Pedro Lopes | University of Illinois at Chicago (original) (raw)
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Papers by Pedro Lopes
PLoS Computational Biology, 2012
Journal of Computational Chemistry, 2009
The polarizable empirical CHARMM force field based on the classical Drude oscillator has been ext... more The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole and purine. Initial parameters for the 6-membered rings were based on benzene with non-bond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of 5-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions and interactions of rare gases with model compounds. The absolute values of the Lennard-Jones parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters and free energies of hydration. Final scaling of the polarizabilities from the gas phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities and isothermal compressibilities, including data as a function of temperature.
Journal of Chemical Theory and Computation, 2010
PLoS Computational Biology, 2012
Journal of Computational Chemistry, 2009
The polarizable empirical CHARMM force field based on the classical Drude oscillator has been ext... more The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole and purine. Initial parameters for the 6-membered rings were based on benzene with non-bond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of 5-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions and interactions of rare gases with model compounds. The absolute values of the Lennard-Jones parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters and free energies of hydration. Final scaling of the polarizabilities from the gas phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities and isothermal compressibilities, including data as a function of temperature.
Journal of Chemical Theory and Computation, 2010