DNA polymerase-mediated DNA synthesis on a TNA template

TNA, or threose nucleic acid, is capable of Watson-Crick base pairing with DNA, RNA, and TNA; coupled with its chemical simplicity, this suggests that TNA is a possible progenitor of RNA. As an initial step toward developing the molecular tools necessary to investigate the functional capabilities of TNA by in vitro selection, we have screened a variety of DNA polymerases for activity on a TNA template. We report that despite having a repeating unit that is one atom shorter than that of DNA, several polymerases showed surprisingly good ability to copy limited stretches of TNA.     

Homeopathic ligand-free palladium as a catalyst in the heck reaction. A comparison with a palladacycle

[reaction: see text] Ligand-free Pd(OAc)(2) can be used as a catalyst in the Heck reaction of aryl bromides as long as the amount of catalyst is kept between 0.01 and 0.1 mol %. At higher concentrations palladium black forms and the reaction stops. The actual catalyst is monomeric. Palladacycles merely serve as a source of ligand-free palladium in Heck reactions of aryl bromides.     

Influence of nano-structure on electrolytic properties in CeO2 based system

Doped ceria (CeO₂) compounds are fluorite type oxides that show oxygen ionic conductivity higher than yttria stabilized zirconia, in oxidizing atmosphere. In order to improve the conductivity, the effective index was suggested to maximize the oxygen ionic conductivity in doped CeO₂ based oxides. In addition, the true microstructure of doped CeO₂ was observed at atomic scale for conclusion of conduction mechanism. Doped CeO₂ had small domains (10-50 nm) with ordered structure in a grain. It is found that the electrolytic properties strongly depended on the nano-structural feature at atomic scale in doped CeO₂ electrolyte. This revised version was published online in August 2006 with corrections to the Cover Date.     

Synthesis and characterization of the new 22-π aromatic furan-containing macrocycle, “ozaphyrin”

The new 22-π, aromatic “pentaplanar” macrocycle, ozaphyrin ( 6 ), has been synthesized by a McMurry coupling of 5,5′-diformyl-4,4′-dipropyl-2,2′-bipyrrole ( 1 ) with 2,5-bis(5-formyl-4-propyl-2-pyrrolyl)furan ( 5 ). This synthetic pathway to ozaphyrin and its characterization by ¹H nmr spectroscopy, uv-visible spectroscopy, cyclic voltammetry, and X-ray crystallography are described. The structure consists of layers of planar, staggered macrocycles stacked perpendicular to the α-axis. Ozaphyrin crystallizes with four formula units in the monoclinic space group C⁵_2h-P2₁/n in a cell of dimensions a = 10.481(7) Å, b = 17.353(17) Å, c = 18.726(12) Å, and β = 102.84(5)° (108 K). The structure has been refined on F² (5171 unique reflections, 411 variables) to R_w(F_o²) = 0.165. The conventional agreement index R(F) is 0.074 for the 3289 reflections have F_o²>2o(F_o²).     

Elektronentransfer und Ionenpaar-Bildung. 40. Mitteilung. Einkristall-Struktur von Bis(Natrium-1,1′-Biphenyl-2-thiolat-Diglyme): Ein Zwischenprodukt der reduktiven Ringöffnung von Dibenzothiophen

Electron Transfer and Ion Pair Formation Single Crystal Structure of Bis(sodium 1,1′-biphenyl-2-thiolate-diglyme): An Intermediate in the Reductive Ring Opening of Dibenzothiophene On Na-metal reduction of dibenzothiophene, the five-membered sulfur ring opens to form a colorless 1,1′-biphenyl-2-thiolate sodium salt, which, according to its single-crystal structure determination, is a dimer containing a four-membered, twice diglyme-solvated ring (diglyme···Na^⊕?SR)₂. Additional measurements provide the following information: cyclic voltammetry in aprotic MeCN solution shows one quasi-reversible electron transfer at E = ?2.58 V. The dibenzothiophene radical anion can be generated in aprotic THF solution at a K mirror and characterized by an 81-line ESR spectrum and its simulation. This blue species is also the first UV/VIS detectable one before the solution changes via green (due to blue + yellow color mixing) to yellow, yielding across an isosbestic point a second and diamagnetic compound. All of the above results suggest a consecutive two-electron reduction followed by an intersystem protonation, M + (e^?) → M^.? (blue) + (e^?) → (M^??, yellow?) + (H^⊕) → MH^? (colorless), to yield the crystallized and structurally characterized reaction intermediate. The diglyme-solvated sodium-salt dimer provides a basis for a quantum-chemical discussion of some facets of the most likely microscopic reduction pathway.     

Effect of glutaraldehyde on the activity of some DNA restriction endonucleases

The effect of the bifunctional crosslinking reagent glutaraldehyde on the activity of the restriction enzymes Bam HI,Hind III, EcoRI, and Tthlll I was investigated. The four enzymes exhibited differential sensitivity to inactivation. Tthlll I was the most sensitive, with activity losses occurring at levels of 0.0025% and above.Hind III was the most stable of the four and remained fully active at concentrations as high as 0.075%. Addition of BSA to incubation mixtures generally had a stabilizing effect. Implications of these results for the design of glutaraldehyde-based methods for the immobilization of restriction endonucleases are discussed.     

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

Contrasting behavior in azide pyrolyses: an investigation of the thermal decompositions of methyl azidoformate, ethyl azidoformate and 2-azido-N, N-dimethylacetamide by ultraviolet photoelectron spectroscopy and matrix isolation infrared spectroscopy

The thermal decompositions of methyl azidoformate (N3COOMe), ethyl azidoformate (N3COOEt) and 2-azido-N,N-dimethylacetamide (N3CH2CONMe2) have been studied by matrix isolation infrared spectroscopy and real-time ultraviolet photoelectron spectroscopy. N2 appears as an initial pyrolysis product in all systems, and the principal interest lies in the fate of the accompanying organic fragment. For methyl azidoformate, four accompanying products were observed: HNCO, H2CO, CH2NH and CO2, and these are believed to arise as a result of two competing decomposition routes of a four-membered cyclic intermediate. Ethyl azidoformate pyrolysis yields four corresponding products: HNCO, MeCHO, MeCHNH and CO2, together with the five-membered-ring compound 2-oxazolidone. In contrast, the initial pyrolysis of 2-azido-N,N-dimethyl acetamide, yields the novel imine intermediate Me2NCOCH=NH, which subsequently decomposes into dimethyl formamide (HCONMe2), CO, Me2NH and HCN. This intermediate was detected by matrix isolation IR spectroscopy, and its identity confirmed both by a molecular orbital calculation of its IR spectrum, and by the temperature dependence and distribution of products in the PES and IR studies. Mechanisms are proposed for the formation and decomposition of all the products observed in these three systems, based on the experimental evidence and the results of supporting molecular orbital calculations.     

Studies on the synthesis of (+/-)-stenine: a combined intramolecular [4 + 2]-cycloaddition/rearrangement cascade

Several cyclic 2-(methylthio)-5-amidofurans containing tethered unsaturation were prepared via the reaction of dimethyl(methylthio)sulfonium tetrafluoroborate (DMSTF) with beta-alkoxy-gamma-dithiane lactams. Thermolysis of these furans resulted in an intramolecular Diels-Alder reaction (IMDAF). The resulting oxa-bridge cycloadducts underwent a subsequent 1,2-methylthio shift to form tricyclic lactams in high yield. Furan 9, annealed to an azepine ring, underwent the IMDAF reaction at or below room temperature. Conformational effects imposed by the placement of a carbonyl group within the tether, combined with a rotational bias about the C(2)-N bond, enhances the rate of the IMDAF reaction of the seven-ring system so that it occurs readily at 25 degrees C. The feasibility of using the cascade sequence in the context of a total synthesis of the Stemona alkaloid (+/-)-stenine was explored. The eventual synthesis of (+/-)-stenine was carried out by an intramolecular Diels-Alder reaction of a 2-amido-5-methylthio-substituted furan containing a trans-pent-3-enoic acid methyl ester side chain in order to create the desired azepinoindole skeleton. This was followed by a series of reductions to set the syn-anti stereochemical relationship at the incipient ring fusion sites present in stenine. All six stereocenters at the azepinoindole core were derived in high stereoselectivity from the functionality present in the rearranged cycloadduct 10. Compound 10 was converted to stenine in 11 additional steps via a sequence that features a Crabtree's-catalyst directed hydrogenation, iodolactonization, and a Keck allylation.     

Cu3(mu-S)2]3+ clusters supported by N-donor ligands: progress toward a synthetic model of the catalytic site of nitrous oxide reductase

By treating Cu(I) complexes of neutral, bidentate N-donor ligands with S8, clusters with novel delocalized mixed-valence [Cu3(mu-S)2]3+ cores have been isolated. X-ray crystal structures and UV-vis and resonance Raman spectral features of these clusters reveal similarities to the tetracopper-sulfide "CuZ" site in nitrous oxide reductase. A delocalized S = 1 ground state for the mixed-valent CuIIICu2II cores is supported by the observation of high symmetry in the X-ray structures and 10-line hyperfine features arising from coupling to three equivalent Cu ions in EPR spectra obtained at room temperature (shown) and 10 K. The delocalization we observe contrasts with the localization reported previously for a [Cu3(mu-O)2]3+ analogue (Root, D. E.; Henson, M. J.; Machonkin, T.; Mukherjee, P.; Stack, T. D. P.; Solomon, E. I. J. Am. Chem. Soc. 1998, 120, 4982), which we rationalized through DFT calculations.