Human telomere sequence DNA in water-free and high-viscosity solvents: g-quadruplex folding governed by kramers rate theory

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.     

Manganese detection in marine sediments: anodic vs. cathodic stripping voltammetry

Three different electroanalytical techniques for the detection of manganese in marine sediments are evaluated. The anodic stripping voltammetry of manganese at an in situ bismuth-film-modified boron-doped diamond electrode and cathodic stripping voltammetry at a carbon paste electrode are shown to lack the required sensitivity and reproducibility whereas cathodic stripping voltammetry at a bare boron-doped diamond electrode is shown to be reliable and selective with a limit of detection, from applying a 60 s accumulation period of 7.4 × 10⁻⁷ M and a sensitivity of 0.24 A M⁻¹. The method was used to evaluate the manganese content of marine sediments taken from Šibenik, Croatia.     

Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins

The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.     

经Opuntia dilenii haw植物提取液绿色合成制备的纳米铝酸锌的催化性质(英文)

Various nanosized zinc aluminate(ZnAl2O4) samples were prepared by a conventional and a mi- crowave method both with and without using Opuntia dilenii haw plant extract,and were charac- terized by X-ray diffraction(XRD),Fourier transform infrared spectroscopy(FT-IR),high resolution scanning electron microscopy(HRSEM),energy dispersion scanning(EDX),temperature dependent conductance measurements, thermoelectric power measurements, ultraviolet-visible (UV-Vis) diffuse reflectance spectroscopy,and photoluminescence spectroscopy.The formation of a pure ZnAl2O4 phase was confirmed by XRD and FT-IR.A change in morphology from nanosized plates to nanosized sheets with,respectively,the conventional and microwave heating methods was clearly shown by HRSEM.UV-Vis diffusion reflectance spectroscopy measured the band gaps of ZnAl2O4 nanosized plates and nanosized sheets as 3.5 and 3.9 eV,respectively.The synthesized ZnAl2O4 was single crystalline and has three photoluminescence emissions at 482,528,and 540 nm.ZnAl2O4 nanosized sheets prepared by the microwave method showed higher catalytic activity for the oxida- tion of benzyl alcohol(85% conversion) than ZnAl2O4 nanosized plates prepared by the convention- al method(60% conversion).     

Investigation of steric and electronic effects in the copper-catalysed asymmetric oxidation of sulfides

Steric and electronic effects in the copper-catalysed asymmetric oxidation of aryl benzyl, aryl alkyl and alkyl benzyl sulfides have been investigated. The presence of an aryl group directly attached to the sulfur is essential to afford sulfoxides with high enantioselectivities, with up to 97% ee for 2-naphthyl benzyl sulfoxide, the highest enantioselectivity achieved to date for copper-catalysed asymmetric sulfoxidation. In contrast, the benzyl substituent can be replaced by sterically comparable groups with no effect on enantioselectivity. Copper-mediated oxidation of substituted aryl benzyl sulfides display modest steric and electronic effects resulting in comparable or lower enantioselectivities to those obtained with the unsubstituted benzyl phenyl sulfide.     

Unusual Structure,Fluxionality, and Reaction Mechanism of Carbonyl Hydrosilylation by Silyl Hydride Complex [(ArN)Mo(H)(SiH2Ph)(PMe3)3]

The reactions of bis(borohydride) complexes [(RN?)Mo(BH₄)₂(PMe₃)₂] ( 4 : R=2,6‐Me₂C₆H₃; 5 : R=2,6‐iPr₂C₆H₃) with hydrosilanes afford new silyl hydride derivatives [(RN?)Mo(H)(SiR′₃)(PMe₃)₃] ( 3 : R=Ar, R′₃=H₂Ph; 8 : R=Ar′, R′₃=H₂Ph; 9 : R=Ar, R′₃=(OEt)₃; 10 : R=Ar, R′₃=HMePh). These compounds can also be conveniently prepared by reacting [(RN?)Mo(H)(Cl)(PMe₃)₃] with one equivalent of LiBH₄ in the presence of a silane. Complex 3 undergoes intramolecular and intermolecular phosphine exchange, as well as exchange between the silyl ligand and the free silane. Kinetic and DFT studies show that the intermolecular phosphine exchange occurs through the predissociation of a PMe₃ group, which, surprisingly, is facilitated by the silane. The intramolecular exchange proceeds through a new non‐Bailar‐twist pathway. The silyl/silane exchange proceeds through an unusual Mo^VI intermediate, [(ArN?)Mo(H)₂(SiH₂Ph)₂(PMe₃)₂] ( 19 ). Complex 3 was found to be the catalyst of a variety of hydrosilylation reactions of carbonyl compounds (aldehydes and ketones) and nitriles, as well as of silane alcoholysis. Stoichiometric mechanistic studies of the hydrosilylation of acetone, supported by DFT calculations, suggest the operation of an unexpected mechanism, in that the silyl ligand of compound 3 plays an unusual role as a spectator ligand. The addition of acetone to compound 3 leads to the formation of [trans‐(ArN)Mo(OiPr)(SiH₂Ph)(PMe₃)₂] ( 18 ). This latter species does not undergo the elimination of a Si? O group (which corresponds to the conventional Ojima′s mechanism of hydrosilylation). Rather, complex 18 undergoes unusual reversible β‐CH activation of the isopropoxy ligand. In the hydrosilylation of benzaldehyde, the reaction proceeds through the formation of a new intermediate bis(benzaldehyde) adduct, [(ArN?)Mo(η²‐PhC(O)H)₂(PMe₃)], which reacts further with hydrosilane through a η¹‐silane complex, as studied by DFT calculations.     

The influence of the liquid crystalline core geometry on the mesogenicity of novel chiral 2-(4-substituted-phenoxy)propanonitriles

Abstract

The synthesis and characterization of seven novel (R)-2-(4-substituted-phenoxy)propanonitriles are described. The propanonitriles were prepared to evaluate their potential use as thermochromics and ferroelectric dopants, as well as to determine their twist sense properties. The materials exhibit smectic and chiral nematic phases of high thermal stability; the mesogenic behaviour of the nitriles is directly related to the type of two-ring core unit employed. The effects of the different molecular geometries and polarizabilities of the liquid crystalline cores on mesophase stability are discussed, particularly in relation to other members of this series. The chiral nematic phase of the propanonitriles is assigned as having a left-handed twist sense from contact preparation studies, and this is in agreement with rules relating absolute configuration and molecular structure to helical twist sense.     

Probes for narcotic receptor mediated phenomena. Part 31: Synthesis of rac-(3R,6aS,11aS)-2-methyl-1,3,4,5,6,11a-hexahydro-2H-3,6a-methanobenzofuro[2,3-c]azocine-10-ol, and azocine-8-ol, the ortho-c and the para-c oxide-bridged phenylmorphan isomers

Two of the 12 possible oxide-bridged phenylmorphans, were synthesized, rac-(3R,6aS,11aS)-2-methyl-1,3,4,5,6,11a-hexahydro-2H-3,6a-methanobenzofuro[2,3-c]azocine-10-ol (7) (the ortho-c compound), and rac-(3R,6aS,11aS)-2-methyl-1,3,4,5,6,11a-hexahydro-2H-3,6a-methanobenzofuro[2,3-c]azocine-8-ol (8) (the para-c compound). Single-crystal X-ray diffraction studies indicated that the dihedral angle between the least squares planes through the phenyl ring and the atoms C₁, C_11a, C₁₂, and C₃ in the piperidine ring in both 7·CHCl₃ and 8·HBr was 6.9°. The C₁₂-C_6a-C_6b-C_10a torsion angle was found to be 139.3° for both compounds. The angular relationship between the phenolic ring and the piperidine ring in phenylmorphans that interact with specific opioid receptors as agonists or antagonists is of considerable theoretical interest.     

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

Summary Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.