iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data

A method was developed to employ National Institute of Standards and Technology (NIST) 2008 retention index database information for molecular retention matching via constructing a set of empirical distribution functions (DFs) of the absolute retention index deviation to its mean value. The effects of different experimental parameters on the molecules' retention indices were first assessed. The column class, the column type, and the data type have significant effects on the retention index values acquired on capillary columns. However, the normal alkane retention index (I(norm)) with the ramp condition is similar to the linear retention index (I(T)), while the I(norm) with the isothermal condition is similar to the Kováts retention index (I). As for the I(norm) with the complex condition, these data should be treated as an additional group, because the mean I(norm) value of the polar column is significantly different from the I(T). Based on this analysis, nine DFs were generated from the grouped retention index data. The DF information was further implemented into a software program called iMatch. The performance of iMatch was evaluated using experimental data of a mixture of standards and metabolite extract of rat plasma with spiked-in standards. About 19% of the molecules identified by ChromaTOF were filtered out by iMatch from the identification list of electron ionization (EI) mass spectral matching, while all of the spiked-in standards were preserved. The analysis results demonstrate that using the retention index values, via constructing a set of DFs, can improve the spectral matching-based identifications by reducing a significant portion of false-positives.     

Quantitative characterization of hydroxyl radicals produced by various photocatalysts

Hydroxyl radicals ((·)OH) have been deemed to be the major active species during the photocatalytic oxidation reaction. In this study, (·)OH produced on various semiconductor photocatalysts in aqueous solution under Xenon lamp irradiation was quantitatively investigated by the photoluminescence (PL) technique using coumarin (COU) as a probe molecule. The results indicated that the formation rate of (·)OH on the surface of irradiated commercial Degussa P25 (P25) was much higher than that of other semiconductor. The pH values of the solution and phase structure of TiO(2) significantly influenced the production rate of (·)OH. The acidic pH environment of the solutions and bi-phase structure (anatase and rutile) of TiO(2) were beneficial to enhancing the formation rate of (·)OH. In addition, the formation rate of (·)OH on anatase TiO(2) and P25 was much faster than that of (·)OH on the other semiconductors (such as rutile TiO(2), ZnO, WO(3), CdS, Bi(2)WO(4) and BiOCl, etc.). A new concept "OH-index" was first proposed to compare photocatalytic activity of photocatalysts, which would provide new insight into the investigation of semiconductor photocatalysts.     

A green method for the synthesis of thiochromene derivatives in ionic liquids

Controlling the pH value by changing the negative ion of ionic liquids, the same reactions of aromatic aldehyde, 2‐(2,3‐dihydrothiochromen‐4‐ylidene) malononitrile and malononitrile product unaromatized and aromatized 6H‐benzo[c]thiochromene derivatives in high yields. The nice features of these procedures include mild reactions condition, simple operations, high yields, and environmentally benign. J. Heterocyclic Chem., (2011).     

1-D Selenidoindates {[In2Se5]}∞ directed by chiral metal complex cations of 1,10-phenanthroline

Two 1-D selenidoindates {[M(phen)(3)]In(2)Se(5)·H(2)O}(n) (M = Ni, Fe) were synthesized by a solvothermal method. The 1-D {[In(2)Se(5)](2-)}(n) anion is a new type of single 1-D structure constituted by an alternately fused four-membered In(2)Se(2) ring and five-membered In(2)Se(3) ring. The chalcogenoindates were separated as mechanical racemic mixtures of single enantiomer crystals, in which the R-helix of 1-D InSe anion is directed by the related clockwise (Δ) cations of [M(phen)(3)](2+) or the L-helix of 1-D anion is directed by the related anticlockwise (Λ) cation. The π···π, C···Se, and C-H···Se oriented interactions of metal complex cations with selenidoindate anions play an important role in the formation of the chiral crystals. The embedded [M(phen)(3)](2+) cations improve the optical absorption of the 1-D semiconductor materials.     

Protein's electronic polarization contributes significantly to its catalytic function

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.     

Nanotubular metal-organic frameworks with high porosity based on T-shaped pyridyl dicarboxylate ligands

Two nanotubular metal-organic frameworks (MOFs), {Cu(L1)·2H(2)O·1.5DMF}(∞) (1) and {Cu(2)(L2)(2)(H(2)O)(2)·7H(2)O·3DMF}(∞) (2), with novel topologies have been constructed based on Cu(2+), 5-(pyridin-4-yl)isophthalic acid (L1) and 5-(pyridin-3-yl)isophthalic acid (L2), respectively. Two MOFs were characterized by IR spectroscopy, thermogravimetry, single-crystal, and powder X-ray diffraction methods. Network analysis reveals a two-nodal (3,6)-connected (4·6(2))(2)(4(2)·6(10)·8(3)) net and a three-nodal (3,4)-connected (4·8(2))(4)(4(2)·8(2)·10(2))(2)(8(4)·12(2)) net. Interpenetration is inherently prevented by both of the topologies of the frameworks. The porosity of MOF 1 was confirmed by N(2) and CO(2) gas adsorption investigations. MOF 1 exhibits remarkable hydrogen sorption hysteresis at low pressure and a H(2) uptake capacity of 1.05 wt% at 77 K and 1 atm.     

Total synthesis of (+)-przewalskin B

An efficient strategy for the total synthesis of (+)-przewalskin B is reported. The key steps feature an intermolecular S(N)2' substitution of iodoallylic phosphate with organocupper reagent, a diastereoselective organocatalytic aldol cyclization, as well as a Rh(2)(OAc)(4)-mediated intramolecular carbene insertion to the tertiary C-H bond.     

SmI2-mediated radical cross-couplings of α-hydroxylated aza-hemiacetals and N,S-acetals with α,β-unsaturated compounds: asymmetric synthesis of (+)-hyacinthacine A2, (-)-uniflorine A, and (+)-7-epi-casuarine

The SmI(2)-mediated radical coupling reactions of β-hydroxylated pyrrolidine/piperidine aza-hemiacetals 8 and 9 and N,S-acetals 6 and 33 with α,β-unsaturated compounds are described. This method allows a rapid access to β-hydroxylated pyrrolidines, piperidines, pyrrolizidinones, and indolizidinones. Starting from N,S-acetal 33 and via a common intermediate 27, the alkaloids hyacinthacine A(2) (2), uniflorine A (3, 6-epi-casuarine), and the unnatural epimer 7-epi-casuarine (37) have been synthesized in four and five steps with overall yields of 34%, 16%, and 13%, respectively. The radical mechanism of the coupling reactions has been confirmed by controlled experiments, which also allowed deducing the anionic mechanism in the coupling between N,S-acetal 6 and carbonyl compounds. This demonstrates that the mechanisms of these SmI(2)-mediated reactions are switchable from Barbier-type anionic to radical by cooperative action of BF(3)·OEt(2) and t-BuOH.     

Highly porous and robust scandium-based metal-organic frameworks for hydrogen storage

The metal-organic frameworks NOTT-400 and NOTT-401, based on a binuclear [Sc(2)(μ(2)-OH)(O(2)CR)(4)] building block, have been synthesised and characterised; the desolvated framework NOTT-401a shows a BET surface area of 1514 m(2) g(-1) with a total H(2) uptake of 4.44 wt% at 77 K and 20 bar.     

A reagentless and disposable electronic genosensor: from multiplexed analysis to molecular logic gates

Reagentless, sensitive and multiplexed analysis of gyrB and K-ras gene biomarkers is achieved based on the proximity changes of two different redox-tags to the electrode surface upon DNA hybridizations, and the presence of the two gene biomarkers also acts as inputs and activates the logic gate.