Structure and vibrational spectra of Ti(IV) hydroxides and their clusters with expanded titanium coordination. DFT study

Equilibrium structures of H(4-n)Ti(OH)n (n = 2-4) molecules and the Ti(OH)4 dimer and trimers were optimized at the B3LYP level of theory. Theoretical vibrational frequencies of TiO stretching modes obtained with several basis sets were compared with the existing experimental frequencies of these vibrations, and the 6-31+G(d) set was chosen for cluster calculations. Only one energy minimum was found for the [Ti(OH)4](2) dimer, but two isomers without symmetry elements stabilized by internal hydrogen bonds and two isomers, belonging to C(s) and C(i) point groups, with free OH groups were found as minima at the [Ti(OH)4](3) potential energy surface. The structure with the linear arrangement of hexacoordinated titanium atoms in the Ti3O12 skeleton may be proposed for trimeric species observed in liquid titanium alkoxides as the only structure satisfying experimental spectroscopic evidence about the presence of center of inversion in these species. Frequency changes of TiO4 modes which accompany the oligomer formation are predicted and discussed.     

Theoretical and experimental investigation on the oxidation of gallic acid by sulfate radical anions

By monitoring the decay of SO4*- after flash photolysis of aqueous solutions of S2O82- at different pH values, the kinetics of the reaction of SO4*- radicals with gallic acid and the gallate ion was investigated. The bimolecular rate constants for the reactions of the sulfate radicals with gallic acid and the gallate ion were found to be (6.3 +/- 0.7) x 10(8) and (2.9 +/- 0.2) x 10(9) M(-1) s(-1), respectively. On the basis of the oxygen-independent second-order decay kinetics and on their absorption spectra, the organic radicals formed as intermediates of these reactions were assigned to the corresponding phenoxyl radicals. DFT calculations in the gas phase and aqueous solution support formation of the phenoxyl radicals by H abstraction from the phenols to the sulfate radical anion. The observed recombination of the phenoxyl radicals of gallic acid to yield substituted biphenyls and quinones is also supported by the calculations. HPLC/MS product analysis showed formation of one of the predicted quinones.     

Effect of thermal treatment on phase composition and ethanol oxidation activity of a carbon supported Pt50Sn50 alloy catalyst

A carbon supported Pt–Sn electrocatalyst in the Pt/Sn atomic ratio 50:50 was prepared by the reduction of Pt and Sn precursors with formic acid and thermally treated at 200 °C (i.e., in the presence of solid tin) and 500 °C (in the presence of molten tin) in flowing hydrogen. In the absence of thermal treatment, X-ray diffraction (XRD) analysis showed a solid solution of Sn in the face centered cubic (fcc) Pt and SnO₂. After thermal treatment, the formation of a main phase of hexagonal PtSn (niggliite) and a secondary phase of cubic Pt₃Sn was observed in the Pt50Sn50 catalyst. The relative amount of the PtSn phase increased with increasing thermal treatment temperature. The presence of molten tin gave rise to the formation of some big particles during annealing at 500 °C. The activity for the ethanol oxidation reaction (EOR) of the as-prepared catalyst was higher than that of both thermally treated catalysts and Pt75Sn25/C and Pt50Ru50/C by E-TEK. The higher activity for the EOR of the as-prepared Pt–Sn catalysts was ascribed to the presence of a large amount of SnO₂. Dedicated to Teresa Iwasita’s 65th birthday.     

Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostics

Mass spectrometry (MS) has become a powerful tool for the quantitative analysis of complex protein samples. A high-throughput strategy for the comparative analysis of multiple protein samples with high complexity becomes more and more important. Two strategies, spectral count and peak intensity, for label-free MS analysis of prefractionated complex mixtures have been described recently to be useful for quantitation. Here we compare both strategies for rapid and quantitative 1-D shotgun LC/MS/MS analyses of highly complex protein mixtures using silica-based monolithic columns. First, we validated linearity and sensitivity of these methods by spiking varying amounts of an internal standard protein in a complex plant protein extract. Secondly, quantitative data of proteins of Medicago truncatula nodules were visualized with independent components analysis using data either obtained from spectral count or peak integration performed with commercial software. Spectral count showed apparent advantages over peak integration because several peptides per protein are automatically averaged, the linear dynamic range of quantitation increases in complex matrices and the number of quantified proteins surpasses the number of proteins using peak integration. Thus, for the need of rapid comparative analysis of highly complex protein samples, spectral count enables sample pattern recognition and identification of biomarkers in nongel based proteomic studies.     

Synthesis and structure of [(Sn(mu-PCy))3(Na x PMDETA)2], containing an electron-deficient [(Sn(mu-PCy))3]2- dianion

The reaction of CyPHNa with Sn(NMe2)2 in the presence of PMDETA (= (Me2NCH2CH2)2NMe) gives the title compound [(Sn(mu-PCy))3(Na x PMDETA)2] (1), containing an electron-deficient [(Sn(mu-PCy))]3(2-) dianion with a novel two-electron, three centre (2e-3c) bonding arrangement.     

Synthesis of molecular motors incorporating para-phenylene-conjugated or bicyclo[2.2.2]octane-insulated electroactive groups

The insulating role of the bicyclo[2.2.2]octane fragment has been theoretically evaluated by comparing the electronic coupling parameter (V(ab)) in 1,4-bis(ferrocenyl)benzene (1) and 1,4-bis(ferrocenyl)bicyclo[2.2.2]octane (2). The geometries were optimized by DFT and an extended Hückel calculation was performed to evaluate V(ab) by the dimer splitting method. The calculations showed a 12-fold decrease of the electronic coupling from 60 meV for 1 to 5 meV for 2. The second part describes the synthesis of two potential molecular motors with one incorporating the insulating bicyclo[2.2.2]octane fragment. These molecules are based on a ruthenium complex bearing a tripodal stator functionalized to be anchored onto surfaces. The ferrocenyl electroactive groups and the cyclopentadienyl (Cp) rotor are connected through a p-phenylene spacer (5) or through a spacer incorporating an insulating bicyclo[2.2.2]octane moiety (6).     

Adsorption of silanes bearing nitrogenated Lewis bases on SiO2/Si (100) model surfaces

The present paper describes the one-pot procedure for the formation of self-assembled thin films of two silanes on the model oxidized silicon wafer, SiO2/Si. SiO2/Si is a model system for other surfaces, such as glass, quartz, aerosol, and silica gel. MALDI-TOF MS with and without a matrix, XPS, and AFM have confirmed the formation of self-assembled thin films of both 3-imidazolylpropyltrimethoxysilane (3-IPTS) and 4-(N-propyltriethoxysilane-imino)pyridine (4-PTSIP) on the SiO2/Si surface after 30 min. Longer adsorption times lead to the deposition of nonreacted 3-IPTS precursors and the formation of agglomerates on the 3-IPTS monolayer. The formation of 4-PTSIP self-assembled layers on SiO2/Si is also demonstrated. The present results for the flat SiO2/Si surface can lead to a better understanding of the formation of a stationary phase for affinity chromatography as well as transition-metal-supported catalysts on silica and their relationship with surface roughness and ordering. The 3-IPTS and 4-PTSIP modified SiO2/Si wafers can also be envisaged as possible built-on-silicon thin-layer chromatography (TLC) extraction devices for metal determination or N-heterocycle analytes, such as histidine and histamine, with "on-spot" MALDI-TOF MS detection.     

Separation of proteins with a molecular mass difference of 2 kDa utilizing preparative double-inverted gradient polyacrylamide gel electrophoresis under nonreducing conditions: application to the isolation of 24 kDa human growth hormone

A method for separating proteins with a molecular mass difference of 2 kDa using SDS-PAGE under nonreducing conditions is presented. A sample mixture containing several human growth hormone (hGH) isoforms was initially separated on a weak anion-exchange column. Fractions rich in 24 kDa hGH as determined by analytical SDS-PAGE were pooled and further separated by cation-exchange chromatography. The fractions pooled from the cation-exchange chromatography contained two hGH isoforms with a 2 kDa molecular mass difference according to SDS-PAGE analysis, 22 and 24 kDa hGH. The 22 and 24 kDa hGH were separated using continuous-elution preparative double-inverted gradient PAGE (PDG-PAGE) under nonreducing conditions. The preparative electrophoresis gel was composed of three stacked tubular polyacrylamide matrices, a 4% stacking gel, a 13-18% linear gradient gel, and a 15-10% linear inverted gradient gel. Fractions containing purified 24 kDa hGH were pooled and Western blot analysis displayed immunoreactivity to antihGH antibodies. PDG-PAGE provides researchers with an electrophoretic technique to preparatively purify proteins under nonreducing conditions with molecular mass differences of 2 kDa.     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Long range ordering in self-assembled Ni arrays on patterned Si

We have succeeded in aligning self-assembled structures by using a lithographically defined stripe. The 140 nm wide by 100 nm high SiO₂ strip is shown to guide the assembly of 500 nm latex spheres so that spheres are aligned along the strip and are in registration on either side of the strip. This method can be used to increase long-range ordering in magnetic storage systems without compromising the density. Inverse sphere Ni arrays were made by electrodeposition through the latex template. We also show that the hexagonal symmetry of the resulting inverse sphere Ni arrays can be simulated using the approach presented below.