title: Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds.
abstract: A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software "parafreq". The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.
authors.affiliation: Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada.
authors.forename: Steven K
authors.initials: SK
authors.lastname: Burger
authors.affiliation: Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada.
authors.forename: Mike
authors.initials: M
authors.lastname: Lacasse
authors.affiliation: Center for Molecular Modeling, Ghent University, 903 Technologiepark, B-9050 Zwijnaarde, Belgium.
authors.forename: Toon
authors.initials: T
authors.lastname: Verstraelen
authors.affiliation: Department of Chemistry, University of Toronto, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6.
authors.forename: Joel
authors.initials: J
authors.lastname: Drewry
authors.affiliation: Department of Chemistry, University of Toronto, 3359 Mississauga Road North, Mississauga, Ontario, Canada L5L 1C6.
authors.forename: Patrick
authors.initials: P
authors.lastname: Gunning
authors.affiliation: Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Ayers