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  • 1990-1994  (766)
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Comparative clinical pathology 4 (1994), S. 146-151 
    ISSN: 1433-2981
    Keywords: Biochemistry ; Development ; Haematology ; Koala
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Haematology and biochemistry of captive pouch young and back young koalas from 165 days to one year old were studied. Distinct changes with age were observed. Packed cell volume, haemoglobin, erythrocyte count, MCV and total plasma protein where lowest in the youngest animals less than 180 days old. Reticulocytes were highest in this age group. Haematological values differed from those of adult animals. Lymphocytosis occurred, especially between 210–330 days of age. Intense erythropoiesis was indicated by reticulocytosis and the presence of erythrocyte granular inclusions, anisocytosis and poikilocytosis on blood films, particularly up to 330 days of age. Microcytosis present on blood films throughout the study period could not be explained by iron deficiency.
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  • 2
    ISSN: 1432-2072
    Keywords: Risperidone ; Antipsychotics ; 5-HT2 antagonism ; D2 antagonism ; Pharmacology ; Receptor binding ; Biochemistry ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review reports on the pharmacodynamics of the new antipsychotic risperidone. The primary action of risperidone is serotonin 5-HT2 receptor blockade as shown by displacement of radioligand binding (Ki: 0.16 nM), activity on isolated tissues (EC50:0.5 nM), and antagonism of peripherally (ED50: 0.0011 mg/kg) and centrally (ED50:0.014 mg/kg) acting 5-HT2 receptor agonists in rats. Risperidone is at least as potent as the specific 5-HT2 receptor antagonist ritanserin in these tests. Risperidone is also a potent dopamine D2 receptor antagonist as indicated by displacement of radioligand binding (Ki: 1.4 nM), activity in isolated striatal slices (IC50: 0.89 nM), and antagonism of peripherally (ED50: 0.0057 mg/kg in dogs) and centrally acting D2 receptor agonists (ED50: 0.056–0.15 mg/kg in rats). Risperidone shows all effects common to D2 antagonists, including enhancement of prolactin release. However, some central effects such as catalepsy and blockade of motor activity occur at high doses only. Risperidone is 4–10 times less potent than haloperidol as a central D2 antagonist in rats and it differs from haloperidol by the following characteristics: predominant 5-HT2 antagonism; LSD antagonism; effects on sleep; smooth dose-response curves for D2 antagonism; synergism of combined 5-HT2/D2 antagonism; pronounced effects on amphetamine-induced oxygen consumption; increased social interaction; and pronounced effects on dopamine (DA) turnover. Risperidone displays similar activity at pre- and postsynaptic D2 receptors and at D2 receptors from various rat brain regions. The binding affinity for D4 and D3 receptors is 5 and 9 times weaker, respectively, than for D2 receptors; interaction with D1 receptors occurs only at very high concentrations. The pharmacological profile of risperidone includes interaction with histamine H1 and α-adrenergic receptors but the compound is devoid of significant interaction with cholinergic and a variety of other types of receptors. Risperidone has excellent oral activity, a rapid onset, and a 24-h duration of action. Its major metabolite, 9-hydroxyrisperidone, closely mimics risperidone in pharmacodynamics. Risperidone can be characterized as a potent D2 antagonist with predominant 5HT2 antagonistic activity and optimal pharmacokinetic properties.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1459
    Keywords: PGAM deficiency ; Myopathy ; Biochemistry ; Muscle culture ; 31P-MR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphoglycerate mutase (PGAM) deficiency has been so far identified in only six patients, five of these being African Americans. We report the results of clinical, morphological, biochemical, muscle culture and31P-MR spectroscopy studies in the first Caucasian patient with muscle PGAM deficiency. A 23-year-old man had a 10-year history of cramps after physical exertion with one episode of pigmenturia. Neurological examination and EMG study were normal. ECG and echocardiography revealed hypertrophy of the interventricular septum and slight dilatation of the left chambers of the heart. Muscle biopsy revealed increased glycogen content and some accumulation of mitochondria. Muscle PGAM activity was markedly decreased (6.5% and 9.7% of control value in two different biopsies). Citrate synthase and other mitochondrial respiratory chain enzyme activities were much higher than normal. In contrast to the marked decrease of PGAM activity observed in muscle biopsy, total enzyme activity in the patient's aneural muscle culture was normal, being represented exclusively by BB isoenzyme. The deficiency of PGAM-MM isoenzyme was reproduced in the patient's innervated muscle culture. Muscle31P-MR spectroscopy showed accumulation of phosphomonoesters only on fast “glycolytic” exercise. On “aerobic” exercise, Vmax, calculated from the work-energy cost transfer function, showed an increase consistent with the morphological and biochemical evidence of mitochondrial proliferation. This might represent a sort of compensatory aerobic effort in an attempt to restore muscle power.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 12-22 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 54-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 90-104 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 132-143 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 155-161 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 190-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy-based three-dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 249-249 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
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  • 11
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 283-299 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 269-282 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical computations on a subset of a large molecule can be performed, at the neglect of diatomic differential overlap (NDDO) level, without further approximation provided that the atomic orbitals of the frontier atoms are replaced by parametrized orthogonal hybrid orbitals. The electrostatic interaction with the rest of the molecule, treated classically by the usual molecular mechanical approximations, is included into the self-consistent field (SCF) equations. The first and second derivatives of energy are obtained analytically, allowing the search for energy minima and transition states as well as the resolution of Newton equations in molecular dynamics simulations. The local self-consistent field (LSCF) method based on these approximations is tested by studying the intramolecular proton transfer in a Gly-Arg-Glu-Gly model tetrapeptide, which reveals an excellent agreement between a computation performed on the whole molecule and the results obtained by the present method, especially if the quantum subsystem includes the side chains and the peptidic unit in between. The merits of the LSCF method are examplified by a study of proton transfer in the Asp69 - Arg71 salt bridge in dihydrofolate reductase. Simulations of large systems, involving local changes of electronic structure, are therefore possible at a good degree of approximation by introducing a quantum chemical part in molecular dynamics studies. This methodology is expected to be very useful for reactivity studies in biomolecules or at the surface of covalent solids. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 333-345 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics force-field parameters for alkyl boronic acids. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 395-404 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 374-374 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 377-384 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates-finite elements, NC-FEM) is provided. Several representative three-dimensional (3D) systems (Henon-Heiles and Eckart potentials, and the H3+ molecule) are studied, and NC-FEM results are compared with those published by other authors. For the H3+, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Tab.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 466-474 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new code has been written to perform relativistic Dirac-Fock self-consistent field (SCF) calculations on closed-shell molecules of any symmetry. The choice of the basis set allows us to work at different levels of approximation depending on the precision required. Calculations on the H2Po molecule show that accurate results on specific problems like geometry optimization can be obtained by evaluating the two-electron integrals on half the basis spinors. © 1994 by John Wiley & Sons, Inc.
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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 455-465 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanics force field for studying some beta-lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.
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  • 20
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 21
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 524-531 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.
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  • 22
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 488-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
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  • 23
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 24
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 627-632 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
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  • 25
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 719-732 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Traditional net atomic charge models were found unsatisfactory for representing the molecular electric potential (MEP) of n-alkanes ethane through decane in their van der Waals envelopes. The MEP of these molecules was calculated by ab initio methods. Mulliken atomic charges were erratic and gave root mean square (rms) relative errors of fit to the MEP ranging from 152 to 607% with the 6-31 + + g** basis set. Fitting the MEP with potential-derived net atomic charges (PD charges) gave errors ranging from 51 to 62% with the same basis set. The use of larger basis sets, inclusion of electron correlation, use of more MEP data points, or relaxation to optimal structural geometry did not improve significantly the representation of the MEP by net atomic charges. In many cases PD charges of hydrogen atoms were negative, and carbon atoms were positive. To improve the representation of the MEP of n-alkanes, augmentation of the model with nonatomic sites was investigated with the program PDM93. Models with additional charge sites located between hydrogens, on a line bisecting the CH2 group, achieved fits to the MEP with errors reduced to 8% or less, except for n-butane, where the fitting error was 16%. The PD models augmented with methylene bisector sites generally show positive hydrogen charges. They also show CH2 group charge alternation along the n-alkane chains. The augmented charge models were consistent with the observed quadrupole moment of ethane and gave satisfactory predictions for the crystal structures of pentane and octane. © 1994 by John Wiley & Sons, Inc.
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  • 26
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 733-746 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi-Newton Broyden-Fletcher-Goldfarb-Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree-Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
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  • 27
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    Journal of Computational Chemistry 15 (1994), S. 782-790 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have applied the FEM-MP2 method (an implementation of the p-version finite element technique within the framework of second-order Møller-Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second-order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed-shell elements. The FEM-MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
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  • 28
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    Journal of Computational Chemistry 15 (1994), S. 820-837 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
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  • 29
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    Journal of Computational Chemistry 15 (1994), S. 561-570 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By nuclear magnetic resonance (NMR), the four ring forms of psicose, α-and β-pyranose and α- and β-furanose, have almost equal concentrations in aqueous solution. Prediction of this equilibrium by molecular mechanics tests both the balance within the force field and the methods for including the many degrees of freedom in the system. For both the α- and β-furanoses, each of 410 different ring shapes was studied in combination with 37 combinations of staggered side-group orientations. Of these, 48 and 57 initial combinations of side-group orientations contributed to the α- and β-furanose energy surfaces. The pyranoses were analyzed in two steps. First, the 38 characteristic ring conformations were optimized with the 63 staggered side-group combinations. All combinations that gave the lowest energy at one or more of the 38 shapes (20 combinations for α-pyranose, 15 for β-pyranose) were then optimized with 4912 different ring forms. Ring conformations were generated by fixing nonadjacent ring atoms (two for furanose rings, three for pyranoses) at increments of 0.1 Å from the plane of the remaining three atoms. At a dielectric constant of 4.0, prediction was in fair agreement with the NMR results. Model northern and southern conformers contribute to the furanose equilibrium, and both chairs are important for α-psicopyranose. © 1994 by John Wiley & Sons, Inc.
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  • 30
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    Journal of Computational Chemistry 15 (1994), S. 588-595 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.
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  • 31
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    Journal of Computational Chemistry 15 (1994), S. 644-652 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have studied the effect of excess charge on the bond strength in the silanes SiH4 and Si2H6 to assess whether charge trapping in a solid-state lattice might promote the technologically important photodegradation of amorphous silicon alloys (the Staebler-Wronski effect). The calculations indicate that both positive and negative charges reduce the strength of Si—H and Si—Si bonds considerably, to the point where they may be broken easily by visible or even infrared light. © 1994 by John Wiley & Sons, Inc.
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  • 32
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    Journal of Computational Chemistry 15 (1994), S. 596-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effects of substituents (X) on the structures and stabilities of CH2X- anions for groups comprised of fourth- and fifth-period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X- anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = Li—F) and third (X = Na—Cl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X- anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X- stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = K—I and QCISD(T)/6-31 + G*/MP2/6-31 + G* + ZPE level] for X = Li—Cl) also show strong π-stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3—PH2—SH—Cl, GeH3—AsH2—SeH—Br, and SnH3—SbH2—TeH—I sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π-accepting ability. © 1994 by John Wiley & Sons, Inc.
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  • 33
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    Journal of Computational Chemistry 15 (1994), S. 633-643 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is developed and applied to characterize the global shape of the hydrogen-bonded networks formed in solvent and solute-solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen-bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large-scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen-bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
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  • 34
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    Journal of Computational Chemistry 15 (1994), S. 662-665 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An X-PLOR scheme for imitating the action of ribosomes in aiding synthesizing peptides to find their ultimate conformations is introduced. The scheme is tested with an example from the Delta-Sleep-Inducing-Peptide mutant family. © 1994 by John Wiley & Sons, Inc.
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  • 35
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    Journal of Computational Chemistry 15 (1994), S. 667-683 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New atom- and group-based spherical-cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom-based method, force switching, leaves short-range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group-based cutoffs is presented: Switched group-shifting shifts the group-group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom-based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen-bonding system consisting of two N-methyl acetamide molecules and by full MD simulation. Thirty-five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom-based shifting are each able to approximate no-cutoff results when a cutoff at or beyond 12 Å is used. However, atom-based potential-energy switching and truncation unacceptably contaminate group-group electrostatic interactions. Group-based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance-dependent dielectric (∊ ∝ r) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom-based spherical cutoffs, whereas switched group-shifting is the preferred group-based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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  • 36
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    Journal of Computational Chemistry 15 (1994), S. 704-718 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulation and thermodynamic integration (TI) techniques have been used to study the relative free energies of the 8-methyl-N5-deazapterin and 8-methyl-pterin cations (N3 protonated) in aqueous solution. The MD simulations were performed at constant temperature and volume, and the mutations between the cations were carried out by changing the coupling parameter continuously and linearly with the MD simulation time (continuous coupling or slow growth method). The free energy changes have been calculated using both linear and nonlinear couplings of the potential energy functions. Free energy changes have also been computed using the perturbation method for comparison. After separation into electrostatic and van der Waals mutations, most (ca. 80%) of the total free energy change is found to be due to mutation of the electrostatic terms. The free energy change is found to be sensitive to the cutoff radii for interactions between solvent molecules, but rather insensitive to the cutoff radii for interactions between cation and solvent. The free energy changes have also been calculated using various cation and solvent models. Atomic charges for the cations were derived from the molecular electrostatic potential at the semiempirical AM1 and ab initio self-consistent field (SCF) (3-21G, 6-31G, 6-31G*, 6-311G**) levels using AM1 and 3-21G optimized geometries. The TIP3P and SPC models were adopted for the solvent. For the TIP3P solvent model, the order of the free energy change is 6-31G 〉 3-21G 〉 6-31G* ≈ 6-311G** 〉 AM1, where the difference between 6-31G and AM1 is approximately 1 kcal/mol. The free energies obtained using 3-21G optimized geometries are approximately 0.7 kcal/mol larger than those obtained using AM1 geometries for the cations. The free energy change computed using the TIP3P/6-311G* model is 0.3 kcal/mol larger than that obtained for the SPC/6-311G* model. © 1994 by John Wiley & Sons, Inc.
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  • 37
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    Journal of Computational Chemistry 15 (1994), S. 752-768 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A CFF931 all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 15 (1994), S. 769-781 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1-difluoro-4,4-dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist-chair 〈 twist-boat 〈 twist-chair) were not observed. The axial-equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2-like rotations, where C2-like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2-like axis in the simulated process, mostly because the C2-like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2-like symmetry of the twist-chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial-equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial-equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 15 (1994), S. 838-846 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
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  • 40
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    Journal of Computational Chemistry 15 (1994), S. 847-857 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water-induced dipoles computed at the 6-31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
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  • 41
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    Journal of Computational Chemistry 15 (1994), S. 866-874 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6-31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3) - O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
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  • 42
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    Journal of Computational Chemistry 15 (1994), S. 919-924 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are used to test the ability of various representations to reproduce bond energies. It is found that expansion in 1/R, where R is the bond length, is remarkably efficient and is consistently better than the usual R expansion. A quadratic form in 1/R is better than a cubic representation in R and sometimes even as good as a quartic representation. A cubic function in 1/R is, in all cases studied, better performing than the quartic expansion in R. It is also found that parameters derived with the 1/R expansion are defined more sharply than those derived for the R expansion. It is suggested that the 1/R expansion may be computationally more efficient for simulations of large biomolecules and for constructions of reactive force fields than the standard bond functions. © 1994 by John Wiley & Sons, Inc.
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  • 43
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    Journal of Computational Chemistry 15 (1994), S. 947-962 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article studies the backbone influence on the side chains of N-methyl N′-acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein φ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone φ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in φ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in φ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
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  • 44
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    Journal of Computational Chemistry 15 (1994), S. 1053-1063 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present potential energy surfaces for Rh—CO obtained from density functional theory for two electronic states of Rh—CO. We have performed local spin-density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom-atom potential for Rh—CO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard-Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of Rh—CO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is -184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠Rh—CO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is -60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with -205 kJ/mol for 2Σ+ and 0.253 nm with -199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠Rh—CO = 30°, with -63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
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  • 45
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    Journal of Computational Chemistry 15 (1994), S. 1105-1112 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
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  • 46
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    Journal of Computational Chemistry 15 (1994), S. 1437-1445 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6-31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.
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  • 47
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    Journal of Computational Chemistry 15 (1994), S. 1127-1138 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.
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  • 48
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    Journal of Computational Chemistry 15 (1994), S. 1176-1185 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 15 (1994), S. 1199-1216 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.
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  • 50
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    Journal of Computational Chemistry 15 (1994), S. 1217-1227 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson-Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric-high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
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  • 51
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method using molecular mechanics to calculate internal energies and the generalized Born/surface area (GB/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from ab initio quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2-Ethanediol, 2-hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the ab initio + MC method in aqueous solution. The GB/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized ab initio values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*//GB/SA predicted most stable conformer for the 1,2-ethandiol system in aqueous solution is in contrast with the ab initio + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*//GB/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in-solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. © 1994 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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  • 53
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 15 (1994), S. 28-43 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher-order multipole moments. The second is an acceleration of the calculations by the particle-particle and particle-mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1-1 kcal/mol, much smaller than the 30-kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
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  • 55
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    Journal of Computational Chemistry 15 (1994), S. 72-79 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We consider the application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard-Jones interaction potential. To accomplish this comparative study of canonical and noncanonical integrators, we computed thermodynamic and structural quantities. Our results indicate that noncanonical methods, with one exception, fail miserably to conserve energy and as a consequence give poor estimates of the other quantities. Also, higher-order canonical methods may offer an advantage over the Störmer/Verlet method. © 1994 by John Wiley & Sons, Inc.
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  • 56
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    Journal of Computational Chemistry 15 (1994), S. 105-123 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration-type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window-type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
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  • 57
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    Journal of Computational Chemistry 15 (1994), S. 149-154 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular dynamics (MD) and Monte Carlo (MC) free energy calculations, the choices of the thermodynamic paths from state a to state b affect the accuracy of the result and the efficiency of the programs. Most of the problems occur at the initial stages of growing in a new particle into a solvent. Based on statistical mechanical perturbation theory, an accurate and efficient direct calculation of inserting a small Lennard-Jones particle into solvent is derived. This eliminates the need for calculation of the initial stages of growing in a new particle by MD or MC simulation. Examples are given to show the utility of direct calculation. The recommended procedure is to use direct calculation for a small Lennard-Jones particle and then use MD or MC simulations to calculate the ΔG of changing the small Lennard-Jones particle into the target molecule. © 1994 by John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 15 (1994), S. 200-207 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 15 (1994), S. 233-240 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 15 (1994), S. 251-268 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
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  • 61
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    Journal of Computational Chemistry 15 (1994), S. 313-321 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Effective core potential (ECP) and full-electron (FE) calculations for MoS4-2, MoO4-2, and MoOCl4 compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo—L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo—L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 15 (1994), S. 346-350 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 15 (1994), S. 351-373 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 15 (1994), S. 405-423 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
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  • 65
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    Journal of Computational Chemistry 15 (1994), S. 433-445 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers - r(AAA) and r(AAG) - obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.
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  • 66
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 67
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    Journal of Computational Chemistry 15 (1994), S. 937-946 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low-energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D-CICADA, and results have been compared to those of the sequential version. D-CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 997-1012 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a novel algorithm of constrained, overdamped dynamics to study the long-time properties of peptides, proteins, and related molecules. The constraints are applied to an all-atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high-frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 103 times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.
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  • 69
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′-tetramethyl-p-diaminobenzene-chloranil complex, the stacking conformations are different from each other. The former prefers the half-stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 1321-1330 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
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  • 71
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    Journal of Computational Chemistry 15 (1994), S. 1-11 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well-established methods for locating transition structures. © 1994 by John Wiley & Sons, Inc.
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  • 72
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    Journal of Computational Chemistry 15 (1994), S. 44-53 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we describe a domain decomposition method for the efficient parallel computation of nonbonded forces and energies in condensed-phase molecular systems. This decomposition is based upon the monotonic logical grid (MLG) approach of Boris [J. Boris, J. Comp. Phys., 66, 1 (1986)] and yields an efficient, scalable algorithm for interparticle interaction computation on private-memory, single-instruction multiple-data (SIMD) parallel computers. We illustrate the application of this technique in a molecular dynamics kernel for rigid molecular solvents by simulating the structural and thermodynamic properties of water and methanol. The performance of this algorithm on the Thinking Machines' CM-2, private-memory SIMD computer, is demonstrated to be good compared to conventional vector/parallel supercomputers. However, as the fluid becomes less structured performance slightly degrades. © 1994 by John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 15 (1994), S. 80-89 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we develop a method to graphically display the flow of energy within molecules. An energy continuity equation is derived leading to a molecular energy flux vector field. Computation of the flux calls for the intramolecular potential, any external interactions, and the phase space trajectories of the molecular motion. The flux provides a means to display energy flow in still frames and as a tool to visualize hitherto undiscovered dynamic pathways in molecules. Examples are presented that show energy flow in three molecular systems and illustrate the point that depiction of energy flux patterns has increasing utility and meaning as one moves to larger molecules. Simple extensions to this work would also allow visualization of the flux of such quantities as linear and angular momentum. © 1994 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 15 (1994), S. 125-131 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To test the applicability of the WKB semiclassical approximation to correctly describe the tunneling frequencies and energy levels in asymmetric double wells, we have considered the cases where the asymmetry comes from the nondegeneracy of the two minima and when it comes from the asymmetry in the shape of the barrier between both minima. To do this, we compare the tunneling frequencies and energy levels obtained through the WKB method for symmetric and asymmetric cases with exact results obtained by a basis set procedure. Our results show that the semiclassical WKB approximation has to be used with caution for asymmetric double wells. © 1994 by John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 15 (1994), S. 183-189 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular O—H…O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics. © 1994 by John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 15 (1994), S. 227-232 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A recent gradient algorithm in nonlinear optimization uses a novel idea that avoids line searches. This so-called spectral gradient algorithm works well when the spectrum of the Hessian of the function to be minimized has a small range or is clustered. In this article, we find a general preconditioning method for this algorithm. The preconditioning method is applied to the stress function, which arises in many applications of distance geometry, from statistics to finding molecular conformations. The Hessian of stress is shown to have a nice block structure. This structure yields a preconditioner which decreases the amount of computation needed to minimize stress by the spectral gradient algorithm. © 1994 by John Wiley & Sons, Inc.
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  • 77
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    Journal of Computational Chemistry 15 (1994), S. 208-226 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Distribution Biased Monte Carlo (DBMC) sampling procedure is developed for the efficient generation of chain conformations in the oriented environment of lipid membranes and other liquid crystalline systems. Conformations of the sn-1 chain of dipalmitoyl phosphatidylcholine (DPPC) were generated by independently sampling torsion angles from continuous distributions in an orienting potential based on a Marcelja mean field; depending on the chain position, the convergence in the deuterium order parameters (SCD) was 100 to 3000 times more efficient with DBMC than with Brownian dynamics. Optimization using joint distribution and torsional potentials of mean force yielded a further threefold increase in sampling efficiency. Overall chain tilt was included using Euler angle rotations and a separate field strength for the anchor. A segmental DBMC procedure was used to generate a set of complete DPPC conformations with well-converged conformationally averaged SCD consistent with experimental values. These conformations show considerable flexibility, not only in the hydrocarbon tails, but additionally in both the glycerol and head-group portions of the lipid. An appendix compares DBMC with a number of other Monte Carlo and stochastic dynamics algorithms using the example of a bistable oscillator, and illustrates the tuning of parameters for optimal convergence. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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  • 78
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 79
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    Journal of Computational Chemistry 15 (1994), S. 241-248 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hyaluronic acid and its derivatives are absorbable polysaccharides which are used extensively in cosmetics and as biomaterials. Two possible mechanisms of degradation, involving an oxocarbenium ion and the corresponding radical cation, are examined by modeling of the saccharide ring and the effects of various ring substituents on the two possible mechanisms. © 1994 by John Wiley & Sons, Inc.
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  • 80
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    Journal of Computational Chemistry 15 (1994), S. 300-312 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite-state models to the backbones of globular proteins. It is demonstrated that a finite-state representation with a reasonably small number of states yields either a small root-mean-square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite-state and reduced-parameter approximations of protein backbone conformations. © 1994 by John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 15 (1994), S. 322-332 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Sets of XNC (X = Li, Na, and K) structures have been investigated using a variety of theoretical methods and basis sets. Two linear and a bridged structure correspond to an energy minimum for LiCN. For NaCN and KCN, the linear isocyanide is a minimum at most levels of theory but becomes a second-order stationary point when correlated levels and large basis sets are used. Two transition structures are involved in the interconversion of the bridged form and each linear isomer. The isomerization of the bridged minimum to the linear XCN involves a substantial barrier in each case, so that the satellite motion of the metal is facile at one end but not at the other. Calculations with large basis sets and with electron correlation, fourth-order Møller-Plesset theory for KNC, and quadratic configuration interaction [QCISD(T)] for LiNC and NaNC give qualitative and quantitative agreement with this experiment. The sodium and potassium cyanide prefer bridged forms, in contrast to the linear isocyanide LiNC. © 1994 by John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 15 (1994), S. 424-432 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Systematic MRD-CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet-singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO-3G results. On an absolute scale, the AM1/MRD-CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between -1.0 and 1.0 eV. The STO-3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ-correlation effects through second-order Epstein-Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.
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  • 83
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    Journal of Computational Chemistry 15 (1994), S. 385-394 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular geometry of 1-fluorosilatrane was optimized fully by restricted Hartree-Fock (HF) calculations using the 3-21G, 3-21G(d) and 6-31G(d) basis sets, with the aim of locating the positions of the local minima on the energy hypersurface. The optimized geometries were compared with available experimental (X-ray and ED) and semiempirical data. The ab initio calculations using polarized basis sets are in good agreement with those of previously reported semiempirical calculations, giving a slightly longer equilibrium Si—N distance (∼ 256 pm) in the case of the endo minimum. However, the exo minimum predicted by the semiempirical methods is not supported. There was no experimental evidence for the existence of this exo minimum, and the present ab initio calculations suggest that it is highly unstable. There is considerable disagreement among the experimental results in the C—N and C—C bond lengths in various silatranes, their differences being as large as 13 pm. The present calculations predict that these differences may appear because the silatrane skeleton is flexible with low-energy, large-amplitude internal motions which introduce considerable uncertainties into the position of ring carbon atoms. © 1994 by John Wiley & Sons, Inc.
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  • 84
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    Journal of Computational Chemistry 15 (1994), S. 446-454 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The cavity used to represent the solute/water interface in Miertus-Scrocco-Tomasi self-consistent reaction field (MST-SCRF) calculations of neutral molecules has been optimized by fitting to experimental data. The study is focused on the refinement of the van der Waals radii of polar and apolar hydrogens and of the van der Waals parameters used to compute the dispersion/repulsion contribution to the total free energy of hydration. When a scaling coefficient of 1.25 is used to build the solute cavity, comparison of 6-31G*/MST results with experimental data demonstrates that the optimum van der Waals radii for hydrogens are around 1.2 Å (apolar) and 0.9 Å (polar). The optimization of the solute cavity and the refinement of the van der Waals parameters lead to root mean square deviations in the computed free energy of hydration of only 0.9 kcal/mol for the 23 molecules considered in this study. © 1994 by John Wiley & Sons, Inc.
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  • 85
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    Journal of Computational Chemistry 15 (1994), S. 475-475 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 86
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    Journal of Computational Chemistry 15 (1994), S. 507-523 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast computer algorithm is presented for complete analytical calculation of van der Waals surfaces and volumes. Connolly's analytical algorithms, computing second- and third-order atomic spheres overlaps, are shown to give insufficient numerical approximations of the exact van der Waals surfaces and volumes. The presented algorithm computes overlaps of any order. Practical situations frequently involve six-order overlaps. Analytical computed surfaces and volumes of 63 chemicals are compared with Monte Carlo measured values. © 1994 by John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 15 (1994), S. 532-552 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the adaptation of the truncated Newton minimization package TNPACK for CHARMM and biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate-gradient technique for solving the Newton equations. The structure of the problem - sparsity of the Hessian - is exploited for preconditioning. Experience with the new version of TNPACK is presented on a series of molecular systems of biological and numerical interest: alanine dipeptide (N-methyl-alanyl-acetamide), a dimer of N-methyl-acetamide, deca-alanine, mellitin (26 residues), avian pancreatic polypeptide (36 residues), rubredoxin (52 residues), bovine pancreatic trypsin inhibitor (58 residues), a dimer of insulin (99 residues), and lysozyme (130 residues). Detailed comparisons among the minimization algorithms available in CHARMM, particularly those used for large-scale problems, are presented along with new mathematical developments in TNPACK. The new TNPACK version performs significantly better than ABNR, the most competitive minimizer in CHARMM, for all systems tested in terms of CPU time when curvature information (Hessian/vector product) is calculated by a finite-difference of gradients (the numeric option of TNPACK). The remaining derivative quantities are, however, evaluated analytically in TNPACK. The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10-8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations. © 1994 by John Wiley & Sons, Inc.
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  • 88
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    Journal of Computational Chemistry 15 (1994), S. 573-579 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The evaluation of gradient vectors of a general operator with one-index, double-one-index, or higher-order one-index transformed integrals is a key operation in multiconfiguration response theory calculations. We describe an integral-driven direct algorithm that carries out this operation efficiently without pretransforming the integrals. The use of this algorithm leads to a considerable reduction in disk space and timing. © 1994 by John Wiley & Sons, Inc.
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  • 89
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    Journal of Computational Chemistry 15 (1994), S. 580-587 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The formation of a charge-transfer complex between carbon dioxide and naphthalene was studied using a molecular modeling program, with the aim of studying the solubility of naphthalene in supercritical carbon dioxide. The orbitals involved in the formation of the complex were studied using MINDO/3 as the semi-empirical method. A solvent cage was constructed, and the maximum number of carbon dioxide molecules to surround naphthalene was found to be 20. The heat of interaction of the complex was obtained using MINDO/3. © 1994 by John Wiley & Sons, Inc.
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  • 90
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    Journal of Computational Chemistry 15 (1994), S. 653-661 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a general approach to the parametrization of linear combinations of Gaussian atomic orbitals, useful for atomic and molecular interactions. We use a Gaussian transform method and Gauss-Legendre quadratures to express hydrogenic atomic orbitals, with varying effective charges, in terms of Gaussian-type orbitals. This procedure provides well-defined rules for calculating exponent factors and combination coefficients of the linear combinations of Gaussians in problems where nuclear distances may vary over large ranges during interactions. © 1994 by John Wiley & Sons, Inc.
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  • 91
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    Journal of Computational Chemistry 15 (1994) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 92
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    Journal of Computational Chemistry 15 (1994), S. 684-703 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The inelastic neutron-scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low-frequency internal dynamics, 〈 200 cm-1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron-derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.
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  • 93
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    Journal of Computational Chemistry 15 (1994), S. 747-751 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New methods for the iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of a generalized eigenvalue problem are proposed. These methods use only multiplication of the A and B matrices on a vector. © 1994 by John Wiley & Sons, Inc.
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  • 94
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    Journal of Computational Chemistry 15 (1994) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 95
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    Journal of Computational Chemistry 15 (1994), S. 814-819 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program has recently been implemented with the aim of extending quasi-particle (QP) band structure calculations to polymers with larger unit cells. The theoretical background is briefly reviewed and the new algorithm described, which has been optimized for machines with vector processors. To illustrate the usefulness of this technique, calculations have been performed on polyparaphenylene (PPP) using a double-zeta basis set. The calculated QP band gap between the valence and conduction bands is 2.3 eV, which compares favorably with the experimental value of 2.8 eV. The self-consistent field (SCF) result with the same double-zeta basis set is 8.7 eV. © 1994 by John Wiley & Sons, Inc.
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  • 96
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    Journal of Computational Chemistry 15 (1994), S. 793-813 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A set of algorithms is presented which establish the topological identity of atoms, bonds, molecules, and ensembles of molecules from a basic connection table. The computationally inexpensive result is a fixed-length hash code which is suited for database applications and structure manipulation programs. The degree of differentiation between structural entities is adjusted easily for stereocenters, isotope labeling, atomic charges, and ionization locations or other properties. Special algorithms are presented which deal with problematic cases of uniform atomic environments. A number of practical applications demonstrate the usefulness of these hash codes. © 1994 by John Wiley & Sons, Inc.
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  • 97
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    Notes: Group theoretic methods are presented for the transformations of integrals and the evaluation of matrix elements encountered in multiconfigurational self-consistent field (MCSCF) and configuration interaction (CI) calculations. The method has the advantages of needing only to deal with a symmetry unique set of atomic orbitals (AO) integrals and transformation from unique atomic integrals to unique molecular integrals rather than with all of them. Hamiltonian matrix element is expressed by a linear combination of product terms of many-center unique integrals and geometric factors. The group symmetry localized orbitals as atomic and molecular orbitals are a key feature of this algorithm. The method provides an alternative to traditional method that requires a table of coupling coefficients for products of the irreducible representations of the molecular point group. Geometric factors effectively eliminate these coupling coefficients. The saving of time and space in integral computations and transformations is analyzed. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 917-917 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 99
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    Journal of Computational Chemistry 15 (1994), S. 893-898 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions with r122n exp( - βr122) factors have been used in variational calculations of the ground state of the helium atom. Additional correlation factors in the form of even powers of rij were introduced to the Gaussian functions with exponential correlation components by differentiating these functions with respect to the correlation exponent β. The algorithm of this method and its computational implementation is described. A number of calculations were performed for the ground state of helium atom to test the performance of the basis sets comparising different numbers of the Gaussians with the exp( - βr122) and r122 exp( - βr122) correlation factors. The numerical results indicate that including functions with r122 factors does not lead to improved results, contrary to what was anticipated initially. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1019-1040 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10-12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water-saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D-glucose and D-mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D-glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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