Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator

Pedro E.M. Lopes, Guillaume Lamoureux, Alexander D. Mackerell

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63 Scopus citations


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 six-membered rings were based on benzene with nonbond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of five-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 were used for the determination of initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones (LJ) 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 LJ 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.

Original languageEnglish (US)
Pages (from-to)1821-1838
Number of pages18
JournalJournal of Computational Chemistry
Issue number12
StatePublished - Sep 2009
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics


  • Ab initio
  • Computational chemistry
  • Condensed phase
  • Crystal simulation
  • Empirical force field
  • Free energy of hydration
  • Heterocycles
  • Molecular modeling
  • Polarization
  • Quantum mechanics


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