Mechanism on two-electron oxidation of ubiquinol at the Qp site in cytochrome bc1 complex: B3LYP study with broken symmetry

The molecular and electronic structures of the Rieske iron-sulfur [2Fe-2S] cluster with an imidazolate and imidazole were investigated by using usual unrestricted and broken symmetry B3LYP methods for the highest and lowest spin states, respectively. The electronic structures of the lowest spin states were determined by the spin contaminations and natural orbital analyses. It was shown that the spin contamination presents the number of pairs of the antiferromagnetic spin couplings. The oxidation mechanism of the ubquinol at the Q(p) site of the cytochrome bc(1) complex was also examined by the broken symmetry B3LYP methods. In the [2Fe-2S] clusters with an imidazolate, the oxidized and lowest spin state, [(Imz(-))FeS](ox)LS, was lowest in energy among four possible states, consistent with experimental observations. In the examination of the mechanism of the ubquinol oxidation, it was confirmed that the ubiquinol docks between the imidazolate of [2Fe-2S] clusters and Glu272(-) of cytochrome b by the hydrogen bonds before the oxidation proceeds, consistent with the experimental proposals. Our results support a "Glu272-first" mechanism that Glu272 serves as an acceptor of the first proton from the ubiquinol and subsequently the proton-coupled electron transfer (PCET) occurs from the ubisemiquinone anion to the Rieske iron-sulfur [2Fe-2S] cluster.     

Potential energy landscape of bis(fluorosulfonyl)amide

The conformational landscape of the bis(fluorosulfonyl)amide, [FSI]-, anion was analyzed using data obtained from Raman spectroscopy, molecular dynamics (MD), and ab initio studies. The plotting of three-dimensional potential energy surfaces and the corresponding MD simulation conformer-population histograms show the existence of two stable isomers, C2 (trans) and C1 (cis) conformers, and confirm the nature of the anion as a flexible molecule capable of interconversion between conformers in the liquid state. In ionic liquids, the two [FSI]- conformers coexist in equilibrium, a result confirmed by the Raman data. The implications of the conformational behavior of the ion [FSI]- are discussed in terms of the solvation properties of the corresponding ionic liquids.     

Control of photobleaching in photodynamic therapy using the photodecarbonylation reaction of ruthenium phthalocyanine complexes via stepwise two-photon excitation

In this study, we have investigated the photochemical properties and photodynamic effects of ruthenium phthalocyanine (RuPc(CO)(Py)) and naphthalocyanine (RuNc(CO)(Py)) complexes. When a nanosecond-pulsed laser is used, the photodecarbonylation of our Ru complexes efficiently proceeds via stepwise two-photon excitation, while the reaction yields are negligibly small when a continuous-wave (CW) laser is employed. The pulsed laser selective photodecarbonylation decreases the Q-band absorbance, which satisfies what the photodynamic therapy (PDT) requires of the photobleaching. For RuPc(CO)(Py), the photochemical reactions including both the photodecarbonylation and just photobleaching occur in HeLa cells in vitro. Toxicity and phototoxicity tests indicate that our RuPc(CO)(Py) and RuNc(CO)(Py) complexes in concentrations of 0.3-1 microM and 1-2 microM, respectively, are applicable as PDT agents. The phototoxicity is consistent with the photochemical properties of these complexes, namely, excited triplet lifetimes (10 and 4.8 micros for the Pc and Nc complexes, respectively) and singlet oxygen yields (0.48 and 0.35 for the Pc and Nc complexes, respectively). On the basis of these results, we propose a novel concept for achieving a greater depth of necrosis in PDT as follows: (1) PDT of upper cellular layers using CW-laser irradiation; (2) efficient photobleaching in upper cellular layers using pulsed dye-laser irradiation, which results in an increase in the therapeutic depth of red light; (3) PDT directed toward deeper tumor tissues using CW laser irradiation. In addition, these Ru complexes are promising as CO release agents for investigative biochemistry.     

Stereoselective synthesis of alpha-glycosyl phosphites and phosphoramidites via O-selective glycosylation of H-phosphonate derivatives

A highly stereo- and chemoselective glycosylation of H-phosphonate derivatives with glycosyl iodides was discovered as a reverse reaction of the formation of a glycosyl iodide from a glycosyl phosphite and I- under mild acidic conditions. Further study on the unique reaction showed that the reaction provided various alpha-glycosyl phosphites and phosphoramidites in a highly stereoselective manner with complete O-selectivity.     

Synthesis of N-allylideneamines and their use for the double nucleophilic addition of ketene silyl (thio)acetals and trimethylsilyl cyanide

N-Allylideneamines 1a, b were prepared from acrolein and diphenylethyl or trityl amine in the presence of Ti(OEt)4. Double nucleophilic addition of various ketene silyl (thio)acetals and trimethylsilyl cyanide to these imines proceeded efficiently to give, after workup with TFA, homoglutamic acid derivatives 3 and valerolactam 5.     

Sulfur standard solution for use in the determination of low sulfur concentration in liquid fuels

A sulfur reference solution at the 1 mg kg⁻¹ level, NMIJ CRM 4215-a, has been issued by the National Metrology Institute of Japan at the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST). The intended use of this CRM is for the calibration of standards used in the determination of sulfur in liquid fuels. The certified value of this CRM was determined using the gravimetric blending method. Thiophene and toluene were chosen as the high purity sulfur compound and the dilution solvent, respectively. Measurements of the trace sulfur in the solvent were performed using the total sulfur analyzer with an enrichment system; the standard addition method was employed. When trace sulfur in the solvent was evaluated, the signal which appears with no sample injection was subtracted as the background.     

Growth process and molecular packing of a self-assembled lipid nanotube: phase-contrast transmission electron microscopy and XRD analyses

Phase-contrast transmission electron microscopy (PC-TEM) and quick freezing method have been combined to study the initial growing process of a self-assembled lipid nanotube in water. The PC-TEM enabled us to detect thin lamellar edge structure and the very fast growth of the newborn edge to a thin tube with high contrast. The thin tube acts as a core structure for further growth into thick complete lipid nanotube. The initially formed nanotube structure is denoted as a "core tube". The core tube has uniform wall structure that consists of five lamellar layers and the inner and outer diameters of the core tube are 130 and 180 nm, respectively. The evaluated lamellar spacing of 4.6 nm is well compatible with that measured by X-ray diffraction. We also discussed the molecular packing of the nanotube from the pitch angle determined by the PC-TEM images, X-ray diffraction pattern in wide-angle region, and IR spectroscopy. The subcell structure of the nanotube is assigned to an orthorhombic type. The twisting angle between the neighboring lipid molecules is determined as ca. 0.26 degrees for the first time; it is a crucial parameter for the formation of a lipid nanotube in chiral packing but has not been elucidated before.     

Arraying heterotypic single cells on photoactivatable cell-culturing substrates

This article describes a photochemical method for the site-selective assembly of heterotypic cells on a glass substrate modified with a silane coupling agent having a caged functional group. Silane coupling agents having a carboxyl (COOH), amino (NH 2), hydroxyl (OH), or thiol (SH) group protected by a photocleavable 2-nitrobenzyl group were synthesized to modify the surfaces of glass coverslips. The caged substrates were first coated by the adsorption of a blocking agent, bovine serum albumin (BSA), to make the entire surface non-cell-adhesive and then irradiated at 365 nm under a standard fluorescence microscope. The photocleavage reaction on the surface was followed by contact angle measurements and X-ray photoelectron spectroscopy. When COS7, NIH3T3, and HEK293 cells were seeded onto these substrates in a serum-free medium, the cells adhered selectively and efficiently to the irradiated regions on the caged NH 2 substrate, whereas the other caged COOH, SH, and OH substrates were nonphotoactivatable for cell adhesion. Qualitative and quantitative analysis of BSA adsorbed to the uncaged substrates revealed that this highly efficient photoactivation on the caged NH 2 substrate arose because of the following reasons: (i) upon photoactivation, BSA adsorbed in advance on the 2-nitrobenzyl groups was readsorbed onto the uncaged functional groups and (ii) BSA readsorbed onto the NH 2 groups became unable to passivate the surface against cell adhesion whereas BSA on the other groups still had normal passivating activity. It was also demonstrated that heterotypic single COS7, NIH3T3, and HEK293 cells were positioned at any desired arrangement on the caged NH 2 substrate by repeating the UV irradiation at optimized array spot sizes and cell seeding in optimized cell concentrations. The present method will be particularly useful in studying the dynamic processes of cell-cell interactions at a single-cell level.     

Determination of the 15N/14N, 17O/16O, and 18O/16O ratios of nitrous oxide by using continuous-flow isotope-ratio mass spectrometry

We developed a rapid, sensitive, and automated analytical system to determine the delta15N, delta18O, and Delta17O values of nitrous oxide (N2O) simultaneously in nanomolar quantities for a single batch of samples by continuous-flow isotope-ratio mass spectrometry (CF-IRMS) without any cumbersome and time-consuming pretreatments. The analytical system consisted of a vacuum line to extract and purify N2O, a gas chromatograph for further purification of N2O, an optional thermal furnace to decompose N2O to O2, and a CF-IRMS system. We also used pneumatic valves and pneumatic actuators in the system so that we could operate it automatically with timing software on a personal computer. The analytical precision was better than 0.12 per thousand for delta15N with >4 nmol N2O injections, 0.25 per thousand for delta18O with >4 nmol N2O injections, and 0.20 per thousand for Delta17O with >20 nmol N2O injections for a single measurement. We were also easily able to improve the precision (standard errors) to better than 0.05 per thousand for delta15N, 0.10 per thousand for delta18O, and 0.10 per thousand for Delta17O through multiple analyses with more than four repetitions with 190 nmol samples using the automated analytical system. Using the system, the delta15N, delta18O, and Delta17O values of N2O can be quantified not only for atmospheric samples, but also for other gas or liquid samples with low N2O content, such as soil gas or natural water. Here, we showed the first ever Delta17O measurements of soil N2O.     

Grain-scale heterogeneities in the stable carbon and oxygen isotopic compositions of the international standard calcite materials (NBS 19, NBS 18, IAEA-CO-1, and IAEA-CO-8)

We determined grain-scale heterogeneities (from 6 to 88 microg) in the stable carbon and oxygen isotopic compositions (delta(13)C and delta(18)O) of the international standard calcite materials (NBS 19, NBS 18, IAEA-CO-1, and IAEA-CO-8) using a continuous-flow isotope ratio mass spectrometry (CF-IRMS) system that realizes a simultaneous determination of the delta(13)C and the delta(18)O values with standard deviations (S.D.) of less than 0.05 per thousand for CO(2) gas. Based on the S.D. of the delta(13)C and delta(18)O values determined for CO(2) gases evolved from the different grains of the same calcite material, we found that NBS 19, IAEA-CO-1, and IEAE-CO-8 were homogeneous for delta(13)C (less than 0.10 per thousand S.D.), and that only NBS 19 was homogeneous for delta(18)O (less than 0.14 per thousand S.D.). On the level of single grains, we found that both IAEA-CO-1 and IAEA-CO-8 were heterogeneous for delta(18)O (1.46 per thousand and 0.76 per thousand S.D., respectively), and that NBS 18 was heterogeneous for both delta(13)C and delta(18)O (0.34 per thousand and 0.54 per thousand S.D., respectively). Closer inspection of NBS 18 grains revealed that the highly deviated isotopic compositions were limited to the colored grains. By excluding such colored grains, we could also obtain the homogeneous delta(13)C and delta(18)O values (less than 0.18 per thousand and less than 0.16 per thousand S.D., respectively) for NBS 18. We conclude that NBS 19, IAEA-CO-1, or pure grains in NBS 18 are suitable to be used as the standard reference material for delta(13)C, and that either NBS 19 or pure grains in NBS 18 are suitable to be used as the reference material for delta(18)O during the grain-scale isotopic analyses of calcite.