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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 82 (1985), S. 2002-2013 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using ab initio SCF molecular orbital techniques, the electric field gradients (efg's) at the oxygen and hydrogen nuclei were calculated for water clusters ranging from dimer to pentamer in an attempt to reproduce the shift in 17O and 2H nuclear quadrupole coupling constants (qcc's) that is observed on going from ice to vapor. For 2H, where the qcc shift is due mostly to the change in O–H bond length, excellent agreement with the experimental vapor → ice shift was obtained. For 17O, the change in the qcc is found to be mainly electronic in origin, effectively due to the polarization of the charge associated with the oxygen atom, and approximately 75% of the observed qcc shift was reproduced. On the basis of the calculations, estimates of the 17O and 2H qcc's in liquid water were made that are consistent with the values obtained from an analysis of the available NMR relaxation data, provided that librational motions are properly taken into account. We also present results of SCF calculations on water interacting with a Li+, Na+, or Cl− ion, indicating that the effect of a nearby ion on the 2H and 17O qcc's is similar to that produced by H bonding.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The electric field gradients (efg's) at the oxygen and hydrogen nuclei in CO,NO+, OH−, H2O, and CH2O, and at the chlorine, lithium, and hydrogen nuclei in HCl, LiCl, and FCl, calculated using ab initio quantum chemical methods, are reported. Using extended Gaussian basis sets, the efg's at the oxygen and chlorine nuclei were computed at the self-consistent field (SCF), singles and doubles configuration interaction [CI(SD)], and coupled pair functional (CPF) levels of theory as the expectation values of the efg operator and also as the energy derivatives of the appropriate perturbed Hamiltonian using the finite field method. The efg's at the hydrogen and lithium nuclei were computed as expectation values. Corrections due to zero point vibrational motions were also calculated. The effect of basis set incompleteness on the calculated efg's is discussed and, where possible, corrected for. The calculated efg's, together with the experimental nuclear quadrupole coupling constants, are used to estimate the 17O, 35Cl, and 2H nuclear quadrupole moments, and to test the quality of the correlated wave functions generated by the CI(SD) and CPF methods. The recommended values on the basis of the present calculations are −2.64±0.03, −8.2±0.2, and 0.278 fm2, respectively, for the 17O, 35Cl, and 2H nuclear quadrupole moments.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Electric field gradients (efg's) at the nitrogen nuclei in N2, NO+, NO, CN, and CN− and at the nitrogen and hydrogen nuclei in HCN, HNC, and NH3, calculated using ab initio quantum chemical methods, are reported. Employing extensive Gaussian basis sets, the efg's were computed at the self-consistent field (SCF), singles and doubles configuration interaction [CI(SD)], and coupled pair functional (CPF) levels of theory as the expectation values of the efg operator and also as the energy derivatives of the appropriate perturbed Hamiltonian using the finite field method. Corrections due to zero point vibrational motions were also calculated. The effect of basis set incompleteness on the calculated efg's, together with the experimental nuclear quadrupole coupling constants, are used to estimate the 14N and 2H nuclear quadrupole moments, and to test the quality of the correlated wave functions generated by the CI(SD) and CPF methods. The recommended values, on the basis of the present calculations, are 2.05±0.02 and 0.29±0.01 fm2, respectively, for the 14N and 2H quadrupole moments.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 89 (1985), S. 2151-2155 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 113 (1991), S. 8247-8256 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1573-4951
    Keywords: Molecular dynamics ; Thermodynamics ; Hydration ; Ligand-protein interactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of 8-methylpterins and 8-methyl-N5-deazapterins to dihydrofolate reductase (DHFR). Methyl-substitution at the 5, 6 and 7 positions in the N-heterocyclic ring gives rise to a variety of ring substituent patterns and biological activity: several of these methyl derivatives of the 8-methyl parent compounds (8-methylpterin and 8-methyl-N5-deazapterin) have been identified as substrates or inhibitors of vertebrate DHFR in previous work. The calculated free energy differences reveal that the methyl-substituted compounds are thermodynamically more stable than the primary compounds (8-methylpterin and 8-methyl-N5-deazapterin) when bound to the enzyme, due largely to hydrophobic hydration phenomena. Methyl substitution at the 5 and/or 7 positions in the 6-methyl-substituted compounds has only a small effect on the stability of ligand binding. Furthermore, repulsive interactions between the 6-methyl substituent and DHFR are minimal, suggesting that the 6-methyl position is optimal for binding. The results also show that similarly substituted 8-methylpterins and 8-methyl-N5-deazapterins have very similar affinities for binding to DHFR. The computer simulation predictions are in broad agreement with experimental data obtained from kinetic studies, i.e. 6,8-dimethylpterin is a more efficient substrate than 8-methylpterin and 6,8-dimethyl-N5-deazapterin is a better inhibitor than 8-methyl-N5-deazapterin.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 15 (1993), S. 426-435 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; free energy ; perturbation theory ; kinetic mechanism ; dissociation constants ; dihydrofolate reductase ; 8-methyl-pterins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism-based pterins, 8-methylpterin and 6,8-dimethylpterin, to dihydrofolate reductase (DHFR), with co-factor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8-dimethylpterin is thermodynamically more stable than DHFR.NADPH.8-methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8-dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH-dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8-dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8-methylpterin. The kinetic data suggest a value of 6.6 ± 0.2 for the pKa of the active site Glu-30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1-10 μM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8-methylpterin and 6,8-dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kcal/mol. © 1993 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 939-950 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition-state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon-Fletcher-Powell/Broyden-Fletcher-Goldfarb-Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable-metric GDIIS is usually equal or superior to static-metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually 〉40%) are also obtained when static-metric GDIIS is used to refine the geometry after the initial application of a transition-state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1496-1512 
    ISSN: 0192-8651
    Keywords: QM/MM ; solvation ; free energy ; hydrogen bonds ; force fields ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods and the TIP3P molecular mechanics model for liquid water is presented. The model was parameterized for each of the three molecular orbital methods using the aqueous solvation free energies of a wide range of neutral organic molecules, many of which are representative of amino acid side chains. The fit to the experimental solvation free energies was achieved by varying the radii in the van der Waals (vdW) terms for interactions between the solute, which was treated quantum mechanically, and the molecular mechanics (TIP3P) solvent molecules. It is assumed that the total free energy can be obtained as the sum of components derived from the electrostatic terms in the Hamiltonian plus a generally smaller “nonelectrostatic” term. The electrostatic contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques; the nonelectrostatic contributions were taken from the literature. It was found that the experimental free energies could be reproduced accurately (to within 1 kcal/mol) from the MD simulations, provided that the vdW parameter associated with hydrogen bonding (H bonding) was allowed to have different values depending on the QM method (AM1, MNDO, or PM3) and the type of functional group involved in the H bonding. Moreover, the radial distribution functions obtained from the MD simulations using such a parameterization scheme showed the expected H-bonded structures between the solute and molecules of the solvent. The solvent-induced dipole moments also compared favorably with the results of other QM/MM model calculations.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1496-1512, 1997
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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