Isotope effects in the dissociation of the B 1A1 state of SiH2, SiHD, and SiD2 using three-dimensional wave packet propagation

Dissociations after the A 1B1-->B 1A1 photoexcitation of SiH2, SiHD, and SiD2 were studied to investigate excited-state dynamics and effects of the initial vibrational state. The cross section (sigma) for the photodissociation relative to SiH2(B)-->Si(1D)+H2 and the rovibrational population of the H2 fragment were computed using the wave packet propagation technique based on the three-dimensional potential energy surfaces (PESs) of the A and B electronic states and the transition dipole surfaces, which were reported in our previous paper [J. Chem. Phys. 122, 144307 (2005)]. The photodissociation spectrum consists of a broadband and a number of sharp peaks. For SiH2 and SiD2, the sharp peaks correspond to the resonance structure of the vibrational levels of the B state and the broadbands are nearly independent of the photon energy. The broadband for SiHD increases steeply with the photon energy above 30,000 cm(-1). The flux leaving the computational grid for SiH2 and SiD2 consists of at least two components, whereas that for SiHD consists of only a faster component. These large isotope effects were discussed based on the valley to the dissociation channel on PES and the difference in the position of the initial wave packet for three isotopomers.     

Using triethynylphosphine ligands bearing bulky end caps to create a holey catalytic environment: application to gold(I)-catalyzed alkyne cyclizations

The synthesis, properties and catalytic uses of phosphinoalkynes bearing bulky end caps at the alkyne termini, that is, tris[(triarylsilyl)ethynyl]phosphines are reported. The most salient feature of the new phosphines is the holey molecular shape possessing a deep and large-scale metal-binding cavity. The holey phosphines displayed remarkable rate enhancement in the gold(I)-catalyzed six- and seven-membered ring forming cyclizations of acetylenic keto esters and 1,7-enynes. It is proposed that the cavity in the ligand forces a nucleophilic center (enol or alkene) of the acetylenic compounds close to the gold-bound alkyne, making ring-closing anti attack feasible.     

Systematics of Mössbauer parameters in Fe57-doped titanate and germanate ilmenites

The Mössbauer spectra of ilmenite (FeTiO₃), Fe²⁺-doped ilmenites, MTiO₃ (M = Cd, Mn, Zn, Co, Mg and Ni) and MGeO₃ (M = Mn, Zn and Mg), have been studied from 4.2 K to room temperature. Systematic variations in the isomer shift and quadrupole splitting at room temperature are correlated with the change in ionic radii of the host M ions and the c/a ratio of the host crystal, respectively. The quadrupole splittings show a remarkable temperature variation; the magnetic ilmenites show either a sudden increase or a sudden decrease of quadrupole splittings below the Néel temperature, depending on the orientation of the spin axis with respect to the c axis.     

Mass spectrometric strategy for the characterization of lipooligosaccharides from Neisseria gonorrhoeae 302 using FTICR

The lipooligosaccharides (LOS) of Neisseria gonorrhoeae 302 were profiled using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Using techniques developed in this laboratory, the topology and some of the linkages of the LOS were determined. Mass spectrometric analysis in the negative ion mode yielded a glycoform of the composition: Hex3 Hep2 Hxn1 PEA1 KDO2 DPLA. The composition was confirmed through exact mass measurements, which showed only a 2 ppm error between the exact mass and theoretical mass. Although the core structure has been postulated previously, the positioning of the three hexose moieties were in question for this particular strain of N. gonorrhoeae. Topology assignment was performed through collision-induced dissociation analysis of the O-deacylated glycoform in the negative ion mode followed by submission to the saccharide topology analysis tool (STAT) computer program, which confirmed the topology assignment. It was found that the three hexoses were added to the Hep[I] of the conserved core of N. gonorrhoeae in a linear fashion, while Hep[II] remains unbranched. Linkage position analysis was performed through application of a mild acid hydrolysis technique followed by collision-induced dissociation of the sodiated precursor ions, yielding a 1 --> 4 linkage between the terminating and penultimate hexoses.     

A carbaboranylmercuric salt catalyzed reaction; highly regioselective cycloisomerization of 1,3-dienes

The combination of carbaboranylmercuric chloride (new type of bulky Lewis acid) and silver triflate efficiently catalyzes cycloisomerization of 1,3-dienes at room temperature. The catalytic system gives allyl-substituted azacycles and cycloalkanes in excellent yields with high to complete regioselectivity.     

Prospects for tertiary structure prediction of RNA based on secondary structure information

We developed a method, called RNA Assembler using Secondary Structure Information Effectively (RASSIE), for predicting RNA tertiary structures using known secondary structure information. We attempted a fragment assembly-based method that uses a secondary structure-based fragment library. For several typical target structures such as stem-loops, bulge-loops, and 2-way junctions, our method provided numerous good quality candidate structures in less computational time than previously proposed methods. By using a high-resolution potential energy function, we were able to select good predicted structures from candidate structures. This method of efficient conformational search and detailed structure evaluation using high-resolution potential is potentially useful for the tertiary structure prediction of RNA.     

Protein-bound uremic toxins in hemodialysis patients measured by liquid chromatography/tandem mass spectrometry and their effects on endothelial ROS production

Cardiovascular disease (CVD) is prevalent in patients with chronic kidney disease (CKD). In hemodialysis (HD) patients, some protein-bound uremic toxins are considered to be associated with CVD. However, it is not yet known which uremic toxins are important in terms of endothelial toxicity. Serum samples were obtained from 45 HD patients before and after HD. Total and free serum concentrations of indoxyl sulfate, indoxyl glucuronide, indoleacetic acid, p-cresyl sulfate, p-cresyl glucuronide, phenyl sulfate, phenyl glucuronide, phenylacetic acid, phenylacetyl glutamine, hippuric acid, 4-ethylphenyl sulfate, and 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid (CMPF) were simultaneously measured by liquid chromatography/electrospray ionization-mass spectrometry/mass spectrometry (LC/ESI-MS/MS). The effects of these solutes at their pre-HD mean and maximum serum concentrations on reactive oxygen species (ROS) production in human umbilical vein endothelial cells (HUVEC) were measured with a ROS probe. Serum levels of 11 of the solutes (all except 4-ethylphenyl sulfate) were significantly increased in HD patients compared to healthy subjects. All 12 solutes showed changes in their protein-binding ratios. In particular, indoxyl sulfate, p-cresyl sulfate, CMPF, and 4-ethylphenyl sulfate showed high protein-binding ratios (>95 %) and low reduction rates by HD (<35 %). Indoxyl sulfate at its mean and maximum pre-HD serum concentrations-even with 4 % albumin-stimulated ROS production in HUVEC most intensely, followed by CMPF. In conclusion, the serum levels of 11 protein-bound uremic toxins were increased in HD patients. Indoxyl sulfate, p-cresyl sulfate, and CMPF could not be removed efficiently by HD due to their high protein-binding ratios. Indoxyl sulfate most intensely induced endothelial ROS production, followed by CMPF.     

Bottom-up Synthesis and Thread-in-Bead Structures of Finite (n,0)-Zigzag Single-Wall Carbon Nanotubes

The last remaining synthetic target of finite single-wall carbon nanotube models, the zigzag nanotube, has been accomplished through bottom-up chemical synthesis. The zigzag nanotube was synthetically accessible without constructing long-sought yet elusive cyclacene structures but with a cycloarylene structure by devising its cutout positions. The persistent tubular shape was also perfected in this last model by cyclization of zigzag-shaped aromatic molecules with a synchronous topological arrangement. The crystal structure of this nanotube further revealed an entangled supramolecular assembly, which showed a novel way to align nanotube molecules by utilizing their open-end functional groups in a thread-in-bead molecular assembly.     

Method validation by interlaboratory studies of improved hydrophilic oxygen radical absorbance capacity methods for the determination of antioxidant capacities of antioxidant solutions and food extracts

Hydrophilic oxygen radical absorbance capacity (H-ORAC) is a method for evaluating antioxidant capacities of solutions of hydrophilic compounds. In this study, we improved the original method for H-ORAC determination, and evaluated the precision of the two improved methods (methods A and B) by interlaboratory studies using 5 antioxidant solutions and 5 food extracts as test samples. An interlaboratory study of method A, in accordance with the harmonized protocol, demonstrated satisfactory performance (intermediate precision relative standard deviations (RSD(int)) ranging from 4.6 to 18.8%; the reproducibility relative standard deviations (RSD(R)) ranging from 7.0 to 21.1%, and the HorRat values ranging from 0.40 to 1.93). However, methodological problems remained, and a further improved method, method B, was thus developed. An interlaboratory study of method B by 5 participating laboratories showed better intermediate precision and reproducibility (RSD(int) and RSD(R) ranging from 1.8 to 9.4%, and from 4.4 to 13.8%, respectively), and all HorRat values for the test samples were less than 1.3, suggesting good performance for the H-ORAC measurement.     

A color-coded backlighted defocusing digital particle image velocimetry system

Defocusing digital particle image velocimetry (DDPIV), as a true three-dimensional (3D) measurement technique, allows for the measurement of 3D velocities within a volume. Initially designed using a single CCD and 3-pinhole mask (Willert and Gharib in Exp Fluids 12:353–358, 1992), it has evolved into a multi-camera system in order to overcome the limitations of image saturation due to multiple exposures of each particle. In order to still use a single camera and overcome this limitation, we have modified the original single CCD implementation by placing different color filters over each pinhole, thus color-coding each pinhole exposure, and using a 3-CCD color camera for image acquisition. Due to the pinhole mask, there exists the problem of a significant lack of illumination in a conventional lighting setup, which we have solved by backlighting the field-of-view and seeding the flow with black particles. This produces images with a white background superimposed with colored triple exposures of each particle. A color space linear transformation is used to allow for accurate identification of each pinhole exposure when the color filters’ spectrum does not match those of the 3-CCD color camera. Because the imaging is performed with a multi-element lens instead of a single-element lens, an effective pinhole separation, d _e, is defined when using a pinhole mask within a multi-element lens. Calibration results of the system with and without fluid are performed and compared, and a correction of the effective pinhole separation, d _e, due to refraction through multiple surfaces is proposed. Uncertainty analyses are also performed, and the technique is successfully applied to a buoyancy-driven flow, where a 3D velocity field is extracted.