Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data

In chromatography-based metabonomic research, retention time (RT) alignment of chromatographic peaks poses a challenge for the accurate profiling of biomarkers. Although a number of RT alignment software has been reported, the performance of these software packages have not been comprehensively evaluated. This study aimed to evaluate the RT alignment accuracy of publicly available and commercial RT alignment software. Two gas chromatography/mass spectrometry (GC/MS) datasets acquired from a mixture of standard metabolites and human bladder cancer urine samples, were used to assess three publicly available software packages, MetAlign, MZmine and TagFinder, and two commercial applications comprising the Calibration feature and Statistical Compare of ChromaTOF software. The overall RT alignment accuracies in aligning standard compounds mixture were 93, 92, 74, 73 and 42% for Calibration feature, MZmine, MetAlign, Statistical Compare and TagFinder, respectively. Additionally, unique trends were observed for the individual software with regards to the different experimental conditions related to extent and direction of RT shifts. Conflicting performance was observed for human urine samples suggesting that RT misalignments still occurred despite the use of RT alignment software. While RT alignment remains an inevitable step in data preprocessing, metabonomic researchers are recommended to perform manual check on the RT alignment of important biomarkers as part of their validation process.     

Prediction of cytochrome P450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines

Statistical learning methods have been used in developing filters for predicting inhibitors of two P450 isoenzymes, CYP3A4 and CYP2D6. This work explores the use of different statistical learning methods for predicting inhibitors of these enzymes and an additional P450 enzyme, CYP2C9, and the substrates of the three P450 isoenzymes. Two consensus support vector machine (CSVM) methods, "positive majority" (PM-CSVM) and "positive probability" (PP-CSVM), were used in this work. These methods were first tested for the prediction of inhibitors of CYP3A4 and CYP2D6 by using a significantly higher number of inhibitors and noninhibitors than that used in earlier studies. They were then applied to the prediction of inhibitors of CYP2C9 and substrates of the three enzymes. Both methods predict inhibitors of CYP3A4 and CYP2D6 at a similar level of accuracy as those of earlier studies. For classification of inhibitors of CYP2C9, the best CSVM method gives an accuracy of 88.9% for inhibitors and 96.3% for noninhibitors. The accuracies for classification of substrates and nonsubstrates of CYP3A4, CYP2D6, and CYP2C9 are 98.2 and 90.9%, 96.6 and 94.4%, and 85.7 and 98.8%, respectively. Both CSVM methods are potentially useful as filters for predicting inhibitors and substrates of P450 isoenzymes. These methods generally give better accuracies than single SVM classification systems, and the performance of the PP-CSVM method is slightly better than that of the PM-CSVM method.     

Synthesis and molecular and extended structures for a diaminonaphthalene-derived bis(amido)stannylene

The cyclic bis(amido)tin(II) compound Sn[1,8-((iPrN)2C10H6] (2) was isolated from the reaction of Li2[1,8-((iPrN)2C10H6] (1) and SnCl2. Solid-state structural analysis of 2 showed it to be a mononuclear species with a pyramidal Sn center as part of a nonplanar metallaheterocycle. The packing diagram of 2 revealed an extended one-dimensional head-to-tail chain structure with short intermolecular Sn/arene-C interactions. Computational examination of 2 (DFT/PW91 and MP2 with 6-31G* and 6-311G** basis functions) indicated that the optimum gas-phase structure of 2,which displays a Sn center in the plane of the naphthyl backbone with a slightly twisted metallaheterocycle, is approximately 24 kcal/mol lower in energy than the X-ray structure. The solid-state geometry of 2 is attributed to the intermolecular donation of the naphthalene pi-electrons to a Lewis acidic Sn center, which leads to the observed supramolecular structure. The crystal structure of 1 is also reported.     

Ultra-performance liquid chromatography/time-of-flight mass spectrometry based metabolomics of raw and steamed Panax notoginseng

At present, metabolite profiling is of growing importance in herbal medicine fields such as breeding, formulation, quality control and clinical trials. This preliminary study indicated that ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOFMS)-based metabolomics allows direct detection of down-stream derivatives of metabolites, arising from the herbal formulation process. This analytical approach allows the discrimination and tentative authentication of unique biomarkers related to different herbal extracts using unsupervised multivariate principal component analysis (PCA). The tentative identification of biomarkers is complemented significantly by the accurate mass measurement of TOFMS and the high resolution and high retention time reproducibility rendered by UPLC. The application of this approach in herbal extract discrimination and ginsenoside biomarker discovery of raw and steamed Panax notoginseng (Burk.) F.H. Chen is demonstrated and discussed.     

Palladium Aryl Sulfonate Phosphine Catalysts for the Copolymerization of Acrylates with Ethene

The reaction of 2‐[bis(2‐methoxy‐phenyl)phosphanyl]‐4‐methyl‐benzenesulfonic acid (a) and 2‐[bis(2′,6′‐dimethoxybiphenyl‐2‐yl)phosphanyl]benzenesulfonic acid (b) with dimethyl(N,N,N′,N′‐tetramethylethylenediamine)‐palladium(II) (PdMe₂(TMEDA)) leads to the formation of TMEDA bridged palladium based polymerization catalysts ( 1a and 1b ). Upon reaction with pyridine, two mononuclear catalysts are formed ( 2a and 2b ). These catalysts are able to homopolymerize ethylene and also copolymerize ethylene with acrylates or with norbornenes. With ligand b , high molecular weight polymers are formed in high yields, but higher comonomer incorporations are obtained with ligand a .

     

New Cu(II) complexes with polydentate chelating Schiff base ligands: Synthesis, structures, characterisations and biochemical activity studies

We have reported herein the synthesis of three new Cu(II) complexes of tri- and tetradentate Schiff base ligands containing N₃ or N₄ donor set along with terminal NNN⁻ or SCN⁻ ligands: [L¹Cu(NCS)]ClO₄ (1), [L²Cu(NCS)₂] (2) and [L³Cu(NNN)]ClO₄ (3) [L¹ = NC₅H₄C(CH₃)=N(CH₂)₃N=C(CH₃)C₅H₄N, L²= Me₂N–(CH₂)₃–N=C(CH₃)C₅H₄N and L³ = NC₅H₄CH=N–(CH₂)₄–N=CHC₅H₄N]. The complexes have been systematically characterised by elemental, spectroscopic and electrochemical techniques. Antimicrobial activities of the Schiff base ligands and their metal complexes have been studied using the disc diffusion method on the strains of Candida tropicalis and Bacillus megaterium. Structures of all the complexes have been unequivocally established from single crystal X-ray diffraction analyses that show the monomeric units containing a five-coordinated copper center in highly distorted square pyramidal geometry with thiocyanate or azide anion coordinated as terminal ligand. The complexes 1 and 3 crystallise in monoclinic (P2₁/c) and 2 in triclinic (P-1) space group, respectively.     

Tetrametallic Reduction of Dinitrogen: Formation of a Tetranuclear Samarium Dinitrogen Complex

The cooperative attack of four (dipyrromethanyl)Sm(II) units on dinitrogen resulted in a novel tetranuclear samarium dinitrogen complex (shown schematically). The presence of halogen atoms inhibited reactivity with dinitrogen through the assembly of divalent samarium clusters. dipyrr=diphenylmethyldipyrrolide dianion.     

A Paramagnetic Diniobium Complex with a Very Short Nb-Nb Distance: Evidence for a Pseudo Nb-Nb Triple Bond?

In spite of the short Nb-Nb distance (2.268 ?) and the presumable existence of an Nb identical withNb bond, the paddle-wheel-shaped diniobium(II) complex 1 is paramagnetic. Theoretical calculations indicate that the presence of LiCl moieties on the intermetallic axis lowers the Nb-Nb bond order and is responsible for the observed paramagnetism.     

Terphenyl ligand systems in lanthanide chemistry: use of the 2,6-di(1-naphthyl)phenyl ligand for the synthesis of kinetically stabilized complexes of trivalent ytterbium, thulium, and yttrium

The molecular structures of terphenyl derivatives of trivalent ytterbium, thulium, and yttrium of general composition DnpLnCl(2)(THF)(2) [Dnp = 2,6-di(1-naphthyl)phenyl] are reported. The complexes (Ln = Yb: 1; Ln = Tm: 2; Ln = Y: 3) are synthesized by reaction of 1 equiv of DnpLi with 1 equiv of LnCl(3) (Ln = Yb, Tm, or Y) in tetrahydrofuran at room temperature in 50% yield. Attempts to prepare a Dnp scandium compound gave heterobimetallic [(THF)(3)Sc(2)OCl(5)Li(THF)](2) (4) in low yield. 1 crystallizes in the monoclinic space group C2/c. Crystal data for 1 at 203 K: a = 14.333(3) A, b = 16.353(3) A, c = 12.427(2) A, beta = 91.021(4) degrees, Z = 4, D(calcd) = 1.637 g cm(-3), R(1) = 4.44%. 2 crystallizes in the monoclinic space group C2/c. Crystal data for 2 at 203 K: a = 14.333(1) A, b = 16.374(2) A, c = 12.404(1) A, beta = 90.934(2) degrees, Z = 4, D(calcd) = 1.628 g cm(-3), R(1) = 3.00%. 3 crystallizes in the monoclinic space group C2/c. Crystal data for 3 at 203 K: a = 14.348(3) A, b = 16.476(3) A, c = 12.356(2) A, beta = 90.987(4) degrees, Z = 4, D(calcd) = 1.441 g cm(-3), R(1) = 5.62%. 4 crystallizes in the monoclinic space group P2(1)/n. Crystal data for 4 at 203 K: a = 11.0975(9) A, b = 11.0976(9) A, c = 21.3305(18) A, beta = 94.718(2) degrees, Z = 2, D(calcd) = 1.051 g cm(-3), R(1) = 3.45%. Complexes 1-3 represent examples of novel chiral (racemic) organometallic complexes of the lanthanide elements ytterbium and thulium and the group 3 element yttrium, respectively. The molecular structures of monomeric 1-3 exhibit distorted trigonal-bipyramidal coordination environments at the metal center, with the two oxygen atoms of the tetrahydrofuran ligands occupying the axial positions of a trigonal-bipyramidal coordination polyeder. The molecular structure of the scandium compound 4 shows a complex polynuclear heterobimetallic arrangement.