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  • 1
    Digitale Medien
    Digitale Medien
    s.l. : American Chemical Society
    Journal of the American Chemical Society 113 (1991), S. 8247-8256 
    ISSN: 1520-5126
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie
    Materialart: Digitale Medien
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  • 2
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: 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.
    Materialart: Digitale Medien
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  • 3
    Digitale Medien
    Digitale Medien
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 82 (1985), S. 2002-2013 
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: 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.
    Materialart: Digitale Medien
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  • 4
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: 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.
    Materialart: Digitale Medien
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  • 5
    Digitale Medien
    Digitale Medien
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 89 (1985), S. 2151-2155 
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
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  • 6
    Digitale Medien
    Digitale Medien
    Springer
    Journal of computer aided molecular design 7 (1993), S. 535-555 
    ISSN: 1573-4951
    Schlagwort(e): Molecular dynamics ; Thermodynamics ; Hydration ; Ligand-protein interactions
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: 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.
    Materialart: Digitale Medien
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  • 7
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 704-718 
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: 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.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 8
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 939-950 
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: 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.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 9
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 977-988 
    ISSN: 0192-8651
    Schlagwort(e): quantum mechanical/molecular mechanical ; free energy ; hydride ion ; molecular dynamics ; catalysis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH3, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 977-988, 1998
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 10
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1598-1611 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Molecular dynamics (MD) simulation methods have been used to study the active site of the ternary complex formed between avian dihydrofolate reductase (DHFR), NADPH cofactor, and the inhibitor 8-methyl-N5-deazapterin in aqueous solution. Spherical shells of water molecules (initially at the bulk-solvent density) are used to solvate the active site and the surrounding protein surface. Two models for treating the effects of the neglected bulk solvent are then considered. The tethered water (TW) model is characterized by the use of harmonic restraining potentials to tether the water molecules to their initial (bulk solvent) positions; whereas, in the capped water (CW) model, water molecules are prevented from escaping from the solvent shell by the use of half-harmonic potentials, but otherwise their motions within the solvation shell are unrestrained. As measured by overall rms differences between coordinates, the distribution of solvent molecules in the active-site region, and the numbers of hydrogen bonds, the TW model compares favorably with the CW model but requires far fewer water molecules, i.e., relatively small solvent shells. The smaller shells of unrestrained water (CW model) gave rise to a distortion in the orientation of the side chain of the active-site residue Tyr-31, whereas no such distortion was apparent in the TW model or for the larger solvent shells in the CW model. A value for the force constant of 0.005 kcal/mol/Å2 for the tethering potential [Solmajer and Mehler, Int. J. Quant. Chem., 44, 291 (1992)] gave satisfactory results for DHFR, although we found that distance-dependent dielectric functions were unable to reproduce accurately the effects of the explicit water models. The free-energy change for the mutation of 8-methyl-N5-deazapterin to 8-methylpterin was computed using both nonsolvated and solvated models. The solvated models gave free energy differences about 1 kcal/mol lower than for nonsolvated models, but the differences between solvated models was much less than 1 kcal/mol. Overall, the calculated differences in thermodynamic stability of the deazapterin and pterin complexes are in fair agreement with experiment, i.e., a small binding differential is predicted. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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