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  • 101
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 102
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 881-894 
    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 report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.
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  • 103
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 895-898 
    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 AM1 and PM3 potential energy surfaces of cyclopentane have been compared and the energy difference between two (boat and chair) cyclohexane conformers analyzed. The effects of reparameterization and different core-repulsion functions (CRFs) have been studied. The H—H, C—H, and C—C CRF energy contributions have been calculated separately. The results show that the CRF energy corrections stabilize the correct (MM2 and ab initio) geometries. The PM3 equilibrium geometry of cyclopentane is closer to the MM2 and ab initio results than the AM1 geometry. It is known that above 190 pm the AM1 H—H CRF curve is smooth and negative but the PM3 H—H CRF curve has a trough and a shoulder. It has been shown that this latter oscillation is not damped by other parameters. As a result, the H—H PM3 energy gradient curve is different from the quasilinear AM1 and ab initio gradient curves. © 1993 John Wiley & Sons, Inc.
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  • 104
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 105
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 639-646 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: For the treatment of hydrogen bonding in SINDO1, 2p orbitals are introduced on hydrogen. The optimization of the orbital exponent together with the generation of approximate formulas for the core attraction integrals is sufficient to obtain good geometries and binding energies in hydrogen bonded systems. The method is applied to the dimers (H2O)2, (NH3)2, (HF)2, (HCOOH)2, (HCN)2, (H2S)2, and (HCI)2, mixed dimers NH3 · H2O and H2O · HCN, and cyclic polymers (HF)n(n = 3, 4, 6). © 1993 John Wiley & Sons, Inc.
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  • 106
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 673-679 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms to reduce the space needed to store information either in memory or magnetic media are presented. These algorithms were designed to pack and unpack two common kinds of data types: sequences of sets of integers that change in a regular fashion and real numbers of fixed absolute precision. One typical application of these techniques is in the storage of electron repulsion integrals in ab initio calculations, where the indices of the basis functions are a good example of data of the first type and the integrals of the second type. In this case, savings in storage space of 50% or more can be obtained with reasonable accuracies in the energies. FORTRAN subroutines are presented for packing/unpacking indices and integrals both in the IBM and IEEE 754 64-bit floating point formats. © 1993 John Wiley & Sons, Inc.
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  • 107
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 685-690 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relative basicities of the lone pairs of the acetate ion have been determined using ab initio calculations for the gas phase and Monte Carlo simulations for the aqueous phase. The syn lone pair is found to be more basic by only 1.25 pKa units. This small difference is the result of a large intrinsic preference for the syn conformer of the conjugate acid in the gas phase, offset by an almost equally large preferential solvation of the anti conformer in the aqueous phase. The better solvation of the anti conformer is due to stronger solute-solvent interactions. © 1993 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 108
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 977-985 
    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 parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four-processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.
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  • 109
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    Journal of Computational Chemistry 14 (1993), S. 995-1005 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom-atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na4 GTP and Na2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.
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  • 110
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    Journal of Computational Chemistry 14 (1993), S. 1027-1035 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three hydrogen-bonded minima on the phenol-water, C6H5OH - H2O, potential energy surface were located with 3-21G and 6-31G** basis sets at both Hartree-Fock and MP2 levels of theory. MP2 binding energies were computed using large “correlation consistent” basis sets that included extra diffuse functions on all atoms. An estimate of the effect of expanding the basis set to the triple-zeta level (multiple f functions on carbon and oxygen and multiple d functions on hydrogen) was derived from calculations on a related prototype system. The best estimates of the electronic binding energies for the three minima are -7.8, -5.0, and -2.0 kcal/mol. The consequences of uncertainties in the geometries and limitations in the level of correlation recovery are analyzed. It is suggested that our best estimates will likely underestimate the complete basis set, full CI values by 0.1-0.3 kcal/mol. Vibrational normal modes were determined for all three minima, including an MP2/6-31G** analysis for the most strongly bound complex. Computational strategies for larger phenol-water complexes are discussed. © John Wiley & Sons, Inc.
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  • 111
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    Journal of Computational Chemistry 14 (1993), S. 751-752 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Some force constants associated with the internal coordinates that sense handedness or chirality can have opposite signs in the enantiomers of chiral molecules. Examples of such force constants include interaction force constants between a torsional and stretching or bending internal coordinates. The sign reversal for these force constants in the enantiomers of chiral molecules or in opposite-handed molecular segments is best recognized by labeling them as chiral force constants. Recognition of chiral force constants suggests that certain guidelines are to be followed in the presentation of internal coordinate force constants. © 1993 by John Wiley & Sons, Inc. © John Wiley & Sons, Inc.
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  • 112
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    Journal of Computational Chemistry 14 (1993), S. 790-798 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three different optimization algorithms are applied to solving the problem of finding the best side-chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.
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  • 113
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    Journal of Computational Chemistry 14 (1993), S. 809-817 
    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 two-step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.
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  • 114
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    Journal of Computational Chemistry 14 (1993), S. 1194-1202 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using a number of different lattice models of proteins, the problems introduced by the discretization of a protein backbone are discussed and examples of the most typical errors arising in low coordination number lattices presented. The geometric properties of different lattices used in the literature are compiled, and for all of them the resulting α-carbon models of proteins are described in detail and compared to the original structures obtained from experiment. © John Wiley & Sons, Inc.
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  • 115
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    Journal of Computational Chemistry 14 (1993), S. 913-921 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relativistic and electron correlation effects in thallium halides TlX and TlX3 (X=F, Cl, Br, and I) are investigated by extensive ab initio configuration interaction calculations. Spin-orbit coupling is included at the Hartree-Fock level for the diatomic TlBr and TlI. At the best level of treatment of electron correlation (quadratic configuration interaction), the calculated molecular properties are in good agreement with experimental results, i.e., for the diatomic thallium halides deviations from experimental values are 〈0.06 Å for bond distances, 〈0.14 mdyn/Å for force constants, 〈35 kJ/mol for dissociation energies, and 〈0.3 D for dipole moments. The convergence of the Møller-Plesset series up to the fourth order is discussed. Two alternative structures of TlI3 are compared. At the Møller-Plesset level of theory, the trigonal planar structure with thallium in the oxidation state + 3 is the preferred gas phase arrangement compared with the bent arrangement containing a linear I3- unit and thallium in the oxidation state + 1, the difference being ca. 95 kJ/mol. Vibrational frequencies are predicted for all trigonal planar thallium(III) halides. © 1993 John Wiley & Sons, Inc.
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  • 116
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    Journal of Computational Chemistry 14 (1993), S. 961-969 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of binding energies and optimum geometries of compounds of the series M(H2O)+ with M = Sc to Zn have been carried out and compared with gas-phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree-Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d-function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d-function space. However, MP2 or higher-level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas-phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.
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  • 117
    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 general procedure is presented for generating one-electron integrals over any arbitrary potential operator that is a function of radial distance only. The procedure outlines that for a nucleus centered at point C integrals over Cartesian Gaussians can be written as linear combinations of 1-D integrals. These Cartesian Gaussian functions are expressed in a compact form involving easily computed auxiliary functions. It is well known that integrals over the Coulomb operator can be expressed in terms of Fn(T) integrals, where \documentclass{article}\pagestyle{empty}\begin{document}$$ F_n \left(T \right) = \int_0^1 {u^{2n} e^{ - Tu^2 } {\rm d}u} $$\end{document} By means of a substitution for Fn(T) by other simple functions, algorithms that form integrals over an arbitrary function can be generated. Formation of such integrals is accomplished with minor editing of existing code based on the McMurchie-Davidson formalism. Further, the method is applied using the inverse-square distance and Yukawa potential operators V(r) over Cartesian Gaussian functions. Thus, the proposed methodology covers a large class of one-electron integrals necessary for theoretical studies of molecular systems by ab initio calculations. Finally, by virtue of the procedure's recursive nature it provides us with an efficient scheme of computing the proposed class of one-electron integrals. © 1993 John Wiley & Sons, Inc.
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  • 118
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    Journal of Computational Chemistry 14 (1993), S. 1019-1026 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Estimating log P (logarithm of “1-octanol to water” partition coefficients) as a measure of lipophilicity for organic compounds is of considerable importance in drug discovery. Several methods have been developed for this purpose, each with its own drawbacks and advantages. In this article, a systematic comparison of three well-documented and fully computerized methods has been attempted for a set of nucleosides and bases. The first method (BLOGP) is based on overall molecular properties derived from a molecular orbital calculation to predict log P. The second method (CLOGP) uses fragmental lipophilicity constants with correction factors and treats log P as an additive-constitutive property. The third method (ALOGP) is based on an additivity scheme of atomic lipophilicity constants, with the constitutive factor governed by an elaborate list of atom types. However, none of these methods take into account conformational flexibility or intramolecular hydrogen bonding, which can cause substantial discrepancy between observations and predictions. A comparison of predictions from each of these methods indicates that the atomic contribution method (ALOGP with r = 0.842 and SD = 0.51) is better than other methods (with r = 0.395 and SD = 1.2 for BLOGP and r = 0.713 and SD = 0.93 for CLOGP) for this class of compounds. Our overall assessment is that we do not have, as yet, a highly reliable, fully computerized log P prediction method applicable to flexible heterocycles such as nucleoside analogs. © John Wiley & Sons, Inc.
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  • 119
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    Journal of Computational Chemistry 14 (1993), S. 1042-1049 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new, generalized, method for measuring the steric size of ligands and substituents has been developed. The method is based on the solid angle concept, the solid angle being generated by the pairwise addition of spheres (atoms). The problem of overlapping spheres (atoms) has been solved analytically and the algorithm provided permits evaluation of the steric space occupied by any combination of spheres (atoms). A range of solid angles for commonly encountered ligands and substituents has been determined and compared to literature values for linear cone angles. © John Wiley & Sons, Inc.
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  • 120
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    Journal of Computational Chemistry 14 (1993), S. 1077-1084 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New combining rules are proposed for the well depth, ∊, and interaction distance, σ, describing nonbonded interatomic forces for rare gas pair interactions. Concepts underlying current combining rules applied in simulations of macromolecular and polymer systems are shown to be incompatible with experimental data on the rare gases. The current combining rules are compared with the new results using the experimental data. Mathematical properties of combining rules are considered, and it is shown how to reduce combining rule formulas from a two-parameter to a single-parameter problem. It is also shown how to graphically analyze combining rules against experimental data. We demonstrate using this analysis technique that the rare gas potentials do not obey a single combining rule for the ∊ parameter but do follow a single combining rule for the σ parameter. Finally, we demonstrate that a combining rule using both ∊ and ω can be used to predict the ∊ parameters for the mixed rare gas pairs. © John Wiley & Sons, Inc.
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  • 121
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    Journal of Computational Chemistry 14 (1993), S. 1259-1271 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulations result in a comprehensive description of molecular motion. However, to gain insight into the dynamic behavior of molecules it is important to be able to identify different types of motions and characterize them. We have developed a novel technique aimed at characterizing the motion of the system using digital signal processing techniques. The amplitudes and phases of the Fourier transform of the atomic fluctuations are used to define the characteristic modes of motion in the MD trajectory. This yields a pictorial description of the oscillatory motions in a manor analogous to normal-mode (NM) analysis. The validity of this method has been tested on small molecules such as water, acetamide, and a blocked polyalanine in a helical conformation. The NMs obtained by diagonalizing the mass-weighted second derivative matrix were combined to generate “NM trajectories” that served as well-characterized test cases. Distinct characteristic modes can be extracted from both NM and MD trajectories. The modes extracted from the NM trajectories were identical to the original NMs. The modes extracted from the MD trajectories were in most cases highly correlated to the corresponding NM. However, intermixing of some of the modes occurred, particularly when conformational changes took place. This technique is flexible and can be applied to the molecular system as a whole or to a subset of atoms of interest. Fourier transform calculations are fast and therefore the analysis stage is not demanding in computational resources. Anharmonicity is included explicitly in the simulations and solvent can be included as well. © John Wiley & Sons, Inc.
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  • 122
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    Journal of Computational Chemistry 14 (1993), S. 1313-1319 
    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 limiting factor to account for the increased rate of intramolecular reactions between functional groups as opposed to their intermolecular counterparts can and has been explained both by proximity effects and by activation energy. Neither explanation has emerged as the single most important reason in all or even the majority of cases studied. We have therefore reexamined the spatiotemporal hypothesis of Menger and the transition-state energy approach of Houk on a consistent set of compounds subjected to the Barton oxidation or related reactions in an effort to more clearly define the reasons for the proximity effect. For the 26 structures studied, neither hypothesis provides a consistent, quantitative explanation although the transitionstate energy hypothesis offered the most promise. © John Wiley & Sons, Inc.
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  • 123
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    Journal of Computational Chemistry 14 (1993), S. 1339-1346 
    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 are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem., 13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time in ab initio computations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley & Sons, Inc.
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  • 124
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    Journal of Computational Chemistry 14 (1993), S. 1385-1395 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Many important problems in chemistry require knowledge of the 3-D conformation of a molecule. A commonly used computational approach is to search for a variety of low-energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low-energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low-energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade-offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.
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  • 125
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    Journal of Computational Chemistry 14 (1993), S. 1407-1414 
    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 demonstrate the use of a genetic algorithm (GA) search procedure for finding low-energy conformations of small to medium organic molecules (1-12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.
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  • 126
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    Journal of Computational Chemistry 14 (1993), S. 1440-1445 
    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 restricted SCF (single-configuration SCF) and MCSCF (multiconfiguration SCF) calculations are performed to compute the ground-state electric dipole moments of four pairs of diatomic molecules - (1) CO and BF; (2) SiO and AlF; (3) CS and BCl; and (4) SiS and AlCl - at a number of internuclear distances on both sides of the equilibrium position. Near Hartree-Fock accuracy is obtained in the SCF calculations. All eight molecules have a range of internuclear distance in which electric dipole moments are of the polarity of A-B+. The shapes of computed electric dipole moment functions are discussed in the language of the molecular orbital method and in relationship to electronegativities of atoms. The present study gives us deeper understanding of electron transfer inside molecules and consequently of the apparent contradiction between electronegativity and the dipole polarity of some molecules. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 1468-1481 
    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 total energies per unit cell of both the undistorted and the Peierls-distorted polyacene polymers are computed from the respective HF/6-311G** and MP2/6-311G** finite-cluster data using 40 different extrapolation schemes. The benchmark calculations, which aim at assessing the efficiency of extrapolation methods, clearly show that the best procedure for obtaining rapidly converging bulk properties should involve computation of the energy differences, followed by rational extrapolation techniques such Wynn's p algorithm or its iteration, both with the interpolation points xn = (n + 1)2, and closely related extrapolation methods, or Wynn's ε algorithm and its close relative, Aitken's iterated Δ2 algorithm. © John Wiley & Sons, Inc.
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  • 128
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    Journal of Computational Chemistry 14 (1993), S. 1504-1518 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges were obtained from ab initio molecular orbital calculations using a variety of procedures to compare them and assess their utility. Two procedures based on the molecular orbitals were examined, the Mulliken population analysis and the Weinhold-Reed Natural Population Analysis. Two procedures using the charge density distribution were included; the Hirshfeld procedure and Bader's Atoms in Molecules method. Charges also were derived by fitting the electrostatic potential (CHELPG) and making use of the atomic polar tensors (GAPT). The procedures were first examined for basis set independence, and then applied to a group of hydrocarbons. The dipole moments for these molecules were computed from the various atomic charges and compared to the total SCF dipole moments. This was followed by an examination of a series of substituted methanes, simple hydrides, and a group of typical organic compounds such as carbonyl derivatives, nitriles, and nitro compounds. In some cases, the ability of the charges to reproduce electrostatic potentials was examined. © John Wiley & Sons, Inc.
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  • 129
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    Journal of Computational Chemistry 14 (1993), S. 1561-1574 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: AM1 semiempirical molecular orbital calculations are reported for 20 ion-neutral complexes, including hydrogen-bonded complexes, presumably involved in the gas-phase unimolecular decomposition of simple organic radical cations. The systems investigated are [C2H4O2]·+, [C2H5NO]·+, [C2H6O]·+, [C2H6O2]·+, [C3H6O]·+, [C3H6O2]·+, [C3H8O]·+, and [C3H8O2]·+. The AM1 results are compared with ab initio molecular orbital calculations at different levels of theory up to MP3/6-31G(d, p)//SCF/6-31G(d) + ZPVE and the available experimental data. AM1 fails to predict some local minima and the equilibrium geometries calculated for several complexes are found to be qualitatively different from those predicted by the ab initio calculations. However, reasonable agreement is generally found for the stabilization energies of the complexes toward dissociation into their loosely bound components. © John Wiley & Sons, Inc.
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  • 130
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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 deuterium quadrupole coupling constant and asymmetry parameter in heavy water were determined using ab initio SCF calculations. Snapshots from a molecular dynamics simulation were used to give liquid water cluster configurations and the influence of simulation parameters on the quadrupole coupling constant was investigated. The electronic potential model and the number of molecules in the molecular dynamics simulation and the pressure of the system were found to have only a small influence on the quadrupole coupling constant. The average value of the quadrupole coupling constant at room temperature, corrected for the known deficiency of the ab initio calculation in the gas phase, yields a quadrupole coupling constant of 253 kHz, in perfect agreement with the most recent experiments. The oxygen - deuterium bond lengths in ice Ih, ice II, and ice IX were determined using experimental quadrupole coupling constants and a model equation. An averaged bond length of 98.9 pm was obtained for the Ih form, which is approximately 2 pm shorter than that determined by neutron diffraction studies, whereas the bond lengths for the four deuterium sites in ice II and the three sites in ice IX are in fair agreement with experiment. © John Wiley & Sons, Inc.
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  • 131
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    Journal of Computational Chemistry 14 (1993), S. 1446-1453 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Pipecolic acid derivatives have proven to be effective P′1 groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31-8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1 position. The binding orientation of Ro 31-8959 is known from X-ray crystallography. However, the bound conformation of the S-hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, the N-alkyl substituents may be equatorial or axial and the 3-carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations, ab initio molecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest-energy N-equatorial rotamer is always at least 3 kcal/mol more stable than the lowest-energy N-axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial-axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for the N-equatorial and N-axial cases. When the molecular dynamics-averaged conformation of the bound S-hydroxy inhibitor is considered, the energy difference between the N-equatorial and N-axial conformers drops to 4-5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline-containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for binding Ro 31-8959. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 3-7 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As probed by ab initio calculations at SCF and MCSCF levels, the rotational barrier of the PC double bond in the title compound is similar in magnitude to the corresponding one in methylenephosphane. The transition state for rotation is dipolaric in nature. On this basis, a combination of electron releasing and electron accepting substituents reduces the magnitude of the rotational barrier in phosphatriafulvene. It is supported by experimental investigations. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 8-12 
    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 data compression algorithm for packing/unpacking floating point numbers is presented. The method has been used to compress large volumes of data commonly generated in ab initio quantum mechanical calculations. To retain an accuracy of 10-6 Hartree on the final energy, the required file space needed is approximately half its original size whereas the CPU time required to solve the Hartree-Fock self-consistent field equations increases with 30-60%. © 1993 John Wiley & Sons, Inc.
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  • 134
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    Journal of Computational Chemistry 14 (1993), S. 263-277 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Combining the modified Urey-Bradley-Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm-1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low-frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1 quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm-1. © 1993 John Wiley & Sons, Inc.
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  • 135
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    Journal of Computational Chemistry 14 (1993), S. 330-348 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The stochastic search method coupled to MM3(92) has been used to locate as many conformers as possible for 6- to 11-membered ring lactones, trans-cycloalkenes, and cis-cycloalkenes. A comparison was carried out between the conformers of lactones and cycloalkenes of the same ring size for each force field. These comparisons were carried out by means of (1) conformational distances, defined as the rms deviation between the dihedral angles of the conformers being compared, and (2), substitution, in which a lactone was transformed into an olefin and vice versa, trying to keep as much as possible the initial geometry, followed by reoptimization. It is found that cycloalkenes and lactones share many common characteristics. The thermodynamic information provided by MM3 was used to study the dependence of conformer population upon (1) temperature and (2) total number of conformers. © 1993 John Wiley & Sons, Inc.
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  • 136
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potential-derived charges for the catecholamine neurotransmitter dopamine were calculated at the STO-3G and 6-31G* basis sets for six different molecular conformations. The degree of variance of the charges with changing conformations was examined. The 6-31G* basis set produced charges that were more sensitive to changes in conformation than those derived from the STO-3G electrostatic potentials. The implication of the charge variations in molecular mechanics calculations was also investigated. The molecular mechanics results in the gas phase exhibited a variance depending upon the charge set used. The force field calculations varied much less when aqueous solvation was included in the calculations through a continuum model. © 1993 John Wiley & Sons, Inc.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Journal of Computational Chemistry 14 (1993), S. 371-377 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: AM1 and PM3 semiempirical calculations are reported for the solvent effects on the tautomeric equilibria of 2-pyridone/2-hydroxypyridine and 4-pyridone/4-hydroxypyridine in the gas phase and solution. The solvent effects on the tautomeric equilibria were investigated by self-consistent reaction field (SCRF) theory implemented in the AMPAC and MOPAC program in two different ways: one in which all the solvent relaxation is included in the quantum mechanics and the total energy must be corrected for the solvent change in energy, method A; and a second in which the quantum mechanics directly includes this term, method B. The calculated (AM1, method A) tautomeric equilibrium constants (log K1) for 2-pyridone in the gas phase, cyclohexane, chloroform, and acetonitrile are -0.3, 0.3, 0.8, and 1.3, respectively, in good agreement with the experimental data (-0.4, 0.24, 0.78, and 2.17, respectively). For 4-pyridone/4-hydroxypyridine differences between calculated log K1 for the gas phase, chloroform and acetonitrile (-6.0, -2.6, and -1.2, respectively) and experimental data (〈 -1, 0.11, and 0.66, respectively) are larger but the experimental values are also less certain. The experimental acetonitrile data are disturbed by specific interactions. An extension of the SCRF for aqueous solutions is reviewed. © 1993 John Wiley & Sons, Inc.
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  • 139
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF3 group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed - molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.
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  • 140
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A systematic SCF study has been undertaken to compare the conventional a posteriori Boys-Bernardi BSSE correction scheme with our recent CHA/F method in which BSSE is excluded in a priori manner. Potential curves have been obtained for nine simple hydrogen-bonded systems by using nine different basis sets for each. It is concluded that the difference between the a posteriori BB and the a priori CHA schemes diminishes much faster when the basis set improves than BSSE disappears from the uncorrected SCF results. This fact gives an additional confidence in the CHA results, permitting one to draw the explicit conclusion that, at the SCF level of theory, the a priori CHA/F scheme can be considered the ultimate solution of the BSSE problem for weakly bonded systems. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 438-444 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD-determined conformations are in the same energy range as the NMR-determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 452-454 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an improvement to Johnson, Gill, and Pople's results for reducing the cost of using the McMurchie-Davidson RNLM recurrence relation for one-center integrals. Recursive replacement of singly referenced and single-term auxiliary integrals results in floating point operation (FLOP) savings of up to 11% and explicit auxiliary integral calculation reductions of up to 76% with respect to the full list and up to 46% with respect to FLOP-reduced lists with no replacement. The programs are written in the string-manipulation language Convert; one of the programs automatically generates a FORTRAN subroutine given an integral list. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 455-470 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics is a fast developing discipline with new methods and potential fields appearing every year. A versatile molecular mechanics program supports many methods and potential fields that make it unavoidably large. There are problems writing and maintaining large programs with traditional methods because of data and other dependencies. Modular programming provides a solution. A program is developed as a collection of highly independent modules containing only related data structures and procedures. These entities are isolated in the module and access to them is provided through a well-defined and controlled interface. The high degree of independence circumscribes programming errors. Most of all, it reduces the cost of revising the program as only a small part of the program needs to be read and understood for each revision. We implemented a molecular mechanics program, yammp, using the modular programming method. © 1993 John Wiley & Sons, Inc.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    Journal of Computational Chemistry 14 (1993), S. 503-509 
    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 natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 549-555 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By using the group symmetrical localized molecular orbitals (SLMOs) as configuration-generating orbitals (CGOs) of many-electron wave functions, the symmetry adaptation of many-electron spaces is greatly simplified, and novel orthogonal bonded functions (OBFs), as complete space- and spin-adapted antisymmetrized products, are introduced. The corresponding programs for the solutions of OBFs are developed. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 566-570 
    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 energy of atoms and molecules may be evaluated accurately by the use of wave functions where the interelectronic distances are explicitly present. In particular, explicitly correlated Gaussian-type functions make these types of calculations feasible and computationally tractable even for more extended systems. The resulting multielectron integrals may be reduced to standard one- and two-electron integrals that are readily evaluated. Initial calculations have been made for the Be atom where all four electrons were correlated at the same time. The preliminary results show that accurate results may be obtained. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 571-578 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A conformational study of the 2,3,6,7-tetrahydroazepine (THA) and closely related systems has been carried out using MM3 and CHARMm molecular mechanics, AM1 semiempirical, as well as Hartree-Fock and local density functional (LDF) ab initio methods. For THA, all methods give similar optimal geometries; however, only MM3 agrees with the Hartree-Fock calculations using a 6-31G* basis set and LDF in the rank order of energies and nature of the stationary points characterized. AM1 shows serious disagreements with those results. Tetrahydrobenzazepines and a D1 receptor agonist containing the THA nucleus were studied using CHARMm, MM3, and AM1 calculations. All methods provide similar descriptions of the geometries of the conformations accessible to these compounds. However, the same disparities in the rank order of energies are observed. © 1993 John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 226-236 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we describe the program MORMIN, which can simultaneously minimize the mechanical energy of a given macromolecular structure, together with a weighted quadratic penalty function of the difference between the observed and computed nuclear Overhauser effect (nOe) peaks. The gradient of the nOe penalty function relatively to the proton coordinates is computed from an exact closed formula of a matrix exponential derivative. To cut CPU time, the molecular system is partitioned into nonoverlapping subsets containing the protons involved in the observed peaks. The algorithm is no longer exact, but if a 1% relative error is accepted it can be run, on a scalar computer, in about the same CPU time as needed for the calculation of the mechanical energy. We have successfully run the program in more than 1000 situations, including cases where the hybrid method failed because of the occurrence of negative eigenvalues. In some cases, the optimization of the Cartesian coordinates could be successfully extended to individual atomic diffusion times. © 1993 John Wiley & Sons, Inc.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Journal of Computational Chemistry 14 (1993), S. 253-262 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present investigations on the use of dielectric continuum models for the self-consistent description of electrostatic solvent effects on the ground state of a molecule and on excitation energies. The electronic structure calculations have been carried out in the framework of the INDO and INDO/S-CI method, respectively. We compare the performance of three implementations of the cavity model that all allow an arbitrary shape of the solute cavity. The procedures differ in the effort spent on the description of the charge density at the cavity surface. Two procedures in the vein of Miertus̆, Scrocco, and Tomasi (MST) rely upon point charges to model the reaction field and differ in the way the cavity surface is modeled. While one implementation divides the surface into flat triangular patches, the improved version uses curved triangles. Alternatively, we investigate a finite element method (FEM) for the calculation of the surface charge density. Applications to rod-shaped organic molecules (including their charge transfer excitations) illustrate the superiority of the improved MST formalism over the primitive one, as it exhibits faster convergence of the results with increasing node density on the cavity surface. The FEM approach, which also employs curved surface patches, leads to a further improvement as it needs less computational effort, especially in the treatment of excited states. © 1993 John Wiley & Sons, Inc.
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  • 152
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    Journal of Computational Chemistry 14 (1993), S. 736-740 
    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 implementation of Pipek-Mezey population localization is described. It is compared with other localization schemes and its use in the framework of the local correlation method is discussed. For such use, this localization is shown to be clearly superior to Boys in the case of physically well-localized systems. Our current algorithm for selection of local virtual spaces is also described. © 1993 John Wiley & Sons, Inc.
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  • 153
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    Journal of Computational Chemistry 14 (1993), S. 741-750 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon-water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon-water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent-induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon-water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.
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  • 154
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    Journal of Computational Chemistry 14 (1993), S. 769-774 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a storage-efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight-binding models of ordered and disordered 2-D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10-4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.
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  • 155
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    Journal of Computational Chemistry 14 (1993), S. 799-808 
    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 systematic study of the suitability of PM3-derived molecular electrostatic potentials (MEPs) is presented. Forty-six MEP minima, 81 electrostatic charges, and 17 electrostatic dipoles were determined at the PM3 level and compared with those obtained from the ab initio 6-31G* wave function, as well as from the semiempirical MNDO and AM1 wave functions. The statistical results of the comparison analysis between semiempirical and ab initio 6-31G* MEPs show that PM3 is in general reliable for the study of the MEP minima but a mediocre method as a source of electrostatic charges. © 1993 John Wiley & Sons, Inc.
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  • 156
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    Journal of Computational Chemistry 14 (1993), S. 831-847 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational behavior of cellobiose (D-glc-ß(1→4)-D-glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic φ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long-lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the 4C1 conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.
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  • 157
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    Journal of Computational Chemistry 14 (1993), S. 867-878 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To make improved treatments of electrostatic interactions in biomacromolecular simulations, two possibilities are considered. The first is the famous particle-particle and particle-mesh (PPPM) method developed by Hockney and Eastwood, and the second is a new one developed here in their spirit but by the use of the multipole expansion technique suggested by Ladd. It is then numerically found that the new PPPM method gives more accurate results for a two-particle system at small separation of particles. Preliminary numerical examination of the various computational methods for a single configuration of a model BPTI-water system containing about 24,000 particles indicates that both of the PPPM methods give far more accurate values with reasonable computational cost than do the conventional truncation methods. It is concluded the two PPPM methods are nearly comparable in overall performance for the many-particle systems, although the first method has the drawback that the accuracy in the total electrostatic energy is not high for configurations of charged particles randomly generated. © 1993 John Wiley & Sons, Inc.
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  • 158
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Complexes of 18-crown-6 with alkali-metal cations (Na+, K+, and Rb+), urea, and the uncomplexed crown ether were studied in vacuo with the molecular dynamics method. Conformational data from these calculations (simulation times in the range from 6-15 ns) was compared with information from the Cambridge Structural Database. Despite the differences in condition between the simulations and the solid state, a number of interesting similarities are observed. © 1993 John Wiley & Sons, Inc.
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  • 159
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    Journal of Computational Chemistry 14 (1993), S. 922-927 
    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 quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO-3G, 3-21G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3-D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions). © 1993 John Wiley & Sons, Inc.
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  • 160
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    Journal of Computational Chemistry 14 (1993), S. 944-960 
    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 modification of Allinger's MM2 force field for the anomeric effect in O—C—N systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3-21G level) and X-ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the C—O—C—N—C moiety as well as C—N bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H-bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force-field approach. © 1993 John Wiley & Sons, Inc.
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  • 161
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    Journal of Computational Chemistry 14 (1993), S. 699-714 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two conformers of protonated pyruvate, CH3C+(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C—C—C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C—COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH3COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C—COO distance of 1.6-1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C—C—O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ⃛ OC hydrogen bond. © 1993 John Wiley & Sons, Inc.
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  • 162
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    Journal of Computational Chemistry 14 (1993), S. 718-727 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method to characterize conformations adopted by chain and cyclic molecules, and to assess their degree of flexibility toward folding, is developed and applied. The proceudure constructs a function A0 from some simple geometric and topological properties of molecular chains. This function provides a global descriptor of the essential shape features of the molecular fold. The descriptor takes a maximum value of 1 for a completely linear or planar structure and a minimum value of 0 for an entangled or globular backbone. In this sense, the function proposed measures the compactness and degree of folding of a configuration. When one monitors the changes in this function along computer-simulated molecular dynamics trajectories, it is possible to assess the differential stability of conformations as a function of time, temperature, and other factors. Molecules that are stable over time toward adopting conformations with radically different folds are characterized as rigid. Consequently, the procedure provides also a quantitative measure of rigidity and flexibility toward folding. In other words, the fluctuations of A0 provide a quantitative measure of stability whereas the value of A0 gives a measure of the actual type of instant folding pattern. The description is characteristic of the given conformation and not relative to the initial nuclear geometry for the dynamics. The procedure is illustrated by comparing conformations of hexane and cyclohexane at various temperatures and contrasting the dynamics of hexane and decane, both starting from similar conformational minima. © 1993 John Wiley & Sons, Inc.
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  • 163
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    Journal of Computational Chemistry 14 (1993), S. 1085-1100 
    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 between geometry optimization in Cartesian coordinates, using an appropriate initial Hessian, and natural internal coordinates. Results on 33 different molecules covering a wide range of symmetries and structural types demonstrate that both coordinate systems are of comparable efficiency. There is a marked tendency for natural internals to converge to global minima whereas Cartesian optimizations converge to the local minimum closest to the starting geometry. Because they can now be generated automatically from input Cartesians, natural internals are to be preferred over Z-matrix coordinates. General optimization strategies using internal coordinates and/or Cartesians are discussed for both unconstrained and constrained optimization. © John Wiley & Sons, Inc.
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  • 164
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    Journal of Computational Chemistry 14 (1993), S. 1112-1122 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics is the integration of a set of coupled differential equations describing the motion of atoms over time. These equations exhibit the unfortunate property of stiffness, that is, terms of the equations (the forces on the atoms) are defined on several scales - ranging from tens of kcal/mol/Å to thousands of kcal/mol/Å. Additional nonconservative and stiff effects occur when a distance cutoff is used for the electrostatics and nonbonded potentials. Because the first derivative at the cutoff is essentially infinite, small variations in positions will cause large variations in energy and violate conservation of energy. The effects are demonstrated in a small system of 125 isolated water molecules. It is possible to greatly reduce and nearly eliminate the stiff integration effects with an improved integrator. The nonconservative effects of the distance cutoff cannot be removed by changing the integrator. © John Wiley & Sons, Inc.
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  • 165
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    Journal of Computational Chemistry 14 (1993), S. 1142-1148 
    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 parallel direct SCF and gradient program for workstation clusters has been implemented on the basis of the ab initio program package TURBOMOLE. Applications on large molecular systems monitor an appreciable speedup in residence time. © John Wiley & Sons, Inc.
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  • 166
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    Journal of Computational Chemistry 14 (1993), S. 848-857 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.
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  • 167
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    Journal of Computational Chemistry 14 (1993), S. 858-866 
    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 monopole “point charges” are routinely determined through a least squares fit to molecular electrostatic potentials [potential-derived (PD) charges]. Previously, it has been shown that these charges vary with variation in molecular conformation. Also, it has been observed that these swings in charges are highly correlated between neighboring atoms. Here, we examine the least squares variance-covariance data matrices for a set of data in the literature and find further indications of high colinearity within the data. These colinearities effectively reduce the dimensionality of the data to a value well below the number of atoms in the molecules. This suggests that the data is not of sufficient dimensionality to support calculation of the charges for all of the atoms in a statistically significant way. We experiment with fixing the charges of atoms whose PD charges reflect large errors in the fit. The resulting estimates of fit of the remaining charges are little degraded from the estimates of fit when the charges of all of the atoms are fit. In addition, the charges that are fit take what would be considered more reasonable and “chemically intuitive” values, often of smaller magnitude. Although most of the free charges continue to vary with molecular conformation, their range is no larger than when all charges were fit and, in some cases, the ranges of the charges for the fit atoms is actually reduced over those that are found when all of the atoms take part in the fitting procedure. The errors of fit are lower and the unconstrained charges appear more reasonable when more chemically “reasonable” charges are used for the fixed values. This suggests that in many cases charges are transferable between molecules. Further, it shows a way to justifiably reduce the large fluctuations in PD charges that occur with variations in conformation. © 1993 John Wiley & Sons, Inc.
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  • 168
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    Journal of Computational Chemistry 14 (1993), S. 907-912 
    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 semidirect implementation of the closed-shell MP2 gradient for efficient use on workstation computers is presented. The approach is based on the algorithm proposed by Frisch and coworkers but includes several modifications to reduce disk storage requirements and exploits nonabelian point group symmetry. The performance of the resulting program MPGRAD (BIOSYM Corp., San Diego, CA) is demonstrated in applications to the molecules [AlSi(CH3)3]4 and ferrocene. The largest calculation involved 492 basis functions and was carried out on IBM RS/6000 workstations with memory sizes of 32 and 128 Mb. The ratio of CPU to wallclock time exceeds 90% in all typical applications. © 1993 John Wiley & Sons, Inc.
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  • 169
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    Journal of Computational Chemistry 14 (1993), S. 1240-1249 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Absolute free energies of hydration have been computed for 13 diverse organic molecules using partial charges derived from ab initio 6-31G* wave functions. Both Mulliken charges and charges fit to the electrostatic potential surface (EPS) were considered in conjunction with OPLS Lennard-Jones parameters for the organic molecules and the TIP4P model of water. Monte Carlo simulations with statistical perturbation theory yielded relative free energies of hydration. These were converted to absolute quantities through perturbations to reference molecules for which absolute free energies of hydration had been obtained previously in TIP4P water. The average errors in the computed absolute free energies of hydration are 1.1 kcal/mol for the 6-31G* EPS charges and 4.0 kcal/mol for the Mulliken charges. For the EPS charges, the largest individual errors are under 2 kcal/mol except for acetamide, in which case the error is 3.7 kcal/mol. The hydrogen bonding between the organic solutes and water has also been characterized. © John Wiley & Sons, Inc.
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  • 170
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    Journal of Computational Chemistry 14 (1993), S. 1491-1497 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By using the dynamically defined reaction path (DDRP) method and starting from various initial polygons, the intrinsic reaction coordinate (IRC) of the H2 + H → H + H2 reaction has been calculated. The numerical stability of the method is illustrated by the evolution phases of the reaction path. Techniques and experiences on the parameter choice and effects of the parameter values on the stability and computer time consumption are discussed. © John Wiley & Sons, Inc.
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  • 171
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom-centered point-charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 14 (1993), S. 1545-1552 
    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 comprehensive study on the gas-phase alkaline hydrolysis of cephalosporins by using the semiempirical AM1 method was carried out. Cephalothin was the model compound used on account of the presence of a good leaving group at C(3′). According to the results obtained, the hydrolysis process takes place via a twostep reaction mechanism that involves the formation of an intermediate with a fully open β-lactam ring that still preserves the acetate group. Likewise, the exo methylene end product is chiefly formed by nucleophilic attack on the β-lactam carbonyl group of cephalosporins containing a good leaving group at C(3′). On the other hand, the alternative mechanism involving hydrolysis of the ester function in the side chain at 3′ and subsequent hydrolysis of the resulting β-lactam yieds essentially the corresponding enamine. The presence of a first solvation layer consisting of five water molecules showed that, even though some potential barriers are slightly increased, the mechanism involved is identical to that of the gas-phase hydrolysis of this antibiotic. © John Wiley & Sons, Inc.
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  • 173
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    Journal of Computational Chemistry 14 (1993) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 174
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    Journal of Computational Chemistry 14 (1993), S. 1423-1428 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A set of simple models of hydrogenated amorphous silicon (a-Si:H) consisting of hypothetical silane molecules with diamond or similar lattices was studied by the semiempirical AM1 method. Densities of states and infrared spectra were calculated for the silane molecules and similar molecules with dangling bonds disorder, and with boron or phosphorus substitution to simulate doping. Some examples are presented, and a comparison is made with experimental properties of a-Si:H. It is proposed to use these models in a study of the Staebler-Wronski photodegradation of a-Si:H and other aspects of amorphous silicon technology. © John Wiley & Sons, Inc.
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  • 175
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    Journal of Computational Chemistry 14 (1993), S. 1250-1257 
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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 reaction mechanism of the model cytochrome P450-mediated desulfuration of thiophosphoryl trifluoride, trimethylphosphine sulfide, and trimethyl phosphorothionate was examined by the semiempirical MNDO-PM3 molecular orbital method. The proposed pathways, involving initial formation of S-oxide followed by rear-rangement to a cyclic phosphoxathiirane and the successive liberation of atomic sulfur to form a phosphate derivative, wee stepwisely analyzed by using the two model active oxygen species, O(1D) and O(3P). Reaction coordinate analysis followed by refinement of transition states in each spin state strongly suggested that the desulfuration of thiophosphorus compounds by O(3P) was energetically more favorable than O(1D). The alternative triplet pathway, abstraction of sulfur by O(3P) forming phosphine and sulfur monoxide followed by recombination between phosphorus and oxygen, was found to be energetically more probable than the rearrangement pathway. © 1993 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 176
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    Journal of Computational Chemistry 14 (1993), S. 1290-1300 
    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 quantification of surface roughness of globular proteins and synthetical macromolecules in the globular state is discussed using the concept of fractality. The Hausdorff dimension as a measure for local and global fractality of surfaces is applied. To calculate the Hausdorff dimension of any surface at a high level of accuracy, a new algorithm is presented that is based on a triangulated solvent-accessible molecular surface. It can be demonstrated that protein surfaces (as calculated on the basis of experimentally determined structures) as well as surfaces of globular polyethylene (PE) conformers (calculated on the basis of structural information basing on extensive Monte Carlo and molecular dynamics simulations) in fact show self-similarity within a reasonable yardstick range, at least in a global statistical sense. The same is true for parts of a protein surface provided that these regions are not too small. The concept of self-similarity breaks down when individual surface points are considered. The results obtained for the fractal dimension of PE surfaces (average fractal dimension D = 2.23) lead to the conclusion that protein surfaces probably do not exhibit a unique and specific degree of geometrical complexity (or surface roughness) characterized by a fractal dimension of approximately D = 2.2 as was argued in the past. It is clear that the concept of self-similarity is helpful for the classification of surface roughness of large molecules, but it seems questionable whether this concept is useful for the identification of active sites or other questions related to the field of molecular recognition. © John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 177
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    Journal of Computational Chemistry 14 (1993), S. 1326-1332 
    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 PM3 quantum-mechanical method is able to model the magic water clusters (H2O)20 and (H2O)21H+. Results indicate that the H3O+ ion is tightly bound within the (H2O)20 cluster by multiple hydrogen bonds, causing deformation to the symmetric (H2O)20 pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H2O)21H+ clusters are presented. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 178
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    Journal of Computational Chemistry 14 (1993), S. 1364-1375 
    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 locally dense basis set approach to the calculation of nuclear magnetic resonance shieldings is one in which a sufficiently large or dense set of basis functions is used for an atom or molecular fragment containing the resonant nucleus or nuclei of interest and fewer or attenuated sets of basis functions employed elsewhere. Provided the dense set is of sufficient size, this approach is capable of determining chemical shieldings nearly as well as a calculation with a balanced basis set of quality equal to the locally dense set, but with considerable savings of CPU time. Detailed comparisons are provided of locally dense and balanced calculations in the gauge including atomic orbital (GIAO) method for the individual principal values, the isotropic shieldings, and the tensor orientations for hydrogen, carbon, nitrogen, oxygen, fluorine, and phosphorus nuclei. It is seen that chemical functional groups can often define the appropriate molecular fragment to be taken locally dense. While the present test cases are for the most part small molecules, the value of the method is that it will allow calculations on systems that would otherwise presently be computationally expensive or inaccessible. © John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 179
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    Journal of Computational Chemistry 14 (1993), S. 1498-1503 
    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 between Miertus-Scrocco-Tomasi (MST) SCRF and free energy perturbation (FEP) estimates of the free energy of hydration of eight small neutral molecules is presented. In both cases, the 6-31G* molecular electrostatic potential is used to describe the electrostatic properties of the molecules. The results demonstrate the ability of both methodologies to provide useful theoretical estimates of the total free energy of hydration; the average errors are only 1.5 kcal/mol (FEP) and 0.8 kcal/mol (MST/SCRF). The largest errors in the FEP and MST/SCRF results are less than 1.5 kcal/mol for all molecules except acetic acid, where the FEP method overestimates the free energy of hydration by 3.3 kcal/mol. © John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 180
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    Journal of Computational Chemistry 14 (1993), S. 1534-1544 
    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 comparative and systematic ab initio study of different models simulating the Si (111) surface has been carried out for a variety of embedding hydrogen atoms including unmodified hydrogen atoms and modified hydrogen atoms described with a STO-4G basis set and a Slater exponent optimized to have the cluster atoms as neutral as possible. The study has been extended to some chemisorption processes as Ag and Al on Si (111). The main conclusion of the present work is that neither the electronic structure of the isolated cluster models nor the nature of the chemisorption bond depend on the kind of embedding hydrogen atoms used to saturate the free valences of the cluster edge atoms. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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