Stereoselective template-directed C-glycosidation. Synthesis of 5-membered oxygen heterocycles via cation-mediated intramolecular cyclization reactions

Construction of 5-membered oxygen heterocycles by intramolecular template-directed C-glycosidation is described. Alkylation of thioglycoside 5 with enone 6 followed by enol etherification gave cyclization substrates 8. Compound 8a underwent silver(I) trifluoromethanesulfonate-mediated ring-closure to give a 1.7:1 mixture of 9 and 9β; isomer 8s gave an 8.5:1 ratio. Some derivatization reactions of the bicyclic products are described.     

Low-magnesium, <Emphasis Type="Italic">trans</Emphasis>-cleavage activity by type III,tertiary stabilized hammerhead ribozymes with stem 1 discontinuities

Background  

Low concentrations of free magnesium in the intracellular environment can present critical limitations for hammerhead ribozymes, especially for those that are designed for intermolecular (trans) cleavage of a host or pathogen RNA. Tertiary stabilizing motifs (TSM's) from natural and artificial ribozymes with a "type I" topology have been exploited to stabilize trans-cleaving hammerheads. Ribozymes with "type II" or "type III" topologies might seem incompatible with conversion to trans-cleavage designs, because opening the loop at the end of stem 1 or stem 2 to accommodate substrate binding is expected to disrupt the TSM and eliminate tertiary stabilization.     

Iminic N-bound iminophosphorano versus nitrilic n-bound iminophosphorano Os(IV) complexes: a new double derivatization of the nitrido ligand

The reactions between trans-[Os(IV)(tpy)(Cl)(2)(NCN)] (1) and PPh(3) and between trans-[Os(IV)(tpy)(Cl)(2)(NPPh(3))](+) (2) and CN(-) provide new examples of double derivatization of the nitrido ligand in an Os(VI)-nitrido complex (Os(VI)N). The nitrilic N-bound product from the first reaction, trans-[Os(II)(tpy)(Cl)(2)(NCNPPh(3))] (3), is the coordination isomer of the first iminic N-bound product from the second reaction, trans-[Os(II)(tpy)(Cl)(2)(N(CN)(PPh(3)))] (4). In CH(3)CN at 45 degrees C, 4 undergoes isomerrization to 3 followed by solvolysis and release of (N-cyano)iminophosphorane, NCNPPh(3). These reactions demonstrate new double derivatization reactions of the nitrido ligand in Os(VI)N with its implied synthetic utility.     

Measurement of PCDDs, PCDFs, and non-ortho-PCBs by comprehensive two-dimensional gas chromatography-isotope dilution time-of-flight mass spectrometry (GC x GC-IDTOFMS)

Comprehensive two-dimensional gas chromatography with isotope-dilution time-of-flight mass spectrometry (GC × GC-IDTOFMS) was used to measure polychlorinated dibenzo-p-dioxin (PCDD), polychlorinated dibenzofuran (PCDF), and coplanar polychlorinated biphenyl (cPCB) concentrations in ash, sediment, vegetation, and fish samples. The GC × GC capability was achieved by using a quad jet, dual stage, thermal modulator. Zone compression of the GC peaks from modulation resulted in a significant increase of the signal intensity over classical GC-IDTOFMS. The GC × GC column set used an Rtx-Dioxin 2 phase as the first dimension (¹D) and an Rtx-500 as the second dimension (²D). The chromatographic separation of the 17 PCDD/Fs and the 4 cPCBs was attained in ¹D except for 2,3,7,8-TCDD and CB126 for which deconvoluted ion currents (DIC) were required to be reported separately. The Rtx-500 phase separated the bulk matrix interfering compounds from the target analytes in ²D. The instrumental limit of detection (iLODs) was 0.5 pg for 2,3,7,8-TCDD. The calibration curves showed good correlation coefficients for all the compounds investigated in the concentration range of 0.5–200 pg. GC × GC-IDTOFMS results compared favorably to those from conventional isotope-dilution one-dimensional gas chromatography-high resolution mass spectrometry (GC-IDHRMS). The comprehensive mass analysis of the TOFMS further permitted the identification of other contaminants of concern in the samples.     

Analysis of rabbit tear proteins by high-pressure liquid chromatography/electrospray ionization mass spectrometry

The aim of this study was to develop a fast and reliable analytical procedure for the display of the protein components of tears that can be used to differentiate the status of the ocular surface. Using this new procedure, we analyzed the tear protein components following a corneal wound in the rabbit. Calibrated 10-microL glass, fire-polished capillary micropipettes were used to collect tears from New Zealand White rabbits prior to and daily for 9 days following a unilateral 6-mm diameter centrally placed anterior keratectomy. Tear proteins were eluted by a reversed-phase high-performance liquid chromatography (RP-HPLC) column and the tear protein profile was monitored by electrospray ionization (ESI) mass spectrometry positive total ion current (TIC) chromatography. Tear proteins were reliably separated into 17 peaks, each of which contained one or a number of protein components. The molecular weight of each protein component was determined by on-line ESI. Major tear protein components, lactoferrin, lysozyme (minimally detectable in rabbit tears), albumin, lipocalin, lipophilin and beta2-microglobulin, were tentatively identified by this method. Based on the mass spectrometric data, beta2-microglobulin was found to be glycosylated with N-acetylhexosamine. ESI-positive TIC chromatograms and mass spectra revealed comparative differences in the tear protein spectra after corneal wounding. One day after wounding, rabbit lysozyme with a molecular weight of 14,717 Da was found to be 8-fold higher in the tears of wounded eyes when compared with tears from unwounded eyes. It dropped back to normal 3 days after wounding. The expression of an unidentified tear protein with the molecular weight of 16,060 Da was also elevated after corneal wounding and returned to normal level by day 5. In this study, LC/ESI-MS was developed as a fast, reproducible and simple method for the identification and analysis of many of the protein components of the tears. Importantly, this technique also allows quantification of each component resolved in the chromatogram. This method is very suitable for mapping peptides and proteins (<80 kDa) in tears.     

Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

Density functionals for inorganometallic and organometallic chemistry

We present a database of 21 bond dissociation energies for breaking metal-ligand bonds. The molecules in the metal-ligand bond energy database are AgH, CoH, CoO+, CoOH+, CrCH3+, CuOH2+, FeH, Fe(CO)5, FeO, FeS, LiCl, LiO, MgO, MnCH3NiCH2+, Ni(CO)4, RhC, VCO+, VO, and VS. We have also created databases of metal-ligand bond lengths and atomic ionization potentials. The molecules used for bond lengths are AgH, BeO, CoH, CoO+, FeH, FeO, FeS, LiCl, LiO, MgO, RhC, VO, and VS and the ionization potentials are for the following atoms: C, Co, Cr, Cu, Ni, O, and V. The data were chosen based on their diversity and expected reliability, and they are used along with three previously developed databases (transition metal dimer bond energies and bond lengths and main-group molecular atomization energies) for assessing the accuracy of several kinds of density functionals. In particular, we report tests for 42 previously defined functionals: 2 local spin density approximation (LSDA) functionals, 14 generalized gradient approximation (GGA) methods, 13 hybrid GGA methods, 7 meta GGA methods, and 8 hybrid meta GGA methods. In addition to these functionals, we also examine the effectiveness of scaling the correlation energy by testing 13 functionals with scaled or no gradient-corrected correlation energy, and we find that functionals of this kind are more accurate for metal-metal and metal-ligand bonds than any of the functionals already in the literature. We also present a readjusted GGA and a hybrid GGA with parameters adjusted for metals. When we consider these 57 functionals for metal-ligand and metal-metal bond energies simultaneously with main-group atomization energies, atomic ionization potentials, and bond lengths we find that the most accurate functional is G96LYP, followed closely by MPWLYP1M (new in this article), XLYP, BLYP, and MOHLYP (also new in this article). Four of these five functionals have no Hartree-Fock exchange, and the other has only 5%. As a byproduct of this work we introduce a convenient diagnostic, called the B1 diagnostic, for ascertaining the multireference character in a bond.     

Comparison by capillary SFC and SFC-MS of soxhlet and supercritical fluid extraction of hamster feces

Components of hamster feces ranging from low molecular weight fatty acids through the expected range of triglycerides have been eluted in a single SFC run with simultaneous pressure and temperature programming. Temperature programming from 140°C to 240°C was required to provide optimum conditions for separation of the fatty acids and to move the elution region of the sterol esters away from that of the triglycerides. Data from chemical ionization and electron impact mass spectrometry of compounds separated by SFC were used to confirm identities suggested by retention measurements and to provide tentative identities of unknown compounds. SFC with flame ionization detection was used to compare Soxhlet extraction, off-line supercritical fluid extraction (SFE), and on-line SFE of the feces. Although samples obtained by Soxhlet extraction and SFE produced very similar chromatograms, SFE required far less time and consumed much smaller quantities of organic solvent.