Density functional study of reactions of phenoxides with polycarbonate

Density functional calculations with simulated annealing have been used to study the reactions of chains of bisphenol A polycarbonate (BPA-PC) with sodium phenoxide (NaOPh), diphenyl carbonate (DPC), and tetraphenylphosphonium phenoxide (PPh4OPh). These calculations extend our work on the reactions of LiOPh, NaOPh, and phenol with the cyclic tetramer of BPA-PC. We study, in particular, chain growth catalyzed by NaOPh and PPh4OH. The energy barriers for reactions with PPh4OPh are somewhat larger than those involving LiOPh and NaOPh, but they are significantly lower than those involving phenol (HOPh), due in part to the collective rearrangement of phenyl groups in the reacting molecules. We discuss in the Appendix the bonds between alkali metal atoms (Na in the present calculations) and other atoms (here oxygen) that are analogous to the more familiar "hydrogen bonds".

Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

Species distribution and coordination of uranyl chloro complexes in acetonitrile

The complex formation of the uranyl ion, UO22+, with chloride ions in acetonitrile has been investigated by factor analysis of UV-vis absorption and U L-3 edge EXAFS (extended X-ray absorption fine structure) spectra. As a function of increasing [Cl-]/[UO22+] ratio, the five monomeric species [UO2(H2O)(5)](2+), [UO2Cl(H2O)(2)(MeCN)(2)](+), [UO2Cl2(H2O)(MeCN)(2)], [UO2Cl3(MeCN)(2)](-), and [UO2Cl4](2-) have been observed. The distances determined in the first coordination sphere are: U-O-ax = 1.77 angstrom, U-O-H2O = 2.43 angstrom, U-N-MeCN = 2.53 angstrom, and U-Cl = 2.68 angstrom. A crystalline material has been obtained from the intermediate solution with the [Cl-]/[UO22+] ratio of similar to 2, where [UO2Cl2(H2O)(MeCN)(2)] is the dominating species. The crystal structure analysis of this material revealed a tetrameric complex, [(UO2)(4)(mu(2)-Cl)(4)(mu(3)-O)(2)(H2O)(2)(CH3CN)(4)]center dot(CH3CN). The crystal data are: monoclinic, space group P2(1)/n, a 10.6388(5) angstrom, b = 14.8441(5) angstrom, c = 10.8521(5) angstrom, beta = 109.164(5)degrees, and Z = 2. The U(VI) coordination of the solution species [UO2Cl2(H2O)(MeCN)(2)] changes during the crystallization by replacing one MeCN molecule with a bridging mu(3)-O atom in the tetramer.

A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes.

The extreme 3'-ends of human telomeres consist of 150–250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang–ligand complexes.

Dimerisation of cyclooctene using Grubbs' catalysts

The dimerisation of cyclooctene (COE) to 1,9-cyclohexadecadiene, a molecule of interest to the fragrance industry, has been achieved using ruthenium catalysts in organic solvents with significantly better selectivities (47-74%) and yields (39-60%) than previously reported (34% and 30%, respectively). Grubbs' first and second generation catalysts, the Hoveyda-Grubbs' catalyst and a phosphonium alkylidene catalyst were tested in a range of organic solvents and ionic liquids (ILs), including 1:1 IL/dichloromethane mixtures and biphasic IL + pentane systems. The best results (74% selectivity, 60% yield) were obtained using Grubbs' first generation catalyst in 1,2-dichloroethane. The formation of trimer, tetramer and other higher molecular mass products were found to be favoured at low catalyst loadings (0.77 mM). Studies of metathesis reactions using 1,9-cyclohexadecadiene as substrate indicated that the monomer-dimer and monomer-trimer reactions are faster than the dimer-dimer reaction. The use of IL media allowed for the recyclability of the catalyst, although a drop in the yield of dimer generally occurred after the first run. Heterogeneized catalysts, where the IL-catalyst system was immobilised onto silica, resulted in fast reactions leading to poor yields of dimer. (C) 2011 Elsevier B.V. All rights reserved.