Highly stereoselective palladium-catalyzed Heck coupling of 5-iodouridine-5′-triphosphates with allylamine: a new efficient method for the synthesis of (E)-5-aminoallyl-uridine-5′-triphosphates

The palladium-catalyzed Heck coupling of 5-iodouridine-5′-triphosphates with allylamine is described. The reaction is highly stereoselective that results in high purity of (E)-5-aminoallyl-uridine-5′-triphosphate with good yields.     

A new class of laser dyes from acridinedione derivatives

Synthesis of 10-aryl-3,4,6,7,9,10-hexahydro-1,8(2H,5H)-acridinedione as a new class of laser dyes is reported. These dyes lase around 475–495 nm and are compared to the standard dye coumarin 102.     

Solid-phase organic synthesis of polyisoprenoid alcohols with traceless sulfone linker

Solid-phase organic synthesis of polyprenols with a traceless sulfone linker is described. The polymer-bound benezenesulfinate is first linked with the "tail" building blocks of isoprenyl chlorides via S-alkylation. With use of dimsyl anion as an appropriate base, the polymer-bound alpha-sulfonyl carbanion is generated and coupled with other "body" building blocks in an efficient manner. After repeated processes and a global palladium-catalyzed desulfonation with LiEt 3BH as the reducing agent, the desired polyprenols with various chain lengths and geometrical configurations are obtained in 32-59% overall yields. The solid-phase synthesis offers the advantage in facile isolation of polyprenols without tedious operation or time-consuming purification.     

ESR, zero-field splitting, and magnetic exchange of exchange-coupled copper(II)-copper(II) pairs in copper(II) tetraphenylporphyrin N-oxide

The crystal structures of the dimer form of copper(II) tetraphenylporphyrin N-oxide, [Cu(tpp-N-O)]2 (3-dimer), and zinc(II) tetraphenylporphyrin N-oxide, [Zn(tpp-N-O)]2 (4-dimer), were established. The geometry at the copper ion in 3-dimer is essentially square-pyramidal with one oxygen bridge [O(1A)] occupying the apical site, giving a much larger Cu-O bond distance compared to those at the basal plane. The respective Cu...Cu distance and Cu-O-Cu angle in the core of 3-dimer are 3.987(4) A and 148.1(3) degrees. The Zn(1) atom in 4-dimer has a distorted square-pyramidal [4 + 1] coordination geometry that gives a tau-value of 0.19. The respective Zn...Zn distance and Zn-O-Zn angle in the dimeric unit of 4-dimer are 4.025(3) A and 148.1(2) degrees. The 3-dimer displays axial X-band electron paramagnetic resonance spectral features (Es = 0) in the powder state at 4 K, giving g parallel = 2.51 (A(parallel,s) = (9.6 +/- 0.2) x 10-3 cm(-1)) and g(perpendicular) = 2.11 and in the same powder state at 293 K giving Ds = 0.0731 cm(-1) (as derived from DeltaMs = 1 lines) or 0.0743 cm(-1) (as derived from the DeltaMs = 2 lines). In addition, 3-dimer displays a DeltaMs = 2 transition at g = 4.17 indicating the presence of spin-exchange coupling. The anisotropic exchange interaction (Ds(ex)= 0.132 cm(-1)) gives the main contribution to Ds in 3-dimer. The theoretical fit of the susceptibility and effective magnetic moment data of 3-dimer in the temperature range of 5-300 K gives 2J = 68 cm(-1), g = 2.01, p = 0.06, and a temperature-independent paramagnetism of 10(-6) cm3 mol(-1). This magnetic susceptibility data indicates that the copper(II) ions in 3-dimer are coupled in a ferromagnetic manner with the ground-spin triplet stabilized by 68 cm(-1) with regard to the singlet.     

Effects of Electron-Transfer Coupled with Collision-Induced Dissociation (ET/CID) on Doubly Charged Peptides and Phosphopeptides

Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c- and z^·-type product ions by randomly cleaving the N–Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in “bottom-up” proteomic analysis.     

Application of Shannon-like diversity measures to cell-based chemistry spaces

The use of multi-dimensional “chemistry spaces” to represent large compound collections has become widespread in pharmaceutical research. In such spaces compounds are treated as points. Points in close proximity represent similar compounds, while distant points represent dissimilar compounds. Assessing the diversity of a compound collection, thus, is tantamount to characterizing the distribution of points in chemistry space. To facilitate many procedures such as selecting subsets of compounds for screening, for compound acquisition and designing combinatorial libraries, chemistry spaces have been partitioned into sets of non-overlapping, multi-dimensional cells, which are generated by dividing each axis into a number of equal-sized bins. This leads to a lattice of (N_bins)^N_dim{(N_{bins})^{N_{\rm dim}}} cells, where N _bins is the number of bins on each axis and N _dim is the dimensionality of the space. One diversity measure that is typically used in cell-based chemistry spaces is identical in form to Shannon entropy, D_Ncpd^cpd{D_{N_{cpd}}^{cpd}} A normalized measure of this Shannon entropy given by, D_rel^cpd{D_{rel}^{cpd}} enables comparison between compound collections that occupy different number of occupied cells. Although D_rel^cpd{D_{rel}^{cpd}} characterizes the uniformity and “spreadout” of the corresponding compound collection, it treats cells as positionally independent. Some of the positional information lost can be recaptured by another diversity measure, which is also related in form to Shannon entropy. This new measure D_Nbin^cell (l){D_{N_{bin}}^{cell} (\lambda)} characterizes the distribution of occupied cells along each axis of chemistry space. The normalized measure á D_rel^cell ñ{\left\langle {D_{rel}^{cell}}\right\rangle} over all axes is given then by the average. Examples illustrating the applicability of these two Shannon-like measures to compound collections are presented.     

Shock tube study on the thermal decomposition of ethanol

The thermal decomposition of C(2)H(5)OH highly diluted in Ar (1 and 3 ppm) has been studied by monitoring H atoms using the atomic resonance absorption spectrometry (ARAS) technique behind reflected shock waves over the temperature range 1450-1760 K at fixed pressure: 1, 1.45, and 2 atm. The rate constant and the product branching fractions have been determined by analyzing temporal profiles of H atoms; the effect of the secondary reactions on the results has been examined by using a detailed reaction mechanism composed of 103 elementary reactions. The apparent rate constant of ethanol decomposition can be expressed as k(1)/s(-1) = (5.28 ± 0.14) × 10(10) exp[-(23,530 ± 980)/T] (T = 1450-1670 K, P = 1-2 atm) without a detectable pressure dependence within the tested pressure range of this study. Branching fractions for producing CH(3) + CH(2)OH (1a) and H(2)O + C(2)H(4) (1b) have been examined by a quantitative measurement of H atoms produced in the successive decompositions of the products CH(2)OH (1a): the pressure dependence of the branching fraction for channel 1a is obtained by a linear least-squares analysis of the experimental data and can be expressed as φ(1a) = (0.71 ± 0.07) - (826 ± 116)/T, (0.92 ± 0.04) - (1108 ± 70)/T, and (1.02 ± 0.10) - (1229 ± 168)/T for T = 1450-1760 K, at P = 0.99, 1.45, and 2.0 atm, respectively. The rate constant obtained in this study is found to be consistent with previous theoretical and experimental results; however, the pressure dependence of the branching fraction obtained in this study is smaller than those of previous theoretical works. Modification of the parameters for the decomposition rate in the falloff region is suggested to be important to improve the practical modeling of the pyrolysis and combustion of ethanol.     

Modification of glassy carbon electrode with a polymer/mediator composite and its application for the electrochemical detection of iodate

A modified glassy carbon electrode was prepared by depositing a composite of polymer and mediator on a glassy carbon electrode (GCE). The mediator, flavin adenine dinucleotide (FAD) and the polymer, poly(3,4-ethylenedioxythiophene) (PEDOT) were electrochemically deposited as a composite on the GCE by applying cyclic voltammetry (CV). This modified electrode is hereafter designated as GCE/PEDOT/FAD. FAD was found to significantly enhance the growth of PEDOT. Electrochemical quartz crystal microbalance (EQCM) analysis was performed to study the mass changes in the electrode during the electrodeposition of PEDOT, with and without the addition of FAD. The optimal cycle number for preparing the modified electrode was determined to be 9, and the corresponding surface coverage of FAD (Γ_FAD) was ca. 5.11 × 10⁻¹⁰ mol cm⁻². The amperometric detection of iodate was performed in a 100 mM buffer solution (pH 1.5). The GCE/PEDOT/FAD showed a sensitivity of 0.78 μA μM⁻¹ cm⁻², a linear range of 4–140 μM, and a limit of detection of 0.16 μM for iodate. The interference effects of 250-fold Na⁺, Mg²⁺, Ca²⁺, Zn²⁺, Fe²⁺, Cl⁻, NO₃⁻, I⁻, SO₄²⁻ and SO₃²⁻, with reference to the concentration of iodate were negligible. The long-term stability of GCE/PEDOT/FAD was also investigated. The GCE/PEDOT/FAD electrode retained 82% of its initial amperometric response to iodate after 7 days. The GCE/PEDOT/FAD was also applied to determine iodate in a commercial salt.