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  • 1
    Electronic Resource
    Electronic Resource
    Ab initio quantum chemical studies of electric field gradients in the hydrogen bonded molecular nitrogen-hydrogen fluoride and molecular nitrogen-hydrogen chloride complexes (1985)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 89 (1985), S. 2151-2155 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100257a005
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  • 2
    Electronic Resource
    Electronic Resource
    The prediction of nuclear quadrupole moments from ab initio quantum chemical studies on small molecules. I. The electric field gradients at the 14N and 2H nuclei in N2, NO, NO+, CN, CN−, HCN, HNC, and NH3 (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 6908-6917 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.452390
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  • 3
    Electronic Resource
    Electronic Resource
    The prediction of nuclear quadrupole moments from ab initio quantum chemical studies on small molecules. II. The electric field gradients at the 17O, 35Cl, and 2H nuclei in CO, NO+, OH−, H2O, CH2O, HCl, LiCl, and FCl (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 416-423 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.453586
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  • 4
    Electronic Resource
    Electronic Resource
    The effect of intermolecular interactions on the 2H and 17O quadrupole coupling constants in ice and liquid water (1985)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 82 (1985), S. 2002-2013 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.448384
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  • 5
    Electronic Resource
    Electronic Resource
    Solvent effects in active-site molecular dynamics simulations on the binding of 8-methyl-N5-deazapterin and 8-methylpterin to dihydrofolate reductase (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1598-1611 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 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.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.2
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  • 6
    Electronic Resource
    Electronic Resource
    Coupled semiempirical molecular orbital and molecular mechanics model (QM/MM) for organic molecules in aqueous solution (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1496-1512 
    Details
    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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  • 7
    Electronic Resource
    Electronic Resource
    Computational strategies for the optimization of equilibrium geometries and transition-state structures at the semiempirical level (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 939-950 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540100712
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 977-988 
    Details
    ISSN: 0192-8651
    Keywords: quantum mechanical/molecular mechanical ; free energy ; hydride ion ; molecular dynamics ; catalysis ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH3, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 977-988, 1998
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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