New aspects of the fragmentation mechanisms of unmodified and methylphosphonate-modified oligonucleotides

A set of pentanucleotides was investigated by electrospray tandem mass spectrometry with the focus on the fragmentation mechanism. Results reveal new aspects of the fragmentation mechanism of modified and unmodified oligonucleotides and demonstrate the influence of the nucleobases on the decomposition of oligonucleotides. Adenine-rich oligonucleotides fragment easily resulting in abundant peaks corresponding to the DNA-typical a-B- and w-ions. On the other hand, thymine was found to have a stabilizing effect, which is reflected by the preferred formation of the w(4)-ions and the relatively low abundance of shorter w-ions upon dissociation of pentanucleotides. Data from investigation of the formation of w(4)-ions support a beta-elimination mechanism. Results obtained by investigation of oligonucleotides with an abasic site confirm this mechanism, which is independent of nucleobase loss. Experiments with methylphosphonate oligonucleotides show a remarkable change in the fragmentation pattern due to the modification. It was found that charges are located on the nucleobases and initiate the fragmentation mechanism. The stability of the oligonucleotide is reduced and no a-B-fragment ions are formed wherever there is a methylphosphonate group within the backbone. This fact also demonstrates that fragmentation is locally controlled.     

Iodochlorination of silyl- and germylphenylacetylenes

Reactions of Si- and Ge-substituted alkynes with KICl₂ were investigated. (1-Germatranyl)-phenylacetylenes and (triphenylsilyl)phenylacetylene gave Z-iodochloroalkenes with chlorine and phenyl groups attached to the same carbon atom. Adduct structures were confirmed by X-ray diffraction studies. © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:169–174, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20001     

Covalent hydration energies for purine analogs by quantum chemical methods

In this work, covalent hydration energies for a variety of azanaphthalenes and purine analogs have been calculated using a variety of quantum chemical methods. On the basis of these results, we recommend the CPCM(UA0)‐B3LYP/6‐31+G(d,p) level for rapid prediction of covalent hydration energies. However, we caution the use of this methodology for computing covalent hydration energies for fluorine‐containing compounds. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Mass spectrometry based cellular phosphoinositides profiling and phospholipid analysis: A brief review

Phospholipids are key components of cellular membrane and signaling. Among cellular phospholipids, phosphoinositides, phosphorylated derivatives of phosphatidylinositol are important as a participant in essential metabolic processes in animals. However, due to its low abundance in cells and tissues, it is difficult to identify the composition of phosphoinositides. Recent advances in mass spectrometric techniques, combined with established separation methods, have allowed the rapid and sensitive detection and quantification of a variety of lipid species including phosphoinositides. In this mini review, we briefly introduce progress in profiling of cellular phosphoinositides using mass spectrometry. We also summarize current progress of matrices development for the analysis of cellular phospholipids using matrix-assisted laser desorption/ionization mass spectrometry. The phosphoinositides profiling and phospholipids imaging will help us to understand how they function in a biological system and will provide a powerful tool for elucidating the mechanism of diseases such as diabetes, cancer and neurodegenerative diseases. The investigation of cellular phospholipids including phosphoinositides using electrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry will suggest new insights on human diseases, and on clinical application through drug development of lipid related diseases.     

An unusual bisnor-clerodane diterpenoid from Polyalthia simiarum

The stem bark of Polyalthia simiarum has yielded a new bisnor-type clerodane diterpenoid, 2-oxo-14,15-bisnor-3,11E-kolavadien-13-one (1), and three previously known clerodane derivatives, kolavenic acid (2), 16beta-hydroxycleroda-3,13(14)Z-dien-15,16-olide (3), and 16-oxocleroda-3,13(14)E-dien-15-oic acid (4). The structures of these compounds were unambiguously determined by extensive NMR studies as well as by comparison with related compounds. Till now this is the second report of the occurrence of any unusual C-18 clerodane diterpenoid from nature. The crude light petroleum extract and the purified compound 3 demonstrated moderate free radical scavenging activity with IC50 values of 21.5 and 23.5 microg/mL, respectively.     

Growth of CdBr2 single crystals by zone refining

CdBr₂ has been purified using a 12-pass zone-refining technique. Single crystals grown from the starting material showed arcing in the X-ray oscillation photographs whereas this is absent in the crystals grown from zone refined material. These crystals are found to be 6R type. In order to study the effect of impurities, DC conductivity studies were made on the crystals at various stages of purification. Surface morphology of the crystals have been studied using an optical microscope.     

Investigation of metal-oligonucleotide complexes by nanoelectrospray tandem mass spectrometry in the positive mode

The formation and fragmentation of multiply metal-coordinated oligonucleotides was studied by nanoelectrospray tandem mass spectrometry in the positive ion mode. Fundamental aspects of the gas-phase behavior of metal-oligonucleotide complexes are revealed. The addition of transition metal ions, such as iron(II), iron(III), and zinc(II), leads to very stable metal-oligonucleotide complexes which show heavily altered fragmentation patterns in contrast to uncomplexed oligonucleotides. The site of metal ion complexation was located by collision-induced dissociation (CID) experiments. It was found that all three metal ions investigated predominantly coordinate to the central phosphate groups of the oligonucleotides. Furthermore, it is demonstrated that the fragmentation of such complexes depends highly upon the metal ion complexed as well as on the sequence of the nucleobases in the oligonucleotide.     

Prediction of a new pathway to presilphiperfolanol

Quantum chemical calculations on the conversion of farnesyl diphosphate to presilphiperfolanol are described. On the basis of the results of this theoretical study, we predict a new mechanism for presilphiperfolanol formation that involves the intermediacy of nerolidyl diphosphate and an unusual reaction step in which a 1,2-alkyl shift and a transannular alkene attack are combined into a concerted process.     

K3[MO4][MO3N] (M=Tc,Re) – Nitridotrioxidorhenate and -technetate from Highly Alkaline Media

The reactions of ammonium perrhenate and pertechnetate in highly alkaline medium led to the isotypic mixed anionic nitridotrioxidorhenate and -technetate K ₃[MO₄][MO₃N] (M= Tc, Re). Both compounds occur as colorless crystals, which were investigated by single crystal X-ray diffraction. Furthermore, K₃[ReO₄][ReO₃N] has been studied by means of X-ray photoelectron spectroscopy to determine the oxidation state of rhenium. The obtained results have been complemented by magnetic measurements. IR and Raman spectroscopy indicated the presence of Re−O as well as Re−N bonds.