Polarization orientation dependence of the far infrared spectra of oriented single crystals of 1,3,5-trinitro-S-triazine (RDX) using terahertz time–domain spectroscopy

The far infrared spectra of (100), (010), and (001)-oriented RDX single crystals were measured as the crystal was rotated about the axis perpendicular to the polarization plane of the incident radiation. Absorption measurements were taken at temperatures of both 20 K and 295 K for all rotations using terahertz time–domain spectroscopy. A number of discrete absorptions were found ranging from 10–100 cm⁻¹ (0.3–3 THz). The absorptions are highly dependent on the orientation of the terahertz polarization with respect to crystallographic axes.     

A conserved helical capping hydrogen bond in PAS domains controls signaling kinetics in the superfamily prototype photoactive yellow protein

PAS domains form a divergent protein superfamily with more than 20?000 members that perform a wide array of sensing and regulatory functions in all three domains of life. Only nine residues are well-conserved in PAS domains, with an Asn residue at the start of α-helix 3 showing the strongest conservation. The molecular functions of these nine conserved residues are unknown. We use static and time-resolved visible and FTIR spectroscopy to investigate receptor activation in the photosensor photoactive yellow protein (PYP), a PAS domain prototype. The N43A and N43S mutants allow an investigation of the role of side-chain hydrogen bonding at this conserved position. The mutants exhibit a blue-shifted visible absorbance maximum and up-shifted chromophore pK(a). Disruption of the hydrogen bonds in N43A PYP causes both a reduction in protein stability and a 3400-fold increase in the lifetime of the signaling state of this photoreceptor. A significant part of this increase in lifetime can be attributed to the helical capping interaction of Asn43. This extends the known importance of helical capping for protein structure to regulating functional protein kinetics. A model for PYP activation has been proposed in which side-chain hydrogen bonding of Asn43 is critical for relaying light-induced conformational changes. However, FTIR spectroscopy shows that both Asn43 mutants retain full allosteric transmission of structural changes. Analysis of 30 available high-resolution structures of PAS domains reveals that the side-chain hydrogen bonding of residue 43 but not residue identity is highly conserved and suggests that its helical cap affects signaling kinetics in other PAS domains.     

Polyfluorination using IF(5)

The polyfluorination of α-(arylthio)carbonyl compounds was achieved by a successive application of polyfluorination using IF(5), Friedel-Crafts arylation, and desulfurizing fluorination using IF(5). Three to six fluorine atoms were selectively introduced to the carbons located between the aromatic ring and the carbonyl group.     

Deferoxamine Iron Chelation Increases δ-Aminolevulinic Acid Induced Protoporphyrin IX in Xenograft Glioma Model

Exogenous administration of δ-aminolevulinic acid (δ-ALA) leads to selective accumulation of protoporphyrin IX (PpIX) in brain tumors, and has shown promising results in increasing extent of resection in fluorescence-guided resection (FGR) of brain tumors. However, this approach still suffers from heterogeneous staining and so some tumor margins may go undetected because of this variation in PpIX production. The aim of this study was to test the hypothesis that iron chelation therapy could increase the level of fluorescence in malignant glioma tumors. Mice implanted with xenograft U251-GFP glioma tumor cells were given a 200 mg kg⁻¹ dose of deferoxamine (DFO), once a day for 3 days prior to δ-ALA administration. The PpIX fluorescence observed in the tumor regions was 1.9 times the background in animal group without DFO, and 2.9 times the background on average, in the DFO pre-treated group. A 50% increase in PpIX fluorescence contrast in the DFO group was observed relative to the control group (t-test P-value = 0.0020). These results indicate that iron chelation therapy could significantly increase δ-ALA-induced PpIX fluorescence in malignant gliomas, pointing to a potential role of iron chelation therapy for more effective FGR of brain tumors.     

Bulge-like Asymmetric Heterodye Clustering in DNA Duplex Results in Efficient Quenching of Background Emission Based on the Maximized Excitonic Interaction

Asymmetric dye clusters with a single fluorophore (Cy3) and multiple quenchers (4'-methylthioazobenzene-4-carboxylate, methyl red, and 4'-dimethylamino-2-nitroazobenzene-4-carboxylate) were prepared. The dye and one-to-five quenchers were tethered through D-threoninol to opposite strands of a DNA duplex. NMR analysis revealed that the clusters with a single fluorophore and two quenchers formed a sandwich-like structure (antiparallel H-aggregates). The melting temperatures of all the heteroclusters were almost the same, although structural distortion should become larger, as the number of quenchers increased. An asymmetric heterocluster of a single fluorophore and two quenchers showed larger excitonic interaction (i.e., hypochromicity of Cy3), than did a single Cy3 and a single quencher. Due to the larger exciton coupling between the dyes, the 1:2 heterocluster suppressed the background emission more efficiently than the 1:1 cluster. However, more quenchers did not enhance quenching efficiency due to the saturation of exciton coupling with two quenchers. Finally, this asymmetric 1:2 heterocluster was introduced into the stem region of a molecular beacon (MB; also known as an in-stem MB) targeting the fusion site in the L6 BCR-ABL fusion gene. With this MB design, the signal/background ratio was as high as 68 due to efficient suppression of background emission resulting from the maximized excitonic interaction.     

Influence of growth temperature on growth of InGaAs nanowires in selective-area metal–organic vapor-phase epitaxy

Indium-rich InGaAs nanowires were grown on an InP (111)B substrate by catalyst-free selective-area metal–organic vapor phase epitaxy, and the growth-temperature dependence of growth rate and composition was studied. In particular, nanowire growth rate rapidly decreases as growth temperature increases. This tendency is opposite (for a similar temperature range) to that found in a previous study on selective-area growth of gallium-rich InGaAs nanowires. This difference between indium-rich and gallium-rich nanowires suggests that the influence of growth temperature on the growth of InGaAs nanowires is dependent on the group-III supply ratio. On the basis of previous experimental observations in InAs and GaAs nanowires, temperature dependence of nanowire growth rate and its dependence on group-III supply ratio are predicted. A guideline to determine the optimum growth conditions of InGaAs nanowires is also discussed.     

Self‐Assembled Monolayers of Alkoxy‐Substituted Octadehydrodibenzo[12]annulenes on a Graphite Surface: Attempts at peri‐Benzopolyacene Formation by On‐Surface Polymerization

Self‐assembled monolayers of a series of tetraalkoxy‐substituted octadehydrodibenzo[12]annulene (DBA) derivatives 1 c – g possessing butadiyne linkages were studied at the 1,2,4‐trichlorobenzene (TCB) or 1‐phenyloctane/graphite interface by scanning tunneling microscopy (STM). The purpose of this research is not only to investigate the structural variation of two‐dimensional (2D) monolayers, but also to assess a possibility for peri‐benzopolyacene formation by two‐dimensionally controlled polymerization on a surface. As a result, the formation of three structures, porous, linear, and lamella structures, were observed by changing the alkyl chain length and the solute concentration. The formation of multilayers of the lamella structure was often observed for all compounds. The selection of molecular networks is basically ascribed to intermolecular and molecule–substrate interactions per unit area and network density. The selective appearance of the linear structure of 1 d is attributed to favorable epitaxial registry matching between the substrate lattice and the overlayer lattice. Even though the closest interatomic distance between the diacetylenic units of the DBAs in the lamella structure (≈0.6 nm) is slightly larger compared to the typical distances necessary for topochemical polymerization, the reactivity toward external stimuli (electronic‐pulse irradiation from an STM tip and UV irradiation) was investigated. Unfortunately, no evidence for polymerization of the DBAs on the surface was observed. The present results indicate the necessity for further designing a suitable system for the on‐surface construction of structurally novel conjugated polymers, which are otherwise difficult to prepare.     

Synthesis of acinetobactin

A structure involving the absolute configuration of acinetobactin (1b) was clarified. It was reconfirmed that preacinetobactin (1a) produced 1b by a rearrangement reaction.     

Dynamical process of complex systems and fractional differential equations

Behavior of dynamical process of complex systems is investigated. Specifically we analyse two types of ideal complex systems. For analysing the ideal complex systems, we define the response functions describing the internal states to an external force. The internal states are obtained as a relaxation process showing a “power law” distribution, such as scale free behaviors observed in actual measurements. By introducing a hybrid system, the logarithmic time, and double logarithmic time, we show how the “slow relaxation” (SR) process and “super slow relaxation” (SSR) process occur. Regarding the irregular variations of the internal states as an activation process, we calculate the response function to the external force. The behaviors are classified into “power”, “exponential”, and “stretched exponential” type. Finally we construct a fractional differential equation (FDE) describing the time evolution of these complex systems. In our theory, the exponent of the FDE or that of the power law distribution is expressed in terms of the parameters characterizing the structure of the system.     

Measurement of the branching fraction, polarization, and asymmetry for decays, and determination of the Cabibbo-Kobayashi-Maskawa phase

We have measured the branching fraction , longitudinal polarization fraction f(L), and CP asymmetry coefficients A and S for B(0) --> rho(+) rho(-) decays with the Belle detector at the KEKB e(+) e(-) collider using 253 Fb(-1) of data. We obtain B = [22.8 +/- 3.8(stat)(+2.3)(-2.6)(syst)] x 10(-6), f(L) = 0.941 (+0.034)(-0.040)(stat) +/- 0.030(syst). A = 0.00 +/- 0.30(stat) +/- 0.09(syst) and S = 0.08 +/- 0.09(syst). These values are used to constrain the Cabibbo-Kobayashi-Maskawa phase ; the solution consistent with the standard model is phi(2) = (88 +/- 17) degrees or 59 degrees < phi(2) < 115 degrees at 90% C.L.