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The gas-phase free energy differences between 20 phenols and their respective anions are estimated by CBS-QB3 method and the CPCM continuum solvation method is employed to calculate the free energy differences of solvation for the phenols and their anions. Absolute pKa calculations with solvated phase of optimized structures for the CPCM calculation yield standard deviations and root-mean-square errors of less than 0.4-pKa units, which is critical and of great importance.

Complete basis set and Gaussian-n models were combined with CPCM continuum solvation methods to gain accurate pKa calculations for caboxylic acids.

The I690C/G743C variant of a C-terminal fragment of the cobalamin-dependent methionine synthase (MetH) is prepared to lock the enzyme into the activation conformation without perturbing any of the residues in the vicinity of the active site. The S-adenosylmethionine substrate requirement has provided MetH a means to suppress deleterious side reactions involving the transiently formed cob(I)alamin ([Co.sup.1+]Cbl) supernucleophile.

The cobalamin-dependent methionine synthase (MetH) from Escherichia co/i is a modular enzyme that catalyzes a methyl group transfer from methyltetrahydrofolate to homocysteine via a methylcob(lll)alamin (MeCbl) intermediate, generating tetrahydrofolate and methionine (Met). Once every ∼2000 turnovers, the cobalamin cofactor is converted to the inactive cob(ll)alamin (Co2+Cbl) form, from which MeCbl has to be recovered for MetH to re-enter the catalytic cycle. A particularly puzzling aspect of this reactivation process is that it requires the reduction of the Co2+CbI species to cob(l)alamin (Co1+Cbl) by flavodoxin, a reaction that would appear to be endergonic on the basis of the corresponding reduction potentials. To explore how MetH may overcome this apparent thermodynamic challenge, we have prepared the 1690C/G743C variant of a C-terminal fragment of MetH (MetHCT) to lock the enzyme into the activation conformation without perturbing any of the residues in the vicinity of the active site. A detailed spectroscopic characterization of this species and the 1690C/G743C1Y1 1 39F MetHCT triple mutant reveals that the strategy employed by MetH to activate Co2+Cbl for Co2+ - Co1+ reduction likely involves (i) an axial ligand switch to generate a five-coordinate species with an axially coordinated water molecule and (ii) a significant lengthening, or perhaps complete rupture, of the Co-OH2 bond of the cofactor, thereby causing a large stabilization of the Co 3d2-based "redox-active" molecular orbital. The lengthening of the Co-OH2 bond is mediated by the Yl 139 active-site residue and becomes much more dramatic when the S-adenosylme- thionine substrate is present in the enzyme active site. This substrate requirement provides MetH a means to suppress deleterious side reactions involving the transiently formed Co1+Cbl "supernucleophile". [ABSTRACT FROM AUTHOR]

Determines the gas-phase free energy differences in phenols and its anions. Charge separation between the negatively charged oxygen and the ring system of phenoxide anions; Structures of the anions; Use of supramolecule-continuum approach in estimating the free energy of proton hydration.

Presents the accurate pK[sub a] calculations for carboxylic acids using Complete Basis Set and Gaussian-n models with CPDM continuum solvation methods. Thermodynamic cycle for proton dissociation; Calculation of the condensed-phase free energies; Conformers of the carboxylic acids; Experimental values for the gas-phase dissociation of acetic acid in thermodynamic cycle.

The naturally occurring G41S mutation to human (Hs) cytochrome (cyt) c enhances apoptotic activity based upon previous in vitro and in vivo studies, but the molecular mechanism underlying this enhancement remains unknown. Here, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and density functional theory (DFT) calculations have been used to identify the structural and electronic differences between wild-type (WT) and G4IS Hs cyt c. S41 is part of the hydrogen bonding network for propionate 7 of heme pyrrole ring A in the X-ray structure of G41S Hs cyt c and, compared to WT, G4IS Hs cyt c has increased spin density on pyrrole ring C and a faster electron self-exchange rate. DFT calculations illustrate an electronic mechanism where structural changes near ring A can result in electronic changes at ring C. Since ring C is part of the solvent-exposed protein surface, we propose that this heme electronic structure change may ultimately be responsible for the enhanced proapoptotic activity of G415 Hs cyt c. [ABSTRACT FROM AUTHOR]