Using chemometrics for navigating in the large data sets of genomics, proteomics, and metabonomics (gpm)

This article describes the applicability of multivariate projection techniques, such as principal-component analysis (PCA) and partial least-squares (PLS) projections to latent structures, to the large-volume high-density data structures obtained within genomics, proteomics, and metabonomics. PCA and PLS, and their extensions, derive their usefulness from their ability to analyze data with many, noisy, collinear, and even incomplete variables in both X and Y. Three examples are used as illustrations: the first example is a genomics data set and involves modeling of microarray data of cell cycle-regulated genes in the microorganism Saccharomyces cerevisiae. The second example contains NMR-metabonomics data, measured on urine samples of male rats treated with either of the drugs chloroquine or amiodarone. The third and last data set describes sequence-function classification studies in a set of G-protein-coupled receptors using hierarchical PCA.     

Sol-Gel Microsphere Pelletisation Process for Fabrication of (U,Pu)O2, (U,Pu)C and (U,Pu)N Fuel Pellets for the Prototype Fast Breeder Reactor in India

A “dust-free” sol-gel microsphere pelletisation (SGMP) process has been developed for fabrication of (U,Pu)O₂, (U,Pu)C and (U,Pu)N fuel pellets containing around 15% plutonium for the forthcoming prototype fast breeder reactor (PFBR) in India. The objective was to produce homogeneous sintered pellets of ∼85% T.D. with a predominantly open-pore structure. Hydrated gel-microspheres of UO₃+PuO₂ and UO₃+PuO₂+C have been prepared from nitrate solutions of uranium and plutonium by the “ammonia internal gelation” process, using hexamethylene tetramine (HMTA) as an ammonia generator and silicone oil at 90±1°C as gelation bath. For oxide fuel pellets, the hydrated UO₃+PuO₂ gel-microspheres were calcined at around 700°C in Ar+8% H₂ atmosphere to produce “non-porous”, “free-flowing” and coarse (around 400 micron) microspheres which could be directly pelletised at 550 MPa to green pellets. The mixed oxide pellets were subjected either to low temperature (∼1100°C) oxidative sintering (LTS) in N₂+air containing ∼1500 ppm O₂ or to high temperature (1650°C) sintering, (HTS) in Ar+8% H₂. For monocarbide and mononitride pellets, hydrated gel-microspheres of UO₃+PuO₂+C were subjected to carbothermic synthesis in vacuum (∼1 Pa) and flowing nitrogen (flow rate: 1.2 m³/h) in the temperature range of 1450–1550°C respectively. The monocarbide and mononitride microspheres thus produced were relatively hard and required higher compaction pressure (∼1200 MPa) for making reen pellets which could be sintered to 85% T.D. in Ar+8% H₂ at 1700°C. The sintered oxide, monocarbide and mononitride pellets had a “blackberry” “open” pore microstructure with fine grain size. The microspheres retained their individual identity in the sintered pellets because during sintering densification took place mainly within and not between the microspheres.     

Comparative energies of Zn(II) cation localization as a function of the distance between two forming cation position aluminium ions in high-silica zeolites

Periodical calculations of Zn(II) metal cation stabilization in cationic positions with distantly placed aluminium ions has been performed for high-silica ferrierite. It was found that decrease of the stabilization energy at large distances between Al ions (more than 10 Å) is about of 2 eV in comparison with nearest possible position of two Al ions in the zeolite lattice and weekly depended on following increase of the Al-Al distance. Main changes in stabilization energy occured within a 3-Å interval of these distances. Only for the localizations of both Al ions in one zeolite ring zinc cationic form is more stable than hydrogen form.     

Quantum chemical topology: The electronic structure of the alkaline nitrites MONO (M = Li,Na, K) studied by means of topological analysis of the electron localization function

In the search of the protocovalent bonding, previously recognized in the nitrous acid (HONO), a nature of the chemical bonds in the alkaline nitrites MONO (M = Li, Na, K) has been studied by means of the topological analysis of the Electron Localization Function (ELF) and Electron Localizability Indicator (ELI‐D). Calculations carried out with the B3LYP and MP2(full) methods, in conjunction with the aug‐cc‐pVTZ and 6‐311++G(3df,3pd) basis sets, revealed the cis (C_2v, more stable) and trans (C_s) isomers as minima on PES. Alkaline nitrites consist of the alkali metal cation M^δ+ interacting, mainly via electrostatic forces, with the nitrite anion [ONO]^δ− (δ ≈ 1e). The covalent N O bonds are characterized by disynaptic basins V(N,O) with the basin populations: 1.58÷1.62e for cis‐M^δ+[ONO]^δ− but 1.39÷1.49e for single N O bond and 1.81÷1.87e for formally double NO bond in trans M^δ+[O NO]^δ−. The protocovalent nitrogen–oxygen bond has not been observed. The N O bonds are slightly polarized towards the nitrogen atom with the polarity index p_NO ≤ 0.12. Two different sets of the hybrid (Lewis) structures are compared leading to different pictures of the bonding. According to NBO data there is a delocalization between the single N O and double NO type bonds, meanwhile results of the ELF analysis emphasize an electron delocalization between the single N O and ionic O⁻N⁺ hybrids. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

The chemical bond in polyphosphides: crystal structures, the electron localization function, and a new view of aromaticity in P4(2-) and P5(-)

The incongruent solvation of M(I)4P6 species (M(I) = K, Rb, Cs) in liquid ammonia leads to a broad variety of polyphosphides such as P7(3-), P11(3-), and the putatively aromatic P4(2-) and P5(-), which we investigated by using NMR spectroscopy and single-crystal X-ray structure analysis. The structures of Cs2P4 x 2 NH3, (K@[18]crown-6)3K3(P7)2 x 10 NH3, Rb3P7 x 7 NH3, and (Rb@[18]crown-6)3P7 x 6 NH3 are discussed and compared. The electron localization function ELF is used in a comparison of the chemical bonding of various phosphorus species. The variances of the basin populations provide a well-established measure for electron delocalization and therefore aromaticity. While comparable variance is calculated for P4(2-) and P5(-) it is observed in the lone pairs rather than in the basin populations of the bonds as in the prototypical aromatic hydrocarbons such as benzene or the cyclopentadienide anion. For this behavior, the term "lone pair aromaticity" is proposed.     

Limitations,mechanism and understanding of the origins of stereocontrol in (S)-dimethylsulfonium-(p-tolylsulfinyl)methylide-mediated epoxidation reactions

The reaction of the (S)-dimethylsulfonium-(p-tolylsulfinyl)methylide with aldehydes gave α,β-epoxy sulfoxides with high enantioselectivity and diastereoselectivity dependent on the aldehyde. The mechanism of the ‘model’ reactions [ylide substituted with Me S(O) or Ph S(O) with MeCHO or PhCHO] has been studied in detail using density functional theory.     

Application of Short Sequential Extraction Procedure（SSEP） for the Determination of Zn, Cu, and Cd Contents in Riverbed Sludge in Hejiagou, Harbin, China

IntroductionThe environment is contaminated by high concen-trations of metals from different sources such as conta-minated soils[1—10], sediments[11—15], and sewage orindustrial sludge[16—20]. However, there has been noreport on the determination of he…     

Screening and insilico analysis of deleterious nsSNPs (missense) in human CSF3 for their effects on protein structure,stability and function

Human granulocyte colony stimulating factor (hG-CSF), known as CSF3, plays an important role in the growth, differentiation, proliferation, survival, and activation of the granulocyte cell lineage such as neutrophils and their precursors. Functional reduction in native CSF3 protein results in reduced proliferation and activation of neutrophils and leads to neutropenia. Single nucleotide polymorphisms (SNPs) in the CSF3 gene may have deleterious effects on the CSF3 protein function. This study was undertaken to find the functional SNPs in the human CSF3 gene. Results suggest that 18.9% of all the SNPs in the dbSNP database for CSF3 gene were present in the coding region. Out of 59 non-synonymous SNPs (nsSNPs), 26 nsSNPs were predicted to be non-tolerable by SIFT whereas 18 and 7 nsSNPs were predicted as probably damaging and possibly damaging, respectively by PolyPhen. Among this 31 nsSNPs, 16 nsSNPs were identified to be potentially deleterious by PANTHER server, and 4 nsSNPs were found to be neutral by PROVEAN. SNPAnalyzer predicted 7 nsSNPs to be neutral phenotype and the remaining 24 nsSNPs to be associated with diseases. Among the predicted nsSNPs, rs144408123, rs144408123, rs145136406, rs145311241, rs373191696, rs762945096, rs763688260, rs767572172, rs775326370, rs777777864, rs777983866, rs781596455, rs139072004, rs757612684, rs772911210, rs139072004, rs746634544, rs749993200, rs763426127, rs772466210 were identified as deleterious and potentially damaging. I-Mutant analysis revealed that th 20 nsSNPs were important for protein stability of CSF3. Therefore, th 20 nsSNPs may be used for the wider population-based genetic studies and also should be taken into account while engineering the recombinant CSF3 protein for clinical use.     

Synthesis,characterization and structure of the Bis(methyl-cyclopentadienyl)vanadium(IV) carboxylates

The 1,1’-dimethylvanadocene dichloride ((C₅H₄CH₃)₂VCl₂) reacts in aqueous solution with various carboxylic acids giving two different types of complexes. The 1,1’-dimethylvanadocene complexes of monocarboxylic acids (C₅H₄CH₃)₂V(OOCR)₂ (R=H,CCl₃, CF₃, C₆H₅) contain two monodentate carboxylic ligands, whereas oxalic and malonic acids act as chelate compounds of the formula (C₅H₄CH₃)₂V(OOC-A-COO) (A=−, CH₂). The structure of the (C₅H₄CH₃)₂ V(OOCCF₃)₂ complex was determined by single crystal X-ray diffraction analysis. The isotropic and anisotropic EPR spectra of all the complexes prepared were recorded. The obtained EPR parameter values were found to be in agreement with proposed structures.     

Synthesis, characterization, electrochemistry, electronic structure, and isomerization of mononuclear oxo-molybdenum(V) complexes: the serine gate hypothesis in the function of DMSO reductases

Crystal structures of DMSO reductases isolated from two different sources and the crystal structure of related trimethylamine-N-oxide reductase indicate that the angle between the terminal oxo atom on the molybdenum and the serinato oxygen varies significantly. To understand the significance of this angular variation, we have synthesized two isomeric compounds of the heteroscorpionato ligand (L1OH) (cis- and trans-(L1O)Mo(V)OCl(2)), where the phenolic oxygen mimics the serinato oxygen donor. Density functional and semiempirical calculations indicate that the trans isomer is more stable than the cis. The lower stability of the cis isomer can be attributed to two factors. First, a strong antibonding interaction between the phenolic oxygen with molybdenum d(xy) orbital raises the energy of this orbital. Second, the strong trans influence of the terminal oxo group in the trans isomer places the phenol ring, and hence the bulky tertiary butyl group, in a less sterically hindered position. In solution, the cis isomer spontaneously converts to the thermodynamically favorable trans isomer. This geometric transformation follows a first-order process, with an enthalpy of activation of 20 kcal/mol and an entropy of activation of -9 cal/mol K. Computational analysis at the semiempirical level supports a twist mechanism as the most favorable pathway for the geometric transformation. The twist mechanism is further supported by detailed mass spectral data collected in the presence of excess tetraalkylammonium salts. Both the cis and trans isomers exhibit well-defined one-electron couples due to the reduction of molybdenum(V) to molybdenum(IV), with the cis isomer being more difficult to reduce. Both isomers also exhibit oxidative couples because of the oxidation of molybdenum(V) to molybdenum(VI), with the cis isomer being easier to oxidize. This electrochemical behavior is consistent with a higher-energy redox orbital in the cis isomer, which has been observed computationally. Collectively, this investigation demonstrates that by changing the O(t)-Mo-O(p) angle, the reduction potential can be modulated. This geometrically controlled modulation may play a gating role in the electron-transfer process during the regeneration steps in the catalytic cycle.     

Fast topological analysis of 2D and 3D grids of data: application to the atoms in molecule (AIM) and the electron localization function (ELF)

The topological analysis of grids of data is used for determination of surfaces or volumes around maxima. The volumes are then related to chemical information such as atoms or bonds, and can be used for integration of local properties such as electronic population. The problem of global connectivity is reversed into the question of local connectivity yielding a linear scaling partition algorithm. Two packages are developed for a very fast analysis and partition of 2D or 3D grids of data, applications being made to C2H2, C2H4, C6H6, H2CO, and H2CS molecules using the Atoms in Molecule (AIM) or Electron Localization Function (ELF).     

Synthesis,X-ray crystal structure,and redox and electronic properties of iron(III)-polyimidazole complexes relevant to the metal sites of iron proteins

A new tripod N(3) ligand (L), containing three imidazole rings, was synthesized in good yield. At variance with usual aromatic ligands with N(2) or N(3) donor sets such as pyridine or pyrazole derivatives, L stabilizes the Fe(III) oxidation state. The corresponding iron(III) complexes [Fe(L)Cl(3)] (1) and [Fe(L)(2)](ClO(4))(3) (2) were prepared and characterized by X-ray structural analysis and spectroscopic methods. The coordination environment around all the Fe(III) centers has a distorted octahedral geometry. [Fe(L)Cl(3)] (1) belongs to the monoclinic system, space group P2(1)/n, a = 9.7406(5) A, b = 17.207(2) A, c = 14.615(2) A, beta = 104.448(9)(o) Z = 4, V = 2372.1(4) A(3); R = 0.044, R(w) = 0.055. [Fe(L)(2)](ClO(4))(3) (2) belongs to the monoclinic system, space group P2(1)/c, a = 16.1057(15) A, b = 11.1079(12) A, c = 26.283(2) A, beta = 102.062(10)(o), Z = 4, V = 4598.2(8) A(3); R = 0.0465, R(w) = 0.0902. The Fe-N((i)PrIm) bond lengths are systematically longer than the Fe-N(MeIm) ones. Compound 2 is a highly anisotropic low-spin Fe(III) complex displaying a rather unusual EPR spectrum with a sharp signal at g = 3.5 and a broad one at g approximately 1.6. The fitting of this EPR spectrum is discussed.     

Investigation of extraction procedures and HPLC-DAD/MS for the determination of the brominated flame retardant tetrabromobisphenol A bis(2,3-dibromopropylether) in environmental samples

A method for the determination of the novel brominated flame retardant tetrabromobisphenol A bis(2,3-dibromopropylether), 1,1′-(isopropylidene)bis[3,5-dibromo-4-(2,3-dibromo-propoxy)-benzene] (TBBPA-dbpe), was developed. Technical TBBPA-dbpe was purified and the results of a thorough physical characterisation are reported. The application of APCI-MS is discussed and the fragmentation patterns are described. Quantification of TBBPA-dbpe was done by HPLC-DAD using external calibration. The validation of the method was accomplished using sediment and sewage sludge samples spiked with defined amounts of authentic TBBPA-dbpe. The average recovery rates of TBBPA-dbpe from spiked samples ranged from 35 to 91% (sediment) and from 57 to 98% (sewage sludge) depending on the respective extraction method. Pressurised fluid extraction (PFE) and fluidised bed extraction were superior to classical Soxhlet and sonication procedures and yielded recovery rates between 90 and 98% with relative standard deviations of 2%. The limits of detection (DTC), identification (ID) and determination (DTM) using HPLC-DAD were 10, 21 and 30 ng g⁻¹ in sediment and 22, 44 and 72 ng g⁻¹ in sewage sludge, respectively.     

Mathematical aspects of the LCAO MO first order density function (1): atomic partition, metric structure and practical applications

Partition of the first order density function within LCAO MO theory permits the definition of Mulliken and Minkowski metric spaces. The metric matrices obtained become useful to connect density atomic partition with quantum similarity measures, Mulliken populations, EHT, expectation values of Hermitian operators and the comparison of two density distributions.     

Acidity in aqueous mixed solvent systems—III : Influence of the organic solvent molecular structure on the acidity of aquo-organic mixtures (acidity function,water structure,hydrophilic and hydrophobic effects)

The acidity functions Ho and H_R have been determined for different aqueous organic mixtures (diols, carbohydrates) at constant acid concentration. We have checked, with a reaction involving a slow proton transfer, that Ho and H_R vary in direct proportion to the acidity of the systems.The results are interpreted in terms of the variations of the proton activity which is dependent on the modifications of the water structure by the organic cosolvent.     

Simple method for the preparation of DNA-poly(o-methoxyaniline) hybrid: structure, morphology, and uncoiling of poly(o-methoxyaniline) on the DNA surface

The DNA-poly(o-methoxyaniline) (POMA) hybrid is prepared by mixing aqueous solutions of POMA [emeraldine salt (ES), doping level [Cl]/[N] = 0.52] and sodium salt of DNA (Na-DNA) and is then freeze-dried after 4 days. Three different compositions (WDNA = 0.25, 0.5, and 0.75, WDNA is the weight fraction of DNA) of the hybrids are prepared. The SEM pictures show a gradation in morphology; for example, for WDNA = 0.75, fibrils are present but, at lower DNA concentration, a fibrillar network structure of the hybrid is observed. The circular dichroism (CD) spectra of the hybrid solutions indicate unchanged DNA conformation and WAXS patterns indicate intact crystal structure of DNA in the hybrid. The UV-vis spectra suggest no denaturation of DNA during the blending process. The UV-vis spectra of the hybrids in aqueous medium show a gradual red shift of the pi band to polaron band transition with time. The plots of these wavelengths with time are sigmoidal, indicating the autocatalytic nature of the process. With an increase in the temperature, the rate of the red shift of the above peak is faster. Arrhenius analysis of the rate (1/tau700 where tau700 is the time required to reach the absorption maximum at the wavelength 700 nm) yields straight lines for the three hybrid compositions with activation energy values of 13-15 kcal/mol. These values are almost equal to the activation energy values of conformational transition of other polymers, supporting the red shift in UV-vis spectra occurs from conformational transition. DNA offers a surface where POMA gets adsorbed and the stable conformational transition resulting in the uncoiling of the POMA chain occurs through repulsive interaction among bound radical cations of POMA (ES) on the DNA surface. The conductivity of the hybrids is on the order of 10(-6) S/cm, and the I-V characteristic curves indicate the semiconducting nature of the hybrids.     

Utilization of W/Mg(NO3)2 modifiers for the direct determination of As and Sb in soils,sewage sludge and sediments by solid sampling electrothermal atomic absorption spectrometry

A simple method has been developed for the determination of arsenic and antimony in environmental samples by solid sampling electrothermal atomic absorption spectrometry, which was validated using certified reference materials of soils (S-VM — Soil Eutric Cambisol; S-MS — Soil Orthic Luvisols; S-SP — Soil Rendzina), sewage sludge (WT-L; WT-M) and sediments (NIES2; GBW07906). The analytical procedure combines solid sampling with utilization of a matrix modifier admixture containing 5 µg of W and 5 µg of Mg. The tungsten in the admixture serves to stabilize the solid matrix during atomisation, which results in dramatically reduced non-specific absorption compared with the conventional palladium modifier. Magnesium was efficient in reducing the accumulation of the matrix residue on the platform. An alternative resonance line of 197.2 nm for arsenic and 206.8 nm for Sb was used in order to eliminate the spectral interferences caused by aluminum compounds, and silicon and iron compounds, respectively. Under optimized experimental conditions, the effective in situ analyte/matrix separation was achieved so that the use of aqueous standards for calibration became possible. With the modifier, a 3 SD detection limit of 0.5 µg g⁻¹ As and 0.1 µg g⁻¹ Sb and 10 SD quantification limit of 1.7 µg g⁻¹As and 0.3 µg g⁻¹ Sb and a characteristic mass of 65 pg As and 53 pg Sb were obtained. For all the matrices under scrutiny, a good agreement with certified values was achieved with RSD values less than 10%.     

Preparation,X-ray crystal structure determination,lattice potential energy,and energetics of formation of the salt S4(AsF6)2.AsF3 containing the lattice-stabilized tetrasulfur [2+] cation. Implications for the understanding of the stability of M(4)2+ and M2+ (M = S,Se, and Te) crystalline salts

S4(AsF6)2.AsF3 was prepared by the reaction of sulfur with arsenic pentafluroide in liquid AsF3 (quantitatively) and in anhydrous HF in the presence of trace amounts of bromine. A single-crystal X-ray structure of the compound has been determined: monoclinic, space group P2(1)/c, Z = 4, a = 7.886(1) A, b = 9.261(2) A, c = 19.191(3) A, beta = 92.82(1) degrees, V = 1399.9(4) A3, T = 293 K, R1 = 0.052 for 1563 reflections (I > 2 sigma (I) 1580 total and 235 parameters). We report a term-by-term calculation of the lattice potential energy of this salt and also use our generalized equation, which estimates lattice energies to assist in probing the homopolyatomic cation thermochemistry in the solid and the gaseous states. We find S4(AsF6)2.AsF3 to be more stable (delta fH degree [S4(AsF6)2.AsF3,c] approximately -4050 +/- 105 kJ/mol) than either the unsolvated S4(AsF6)2 (delta fH degree [S4(AsF6)2,c] approximately -3104 +/- 117 kJ/mol) by 144 kJ/mol or two moles of S2AsF6 (c) and AsF3 (1) by 362 kJ/mol. The greater stability of the S(4)2+ salt arises because of the greater lattice potential energy of the 1:2 solvated salt (1734 kJ/mol) relative to twice that of the 1:1 salt (2 x 541 = 1082 kJ/mol). The relative lattice stabilization enthalpies of M(4)2+ ions relative to two M2+ ions (i.e., in M4(AsF6)2 (c) with respect to two M2AsF6 (c) (M = S, Se, and Te)) are found to be 218, 289, and 365 kJ/mol, respectively. Evaluation of the thermodynamic data implies that appropriate presently available anions are unlikely to stabilize M2+ in the solid phase. A revised value for delta fH degree [Se4(AsF6)2,c] = -3182 +/- 106 kJ/mol is proposed based on estimates of the lattice energy of Se4(AsF6)2 (c) and a previously calculated gasphase dimerization energy of 2Se2+ to Se(4)2+.     

Synthesis, structure determination, and (radio-)fluorination of novel functionalized phosphanes suitable for the traceless Staudinger ligation

An elegant and efficient synthesis approach for the preparation of novel benzoate and nicotinate containing phosphanes is presented. This reaction path has a broad substrate scope. Thus, various functionalized phosphanes were obtained in high yields using an esterification procedure under Steglich conditions. A facile blocking of the phosphorus atom with BH₃ was carried out. BH₃ as easily insertable and removable protecting group enables a further derivatization of the benzoate residue. The prepared phosphane derivatives proved to be valuable labeling building blocks for the implementation of a bioorthogonal (radio-)fluorination strategy and were applied for labeling purposes using the traceless Staudinger ligation. For this purpose, a selection of azide-functionalized small organic and bioactive sample molecules was prepared. Furthermore, a mild and selective (radio-)fluorination of these derivatives is demonstrated adopting this bioorthogonal ligation method.     

Electronic structure, X-ray absorption, and optical spectroscopy of LaCoO(3) in the ground-state and excited-states

We present the magnetic and optical properties of various combinations of ordered spin state configurations between low-spin (LS) state, intermediate-spin (IS) state, and high-spin (HS) state of LaCoO(3) . In this study, we use the state-of-the-art first principles calculations based on generalized gradient (GGA) + Hubbard U approach. The excited-state properties of different spin configurations of LaCoO(3) such as the X-ray absorption spectra, optical conductivity, reflectivity, and electron energy loss are calculated. We have demonstrated that the optical spectra results can be used for analyzing the spin state of Co(3+) ion. The first specie is the local excitation of IS cobalt ions in the LS ground state. The second excitation leads to the stabilization of the mixed IS/HS Co(3+) metallic state. At low temperature, the comparison between O 2p and Co 3d projected density of states with the experimental valence band spectra indicates significant IS Co(3+) ions and this is in sharp contrast to the HS state which is negligible. The line shape of O 2s and Co 3d core level spectra are well reproduced in this study. The present results are in excellent agreement with the available experimental data. The variation in the spectra of different configurations of LaCoO(3) suggests a changing in the spin state as the temperature is enhanced from 90 to 500 K.