Rate constants for the reactions of OH radicals with dimethyl phosphonate [DMHP, (CH(3)O)(2)P(O)H] and dimethyl methylphosphonate [DMMP, (CH(3)O)(2)P(O)CH(3)] have been calculated by ab initio structural methods and semiclassical dynamics modeling and compared with experimental measurements over the temperature range 250-350 K. The structure and energetics of reactants and transition structures are determined for all hydrogen atom abstraction pathways that initiate the atmospheric oxidation mechanism. Structures are obtained at the CCSD/6-31++G** level of chemical theory, and the height of the activation barrier is determined by a variant of the G2MP2 method.
View Article and Find Full Text PDFIn this paper, we test the performance of the molecular truncation method of Mallik et al., which was originally applied at the semiempirical NDDO level, in ab initio MBPT methods. Pseudoatoms developed for the replacement of -OCH(3) and -OCH(2)CH(3) functional groups are used in optimizations of selected clusters, and the resulting geometries are compared to reference values taken from the full molecules.
View Article and Find Full Text PDFCavity complementation has been observed in many proteins, where an appropriate small molecule binds to a cavity-forming mutant. Here, the binding of compounds to the W191G cavity mutant of cytochrome c peroxidase is characterized by X-ray crystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, the W191G cavity does not bind neutral or hydrophobic compounds, but displays a strong specificity for heterocyclic cations, consistent with the role of the protein to stabilize a tryptophan radical at this site.
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