Ru9Zn7Sb8: a structure with a 2 × 2 × 2 supercell of the half-Heusler phase

The title compound Ru(9)Zn(7)Sb(8) was synthesized via a high-temperature reaction from the elements in a stoichiometric ratio, and its structure was solved by a single-crystal X-ray diffraction method. The structure [cubic, space group Fm3m, Pearson symbol cF96, a = 11.9062(14) ? (293 K), and Z = 4] adopts a unique 2a(hh) × 2a(hh) × 2a(hh) supercell of a normal half-Heusler phase and shows abnormal features of atomic coordination against the Pauling rule. The formation of this superstructure was discussed in light of the valence electron concentration per unit cell. It is a metallic conductor [ρ(300 K) = 16 μΩ·m], and differential scanning calorimetry revealed that Ru(9)Zn(7)Sb(8) undergoes a transformation at 1356(1) K and melts, by all indications, congruently at 1386 K. At room temperature, its thermal conductivity is about 3 W/m·K, which is only one-quarter of that of most normal half-Heusler phases. Ru(9)Zn(7)Sb(8) as well as its analogues of iron-, cobalt-, rhodium-, and iridium-containing compounds are expected to serve as a new structure type for exploring new thermoelectric materials.     

Helix formation in synthetic polymers by hydrogen bonding with native saccharides in protic media

Water-soluble poly(m-ethynylpyridine)s were designed to realize saccharide recognition in protic media. UV/Vis, 1H NMR, and fluorescence measurements revealed that the polymer forms a helical higher order structure by solvophobic interactions between the ethynylpyridine units in the protic medium. The resulting pore in the helix behaves like a binding pocket in proteins, by taking advantage of inwardly directed hydrogen-bonding functional groups of the polymers. Molecular recognition of native saccharides by the polymers was investigated by circular dichroism (CD). The chirality of the saccharide was transferred to the helical sense of the polymers, accompanied by the appearance of induced CDs (ICDs) in the absorptive region of the polymers. In MeOH/water (10/1), mannose and allose showed intense ICDs, and the apparent association constant between the polymer and D-mannose was 14 M(-1).     

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

Here we improved our hybrid QM/MM methodology (Houjou et al. J Phys Chem B 2001, 105, 867) for evaluating the absorption maxima of photoreceptor proteins. The renewed method was applied to evaluation of the absorption maxima of several retinal proteins and photoactive yellow protein. The calculated absorption maxima were in good agreement with the corresponding experimental data with a computational error of <10 nm. In addition, our calculations reproduced the experimental gas-phase absorption maxima of model chromophores (protonated all-trans retinal Schiff base and deprotonated thiophenyl-p-coumarate) with the same accuracy. It is expected that our methodology allows for definitive interpretation of the spectral tuning mechanism of retinal proteins.     

Duty cycle enhancement of an orthogonal acceleration TOF mass spectrometer using an axially-resonant excitation linear ion trap

We report a new technique to enhance detection duty cycle of an orthogonal-acceleration time-of-flight mass spectrometer (oaTOF) over a broad mass range. To this end, we used an axially-resonant-excitation linear ion trap, which ejects ions axially and mass selectively into a non-mass-selective linear ion trap in front of the TOF pusher. A delay between the ejection timing of the non-mass-selective LIT and the push timing of the oaTOF was swept mass-synchronously with the axially-resonant-excitation linear ion trap, so that ions are detected with duty cycle larger than 60% over a wide mass range from m/z 174.1 to 1922.0, which is 3 to 10 times better than conventional oaTOF.     

'Information-Based-Acquisition' (IBA) technique with an ion-trap/time-of-flight mass spectrometer for high-throughput and reliable protein profiling

Highly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS). In an LC/MS run, intense peptide ions originating from high-abundance proteins are preferentially analyzed using tandem mass spectrometry (MS(2)), so obtaining the MS(2) spectra of peptide ions from low-abundance proteins is difficult even if such ions are detected. Furthermore, the MS(2) spectra may produce insufficient information to identify the peptides or proteins. To solve these problems, we have developed a real-time optimization technique for MS(2), called the Information-Based-Acquisition (IBA) system. In a preliminary LC/MS run, a few of the most intense ions detected in every MS spectrum are selected as precursors for MS(2) and their masses, charge states and retention times are automatically registered in an internal database. In the next run, a sample similar to that used in the first run is analyzed using database searching. Then, the ions registered in the database are excluded from the precursor ion selection to avoid duplicate MS(2) analyses. Furthermore, real-time de novo sequencing is performed just after obtaining the MS(2) spectrum, and an MS(3) spectrum is obtained for accurate peptide identification when the number of interpreted amino acids in the MS(2) spectrum is less than five. We applied the IBA system to a yeast cell lysate which is a typical crude sample, using a nanoLC/ion-trap time-of flight (IT/TOF) mass spectrometer, repeating the same LC/MS run five times. The obtained MS(2) and MS(3) spectra were analyzed by applying the Mascot (Matrix Science, Boston, MA, USA) search engine to identify proteins from the sequence database. The total number of identified proteins in five LC/MS runs was three times higher than that in the first run and the ion scores for peptide identification also significantly increased, by about 70%, when the MS(3) spectra were used, combined with the MS(2) spectra, before being subjected to Mascot analysis.     

Analysis of protein-protein interactions with a multi-capillary electrophoresis instrument

Protein-protein interactions were analyzed by zone electrophoresis of premixed equilibrium mixtures of a fluorescence-labeled protein at a constant concentration and unlabeled protein at a variety of concentrations using a 96-CE instrument equipped with a LIF detector. The interactions between labeled-con A versus succinylated ovalbumin, labeled-trypsin versus four proteinaceous trypsin inhibitors and labeled-insulin versus seven anti-insulin monoclonal antibodies were analyzed using a dual buffer system, in which a 60 mM borate-Na buffer (pH 9.35) was used as electrophoresis buffer and 60 mM MOPS-Na (pH 7.35) containing 0.1% Tween 20 was used as a sample buffer. The dual buffer system allowed fast and reproducible analyses of interactions at a physiological pH using uncoated fused-silica capillaries. The change in the mobility moment, the first statistical moment of an electropherogram on the mobility axis (Shimura, K., Uchiyama, N., Enomoto, M., Matsumoto, H., Kasai, K., Anal. Chem. 2005, 77, 564-572), of the labeled proteins were analyzed as a function of the concentration of unlabeled proteins. The dissociation constants for seven antibodies ranging from sub nanomolar to micromolar was determined based on the results of one cycle of parallel electrophoresis runs, which completed in 30 min using 20 pmol (120 ng) of labeled insulin and 5 pmol (750 ng) each of the mAb.     

Strange behaviors of interior-point methods for solving semidefinite programming problems in polynomial optimization

We observe that in a simple one-dimensional polynomial optimization problem (POP), the ??optimal?? values of semidefinite programming (SDP) relaxation problems reported by the standard SDP solvers converge to the optimal value of the POP, while the true optimal values of SDP relaxation problems are strictly and significantly less than that value. Some pieces of circumstantial evidences for the strange behaviors of the SDP solvers are given. This result gives a warning to users of the SDP relaxation method for POPs to be careful in believing the results of the SDP solvers. We also demonstrate how SDPA-GMP, a multiple precision SDP solver developed by one of the authors, can deal with this situation correctly.     

Molecular cluster theory for chemisorption of first row atoms on nickel (100) surfaces

Self-consistent Hartree-Fock-Slater molecular cluster models for the chemisorption of first row atoms on Ni(100) surfaces are presented. Energy levels and ground state charge distributions for XNi_S clusters with the adatom X = H, C, N, O located in C_{4 V} symmetry at a fixed height of h = 2.0 au above the surface are given. The variation of properties with h was studied in detail for the case of oxygen. Theoretical results compare rather well with experimental photoelectron and energy loss data. Local-densities-of-states diagrams are used to clarify the interaction between adsorbate levels and metal conduction bands.