Efficient primer strand extension beyond oxadiazole carboxamide nucleobases

Two oxadiazole carboxamide deoxyribonucleoside analogues are described that can be incorporated and efficiently extended by Taq DNA polymerase. The primer strand extension beyond oxadiazole nucleoside analogues occurs at rates similar to the values observed for the canonical Watson-Crick base pairs irrespective of the template nucleobase. These distinctive chemical effects in DNA polymerase extensions are attributed to the smaller size and unique electronic properties of the oxadiazole nucleobase.     

Synthesis,spectroscopic studies,and x-ray crystallographic analysis of the organotin carbohydrate: 1,2∶3,4-di-O-isopropylidene-6-O-triphenylstannylmethyl-α-D-galactopyranose

The title organotin carbohydrate, C₃₁H₃₆O₆Sn, has been synthesized and its molecular structure has been determined in solution and in the solid state. NMR, infrared, mass and X-ray crystallographic techniques were used. The chiral molecules crystallize in the monoclinic space group P2₁ withZ=2. The triphenyltin and carbohydrate moieties are linked by a trans methylene-oxygen-methylene arrangement. The pyranosyl ring adopts a twist-boat conformation and the isopropylidene rings adopt different (half-chair and envelope) forms. Solution and solid-state conformations are similar as only three ¹³C shift values are greater than 2ppm; the ¹¹⁹Sn value is 12 ppm.     

Metal-containing ditopic receptors for molecular recognition of diammonium cations

Two new ditopic receptors for α,ω-alkanediyldiammonium cations based on a tetraazamacrocyclic (cyclidene) nickel(II) complex bearing two crown-ether residues were synthesized. The studies of the host-guest interaction between the receptors and a series of α,ω-diammonium salts by NMR titration in acetonitrile-d₃ showed that 1:1 complexes are formed with K_assoc∼10³-10⁵ M⁻¹. Receptor 1 with benzo-15-crown-5 arms showed substantial selectivity in binding of trimethylene- and tetramethylenediammonium dications, and 1-2 orders of magnitude weaker binding of shorter (C₂) or longer (C₅ and C₆) diammonium cations. Receptor 2 with benzo-18-crown-6 arms showed higher affinity to all studied diammonium cations, but the recognition of the length of α,ω-diammonium cations was less pronounced.     

Novel radial oligothienyl silanes

A series of thiophene-based homologues with a silicon core surrounded by mono-, bi-, terthiophene, and their derivatives with alkylsilyl linkages has been prepared using hydrosilylation and Stille coupling methods.     

Proton-induced supramolecular dimerization of aminomethylbenzo-15-crown-5 accompanied by a covalent dimerization of cyanoborohydride anion

Reductive amination of 4′-formyl[benzo-15-crown-5] with sodium cyanoborohydride in the NH₄Ac/MeOH medium followed by acid addition and extraction with CHCl₃ unexpectedly lead to the isolation of the salt (B15C5-CH₂-NH₃)⁺-(H₃BCNBH₂CN)⁻ with an unusual dicyanodiborohydride anion. The self-complementary 4′-ammoniomethyl[benzo-15-crown-5] cation was found to exist as a supramolecular dimer in the solid state, acetonitrile solution, and gas phase as revealed by X-ray crystallography, NMR and mass spectrometry, respectively.     

A simple procedure for the quantitative microdetermination of rhamnose

Summary A simple spectrophotometric procedure for microdetermination of rhamnose is described. It is based on breakdown of the sugar with sulphuric acid followed by treatment withp-hydroxydiphenyl. The coloured product is measured spectrophotometrically at 560 nm. A linear relationship exists between the amount of rhamnose (10-0g–) and the absorbance. The method is recommended for determination of rhamnose in samples containing rhamnose, different neutral sugars, amino-sugars, sugar alcohols, uronic acids, and muramic acid.

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Zusammenfassung Ein einfaches spektralphotometrisches Verfahren zur Mikrobestimmung von Rhamnose wurde beschrieben. Es beruht auf der Spaltung des Zuckers mit Schwefelsäure und nachfolgender Behandlung mit p-Hydroxydiphenyl. Das gefärbte Reaktionsprodukt wird spektralphotometrisch bei 560 nm gemessen. Die Extinktion steht mit der Rhamnosemenge in linearer Beziehung. Das Verfahren wird für die Rhamnosebestimmung in Proben empfohlen, die verschiedene Neutralzucker, Aminozucker, Zuckeralkohole, Uronsäuren und Muramsäure enthalten.

     

Time-resolved chemically induced dynamic nuclear polarization studies of structure and reactivity of methionine radical cations in aqueous solution as a function of pH

Using time-resolved chemically induced dynamic nuclear polarization (CIDNP) techniques, we have studied the mechanism of the photoreactions of triplet excited 4-carboxybenzophenone (CBP) with l-methionine (Met) and 3-(methylthio)propylamine (MTPA) in aqueous solution and the details of the formation of CIDNP at pH from 6.7 to 13.6. At a pH below the pKa of the nitrogen atom of Met, the CIDNP is strongly affected by degenerate electron exchange between the S-S cationic radical dimer and the zwitterionic form of Met with the rate constant kex = 3.4 x 10(8) s(-1) providing an exhaustive explanation of the pH dependence of steady-state CIDNP that was previously interpreted as a manifestation of fast interconversion among three different methionine radical species (Goez, M.; Rozwadowski, J. J. Phys. Chem. A 1998, 102, 7945-7953). By analyzing the polarization of different protons formed in geminate recombination as a function of the pH, we obtained the branching ratio between two reaction pathways for oxidative quenching of (T)CBP via electron transfer from the sulfur and nitrogen atoms of Met and MTPA. Nuclear spin-lattice relaxation times were determined in the dimeric cation radical of Met (T1,S = 8.5 micros). In the cyclic radical cation of MTPA with a three-electron two-center S-N bond, the estimated paramagnetic relaxation is comparatively slow for all protons. Fast deprotonation of the primary aminium radical cation of MTPA and Met in strongly basic solution takes place on the submicrosecond time scale leading to efficient formation of CIDNP in the neutral aminyl radical.     

Relative reactivity of peracids versus dioxiranes (DMDO and TFDO) in the epoxidation of alkenes. A combined experimental and theoretical analysis

Comparative analysis of the calculated gas-phase activation barriers (DeltaE++) for the epoxidation of ethylene with dimethyldioxirane (DMDO) and peroxyformic acid (PFA) [15.2 and 16.4 kcal/mol at QCISD(T)// QCISD/6-31+G(d,p)] and E-2-butene [14.3 and 13.2 kcal/mol at QCISD(T)/6-31G(d)//B3LYP/6-311+G(3df,2p)] suggests similar oxygen atom donor capacities for both oxidants. Competition experiments in CH(2)Cl(2) solvent reveal that DMDO reacts with cyclohexene much faster than peracetic acid/acetic acid under scrupulously dried conditions. The rate of DMDO epoxidation is catalyzed by acetic acid with a reduction in the classical activation barrier of 8 kcal/mol. In many cases, the observed increase in the rate for DMDO epoxidation in solution may be attributed to well-established solvent and hydrogen-bonding effects. This predicted epoxidative reactivity for DMDO is not consistent with what has generally been presumed for a highly strained cyclic peroxide. The strain energy (SE) of DMDO has been reassessed and its moderated value (about 11 kcal/mol) is now more consistent with its inherent gas-phase reactivity toward alkenes in the epoxidation reaction. The unusual thermodynamic stability of DMDO is largely a consequence of the combined geminal dimethyl- and dioxa-substitution effects and unusually strong C-H and C-CH(3) bonds. Methyl(trifluoromethyl)dioxirane (TFDO) exhibits much lower calculated activation barriers than DMDO in the epoxidation reaction (the average DeltaDeltaE++ values are about 7.5 kcal/mol). The rate increase relative to DMDO of approximately 10(5), while consistent with the higher strain energy for TFDO (SE approximately 19 kcal/mol) is attributed largely to the inductive effect of the CF(3) group. We have also examined the effect of alkene strain on the rate of epoxidation with PFA. The epoxidation barriers are only slightly higher for the strained alkenes cyclopropene (DeltaE++ = 14.5 kcal/mol) and cyclobutene (DeltaE++ = 13.7 kcal/mol) than for cyclopentene (DeltaE++ = 12.1 kcal/mol), reflecting the fact there is little relief of strain in the transition state. Alkenes strained by twist or pi-bond torsion do exhibit much lower activation barriers.     

Rapid detection of an anthrax biomarker by surface-enhanced Raman spectroscopy

A rapid detection protocol suitable for use by first-responders to detect anthrax spores using a low-cost, battery-powered, portable Raman spectrometer has been developed. Bacillus subtilis spores, harmless simulants for Bacillus anthracis, were studied using surface-enhanced Raman spectroscopy (SERS) on silver film over nanosphere (AgFON) substrates. Calcium dipicolinate (CaDPA), a biomarker for bacillus spores, was efficiently extracted by sonication in nitric acid and rapidly detected by SERS. AgFON surfaces optimized for 750 nm laser excitation have been fabricated and characterized by UV-vis diffuse reflectance spectroscopy and SERS. The SERS signal from extracted CaDPA was measured over the spore concentration range of 10(-14)-10(-12) M to determine the saturation binding capacity of the AgFON surface and to calculate the adsorption constant (Kspore=1.7 x 10(13) M(-1)). At present, an 11 min procedure is capable of achieving a limit of detection (LOD) of approximately 2.6 x 10(3) spores, below the anthrax infectious dose of 10(4) spores. The data presented herein also demonstrate that the shelf life of prefabricated AgFON substrates can be as long as 40 days prior to use. Finally, these sensing capabilities have been successfully transitioned from a laboratory spectrometer to a field-portable instrument. Using this technology, 10(4) bacillus spores were detected with a 5 s data acquisition period on a 1 month old AgFON substrate. The speed and sensitivity of this SERS sensor indicate that this technology can be used as a viable option for the field analysis of potentially harmful environmental samples.