, vibrational corrections of calculated crystal structures, and a multidimensional driver to scan the energy hypersurface. Used in force field optimization mode, the program employs a least-squares method to fit the force field parameters to a set of experimental data.
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    Journal of Computational Chemistry 13 (1992), S. 318-328 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock self-consistent field calculations on the 3-21G(*) level of approximation have been performed to phosphorylcholine and its derivatives in a geometry close to an X-ray structure of an antibody/antigen complex. Wave functions have been analyzed using different methods for derivation of atomic charges used as Coulomb charges in empirical force fields for molecular dynamics simulations. Among the three applied methods - Mulliken population analysis, natural population analysis, and electrostatical fit - the natural population analysis seems to give best results for these molecules.
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    Journal of Computational Chemistry 13 (1992), S. 362-370 
    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 solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying Lennard-Jones 6-12 and 10-12 perturbations to the hydrogen-bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 program package that allows an interaction described by a Lennard-Jones 6-12 potential to be changed into one described by a hydrogen bond 10-12 potential. The algorithm applied allows this change to occur smoothly without the generation of more extrema on the potential surface. Results using this algorithm have been compared with those determined using the standard AMBER 3.0 Revision A program package, which provides for 6-12 to 6-12 parameter perturbations only. We have also developed a procedure to perform pyrimidine to purine nucleoside mutations to calculate the relative free energies of solvation directly. The theoretical results are compared to experimental energies derived from solvation and vaporization data taken from the literature. The free energies calculated using the new algorithm show good agreement with the derived experimental values. This is also true for the calculations that employ the 6-12 function only, but with 6-12 parameters modified to reflect the correct hydrogen-bonding interactions. However, perturbation of the “standard” 6-12 parameters without changing the functional form proves to be less effective in determining solvation free energies correctly, and demonstrates the importance of accurate hydrogen bond descriptions in free energy simulations.
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  • 53
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    Journal of Computational Chemistry 13 (1992), S. 399-407 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are reported for dimerization-induced changes, Δk, in the harmonic force constant k of the H-bonded OH in water dimer. Two dimer geometries are considered. Δk is obtained by considering the perturbation of a given monomer OH potential by the interaction energy in the dimer in question. The interaction energy is partitioned to identify the role of the various contributions to Δk. The sensitivity of Δk to the choice of the one-electron basis set is studied by using five different basis sets, some of which have a set of bond functions in the H—O bond. At the correlated level, correction for basis set superposition error is found to be essential. A comparison is made of the correlation contribution to Δk as given by the CEPA1, MP2, MP3, and MP4 methods. Of these, MP2 gives exaggerated results. Nevertheless, for economical and reasonably accurate calculations on large systems the MP2 approach in the ESPB basis set is advocated. The most accurate calculations yield a shift Δv0-;1 of - 121 cm-1 for the uncoupled donor O-H vibrational frequency in water dimer.
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  • 54
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    Journal of Computational Chemistry 13 (1992), S. 414-422 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In ab initio Hartree - Fock crystal orbital calculations of chemical and physical properties of polymers, the huge number of two-electron integrals restricts the size of the elementary cell. Therefore, the question arises how the storage and computation resources of modern parallel supercomputers can be exploited. In this work, we report the parallelization of the one- and two-electron integral programs, respectively, for the parallel computer SUPRENUM. A short description of the hardware and software environment of this supercomputer is given. The results are discussed with respect to speed-up and efficiency.
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  • 55
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    Journal of Computational Chemistry 13 (1992), S. 505-524 
    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 ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor-dependent terms in the potential function at points on a three-dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
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    Journal of Computational Chemistry 13 (1992), S. 533-538 
    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 investigate and test an algorithm suitable for the parallel calculation of the potential energy of a protein, or its spatial gradient, when the protein atoms interact via pair potentials. This algorithm is similar to one previously proposed, but it is more efficient, having half the interprocessor communications costs. For a given protein, we show that there is an optimal number of processors that gives a maximum speedup of the potential energy calculation compared to a sequential machine. (Using more than the optimum number of processors actually increases the computation time). With the optimum number the computation time is proportional to the protein size N. This is a considerable improvement in performance compared to sequential machines, where the computation time is proportional to N2. We also show that the dependence of the maximum speedup on the message latency time is relatively weak.
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    Journal of Computational Chemistry 13 (1992), S. 560-564 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Among some 2-substituted 4H-1,3,2-benzodioxaphosphorin 2-sulfides, the 2-OMe derivative has the sulfur atom mainly in the quasiequatorial position. On the other hand, the conformation in which the sulfur is quasiaxial is favored in the 2-NHMe and 2-Et derivatives. We have done ab initio molecular orbital calculations for the model compounds, and such a substituent effect was reproduced. Moreover, the effect was discussed in terms of the intramolecular electrostatic interactions and the degree of charge distribution.
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  • 58
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    Journal of Computational Chemistry 13 (1992), S. 570-578 
    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 Tyson-Fife reaction-diffusion equations are solved numerically using a locally implicit approach. Since the variables evolve at very different time scales, the resulting system of equations is stiff. The reaction term is responsible for the stiffness and the time step is increased by using an implicit method. The diffusion operator is evaluated explicitly and the system of implicit nonlinear equations is decoupled. The method is particularly useful for parameter values in which the equations are very stiff, such as the values obtained directly from the experimental reaction rate constants. Previous efforts modified the parameters on the equations to avoid stiffness. The equations then become a simplified model of excitable media and, for those cases, the locally implicit method gives a faster although less accurate solution. Nevertheless, since the modified equations no longer represent a particular chemical system an accurate solution is not as important. The algorithm is applied to observe the transition from simple motion to compound motion of a spiral tip.
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  • 59
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    Journal of Computational Chemistry 13 (1992) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 60
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    Journal of Computational Chemistry 3 (1982) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 61
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Orbital mapping analysis based on CNDO/2 molecular orbitals has been used to survey the thermal ring-opening isomerizations of cyclobutenes and benzocyclobutenes. Isoelectronic substitutions within the molecular framework of cyclobutene (e.g., CH2 replaced by CH-, OH+, NH, NH2+) result in ground-state orbital correlations via both conrotatory and disrotatory pathways in several cases, in contrast to the parent hydrocarbon conrotatory stereochemistry. The results substantiate the heteroatom effects previously revealed by orbital mapping for the disrotatory thermal isomerizations of isoelectronic Dewar benzenes. Qualitative patterns, such as nodal shifts in the butadiene π orbital, are discussed in relation to the mapping correlations. The isoelectronic benzocyclobutenes give ground-state orbital correlations via conrotatory pathways only, which suggests that delocalization may reduce the heteroatom perturbation.
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  • 62
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    Journal of Computational Chemistry 3 (1982), S. 471-476 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The distance geometry approach to conformational calculation has been shown to be very effective at producing large molecular structures satisfying many given, long-range constraints on the interatomic distances. I now present a significant extension of the method that handles strictly geometric constraints as well as before while also locating conformers of very low energy. The main feature of the algorithm is a projection of the molecule from a low energy conformation in a high dimensional space to three dimensions in such a way as to perturb the energy as little as possible. Tests of the method on very small systems with simple energy functions completely explored by independent means show that the global minimum of energy is sometimes attained. In every case the final energy is very low, and geometric constraints are completely satisfied.
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  • 63
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    Journal of Computational Chemistry 3 (1982), S. 486-494 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MNDO-UHF method has been applied to a large number of organic and inorganic radical species. The obtained results demonstrate that thermodynamical data as well as their equilibrium structures are in reasonable agreement with experimental findings.
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  • 64
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The O—H bond length and the quadratic, cubic, and quartic stretching force constants, calculated ab initio using the unscaled 4-31G basis set with full geometry optimization, are reported for 30 planar conformers of ten molecules contaning either the C—OH, N—OH, or O—OH group. The data are analyzed in terms of the general form of Clark's equation, and the power functions and exponential functions proposed by Herschbach and Laurie. In the case of the quadratic constants, significant trends are found in the values of the parameters depending on whether the O—H group is bonded to carbon, nitrogen, or oxygen, and whether it is non-hydrogen-bonded or involved in intramolecular hydrogen bond formation in four-, five-, or six-membered rings. Using data for diatomic molecules, O—H, and C—H bonds, and the C=O and C—C bonds in planar monosubstituted carbonyl compounds, the parameter dij in the power function equation for quadratic constants, which can be regarded as the distance of closest approach of the two nuclei, is shown to increase progressively along the series (i) diatomic molecule; (ii) similar bond in a polyatomic environment with one of the two atoms covalently bonded to a neighboring atom; (iii) as in (ii) but with the second atom hydrogen bonded; and (iv) with both atoms covalently bonded to neighboring atoms.
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    Journal of Computational Chemistry 3 (1982), S. 556-560 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An improved version of the direct inversion in the iterative subspace algorithm is developed. The method is significantly more efficient than the previous version, and is applicable to intrinsically divergent or slowly convergent cases. Comparisons indicate that the method is superior to the recently proposed quadratically convergent (QC-SCF) method of Bacskay.
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  • 66
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    Journal of Computational Chemistry 3 (1982), S. 571-579 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electronic states and barriers to internal rotation in allene (1a), 1-silaallene (2a), and 2-silaallene (3a) are investigated computationally using ab-initio molecular orbital methods. Planar geometries with two-, three-, and four-π-electron configurations have been considered as possible transition states (1b-3d). Structures have been optimized at the Hartree-Fock level with a small split valence basis set (3-21G) and higher level calculations with basis sets of split valence (6-31G) and split valence plus polarization function (6-31G*) quality include correlation energy estimates from Møller-Plesset second-and third-order perturbation theory. The electronic barrier to internal rotation in allene is estimated near 53 kcal/mol whereas the corresponding barriers in 1-silaallene and 2-silaallene are considerably smaller, ca. 35 and 20 kcal/mol, respectively. The transition states are predicted to possess bent geometries in all three molecules with open-shell singlet, three-π-electron configurations in 1 and 2 (1c, 2c) but a closed-shell singlet, two-π-electron configuration in 3 (3d).
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    Journal of Computational Chemistry 3 (1982), S. 603-603 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 3 (1982) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 3 (1982), S. 23-27 
    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 reaction between atomic oxygen and carbon disulfide is predicted to lead to at least two primary products, which are the dithiiranone (1) and the oxathiirane-thione (2) and/or the carbon disulfide S-oxide (4). The possible intramolecular equilibria 1 ⇄ 2, 1 ⇄ 3, 2 ⇄ 4, and 2 ⇄ 5 as well as the fragmentations of the possible intermediates 1-5 have been studied theoretically within the semiempirical CNDO/B framework as conceivable ground-state reactions. On the basis of MO correlations and potential energy changes along the reaction paths, supplementary with previously reported experimental data, the single molecular transformations and the eventual product formations are discussed.
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    Journal of Computational Chemistry 3 (1982), S. 28-36 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The topological resonance energy (TRE) model was introduced independently by the Zagreb Group (in 1975) and by Aihara (in 1976). Several practical obstacles arise in the computation of TRE. Ways to surmount them are pointed out. Descriptions of algorithms, optimizations, and the efficient computer program are presented. Possible numerical instability is discussed.
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  • 71
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular structures of tricyclohexane, norbornane, quadricyclane, and cubane were completely refined by standard ab initio force relaxation on the 4-21G level. The results can be used as a basis to interpret some contradictory experimental reports found in the literature and to establish some hitherto unobserved structural trends involving the C—C and C—H bond distances of the cases studied. Group Delta;E values for C—(H)3(C), C—(H)2(C)2, and C—(H)(C)3 (Benson's notation) derived from the total energies of the completely relaxed 4-21G geometries of a number of unstrained hydrocarbons are also listed. The values are used to estimate the strain energies of the systems studied and of the optimized 4-21G geometries of cyclopropane, cyclobutane, cyclohexane, and bicyclo (2.1.0)pentane. Cooperative effects in the strain energies are discussed.
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    Journal of Computational Chemistry 3 (1982), S. 75-88 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article develops computer programs for computer generation of nuclear spin species and nuclear spin statistical weights of rovibronic levels. The programs developed here generate nuclear spin species and statistical weights from the group structures known as generalized character cycle indices (GCCIs) which are computed easily from the character table of the PI group of the molecule under consideration. Procedures are illustrated with examples.
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    Journal of Computational Chemistry 3 (1982) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 3 (1982), S. 135-139 
    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 well known that if the formation of hydrocarbons during Fischer-Tropsch synthesis occurs via the condensation polymerization mechanism, there is little hope for selectivity enhancement in the desired range of products. Recent data on low surface area model catalysts, where readsorption is unlikely, have shown that at low conversions, the product distribution obeys the condensation polymerization mechanism and the distribution of products is shifted to lower-molecular-weight hydrocarbons. We have used a computer simulation of the growth of hydrocarbon chains to obtain a picture of the catalyst surface under synthesis conditions. Such an approach could prove useful in distinguishing between various theoretical models. We have applied the simulation to compare the changes in selectivity when readsorption occurs and when it does not. The dynamic behavior of the reacting system which is obtained from the computer results has shown that selectivity to lower-molecular-weight hydrocarbons is a stronger function of the extent of reaction than the incorporation of readsorption into the chain growth mechanism.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Bond correlation energies ∊(XY) have been derived by partitioning second-order Rayleigh-Schrödinger-Møller-Plesset (RSMP) correlation energies. Values of ∊(XY) depend on the type of bonding between atoms X and Y. They can be considered as comprising correlation energies of bond, lone, and inner-shell electron pairs of the group XY. Once a set of appropriate increments ∊(XY) has been obtained, it is possible to estimate unknown RSMP energies of larger molecules. This concept also can be used when estimating total correlation energies E(CORR). For this purpose e(XY) values have been derived from known E(CORR) energies of small molecules. It is shown that ∣∊(XY)∣ increments increase linearly with the number n of electron pairs of the group XY. The function ∊(n) becomes zero for n = 1/2 (one uncorrelated electron) and passes through -0.042 for n = 1, which is approximately the correlation energy of the bonding electron pair of H2 or a 1s inner-shell pair. With the aid of estimated E(CORR) and HF limit energies, Schrödinger energies and theoretical heats of formation of relatively large molecules are obtained.
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    Journal of Computational Chemistry 3 (1982), S. 191-207 
    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 that even the CPMET approximation for the contributions of fourfold excitations can be replaced by a more sophisticated method. Furthermore, an approximation is presented for the contributions of threefold excitations which are neglected in CPMET. Finally, it is described how the advantages of different CEPA methods can be united in a single CEPA scheme (called CEPA-U). The various approximations are discussed in terms of Slater determinants, and it is shown how the relatively large amount of details can be handled with the help of computer programs, i.e., how knowledge engineering can be successfully applied here.
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    Journal of Computational Chemistry 3 (1982), S. 229-233 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Fifty-one structures have been calculated by the MINDO/3 method to evaluate the errors introduced by branching and by the presence of the heteroatom. The structures are evaluated by comparisons which reveal that the calculated ΔHf values reflect a bias because of the presence of the heteroatom. With two carbons or more in a chain attached to a heteroatom group, a linear relationship exists which makes possible the calculation of reasonably accurate ΔHf values for unbranched alcohols, primary or secondary amines, ethers, thioethers, thiols, and alkyl chlorides. Branching errors do not seem to be linearly related among the systems. Some errors in calculations of geometries are also discussed.
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    Journal of Computational Chemistry 3 (1982), S. 234-250 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical HF/6-31G* (Hartree-Fock, 6-31G* basis set) and MP2/6-31G* (second-order Møller-Plesset, 6-31G* basis set) vibrational frequencies based on complete quadratic force fields have been obtained for a set of 36 one- and two-heavy-atom molecules comprising first-row elements for which experimental spectroscopic data are available. Frequencies calculated at the HF/6-31G* level are an average of 12.6% higher than experimental values. Partial treatment of electron correlation via the perturbation method of Møller and Plesset, terminated at second order, leads to a significant reduction in this error, although theoretical MP2/6-31G* frequencies are still larger than the experimental quantities by 7.3%. Part of the difference may be traced to the restriction of quadratic force fields, as comparison with experimental harmonic frequencies shows deviations of only 9.5% and 4.7% for the two levels, respectively. The calculated frequencies are used in conjunction with the corresponding theoretical equilibrium structures to obtain absolute molecular entropies, which may in turn be used to yield entropies of reaction. These latter quantities are generally in good accord with entropies derived using experimental structures and frequencies.
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    Journal of Computational Chemistry 3 (1982), S. 273-273 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular structure of the stretched form of n-nonane, as a typical long-chain hydrocarbon, was refined by geometrically unconstrained ab initio force relaxation on the 4-21G level. The C—C bonds and C—H bond distances in the interior of the hydrocarbon chain are found to be longer (by about 0.001 Å and 0.002 Å, respectively) than those near the end of the chain. Similarly, interior C—C—C bond angles are 0.4° larger than the terminal angles. The variation of structural parameters with distance from the molecular ends levels off after the second carbon atom, and the geometry of methylene is practically constant from C3 on. However, if one end of the system is perturbed by moving the inplane methyl hydrogen away from equilibrium, the resulting destabilizing electronic effects are transmitted through the C—C bond distance chain in such a way that significant perturbations are still experienced at C5. Molecular mechanics (MM2) gives a structure in which the small changes in bond lengths and angles with chain location are well reproduced.
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    Journal of Computational Chemistry 3 (1982), S. 305-316 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The formalism developed in the preceding article is used in a normal coordinate analysis of the pyrimidine base cytosine. The results of both planar and nonplanar vibrations are reported. The model yields 66 frequencies with an average error of about 6.5 cm-1 (ca. 0.5%). The vibrational modes are compared with experimental data and discussed in terms of potential energy distributions and Cartesian displacements. Two isolated low-frequency (near 200 cm-1) out-of-plane modes are predicted in the vicinity of where two such modes are believed to occur. In addition, the model has taken into account the observed coalescence of the torsional and wagging modes of the amino group upon deuteration of the amino group. Recent data from sulfur-substituted cytosine (2-thiocytosine) were useful in making assignments.
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    Journal of Computational Chemistry 3 (1982), S. 329-334 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The coefficients of a 1/R expansion (containing long-range electrostatic interaction, medium-range electrostatic-induced dipole attraction, short-range dispersive attraction, and very short overlap interaction terms) have been determined, within a semiempirical approach, from the results of a priori calculations. The formulation has been applied to the study of the stable conformations of benzene complexes.
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    Journal of Computational Chemistry 3 (1982), S. 354-362 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The experimental IR and Raman spectra of ethylene oxide have been reinvestigated with particular attention to the intensities. The absolute IR intensities have been measured for the gaseous state. The spectra have been simulated by using a normal coordinate analysis coupled with a CNDO determination of the intensities. The intensity calculation using polarization functions appears to be more reliable than the standard version. Furthermore, the force field has been extended for ethylene sulfide.
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  • 84
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    Journal of Computational Chemistry 3 (1982), S. 385-399 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The principles and structure of an LCAO-MO ab-initio computer program which recalculates all two-electron integrals needed in each SCF iteration are formulated and discussed. This approach - termed “direct SCF” - is found to be particularly efficient for calculations on very large systems, and also for calcuations on small and medium-sized molecules with modern minicomputers. The time requirements for a number of sample calculations are listed, and the distribution of two-electron integrals according to magnitude is investigated for model systems.
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  • 85
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    Journal of Computational Chemistry 3 (1982), S. 417-420 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 force field has been used to calculate the strain energies of a representative series of bridgehead alkenes, and the results compared to similar previous calculations using the MM1 force field. The new results roughly parallel the old ones, although the strain energy of a given compound is normally higher with MM2 than MM1. These differences are largely negated, however, when the OS (olefinic strain) value is considered.
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  • 86
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: With the purpose of deciphering conformational inversion processes of typical mobile bicyclic molecules, torsional energy surfaces near the enantiomers of bicyclo[4.2.1]nonan-9-one (1) and bicyclo-[4.2.2]decane (2) were prepared using molecular mechanics with an improved two-bond drive technique. Inversion of 1 takes place most favorably via a Cs transition state with the tetramethylene chain over the ethano bridge [1B, ΔH± 6.1 (calculated) vs. 6.8 (observed) kcal/mol]. An alternative pathway involving a Cs local energy minimum (1C), in which the tetramethylene chain is bent over the carbonyl, has a barrier 2.4 kcal higher than 1B. The global energy minimum conformation of 2 has boat-chair cyclooctane and twist-boat cyclohexane rings (BCTB), and enantiomerizes into its mirror image (BCTB') via three intermediates: TCTB, CB, and TCTB'. The highest point in the proposed pathway, a saddlepoint CB, is calculated to lie 8.0 kcal/mol above BCTB (observed ΔH± 7.8 kcal/mol). The advantage of the two-parametric over the one-parametric torsional energy surface is discussed.
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  • 87
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Existing schemes for evaluation of the characteristic polynomial of a graph suffer from limited practicality. Their application to large molecules inordinately increases the amount of labor. Here a procedure is outlined which is useful even for large molecules. It is based on a not widely known property of the collection of characteristic polynomials for Ulam's subgraphs, which, when added, give the derivative of the characteristic polynomial of the initial graph. The characteristic polynomials for Ulam's subgraphs are, as a rule, easier to derive due to the presence of many pending bonds in graphs of chemical interest. The last step requires an integration of a polynomial (which is a straightforward step) and determining the constant of integration, which represents the determinant of the adjacency matrix. The available methods for determing the additive constant (the determinant) are combinatorially much simpler than the initial task of finding all of the coefficients of the characteristic polynomial. The approach is illustrated on selected benzenoid hydrocarbons, nonbenzenoid, and nonalternant systems. Construction of the characteristic polynomials can be accelerated by considering auxiliary fragments and irreducible subgraphs separately and combining them in the final expression. Many auxiliary fragments allow their characteristic polynomials to be expressed in a closed form using recursive relations. The results for complex molecules can thus be written in a relatively compact form. Finally, the derivative of the characteristic polynomial, expressed in terms of selected auxiliary functions and irreducible components, can be integrated directly to give the result in terms of contributions signifying various fragments rather than as an explicit function of x.
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  • 88
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    Journal of Computational Chemistry 3 (1982), S. 451-467 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The application of the self-consistent field (SCF) local-impurity formalism to quasi-one-dimensional systems is discussed. We describe a general procedure for an accurate numerical determination of the Green's function matrix elements of the unperturbed system. An application to a local impurity in a model chain with two orbitals per unit cell is reported. The changes in the charge-bond-order matrix and in local and total density of states due to the impurity are discussed with special emphasis on the changes at the critical points (van Hove singularities) at the band edges. The Green's matrix approach is used to reexamine long-range Friedel oscillations caused by an impurity in a strictly one-dimensional metal. The extent of the long-range tail of the perturbed charge density is in an inverse relation to the localization length of the impurity state: the stronger the perturbation the more localized is the bound state and the more extended are the oscillations in the charge distribution. The results for the model chain with two orbitals per unit cell indicate that the impurity-induced change in charge distribution may be locally screened by redistribution of the population of the on-site orbitals, therefore damping possible oscillations and leading to a faster decay than in strictly one-dimensional systems.
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  • 89
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    Journal of Computational Chemistry 3 (1982), S. 507-511 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The inadequate description of molecular systems involving lone pairs by the original PCILO method is analyzed on some examples. A modified PCILO version for the lone-pair description is proposed. The success of this method is represented in the same examples.
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  • 90
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    Journal of Computational Chemistry 3 (1982), S. 552-555 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Localized molecular orbital (LMO) energies obtained from the canonical molecular orbital (CMO) energies and unitary transformation or from the matrix of the Fock operator and the LMOs are described. The results for water and ethylene are given, and compared with earlier work of Wilhite and Whitten.
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  • 91
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    Journal of Computational Chemistry 3 (1982), S. 525-547 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute-solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN/2 potential for methane-water interactions) and 124 water molecules (using the MCY potential for water-water interactions). Again, the convergence of solute-solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN/2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.
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  • 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: Ab-initio studies were conducted on quantitative aspects of π-nonbonded, σ-σ*, n-σ*, and throughbond interactions in R1CH2(CH2)N-1 CH2 R2, where R1 and R2 are H and/or nonbonding AO, n, and N = 2, 3, and 4. Geometrical preferences were found to depend both on π-nonbonding and bond-antibonding interactions, the latter being more important. Level orderings and energy splittings involved in the through-bond interactions of diradicals can be qualitatively predicted by examining the signs of the overlap between the n orbitals and a common vicinal σ* bond orbital, using simple orbital patterns and paying special attention to the “backside” tails of bond orbitals.
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  • 93
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    Journal of Computational Chemistry 3 (1982), S. 588-592 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An analysis has been made of the applicability of various sets of nonbonded interaction potential parameters which do not consider hydrogen atoms explicitly, to represent molecular packing interactions in crystals of ferrous porphyrin complexes, which are models for deoxyhemoglobin. Ordered regions of the structures are well described, but disordered solvent or ligands cause difficulty.
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  • 94
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    Journal of Computational Chemistry 3 (1982), S. 593-602 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: SCF-MO-LCAO ab-initio computations were carried out for the four tautomers 2-pyridone, 2-hydroxypyridine, 3-pyridone, and 3-hydroxypyridine interacting with a water molecule placed at different positions and orientations around each of them. The computed interaction energies were fitted by an analytical potential consisting of a 6-12 Lennard-Jones term plus a Coulombic one. The root-mean-square deviation of the fit is 2.5 kJ/mol. We report isoenergy contour maps for some important cross sections and obtain a qualitative trend of the solvation entropy, in agreement with available experimental data. The obtained potentials were used for Monte Carlo simulation of four clusters consisting of a tautomer molecule as solute and 50 water molecules, at 300 K. The problem of the transferability of fitting constants is also examined.
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  • 95
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    Journal of Computational Chemistry 13 (1992), S. 17-32 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An overall adsorption quantity for a heterogeneous solid is usually expressed by an integral equation, which contains a distribution function that describes heterogeneous properties of this solid. The calculation of this distribution function is an ill-posed problem. The current article shows that the difficulties arising from the ill-posed nature of an adsorption equation can be overcome with the regularization method. This work presents general principles of regularization for solving the ill-posed problems without detailed mathematical considerations. The application of the regularization method to calculate a distribution function from any overall adsorption functions is illustrated with both simulated and experimental adsorption isotherms.
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  • 96
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    Journal of Computational Chemistry 13 (1992), S. 66-69 
    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 used Brownian dynamics simulations of substrate O2- encounters with the enzyme bovine erythrocyte Cu, Zn superoxide dismutase (SOD) to study the effects of multiple charge modifications in the enzyme on the kinetics of its diffusion-controlled reaction. When the charges of two or three residues were changed, the calculated rate consant relative to that for the unmodified enzyme was usually found to be the product of relative rate constants for the enzymes with the corresponding single-site changes. This “multiplicativity” rule may be useful in the design of enzymes that operate with diffusion-controlled kinetics. Residues that deviate from the general rule are found in the active site channel of SOD, and the origin of these deviations is considered.
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  • 97
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    Journal of Computational Chemistry 13 (1992), S. 85-92 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The semiempirical MO method SINDO1, originally suitable for first- and second-row atoms, is extended to transition metals from scandium to zinc. The core Hamiltonian elements in a symmetrically orthogonalized atomic orbital (OAO) basis set are modified and the parameters are optimized to reproduce the experimental geometries, heats of formation, and ionization potentials. An application of the method to a selected number of molecules, as well as a comparison between calculated and experimental data is reported.
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  • 98
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: From the standpoint of models that use a polarizable continuum to represent the solvent in studying the phenomenon of solvation, a systematic and detailed analysis is made of the influence of the cavity size and shape on calculated energies. The solute is represented by its ab initio wavefunction, and the electronic part of the solvation energy is calculated including terms that take into account electron correlation up to third order. The analysis shows the convenience of modeling the cavity according to considerations of homogeneity, which are based fundamentally on how the solute wavefunction is constructed, i.e., the basis set used.
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  • 99
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    Journal of Computational Chemistry 13 (1992), S. 155-159 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Elementary Jacobi Rotations are used as the basic tools to obtain eigenvalues and eigenvectors of arbitrary real symmetric matrices. The proposed algorithm has a complete concurrent structure, that is: every eigenvalue-eigenvector pair can be obtained in any order and in an independent way from the rest. Examples based on diagonally dominant real symmetric matrices are given.
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  • 100
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    Journal of Computational Chemistry 13 (1992), S. 214-228 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational space available to four inhibitors of the bacterial enzyme thermolysin has been searched in the enzyme binding site using a method that combines Monte Carlo type techniques with energy minimization for exploration of the conformational potential energy hypersurface. Molecular mechanics methodology using the AMBER force field was employed for computation of the molecular energetics. Solvation energies were also included in the calculations by employing a technique that estimates hydration energies based on the exposed solvent accessible surface area for each atom of the inhibitor and active site. It was found that in each case, the crystallographically observed conformation was among the low energy conformers discovered. In fact, in three of the calculations it was the lowest energy conformation. The methodology described in this article is expected to be quite useful for studies involving computer aided design and evaluation of enzyme inhibitors.
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