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Transition-metal centers are the active sites for a broad variety of biological and inorganic chemical reactions. Notwithstanding this central importance, density-functional theory calculations based on generalized-gradient approximations often fail to describe energetics, multiplet structures, reaction barriers, and geometries around the active sites. We(More)
We present here a computational study of reactions at a model complex of the SyrB2 enzyme active site. SyrB2, which chlorinates L-threonine in the syringomycin biosynthetic pathway, belongs to a recently discovered class of alpha-ketoglutarate (alphaKG), non-heme Fe(II)-dependent halogenases that share many structural and chemical similarities with(More)
Enzymatic methyl transfer, catalyzed by catechol-O-methyltransferase (COMT), is investigated using binding isotope effects (BIEs), time-resolved fluorescence lifetimes, Stokes shifts, and extended graphics processing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches. The WT enzyme is compared with mutants at Tyr68, a conserved(More)
Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the(More)
Both first-principles molecular dynamics and theoretical X-ray absorption spectroscopy have been used to investigate the aqueous solvation of cations in 0.5 M MgCl(2), CaCl(2), and NaCl solutions. We focus here on the species-specific effects that Mg(2+), Ca(2+), and Na(+) have on the X-ray absorption spectrum of the respective solutions. For the divalent(More)
Catechol O-methyltransferase (COMT) is a SAM- and Mg2+-dependent methyltransferase that regulates neurotransmitters through methylation. Simulations and experiments have identified divergent catecholamine substrate orientations in the COMT active site: molecular dynamics simulations have favored a monodentate coordination of catecholate substrates to the(More)
We employ error-corrected density functional theory methods to map out the dependence of reactivity on substrate position for SyrB2, a member of a family of non-heme iron halogenases and hydroxylases that are only reactive toward amino acid substrates delivered via prosthetic phosphopantetheine arms. For the initial hydrogen abstraction step, the inherent(More)
An extensive redistribution of spin density in TBrPP-Co molecules adsorbed on a Cu(111) surface is investigated by monitoring Kondo resonances at different locations on single molecules. Remarkably, the width of the Kondo resonance is found to be much larger on the organic ligands than on the central cobalt atom-reflecting enhanced spin-electron(More)
We present a detailed analysis of the addition-elimination reaction pathways for the gas-phase conversion of molecular hydrogen and methane on FeO(+) to water and methanol, respectively, using first-principles calculations. These two reactions represent paradigmatic, challenging test cases for electronic structure approaches to transition-metal catalysis.(More)