Dipyrrylmetheneboron Difluorides as Labels in Two-Photon Excited Fluorometry. Part II–Nucleic Acid Hybridization Assays

Five two-photon excitable dipyrrylmetheneboron difluoride labels (dipyrrylmethene-BF₂ labels) with fluorescence emission maximum between 530 and 590 nm, and a frequently used rhodamine label, TAMRA, were conjugated to aminomodified oligonucleotides. The performance of the labeled oligonucleotides was studied in a separation-free nucleic acid hybridization assay using ArcDia^™ TPX bioaffinity assay technology. The results show that oligonucleotide conjugates of dipyrrylmethene-BF₂ labels provide higher two-photon excited fluorescence yield and better assay sensitivity than corresponding TAMRA conjugate. The effect of conjugation on photophysical properties of the labels and performance of the labeled oligonucleotides in separation-free hybridization assay is discussed.     

Insights into the Pamamycin Biosynthesis

Pamamycins are macrodiolides of polyketide origin with antibacterial activities. Their biosynthesis has been proposed to utilize succinate as a building block. However, the mechanism of succinate incorporation into a polyketide was unclear. Here, we report identification of a pamamycin biosynthesis gene cluster by aligning genomes of two pamamycin‐producing strains. This unique cluster contains polyketide synthase (PKS) genes encoding seven discrete ketosynthase (KS) enzymes and one acyl‐carrier protein (ACP)‐encoding gene. A cosmid containing the entire set of genes required for pamamycin biosynthesis was successfully expressed in a heterologous host. Genetic and biochemical studies allowed complete delineation of pamamycin biosynthesis. The pathway proceeds through 3‐oxoadipyl‐CoA, a key intermediate in the primary metabolism of the degradation of aromatic compounds. 3‐Oxoadipyl‐CoA could be used as an extender unit in polyketide assembly to facilitate the incorporation of succinate.     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

Synthesis and NMR characterization of the cis and trans isomers of [Pt(II)(N9-adeH)2(pz)2] and X-ray crystallography of the trans isomer

The reaction of tetrapyrazine Pt(II) with adenine under basic conditions yielded two products both disubstituted by adenine and bound in all cases to the N-9 nitrogen of adenine. Crystals amenable to X-crystallographic analysis were obtained for one product which was consequently identified as trans-[Pt(II)(N9-adeH)2(pz)2](NO3)(4).H2O. The other product, though, was identified as the cis isomer based on extensive and comparative NMR structural studies whereby the two compounds were examined as both neutral and tetraprotonated species in solution. The major product of the reaction was unexpectedly the cis isomer, thus obtained in contrast to the trans effect, and the reason for this result is speculated on. Computational calculations using DFT at the B3LYP/TZVP-MARI-J level of theory provided the head-to-tail conformer as the overwhelmingly more stable species over the head-to-head conformer for both compounds whilst the trans product was found to be more stable than the cis. Thus the reaction does not follow a thermodynamic course and rather is kinetically controlled in concert with the speculated mode of reaction.     

LC–MS Analysis of the Essential Oils of Achillea millefolium and Achillea crithmifolia

The chemical composition of the hydro-distilled essential oils of Achillea millefolium and Achillea crithmifolia was analyzed by GC, GC–MS, ¹³C NMR and high resolution LC–MS. For the first time, the use of the combination of different chromatographic and spectral methods, primarily the advantage of LC-Orbitrap over standard methods, enabled the detection of azulenes and their progenitors, in minute quantities, in previously believed proazulene free Achillea taxon (A. crithmifolia). Furthermore, the LC-Orbitrap hyphenated method provided the means for detection of these and related non-volatile (GC-injector compared to water steam distillation) metabolites up to know unreported as essential oil constituents.     

Hot-electron-driven enhancement of spin-lattice coupling in Gd and Tb 4f ferromagnets observed by femtosecond x-ray magnetic circular dichroism

Femtosecond x-ray magnetic circular dichroism was used to study the time-dependent magnetic moment of 4f electrons in the ferromagnets Gd and Tb, which are known for their different spin-lattice coupling. We observe a two-step demagnetization with an ultrafast demagnetization time of 750 fs identical for both systems and slower times which differ sizeably with 40 ps for Gd and 8 ps for Tb. We conclude that spin-lattice coupling in the electronically excited state is enhanced up to 50 times compared to equilibrium.     

Complete assignment of the 1H and 13C NMR spectra of antimicrobial 4‐arylamino‐ 3‐nitrocoumarin derivatives

Herein, we describe the synthesis and complete assignment of the ¹H and ¹³C NMR chemical shifts of a series of antimicrobial 4‐arylamino‐3‐nitrocoumarin derivatives based on a combination of ¹H and ¹³C NMR, ¹H‐¹H‐COSY, NOESY, HSQC and HMBC experiments. Conformational effects upon the chemical shifts of the coumarin moiety arising from the anisotropy of the aryl side group are briefly discussed. This study provides the first complete and fully assigned NMR data for this important group of antimicrobial compounds and bridges the gap existing in the literature with regard to NMR structural data for 4‐arylamino‐3‐nitrocoumarins. Copyright © 2010 John Wiley & Sons, Ltd.