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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 5 (1999), S. 271-280 
    ISSN: 0948-5023
    Keywords: Melatonin ; Conformation ; Solvation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The conformational space of melatonin, as defined by dihedral angles representing different orientations of the carboxamido ethyl side chain, was calculated in vacuum and aqueous solution, using the AM1 semiempirical methodology, and the AM1-SM2.2 solvation model, respectively. The effects of conformation and aqueous solvation on several molecular properties typically used as descriptors in structure-activity relationship studies, such as Mulliken charges and the HOMO-LUMO gap, were considered. In the case of the charges on the O(3) and N(4) atoms, the effects of conformation were shown to be larger than those due to structural changes, while the charge on O(16) was greatly affected by structural and very little by conformational changes. Based on the computed values for this charge in analogs with different binding affinities, we suggest that the electrostatic features of the 5-methoxy moiety do not modulate binding affinity. Taken together, our results suggest that conformational and solvation effects should be considered in order to obtain realistic structure-activity relationships of the melatonin system.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 7059-7061 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Hill determinant method is shown to be useful in obtaining the eigenvalues of central-field systems with potentials that can be expanded in the Taylor series. Some model potentials for diatomic molecules are considered as illustrative examples.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 7201-7212 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Multiconfigurational floating Gaussian electronic wave functions are obtained for a variety of 2-electron atoms and for H2. These correlated wave functions are unusual in that they are constructed without taking excitations from a reference configuration. The description of electron correlation, the degree to which the proper ground state symmetry is attained, and the behavior of wave functions obtained by simulated annealing as a function of nuclear position are analyzed for two types of basis functions, product Gaussians and a second type of basis function that explicitly includes electron correlation. This work is aimed toward applications in mixed quantum/classical condensed phase simulations. Several recent studies have used simulated annealing to build floating Gaussian electronic wave functions in condensed phase or cluster simulations. We analyze the ability of the simulated annealing method to follow the optimum, or near optimum wave functions as nuclear positions move.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 7187-7200 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Born–Oppenheimer electronic surfaces for NaArn clusters are calculated using simulated annealing with a floating Gaussian basis set. The electronic energy levels are obtained during a molecular dynamics simulation of nuclear motion. Classical dynamics is used to search for local minima of the cluster potential energy surface. Results are presented for NaArn, n=1, 2, 3, 4, and for two large clusters, NaAr20 and NaAr24. Predictions of vertical transition energies of the cluster solvated sodium atom are given. The blueshifted transition frequencies for NaAr20 and NaAr24, clusters in which the metal atom is densely surrounded by rare gas solvent, are comparable to the largest sodium blueshifts observed in argon matrix spectra.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 117 (2002), S. 2718-2725 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A hybrid quantum-classical computational algorithm, which couples a density functional Hamiltonian to a classical bath, is applied to investigate symmetry breaking and the vibrational spectrum of [NO3]− in aqueous clusters. The nitrate ion was modeled using density functional theory with a Gaussian basis set; two different force fields for the classical bath were investigated: the TIP4P-FQ fluctuating charge and the TIP4P mean-field potentials. The choice of basis sets, functionals, and force field parameters has been validated by performing calculations on small complexes [NO3(H2O)n]− (n=1,2) at 0 K. We have found different asymmetrical configurations, mostly of Cs symmetry, with characteristic lifetimes in the picosecond range in a molecular dynamics (MD) simulation of [NO3 (H2O)124]− using the TIP4P potential. The vibrational density of states (DOS), computed by calculating the Fourier transform of the velocity autocorrelation function, shows two distinctive peaks corresponding to the antisymmetric N–O stretching (around 1500 cm−1) for each configuration, in contrast with the degenerate peak observed in the isolated solute. The DOS corresponding to the whole simulation, in which several configurations were visited, is similar to the broad band observed experimentally in aqueous solution. The structural and DOS results obtained for a TIP4P simulation of [NO3]− solvated with 256 water molecules do not differ significantly from those obtained with the smaller cluster, confirming that the main features of solvation are already present in the smaller system. In order to assess the influence of solvent polarization, we have performed a hybrid simulation employing the fluctuating charge TIP4P-FQ water potential. We obtain similar results to those obtained using the mean-field potential, except that residence times of each asymmetric configuration are larger than in the TIP4P case. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 5653-5660 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 6560-6568 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Acid ionization in aprotic media is studied using molecular dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as 30 molecules. For smaller clusters or for large ion pair separations cluster finite-size effects come into play in a significant fashion. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 9039-9047 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Energetics, structural features, polarity, and melting transitions in water clusters containing up to eight molecules were studied using ab initio methods and empirical force field models. Our quantum approach was based on density functional theory performed at the generalized gradient approximation level. For the specific case of (H2O)6, we selected five conformers of similar energy with different geometries and dipolar moments. For these cases, the cyclic arrangement was found to be the only nonpolar aggregate. For (H2O)8, the most stable structures corresponded to nonpolar, cubic-like, D2d and S4 conformers. Higher energy aggregates exhibit a large spectrum in their polarities. The static polarizability was found to be proportional to the size of the aggregates and presents a weak dependence with the number of hydrogen bonds. In order to examine the influence of thermal fluctuations on the aggregates, we have performed a series of classical molecular dynamics experiments from low temperature up to the melting transition using two different effective pseudopotentials: the TIP4P and MCY models. Minimum energy structures for both classical potentials were found to reproduce reasonably well the results obtained using ab initio methods. Isomerization and phase transitions were monitored by following changes in dipole moments, number of hydrogen bonds and Lindemann's parameter. For (H2O)6 and (H2O)8, the melting transitions were found at Tm(approximate)50 and 160 K, respectively; for both aggregates, we observed premelting transitions between well differentiated conformers as well. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 96 (1992), S. 5325-5331 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 7977-7991 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Absorption spectra of a sodium atom chromophore clustered with four or six argon atoms are calculated as a function of temperature. Certain spectral features are sensitive to isomerization and phase transitions, particularly the peak which arises from transitions to the middle of the three sodium 3P levels distorted by the cluster environment. Nonlocal pseudopotentials for the sodium core and argon solvent are used to reduce the electronic problem to that of one valence electron. Ground and excited Born–Oppenheimer states of the sodium chromophore are obtained during a molecular dynamics simulation via simulated annealing. Implications of our results for more complicated experiments are also discussed.
    Type of Medium: Electronic Resource
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