title: Ab initio parameterization of YFF1, a universal force field for drug-design applications.
abstract: The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds.
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada. ayakovenko@bcgsc.ca
authors.forename: Olexandr Ya
authors.initials: OY
authors.lastname: Yakovenko
authors.forename: Yvonne Y
authors.initials: YY
authors.lastname: Li
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Oliferenko
authors.forename: Ganna M
authors.initials: GM
authors.lastname: Vashchenko
authors.forename: Volodymyr G
authors.initials: VG
authors.lastname: Bdzhola
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D000465:Algorithms; D002412:Cations / Q000737:chemistry; D003198:Computer Simulation; D015195:Drug Design; D008958:Models, Molecular; D015203:Reproducibility of Results
chemical_list: D002412:Cations