Permutational isomerization of caged polycyclic oxyphosphoranes

Full Conformational Analyses of the Ultrafast Isomerization in Penta-coordinated Ru(S2C2(CF3)2)(CO)(PPh3)2: One Compound, Two Crystal Structures, Three CO Frequencies, 24 Stereoisomers, and 48 Transition States

The stereodynamics of an ultrafast (picosecond) isomerization in a penta-coordinated ruthenium complex, Ru(S₂C₂(CF₃)₂)(CO)(PPh₃)₂, were characterized by density functional theory (DFT). The ruthenium complex crystallizes in two almost-square pyramidal (SP) forms. The violet form has an apical PPh₃ ligand, the orange form has an apical CO ligand, and their solution displays three CO stretching frequencies. With 4 possible centers of chirality (1 ruthenium, 2 phosphines, and 1 dithiolate), there are 24 stereoisomers. DFT calculations of these stereoisomers show structures ranging from almost-perfect SP (τ₅ ≈ 0) to structures significantly distorted toward trigonal bipyramidal (TBP) (τ₅ ≈ 0.6). The stereoisomers fall neatly into three groups, with ν_CO ≈ 1960 cm^-1, 1940 cm^-1, and 1980 cm^-1. These isomers were found to interconvert over relatively small barriers via Ru-S bond twisting, CF₃ rotation, phenyl twisting, PPh₃ rotation, and, in some cases, by coupled motions. The composite energy surface for each CO frequency group shows that interconversions among the low-energy structures are possible via both the direct and indirect pathways, while the indirect pathway via isomers in the ν_CO ≈ 1980 cm^-1 group is more favorable, which is a result consistent with recent experimental work. This work provides the first complete mechanistic picture of the ultrafast isomerization of penta-coordinated, distorted SP, d⁶-transition-metal complexes.

Kinetic mechanism of the Mg2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases

The Mg(2+)-dependent adenylylation of the T4 DNA and RNA ligases was studied in the absence of a DNA substrate using transient optical absorbance and fluorescence spectroscopy. The concentrations of Mg(2+), ATP, and pyrophosphate were systematically varied, and the results led to the conclusion that the nucleotidyl transfer proceeds according to a two-metal ion mechanism. According to this mechanism, only the di-magnesium-coordinated form Mg(2)ATP(0) reacts with the enzyme forming the covalent complex E.AMP. The reverse reaction (ATP synthesis) occurs between the mono-magnesium-coordinated pyrophosphate form MgP(2)O(7)(2-) and the enzyme.MgAMP complex. The nucleotide binding rate decreases in the sequence ATP(4-) > MgATP(2-) > Mg(2)ATP(0), indicating that the formation of the non-covalent enzyme.nucleotide complex is driven by electrostatic interactions. T4 DNA ligase shows notably higher rates of ATP binding and of subsequent adenylylation compared with RNA ligase, in part because it decreases the K(d) of Mg(2+) for the enzyme-bound Mg(2)ATP(0) more than 10-fold. To elucidate the role of Mg(2+) in the nucleotidyl transfer catalyzed by T4 DNA and RNA ligases, we propose a transition state configuration, in which the catalytic Mg(2+) ion coordinates to both reacting nucleophiles: the lysyl moiety of the enzyme that forms the phosphoramidate bond and the alpha-beta-bridging oxygen of ATP.