title: Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.
abstract: Benchmark calculations of proton affinities and gas-phase basicities of molecules most relevant to biological phosphoryl transfer reactions are presented and compared with available experimental results. The accuracy of proton affinity and gas-phase basicity results obtained from several multi-level model chemistries (CBS-QB3, G3B3, and G3MP2B3) and density-functional quantum models (PBE0, B1B95, and B3LYP) are assessed and compared. From these data, a set of empirical bond enthalpy, entropy, and free energy corrections are introduced that considerably improve the accuracy and predictive capability of the methods. These corrections are applied to the prediction of proton affinity and gas-phase basicity values of important biological phosphates and phosphoranes for which experimental data does not currently exist. Comparison is made with results from semiempirical quantum models that are commonly employed in hybrid quantum mechanical/molecular mechanical simulations. Data suggest that the design of improved semiempirical quantum models with increased accuracy for relative proton affinity values is necessary to obtain quantitative accuracy for phosphoryl transfer reactions in solution, enzymes, and ribozymes.
authors.affiliation: Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0431, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Range
authors.forename: Demian
authors.initials: D
authors.lastname: Riccardi
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
authors.forename: Marcus
authors.initials: M
authors.lastname: Elstner
authors.forename: Darrin M
authors.initials: DM
authors.lastname: York
mesh_terms: D000465:Algorithms; D019985:Benchmarking; D001665:Binding Sites; D001692:Biological Transport; D001704:Biopolymers / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D004735:Energy Transfer; D008954:Models, Biological; D008956:Models, Chemical; D044367:Phase Transition; D010710:Phosphates / Q000737:chemistry* / Q000378:metabolism; D010766:Phosphorylation; D011522:Protons; D016337:RNA, Catalytic / Q000032:analysis / Q000737:chemistry*; D012984:Software; D012986:Software Validation
chemical_list: D001704:Biopolymers; D010710:Phosphates; D011522:Protons; D016337:RNA, Catalytic