Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene

Photolysis (λ \u3e 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively)

Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana

Array-based comparative genomic hybridization (Array-CGH) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs) are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM)

Coccolithophores as palaeoecological indicators for shifts of the ITCZ in the Cariaco Basin during the late Quaternary

Coccoliths were studied from the ODP Hole 1002C and core PL07-39PC in the Cariaco Basin. Increases in Emiliania huxleyi are synchronous with decreases of Gephyrocapsa oceanica and vice versa. A new index (GEX) based on the relative abundances of these two taxa is proposed, and correlates with various other proxies. It is shown that GEX can serve as upwelling proxy. This confirms that the Intertropical Convergence Zone shifted north during the Bølling/Allerød, south during the Younger Dryas and back north during the Preboreal. The upwelling proxy shows few discrepancies with the terrigenous record

A stable ketene-pyridine prereactive intermediate: Experimental and theoretical identifications of the C3O2... pyridine complex

structure and energy of the 1:1 pyridine/C3O2 complex have been investigated in solid argon matrixes using FTIR spectroscopy as well as ab initio and density functional theory (up to B3LYP/6-31 1SG(3df,2p)) calculations. Computationally, the complex may exist in a T-shaped form, T-Nu, Of either C-2v or C-s symmetry. The complex trapped in argon matrix is characterized by a large shift of the antisymmetric CCO stretching mode to lower frequency (Delta nu = 90 cm(-1)). The predicted frequency shifts for the C-2 nu structure Of the T-Nu complex are in good agreement with the observed vibrational frequency shifts. This complex is indicative of electrostatic interaction between the nitrogen atom of the pyridine molecule and the C-2 and C-4 atoms of the C3O2 moiety (intermolecular bond distance = 3.28 Angstrom). The agreement between calculated and experimental IR spectra together with the calculated structure suggests the presence of a prereactive intermediate of a nucleophilic addition reaction. No stable zwitterionic type structure was observed