N-K near-edge x-ray-absorption fine structures of acetonitrile in gas phase

The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu(CN) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.     

Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology

Simulations of coupled interactions involving two opposite enzymatic reactions, solute diffusions, and electrostatic interactions between membrane charges and charged solutes were conducted under a fixed kinase-channel-phosphatase (KCP) topology oriented from the outside to the inside of a porous membrane structure. Depending on the kinase and phosphatase locations, we recently demonstrated that an active transport of a phosphorylated substrate may occur via the opposite topology, that is, a PCK topology. The present analysis demonstrates that, under a KCP membrane topology, which also behaves as a specific ATP-dependent transporter, the active transport of a neutral substrate may occur. This analogous active transport appears to be dependent on the phosphatase location and on the membrane surface potentials. A broad analysis of the role played by the main parameters taken into account in the model was conducted in order to define precisely the physico-chemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

Trimeric perfluoro-ortho-phenylenemercury: a versatile Lewis acidic host

Trimeric perfluoro-ortho-phenylenemercury (1) constitutes one of the simplest trifunctional Lewis acidic hosts. In addition to cooperative effects arising from the proximity of the mercury(II) centers, the electron-withdrawing properties of the backbone and the accessibility of the electrophilic sites lead to the facile complexation of neutral and electron rich substrates. The planarity of the structure as well as its overall polarizability compounded with relativistic effects at mercury also permits the occurrence of non-covalent interactions and accounts for the tendency of this compound to form cofacial dimers. Collectively, the Lewis acidic properties of 1 as well as its ability to engage in non-covalent interactions can be held responsible for its ability to form extended binary supramolecular stacks with arenes. The photoluminescence observed in some of these supramolecular complexes corresponds to the phosphorescence of the aromatic substrate and indicate the occurrence of a mercury heavy atom effect.     

Energetic and topological analyses of the oxidation reaction between Mo(n) (n = 1, 2) and N2O

The interaction between molybdenum, atom, and dimer, with nitrous oxide has been investigated using density functional theory. The analysis of the potential energy surfaces for both reactions has revealed that a single molybdenum atom can activate the N--O bond of N2O requiring a small activation energy. However, the presence of several intersystem crossings between three different spin states, namely, septet, quintet and triplet states, seems to be the major constraint to the Mo + N2O reaction. Contrarily, the low-lying excited states (triplet and quintet) do not participate in the reaction between the molybdenum dimer and N2O. The latter reaction fully evolves on the singlet spin surface. Three different regions have been distinguished along the pathway: formation of an adduct complex, formation of an inserted compound, and the N2 detachment. The connection between the two first regions has been characterized by the formation of a special complex in which the N--O bond is so weakened that it could be considered as a first step in the insertion process. It has been shown that the topological changes along the pathways provide a clear explanation for the geometrical changes that occur along the reaction pathway. In summary, the detachment of the N2 molecule is found to be kinetically an effective process for both reactions, owing to the high exothermicity and consequently to the high internal energy of the insertion intermediates. However, in the case of Mo atom, the reaction should be a slow process due to the presence of spin-forbidden transitions. These results fully agree with previous experimental works.     

Synthesis of Jasminaldehyde by Solid-Liquid Phase Transfer Catalysis Without Solvent,Under Microwave Irradiation

α-n-amylcinnamaldehyde (jasminaldehyde) was obtained with 82 % yield by solid-liquid phase transfer catalysis without solvent within 3 days at room temperature. By use of domestic microwave irradiation, the same yield was obtained within 1 minute at a power of 600 W.     

Ultra performance liquid chromatography – mass spectrometry studies of formalin‐induced alterations of human brain lipidome

The development of ‘omics’ sciences offers new opportunities for the study of neurodegenerative diseases but increases at the same time the sample demand on brain banks that collect and store valuable human post‐mortem tissue. Our study aims to evaluate in lipidomics the potential of formalin‐fixed tissue compared with the cryopreservation method, considered as the gold standard for biochemical research. Two complementary liquid chromatography/mass spectrometry analytical platforms were used on the basis of hybrid quadrupole time‐of‐flight and triple quadrupole mass spectrometers. Untargeted fingerprinting, semitargeted profiling of specific lipid classes and targeted monitoring of lipid species were performed in formalin‐fixed and cryopreserved samples to provide detailed information at the molecular level on the formalin‐induced alterations of the brain tissue. In vitro incubations of lipid standards were also performed to further describe the degradation processes induced by formaldehyde. Phospholipid compounds were found to be extensively hydrolysed, whilst the sphingolipid ones were preserved. N‐methylation and N‐formylation of amine‐containing phospholipids have also been evidenced. These findings show that the potential detrimental effect of formalin on the analytes of interest must be taken into account when analysing formalin‐fixed samples. Copyright © 2014 John Wiley & Sons, Ltd.     

RNA Ligation for Mono and Dually Labeled RNAs

Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3′-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3′,5′-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5′-fluorescently labeled m⁷Gp₃A_m-capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.