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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 139-149 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program for automatic resonance assignment of nuclear magnetic resonance (NMR) spectra of proteins, GARANT (General Algorithm for Resonance Assignment), is introduced. Three principal elements used in this approach are: (a) representation of resonance assignments as an optimal match of two graphs describing, respectively, peaks expected from combined knowledge of the primary structure and the magnetization transfer pathways in the spectra used, and experimentally observed peaks; (b) a scoring scheme able to distinguish between correct and incorrect resonance assignments; and (c) combination of an evolutionary algorithm with a local optimization routine. The score that evaluates the match of expected peaks to observed peaks relies on the agreement of the information available about these peaks, most prominently, but not exclusively, the chemical shifts. Tests show that the combination of an evolutionary algorithm and a local optimization routine yields results that are clearly superior to those obtained when using either of the two techniques separately in the search for the correct assignments. GARANT is laid out for assignment problems involving peaks observed in two- and three-dimensional homonuclear and heteronuclear NMR spectra of proteins. © 1997 by John Wiley & Sons, Inc.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 159-168 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A parallel implementation of the computation of RHF energy second derivatives with respect to the nuclear coordinates is described. The algorithm and organization of the code are described in detail on the most computationally demanding steps with special emphasis on the integral transformation code. Key features of the proposed algorithm are its large degree of concurrency, limited interprocessor communication, and critical memory needs distributed over the processors. The cpu times and computer and network resources used are reported and discussed for a few examples. © 1997 by John Wiley & Sons, Inc.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 198-210 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: All four possible Diels-Alder reactions between 2H-phosphole and phosphaethene were examined at various theoretical levels, including HF, MP4SDQ, CCSD(T), and CASSCF. MP2/6-31G* geometry optimizations could not be employed since the potential energy surface is qualitatively incorrect at this level of theory, due to the inherent underestimation of the activation energies (ameliorated at higher-order MP or coupled-cluster levels). Solvent effects were examined employing the Onsager, polarized continuum, and isodensity and surface polarized continuum models. At MP4SDQ/6-31G*//HF/6-31G* these reactions are exothermic by 34-38 kcal mol-1 and have very low activation energies, 5-7 kcal mol-1. The P—P/C—C regioisomer products are lower in energy than the C—P isomers and, within each pair, the exo isomer is lower in energy. At low computational levels the smallest activation energy is for the reaction leading to the C—P endo product. Larger basis sets, electron correlation, and solvent favor the transition state leading to the experimentally observed P—P/C—P endo isomer. The dimerization of phosphole is, therefore, kinetically controlled. Based on geometric and electron density analysis, the reactions are concerted and synchronous. © 1997 by John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 9-19 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A G2 search of the triplet [H4, Si, P]+ potential energy surface (PES) was carried out, along with a study of a number of mechanisms for the reaction of the P+ (3P) ion with silane. The most stable isomer, which corresponds to the species resulting from transferring three hydrogen atoms from the silicon to the phosphorus atom, lies 67.3 kcal/mol below the reactants' level. The P+—SiH4 ion-molecule complex also has remarkable stability, 20.4 kcal/mol. Bond properties were calculated and are discussed for all the stable species found on the PES. Various exothermic reaction paths were also fully characterized. The abstractions of a hydrogen molecule and a hydrogen atom, yielding species with P—Si bonds, have comparable kinetic hindrance, although release of molecular hydrogen was found to be more exothermic. Finally, hydrogen and/or charge transfer reactions between P+ (3P) and silane are also discussed. © 1997 by John Wiley & Sons, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 449-462 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four commonly used molecular mechanics force fields, CHARMM22, OPLS, CVFF, and GROMOS87, are compared for their ability to reproduce experimental free energies of hydration (ΔGhydr) from molecular dynamics (MD) simulations for a set of small nonpolar and polar organic molecules: propane, cyclopropane, dimethylether, and acetone. ΔGhydr values were calculated by multiconfiguration thermodynamic integration for each of the different force fields with three different sets of partial atomic charges: full charges from an electrostatic potential fit (ESP), and ESP charges scaled by 0.8 and 0.6. All force fields, except for GROMOS87, give reasonable results for ΔGhydr · if partial atomic charges of appropriate magnitude are assigned. For GROMOS87, the agreement with experiment for hydrocarbons (propane and ethane) was improved considerably by modifying the repulsive part of the carbon-water oxygen Lennard-Jones potential. The small molecules studied are related to the chemical moieties constituting camphor (C10Hl6O). By invoking force-field transferability, we calculated the ΔGhydr for camphor. With the modified GROMOS force field, a ΔGhydr within 4 kJ/mol of the experimental value of -14.8 kJ/mol was obtained. Camphor is one of the largest molecules for which an absolute hydration free energy has been calculated by molecular simulation. The accuracy and reliability of the thermodynamic integration calculations were analyzed in detail and we found that, for ΔGhydr calculations for the set of small molecules in aqueous solution, molecular dynamics simulations of 0.8-1.0 ns in length give an upper statistical error bound of 1.5 kJ/mol, whereas shorter simulations of 0.25 nm in length given an upper statistical error bound of 3.5 kJ/mol. © 1997 by John Wiley & Sons, Inc.
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  • 6
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe the implementation of the cell multipole method (CMM) in a complete molecular dynamics (MD) simulation program (MPSim) for massively parallel supercomputers. Tests are made of how the program scales with size (linearly) and with number of CPUs (nearly linearly) in applications involving up to 107 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry. © 1997 by John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 712-721 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; neolignans ; conformational analysis ; environment effect ; active conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational analysis of 20 neolignans was performed to determine the most probable conformer that may fit the receptor. The molecular mechanics method (MM2) was employed to construct conformational maps in both a vacuum and a biological environment. Boltzmann's distribution among several local minima was calculated. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 712-721, 1997
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  • 8
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 723-743 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Monte Carlo docking procedure that combines random displacements of the substrate and protein side chains with minimization of the enzyme - substrate complex is described and applied to finding the binding mode of the blocked tetrapeptide N-acetyl-Leu-Pro-Phe-methylamide to the FK506 binding protein (FKBP). The tetrapeptide, an analog of the preferred FKBP substrate, and the FKBP binding site are flexible during the docking procedure. The twisted-imide transition-state form of the substrate is used during docking. The enzyme charges are scaled individually to account for solvent screening of specific binding site residues during the Monte Carlo sampling. To evaluate the relative binding free energies of the resulting structures, a rapid method for calculating polar and nonpolar solvation effects is introduced. Accurate electrostatic solute - solvent energies are calculated by solving the finite-difference linearized Poisson - Boltzmann equation; nonpolar contributions to the stability of the different conformers are estimated by the free energy of cavity formation, which is obtained from the molecular surface, and the solute - solvent van der Waals energy, which is calculated with a continuum approach. In the conformation of the enzyme - substrate complex with the lowest free energy, the tetrapeptide is bound as a type VIa proline turn with solvent accessible ends to permit longer polypeptide chains to act as substrates. Except for the imide carbonyl, which is involved in polar interactions with aromatic side chains of the FKBP binding site, all of the seven potential hydrogen bond donors or acceptors of the tetrapeptide are satisfied. The FKBP binding site has a similar conformation in the substrate complex as in the FKBP-FK506 cocrystal structure, except for the predicted reorientation of the Tyr 82 hydroxyl, which plays an important role in substrate binding. The present model for the FKBP - substrate complex is in agreement with the recently determined crystal structure of a cyclic peptide - FK506 hybrid bound to FKBP and supports the structure obtained previously by iterative model building. In addition, it is consistent with the observed effects of FKBP point mutations on the enzyme activity. The approach described here should be useful, in general, for the prediction of the structure of a molecule in solution or as part of a complex. It provides for the effective sampling of conformational space and for the inclusion of solvent effects. © 1997 by John Wiley & Sons, Inc.
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  • 9
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 796-811 
    ISSN: 0192-8651
    Keywords: DNA ; normal mode ; flexibility ; modeling ; DNA bending ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility. Normal modes are analyzed in terms of helicoidal and backbone parameter variations with special attention being paid to global deformations of the double helix such as bending, twisting, or stretching. Results show that the allomorphic form of DNA has the largest influence on the flexibility of the sugar-phosphate backbone. Amplitudes of these vibrations follow the order: B 〉 Z 〉 A. In contrast, the amplitudes of helicoidal parameter variations are much more dependent on the base sequence. Global deformations of the double helix occur with characteristic times in the range of 1 to 10 ps and can be of mixed character, the strongest bending mode being at the same the time strongest stretching mode. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 796-811, 1997
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  • 10
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 381-392 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present the results of simulations of the structures and optical absorption spectra of Na atoms in solid and liquid Ar at its triple point, and in critical-point Ar fluid. The spectral simulations combine a classical Monte Carlo scheme for generating thermally accessible ground state configurations, along with a first-order perturbation theory treatment of the interactions between the excited Na*(3p 2P) atom and the surrounding Ar perturbers [Boatz and Fajardo, J. Chem. Phys., 101, 3472 (1994)]. These simulations predict a “triplet” (i.e., three peaks) absorption lineshape for Na atoms in solid and liquid Ar at its triple point, and an asymmetrical, blue degraded absorption band for Na atoms in critical Ar fluid. We also note and discuss the similarities between the simulated Na/Ar(1) lineshape and an experimental Li/Ar/Xe mixed host matrix spectrum, and the similarities between the simulated spectrum of Na atoms in critical point Ar fluid, and an experimental Li/H2 matrix absorption spectrum. © 1997 by John Wiley & Sons, Inc.
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  • 11
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 403-415 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method has been developed for minimizing the energy of a polypeptide with rigid geometry while keeping all disulfide loops closed exactly. Exact closure of disulfide loops implies that some dihedral angles become implicit functions of the remaining dihedral angles in the polypeptide; the efficacy of the method is related to the manner in which the implicitly defined dihedral angles are chosen. The method has been used to find minimum-energy conformations of bovine pancreatic trypsin inhibitor, ribonuclease A, crambin, the defensin HNP3 dimer, and ω-conotoxin. For the first two proteins, the starting conformations for energy minimization had been derived previously from crystal structures using pseudopotentials to keep the disulfide loops almost closed. Starting conformations for the remaining three proteins were derived from their crystal or NMR structures by similar procedures. In all cases, the energy-minimized structures had a significantly and, in some cases, substantially, lower energy than the starting structures. The RMS deviations between the exactly closed energy- minimized structures and the crystal or NMR structures from which they were derived ranged from 0.9 Å to 1.9 Å, suggesting that the computed structures can serve as “regularized” native structures for these proteins. The energy of a ribonuclease derivative lacking the 65-72 disulfide bridge was minimized using the procedure; the result showed that this derivative has a low-energy structure with a conformation very close to that of native ribonuclease, and is consistent with its postulated role in the folding of ribonuclease. These results offer strong support for the validity of the rigid-geometry model in the studies of the conformational energy of proteins. © 1997 by John Wiley & Sons, Inc.
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  • 12
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational scheme is presented which combines quantum mechanical ab initio techniques with methods using analytical potential functions. The scheme is designed for use in structure optimizations and is also applicable to molecular dynamics simulations. The implementation covers both molecular and periodic systems. The problem of the link atoms is solved by a subtraction scheme which is easily implemented for any combination of methods. As a first application dense and microporous silica polymorphs are studied. The Hartree-Fock method is combined with both a force field and an ion pair shell model potential. Comparison is made with lattice energy minimizations which use the force field or the shell model potential alone as well as with free cluster optimizations and optimizations in which the outer part of the cluster is kept fixed. © 1997 by John Wiley & Sons, Inc.
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  • 13
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 489-500 
    ISSN: 0192-8651
    Keywords: benzofuroxan ; ortho-dinitrosobenzene ; nitrosobenzene ; vibrational spectra ; tautomerism ; density functional theory (DFT) ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular rearrangement of benzofuroxan was studied by comparing calculated and experimental IR spectra, the latter taken before and during the reaction. All calculations were performed at the B3-LYP/6-31G(d) density functional level with a further refinement of the computed force constants done by applying the scaled quantum mechanical force field (SQM) technique. Complete assignments for the IR spectra of benzofuroxan and nitrosobenzene are given. The agreement between computed and experimental spectra is excellent, but in benzofuroxan these spectra are very different from previously calculated data. The conformation of the ortho-dinitrosobenzene intermediate of this tautomeric reaction was identified by modeling a composite IR spectrum of four possible components. It shows good agreement with an experimental spectrum that was obtained after photolysing benzofuroxan in Xe matrix. Knowing the conformation of the intermediate provides insight into the reaction mechanism and allows inferences for the thermal reaction, which could not be clarified conclusively by energetic considerations only. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 489-500, 1997
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  • 14
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    Journal of Computational Chemistry 18 (1997), S. 533-551 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full) /6-31G* level. Hence, the force field should provide good starting structures for ab initio calculations. The π-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6-31G*//MP2(full)/6-31G* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1-3 π-interactions in allyl cations are quite significant, but are reduced by alkyl groups hyperconjugatively and sterically. © 1997 by John Wiley & Sons, Inc.
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  • 15
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    Journal of Computational Chemistry 18 (1997), S. 569-583 
    ISSN: 0192-8651
    Keywords: fast multigrid boundary element method ; macromolecular electrostatic calculations ; poisson equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast multigrid boundary element (MBE) method for solving the Poisson equation for macromolecular electrostatic calculations in a solvent is developed. To convert the integral equation of the BE method into a numerical linear equation of low dimensions, the MBE method uses an adaptive tesselation of the molecular surface by BEs with nonregular size. The size of the BEs increases in three successive levels as the uniformity of the electrostatic field on the molecular surface increases. The MBE method provides a high degree of consistency, good accuracy, and stability when the sizes of the BEs are varied. The computational complexity of the unrestricted MBE method scales as O(Nat), where Nat is the number of atoms in the macromolecule. The MBE method is ideally suited for parallel computations and for an integrated algorithm for calculations of solvation free energy and free energy of ionization, which are coupled with the conformation of a solute molecule. The current version of the 3-level MBE method is used to calculate the free energy of transfer from a vacuum to an aqueous solution and the free energy of the equilibrium state of ionization of a 17-residue peptide in a given conformation at a given pH in ∼ 400 s of CPU time on one node of the IBM SP2 supercomputer. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 569-583, 1997
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  • 16
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    Journal of Computational Chemistry 18 (1997), S. 584-593 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A homomolecular differential bond separation reaction may be defined as the difference between the conventional bond separation reactions involving the unsaturated system and its saturated counterpart. Such a reaction is homomolecular in that the basic molecular structures involved are the same on both sides of the reaction. The type of homodesmotic reaction that also conserves structure in this way may be termed a homomolecular homodesmotic reaction. Both types of homomolecular reactions are readily related to hydrogenation reactions and, more importantly, to each other. Δ B(n), the energy of the homomolecular differential bond separation reaction involving a system with n double bonds, and H(n), the corresponding homomolecular homodesmotic reaction, are related by: $$\Delta B(n)-H(n)= n \cdot (h(1)-h(e))$$ where h(1) and h(e) are the hydrogenation energies of the system's monoene and of ethylene, respectively. Both types of reactions yield measures of cyclic conjugation energies that for certain classifications of molecules are simply related to each other. Consideration of extra conjugation in the monoenes allows a ready interpretation of those cases in which a simple classification is not obtained. Ab initio calculations illustrating these effects have been carried out on a variety of molecules including many five- and six-membered ring systems using second order Møller-Plesset and density functional approaches. © 1997 by John Wiley & Sons, Inc.
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  • 17
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    Journal of Computational Chemistry 18 (1997), S. 1-8 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The polarizable continuum model of Miertus et al. was implemented in the semiempirical molecular orbital method SINDO1. A fast and precise method for the calculation of solvation energies is achieved based on isodensity surfaces for the cavity surface and on approximated electrostatic potentials. The calculated solvation energies in water agree well with experimental and other calculated data. © 1997 by John Wiley & Sons, Inc.
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  • 18
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    Journal of Computational Chemistry 18 (1997), S. 28-44 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6-31G* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.
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  • 19
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    Journal of Computational Chemistry 18 (1997), S. 45-55 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry optimization using natural internal coordinates was applied for transition metal complexes. The original definitions were extended here for the skeletal degrees of freedom which are related to the translational and rotational displacements of the ηn-bonded ligands. We suggest definitions for skeletal coordinates of ηn-bonded small unsaturated rings and chains. The performance of geometry optimizations using the suggested coordinates were tested on various conformers of 14 complexes. Consideration was given to alternative representations of the skeletal internal coordinates, and the performance of optimization is compared. Using the skeletal internal coordinates presented here, most transition metal complexes were optimized between 10 and 20 geometry optimization cycles in spite of the usually poor starting geometry and crude approximation for the Hessian. We also optimized the geometry of some complexes in Cartesian coordinates using the Hessian from a parametrized redundant force field. We found that it took between two and three times as many iterations to reach convergence in Cartesian coordinates than using natural internal coordinates. © 1997 by John Wiley & Sons, Inc.
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  • 20
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    Journal of Computational Chemistry 18 (1997), S. 80-85 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for generating a full backbone protein structure from the coordinates of α-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the basic advantage of the presented method is its simplicity and speed. In a test run, the present program is shown to be much faster than existing database searching algorithms, and reconstructs about 8000 residues per second. Thus, it may be included as an independent procedure in protein folding algorithms to rapidly generate approximate coordinates of backbone atoms. © 1997 by John Wiley & Sons, Inc.
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  • 21
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    Journal of Computational Chemistry 18 (1997), S. 115-125 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the molecular surface and the accessible surface lead to exactly the same results when calculating solvation free energies and transfer free energies, from methods using the surface tension as a parameter if the exact geometric curvature is used with the accessible surface. However, the use of the exact curvature is not necessarily the best approach chemically. Other modifications, including an approximate curvature improves the approach. Such modifications are difficult to include in methods in which the molecular surface rather than the accessible surface is used to calculate solvent effects. A modification of a Gaussian curvature term is necessary if dissociation is to be accounted for properly. The inclusion of a Gaussian curvature term, in addition to the usual mean curvature term, reconciles the difference in magnitude of the microscopic and macroscopic surface tension in the case of the accessible surface area. © 1997 by John Wiley & Sons, Inc.
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  • 22
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The five energetically lowest minima on the potential energy surface of N-acetyl-N′-methylalaninamide were optimized at the Becke3LYP/DZd level of theory to compare these density functional theory results with the literature findings at restricted Hartree-Fock/3-21G. While the relative energies are very similar, the amide moiety is predicted to be much more flexible at Becke3LYP/DZd. As a consequence, the three minima that favor a nonplanar amide group differ by up to 14° in their φ and ψ values between the two levels. To compare the change in the density functional NMR chemical shifts with respect to φ and ψ with experimental results, Becke3LYP/DZd was employed to optimize a structure for N-acetyl-N′-methylalaninamide at each 30° interval on the (φ, ψ) surface in the regions that correspond to the α helix and the β-pleated sheet and at each 60° interval elsewhere. The corresponding NMR chemical shielding surface was computed with the density functional program deMon. The resultant NMR chemical shielding surfaces for N and Cβ are in good agreement with the experiment, while the change in the NMR chemical shielding of C′ and Cα cannot be described only in terms of φ and ψ. The chemical shifts for those atoms also depend on the nonplanarity of the amide moiety. We evaluated this dependence for N-methylacetamide as a model system. Estimates of the parameters derived from N-methyl-acetamide allowed the NMR-shielding surfaces of C′ and Cα to be corrected for the nonplanar nitrogen influence. Although the effect is less pronounced with lower level theoretical geometries, due to the smaller degree of pyramidalization of the amide nitrogen, the (φ, ψ) NMR chemical shielding surfaces will need to be corrected. The agreement with the experiment was much better for the corrected surface of C′ when the nitrogen in the α helix had a nonplanar environment. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 211-220 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Test particle calculations are employed to derive van der Waals parameters for methane. It is shown that it is possible to derive these parameters completely based on ab initio calculations. The newly derived parameters are tested in molecular dynamics calculations of liquid methane and the results are compared with the results of existing force fields. It is shown that the newly derived parameters perform better in the prediction of the density, the heat of vaporization, and the self-diffusion coefficient of methane. Scaling of the parameters to account for systematic errors in the employed ab initio method does not generally improve the parameters with respect to the properties calculated. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 221-239 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force field parameters for nicotinamide (NIC+) and 1,4-dihydronicotinamide (NICH) were developed for use in modeling of the coenzymes nicotinamide adenine dinucleotide (NAD+) and NAD hydride (NADH). The parametrization follows the methodology used in the development of the CHARMM22 all-hydrogen parameters for proteins, nucleic acids, and lipids. Parametrization of inorganic phosphate for use in adenosine di- and triphosphates (e.g., ADP and ATP) is also presented. While high level ab initio data, such as conformational energies, dipole moments, interactions with water, and vibrational frequencies, were adequately reproduced by the developed parameters, strong emphasis was placed on the successful reproduction of experimental geometries and crystal data. Results for molecular dynamics crystal simulations were in good agreement with available crystallographic data.Simulations of NAD+ in the enzyme alcohol dehydrogenase compared quite favorably with experimental geometries and protein matrix interactions. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 260-267 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the claims that density functional theory (DFT) can handle orbitally degenerate states are ungrounded. The constraint search formulation of DFT allows one to determine a set of densities and eigenvalues for the degenerate term that, however, are neither observables, nor can they be used to solve the system of coupled equations for the nuclear motions to obtain observables, as in the wave function presentation. A striking example of the failure of the existing versions of DFT to describe degenerate states is provided by the Berry phase problem: the strong dependence of the results on the phase properties of the electronic wave function that are smeared out in the density formulation. The solution of the Jahn-Teller E-e problem illustrates these statements. For nondegenerate states with the full wave function taken in the adiabatic approximation as a product of the electronic and nuclear parts, the formulation of DFT is rigorous if and only if the dependence of the electronic wave function on nuclear coordinates is ignored. This lowers the accuracy of the results, in general, and may lead to erroneous presentation as in the case of molecular systems in strong magnetic fields. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 290-299 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The development of a crystal indexing computer program using interplanar angles and lattice spacings is very useful, particularly in nanocrystal research by transmission electron microscopy. However, the indexing involves a large number of possible variables, which prohibits the use of simple mathematical techniques. This article is concerned with an application of a combinatorial optimization technique using the simulated annealing algorithm for solving the crystal indexing problem where traditional descent optimization cannot be used. We show that the program can unambiguously identify the Miller indices using a set of interplanar angles even for crystals with low symmetry elements. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 313-322 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present the theory and implementation of a new approach for studying solvent effects. The electronic structure of the solute, calculated at the ab initio level, is obtained in the presence of the surrounding medium. We employ a mean field theory in which the solvent response is described by means of point charges chosen in such a way that they reproduce the average value of the solvent electrostatic potential calculated from molecular dynamics data. In this way, the complete solvent potential can be introduced into the solute Hamiltonian without making use of a one-center multiple expansion of the solute-solvent potential. In the proposed method, only one quantum calculation has to be performed and a great number of configurations can easily be included making the calculation statistically significant. We show that, despite the large fluctuations in the solute charge distribution induced by the solvent, the proposed mean field theory adequately reproduces the energetics and properties of formamide and water molecules in aqueous solution. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 368-380 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A potential energy model is developed to study the intramolecular proton transfer in the enol form of acetylacetone. It makes use of the empirical valence bond approach developed by Warshel to combine standard molecular mechanics potentials for the reactant and product states to reproduce the interconversion between these two states. Most parameters have been fitted to reproduce the key features of an ab initio potential surface obtained from 4-31G* Hartree-Fock calculations. The partial charges have been fitted to reproduce the electrostatic potential surface of 6-31G* Hartree-Fock wave functions, subject to total charge and symmetry constraints, using a fitting procedure based on generalized inverses. The resulting potential energy function reproduces the features most important for proton transfer simulations, while being several orders of magnitude faster in evaluation time than ab initio energy calculations. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 393-402 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The thermal effect of a reaction makes the temperature inside the reaction system deviate from a prescribed heating program. To take into account the effect of such temperature deviations on kinetic evaluations, a computational method applicable to an arbitrary variation in temperature has been developed. The method combines the isoconversional principle of evaluating the activation energy with numerical integration of the equation, dα/dt = k[T(t)]f(α), over the actual variation of the temperature with the time, T(t). Details of the numerical algorithm are reported. A model example has been used to verify the reliability of this method as compared to an analogous method which does not account for the deviations of the temperature from a prescribed program. The method has been tested for tolerance for noise in the temperature. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 430-448 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A massively parallel version of the configuration interaction (CI) section of the COLUMBUS multireference singles and doubles CI (MRCISD) program system is described. In an extension of our previous parallelization work, which was based on message passing, the global array (GA) toolkit has now been used. For each process, these tools permit asynchronous and efficient access to logical blocks of 1- and 2-dimensional (2-D) arrays physically distributed over the memory of all processors. The GAs are available on most of the major parallel computer systems enabling very convenient portability of our parallel program code. To demonstrate the features of the parallel COLUMBUS CI code, benchmark calculations on selected MRCI and SRCI test cases are reported for the CRAY T3D, Intel Paragon, and IBM SP2. Excellent scaling with the number of processors up to 256 processors (CRAY T3D) was observed. The CI section of a 19 million configuration MRCISD calculation was carried out within 20 min wall clock time on 256 processors of a CRAY T3D. Computations with 38 million configurations were performed recently; calculations up to about 100 million configurations seem possible within the near future. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 478-488 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The implementation of parallel molecular dynamics techniques is discussed in the context of the simulation of single-site anisotropic potentials. We describe the use of both replicated data and domain decomposition approaches to molecular dynamics and present results for systems of up to 65536 Gay-Berne molecules on a range of parallel computers (Transtech i860/XP Paramid, Intel iPSC/860 Hypercube, Cray T3D). We find that excellent parallel speed-ups are possible for both techniques, with the domain decomposition method found to be the most efficient for the largest systems studied. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 522-532 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon - carbon rather than carbon - nitrogen bonds. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 562-568 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A number of cluster models used to study the interaction of NH3 and NH-4 with the Bronsted sites of the acidic zeolite, chabazite, are assessed by comparison with the results from full periodic Hartree-Fock calculations. Corrections to bare cluster models to take account of the electrostatic environment due to the periodic zeolite are found to agree well with periodic calculations, and appear to be more successful than a more sophisticated embedding procedure. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 594-599 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm is presented for the location of the global minimum of a multiple minima problem. It begins with a series of randomly placed probes in phase space, and then uses an iterative Gaussian redistribution of the worst probes into better regions of phase space until all probes converge to a single point. The method quickly converges, does not require derivatives, and is resistant to becoming trapped in local minima. Comparison of this algorithm with others using a standard test suite demonstrates that the number of function calls has been decreased conservatively by a factor of about three with the same degree of accuracy. A sample problem of a system of seven Lennard-Jones particles is presented as a concrete example. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 638-645 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article a new method is described to superimpose molecules using a crystallographic Fourier transform approach. Superimposed molecules, among other purposes, serve as a basis for three-dimensional (3D) QSAR analyses in drug design and therefore an objective and reproducible method of molecule alignment is of major importance. Fourier data are generated for hypothetical crystals of cubic symmetry for the compounds under consideration. A Patterson-density-based similarity index is used to optimize rotational alignment of the molecules. After optimization of rotational orientation, an electron density derived similarity index is used to further optimize overlap of electron density as a function of translation of the molecules. Both similarity indices are maximized by a simple optimization routine, thus enabling automated superposition. The use of Fourier space offers several advantages. First, rotational and translational parameters can be optimized separately, thus providing a small parameter space. Second, a limited number of data already provide an adequate, continuous description of the electron (or Patterson) density distribution. Third, crystallography provides simple methods to calculate the Fourier transforms that are needed. The resolution of the Patterson (electron) density representation used for superposition can be varied in a straightforward manner. Results are shown for the superposition of two antiviral agents, 2rs1 and 2r04; the dihydrofolate reductase ligands, methotrexate and dihydrofolate; and a set of three ε-thrombin inhibitors. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 677-693 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 702-711 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The typical shallowness of the potential surfaces of weakly bound clusters implies sizable ground-state vibrational excursions in the weak modes, a feature often complicated by considerable anharmonicity. The difficulties of vibrational analysis are exacerbated as the number of weak modes increases with the number of molecules in a cluster. Quantum Monte Carlo (QMC) approaches offer a general suitability to the problem of vibrational dynamics of weakly bound clusters in that they can fully account for anharmonicity and large amplitude motions. We report on the effectiveness and convergence behavior of diffusion quantum Monte Carlo for both energies and the key spectroscopic values of vibrationally averaged rotational constants. QMC involves recurring evaluations of the interaction potential, and we show how property-based, two-and three-body potentials (e.g., those involving intrinsic molecular tensor properties) may be carefully linked to the QMC propagation steps. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 757-774 
    ISSN: 0192-8651
    Keywords: O(SINGLE BOND)H ··· O hydrogen bond ; intermolecular perturbation theory ; crystal structures ; directionality ; esters ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An attractive way to study intermolecular hydrogen bonding is to combine analysis of experimental crystallographic data with ab initio - based energy calculations. Using the Cambridge Structural Database (CSD), a distributed multipole analysis (DMA)-based description of the electrostatic energy, and intermolecular perturbation theory (IMPT) calculations, hydrogen bonding between donor alkanol hydroxyl groups and oxygen acceptor atoms in ketone, ether, and ester functional groups is characterized. The presence and absence of lone pair directionality to carbonyl and ether or ester oxygens, respectively, can be explained in terms of favored electrostatic energies, the major attractive contribution in hydrogen bonding. A hydrogen bond in its optimum geometry is only slightly stronger when formed to a ketone group than to an ether group. Hydrogen bonds formed to carbonyl groups have similar properties in a ketone or ester, but the ester O2 differs from an ether oxygen due to various environmental effects rather than a change in its intrinsic properties. For (E)-ester oxygens, there are few hydrogen bonds found in the CSD because of the competition with the adjacent carbonyl group, but the interaction energies are similar to an ether. Hydrogen bonds to O2 of (Z)-esters are destabilized by the repulsive electrostatic interaction with the carbonyl group. The relative abundance of nonlinear hydrogen bonds found in the CSD can be explained by geometrical factors, and is also due to environmental effects producing slightly stronger intermolecular interaction energies for an off-linear geometry. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 757-774, 1997
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    Journal of Computational Chemistry 18 (1997), S. 826-846 
    ISSN: 0192-8651
    Keywords: molecular quantum similarity measures (MQSM) ; atomic shell approximation (ASA) ; global maximization ; molecular alignments ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A quantum similarity measure between two molecules is normally identified with the maximum value of the overlap of the corresponding molecular electron densities. The electron density overlap is a function of the mutual positioning of the compared molecules, requiring the measurement of similarity, a solution of a multiple-maxima problem. Collapsing the molecular electron densities into the nuclei provides the essential information toward a global maximization of the overlap similarity function, the maximization of which, in this limit case, appears to be related to the so-called assignment problem. Three levels of approach are then proposed for a global search scanning of the similarity function. In addition, atom - atom similarity Lorentzian potential functions are defined for a rapid completion of the function scanning. Performance is tested among these three levels of simplification and the Monte Carlo and simplex methods. Results reveal the present algorithms as accurate, rapid, and unbiased techniques for density-based molecular alignments. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 826-846, 1997
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    Journal of Computational Chemistry 18 (1997), S. 902-919 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a comparison of four free energy calculation methods: thermodynamic integration (TI); traditional free energy perturbation (FEP); Bennett's acceptance ratio method (IPS); and a method that is related to an implementation of the WHAM method (CRS). The theoretical bases of the methods are first described, then calculations of the solvation free energies of methane and ethane are performed to determine the magnitude of the errors for the different methods. We find that the methods give similar errors when many intermediate states (windows) are used, but the IPS and CRS methods give smaller errors than the TI and FEP methods when no intermediate states are used. We also present a new procedure (based on the CRS method) that uses coordinates from simulations of a set of solutes to calculate the salvation free energies of additional solutes for which no simulations were performed. Solvation free energies for nine solutes (methanol, dimethylether, methylamine, methylammonium, dimethylamine, fluoromethane, difluoromethane, trifluoromethane, and tetrafluoromethane) are estimated based only on simulations of set of small hydrophobic solutes (including methane, ethane, and propane). These estimates can be surprisingly accurate and appear to be useful for making rapid estimates of solvation free energies. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 902-919, 1997
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    Journal of Computational Chemistry 18 (1997), S. 955-969 
    ISSN: 0192-8651
    Keywords: electrostatic ; potential ; charge ; PRDDO ; PESP ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e- with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955-969, 1997
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    Journal of Computational Chemistry 18 (1997), S. 980-991 
    ISSN: 0192-8651
    Keywords: molecular electrostatic potential (MEP) ; density functional method (DFT) ; electrostatic potential (ESP) derived charges ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A systematic analysis was performed on the suitability of the molecular electrostatic potential (MEP) and MEP-derived properties determined by means of density functional (DFT) methods. Attention was paid to the electrostatic potential (ESP) derived charges, the ESP and exact quantum mechanical dipole moments, the depth of MEP minima, and the MEP distribution in layers around the molecule for a large series of molecules. The electrostatic properties were determined at either local or nonlocal DFT levels using different functionals. The results were compared with the values estimated from quantum mechanical calculations performed at Hartree-Fock, Møller-Plesset up to fourth order, and CIPSI levels. The suitability of the MEP-derived properties estimated from DFT methods is discussed for application in different areas of chemical interest. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 980-991, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1011-1022 
    ISSN: 0192-8651
    Keywords: line search minimization algorithm ; topography ; multidimensional potential energy surfaces ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The most robust numerical algorithms for unconstrained optimization that involve a line search are tested in the problem of locating stable structures and transition states of atomic microclusters. Specifically, the popular quenching technique is compared with conjugate gradient and variable metric algorithms in the Mg+Arn clusters. It is found that the variable metric method BFGS combined with an approximate line minimization routine is the most efficient, and it shows global convergence properties. This technique is applied to find a few hundred stationary points of Mg+Ar12 and to locate isomerization paths between the two most stable icosahedral structures found for Mg+Ar12. The latter correspond to a solvated and a nonsolvated ion, respectively. © 1997 John Wiley & Sons, Inc. J Comput Chem 18:1011-1022, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1056-1060 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Following the publication of a comparison of several molecular mechanics methods [Gundertofte et al., J. Comput. Chem. 17, 429 (1996)], we have expanded the set of force fields tested by examining CHARMm 23.0 with its associated parameter set (version 22.0) relative to the gas-phase data used in the Gundertofte et al. study. CHARMm calculated rotational barriers and conformational energies within the same range of accuracy as the most accurate ones of the other force fields. The average absolute error was 0.64 kcal/mol, and 0.52 kcal/mol when the rotational barriers were excluded. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1056-1060, 1997
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  • 45
    ISSN: 0192-8651
    Keywords: force field ; open-shell amino acids ; peptides ; glycine ; glycine radical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters suitable for extending the AMBER force field for nucleic acids and proteins to open-shell derivatives of amino acid residues are proposed and tested. Two new atom types (radical carbon [CE] and hydrogen directly bonded to it [HE]) are introduced, whose parameters have been determined by a best fitting of quantum-mechanical computations of the simplest analogue of glycine radical (GlyR) in a peptide. The new force field is able to fit the reference results concerning both the structural parameters and the relative stabilities of the different conformers. It has been next applied to a conformational study of the distortions induced by extraction of the glycine Hα atom in an initially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure corresponds to a local energy minimum, but deeper minima are found which correspond to a fully planar GlyR residue included in a distorted helical sequence.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1720-1728, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1773-1784 
    ISSN: 0192-8651
    Keywords: three-membered ring formation ; intramolecular nucleophilic substitution ; ab initio molecular orbital method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three-membered ring (3MR) forming processes of -X(SINGLE BOND)CH2(SINGLE BOND)CH2(SINGLE BOND)F and -CH2(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH2(SINGLE BOND)F (X(DOUBLE BOND)CH2, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (SNi) are studied theoretically using the ab initio molecular orbital method with the 6-31+G* basis set. When electron correlation effects are considered, the activation (ΔG≠) and reaction energies (ΔG0) are lowered by ca. 10 kcal mol-1, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (-TΔS≠) at 298 K to ΔG≠ is very small, and the reactions are enthalpy controlled. The ΔG≠ and ΔG0 values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell-Evans-Polanyi principle applies well to all these reaction series.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1773-1784, 1997
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  • 47
    ISSN: 0192-8651
    Keywords: diborylmethane ; conrotation and disrotation ; 1,3 H exchange ; orbital deletion procedure ; gradient line reaction path ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The paths of correlated internal disrotation (barrier less than 0.4 kcal/mol) and conrotation (barrier around 1.9 kcal/mol) of the two BH2 groups in H2BCH2BH2 have been computed employing ab initio [MP2(full)/6-31G**] and density functional theory (Becke3LYP/6-311+G**) methods. Two B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative interactions stabilize the Cs symmetric H2BCH2BH2 isomer (1). The B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative stabilization, evaluated by homodesmotic reactions and using the orbital deletion procedure (which “deactivates” the “vacant” born p orbital), is less than 6 kcal/mol in diborylmethane. The B(SINGLE BOND)C(DOTTED BOND)B(p) stabilization is shown to be remarkably large in C4B6H10 (Td). At MP2(fu)/6-31G**, disproportionation into 1 and methane is only 5.6 kcal/mol exothermic. The 1,3 H exchange in diborylmethane is an asynchronous process and proceeds via a doubly bridged cyclic intermediate with 9.3 kcal/mol barrier. Structures with “planar tetracoordinate” carbon are stabilized considerably by BH2 substituents, but they are still high in energy.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1792-1803, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1827-1847 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; sulfides ; mercaptans ; vibrational spectra ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM4 force field has been extended to the title class of compounds. The vibrational spectra, structures, conformational equilibria, and heats of formation have been studied for 47 conformers of 29 compounds. In general, the properties may be calculated with accuracy that is competitive with that for hydrocarbons. The structures are better fit than previously because of the inclusion of a torsion-bend interaction term, which has its origin in the lone pair (Bohlmann) effect. Available experimental data do not suffice to yield detailed torsional potentials, or geometries as a function of torsion angle, and these quantities were determined by ab initio calculations at the MP2/6-31G* level. The rms error in the calculated frequencies of seven representative structures (with a total of 64 experimental and 96 ab initio frequencies) is 25 cm-1. The heats of formation for 23 compounds have a weighted rms error of 0.36 kcal/mol.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1827-1847, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1848-1862 
    ISSN: 0192-8651
    Keywords: molecular dynamics ; biomolecules ; electrostatics ; software ; reversible multiple time-step algorithms ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines state-of-the-art molecular dynamics (MD) algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, reversible reference system propagation algorithm) specifically designed and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps of standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1848-1862, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1760-1772 
    ISSN: 0192-8651
    Keywords: computer simulations ; wavepacket ; zero-point vibration ; activation energy ; reaction coordinate ; empirical valence bond ; Fourier transform ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results of mixed quantum-classical molecular dynamics simulations of the intramolecular proton transfer in acetylacetone. Simulations are performed starting from the reactant and transition state configurations with initial velocities at each configuration chosen from an ensemble at 300 K. The proton motion is treated quantum mechanically and the remaining degrees of freedom are treated classically. Two mixed quantum-classical molecular dynamics methods are implemented. In the first, a quantum-classical time-dependent self-consistent field method (QC/TDSCF), the time-dependent Schrödinger equation for the proton is solved using the split operator approach and a plane-wave basis. In the second, a mixed quantum-classical adiabatic method (QC/A), the instantaneous ground state wave function is calculated by solving the time-independent Schrödinger equation for the configurations of the classical particles by propagating in imaginary time using the split operator approach and the same plane-wave basis. A comparison of the two approaches with classical trajectories is presented. The QC/TDSCF and QC/A results are very similar for trajectories started from the reactant configuration. The two methods, however, yield somewhat different results when the trajectories are started from the transition state configuration. The proton wave function of the QC/A method adjusts instantaneously to the position of the classical particles, whereas the motion of the QC/TDSCF wavepacket more faithfully represents the true proton dynamics.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1760-1772, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1804-1811 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; geometric statement function method ; in-plane and out-of-plane bend ; improper torsion ; MM2, MM3, and MM4 force fields ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simple and very efficient formulas are presented for four-body out-of-plane bend (used in MM2 and MM3 force fields) and improper torsion (used in the MM4 force field) internal coordinates and their first and second derivatives. The use of a small set of bend and stretch intermediates allows for order of magnitude decreases in calculation time for potential energies and their first and second derivatives, which are required in molecular mechanics calculations. The formulas are eminently suitable for use in molecular simulations of systems with complicated bond networks.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1804-1811, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1863-1874 
    ISSN: 0192-8651
    Keywords: electronic structure ; transition metals ; pseudospectral methods ; Hartree-Fock theory ; density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a parameterization enabling ab initio electronic structure calculation via the PS-GVB program on transition-metal-containing systems using two standard effective core potential basis sets. Results are compared with Gaussian-92 for a wide range of complexes, and superior performance is demonstrated with regard to computational efficiency for single-point energies and geometry optimization. Additionally, the initial guess strategy in PS-GVB is shown to provide considerably more reliable convergence to the ground state.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1863-1874, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1875-1892 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article outlines an original method for matching discrete structures when atom correspondences are unknown. This method avoids the current atom-by-atom treatment (and its inherent combinatorial problems) and considers the structures to be compared in their totality. The basic idea is to first obtain the atom correspondences by fitting one of the two discrete structures onto a spline approximation of the other, rather than optimizing in discrete space, and, second, to overlap the two discrete structures on the basis of the proposed assignment. As starting data, the method requires only the Cartesian coordinates of the two structures. No connectivity information, neither atom labeling nor matching tolerance is required. This method can readily handle matches of molecules with a few hundred atoms. It is able to search for a given 3D pattern as well as for a pattern common to two structures.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1875-1892, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1918-1929 
    ISSN: 0192-8651
    Keywords: effective core potential ; basis functions ; generator coordinate method ; molecular properties ; MP2 ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new approach for developing of basis sets to be used along with effective core potential is systematically studied. The behavior of the LCAO coefficients versus the ln(α) of the respective primitives can provide simple guidelines to establish the range over which the basis set should be developed or modified, especially when using effective core potential. Double-zeta basis sets were modeled for SBK pseudopotential from all-electron basis sets for a series of compounds containing elements of the second period of the periodic table. Application of the modeled basis sets at the Hartree-Fock and MP2 levels of theory shows that the new method provides molecular properties as accurate as those calculated by all-electron calculations.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1918-1929, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1943-1953 
    ISSN: 0192-8651
    Keywords: conducting polymers ; band gap problem ; density functional theory ; hybrid functionals ; ionization potentials and electron affinities ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Band gaps in solids and excitation energies in finite systems are underestimated significantly if estimated from differences between eigenvalues obtained within the local spin density approximation (LSDA). In this article we present results on 20 small- and medium-sized π-systems which show that HOMO-LUMO energy differences obtained with the B3LYP, B3P86, and B3PW91 functionals are in good agreement with vertical excitation energies from UV-absorption spectra. The improvement is a result of the use of the exact Hartree-Fock exchange with hybrid methods. Negative HOMO energies and negative LUMO energies do not provide good estimates for IPs and EAs. In contrast to Hartree-Fock theory, where IPs are approximated well and EAs are given poorly, DFT hybrid methods underestimate IPs and EAs by about the same amount. LSDA yields reasonable EAs but poor IPs.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1943-1953, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1985-1992 
    ISSN: 0192-8651
    Keywords: density functional ; relativistic ; calculation ; transition metal ; carbonyl ; trans effect ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Relativistic density functional calculations have been carried out for the group VI transition metal carbonyls M(CO)5L (M=Cr, Mo, W; L=OH2, NH3, PH3, PMe3, N2, CO, OC (isocarbonyl), CS, CH2, CF2, CCl2, NO+). The optimized molecular structures and M(SINGLE BOND)L bond dissociation energies, as well as the metal-carbonyl bond energy of the trans CO group, have been calculated. Besides the marked dependence of the trans M(SINGLE BOND)CO bond length on the type of ligand L, such an effect on the that bond energy is also observed. For the chromium compounds, the trans Cr(SINGLE BOND)CO bond length varies from 184 to 199 pm and its bond energy from 242 to 150 kJ/mol. For the molybdenum compounds, the range is 197 to 216 pm and 253 to 128 kJ/mol and, for tungsten, 198 to 214 pm and 293 to 159 kJ/mol. The observed trends can be explained with the π acceptor strength of the L ligand.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1985-1992, 1997
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    Journal of Computational Chemistry 18 (1997), S. 2012-2022 
    ISSN: 0192-8651
    Keywords: tetramethylammonium (binding to aromatics) ; cation-π interaction ; benzene ; pyrrole ; imidazole ; pyridine ; phenylalanine ; tyrosine ; tryptophan ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio computations including correlation have been performed in a comparative study of complexes of tetramethylammonium (TMA) with benzene, pyrrole, pyridine, and imidazole, using polarized Gaussian basis sets of different accuracies. With the best basis (optimized on molecular polarizabilities), the BSSE-corrected binding energies in the most stable complexes of these four ligands are 9.1, 10.7, 13.3, and 16.3 kcal/mol, respectively, with benzene and pyrrole binding in a plane perpendicular to the TMA axis, and pyridine and imidazole inserting their nitrogen lone pair essentially along the TMA axis. The characteristics of secondary sites of binding of benzene are also determined and the overall results are discussed in connection with the possible role of aromatic amino acids in proteins.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 2012-2022, 1997
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    Journal of Computational Chemistry 18 (1997), S. 2093-2093 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
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    Journal of Computational Chemistry 18 (1997), S. 20-27 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The computation of the relativistic correction to the first order in 1/c2, where c is the velocity of light, is implemented at the levels of coupled cluster and many-body perturbation theory. The relativistic correction is obtained by applying direct perturbation theory through the first order, and it is shown that its implementation is straightforward if analytical energy gradients of the methods under consideration are available. Preliminary results were obtained by a numerical procedure and are reported for some closed-shell atoms (He, Be, Ne, and Ar) and molecules (CuH and SiH4). © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 70-79 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The gas-phase interaction energies of methane and neopentane dimers are calculated at various intermolecular distances and geometries using several molecular mechanics and semiempirical parameter sets. For comparisons, a set of reference calculations are also performed using the 6-311G (2d, 2 p) basis set with the inclusion of second-order Möller-Plesset energies (MP2) and basis set superposition corrections. These calculations are further used to examine the mechanism by which the AM1 and PM3 methods account for dispersion interactions in molecular systems. While no specific parameter(s) are included in semiempirical energy functions to capture such effects, the results indicate that both methods produce favorable interaction energies at near contact distances for the dimer systems. AM1 energies, however, show much closer agreement with the reference calculations, indicating potential deficiencies in the PM3 parameter set. Although the source of the dispersion energy could be traced to the attractive Gaussians of the core repulsion function in the AM1 Hamiltonian, a similar link could not be established for PM3. In contrast, PM3 dispersion energies apparently stem from a collection of contributions implicitly included during parameter optimization, providing no clear mechanism for correction or adjustment. Based on the analysis presented, an approach is also suggested for improving the AM1 parameter set. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 108-114 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Isodesmic reactions are commonly used in ab initio studies to partially cancel errors associated with incomplete basis sets and incomplete correction for electron correlation. The errors associated with these reactions have been examined using the 6-31G* basis set at the theoretical levels HF, MP2, MP3, MP4, and B3LYP, and using the 6-311 + G* basis set at the HF, MP2, and B3LYP levels. As a comparison, the recently developed model chemistries, CBS-4 and CBS-Q, were also used. With hydrogenation and hydrogenolysis reactions, only the HF level gave large deviations from the experimental reaction energies. The use of hydrogen transfer reactions improved the HF calculated energies, but mixed results were obtained at the correlated levels. Some isomerization reactions and reactions of carbocations also were examined. The MP4/6-31G* and CBS-Q levels of theory were uniformly the more satisfactory. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 240-253 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Monte Carlo minimization (MCM) method of Li and Scheraga is an efficient tool for generating low energy minimized structures of peptides, in particular the global energy minimum (GEM). In a recent article we proposed an enhancement to MCM, called the free energy Monte Carlo minimization (FMCM) procedure. With FMCM the conformational search is carried out with respect to the harmonic free energy, which approximates the free energy of the potential energy wells around the energy minimized structures (these wells are called localized microstates). In this work we apply both methods to the pentapeptide Leu-enkephalin described by the potential energy function ECEPP, and study their efficiency in identifying the GEM structure as well as the global harmonic free energy (GFM) structure. We also investigate the efficiency of these methods to generate localized microstates, which pertain to different energy and harmonic free energy intervals above the GEM and GFM, respectively. Such microstates constitute an important ingredient of our statistical mechanical methodology for analyzing nuclear magnetic resonance data of flexible peptides. Aspects of this methodology related to the stability properties of the localized microstates are examined. © 1997 by John Wiley & Sons, Inc.
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  • 63
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common problem in the calculation of electrostatic potentials with the Poisson-Boltzmann equation using finite difference methods is the effect of molecular position relative to the grid. Previously a uniform charging method was shown to reduce the grid dependence substantially over the point charge model used in commercially available codes. In this article we demonstrate that smoothing the charge and dielectric values on the grid can improve the grid independence, as measured by the spread of calculated values, by another order of magnitude. Calculations of Born ion solvation energies, small molecule solvation energies, the electrostatic field of superoxide dismutase, and protein-protein binding energies are used to demonstrate that this method yields the same results as the point charge model while reducing the positional errors by several orders of magnitude. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 301-312 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Approximate molecular electrostatic potentials (MESPs) are calculated with the asymptotic density model (ADM) on the basis of semiempirical wavefunctions generated by the SINDO1 method. The approximate MESP is adjusted to obtain good agreement with the exact MESP from 6-31G* ab initio calculations for small molecules. This form of the MESP is used for the study of the reactivity of small and medium size silicon clusters with 5 to 45 atoms. Special attention is given to the reactivity of various Si45 structures proposed in the literature. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 330-342 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational space of 1C4 α-L-fucose was searched by the MM2*-SUMM molecular mechanics conformational search technique. The molecular geometries of the first 17 structures of lowest energy were analyzed at the HF/3-21G, 6-31G(d), and generalized gradient approximation (GGA) DFT levels of theory. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 351-367 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A force field to be used in molecular mechanics studies of sulfated polysaccharides with explicit account of water and counterion interactions was derived from the analysis of six crystal structures of sulfated monosaccharide salts. The force field is based on Allinger's MM2, and was developed starting from the parameters used in previous studies of heparin and related oligosaccharides. While the novel parameters have been derived empirically, use of the atomic charge distribution obtained from ab initio quantum-mechanical computations, at the 6-31 + G** level, improves the quality of structural fitting significantly. The overall discrepancy between the positions of the nonhydrogen atoms determined by X-ray diffractometry and those corresponding to the minimum-energy structure is 0.21 Å. While most geometrical features of both carbohydrate and sulfate moieties are reproduced satisfactorily, in some cases (particularly in the case of the Na+ salt of α-methyl-4-O-sulfogalactopyranoside) the hydrogen bond pattern is altered by energy minimization, probably due to errors in the balance of the strong electrostatic forces. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 416-429 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical studies of the electron density topology at the bond critical point for some small molecules, Ti, and Mo organometallic complexes were undertaken in order to understand the reason for the failure of the topological analysis of the coreless electron densities obtained from a pseudopotential calculation. We show that the absence of the core electron density is the main reason for such behavior. The erratic behavior of the effective core potentials electron densities can be corrected by adding atomic electron core density obtained from a single-atom Hartree-Fock calculation. The effect of orthogonalization of the core orbital with the valence orbitals was also investigated. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 56-69 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The relative stabilities of the keto and enol forms [Δ E0 (enol-keto)] and the energy barriers to enolization of the keto forms [Δ E≠ (transition state-keto)] for CH3COR (R = CH3, H, F, and CN) and CH3CHY (Y = CH2, NH, and S) are investigated theoretically by Hartree-Fock and Möoller-Plesset second-order calculations with 6-31G** basis sets. Specific and bulk solvent effects are considered by incorporating one water molecule and applying the self-consistent reaction field (SCRF) method to the reaction system, respectively. The Δ E0MP2 values are all positive, in agreement with the lower stability of the enol form in the gas phase as well as in solution. In contrast to a relatively small effect of specific as well as bulk solvation on Δ E0, there is a large lowering of Δ E≠ (by ca. 30 kcal/mol) when solvent effects are accounted for. In general, both Δ E0 and Δ E≠ are depressed in solution and hence enolization is favored thermodynamically as well as kinetically. The keto form is strongly stabilized by a π donor, whereas the enol isomer is stabilized by a π as well as a σ-acceptor substituent, R. As a result, substituent R = F is the most unfavorable whereas R = CN is the most favorable for the enolization. The water catalyzed enolization in the neutral water proceeds concertedly, but carbon deprotonation is more important than carbonyl-oxygen protonation by water in the rate determining step. © 1997 by John Wiley & Sons, Inc.
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  • 69
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    Journal of Computational Chemistry 18 (1997), S. 86-107 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article addresses the systematic and complete enumeration of all the substructures of any size present in a given molecule. The study is not restricted to features which could be defined a priori such as rings or chains. Contrary to prior expectation the exhaustive enumeration is tractable with current computational tools. Results are presented for several families of skeletons which are widespread in chemistry. It is shown that the numbers of constituent substructures of each size are related to the molecular topology, in particular the degree of branching. The number substructures which are distinct depends additionally on the number of different atom and bond types present. The overall shapes of the distribution of substructure counts as a function of substructure size are found to be similar within particular classes of molecules. These distributions are compared and found to be characteristic of certain topologies. For several simple classes of molecule, analytic expressions are provided for the numbers of substructures as a function of fragment and molecule size. These results hold promise for identifying potentially useful scaffolds for use in combinatorial chemistry. © 1997 by John Wiley & Sons, Inc.
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  • 70
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    Journal of Computational Chemistry 18 (1997), S. 151-158 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A steepest descent method for optimizing the Carbó molecular similarity index was implemented and evaluated. Comparisons were made between this procedure and the extensively used simplex method. Several data sets were considered, and in each case the gradient method showed a substantial improvement in the time taken for the optimization to converge while comparable similarity values were obtained. In some cases, performance enhancements of up to an order of magnitude were observed. © 1997 by John Wiley & Sons, Inc.
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  • 71
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    Journal of Computational Chemistry 18 (1997), S. 169-181 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to perform essential dynamics using different subsets of atoms and compare these to the basic C-α analysis. Essential dynamics analyses are also compared to the normal modes method. The stability of the essential space during a simulation is investigated by comparing the two halves of a trajectory. Apart from the analyses in Cartesian space, the essential dynamics in φ/ψ torsion angle space is discussed. © 1997 by John Wiley & Sons, Inc.
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  • 72
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The new transferable atom equivalent (TAE) method for rapid molecular electron density reconstruction was used to compute a set of molecular surface property descriptors. These descriptors were then used to construct HPLC column capacity factor PLS models for a series of high-energy materials. The new TAE-derived surface property indices are also available from ab initio or semiempirical wave functions, but the speed and accuracy of TAE reconstruction make it the method of choice for obtaining these indices. The new QSPR indices are based upon the extrema, distributions, and surface integrals of the electronic kinetic energy density, the Politzer average local ionization potential (pip), and the electrostatic potential, as well as the rates at which these properties change normal to the 0.002-e/au3 molecular surface. The distribution of the properties were recorded as surface histograms. While property extrema and surface integral averages proved to be descriptive, the most useful new indices were found to correspond to histogram bin data computed for K and G surface kinetic energy densities. All-subsets-regression modeling showed that when mixtures of traditional connectivity indices, theoretical linear solvation energy relations (TLSERs), and generalized interaction properties functions (GIPFs) were included with the new indices in the variable sets, the new indices were consistently involved in the best 2% of the capacity factor models. Peak retention time data from two different columns were examined (a Hypersil “CPS” cyanoalkylated column and a standard reverse-phase Hypersil “ODS” column) using a phosphate buffer mobile phase at pH 3.0. The result were compared to an earlier TLSER correlation analysis of the same data by Lowrey and Famini. The TAE-generated surface property descriptors were shown to provide superior PLS models for both sets of columns and conditions. © 1997 by John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 18 (1997), S. 254-259 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The 1,5-cyclooctadiene (COD) molecule can easily form complexes with transition metals with the molecular structure of various of these complexes being proposed with the aid of X-ray diffraction methods. The fact that the complexes exhibit weak metal-COD bonds makes it very important in inorganic synthesis and catalysis. In this work the potential energy surface (PES) for the COD molecule was comprehensively investigated: first with molecular mechanics (using the MM3 force field); and, in a second stage, at the ab initio Hartree-Fock level of theory employing the 3-21G*, 6-31G, and 6-31G* basis sets and also including electron correlation effects at the Moller-Plesset second-order perturbation theory level. This work revealed that there are three distinct conformers of the COD molecule with the predicted lowest energy conformation being in agreement with the proposed structure based on experimental electron diffraction data. © 1997 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 18 (1997), S. 277-289 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm, complementarity, is developed for conformational search of macrocyclic molecules. The algorithm scans a large number of candidate conformations and energy-minimizes only the promising ones. These candidates can be generated by two operators that construct new conformations from known minima. The candidates have similar bonded-interaction energy as the known minima and possibly lower nonbonded interaction energy. This algorithm is 9 to 11 times faster than the existing methods when tested on two large rings, cycloheptadecane and rifamycin SV. © 1997 by John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 18 (1997), S. 323-329 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the application of the adaptive simulated annealing (ASA) method as a global optimization approach to biomolecular structure determination, using the ECEPP/2 (empirical conformation energy program for peptides) potential energy form. As applied to Met-enkephalin, our optimization results in a conformation that is in agreement with other studies. In addition, a dominant right-handed α-helical conformation is predicted for a 14-residue poly (L-alanine) model peptide in a limited search range. These results show that ASA is an efficient and robust algorithm for conformational analysis. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 343-350 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of how to calculate the electrostatic interactions between molecules and a solvent is a very important one in theoretical chemistry and biophysics. One of the more commonly used methods has been to represent the solvent by a dielectric continuum and then to solve the Poisson (or the Poisson-Boltzmann) equation for the potential due to the charge distribution of the solute. The solution of the equation has, up to now, been largely carried out using finite-difference grid-based methods. In this article, we investigate the use of an alternative method, based on a basis set expansion of the potential. The choice of basis functions, the representation of the dielectric function and the accuracy that can be obtained are discussed and illustrated by example calculations on small molecules. © 1997 by John Wiley & Sons, Inc.
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  • 77
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    Keywords: parallel computation ; SCF NMR chemical shifts ; GIAO ; pseudodiagonalization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We implemented our gauge-including atomic orbital (GIAO) NMR chemical shielding program on a workstation cluster, using the parallel virtual machine (PVM) message-passing system. On a modest number of nodes, we achieved close to linear speedup. This program is characterized by several novel features. It uses the new integral program of Wolinski that calculates integrals in vectorized batches, increases efficiency, and simplifies parallelization. The self-consistent field (SCF) step includes a multi-Fock algorithm, i.e., the simultaneous calculation of several Fock matrices with the same integral set, increasing the efficiency of the direct SCF procedure. The SCF diagonalization step, which is difficult to parallelize, has been replaced by pseudodiagonalization. The latter, widely used in semiempirical programs, becomes important in ab initio type calculations above a certain size, because the ultimate scaling of the diagonalization step is steeper than that of integral computation. Examples of the calculation of the NMR shieldings in large systems at the SCF level are shown. Parallelization of the density functional code is underway. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 816-825, 1997
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  • 78
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    Keywords: protein structure prediction ; united-residue representation of a polypeptide chain ; potential of mean force ; radial and angular distribution functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A two-stage procedure for the determination of a united-residue potential designed for protein simulations is outlined. In the first stage, the long-range and local-interaction energy terms of the total energy of a polypeptide chain are determined by analyzing protein-crystal data and averaging the all-atom energy surfaces. In the second stage (described in the accompanying article), the relative weights of the energy terms are optimized so as to locate the native structures of selected test proteins as the lowest energy structures. The goal of the work in the present study is to parameterize physically reasonable functional forms of the potentials of mean force for side-chain interactions. The potentials are of both radial and anisotropic type. Radial potentials include the Lennard-Jones and the shifted Lennard-Jones potential (with the shift parameter independent of orientation). To treat the angular dependence of side-chain interactions, three functional forms of the potential that were designed previously to describe anisotropic systems are evaluated: Berne-Pechukas (dilated Lennard-Jones); Gay-Berne (shifted Lennard-Jones with orientation-dependent shift parameters); and Gay-Berne-Vorobjev (the same as the preceding one, but with one more set of variable parameters). These functional forms were used to parameterize, within a short-distance range, the potentials of mean force for side-chain pair interactions that are related by the Boltzmann principle to the pair correlation functions determined from protein-crystal data. Parameter determination was formulated as a generalized nonlinear least-squares problem with the target function being the weighted sum of squares of the differences between calculated and “experimental” (i.e., estimated from protein-crystal data) angular, radial-angular, and radial pair correlation functions, as well as contact free energies. A set of 195 high-resolution nonhomologous structures from the Protein Data Bank was used to calculate the “experimental” values. The contact free energies were scaled by the slope of the correlation line between side-chain hydrophobicities, calculated from the contact free energies, and those determined by Fauchere and Pliška from the partition coefficients of amino acids between water and n-octanol. The methylene group served to define the reference contact free energy corresponding to that between the glycine methylene groups of backbone residues. Statistical analysis of the goodness of fit revealed that the Gay-Berne-Vorobjev anisotropic potential fits best to the experimental radial and angular correlation functions and contact free energies and therefore represents the free-energy surface of side-chain-side-chain interactions most accurately. Thus, its choice for simulations of protein structure is probably the most appropriate. However, the use of simpler functional forms is recommended, if the speed of computations is an issue. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 849-873, 1997
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    Journal of Computational Chemistry 18 (1997), S. 920-933 
    ISSN: 0192-8651
    Keywords: Monte Carlo ; generalized ensemble ; protein folding ; multiple-minima problem ; global energy minimization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We numerically compare the effectiveness of three recently proposed algorithms, multicanonical algorithm, simulations in a 1/k-sampling, and simulated tempering, for the protein folding problem. We perform simulations with high statistics for one of the simplest peptides, met-enkephalin. While the performances of all three approaches is much better than traditional methods, we find that the differences among the three are only marginal. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 920-933, 1997
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    Journal of Computational Chemistry 18 (1997), S. 992-1003 
    ISSN: 0192-8651
    Keywords: location of funnels ; conical intersections ; crossing points ; reduced-quasi-Newton-Raphson method ; restricted step algorithm ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a method for the location and optimization of an intersection energy point between two potential energy surfaces. The procedure directly optimizes the excited state energy using a quasi-Newton-Raphson method coupled with a restricted step algorithm. A linear transformation is also used for the solution of the quasi-Newton-Raphson equations. The efficiency of the algorithm is analyzed and demonstrated in some examples. © 1997 John Wiley & Sons, Inc. J Comput Chem 18:992-1003, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1036-1042 
    ISSN: 0192-8651
    Keywords: crystal structure prediction ; fast clustering ; equivalent structures ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Most methods of crystal structure prediction generate many trial structures. Because these may differ in choice of unit cell, it is not always immediately obvious whether or not two such structures are equivalent. A method to answer this question is described for the case where the asymmetric unit contains one molecule in a general position, defined by the rotation and translation of that molecule with respect to some reference geometry. In the comparison of two structures, the rotation needed to transform one orientation into the other is determined first. Then it is checked whether this rotation corresponds to a transformation that is compatible with the imposed space group symmetry. A final test compares the cell lengths, the cell angles, and the molecular centers of gravity after the transformation of one structure into the other. The method is implemented for triclinic, monoclinic, and orthorhombic systems and is found to be very fast in tests on hypothetical crystal structures of acetic acid. © 1997 John Wiley & Sons, Inc. J Comput Chem 18:1036-1042, 1997
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    Journal of Computational Chemistry 18 (1997), S. 617-628 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The importance of the inclusion of the Madelung potential in cluster models of ionic surfaces is the subject of this work. We have determined Hartree-Fock all electron wave functions for a series of MgO clusters with and without a large array of surrounding point charges (PC) chosen to reproduce the Madelung potential. The phenomena investigated include: the reactivity of surface oxygens toward CO2, atomic hydrogen, and H+; the geometry and adsorption energy of water and the vibrational shift of CO adsorbed at Mg2+ sites; the electronic structure and the hyperfine coupling constants of oxygen vacancies, the paramagnetic Fs+ centers. While some clusters give results which are virtually independent of the presence of the PCs, other clusters, typically of small size, give physically incorrect results when the PCs are not included. The embedding of the cluster in PCs guarantees a similar response for clusters of different size, at variance with the bare clusters, where the long range coulombic interactions are not included. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 609-616 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The [3 + 2] cycloaddition reaction of phosphaacetylene with diazomethane was investigated by means of high level ab initio calculations. It was deduced that the aromatic diazaphosphole is formed via a nonaromatic intermediate. The regiospecificity of the reaction is thus determined by the energy difference between the two transition states that lead to the two possible regioisomeric intermediates. Of the transition states in the concerted pathways, the one leading to the regioisomer with two PC bonds (3) was found to be more stable at all the levels of theory investigated, including coupled-cluster singles doubles (CCSD)(T)/6-311 + G*//Møller-Plessett(MP)2/6-311 + G* (+ basis set superposition, BSSE, correction). The energy difference between the two transition states, however, is always less than 2 kcal/mol. When the free energies in the two reactions are calculated by use of the harmonic frequencies, the energy separation between the two transition structures remains practically unchanged. The free energy of activation ΔG† was 21 kcal/mol at the CCSD(T)/6-311 + G* level of theory and use of the MP2/6-31 + G* frequencies. At the MP2 level, a rather stable complex is obtained in the initial phase of the reaction. However, the stability of the complexes decreases at the CCSD(T) level, and application of the BSSE correction results in unstable complexes. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 629-637 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities of PAHs including one five-membered ring are calculated by using the AM1 Hamiltonian for the determination of ΔHfo of the neutral and protonated molecules. The calculated PAs are compared to experimental PAs measured by chemical ionization mass spectrometry, using a new method based on competition between charge transfer and proton transfer occurring during the ionization process. A procedure is proposed to validate AM1-calculated PAs from experimental PAs after rescaling the calculated and measured PA values. The site of protonation is first determined on the criterion of the lowest loss of aromaticity, then on the criterion of the largest HOMO coefficient. For indene, the corrected result is compared to an ab initio calculation at the MP2/6-31G*//HF/6-31G* level and to a DFT calculation at the B3LYP/6-31G* and the B3LYP/6-311 + G** levels. Five new PAs are thus established and one published experimental PA is revised. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 646-659 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A direct transfer of Cartesian molecular force fields (FF) and electric property tensors is tested on model systems and compared to transfer in internal coordinates with an aim to improve simulation of vibrational spectra for larger molecules. This Cartesian transformation can be implemented easily and offers greater flexibility in practical computations. It can be also applied for transfer of anharmonic derivatives. The results for model calculations of the force field and vibrational frequencies for N-methylacetamide show that our method removes errors associated with numerical artifacts caused by nonlinearity of the otherwise required Cartesian to internal coordinate transformation. For determination of IR absorption and vibrational circular dichroism intensities, atomic polar and axial tensors were also transferred in the Cartesian representation. For the latter, which are dependent upon the magnetic dipole operator, a distributed origin gauge is used to avoid an origin dependence. Comparison of the results of transferring ab initio FF and intensity parameters from an amide dimer fragment onto a tripeptide with those from a conventionally determined tripeptide FF document some limitations of the transfer method and its possible applications in the vibrational spectroscopy. Finally, application to determination of the FF and spectra for helical heptapeptide are presented and compared to experimental results. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 694-701 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We extended Mayer's chemical Hamiltonian approach methods to N interacting subsystems at the self-consistent field and density functional levels of theory and discussed an efficient algorithm for the implementation. As an example, the energetics of linear (HF)n chains (n varies from 2 to 8) were calculated. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 744-756 
    ISSN: 0192-8651
    Keywords: computational chemistry ; semiempirical MO methods ; ESP atomic charges ; QSAR ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic point charges obtained on the number of grid points used in the fitting procedure is examined. For “buried” atoms a high density grid is necessary. It is possible to obtain 6-31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 744-756, 1997
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    Journal of Computational Chemistry 18 (1997), S. 775-795 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The performance of four commonly used density functionals (VWN, BLYP, BP91, and Becke's original three-parameter approximation to the adiabatic connection formula, referred to herein as the adiabatic connection method or ACM) was studied with a series of six Gaussian-type atomic basis sets [DZP, 6-31G**, DZVP, TZVP, TZ2P, and uncontracted aug-cc-pVTZ (UCC)]. The geometries and dipole moments of over 100 first-row and second-row molecules and reaction energies of over 300 chemical reactions involving such molecules were computed using each of the four density functionals in combination with each of the six basis sets. The results were compared to experimentally determined values. Based on overall mean absolute theory versus experiment errors, it was found that ACM is the best choice for predictions of both energies of reaction [overall mean absolute theory versus experiment error (MATvEE) of 4.7 kcal/mol with our most complete (UCC) basis set] and molecular geometries (overall MATvEE of 0.92 pm for bond distances and 0.88° for bond angles with the UCC basis set). For routine calculations with moderate basis sets (those of double-ζ type: DZP, 6-31G**, and DZVP) the DZVP basis set was, on average, the best choice. There were, however, examples of reactions where significantly larger basis sets were required to achieve reasonable accuracy (errors ≤ 5 kcal/mol). For dipole moments, ACM, BP91, and BLYP performed comparably (overall MATvEE of 0.071, 0.067, and 0.059 debye, respectively, with the UCC basis set). Basis sets that include additional polarization functions and diffuse functions were found to be important for accurate density functional theory predictions of dipole moments. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 812-815 
    ISSN: 0192-8651
    Keywords: computer simulation ; solvent layer ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that, by optimizing the placement of a solute in a solvent droplet or in a periodic simulation cell, the number of solvent molecules can be reduced without affecting the quality of the simulation. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 812-815, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1407-1414 
    ISSN: 0192-8651
    Keywords: neural network ; network ; correlation energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electronic correlation energy of diatomic molecules and heavy atoms is estimated using a back propagation neural network approach. The supervised learning is accomplished using known exact results of the electronic correlation energy. The recall rate, that is, the performance of the net in recognizing the training set, is about 96%. The correctness of values given to the test set and prediction rate is at the 90% level. We generate tables for the electronic correlation energy of several diatomic molecules and all the neutral atoms up to radon (Rn).   © 1997 by John Wiley & Sons, Inc.   J Comput Chem 18: 1407-1414, 1997
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  • 91
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1431-1439 
    ISSN: 0192-8651
    Keywords: electron localization function ; core-valence separation ; d electrons ; valence density ; Pauh kinetic energy density ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electron localization function (ELF) shows too-high values when computed from valence densities only (instead of using the total density). This effect is mainly found when d electrons are present in the outermost shell of the core. Although no pronounced qualitative differences could be noticed in the examples studied up to now, it is found that the quantitative differences between the values of ELF obtained from the valence densities only or from the total densities can be large. We also show, for the first time, an example (the Be atom) where ELF is obtained directly from the density. This exemplifies the possibility of computing ELF from highly accurate calculations (or from experimental data).   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1431-1439, 1997
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  • 92
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    Journal of Computational Chemistry 18 (1997), S. 1463-1472 
    ISSN: 0192-8651
    Keywords: constraints ; molecular dynamics ; Langevin dynamics ; SHAKE ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1463-1472, 1997
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  • 93
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1513-1522 
    ISSN: 0192-8651
    Keywords: general bond network ; molecular simulation ; geometric statement function ; internal coordinates ; polymer ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: One of the most formidable difficulties in the computer programming of molecular simulations is the sometimes complicated bookkeeping required for keeping track of internal coordinates and their derivatives. A completely general method for keeping track of stretch (two-body), bend (three-body), and torsion, wag, and other four-body interactions for ANY bond network is presented. Computer code using this method for calculating internal coordinates and their derivatives can be used for completely different types of bond networks, no matter how complex, with little or no modification. The method is designed to incorporate recent improved formulas for calculating internal coordinates and their derivatives to ensure the most optimal calculation sequence.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1513-1522, 1997
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  • 94
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    Journal of Computational Chemistry 18 (1997), S. 1534-1545 
    ISSN: 0192-8651
    Keywords: self-interaction error ; hybrid functionals ; H2, total energy ; equilibrium bond length ; electron density ; KS potential ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The performance of the currently used generalized gradient approximation density functionals is analyzed using several simple, yet critical requirements. We analyze the effects of the self-interaction error, the inclusion of the exact exchange, and the parameter settings used in the popular three-parameter hybrid density functionals. The results show that the elimination of the self-interaction error from the current density functionals lead to very poor results for H2. The inclusion of the exact exchange does not significantly influence the self-interaction corrected results. The variation of the A, B, and C parameters of a hybrid DFT method influences the H(SINGLE BOND)H equilibrium bond length through a very simple linear equation, and it is possible to reproduce the experimental H(SINGLE BOND)H distance with appropriate selection of these parameters, although an infinite number of solutions exists. Similar results were obtained for the total energy and the electron density along the internuclear axis. The analysis of the exact KS potential at the bond critical point of the dissociating H2 molecule shows that, for this property, the second order Moller-Plesset perturbation theory yields a better potential than the density functionals studied in this article.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1534-1545, 1997
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  • 95
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1591-1608 
    ISSN: 0192-8651
    Keywords: dielectric continuum ; Poisson-Boltzmann equation ; finite element ; electrostatics ; solvation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson-Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary element calculations using our triangulated molecular surface. The overall scaling of the method is found to be approximately linear in the number of atoms in the system. The finite element mesh structure can be exploited to compute the gradient of the polarization energy in 10-20% of the time required to solve the equation itself. The resulting timings for the larger systems considered indicate that energies and gradients can be obtained in about half the time required for a finite difference solution to the equation. The development of a multilevel version of the algorithm as well as future applications to structure optimization using molecular mechanics force fields are also discussed.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1591-1608, 1997
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  • 96
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1609-1631 
    ISSN: 0192-8651
    Keywords: glycine ; conformational equilibrium ; density functional theory ; biomolecular modeling ; microwave structure ; adiabatic connection method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surface of un-ionized glycine has been explored with density functional theory. The performance of several nonlocal functionals has been evaluated and the results are presented in the context of available experimental information and post-Hartree-Fock quantum chemical results. The zero-point and thermal vibrational energies along with vibrational entropies play a very important role in determining the relative stability of glycine conformers; the realization of this has led to some revision and reinterpretation of the experimental results. Uncertainties in the vibrational contributions to the energy differences of several tenths of a kilocalorie/mole remain. The uncertainty in the vibrational free energy is even larger, about 1 kcal/mol. In the final analysis, we suggest that the best estimate of the electronic energy difference between the two lowest glycine conformers should be revised downward from 1.4 to 1.0 kcal/mol. Thirteen stationary points on the potential energy surface have been localized. For the majority of these, there is close agreement among various nonlocal density functionals and the post-Hartree-Fock methods. However, the second conformer (IIn), which has a strong hydrogen bond between the hydroxyl hydrogen and the nitrogen of the amine group, presents a distinct challenge. The relative energy of this conformer is extremely sensitive to the basis set, the level of correlation, or the functional used. The widely used BP86, PP86, and BP91 nonlocal functionals overestimate the strength of the hydrogen bond and predict that this conformer is the lowest energy structure. This contradicts both experiment and high-level post-Hartree-Fock studies. The adiabatic connection method (ACM) and the BLYP functional yield the correct order. The ACM method, in particular, gives energies which are in reasonable agreement with MP2, although these are somewhat low as compared with experiment. Based on this study, ACM should perform well for this type of bioorganic application, with typical errors of a few tenths of a kilocalorie/mole and only rarely exceeding 0.5 kcal/mol.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1609-1631, 1997
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  • 97
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1664-1667 
    ISSN: 0192-8651
    Keywords: force constant ; electric field Hellman-Feynman theorem ; diatomic molecules ; bond length ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The change in the electric field at a nucleus in a molecule due to bond stretch is related to the force constant of the stretched bond. The validity of this relationship using approximate wave functions at the SCF and MP2 levels of theory is tested for the diatomic molecules H2, HF, CO, and N2. The effect of basis set variation on H2 is also investigated.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1664-1667, 1997
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  • 98
    ISSN: 0192-8651
    Keywords: singlet oxygen ; addition to double bond ; hydroperoxides ; MCSCF calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The reaction path of singlet (1Δg) oxygen addition to ethenol (vinyl alcohol) - a model of the reactions of singlet oxygen with aromatic and unsaturated compounds bearing the hydroxy groups - has been studied by means of MCSCF calculations, using various active spaces and basis sets. The effects of dynamic correlation (at the PT2 level) and basis set superposition error (BSSE) on relative energies were also investigated. It was found that including polarization functions is necessary to obtain geometries of the oxygen moiety consistent with the available experimental data. Two possible reaction products were considered: 1-hydroxy-1,2-dioxethane (peroxide) and 2-hydroperoxyethanal-1 (hydroperoxide); their energies are 24.1 and 36.6 kcal/mol (44.1 and 78.2 kcal/mol with the PT2 contribution and BSSE correction) below the dissociation limit, respectively (all energies reported here refer to the 6-31G** basis set and an active space composed of eight orbitals and ten electrons). A common stage of both reactions is the formation of a peralcoxyl intermediate with one of the oxygen atoms attached to the unsubstituted carbon atom; the energies of the respective transition state and that of the intermediate are 30.2 and 18.7 kcal/mol (15.9 and 10.3 kcal/mol with the PT2 contribution and BSSE correction) above the dissociation limit, respectively. The energy of this transition state is the dominant energy barrier to the reaction. The intermediate can then undergo conversion to the dioxethane product, to the perepoxide intermediate, or via a proton transfer, directly to the hydroperoxide, the last route being the most probable one. The perepoxide intermediate, after a proton transfer, also readily gives the hydroperoxide. It was also found that the unimolecular conversion from dioxethane to hydroperoxide via a proton transfer from the hydroxy group accompanied with ring cleavage requires an activation energy of at least 56 kcal/mol, making this reaction path highly improbable.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1668-1681, 1997
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  • 99
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1750-1759 
    ISSN: 0192-8651
    Keywords: Langevin dynamics ; Monte Carlo ; Poisson-Boltzmann equation ; alanine dipeptide ; continuum solvent ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We apply a combination of stochastic dynamics and Monte Carlo methods (MC/SD) to alanine dipeptide, with solvation forces derived from a Poisson-Boltzmann model supplemented with apolar terms. Our purpose is to study the effects of the model parameters, such as the friction constant and the size of the electrostatic finite difference grid, on the rate of conformational sampling and on the accuracy of the resulting free energy map. For dialanine, a converged Ramachandran map is produced in significantly less time than what is required by stochastic dynamics or Monte Carlo alone. MC/SD is also shown to be faster, per timestep, than explicit methods.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1750-1759, 1997
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  • 100
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1354-1364 
    ISSN: 0192-8651
    Keywords: molecular dynamics of polymers ; internal coordinate molecular dynamics ; constraint dynamics ; molecular dynamics in torsion angle space ; implicit leapfrog integrator ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conventional molecular dynamics simulations of macromolecules require long computational times because the most interesting motions are very slow compared to the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is, with bond lengths, bond angles, and torsions as independent variables, gives a theoretical possibility of eliminating all uninteresting fast degrees of freedom from the system. This article presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived that are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations of a 56 residue globular protein. For the first time it was possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is, with fixed bond lengths, bond angles, and rigid aromatic groups, the characteristic step size is 4 fs, which is 2 times higher than with fixed bond lengths only. The step size can be increased up to 11 fs when rotation of hydrogen atoms is suppressed.   © 1997 by John Wiley & Sons, Inc.   J Comput Chem 18: 1354-1364, 1997
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