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  • Inorganic Chemistry  (6,769)
  • Theoretical, Physical and Computational Chemistry  (1,576)
  • 1995-1999  (3,353)
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  • 101
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 535-547 
    ISSN: 0192-8651
    Keywords: force field parametrization ; liquid alkanes ; van der Waals interactions ; molecular dynamics ; GROMOS96 ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The derivation of the van der Waals parameters for the aliphatic CHn united atoms of the GROMOS96 force field is presented. The parameters have been adjusted to reproduce the experimental enthalpies of vaporization and vapor pressures or densities of a set of nine alkanes in the liquid state at 298 K (or at the boiling point in the case of methane), using a cutoff radius for the van der Waals interactions of 1.6 nm. Force fields to be used in molecular simulations are bound to the conditions chosen for their parametrization, for example, the temperature, the densities of the systems included in the calibration set, or the cutoff radius used for the nonbonded interactions. Van der Waals parameters for the CHn united atoms of earlier GROMOS force fields were developed using a cutoff radius of 0.8 nm for the van der Waals interactions. Because the van der Waals interaction energy between aliphatic groups separated by distances between 0.8 and 1.4 nm is not negligible at liquid densities, the use of these parameters in combination with longer cutoffs leads to an overestimation of the attractive van der Waals interaction energy. The relevance of this excess attraction depends on the size of the groups that are interacting, as well as on their local densities. Free energies of hydration have been calculated for five alkanes.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 535-547, 1998
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  • 102
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 575-584 
    ISSN: 0192-8651
    Keywords: Boys-Bernardi scheme ; chemical Hamiltonian approach ; hydrogen bond ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparative study of intermolecular potential energy curves is performed on the complexes H2O(SINGLE BOND)HF, H2O(SINGLE BOND)H2O, H2O(SINGLE BOND)H2S, and H2S(SINGLE BOND)H2S using nine different basis sets at the MP2 and DFT (BLYP and B3LYP) levels of theory. The basis set superposition error is corrected by means of the counterpoise scheme and based on the “chemical Hamiltonian approach.” The counterpoise and CHA-corrected DFT curves are generally close to each other. Using small basis sets, the B3LYP functional cannot be favored against the BLYP one because the BLYP results sometimes get closer to the MP2 values than those of B3LYP. From the results - including the available literature data - we suggest that one has to use at least polarized-valence triple-zeta-quality basis sets (TZV, 6-311G) for the investigation of hydrogen-bonded complexes. Special attention must be paid to the physical nature of the binding. If the dispersion forces become significant DFT methods are not able to describe the interaction. Proper correction for the basis set superposition error is found to be mandatory in all cases.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 575-584, 1998
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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 51-59 
    ISSN: 0192-8651
    Keywords: MolSurf ; QSAR ; amino acid descriptors ; quantum chemistry ; PLS ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This work describes a new set of amino acid descriptors based on ab initio quantum mechanical calculations and MolSurf technology. These descriptors have been applied to two dipeptide data sets using partial least squares as the statistical engine. Statistically significant models for both data sets have been developed. The results from the derived peptide QSAR models are easy to interpret in terms of the theoretically computed MolSurf parameters of physicochemical nature.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 51-59, 1998
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  • 104
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 38-50 
    ISSN: 0192-8651
    Keywords: quantum mechanics ; molecular mechanics ; self-consistent Madelung potential ; polar molecular crystals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion-repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 38-50, 1998
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  • 105
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 21-37 
    ISSN: 0192-8651
    Keywords: antisteroid antibody ; progesterone ; thrombin ; NAPAP ; flexible docking ; MSNI ; MCM ; finite-difference Poisson-Boltzmann technique ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A novel procedure for docking ligands in a flexible binding site is presented. It relies on conjugate gradient minimization, during which nonbonded interactions are gradually switched on. Short Monte Carlo minimization runs are performed on the most promising candidates. Solvation is implicitly taken into account in the evaluation of structures with a continuum model. It is shown that the method is very accurate and can model induced fit in the ligand and the binding site. The docking procedure has been successfully applied to three systems. The first two are the binding of progesterone and 5β-androstane-3,17-dione to the antigen binding fragment of a steroid binding antibody. A comparison of the crystal structures of the free and the two complexed forms reveals that any attempt to model binding must take protein rearrangements into account. Furthermore, the two ligands bind in two different orientations, posing an additional challenge. The third test case is the docking of Nα-(2-naphthyl-sulfonyl-glycyl)-D-para-amidino-phenyl-alanyl-piperidine (NAPAP) to human α-thrombin. In contrast to steroids, NAPAP is a very flexible ligand, and no information of its conformation in the binding site is used. All docking calculations are started from X-ray conformations of proteins with the uncomplexed binding site. For all three systems the best minima in terms of free energy have a root mean square deviation from the X-ray structure smaller than 1.5 Å for the ligand atoms.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 21-37, 1998
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  • 106
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 60-70 
    ISSN: 0192-8651
    Keywords: molecular-dynamics minimization ; conformational search ; water cluster ; Lennard-Jones clusters ; Coulombic clusters ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new conformational search method, molecular dynamics-minimization (MDM), is proposed, which combines a molecular dynamics sampling strategy with energy minimizations in the search for low-energy molecular structures. This new method is applied to the search for low energy configurations of clusters of coulombic charges on a unit sphere, Lennard-Jones clusters, and water clusters. The MDM method is shown to be efficient in finding the lowest energy configurations of these clusters. A closer comparison of MDM with alternative conformational search methods on Lennard-Jones clusters shows that, although MDM is not as efficient as the Monte Carlo-minimization method in locating the global energy minima, it is more efficient than the diffusion equation method and the method of minimization from randomly generated structures. Given the versatility of the molecular dynamics sampling strategy in comparison to Monte Carlo in treating molecular complexes or molecules in explicit solution, one anticipates that the MDM method could be profitably applied to conformational search problems where the number of degrees of freedom is much greater.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 60-70, 1998
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  • 107
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 71-85 
    ISSN: 0192-8651
    Keywords: molecular docking ; protein folding ; grid approximation ; trilinear interpolation ; potential energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is described for molecular mechanics calculations based on a cubic B-spline approximation of the potential energy. This method is useful when parts of the system are allowed to remain fixed in position so that a potential energy grid can be precalculated and used to approximate the interaction energy between parts of a molecule or between molecules. We adapted and modified the conventional B-spline method to provide an approximation of the Empirical Conformational Energy Program for Peptides (ECEPP) potential energy function. The advantage of the B-spline method over simpler approximations is that the resulting B-spline function is C2 continuous, which allows minimization of the potential energy by any local minimization algorithm. The standard B-spline method provides a good approximation of the electrostatic energy; but in order to reproduce the Lennard-Jones and hydrogen-bonding functional forms accurately, it was necessary to modify the standard B-spline method. This modification of the B-spline method can also be used to improve the accuracy of trilinear interpolation for simulations that do not require continuous derivatives. As an example, we apply the B-spline method to rigid-body docking energy calculations using the ECEPP potential energy function. Energies are calculated for the complex of Phe-Pro-Arg with thrombin. For this system, we compare the performance of the B-spline method to that of the standard pairwise summation in terms of speed, accuracy, and overhead costs for a variety of grid spacings. In our rigid-body docking calculations, the B-spline method provided an accurate approximation of the total energy of the system, and it resulted in an 180-fold reduction in the time required for a single energy and gradient calculation for this system.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 71-85, 1998
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  • 108
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 902-911 
    ISSN: 0192-8651
    Keywords: catalysis ; effective core potentials ; mercury chemistry ; methane activation ; quantum chemistry ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational investigation of methane activation by HgII complexes is reported. Calculated geometries and energetics of Hg(II)-containing reactants and products are consistent with available experimental data for a wide range of diverse ligand types. Calculated reaction enthalpies and activation barriers for HgII complexes cover a wide range of values for different ligands. This diversity suggests that the kinetics and thermodynamics of methane activation by Hg(II) and related medium-valent complexes can be tailored through rational modification of the ligand environment. Calculated activation barriers and reaction enthalpies for methane activation by Hg(II) complexes indicates that harder, more electronegative, ligands are kinetically and thermodynamically preferred. Potential donor groups on the activating ligand can stabilize the transition state versus the ground state reactants and hence result in substantially lower methane activation barriers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 902-911, 1998
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  • 109
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 754-768 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; spectroscopically determined force field ; infrared intensities ; electrostatic model ; alkanes ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new electrostatic model for the calculation of infrared intensities in molecular mechanics and molecular dynamics is presented. The model is based on atomic charges, atomic charge fluxes, and internal coordinate dipoles and their fluxes. The internal coordinate dipoles are used instead of atomic dipoles, thus simplifying the derivation of parameters. The model is designed to reproduce ab initio dipole derivatives, and the parameters can be obtained by (iterative) transformations from these, or by linear least squares fitting to them. A first application to linear alkanes has been made. For these molecules, the intensities can be predicted with an average accuracy of 30-40%.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 754-768, 1998
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  • 110
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 781-796 
    ISSN: 0192-8651
    Keywords: molecular electronic spectroscopy ; band shape ; solvent effects ; stochastic methods ; ZINDO ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for approximating the band shape of molecular electronic transitions based on a single geometric configuration is described. The band shape is modeled using an empirical parameter to estimate the width at half-height for each transition. In addition to generating a shape for allowed transitions, a procedure is developed for approximating the oscillator strength for the symmetry forbidden bands. The results obtained using these two approximations are then compared with experimental spectra and to the results obtained from stochastic methods for simple organic molecules, such as benzene, naphthalene, and the diazobenzenes.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 781-796, 1998
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  • 111
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 797-808 
    ISSN: 0192-8651
    Keywords: van der Waals surface area (vdWSA) ; solvent-accessible surface area (SASA), numerical calculation ; neighbor list ; united- and all-atom representations ; protein structures ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general, fast, and exact optimization, called neighbor-list reduction (NLR), is presented, which can be used to accelerate the computation of hard-sphere molecular surface areas. NLR allows selected neighbors of a central atom to be removed from the computation in a preprocessing step, thus allowing the calculation of the atom's surface area to proceed with a shorter list of neighbors. The atoms removed are those having intersections with the central atom falling entirely within unions of other atoms' intersections with the central atom. We describe explicit methods for two levels of neighbor-list reduction: 3NLR considers three hard spheres at a time - the central atom, the candidate for removal, and one other neighbor; whereas 4NLR considers two other neighbors. We demonstrate the correctness and efficiency of this optimization by means of a modified version of the NACCESS program, which computes atomic and molecular surface areas numerically. As test cases we used compounds of different size and class, with and without explicit hydrogens. When van der Waals surface (vdWSA) is computed, the NLR methods reduce the length of the neighbor list by as much as 41%; when solvent-accessible surface area (SASA) is computed, the reduction is as great as 74%. The overall speed improvement due to these reductions is a factor of only about 1.2 for vdWSA, but is about 2.0 for the computation of SASA, in the context of this particular program. All 39,554 calculated atomic surface areas (vdWSA and SASA) were found to be identical to within 0.001 Å2 to those obtained without NLR.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 797-808, 1998
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  • 112
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 977-988 
    ISSN: 0192-8651
    Keywords: quantum mechanical/molecular mechanical ; free energy ; hydride ion ; molecular dynamics ; catalysis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH3, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 977-988, 1998
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  • 113
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 882-892 
    ISSN: 0192-8651
    Keywords: photoelectron spectroscopy ; bond order ; through bond interaction ; Lewis structures ; vibrational structures ; natural bond orbitals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: When canonical molecular orbitals are expanded in terms of a set of localized molecular orbital building blocks, called bond orbitals, the character of the canonical molecular orbitals can be characterized according to the component bond orbitals resembling the core, lone pair, and localized bond building blocks in an intuitive Lewis structure. Weinhold's natural bond orbital method can produce a unique Lewis structure with total occupancy of its occupied bond orbitals exceeding 99.9% of the total electron density for simple molecules. Two useful indices, Lewis bond order and weight of lone pair orbitals, can be defined according to the weights of the bonding and lone pair components of this unique Lewis structure. Calculation results for molecules N2, CO, CS, NO, HCN, C2H2, H2O, and H2S show that the former index can account for the vibrational structures of photoelectron spectroscopy, whereas the latter index can account for the band intensity enhancement of Penning ionization electron spectroscopy.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 882-892, 1998
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  • 114
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    Journal of Computational Chemistry 19 (1998), S. 1030-1038 
    ISSN: 0192-8651
    Keywords: pseudospectral ; parallel ; localized Møller-Plesset, scalable ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a parallel version of our pseudospectral localized Møller-Plesset electronic structure code. We present timings for molecules up to 1010 basis functions and parallel speedup for molecules in the range of 260-658 basis functions. We demonstrate that the code is scalable; that is, a larger number of nodes can be efficiently utilized as the size of the molecule increases. By taking advantage of the available distributed memory and disk space of a scalable parallel computer, the parallel code can calculate LMP2 energies of molecules too large to be done on workstations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1030-1038, 1998
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  • 115
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1039-1052 
    ISSN: 0192-8651
    Keywords: kinetics ; thermal rate constants ; direct dynamics ; variational transition-state theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We introduce TheRate (THEoretical RATEs), a complete application program with a graphical user interface (GUI) for calculating rate constants from first principles. It is based on canonical variational transition-state theory (CVT) augmented by multidimensional semiclassical zero and small curvature tunneling approximations. Conventional transition-state theory (TST) with one-dimensional Wigner or Eckart tunneling corrections is also available. Potential energy information needed for the rate calculations are obtained from ab initio molecular orbital and/or density functional electronic structure theory. Vibrational-state-selected rate constants may be calculated using a diabetic model. TheRate also introduces several technical advancements, namely the focusing technique and energy interpolation procedure. The focusing technique minimizes the number of Hessian calculations required by distributing more Hessian grid points in regions that are critical to the CVT and tunneling calculations and fewer Hessian grid points elsewhere. The energy interpolation procedure allows the use of a computationally less demanding electronic structure theory such as DFT to calculate the Hessians and geometries, while the energetics can be improved by performing a small number of single-point energy calculations along the MEP at a more accurate level of theory. The CH4+H↔CH3+H2 reaction is used as a model to demonstrate usage of the program, and the convergence of the rate constants with respect to the number of electronic structure calculations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1039-1052, 1998
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  • 116
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    Journal of Computational Chemistry 19 (1998), S. 1101-1109 
    ISSN: 0192-8651
    Keywords: parallel computation ; divide-and-conquer ; semiempirical ; quantum mechanical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have implemented a parallel divide-and-conquer method for semiempirical quantum mechanical calculations. The standard message passing library, the message passing interface (MPI), was used. In this parallel version, the memory needed to store the Fock and density matrix elements is distributed among the processors. This memory distribution solves the problem of demanding requirement of memory for very large molecules. While the parallel calculation for construction of matrix elements is straightforward, the parallel calculation of Fock matrix diagonalization is achieved via the divide-and-conquer method. Geometry optimization is also implemented with parallel gradient calculations. The code has been tested on a Cray T3E parallel computer, and impressive speedup of calculations has been achieved. Our results indicate that the divide-and-conquer method is efficient for parallel implementation.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1101-1109, 1998
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  • 117
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    Journal of Computational Chemistry 19 (1998), S. 1111-1129 
    ISSN: 0192-8651
    Keywords: anomer ; conformational analysis ; glucose ; molecular orbital theory ; molecular modeling ; quantum mechanics ; solvation ; stereoelectronic effects ; sugars ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The relative energies of 11 different conformers of D-glucose, including different exo-anomeric orientations and at least one of each hydroxymethyl conformer (G-, G+, and T) for each of the two anomeric forms (α and β), were calculated at much more complete levels of quantum mechanical (QM) electronic structure theory than previously available, and relative free energies in solution were calculated by adding rotational, vibrational, and aqueous solvation effects. The gas-phase results are based on very large basis sets (up to 624 contracted basis functions) and the coupled cluster method for electron correlation. Solvation Model 5.4/ AM1 was used to calculate the effects of aqueous solvation. Factors contributing to the relative energies of these conformers have been analyzed. Relative energies varied considerably (up to 4.5 kcal/mol), depending on the theoretical level, and different levels of theory disagreed as to which anomer was lower in energy. The highest-level gas-phase calculations predicted the α-anomer to be lower in free energy by 0.4 kcal/mol (Boltzmann average). Gas-phase energies from several different classical force fields were compared to QM results. The QM structures optimized at the MP2/cc-pVDZ level of theory compared well with experiment for three different crystal structures. In water, the β-anomers were better solvated than the α-anomers by 0.6 kcal/mol (Boltzmann average). Contributions of individual hydrophilic groups to the solvation free energies were analyzed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1111-1129, 1998
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  • 118
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    Journal of Computational Chemistry 19 (1998), S. 1229-1240 
    ISSN: 0192-8651
    Keywords: free energy calculations ; molecular dynamics ; ribonuclease A ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The calculation of free energies by computer simulation represents one of the most promising areas in molecular modeling. While the computational methods developed so far give reliable results for liquids or solutions, they are not satisfactory for globular proteins. The reproducibility of the data is poor due to several sources of error. The most important are due to the magnitude of the molecule's phase space, to the long relaxation time of the system, and to the singularity occurring when creating or annihilating atoms. In a previous study Simonson and Brünger reported the free energy differences calculated for three successive mutations in the ribonuclease-S system and revealed several sources of error. These errors were reanalyzed and the performance of several methods studied in order to reduce them. Different approaches of mutating the Hamiltonian are compared using the method proposed by Resat and Mezei and a modification of the method proposed by Cross. Procedures are also proposed to reduce the effects of the long relaxation time of the molecule, to bias the simulation toward the experimental structure, and to reduce large free energy derivative fluctuations. All these methods give reliable results when the mutation is carried out in a peptide in solution. When the mutation is carried out in a globular protein, the sources of errors are reduced but not eliminated. Although the investigated procedures and methods increase the reliability of free energy calculation, further improvements will be required.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1229-1240, 1998
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  • 119
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    Journal of Computational Chemistry 19 (1998), S. 1294-1299 
    ISSN: 0192-8651
    Keywords: Monte Carlo ; molecular dynamics ; free energy simulation ; simulation convergence ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A comparative study was carried out to test the efficiency with which Metropolis Monte Carlo (MC) and stochastic dynamics (SD) sample the potential energy surface of the N-acetyl glycyl glycine methylamide peptide as defined by the united atom AMBER* force field. Boltzmann-weighted ensembles were generated with variations of all internal degrees of freedom (i.e., stretch, bend, and torsion) for a single N-acetyl glycyl glycine methylamide molecule at 300 K by 108-step MC and 100-ns SD simulations. As expected, both methods gave the same final energetic results. However, convergence was found to be ∼10 times faster with MC than with SD as measured by comparisons of the populations of all symmetrically equivalent conformers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1294-1299, 1998
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  • 120
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    Journal of Computational Chemistry 19 (1998), S. 1179-1186 
    ISSN: 0192-8651
    Keywords: liquid water ; density ; Monte Carlo simulations ; water models ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo statistical mechanics simulations have been carried out with the TIP3P, SPC, and TIP4P models for liquid water at 13 temperatures from -50°C to 100°C at 1 atm. Long runs with 512 water molecules provided definitive results for densities. Although the TIP4P model yields a flat region in the density profile and a temperature of maximum density near -15°C, the SPC and TIP3P models show monotonically increasing density with decreasing temperature. Results for heats of vaporization, isothermal compressibilities, and coefficients of thermal expansion and their convergence characteristics are also reported.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1179-1186, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1663-1674 
    ISSN: 0192-8651
    Keywords: normal mode ; decomposition ; vibration ; vector projection ; phenol ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for quantitatively comparing calculated vibrational modes is described that relies on projecting the vectors describing the normal modes of one molecule onto those of a basis molecule. The procedure virtually automates the assignment of vibrational modes from one molecule to a second, structurally similar one. We illustrate the concept by using the classical Wilson modes of benzene as a basis for describing normal modes of the monosubstituted benzene derivatives phenol, phenol-d5, and phenol radical cation. These examples demonstrate the method's power for accurately assigning and comparing the normal modes of molecules perturbed by chemical substitution, isotopic substitution, or oxidation state. The vibrational projection analysis method - a special case of vector projection analysis - is compared and contrasted with total energy distribution analysis, perhaps the most commonly used technique for quantitatively comparing vibrational modes, and is found superior in each case when comparing normal modes. Vibrational projection analysis need not be limited to single molecules and quantum calculations, because normal modes may be obtained for much larger systems using molecular mechanics or molecular dynamics techniques. The method should therefore prove useful for interpreting the normal modes of ordered periodic solids and structures perturbed by noncovalent contacts, including proteins and polymers. The method may also prove useful in evaluating new computational methods by allowing direct, quantitative comparison of the vibrational modes obtained from different techniques. The power of this technique will make vibrational projection analysis a valuable tool for computational chemists as well as those using calculations to complement vibrational spectroscopic measurements.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1663-1674, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1689-1697 
    ISSN: 0192-8651
    Keywords: hybrid Monte Carlo ; generalized ensemble ; reweighting ; n-butane ; triribonucleotide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A hybrid Monte Carlo method with adaptive temperature choice is presented that exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. The algorithm is tested by comparing analytical and numerical results for the small n-butane molecule before simulations are performed for a triribonucleotide. Sampling the complex multiminima energy landscape of this small RNA segment, we observe enforced crossing of energy barriers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1689-1697, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1746-1757 
    ISSN: 0192-8651
    Keywords: ab initio ; density functional ; parallelization ; quantum chemistry ; message passing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The parallelization of density functional treatments of molecular electronic energy and first-order gradients is described, and the performance is documented. The quadrature required for exchange correlation terms and the treatment of exact Coulomb interaction scales virtually linearly up to 100 nodes. The RI-J technique to approximate Coulomb interactions (by means of an auxiliary basis set approximation for the electron density) even shows superlinear speedup on distributed memory architectures. The bottleneck is then linear algebra. Demonstrative application examples include molecules with up to 300 atoms and 3000 basis functions that can now be treated in a few hours per geometry optimization cycle in C1 symmetry.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1746-1757, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1786-1794 
    ISSN: 0192-8651
    Keywords: gear effect ; internal rotation ; molecular mechanics ; MM3 force field ; hindered systems ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MM3-based calculations showed that bicycles and polycycles with four- to six-membered rings-components of the bi- and polycyclic backbone are sufficiently rigid to keep a syn-periplanar orientation of vicinal tert-butyl substituents. As a result of the spatial proximity of these groups, their rotation occurs in a concerted manner as demonstrated by conformational schemes that are built using MM3-derived methodology. Only correlated disrotation in saturated systems with four- to five-membered rings-components and in the adamantane system leads to isochronism for Me groups of the tert-Bu substituents (i.e., to dynamic gearing in Mislow's terms). Moreover, correlated rotation of these substituents is coupled with a change of the backbone geometry (pseudorotation) except in the most rigid bicyclo[2.1.1]hexa-2-ene system. Thus, a new type of dynamic gearing, correlated rotation-rotation-pseudorotation, is predicted for quasirigid bi- and polycycles with syn-periplanar oriented tert-Bu substituents.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1786-1794, 1998
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    Journal of Computational Chemistry 19 (1998), S. 847-857 
    ISSN: 0192-8651
    Keywords: exchange-repulsion ; methane ; methane dimer ; anisotropic model potential ; potential energy surface ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The procedure previously proposed for the parameterization of the exchange-repulsion energy using probe atom calculations is applied here to the study of the methane dimer and refined to give a very accurate anisotropic model potential in terms of atomic parameters. The most accurate model uses sites on C and H atoms and requires 12 parameters, but a description using just four isotropic sites shifted inward from the H atoms by 15% of the bond length is almost as accurate and is very simple in form.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 847-857, 1998
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    Journal of Computational Chemistry 19 (1998), S. 858-865 
    ISSN: 0192-8651
    Keywords: generator coordinate Hartree-Fock method ; adapted Gaussian basis sets ; total energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have applied a discretized version of the generator coordinate Hartree-Fock method to generate adapted Gaussian basis sets for atoms Cs (Z=55) to Lr (Z=103). Our Hartree-Fock total energy results, for all atoms studied, are better than the corresponding Hartree-Fock energy results attained with previous Gaussian basis sets. For the atoms Cs to Lr we have obtained an energy value within the accuracy of 10-4 to 10-3 hartree when compared with the corresponding numerical Hartree-Fock total energy results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 858-865, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1534-1552 
    ISSN: 0192-8651
    Keywords: molecular dynamics simulation ; protein dynamics ; problem adapted accuracy ; multiple time step method ; relevant observables ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We evaluate several multiple time step (MTS) molecular dynamics (MD) methods with respect to their suitability for protein dynamics simulations. In contrast to the usual check of conservation of total energy or comparisons of trajectory details, we chose a problem-oriented approach and selected a set of relevant observables computed from extended test simulations. We define relevance of observables with respect to their role in the description of protein function. Accordingly, the use of quantities that exhibit chaotic behavior, like trajectory details, is shown to be inappropriate for the sake of the evaluation of methods. The accuracy of a cutoff method and of six MTS methods is evaluated, which differ in their treatment of the computationally crucial long-ranged Coulomb interactions. For each of the observables considered, the size of purely statistical fluctuations is determined to allow identification of algorithmic artifacts. The obtained ranking of the considered MD methods differs significantly from that obtained by the usual measures of algorithmic accuracy. One particular distance class method, DC-1d, is shown to be clearly superior in that no algorithmic artifacts were detected.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1534-1552, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1553-1554 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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    Journal of Computational Chemistry 19 (1998), S. 1596-1603 
    ISSN: 0192-8651
    Keywords: direct perturbation theory ; MP2 gradients ; density functional theory ; relativistic effects ; nonadditivity of relativity and correlation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The evaluation of the first-order scalar relativistic corrections to MP2 energy based on either direct perturbation theory or the mass-velocity and Darwin terms is discussed. In a basis set of Lévy-Leblond spinors the one- and two-electron matrix elements of the relativistic Hamiltonian can be decomposed into a nonrelativistic part and a relativistic perturbation. Thus, a program capable of calculating nonrelativistic energy gradients can be used to calculate the cross-term between relativity and correlation. The method has been applied to selected closed-shell atoms (He, Be, Ne, and Ar) and molecules (CuH, AgH, and AuH). The calculated equilibrium distances and harmonic frequencies were compared with results from first-order relativistic density functional calculations. It was found that the cross-term is not the origin of the nonadditivity of relativistic and correlation effects.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1596-1603, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1604-1611 
    ISSN: 0192-8651
    Keywords: electron correlation ; relativistic effects ; tungsten hexahydride ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries and relative stabilities of several structural isomers of tungsten hexahydride, WH6, have been obtained at different levels of quantum chemical calculations. The performance of various strategies to (i) include electron correlation, viz. density functional theory based approaches, Møller/Plesset perturbation and coupled cluster theory, and to (ii) account for scalar relativistic effects, viz. various relativistic effective core potentials, first order perturbation theory, a quasi-relativistic treatment employing a Pauli Hamiltonian, and use of the Douglas/Kroll operator, are compared to the best theoretical data available. It is shown that relativistic and electron correlation effects are most important for the high-symmetry species, that these effects give rise to opposite trends in relative energies, and that overall the relativistic effects dominate. The most efficient way to incorporate relativistic effects appears to be via the use of relativistic effective core potentials, while the correlation energies are best taken account of using a conventional method such as CCSD(T).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1604-1611, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1698-1715 
    ISSN: 0192-8651
    Keywords: MNDO ; MNDO/d ; polarizabilities ; hyperpolarizabilities ; H2Sn ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structure-polarization relationship was investigated in a series of polysulfanes, H2Sn. The reported results demonstrate that the forms of change of the polarizability components, αii, and the second hyperpolarizability components, γiiii, as well as the average values α and γ, respectively, of H2Sn with n are similar. This shows that polarizability components can be easily used to determine corresponding hyperpolarizability data. A remarkable change of the hyperpolarizabilities with the molecular geometry of H2Sn was found. This result can be used for the design of nonlinear optical materials with optimum properties. The present study uses the flexible σ bonded H2Sn and is complementary to the works that considered the effect of conformational changes of π-conjugated systems on their hyperpolarizabities. The present computations were performed using the semiempirical approaches MNDO and MNDO/d, as well as ab initio methods with STO-3G, extended with polarization and diffuse functions, and [3s2p/7s5p2d] sets for H2Sn. At the ab initio level, the electronic and the vibrational contributions to polarizabilities and hyperpolarizabilities were both computed for several members of H2Sn. The frequency dependence of the above contributions and the static limit were discussed. Electron correlation was taken into account for several test cases using MP2 theory. The selected methods and the variety of the approximations on which they rely allow the systematic consideration of the effect of changes of the geometry of H2Sn on their polarizabilities and second hyperpolarizabilities.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1698-1715, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1716-1723 
    ISSN: 0192-8651
    Keywords: internal coordinates ; Hessian ; parallel algorithm ; message passing interface ; Newton-Raphson optimization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A parallel algorithm for efficient calculation of the second derivatives (Hessian) of the conformational energy in internal coordinates is proposed. This parallel algorithm is based on the master/slave model. A master processor distributes the calculations of components of the Hessian to one or more slave processors that, after finishing their calculations, send the results to the master processor that assembles all the components of the Hessian. Our previously developed molecular analysis system for conformational energy optimization, normal mode analysis, and Monte Carlo simulation for internal coordinates is extended to use this parallel algorithm for Hessian calculation on a massively parallel computer. The implementation of our algorithm uses the message passing interface and works effectively on both distributed-memory parallel computers and shared-memory parallel computers. We applied this system to the Newton-Raphson energy optimization of the structures of glutaminyl transfer RNA (Gln-tRNA) with 74 nucleotides and glutaminyl-tRNA synthetase (GlnRS) with 540 residues to analyze the performance of our system. The parallel speedups for the Hessian calculation were 6.8 for Gln-tRNA with 24 processors and 11.2 for GlnRS with 54 processors. The parallel speedups for the Newton-Raphson optimization were 6.3 for Gln-tRNA with 30 processors and 12.0 for GlnRS with 62 processors.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1716-1723, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1736-1745 
    ISSN: 0192-8651
    Keywords: Monte Carlo ; conformational free energies ; free energy simulations ; multiple minimum problem ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Many of the most common molecular simulation methods, including Monte Carlo (MC) and molecular or stochastic dynamics (MD or SD), have significant difficulties in sampling the space of molecular potential energy surfaces characterized by multiple conformational minima and significant energy barriers. In such cases improved sampling can be obtained by special techniques that lower such barriers or somehow direct search steps toward different low energy regions of space. We recently described a hybrid MC/SD algorithm [MC(JBW)/SD] incorporating such a technique that directed MC moves of selected torsion and bond angles toward known low energy regions of conformational space. Exploration of other degrees of freedom was left to the SD part of the hybrid algorithm. In the work described here, we develop a related but simpler simulation algorithm that uses only MC to sample all degrees of freedom (e.g., stretch, bend, and torsion). We term this algorithm MC(JBW). Using simulations on various model potential energy surfaces and on simple molecular systems (n-pentane, n-butane, and cyclohexane), MC(JBW) is shown to generate ensembles of states that are indistinguishable from the canonical ensembles generated by classical Metropolis MC in the limit of very long simulations. We further demonstrate the utility of MC(JBW) by evaluating the room temperature free energy differences between conformers of various substituted cyclohexanes and the larger ring hydrocarbons cycloheptane, cyclooctane, cyclononane, and cyclodecane. The results compare favorably with available experimental data and results from previously reported MC(JBW)/SD conformational free energy calculations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1736-1745, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1758-1776 
    ISSN: 0192-8651
    Keywords: DefPol ; molecular surfaces ; continuum solvation methods ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a method to define van der Waals, solvent-accessible, and solvent-excluding molecular surfaces with their partition in nonoverlapping surface portions (tesserae). The procedure is more efficient than those available in the literature to describe solvent effects on molecular systems of large size, and it can also be applied to solutes of small size without reducing the accuracy of the output and without increasing computational times. All the tesserae are expressed in terms of spherical triangles, having all the characterizing elements (vertices, centers, etc.) analytically defined. The method was tested by comparing the results for the surface area and the solvation free energy (decomposed in electrostatic, dispersion, and steric contributions) obtained using the GEPOL procedure within the framework of the polarizable continuum model solvation method. These comparisons regard 87 molecules at the molecular mechanics level and 28 molecules at the ab initio Hartree-Fock level: the results are quite satisfactory.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1758-1776, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1805-1815 
    ISSN: 0192-8651
    Keywords: molecular surface ; molecular graphics ; molecular recognition ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm is proposed for approximation to the molecular surface. It starts with a triangular mesh built on an ellipsoid embracing the whole molecular surface. The triangular mesh is obtained from an icosahedron subdivision sphere with highly uniform vertex distribution, and the embracing surface is deflated stepwise to the best adherence of its triangles onto the surface of the molecule. The deflating direction of each vertex of a triangle is defined by the vector normal at this point to the previous deflated embracing surface. Our results show that the speed of the triangulation embracing ellipsoid method and the quality of the surface obtained by the method are faster and better than the method that starts with a quadrilateral mesh built from meridian and parallel representations on an embracing sphere to get the molecular surface. Furthermore, the surface obtained by the method can be used directly to approximate the molecular surface by spherical harmonic expansions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1805-1815, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1816-1825 
    ISSN: 0192-8651
    Keywords: HCl dimer ; intermolecular potential ; nonspherical atom-atom exchange repulsion ; virial coefficient ; r2 expectation values ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The intermolecular part of the potential energy surface for the HCl dimer has been studied with ab initio quantum chemical methods. An intermolecular potential, based on quantum chemical calculations has been constructed. The interaction energy consists of electrostatic, induction, and dispersion terms calculated from the monomer properties of the interacting molecules and an exchange repulsion term. The latter term was parameterized from the results of the quantum chemical calculations and estimates of the electrostatic and induction energies. It was found necessary to use nonspherical atom-atom exchange repulsion interaction parameters, and the parameters describing the deviation from spherical behavior could be obtained from the expectation values of r2 for the electrons assigned to an atom.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1816-1825, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1834-1852 
    ISSN: 0192-8651
    Keywords: cluster ; flexibility ; similarity ; docking ; reaction ; conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1834-1852, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1862-1876 
    ISSN: 0192-8651
    Keywords: protonation of glycine ; ab initio calculations ; conformational analysis ; gas-phase basicity ; amino acids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller-Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH3+ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)2+. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0-10 and 30-40 kcal mol-1. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1862-1876, 1998
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    Journal of Computational Chemistry 19 (1998), S. 86-93 
    ISSN: 0192-8651
    Keywords: molecular dynamics simulation ; ortho-terphenyl ; 1,3,5-tri-α-naphthyl benzene ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer code was prepared for the molecular dynamics (MD) simulation of a multimolecular system to atomic resolution. Based on a widely accepted force field and aided by simulated annealing of single molecules, $\tilde V$ and $\tilde E$ were computed for ortho-terphenyl and 1,3,5-tri-α-naphthyl benzene across an extended range of temperatures. Although neither the simulation time (40-100 ps) nor the system size (27 and 64 molecules) appeared to affect the computational results to an appreciable extent, it was clear that a longer simulation time or a larger system tended to yield a more consistent set of data. In comparison to experimental observations, simulation was capable of representing $\tilde V$ to within 2-7%, Tg to within 10 K, and ΔCp across Tg to within 10%.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 86-93, 1998
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    Journal of Computational Chemistry 19 (1998), S. 250-257 
    ISSN: 0192-8651
    Keywords: fluorosulfonic acid ; protonation energies ; solvation ; acidities ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic solvation free energies were computed for several small neutral bases and their conjugate acids using a continuum solvation model called the self-consistent isodensity polarizable continuum model (SCIPCM). The solvation energies were computed at the restricted Hartree-Fock (RHF) and second-order Møller-Plesset (MP2) levels of theory, as well as with the Becke3-Lee-Yang-Parr (B3LYP) density functional theory, using the standard 6-31G** Gaussian basis set. The RHF solvation energies are similar to those computed at the correlated MP2 and B3LYP theoretical levels. A model for computing protonation enthalpies for neutral bases in fluorosulfonic acid solvent leads to the equation ΔHprot, HSO3F(B)=-PA(B)+ΔEt(BH+)-ΔEt(B)+β, where PA(B) is the gas phase proton affinity for base B, ΔEt(BH+) is the SCIPCM solvation energy for the conjugate acid, and ΔEt(B) is the solvation energy for the base. A fit to experimental values of ΔHprot, HSO3F(B) for 10 neutral bases (H2O, MeOH, Me2O, H2S, MeSH, Me2S, NH3, MeNH2, Me2NH, and PH3) gives β=238.4±2.9 kcal/mol when ΔΔEt is computed using the 0.0004 e⋅bohr-3 isodensity surface for defining the solute cavity at the RHF/6-31G** level. The model predicts that for carbon monoxide ΔHprot, HSO3F(CO)=10 kcal/mol. Thus, protonation of CO is endothermic, and the conjugate acid HCO+ (formyl cation) behaves as a strong acid in fluorosulfonic acid.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 250-257, 1998
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  • 141
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    Journal of Computational Chemistry 19 (1998), S. 290-299 
    ISSN: 0192-8651
    Keywords: solvation ; density functional ; polarizable continuum model (PCM) ; reaction profiles ; hydration energy ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient version of the polarizable continuum model for solvation has been implemented in the Gaussian density-functional-based code called deMon. Solvation free energies of representative compounds have been calculated as a preliminary test. The hydration effects on the reaction profile of the Cl-+CH3Cl→ClCH3+Cl- reaction and the thermodynamics of the Menschutkin reaction have also been investigated. Finally, the conformational behavior of the 1,2-diazene cis-trans isomerization process in water was examined. Comparisons between the results obtained and the available experimental data and previous theoretical computations have been made.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 290-299, 1998
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  • 142
    ISSN: 0192-8651
    Keywords: Broyden-Fletcher-Goldfarb-Shanno formula ; update Hessian formula ; transition structures ; optimization ; saddle points ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Based on a study of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) update Hessian formula to locate minima on a hypersurface potential energy, we present an updated Hessian formula to locate and optimize saddle points of any order that in some sense preserves the initial structure of the BFGS update formula. The performance and efficiency of this new formula is compared with the previous updated Hessian formulae such as the Powell and MSP ones. We conclude that the proposed update is quite competitive but no more efficient than the normal updates normally used in any optimization of saddle points.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 349-362, 1998
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  • 143
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    Journal of Computational Chemistry 19 (1998), S. 628-646 
    ISSN: 0192-8651
    Keywords: natural resonance theory ; resonance theory ; bonding ; chemical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe quantitative numerical applications of the natural resonance theory (NRT) to a variety of chemical bonding types, in order to demonstrate the generality and practicality of the method for a wide range of chemical systems. Illustrative applications are presented for (1) benzene and polycyclic aromatics; (2) CO2, formate, and related acyclic species; (3) ionic and polar compounds; (4) coordinate covalent compounds and complexes; (5) hypervalent and electron-deficient species; (6) noncovalent H-bonded complex; and (7) a model Diels-Alder chemical reaction surface. The examples exhibit the general harmony of NRT weightings with qualitative resonance-theoretic concepts and illustrate how these concepts can be extended to many new types of chemical phenomena at a quanitative ab initio level.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 628-646, 1998
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  • 144
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    Journal of Computational Chemistry 19 (1998), S. 647-657 
    ISSN: 0192-8651
    Keywords: simulated annealing ; molecular dynamics ; Tsallis machine ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We propose a stochastic optimization technique based on a generalized simulated annealing (GSA) method for mapping minima points of molecular conformational energy surfaces. The energy maps are obtained by coupling a classical molecular force field (THOR package) with a GSA procedure. Unlike the usual molecular dynamics (MD) method, the method proposed in this study is force independent; that is, we obtain the optimized conformation without calculating the force, and only potential energy is involved. Therefore, we do not need to know the conformational energy gradient to arrive at equilibrium conformations. Its utility in molecular mechanics is illustrated by applying it to examples of simple molecules (H2O and H2O3) and to polypeptides. The results obtained for H2O and H2O3 using Tsallis thermostatistics suggest that the GSA approach is faster than the other two conventional methods (Boltzmann and Cauchy machines). The results for polypeptides show that pentalanine does not form a stable α-helix structure, probably because the number of hydrogen bonds is insufficient to maintain the helical array. On the contrary, the icoalanine molecule forms an α-helix structure. We obtain this structure simulating all Φ, Ψ pairs using only a few steps, as compared with conventional methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 647-657, 1998
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  • 145
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    Journal of Computational Chemistry 19 (1998), S. 673-684 
    ISSN: 0192-8651
    Keywords: molecular interaction potential ; molecular electrostatic potential ; dibenzo-p-dioxin ; induced molecular dipole moments ; π-charge interaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand-probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 673-684, 1998
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    Journal of Computational Chemistry 19 (1998), S. 695-715 
    ISSN: 0192-8651
    Keywords: nucleic acid ; multivariate analysis ; Ramachandran plots ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method to construct the equivalent of multidimensional Ramachandran plots for nucleic acids on the basis of singular value decomposition (SVD) is presented. For this purpose, a data matrix containing 244 DNA dinucleoside monophosphate steps, represented by nine torsion angles, was decomposed into a score and loading matrix. It is shown that biplots, containing both score points and loading vectors, provide a simple tool to interpret the principles of DNA class separation. Scores separate the data matrix into one A-DNA class, two different B-DNA classes, and one so-called crankshaft class. Loading vectors correlate torsion angles. The projections of scores on loading vectors indicate which torsion angles play a dominant role in DNA class separation. The results of the biplots are supported by (simple) physical interpretations. From a three-dimensional score space the nine original torsion angles can be reconstructed. Hence, the potential to create the multidimensional equivalent of a Ramachandran plot is available; that is, forbidden and accessible regions in the reduced space reflect these same regions in the nine-dimensional original space.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 695-715, 1998
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    Journal of Computational Chemistry 19 (1998), S. 726-740 
    ISSN: 0192-8651
    Keywords: molecular dynamics ; energy equipartition ; macromolecular simulations ; constant temperature simulations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes an unexpected phenomenon encountered during MD simulations: velocity rescaling using standard protocols can systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees of freedom. Under these conditions, the simulation violates the principle of equipartition of energy, which requires a mean kinetic energy of RT/2 in each degree of freedom. A particularly pathological form of this problem occurs if one does not periodically remove the net translation of (and rotation about) the center of mass. In this case, almost all of the kinetic energy is converted into these two kinds of motion, producing a system with almost no kinetic energy associated with the internal degrees of freedom. We call this phenomenon “the flying ice cube.” We present a mathematical analysis of a simple diatomic system with two degrees of freedom, to document the origin of the problem. We then present examples from three kinds of MD simulations, one being an in vacuo simulation on a diatomic system, one involving a low resolution model of DNA in vacuo, and the third using a traditional all-atom DNA model with full solvation, periodic boundary conditions, and the particle mesh Ewald method for treating long-range electrostatics. Finally, we discuss methods for avoiding the problem.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 726-740, 1998
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    Journal of Computational Chemistry 19 (1998), S. 741-753 
    ISSN: 0192-8651
    Keywords: isotopic labeling ; reaction mechanism ; elucidation ; MECHEM program ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Isotopic labeling experiments can be highly informative in reaction pathway studies, but inferring the implications of a mechanistic hypothesis can be difficult, especially in the case of complex reactions. We report systematic methods for predicting the distribution of labeled products and intermediates given: (1) a mechanistic hypothesis; and (2) a proposed labeling experiment. The methods have been implemented with MECHEM - a computer aid for elucidating reaction mechanisms. As an illustration, we predict the outcomes of ethylene and propylene hydrogenation and n-heptane dehydrocyclization, for a variety of mechanisms and labeling experiments.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 741-753, 1998
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    Journal of Computational Chemistry 19 (1998), S. 935-946 
    ISSN: 0192-8651
    Keywords: consistent valence force-field (CVFF) ; parameterization of bond lengths and bond angles ; Hessian matrix ; dopamine D3-receptor agonists ; heterocyclic systems ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To secure a broad utilization of molecular mechanics in medicinal chemistry appropriate parameters (e.g., reference values and force constants) are required to describe correctly all possible atomic interactions. For this purpose parameters for bond lengths and bond angles were derived for some heterocyclic dopamine D3-receptor agonists. Some new atom types were introduced and consistent valence force-field (CVFF) was supplied with several bond-stretching and angle-bending force constants as well as reference values. Representative fragments containing these missing parameters were minimized at the HF/6-31G* level of theory using Gaussian-92. After frequency calculation, corresponding force constants were extracted from the Hessian matrix. The values were then appropriately converted and scaled. Also, reference values were taken from quantum mechanically minimized structures, applying the same basis set. The transferability of the calculated force constants to CVFF was investigated using fragments with already known parameters. The quality of the extended force field was checked in comparison with “automatic parameters” and ab initio-minimized structures. Finally, the evaluated procedure was applied successfully to related structures.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 935-946, 1998
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    Journal of Computational Chemistry 19 (1998), S. 222-231 
    ISSN: 0192-8651
    Keywords: vinylcyclopropane ; sigmatropic shift ; cyclopropane stereo-mutations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The thermal isomerization of vinylcyclopropane to cyclopentene was discovered in 1960 and soon recognized as the simplest known example of a [1,3] sigmatropic shift. Experimental observations for the parent rearrangement and for isomerizations shown by substituted systems suggest that diradical transition structures are involved; recent theoretical treatments of the reaction find no minima corresponding to diradical intermediates. The common dichotomy opposing concerted versus diradical and thus necessarily stepwise mechanisms appears inappropriate. The reaction of vinylcyclopropane may involve four energetically concerted paths traversed by different conformational forms of nearly isoenergetic diradical species leading through four isometric diradical transition structures to cyclopentene.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 222-231, 1998
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  • 151
    ISSN: 0192-8651
    Keywords: bicyclic azirine intermediates ; ring cleavage ; ab initio calculations ; DFT calculations ; coarctate transition structures ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed investigation of the reaction path for the thermal rearrangement of 3,4-dihydro-1aH-azirine[2,3-c]pyrrol-2-one to yield a cyanoketene-formaldimine complex is carried out at the MP2/6-31G* and B3LYP/6-31G* levels of theory. The ring opening of the five-membered pyrrolinone ring and the formation of the nitrile group takes place in a concerted manner, presenting a significant strain energy release and allowing for an electronic stabilization by coarctate conjugation of the transition structure (TS). These two factors make possible a moderate energy barrier. Although the structural features B3LYP/6-31G* theoretical levels, it is found that the MP2 energy barrier (28.8) CCSD(T)/6-31G*//MP2/6-31G* value (17.1 kcal/mol). The complex electronic rearrangement can be rationalized using the theory of coarctate transition structures developed by Herges as the evolution of an azirine structure without referring to a hypothetical vinyl nitrene intermediate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 912-922, 1998
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    Journal of Computational Chemistry 19 (1998), S. 319-333 
    ISSN: 0192-8651
    Keywords: solvation energy ; solvent accessible surface area ; atomic solvation parameters ; Monte Carlo simulation ; FANTOM ; avian pancreatic polypeptide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss-Bonnet theorem. The surface routine was implemented in FANTOM, a program for energy minimization and Monte Carlo simulation, and tested for accuracy and efficiency in extensive energy minimizations of Met-enkephalin, the α-amylase inhibitor tendamistat, and avian pancreatic polypeptide (APP). The CPU time for the exact calculation of the accessible surface areas and their gradients has been reduced by factors of 2.2 (Met-enkephalin) and 3.2 (tendamistat) compared with our previous approach. The efficiency of our exact method is similar to the recently described approximate methods MSEED and SASAD. The performance of several atomic solvation parameter sets was tested in searches for low energy conformations of APP among conformations near the native X-ray crystal structure and highly distorted structures. The protein solvation parameters from Ooi et al. [Proc. Natl. Acad. Sci. USA, 84, 3086 (1987)] and from Wesson and Eisenberg [Prot. Sci., 1, 227 (1992)] showed a good correlation between solvation energies of the conformations and their root-mean-square deviations from the X-ray crystal structure of APP.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 319-333, 1998
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  • 153
    ISSN: 0192-8651
    Keywords: anomeric effects ; boat conformers, dihydrodioxins ; 3,4-dihydro-1,2-dithiin ; 3,6-dihydro-1,2-dithiin ; 4H-1,3-dithiin ; 2,3-dihydro-1,4-dithiin ; dihydrodithiins ; half-chair conformers ; hyperconjugative orbital interactions ; relative energies ; stereoelectronic effects ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Optimized geometries and energies for 3,4-dihydro-1,2-dithiin (1), 3,6-dihydro-1,2-dithiin (2), 4H-1,3-dithiin (3), and 2,3-dihydro-1,4-dithiin (4) were calculated using ab initio 6-31G* and MP2/6-31G*//6-31G* methods. At the MP2/6-31G*//6-31G* level, the half-chair conformer of 4 is more stable than those of 1, 2, and 3 by 2.5, 3.5, and 3.6 kcal/mol, respectively. The half-chair conformers of 1, 2, 3, and 4 are 2.9, 7.1, 2.0, and 5.6 kcal/mol, respectively, more stable than their boat conformers. The calculated half-chair structures of 1-4 are compared with the calculated chair conformer of cyclohexane and the half-chair structures for cyclohexene, 3,4-dihydro-1,2-dioxin (5), 3,6-dihydro-1,2-dioxin (6), 4H-1,3-dioxin (7), and 2,3-dihydro-1,4-dioxin (8).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1064-1071, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1087-1100 
    ISSN: 0192-8651
    Keywords: saddle point ; distinguished coordinate ; valley-ridge inflection point ; H2CO potential energy surface ; HCN⇌CNH isomerization ; azidoazomethine⇌1H-tetrazole isomerization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The old coordinate driving procedure to find transition structures in chemical systems is revisited. The well-known gradient criterion, ∇E(x)=0, which defines the stationary points of the potential energy surface (PES), is reduced by one equation corresponding to one search direction. In this manner, abstract curves can be defined connecting stationary points of the PES. Starting at a given minimum, one follows a well-selected coordinate to reach the saddle of interest. Usually, but not necessarily, this coordinate will be related to the reaction progress. The method, called reduced gradient following (RGF), locally has an explicit analytical definition. We present a predictor-corrector method for tracing such curves. RGF uses the gradient and the Hessian matrix or updates of the latter at every curve point. For the purpose of testing a whole surface, the six-dimensional PES of formaldehyde, H2CO, was explored by RGF using the restricted Hartree-Fock (RHF) method and the STO-3G basis set. Forty-nine minima and saddle points of different indices were found. At least seven stationary points representing bonded structures were detected in addition to those located using another search algorithm on the same level of theory. Further examples are the localization of the saddle for the HCN⇌CNH isomerization (used for steplength tests) and for the ring closure of azidoazomethine to 1H-tetrazole. The results show that following the reduced gradient may represent a serious alternative to other methods used to locate saddle points in quantum chemistry.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1087-1100, 1998
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    Journal of Computational Chemistry 19 (1998), S. 404-417 
    ISSN: 0192-8651
    Keywords: geometry optimization ; polarizable continuum model ; density functionals ; fixed cavity ; mobile cavity ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new implementation of analytical gradients for the polarizable continuum model is presented, which allows Hartree-Fock and density functional calculations taking into account both electrostatic and nonelectrostatic contributions to energies and gradients for closed and open shell systems. Simplified procedures neglecting the derivatives of the cavity surface and/or using single spheres for XHn groups have also been implemented and tested. The solvent-induced geometry relaxation has been studied for a number of representative systems in order to test the efficiency of the procedure and to investigate the role of different contributions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 404-417, 1998
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    Journal of Computational Chemistry 19 (1998), S. 475-487 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; correlation energies ; conjugated polyenes ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electron correlation at the Møller-Plesset second-order level was incorporated into the π-system portion of MM3 calculations for several conformers of [10]annulene, [18]annulene, bicyclo[5.3.1]undecapentaene, and bicyclo[4.4.1]undecapentaene. The conformers with “localized” C(SINGLE BOND)C π bonds (strongly alternating bond lengths) were found to be of lower energy than their counterparts with “delocalized” C(SINGLE BOND)C π bonds (similar bond lengths) before correlation energy was included. Correlation always lowered the energies of the delocalized conformation more than it did that of the localized conformation, such that often the latter was found to be more stable after correlation energy was included in the calculation. When a delocalized structure was not at a stationary point on the MM3 energy surface, such comparison could not be made. An example is the porphin molecule.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 475-487, 1998
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    Journal of Computational Chemistry 19 (1998), S. 459-474 
    ISSN: 0192-8651
    Keywords: crystal structure prediction ; distributed multipoles ; molecular dynamics ; symmetry constraints ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Possible crystal structures of acetic acid were generated, considering eight space groups and assuming one molecule in the asymmetric unit. Our grid-search method was compared with a Monte Carlo approach as implemented in the Biosym/MSI Polymorph Predictor. This revealed no sampling deficiencies. A large number of possible crystal structures were found (∼100 within only 5 kJ/mol), including the experimental structure. Energy minimizations were done with a united-atoms force field (GROMOS), an all-atoms force field (AMBER), and a potential that describes the electrostatic interactions with distributed multipoles (DMA). In all cases, the experimental structure had a low lattice energy. The number of hypothetical crystal structures was reduced considerably by removing space-group symmetry constraints, or by a primitive molecular dynamics shake-up. Nevertheless, sufficient structures of equal or lower energy compared with the experimental structure remained to suggest that other factors need to be considered for genuine structure prediction.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 459-474, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1402-1420 
    ISSN: 0192-8651
    Keywords: antiaromatic destabilization energies ; singlet-triplet separation ; structures and heats of formation ; stabilization by 1,3 π-overlaps ; homoallylic t-butylcyclopentadienyl cation structure ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report ab initio [MP2(full)/6-31G*] and force field (MMP2 extended to carbocations) results on the parent and alkylated singlet cyclopentadienyl cations. The ab initio results are complemented by force field calculations of 1,3 π-interactions and antiaromatic destabilization energies. The antiaromatic destabilization of the singlet cyclopentadienyl cation is larger than that of cyclobutadiene. The MMP2 heats of formation of various cyclopentadienyl cations agree with experimental and ab initio data. Two Jahn-Teller distorted isomeric structures with almost identical energies are found for the parent singlet cyclopentadienyl cation. Dynamic and nondynamic correlation calculations employing the CASSCF(4,5)/6-31G*//MP2(full)/6-31G* and CASPT2(4,5)/6-31G*//MP2(full)/6-31G* levels of theory clearly show the energetic favorability of an allylic structure for the parent singlet cyclopentadienyl cation. Aklylated cyclopentadienyl cations prefer one of the two possible isomeric cyclopentadienyl cation forms. The substitution pattern determines the preferred cyclopentadienyl structure. As a consequence of its strong antiaromatic destabilization the singlet t-butylcyclopentadienyl cation is predicted to rearrange to a homoallylic 2-(1-methyl-2,4-cyclopentadienyl)-2-propyl cation.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1402-1420, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1445-1455 
    ISSN: 0192-8651
    Keywords: conformational optimization ; energy minimization ; peptides ; simulated annealing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general method designed to isolate the global minimum of a multidimensional objective function with multiple minima is presented. The algorithm exploits an integral “coarse-graining” transformation of the objective function, U, into a smoothed function with few minima. When the coarse-graining is defined over a cubic neighborhood of length scale ∊, the exact gradient of the smoothed function, U∊, is a simple three-point finite difference of U. When ∊ is very large, the gradient of U∊ appears to be a “bad derivative” of U. Because the gradient of U∊ is a simple function of U, minimization on the smoothed surface requires no explicit calculation or differentiation of U∊. The minimization method is “derivative-free” and may be applied to optimization problems involving functions that are not smooth or differentiable. Generalization to functions in high-dimensional space is straightforward. In the context of molecular conformational optimization, the method may be used to minimize the potential energy or, preferably, to maximize the Boltzmann probability function. The algorithm is applied to conformational optimization of a model potential, Lennard-Jones atomic clusters, and a tetrapeptide.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1445-1455, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1215-1228 
    ISSN: 0192-8651
    Keywords: configuration interaction ; parallel computation ; quantum chemistry ; electronic structure ; electron correlation ; 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 internally contracted (IC) multireference configuration (MRCI) module of the MOLPRO quantum chemistry program is described. The global array (GA) toolkit has been used in order to map an existing disk-paging small-memory algorithm onto a massively parallel supercomputer, where disk storage is replaced by the combined memory of all processors. This model has enabled a rather complicated code to be ported to the parallel environment without the need for the wholesale redesign of algorithms and data structures. Examples show that the parallel ICMRCI program can deliver results in a fraction of the time needed for equivalent uncontracted MRCI computations. Further examples demonstrate that ICMRCI computations with up to 107 variational parameters, and equivalent to uncontracted MRCI with 109 configurations, are feasible. The largest calculation demonstrates a parallel efficiency of about 80% on 128 nodes of a Cray T3E-300.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1215-1228, 1998
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  • 161
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    Journal of Computational Chemistry 19 (1998), S. 1255-1267 
    ISSN: 0192-8651
    Keywords: conformation space ; potential energy surface ; energy landscape ; principal component analysis ; principal coordinate analysis ; peptide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Obtaining useful representations of molecular conformation spaces and visualizing the associated potential energy surfaces is a complex task, mainly due to the high dimensionality of these spaces. Principal component analysis (PCA), which projects multidimensional data on low-dimensional subspaces, is thus becoming a common technique for studying such spaces. Three issues, relating to the use of principal component techniques for mapping molecular potential energy surfaces, are discussed in this study: the effectiveness of the projection; its accuracy; and the mapping procedure. The effectiveness of PCA is demonstrated through detailed analyses of principal component projections of several peptides. In these cases PCA projected conformation space into a subspace smaller even than that defined by the peptide's backbone dihedral angles. The average accuracy as well as the distribution of errors in the projection (i.e., the errors in reproducing individual distances) are studied as a function of the dimensionality of the projection. The wide variation in accuracy between different systems suggests that it is imperative to indicate the accuracy of the projection whenever PCA projections are used. Furthermore, when projecting potential energy surfaces on the principal two-dimensional (2D) plane, the projection errors result in artificial roughening of the surface. A new mapping procedure, the “minimal energy envelope” procedure, is introduced to overcome this problem. This procedure yields relatively smooth “energy landscapes,” which highlight the basin structure of the real multidimensional energy surface. It is demonstrated that the projected potential energy maps can be used for charting conformational transitions or dynamic trajectories in the system.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1255-1267, 1998
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  • 162
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    Journal of Computational Chemistry 19 (1998), S. 1284-1293 
    ISSN: 0192-8651
    Keywords: reference program ; molecular calculations ; Slater-type orbitals ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A program for computing all the integrals appearing in molecular calculation with Slater-type orbitals is reported. The program is mainly intended as a reference for testing and comparing other algorithms and techniques. An analysis of the performance of the program is presented, paying special attention to the computational cost and the accuracy of the results. Results are also compared with others obtained with Gaussian basis sets of similar quality.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1284-1293, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1325-1336 
    ISSN: 0192-8651
    Keywords: cyanate ; isocyanate ; ambident ; ion pair ; SN2 reaction ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structure of lithium and sodium cyanates and isocyanates and their related ion pair SN2 reactions were investigated using molecular quantum mechanics at the Hartree-Fock (HF)/6-31G**//HF/6-31G** level. Extensive further calculations of some of the lithium systems at higher levels gave no significant changes in relative properties. The isocyanate ion pairs are the most stable monomeric forms. The lowest energy dimers are planar eight-membered rings. For the ionic SN2 reaction of cyanate ion and methyl fluoride and chloride, methyl isocyanate is the predicted major product. The monomer ion pair inversion mechanism is predicted to preferentially form methyl cyanate but the calculations also indicate that reaction with dimeric ion pairs have no clear preference for forming methyl cyanate or isocyanate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1325-1336, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1337-1344 
    ISSN: 0192-8651
    Keywords: density averaging ; average conformation ; molecular deformations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The concepts of averaged electron densities and averaged nuclear arrangements are discussed with reference to small nuclear distortions and an electron density transformation based on the inverse Löwdin transform.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1337-1344, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1853-1861 
    ISSN: 0192-8651
    Keywords: pyrrolizidine alkaloids ; necine bases ; retronecine ; heliotridine ; conformational analysis ; molecular structure ; hydrogen bond ; molecular mechanics ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo-exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo-endo interconversion of heliotridine. Reactivity behaviors and 1H-NMR data of both diasterisomers were elucidated in light of the theoretical results.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1853-1861, 1998
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  • 166
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    Journal of Computational Chemistry 19 (1998), S. 1887-1898 
    ISSN: 0192-8651
    Keywords: Hartree-Fock exchange plus correlation functionals SCF calculations ; two-body density ; ionization potentials ; electron affinities ; polarizabilities ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Self-consistent field calculations are done using two-body density functionals for the correlation energy. The corresponding functional derivatives are obtained and used in pseudo-eigenvalue equations analogous to the Kohn-Sham ones. The examples studied include atomic systems from He to Ar. The values obtained for ionization potentials, electron affinities, dipole polarizabilities, and virial ratios from these calculations are given, and the effect of exchange is addressed. The results obtained are in good agreement with experimental values, and are of the same quality as those given by accurate exchange-correlation functionals.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1887-1898, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1-20 
    ISSN: 0192-8651
    Keywords: crystal structure prediction ; polymorphism ; atom-atom potential method ; force fields ; crystal structure solution ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The approach of Karfunkel and Gdanitz has been used to predict possible crystal structures of acetic acid and three of its monohalogenated analogs starting with the molecular structure alone. The results demonstrate that this approach is capable of finding many, if not all, of the possible packing arrangements of molecules of this size, but that it is not currently capable of correctly ranking these structures in terms of their enthalpy. This deficiency is probably due to inadequacies in the force field used to minimize the structures. The inadequacies relate to the description of acidic hydrogen bonds and halogen-halogen interactions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1-20, 1998
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    Journal of Computational Chemistry 19 (1998), S. vii 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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    Journal of Computational Chemistry 19 (1998), S. 102-111 
    ISSN: 0192-8651
    Keywords: QSHAKE ; bond constraints ; semirigid molecules ; molecular dynamics simulations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE-ing” bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is significantly more efficient whenever SHAKE requires triangles (or tetrahedra) of constraints to maintain molecular shape. Efficiencies are gained because QSHAKE reduces the number of holonomic constraints that must be solved iteratively and requires fewer iterations to obtain convergence. The gains in efficiency are most noticeable when a high degree of precision is imposed on the constraint criteria. QSHAKE is also stable at larger time steps than SHAKE, thus allowing for even more efficient exploration of phase space for semirigid molecules.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 102-111, 1998
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    Journal of Computational Chemistry 19 (1998), S. 154-167 
    ISSN: 0192-8651
    Keywords: density functional theory ; free radicals ; alkane fragmentation ; Chemistry ; Theoretical, Physical and Computational Chemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Density functional methods at the 6-31G* level are applied to the rupture of n-octane into methyl-heptyl, ethyl-hexyl, propyl-pentyl, and butyl-butyl radical fragments. The energetics of the radicals at UMP3, UMP2/6-31G*//UHF/6-31G* (hereafter referred to as UMP), are compared to UB3LYP/6-31G* results (referred to as UB). Although the UMP approach matches additivity energies to within 5 kcal/mol, it fails to mimic the overall energetic trend. The UB energies agree with additivity estimates and trends to within 1-2 kcal/mol and radical entropies deviate by only 2 e.u. from available experimental data.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 154-167, 1998
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  • 171
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    Keywords: bond polarizabilities ; localized orbitals ; bicyclo[1.1.1]pentanes ; NMR coupling constants ; CLOPPA-IPPP ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: In the present work, the relationship between the large substituent effects on 3J(C1H) in 1-X-3-M-bicyclo[1.1.1]pentanes, I, and the polarizability of the bridgehead C3(SINGLE BOND)Mα bond is investigated. The existence of such a relationship is suggested by the finding that the effect of an electronegative substituent X on 3J(C1Mα) couplings in I (M=H) is due to a distortion of the C3(SINGLE BOND)H bond toward the C1 center, which enhances the Fermi contact interaction. If such distortion originates in an electrostatic effect, then in other members of this series it can be expected that the substituent effects on 3J(C1Mα) couplings should depend strongly on the C3(SINGLE BOND)Mα bond polarizability. Two approaches are followed. First, the ab initio CLOPPA-IPPP method is applied to study the C3(SINGLE BOND)Mα bond contribution to the molecular static polarizability tensor in I (M=H, F, CH3). Such bond polarizabilities are found to follow the same trend as calculated as well as experimentally determined substituent effects on 3J(C1Mα) couplings, which were measured as part of this work in I [X=H, Cl; M=F, CH3 and X=OCH3; M=Sn(CH3)3]. Second, 3J(C1Mα) couplings (M=H, CH3) are calculated at an ab initio level for X=H, F, and they are compared with those obtained in the parent compound (X=H) if the calculation is carried out in the presence of an inhomogeneous electric field.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 181-188, 1998
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    Journal of Computational Chemistry 19 (1998), S. 203-214 
    ISSN: 0192-8651
    Keywords: structure ; stability ; B+13 clusters ; B3LYP/6-31G* density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures and energies of B+13, observed experimentally to be an unusually abundant species among cationic boron clusters, have been studied systematically with B3LYP/6-31G* density functional theory. The most thermodynamically stable B+12 and B+13 clusters are confirmed to have planar or quasiplanar rather than globular structures. However, the computed dissociation energies of the 3-dimensional B+13 clusters are much closer to the experimental values than those of the planar or quasiplanar structures. Hence, planar and 3-dimensional B+13 may both exist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 203-214, 1998
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    Journal of Computational Chemistry 19 (1998), S. 833-846 
    ISSN: 0192-8651
    Keywords: continuum solvation models ; ab initio calculations ; solvation free energy ; solute-solvent interactions ; cavity errors ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a formal and numerical analysis of the errors related to the use of molecular cavities in the continuum description of solute-solvent electrostatic interactions. In this approximation the solvent response is fully described by an apparent charge distribution induced on the cavity surface. The latter is then discretized into a set of point charges that are generally affected by errors of different origin but all depending on the definition of the cavity boundaries, and the way its surface is partitioned. The numerical analysis is based on results obtained for a set of couples of neutral/anionic solutes obtained with various versions of PCM methods, exploiting different correction procedures, as well as with two recently developed continuum methods, complementing PCM.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 833-846, 1998
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    Journal of Computational Chemistry 19 (1998), S. 866-881 
    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 strategy to introduce multipole-induced polarization effects into quantum mechanical particles is presented. The strategy takes advantage of perturbation theory, and allows one to introduce polarization effects into the generalized molecular interaction potential (GMIP) previously defined by our group. The resulting parameter provides a complete and accurate picture of molecular interactions at a reduced computational cost. It is suggested that this polarized potential (GMIPp) can be used as an effective Hamiltonian for mixed QM/MM calculations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 866-881, 1998
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    Journal of Computational Chemistry 19 (1998), S. 168-180 
    ISSN: 0192-8651
    Keywords: symmetry theory ; group theory ; point group ; space group ; cluster group ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two types of symmetry groups are commonly used in chemistry. Point groups are used for molecules, whereas, for solids, the 230 space groups are used. Neither of these types of symmetry groups are suitable for representing unit cells in solids, the symmetry of which is intermediate between that of point groups and space groups. To represent the symmetry of unit cells in an infinite lattice, a third type of symmetry group must be used. An algorithmic method of generating these symmetry groups is described. It can be demonstrated that these groups are valid by use of conventional symmetry group theory. This technique has been applied to the two-dimensional graphite lattice. Because the new method generates symmetry tables using only the topology of the system, the symmetry properties of graphs can also readily be derived. Last, the relationship between these groups and the other two types of groups is identified.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 168-180, 1998
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    Journal of Computational Chemistry 19 (1998), S. 189-194 
    ISSN: 0192-8651
    Keywords: fullerene, ab initio ; carbon-13 ; nuclear magnetic resonance ; density functional ; buckyball ; MM3 ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio studies at the HF/6-31G* and B3LYP/6-31G* levels are reported for two bowl-shaped hydrocarbons related to C60: C30H12 and C36H12, of C3 and C3v symmetry, respectively. The former has an approximate heat of formation of 211 kcal/mol. Bowl-to-bowl interconversion may occur through a planar (C3h) form of ca. 64 kcal/mol greater energy having one imaginary vibrational frequency. The larger C36H12 bowl has a calculated ΔH°f of 265 kcal/mol. Its HF/6-31G*, B3LYP/6-31G*, and MM3 bond lengths are in good agreement with a recent X-ray structure. Chemical shifts for both compounds calculated by the GIAO method are in good agreement with the measured NMR spectra. The observed 13C chemical shifts increase with the extent of pyramidalization.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 189-194, 1998
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    Journal of Computational Chemistry 19 (1998), S. 195-202 
    ISSN: 0192-8651
    Keywords: 1,3-dipolar cycloaddition ; regiochemistry ; softness ; local HSAB principle ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The principle of hard and soft acids and bases is applied in the local sense to rationalize the regiochemistry in the cycloaddition reactions of a few typical 1,3-dipoles, in particular those with phosphorus-containing dipolarophiles. Local softnesses are calculated using density functional theory. It is observed that the regioselectivity can be explained using these new reactivity descriptors based solely on the properties of the reactants.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 195-202, 1998
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    Journal of Computational Chemistry 19 (1998), S. 232-239 
    ISSN: 0192-8651
    Keywords: endohedral metallofullerenes ; cage structures and symmetry ; metal positions and motion ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structural determination of endohedral metallofullerenes has attracted special attention in disclosing the formation mechanism and developing new routes to bulk production. Recent advances in the theoretical and experimental studies are summarized with representative mono- and dimetallofullerenes such as M@C82 (M=Ca, Sc, Y, and La), Sc2@C84, and La2@C80.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 232-239, 1998
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    Journal of Computational Chemistry 19 (1998), S. 215-221 
    ISSN: 0192-8651
    Keywords: nitroxide radical trapping ; steric substituent parameter ΩS ; molecular mechanics ; correlation analysis ; reactivity ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The reactivity of nitroxide radical trapping (NRT), where stable nitroxide radicals react with transient carbon-centered radicals to form diamagnetic molecules, was evaluated. This was done with the use of the steric substituent parameter of both radicals by correlation analysis on the basis of the reactivity data determined by Ingold's group. In the case where the transient carbon-centered radicals were not resonance stabilized, the rate constant could be well correlated by using only ΩS parameters of R2NO⋅ and U⋅. If the transient radicals were stabilized by resonance, the parameter to estimate the amount of the resonance stabilization of U⋅ was necessary in the regression equation to evaluate the reactivity correctly. When the spin density, calculated by PM3 UHF molecular orbital calculations, was used as the resonance stabilization parameter, the rate constant could be well evaluated by a dual-parameter regression equation.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 215-221, 1998.
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    Journal of Computational Chemistry 19 (1998), S. 240-249 
    ISSN: 0192-8651
    Keywords: furan ; decomposition mechanism ; ab initio ; DFT ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Density functional theory and high-level ab initio calculations were carried out to investigate three unimolecular decomposition channels of furan. All equilibrium and transition state structures along the proposed decomposition channels are fully optimized by B3LYP/6-31G** and characterized at the same level of theory by vibrational and intrinsic reaction coordinate analyses. Relative energies of the optimized structures were evaluated at theoretical levels up to QCISD(T)/6-311++G**. The theoretical results suggest that the unimolecular decomposition channel of isoxazole, proposed in an experimental study and implied to be the main decomposition channel of furan, is responsible only for the formation of HC(TRIPLE BOND)CH and H2O(DOUBLE BOND)C(DOUBLE BOND)O, minor products of furan thermal decomposition. A new decomposition mechanism, proposed in the present study, is shown to be more likely responsible for the formation of CH3C(TRIPLE BOND)CH and CO, major products of furan thermal decomposition.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 240-249, 1998
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    Journal of Computational Chemistry 19 (1998), S. 334-348 
    ISSN: 0192-8651
    Keywords: parameters ; parametrization ; neon ; helium ; CHARMM ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Obtaining accurate Lennard-Jones (L-J) parameters is a vital part of the optimization of empirical force fields due to their significant contribution to condensed-phase properties. We present a novel approach to optimize L-J parameters via the use of ab initio data on interactions between rare gas atoms and model compounds combined with the reproduction of experimental pure solvent properties. Relative values of ab initio minimum interaction energies and geometries between helium or neon and model compounds were used to optimize the relative magnitude of the L-J parameters. Absolute values of the L-J parameters were determined by reproducing experimental heats of vaporization and molecular volumes for pure solvents. Application of the approach was performed on methane, ethane, and propane. Free energies of aqueous solvation and butane pure solvent and aqueous solvation calculations were used to test the developed L-J parameters. The new alkane parameters are similar or improved as compared with current empirical force field parameters with respect to experimental pure solvent properties and free energies of aqueous solvation. Also included is a description of the internal portion of the force field.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 334-348, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1268-1277 
    ISSN: 0192-8651
    Keywords: molecular surface ; marching tetrahedra ; meshing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented to generate and triangulate molecular surfaces rapidly. It is based on the ‘marching tetrahedra’ approach. The method is fast, simple and easy to implement. Our approach is not analytical in nature. Hence no special treatment is required for complications with singularity, degeneracy, or with self-intersecting re-entrant surfaces. A quick test for determining the solvent accessibility of a point in space forms an important part of the method. This test has potential use outside of the surface generation algorithm such as in molecular field analysis where the solvent accessibility of a point needs to be determined. The triangulated surface generated is suitable for molecular graphics display as well as boundary element continuum dielectric calculations.   © 1998, Government of Canada. Exclusive worldwide publication rights in the article have been transferred to John Wiley & Sons, Inc. in perpetuity.   J Comput Chem 19: 1268-1277, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1205-1214 
    ISSN: 0192-8651
    Keywords: silicon monoxide halides ; IR spectra ; DFT ; electron localization function ; bonding analysis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The spectroscopic properties of XSiO (X=F, Cl, or Br) have been predicted using the B3-LYP/6-311+G(2d) level of theory. It has been shown that the halogen atom is Si bonded in a bent structure, with ∠(XSiO) bond angles close to 126°. The binding energy of the halogen with the SiO subunit was calculated to be -80.1, -40.9, and -29.3 kcal/mol for FSiO, ClSiO, and BrSiO, respectively. The harmonic frequencies and isotopic shifts have been calculated. A comparison between XSiO and X2SiO has also been made. For the X2SiO (X=F or Cl) compounds, the calculated frequencies are in fair agreement with the available experimental data. Characterization of bonding has been investigated with different approaches (natural bond orbital approach, topological analysis of the charge density, and of the electron localization function ELF).   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1205-1214, 1998
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  • 184
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    Journal of Computational Chemistry 19 (1998), S. 1187-1204 
    ISSN: 0192-8651
    Keywords: vibrational spectra ; SQM force fields ; fluorocarbons ; density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the scaled quantum-mechanical (SQM) force field approach with direct scaling of individual primitive force constants, we derive optimal scaling factors by a least-squares fit to the experimentally observed fundamentals of some selected “simple” fluorocarbons. We use the derived scaling factors to predict the vibrational spectra of all possible fluoromethanes, fluoroethylenes, fluoroethanes, and monofluoropropenes, proposing a reassignment of some experimental fundamentals. Two separate sets of scaling factors are derived for both traditional Hartree-Fock (HF) calculations and density functional theory (DFT) calculations using the hybrid three-parameter B3-PW91 density functional. With the split-valence 6-31G(d) basis set, our scaling procedure gives an average error of less than 9 cm-1 in the scaled frequencies with the B3-PW91 functional. The average percentage error is around 1%. The HF results are not as good - the average error is 12.6 cm-1 - showing that hybrid density functional SQM schemes are better for predicting vibrational spectra than basic Hartree-Fock.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1187-1204, 1998
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  • 185
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    Journal of Computational Chemistry 19 (1998), S. 1470-1481 
    ISSN: 0192-8651
    Keywords: protein folding ; simulated annealing ; Monte Carlo dynamics ; multiple minima problem ; global minimum conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new and efficient method for overcoming the multiple minima problem of polypeptides, the systematic stepsize variation (SSV) method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly chosen dihedral angles are updated starting with a small stepsize (i.e., magnitude of rotation). A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of ±0.0004 kcal/mol from the reference structure and, consequently, are perfectly superposable. For comparison, Metropolis Monte Carlo simulated annealing (MMC-SA) is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1470-1481, 1998
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  • 186
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    Journal of Computational Chemistry 19 (1998), S. 1575-1583 
    ISSN: 0192-8651
    Keywords: 1-octanol/water partition coefficient ; molecular quantum similarity measures ; atomic shell approximation ; promolecular densities ; QSAR ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new molecular descriptor of hydrophobicity based on molecular quantum similarity measures (MQSM), which can be used to replace the log P parameter in QSAR studies, is proposed. Unlike the majority of existing approaches for calculation of log P, the present methodology does not rely on the use of fragment additive contributions, but rather it is based on the comparison of quantum chemically calculated electron density distributions of a given molecule in water and in 1-octanol, using MQSM. The method has been tested on a broad series of 58 molecules including such structural types as aliphatic hydrocarbons, alcohols, amines, halides, carboxylic acids, esters, amides, and ketones, as well as more complex systems with two functional groups. In all cases investigated, an excellent linear relationship between calculated MQSM and log P values was found. Additionally, an example of QSAR analysis is presented using MQSM instead of log P values, corresponding to predict the narcosis of tadpoles.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1575-1583, 1998
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  • 187
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    Journal of Computational Chemistry 19 (1998), S. 1632-1638 
    ISSN: 0192-8651
    Keywords: Monte Carlo simulation ; QM/MM method ; perturbation theory ; microsolvation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We introduce error weighting functions into the perturbative Monte Carlo method for use with a hybrid ab initio quantum mechanics/molecular mechanics (QM/MM) potential. The perturbative Monte Carlo approach introduced earlier provides a means to reduce the number of full SCF calculations in simulations using a QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of an MM molecule. The use of weighting functions, introduced here, allows an optimal number of MM molecule displacements to occur between the performance of the full self-consistent field calculations. This will allow the ab initio QM/MM approach to be applied to systems that require more accurate treatment of the QM and/or MM regions.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1632-1638, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1345-1352 
    ISSN: 0192-8651
    Keywords: ab initio calculations ; low-barrier hydrogen bonds ; enzyme catalysis ; density functional calculations ; hydrogen bonding ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: High-level ab initio and DFT molecular orbital calculations have been used to investigate the physical properties of a model low-barrier hydrogen bond (LBHB) system: formic acid-formate anion. In the gas phase, it is found that the hydrogen bond formed is extraordinarily short and strong [ca. 27 kcal/mol at B3LYP/6-31++G(d, p)], with a calculated enthalpy of activation for proton transfer from donor to acceptor that is less than the zero-point vibrational energy available to the system. Several perturbations to this system were studied. Forcing a mismatch of pKas between donor and acceptor, via the use of substituents, causes the strength of the hydrogen bond to decrease. Microsolvation of the hydrogen-bonded complex does not affect the strength of the low-barrier hydrogen bond very much. Small variations in the structure of the LBHB results in a decrease in hydrogen-bond strength. Increasing the effective polarity of the cavity surrounding the LBHB was found to have a significant impact on the strength of the hydrogen bond. Implications for enzyme catalysis are discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1345-1352, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1353-1369 
    ISSN: 0192-8651
    Keywords: ab initio ; density functional theory ; oxidation reactions ; dioxiranes ; carbonyl oxides ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The relative reactivity of a series of nucleophiles that includes ethylene, sulfides, sulfoxides, amines, and phosphines toward dioxirane, dimethyldioxirane, carbonyloxide and dimethylcarbonyloxide has been examined at the MP4/6-31G*//MP2/6-31G*, QCISD(T)/6-31G*//MP2/6-31G*, and B3-LYP/6-31G* levels of theory. The barriers for the oxidations with dimethyldioxirane are higher (up to 2.5 kcal/mol for the oxidation of H2S) than those for the oxidations with the parent dioxirane. The oxidation barriers for dioxirane are larger than those for the oxidations with peroxyformic acid, except the barriers for the oxidation of sulfoxides. The reactivity of dimethylsulfide toward dimethyldioxirane was found to be comparable to that of dimethylsulfoxide both in the gas phase and in solution (chloroform). The classical gas phase barrier for the oxidation of trimethylamine to trimethylamine oxide was higher (6.3 kcal/mol at the MP4//MP2/6-31G* level) than that for oxygen atom transfer to trimethylphosphine. When the transition states were examined by self-consistent reaction field (SCRF) methods, the predicted barriers for the oxidation of amines and phosphines were found to be in good agreement with experiment. The general trend in reactivity for oxidation by dioxirane was R2S≈R2SO, R3P〉R3N in the gas phase, and R2S≈R2SO, R3N≈R3P (R=Me) in solution. The oxidation barriers calculated using the B3-LYP functional were lower than those computed at the MP4 and QCISD(T) levels.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1353-1369, 1998
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  • 190
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    Journal of Computational Chemistry 19 (1998), S. 1505-1514 
    ISSN: 0192-8651
    Keywords: protein design ; dead-end elimination ; rotamers ; combinatorial optimization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Recent advances in protein design have demonstrated the effectiveness of optimization algorithms based on the dead-end elimination theorem. The algorithms solve the combinatorial problem of finding the optimal placement of side chains for a set of backbone coordinates. Although they are powerful tools, these algorithms have severe limitations when the number of side chain rotamers is large. This is due to the high-order time dependence of the aspect of the calculation that deals with rotamer doubles. We present three independent algorithmic enhancements that significantly increase the speed of the doubles computation. These methods work by using quantities that are inexpensive to compute as a basis for forecasting which expensive calculations are worthwhile. One of the methods, the comparison of extrema, is derived from analytical considerations, and the remaining two, the “magic-bullet” and the “qrs” and “quv” metrics, are based on empirical observation of the distribution of energies in the system. When used together, these methods effect an overall speed improvement of as much as a factor of 47, and for the doubles aspect of the calculation, a factor of 95. Together, these enhancements extend the envelope of inverse folding to larger proteins by making formerly intractable calculations attainable in reasonable computer time.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1505-1514, 1998
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  • 191
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    Journal of Computational Chemistry 19 (1998), S. 811-819 
    ISSN: 0192-8651
    Keywords: hydroxyl radical ; alkenes ; atmospheric reactions ; OH addition ; reaction mechanism ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MP2 calculations with full geometry optimizations were performed with a double- and a triple-zeta basis set to obtain the energy profile for reactions of propene+OH and ethene+OH at low pressures. In these conditions, the β-hydroxyalkyl radicals formed after OH addition to the alkene double bond may go through a rearrangement reaction to form easily identifiable aldehydes and ketones. The theoretical results obtained reproduce the available experimental data well and shed light on the mechanism of reactions characterized by negative activation energies.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 811-819, 1998
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  • 192
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    Journal of Computational Chemistry 19 (1998), S. 1072-1086 
    ISSN: 0192-8651
    Keywords: three-membered rings ; G2 theory ; ring-strain ; hydrogenation energies ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: G2 ab initio calculations on all ABX three-membered rings (TMRs) that can be derived from cyclopropane by systematic substitution of the (SINGLE BOND)CH2 groups by (SINGLE BOND)NH or (SINGLE BOND)O groups have been performed. Our results show that the decrease in the A(SINGLE BOND)B bond length as the electronegativity of X increases is significantly larger than that found for the corresponding acyclic analogs. In general, a systematic substitution of the (SINGLE BOND)CH2 groups of cyclopropane by (SINGLE BOND)NH or (SINGLE BOND)O groups implies significant geometric changes that are not reflected in a parallel change of the corresponding conventional ring strain energy (CRSE). When the electronegativity of the groups forming the TMR increases the effect on the CRSE of the system is small, although the charge delocalization inside the ring decreases. The near constancy of the CRSE along the series can be explained in terms of the charge redistribution of the system where the (SINGLE BOND)CH2 groups play a crucial role. There are, however, significant changes in the hydrogenation energies of the TMR investigated; our results show that, when in an ABX three-membered ring, the electronegativity of X increases the hydrogenation energy of A(SINGLE BOND)B bond decreases and vice versa.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1072-1086, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1110-1110 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: No abstract.
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  • 194
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    Journal of Computational Chemistry 19 (1998), S. 1146-1166 
    ISSN: 0192-8651
    Keywords: automatic parameterization ; force field development ; molecular mechanics ; MM3 ; Newton-Raphson and simplex optimization ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general set of procedures for automated parameterization of molecular mechanics force fields is presented. The current implementation for MacroModel force fields can easily be adapted to other programs running under Unix. Several variants of numerical Newton-Raphson and simplex methodologies are used to fit simultaneously both experimental and quantum mechanical data. In a sample parameterization of ethane, 24 different modes of combining various sources of reference data are compared. The best cost/performance ratio for generating quantum mechanical source data was obtained with the B3LYP/6-31G* method. The best optimization strategy consists of initial subset optimizations with a modified simplex method, followed by Newton-Raphson optimization using Lagrange multipliers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1146-1166, 1998
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  • 195
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    Journal of Computational Chemistry 19 (1998), S. 1167-1178 
    ISSN: 0192-8651
    Keywords: metals ; force field ; coordination ; organometallic compounds ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Transition metal complexes have been treated by a molecular mechanics approach using an MM2-like valence force field for the ligands and a Urey-Bradley force field about the metal. Metal-ligand atom bonds are parameterized with dependence on the metal covalent radius. The current metal-ligand distances and covalent radii were determined by a Simplex minimization and visual optimization of the deviations in bond distance between 230 structures from the Cambridge Crystallographic Structure Database and the force field calculated values. Moderately good reproducibility of structures is obtained with a variety of metal types with different oxidation states, and degree of unsaturation and with square-planar compounds. The current model also includes coordination of π ligands to the metal center with a 1/r6 attractive term whose minimum is 25 kcal/mol per p orbital at a distance dependent on the covalent radius of the metal and an angular attentuation factor.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1167-1178, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1241-1254 
    ISSN: 0192-8651
    Keywords: integral transformation ; low-order scaling ; second-order Møller-Plesset calculations ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is presented for the four-index transformation of electron repulsion integrals to a localized molecular orbital (MO) basis. Unlike in most programs, the first two indices are transformed in a single step. This and the localization of the orbitals allows the efficient neglect of small contributions at several points in the algorithm, leading to significant time savings. Thresholds are applied to the following quantities: distant orbital pairs, the virtual space before and after the orthogonalizing projection to the occupied space, and small contributions in the transformation. A series of calculations on medium-sized molecules has been used to determine appropriate thresholds that keep the truncation errors small (below 0.01% of the correlation energy in most cases). Benchmarks for local second-order Møller-Plesset perturbation theory (MP2; i.e., MP2 with a localized MO basis in the occupied subspace) are presented for several large molecules with no symmetry, up to 975 contracted basis functions, and 60 atoms. These are among the largest MP2 calculations performed on a single processor. The computational time (with constant basis set) scales with a somewhat lower than cubic power of the molecular size, and the memory demand is moderate even for large molecules, making calculations that require a supercomputer for the traditional MP2 feasible on workstations.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1241-1254, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1278-1283 
    ISSN: 0192-8651
    Keywords: SHAKE ; CHARMM ; molecular mechanics ; free energy perturbation ; molecular dynamics simulation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: When calculating free energy differences between two molecular systems by means of molecular dynamics simulation, accessory potential functions can help eliminate uninteresting configurational entropy contributions, improve convergence, and facilitate reversibility. In this work, we demonstrate that the use of a harmonic potential function to restrain key portions of a molecular system in a free energy perturbation dual-topology molecular dynamics approach dramatically improves convergence and precision of the calculation. Limitations of this technique are illustrated, and its use in conjunction with a fixed bond-length constraint is developed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1278-1283, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1300-1314 
    ISSN: 0192-8651
    Keywords: Gaussian fits ; Prony's method ; pseudospectral methods ; electron correlation ; aliasing error ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a method of fitting arbitrary functions to linear combinations of Gaussians. In particular, we discuss an adaptation of Prony's method, or separation of exponentials, which allows us to automatically select appropriate exponents for these Gaussians. We then apply this technique to the selection of dealiasing sets for pseudospectral electron correlation methods. We show that it can successfully choose functions that generally improve the accuracy of pseudospectral correlation energies while reducing the size of the dealiasing set chosen.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1300-1314, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1315-1324 
    ISSN: 0192-8651
    Keywords: ab initio ; anharmonicity ; force field ; Morse potential ; vibrational frequency ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four alternatives are compared for estimating vibrational anharmonicity constants without explicitly calculating the expensive fourth derivatives of the potential curves. In the first, semiempirical approach, fourth derivatives for 53 diatomic molecules are estimated from ab initio second and third derivatives by using the Morse model potential. Vibrational anharmonicities ωexe are then computed from the third and fourth derivatives. The second approach invokes a purely empirical linear correlation between ωexe and the harmonic frequencies ωe. The third and fourth empirical approaches suppose that the effective harmonic and anharmonic force constants are proportional (with an additive constant in the fourth approach). Experimental values for ωexe are compared with empirical predictions and with semiempirical estimates based upon Hartree-Fock (HF), Møller-Plesset (MP2), and local, nonlocal, and hybrid density-functional theories (DFT), using the small 6-31G* basis set. Ab initio values of ωe and bond lengths re are also compared against experiment. The (U)MP2 results are the worst and include several anomalies. The other semiempirical methods yield results of comparable accuracy for ωexe of hydrides, although the DFT methods are markedly better for ωe and re and for ωexe of nonhydrides. The empirical estimates are nearly as good as the semiempirical ones. We conclude that: (1) both empirical and semiempirical approximations are useful for predicting stretching anharmonicity constants ωexe to precisions of σ≈5 cm-1 for hydrides and σ≈1.5 cm-1 for nonhydrides; and (2) MP2 theory is relatively unreliable for such calculations. In addition, we find the following tests to be useful when evaluating the reliability of vibrational constants calculated at the UMP2 level: (a) the calculated values of ωe and ωexe should not deviate substantially from the empirical relations; (b) harmonic frequencies and intensities calculated at the MP2 level should be smaller than those calculated at the corresponding HF level; (c) a large distance-dependence of the spin contamination, d〈S2〉/dR≳0.05 Å-1, suggests that calculated constants are too large.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1315-1324, 1998
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    Journal of Computational Chemistry 19 (1998), S. 1387-1401 
    ISSN: 0192-8651
    Keywords: acyl halides ; MM3 ; ab initio calculations ; IR ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A newly developed acyl halide molecular mechanics (MM3) force field can accurately calculate molecular geometry, usually to within experimental error. The new force field can also calculate vibrational frequencies. The acyl halides studied were formyl halides, acetyl halides, propionyl halides, n-butyryl halides, 2-methylpropionyl halides, and 2,2-dimethylpropionyl halides. The rms deviation for vibrational frequencies was 28 cm-1.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1387-1401, 1998
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