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]     

Metal complexes of porphycene,corrphycene, and hemiporphycene: stability and coordination chemistry

Porphyrin (P), porphycene (Pc), corrphycene (Cn), and hemiporphycene (Hpc) represent a series of well defined "4-N in" constitutional porphyrin isomers. These isomers, in the form of their octaethyl derivatives, represent a congruent set of porphyrinoids whose properties can be compared. In this study we report how variations in electronic structure and nitrogen-core size in the free-base forms of these four systems are reflected in the properties of their corresponding metal complexes. Specifically, the effects that these differences have on the axial ligation properties of the Zn(II), Mg(II), Ni(II), and Co(II) complexes of P, Pc, Cn, and Hpc in toluene using pyridine as the axial ligand are detailed. Also reported are the relative stabilities of these complexes under acidic conditions. It is shown that for the zinc, magnesium, and cobalt complexes, there are distinct differences in the ability to maintain four-, five-, or six-coordinate geometries in the presence of similar concentrations of pyridine. By contrast, no apparent differences in axial ligand binding affinity are seen for the four nickel complexes. Little difference in stability was likewise seen when these same complexes were subject to acid-mediated demetallation, with all four falling into stability class II, according to the accepted porphyrin stability ranking system. High stabilities were also seen in the case of the cobalt complexes, with the Pc and Cn complexes being of stability class III and the P and Hpc derivatives falling into stability class II. The Zn(II) and Mg(II) complexes were all far less stable than the corresponding Ni(II) and Co(II) complexes. In this case, semiquantitative analyses of the rate of acid-induced decomposition revealed the following stability sequence P>Cn>Hpc>Pc for both the Zn(II) and Mg(II) complexes. Single-crystal X-ray diffraction structures were solved for the Zn(II), Mg(II), and Ni(II) complexes of the octaethyl derivatives of Hpc, Cn, and Pc as well as a Co(II) octamethylcorrphycene and are reported as part of this study. These solid-state structures confirm four-coordinate species for the Ni(II) complexes, four- and five-coordinate species for the Mg(II) and Zn(II) complexes, and a six-coordinate species for the lone Co(II) complex.     

Benchmark calculations for He2 and LiH molecules using explicitly correlated Gaussian functions

Explicitly correlated Gaussian (ECG) functions with carefully optimized non-linear parameters are used to calculate the electronic energies of He₂⁺ and LiH at their equilibrium internuclear distances. The obtained variational upper bounds (−4.99464392 and −8.070538 hartree, respectively) are the lowest reported to date. By extrapolating results obtained with various expansion lengths, the estimations of the Born–Oppenheimer limits are made.     

Passive sampling and/or extraction techniques in environmental analysis: a review

The current state-of-the-art of passive sampling and/or extraction methods for long-term monitoring of pollutants in different environmental compartments is discussed in this review. Passive dosimeters that have been successfully used to monitor organic and inorganic contaminants in air, water, sediments, and soil are presented. The application of new approaches to the determination of pollutants at the sampling stage is discussed. The main milestones in the development of passive techniques for sampling and/or extraction of analytes, and in biomonitors used in environmental analysis, are summarized in this review. Passive samplers and biomonitors are compared.     

Thermolytic carbonates for potential 5'-hydroxyl protection of deoxyribonucleosides

Thermolytic groups structurally related to well-studied heat-sensitive phosphate/thiophosphate protecting groups have been evaluated for 5'-hydroxyl protection of deoxyribonucleosides as carbonates and for potential use in solid-phase oligonucleotide synthesis. The spatial arrangement of selected functional groups forming an asymmetric nucleosidic 5'-O-carbonic acid ester has been designed to enable heat-induced cyclodecarbonation reactions, which would result in the release of carbon dioxide and the generation of a nucleosidic 5'-hydroxyl group. The nucleosidic 5'-O-carbonates 3-8, 10-15, and 19-21 were prepared and were isolated in yields ranging from 45 to 83%. Thermolytic deprotection of these carbonates is preferably performed in aqueous organic solvent at 90 degrees C under near neutral conditions. The rates of carbonate deprotection are dependent on the nucleophilicity of the functional group involved in the postulated cyclodecarbonation reaction and on solvent polarity. Deprotection kinetics increase according to the following order: 4 < 5 < 10 < 6 < 12 < 7 < 13 < 8 < 14 congruent with 19-21 and CCl4 < dioxane < MeCN < t-BuOH < MeCN:phosphate buffer (3:1 v/v, pH 7.0) < EtOH:phosphate buffer (1:1 v/v, pH 7.0). Complete thermolytic deprotection of carbonates 7, 8, 13, and 14 is achieved within 20 min to 2 h under optimal conditions in phosphate buffer-MeCN. The 2-(2-pyridyl)amino-1-phenylethyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups are particularly promising for 5'-hydroxyl protection of deoxyribonucleosides as thermolytic carbonates.     

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.     

Retention behaviour of some high-intensity sweeteners on different SPE sorbents

The objective of this paper is to provide information about application of solid-phase extraction (SPE) for isolation of nine high-intensity sweeteners (acesulfame-K, alitame, aspartame, cyclamate, dulcin, neotame, saccharin, sucralose and neohesperidin dihydrochalcone) from aqueous solutions. The influence of several types of LC-MS compatible buffers (different pH values and compositions) on their recovery has been studied and discussed. A number of commercially available SPE cartridges, such as Chromabond C18ec, Strata-X RP, Bakerbond Octadecyl, Bakerbond SDB-1, Bakerbond SPE Phenyl, Oasis HLB, LiChrolut RP-18, Supelclean LC-18, Discovery DSC-18 and Zorbax C18 were tested in order to evaluate their applicability for the isolation of analytes. Very high recoveries (better than 92%) of all studied compounds were obtained using formic acid-N,N-diisopropylethylamine buffer adjusted to pH 4.5 and C₁₈-bonded silica sorbents. Behaviour of polymeric sorbents strongly depends on their structure. Strata-X RP behaves much like a C₁₈-bonded silica sorbent. Recoveries obtained using Oasis HLB were comparable with those observed for silica-based sorbents. The only compound less efficiently (83%) retained by this sorbent was cyclamate. Bakerbond SDB-1 shows unusual selectivity towards aspartame and alitame. Recoveries of these two sweeteners were very low (26 and 42%, respectively). It was also found that aspartame and alitame can be selectively separated from the mixture of sweeteners using formic acid-triethylamine buffer at pH 3.5.     

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.     

Photophysics,Excited‐state Double‐Proton Transfer and Hydrogen‐bonding Properties of 5‐Deazaalloxazines

The photophysical properties of 5‐deazaalloxazine and 1,3‐dimethyl‐5‐deazaalloxazine were studied in different solvents. These compounds have higher values of fluorescence quantum yields and longer fluorescence lifetimes, compared to those obtained for their alloxazine analogs. Electronic structure and S₀–S_i transitions were investigated using the ab initio methods [MP2, CIS(D), EOM‐CCSD] with the correlation‐consistent basis sets. Also the time‐dependent density functional theory (TD‐DFT) has been employed. The lowest singlet excited states of 5‐deazaalloxazine and 1,3‐dimethyl‐5‐deazaalloxazine are predicted to have the π, π* character, whereas similar alloxazines have two close‐lying π, π* and n, π* transitions. Experimental steady‐state and time‐resolved spectral studies indicate formation of an isoalloxazinic excited state via excited‐state double‐proton transfer (ESDPT) catalyzed by an acetic acid molecule that forms a hydrogen bond complex with the 5‐deazaalloxazine molecule. Solvatochromism of both 5‐deazaalloxazine and its 1,3‐dimethyl substituted derivative was analyzed using the Kamlet–Taft scale and four‐parameter Catalán solvent scale. The most significant result of our studies is that the both scales show a strong influence of solvent acidity (hydrogen bond donating ability) on the emission properties of these compounds, indicating the importance of intermolecular solute–solvent hydrogen‐bonding interactions in their excited state.