Ultrafast spectroscopic study of the photochemistry and photophysics of arylhalodiazirines: direct observation of carbene and zwitterion formation

Ultrafast photolysis (lambdaex = 270, 350, or 360 nm) of bromophenyl, chlorophenyl, fluorophenyl, and fluoro-para-trifluoromethylphenyl diazirines produces transient species which absorb broadly in the UV and visible regions. Transient decay can be fit to either mono- or biexponential functions (tau1 approximately 0.3-10 ps, tau2 approximately 10-350 ps; dependent on solvent and halogen). Fluoro- and chlorophenylcarbene are formed within the time resolution of the spectrometer (300 fs, 270 nm excitation). Bromophenyl diazirine decay (270 nm excitation) correlates with the growth of bromophenylcarbene. Solvent and substituent effects on the slower decays of the transient absorptions are consistent with assigning the carriers of transient absorption in the visible region to ring-opened zwitterionic species.     

The IINS, IR and DFT studies of hydrogen bonds in 6-Furfuryl and 6-Benzylaminopurines

FTIR and IINS spectra of 6-Furfurylaminopurine (6-FAP) and 6-Benzylaminopurine (6-BAP) taken at different temperatures have been analysed and compared with the spectra calculated by the ab initio DFT/B3LYP method and the semiempirical PM3 method in the isolated molecule approximation, for the tautomers N3-H, N7-H and N9-H, and dimers with hydrogen bonds. For 6-FAP the best agreement between the calculated and experimental (at 20 K) spectra has been found for the N9-H tautomer, whose structure was established by X-ray diffraction. For 6-BAP the analogous agreement for the N9-H tautomer structure has been poor and much better for the N7-H tautomer. The vibrational spectra calculated for dimers of the molecules studied involved in hydrogen bonds, permitted also an interpretation of the bands whose positions and FWHM in the FTIR spectra changed with temperature.     

New method to measure packing densities of self-assembled thiolipid monolayers

For a monolayer of 2,3-di-phytanyl-sn-glycerol-1-tetraethylene glycol-D,L-a-lipoic acid ester lipid (DPTL) self-assembled (SAM) at a gold electrode surface we propose a new method to determine the charge number per adsorbed molecule and the packing density (area per molecule) in the monolayer. The method relies on chronocoulometry to measure the charge density at the SAM covered gold electrode surface. Two series of measurements have to be performed. In the first series, charge densities are measured for a monolayer transferred from the air-solution to the metal-solution interface using the Langmuir-Blodgett (LB) technique. This series of measurements allows one to determine charge numbers per adsorbed DPTL molecule. The second series is performed using a gold electrode covered with a self-assembled monolayer. The charge densities obtained in this series are then used to calculate the packing density with the help of charge numbers per adsorbed DPTL determined in the first series. The area per adsorbed molecule determined by the new method was compared to the area per molecule determined by the popular reductive desorption method. The molecular area determined with the new method is about 20% larger than the area calculated from the van der Waals model, which is a physically reasonable result. In contrast, the popular reductive desorption method gives an area per molecule 20% lower than the minimum estimated based on a van der Waals model. This is a physically unreasonable result. It is also shown that the charge numbers per adsorbed molecule depend on the electrode potential and may assume values smaller than the number of electrons participating in the reductive desorption step. An explanation of the origin of the "partial charge numbers" is provided. We recommend the new method be used in future studies of thiol adsorption at metal surfaces.     

Models for the Investigation of the Structure of Vulcanizates

For the investigation of vulcanizates structure, new models have been developed relating the modulus of vulcanizates and the volume fraction of filler. The parameters of the models are the filler distribution and the properties of the shell surrounding the filler particles. Three functions of filler distribution have been assumed. Dynamic mechanical properties of a series of vulcanizates were tested and the parameters of the models were computed. The obtained data allows estimating the properties of the shell formed around filler particles in vulcanizates and to distinguish the functions of filler distribution.     

Synthesis of Functionalized (2-Thienylcarbonyl)thiazoles and 4-(2-Thienyl)pyridines by Reaction of (2-Thienylcarbonyl)thioacetanilides and their Enamine Derivatives

Summary. The condensation of two molecules of 2-(2-thienylcarbonyl)thioacetanilides catalyzed by piperidine yielded thiazole derivatives as confirmed by X-ray crystal structure analysis. The reaction of malononitrile with 3-morpholino-3-(2-thienyl)acrylic acid thioanilides furnished 6-amino-1-aryl-4-(2-thienyl)-1,2-dihydro-2-thioxopyridine-5-carbonitriles. A similar reaction of malononitrile with 3-morpholino-3-(2-thienyl)acrylic acid anilides provided 2-oxopyridine-5-carbonitriles.     

Vibrational spectroscopy differentiates between multipotent and pluripotent stem cells

Over the last few years, there has been an increased interest in the study of stem cells in biomedicine for therapeutic use and as a source for healing diseased or injured organs/tissues. More recently, vibrational spectroscopy has been applied to study stem cell differentiation. In this study, we have used both synchrotron based FTIR and Raman microspectroscopies to assess possible differences between human pluripotent (embryonic) and multipotent (adult mesenchymal) stem cells, and how O(2) concentration in cell culture could affect the spectral signatures of these cells. Our work shows that infrared spectroscopy of embryonic (pluripotent) and adult mesenchymal (multipotent) stem cells have different spectral signatures based on the amount of lipids in their cytoplasm (confirmed with cytological staining). Furthermore, O(2) concentration in cell culture causes changes in both the FTIR and Raman spectra of embryonic stem cells. These results show that embryonic stem cells might be more sensitive to O(2) concentration when compared to mesenchymal stem cells. While vibrational spectroscopy could therefore be of potential use in identifying different populations of stem cells further work is required to better understand these differences.     

Structural changes accompanying excited-state electron transfer in meta- and para-dialkylaminopyridines

The electronic structure of the lowest excited singlet states and molecular geometries of a series of dialkylaminopyridines (DAAPs) representing electron donor–acceptor systems were studied by photostationary and time-resolved UV–vis spectroscopic methods and quantum chemical calculations. The comparative studies allow us to rationalize dual luminescence of 4-DAAPs in terms of the TICT state model—the analysis of the electronic transition dipole moments indicates a nearly orthogonal conformation of the fluorescent ICT states. Introduction of the amino group at meta position as in 3-diisopropylaminopyridine completely changes photophysics of these pyridine derivatives: (i) the Franck-Condon excited state initially reached upon excitation and the solvent equilibrated fluorescent state are most probably of the same nature (both excited states do not correspond to a full separation of charges) and (ii) the electronic structure and geometry of the fluorescent CT states of m-DIAP are solvent dependent.     

Quantitative measurement of different ceramide species from crude cellular extracts by normal-phase high-performance liquid chromatography coupled to atmospheric pressure ionization mass spectrometry

Normal-phase high-performance liquid chromatography (NP-HPLC) coupled to atmospheric pressure ionization mass spectrometry (APCI-MS) allows quantitative analysis of endogenous ceramide and dihydroceramide species from crude lipid extracts. Qualitative information for the species comes from observation of differences in chromatographic and mass spectrometric behavior between species (Pettus et al. Rapid Commun. Mass Spectrom. 2003; 17: 1017-1026). Quantitative analysis is achieved by (1) use of a synthetic internal standard as an extraction and injection control, (2) lack of salt adduction, ion suppression, or other matrix effects in APCI mode, and (3) consistent fragmentation and ionization of external standards across the physiologically relevant concentration range found in endogenous lipid samples. Application to the analysis and quantitation of ceramide and dihydroceramide from various cell lines is demonstrated. The results from APCI-MS analysis corroborate and enhance information acquired from use of the diacylglycerol kinase assay for total ceramide measurement. This technique readily allows simultaneous quantitation of ceramide and dihydroceramide species.     

Assessment of 4-nitrogenated benzyloxymethyl groups for 2'-hydroxyl protection in solid-phase RNA synthesis

The search for a 2'-OH protecting group that would impart ribonucleoside phosphoramidites with coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites led to an assessment of 2'-O-(4-nitrogenated benzyloxy)methyl groups through solid-phase RNA synthesis using phosphoramidites 2a-d, 12a, and 14a. These phosphoramidites exhibited rapid and efficient coupling properties. Particularly noteworthy is the cleavage of the 2'-O-[4-(N-methylamino)benzyloxy]methyl groups in 0.1 M AcOH, which led to U19dT within 15 min at 90 degrees C. [reaction: see text]     

The 2‐Cyano‐2,2‐dimethylethanimine‐N‐oxymethyl Group for the 2′‐Hydroxyl Protection of Ribonucleosides in the Solid‐Phase Synthesis of RNA Sequences

The reaction of 2‐cyano‐2‐methyl propanal with 2′‐O‐aminooxymethylribonucleosides leads to stable and yet reversible 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl)ribonucleosides. Following N‐protection of the nucleobases, 5′‐dimethoxytritylation and 3′‐phosphitylation, the resulting 2′‐protected ribonucleoside phosphoramidite monomers are employed in the solid‐phase synthesis of three chimeric RNA sequences, each differing in their ratios of purine/pyrimidine. When the activation of phosphoramidite monomers is performed in the presence of 5‐benzylthio‐1H‐tetrazole, coupling efficiencies averaging 99 % are obtained within 180 s. Upon completion of the RNA‐chain assemblies, removal of the nucleobase and phosphate protecting groups and release of the sequences from the solid support are carried out under standard basic conditions, whereas the cleavage of 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl) protective groups is effected (without releasing RNA alkylating side‐products) by treatment with tetra‐n‐butylammonium fluoride (0.5 m) in dry DMSO over a period of 24–48 h at 55 °C. Characterization of the fully deprotected RNA sequences by polyacrylamide gel electrophoresis (PAGE), enzymatic hydrolysis, and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry confirmed the identity and quality of these sequences. Thus, the use of 2′‐O‐aminooxymethylribonucleosides in the design of new 2′‐hydroxyl protecting groups is a powerful approach to the development of a straightforward, efficient, and cost‐effective method for the chemical synthesis of high‐quality RNA sequences in the framework of RNA interference applications.