Kinetic Destabilization Research Articles

Ab Initio calculations of the potential surfaces for rearrangement of methylenecyclopropane and 2,2-difluoromethylenecyclopropane. Why do the geminal fluorines have little effect on lowering the activation energy? †

(4/4)CASSCF and CASPT2 calculations with the 6-31G* basis set have been performed in order to understand the experimental observation that the geminal fluorines in 2,2-difluoromethylenecyclopropane (2) have only a small effect on lowering the activation energies for its degenerate and non-degenerate methylenecyclopropane rearrangements, relative to the activation energy for the rearrangement of the hydrocarbon (1). As expected from previous experimental and computational studies, the geminal fluorines are calculated to destabilize the three-membered ring in 2 thermodynamically. The small amount of kinetic destabilization of 2 is shown to be due to a nearly equal destabilization of the transition structures for its rearrangements. The high energies of the transition structures are attributed to the strong preference of a CF2 group for a pyramidal geometry. This preference is found to destabilize the transition structures both for forming a σ bond to the fluorinated carbon in the degenerate methylenecyclopropane rearrangement of 2 and for making a π bond to this carbon in the non-degenerate rearrangement of 2 to (difluoromethylene)cyclopropane (4).

Differential Effects of Vinblastine on Polymerization and Dynamics at Opposite Microtubule Ends

We have characterized the effects of vinblastine on the growing and shortening dynamics at opposite ends of individual bovine brain microtubules at steady state in vitro by video microscopy. Vinblastine exerted strikingly different effects on the dynamics and polymer mass at the plus and minus ends of microtubules. At concentrations between 0.1 and 0.4 microM, the drug strongly depolymerized microtubules at minus ends, whereas it did not significantly depolymerize microtubules at plus ends. Vinblastine stabilized plus ends by suppressing the rate and extent of growth and shortening, decreasing the catastrophe frequency, and increasing the rescue frequency. In contrast, vinblastine destabilized minus ends by increasing the catastrophe frequency and decreasing the rescue frequency, whereas it had no effect on the rate or extent of growth or shortening. Thus, vinblastine moderately increased the overall dynamicity at minus ends while strongly suppressing dynamicity at plus ends. Both the kinetic destabilization of microtubules at minus ends and the stabilization at plus ends may contribute to the altered function of mitotic spindle microtubules of cells blocked in mitosis by low concentrations of vinblastine.

Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilization of the minor groove hydration of d-(TTAA)2 versus d-(AATT)2 segments.

The residence times of the hydration water molecules near the base protons of d-(GTGGAATTCCAC)2 and d-(GTGGTTAACCAC)2 were investigated by nuclear magnetic resonance (NMR) spectroscopy. Nuclear Overhauser effects (NOE) were observed between base protons of the DNA and hydration water in NOESY and ROESY experiments. Large positive NOESY cross peaks observed between the resonances of the water and the adenine 2H protons of the central d-(AATT)2 segment in the duplex d-(GTGGAATTCCAC)2 indicate the presence of a 'spine of hydration' with water molecules exhibiting residence times on the DNA longer than 1 nanosecond. In contrast, no positive intermolecular NOESY cross peaks were detected in the d-(TTAA)2 segment of the duplex d-(GTGGTTAACCAC)2, indicating that no water molecules bound with similarly long residence times occur in the minor groove of this fragment. These results can be correlated with the larger width of the minor groove in d-(TTAA)2 segments as compared to that in d-(AATT)2 segments, as observed previously in single crystal structures of related oligonucleotide duplexes in B type conformation. The present experiments confirm earlier experimental results from single crystal studies and theoretical predictions that a 5'-dTA-3' step in the nucleotide sequence interrupts the spine of hydration in the minor groove.

Kinetic destabilization of the hydroperoxy flavin intermediate by site-directed modification of the reactive thiol in bacterial luciferase.

Bacterial luciferase catalyzes the formation of visible light, FMN, and a carboxylic acid from FMNH2, O2, and the corresponding aldehyde. The reactive cysteinyl residue at position 106 of the alpha subunit has been replaced by serine, alanine, and valine by site-directed mutagenesis (Baldwin, T. O., Chen L. H., Chlumsky, L. J., Devine, J. H., and Ziegler, M. M. (1989) J. Biolumin. Chemilumin. 4, 40-48) and the kinetics of the reaction catalyzed by each mutant protein measured by stopped-flow spectrophotometry at pH 7 and 25 degrees C. The time courses for the formation and decay of the various intermediates for the three alpha C106 mutants have been followed by monitoring the absorbance at 380 and 445 nm and the emission of visible light using n-decanal as the aldehyde substrate. The time courses for these events have been incorporated into a comprehensive kinetic model; 16 individual rate constants have been obtained for this model by numeric simulations of the time courses for the wild-type enzyme and for the three alpha C106 mutants. The mutants catalyzed the production of visible light demonstrating that the reactive thiol is not involved in the bioluminescence reaction. All three mutants have been found to catalyze the formation of the C4a-hydroperoxy flavin intermediate with rate constants equal to that of the wild-type enzyme. These results are incompatible with those reported by Xi et al. who have suggested that the major pathway for the oxidation of alpha C106V-bound FMNH2 does not involve the C4a-hydroperoxy flavin as an intermediate (Xi, L., Cho, K.-W., Herndon, M.E., and Tu, S.-C. (1990) J. Biol. Chem. 265, 4200-4203). The rates of decay of the C4a-hydroperoxy flavin intermediate with the mutant enzymes were found to be two orders of magnitude faster than that of the wild-type enzyme. Luciferase has been shown to be inhibited at high levels of aldehyde substrate when the enzyme is assayed by injecting FMNH2 into an aerobic mixture of enzyme and aldehyde. This aldehyde inhibition has been shown to occur by the formation of a dead-end enzyme-aldehyde complex which blocks the binding of FMNH2 to the enzyme; loss of activity is due to the rapid nonenzymatic decomposition of the reduced flavin with molecular oxygen.

Analysis of cyclotron harmonic emissions at the outer planets

The flyby missions of Voyagers 1 and 2 at Jupiter, Saturn and Uranus revealed intense waves above the electron gyrofrequency. Observation of waves at the upper hybrid frequency is often accompanied by power at adjacent electron Bernstein harmonics, and the relative power in these modes depends both on the density and temperature ratios of the cold background electron population and the hot magnetospheric electrons which drive the instability. A model of electron distributions which is consistent with observations is used for analysis of the excited waves, their dependence upon plasma parameters, and the time scales of the saturation processes. It is shown that in the presence of two-temperature electron distributions the linear excitation is due to a fluid-like coupling of two eigenmodes for perpendicular propagation and to kinetic destabilization of oblique modes. The dependence of linear growth rates on propagation angle is presented, along with results from particle simulations. A quasilinear diffusion time for relaxing the hot electron loss cone is calculated and compared with simulation results. This time scale is faster than for local saturation by heating the cold population, and also the convective amplification time scale, suggesting that the waves saturate at quasilinear levels, while being convectively localized to the equatorial regions of the outer planetary magnetospheres.

Contribution of nonbonded interactions to the kinetic destabilization of a Group 14 bicyclo[1.1.1]pentane

Synthesis of a bicyclo [1.1.1]pentastannane derivative, by two complementary routes, and its anomalous chemical and spectroscopic behavior, which further reveals how nonbonded interactions in synthetic derivatives of heavy-atom polycyclic compounds can influence another feature of theoretical interest, stability

Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA X dC mismatch site.

Deoxyadenosine-deoxycytidine pairing at symmetrically related dA X dC mismatch sites in the d(C1-G2-C3-G4-A5-A6-T6-T5-C4-A3-C2-G1) self-complementary duplex (henceforth called 12-mer AC) has been investigated by proton and phosphorus NMR studies in aqueous solution. We demonstrate that base pairing is maintained on either side of the mismatch site in the 12-mer AC duplex at low temperature. The proton chemical shifts and NOE measurements rule out models in which the H-2 proton of adenosine at the mismatch site is stacked over adjacent dG X dC base pairs. A comparison of the hydrogen-exchange kinetics in the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex (henceforth called 12-mer) with standard dG X dC base pairs at position 3 from either end with the 12-mer AC duplex, which contains dA X dC mismatches at these positions, demonstrates kinetic destabilization at dG X dC base pair 4 adjacent to the mismatch site and at dA X dT base pairs 5 and 6 far from this site. This contrasts with previous hydrogen-exchange studies on the 12-mer GT and 12-mer GA duplexes where the kinetic destabilization was localized to base pair 4, which is adjacent to the mispairing site. The melting temperature of the 12-mer AC duplex in 0.1 M phosphate is approximately 30 degrees C lower than the corresponding value for the 12-mer duplex.(ABSTRACT TRUNCATED AT 250 WORDS)