Vacuum fusion determination of micro-quantities of bulk gases in low carbon iron without an effect of surface gases

Summary Vacuum Fusion Determination of Micro-quantities of Bulk Gases in Low Carbon Iron Without an Effect of Surface Gases Micro-quantities of bulk and surface oxygen and hydrogen in low carbon iron was simultaneously determined by the surface-area-variation method using vacuum fusion analysis. Among the difference of three surface treatments, silicon carbide abrasive, electropolishing and hydrogen reduction methods, bulk oxygen and hydrogen were in agreement within their errors, however, surface oxygen and hydrogen were influenced from the surface treatments. Even in the case of electropolishing, which gave the smallest surface oxygen value, bulk oxygen less than 10g/g is needed to discriminate from the surface oxygen. Bulk hydrogen of 0.03g/g was determined without the effect of surface hydrogen in the hydrogen reduction treatment.     

Synthesis and anti-HIV-1 activity of novel 10-thiaisoalloxazines,a structural analog of C-5 and/or C-6 substituted pyrimidine acyclonucleoside

A series of novel 10-thiaisoalloxazine derivatives bearing an alkoxymethyl or benzyloxymethyl moiety at the N-1 position has been synthesized through the bromination of 1-substituted-5-hydroxyuracils and subsequent condensation with aminobenzenethiol in a one-pot reaction. Contrary to the previous report, the formation of intermediary 5,6-diethoxy-5-hydroxy-5,6-dihydrouracil seems to be not the necessary factor for the formation of the thiaisoalloxazines, since the reaction proceeds in tetrahydrofuran (THF) or acetonitrile far more smoothly than in ethanol. The anti-human immunodeficiency virus (HIV)-1 activity of the resulted thiaisoalloxazine derivatives was evaluated in lymphocyte cells based on the inhibitory activity against the viral-induced cytopathic activity. Among the derivatives, compounds 6, 7, and 8 bearing an alkoxymethyl moiety at the N-1 position exhibited modest inhibitory activity towards the cytotopathic effect of HIV-1.     

Synthesis and properties of thermotropic liquid-crystalline polyesters containing 9,10-diphenylanthracene moiety in the main chain

We synthesized thermotropic liquid-crystalline polyesters in which 9,10-diphenylanthracene moieties are incorporated into the main chain type of polyester forming the chiral smectic C (Sm C*). The polymers were prepared by the isopropyltitanate-catalyzed reaction of biphenyldicarboxylic acid and the corresponding diols, with different ratios of diol of 9,10-diphenylanthracene moiety to the alkane diols (1, 5, and 10 mol %) under nitrogen atmosphere. The polymers exhibited thermotropic liquid crystals despite the presence of a bulky diphenylanthracene moiety in the main chain. The circular dichroism spectra revealed that a Sm C* phase was formed in the polymer with 1 mol % of anthracene moiety, although only an Sm A phase was formed in the other polymers. This is the first example of a Sm C* polyester containing a diphenylanthracene moiety in the main chain. Furthermore, we measured the optical properties of the polymers and found that they exhibited very high fluorescent efficiency. The fluorescence spectra of the thin film differed from that of a CH₂Cl₂ solution.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Four guaianolides from Sinodielsia yunnanensis

Four new guaianolides, sinodielides A-D (1-4), were isolated from Sinodielsia yunnanensis WOLFF together with a known polyacetylene, falcarindiol, and two known coumarins, bergapten and scopoletin. Their structures were established by spectral and X-ray analyses.     

Theoretical studies on magnetic interactions between Cu(II) ions in hydroxypyridone nucleobases

The origin of a ferromagnetic interaction between Cu²⁺ ions in the Cu²⁺–DNA system which reported by Tanaka et al. is examined by using DFT calculations. In order to consider effects of an entanglement and a dis-entanglement of the double helix chain, three types of structural disorders i.e. distance, rotation angle and discrepancy in XY-plane, are considered in the model dimer structure. All calculated results show that J_ab values are weak anti-ferromagnetic couplings. Boltzmann distribution simulation indicates that the high spin (HS) species exist 21% at 1.5 K by thermal excitation within the model structure.     

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: Application to the folding of a mini‐protein,chignolin

The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time‐scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini‐protein, chignolin, and automatically sampled the native structure (C_α root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long‐time 1‐µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape. © 2015 Wiley Periodicals, Inc.     

Third-order nonlinear optical properties of open-shell supermolecular systems composed of acetylene linked phenalenyl radicals

The third-order nonlinear optical (NLO) properties, at the molecular level, the static second hyperpolarizabilities, γ, of supermolecular systems composed of phenalenyl and pyrene rings linked by acetylene units are investigated by employing the long-range corrected spin-unrestricted density functional theory, LC-UBLYP, method. The phenalenyl based superethylene, superallyl, and superbutadiene in their lowest spin states have intermediate diradical characters and exhibit larger γ values than the closed-shell pyrene based superpolyene systems. The introduction of a positive charge into the phenalenyl based superallyl radical changes the sign of γ and enhances its amplitude by a factor of 35. Although such sign inversion is also observed in the allyl radical and cation systems in their ground state equilibrium geometries, the relative amplitude of γ is much different, that is, |γ(regular allyl cation)/γ(regular allyl radical)| = 0.61 versus |γ(phenalenyl based superallyl cation)/γ(phenalenyl based superallyl radical)| = 35. In contrast, the model ethylene, allyl radical/cation, and butadiene systems with stretched carbon-carbon bond lengths (2.0 ?), having intermediate diradical characters, exhibit similar γ features to those of the phenalenyl based superpolyene systems. This exemplifies that the size dependence of γ as well as its sign change by introducing a positive charge on the phenalenyl based superpolyene systems originate from their intermediate diradical characters. In addition, the change from the lowest to the highest π-electron spin states significantly reduces the γ amplitudes of the neutral phenalenyl based superpolyene systems. For phenalenyl based superallyl cation, the sign inversion of γ (from negative to positive) is observed upon switching between the singlet and triplet states, which is predicted to be associated with a modification of the balance between the positive and negative contributions to γ. The present study paves the way toward designing a variety of open-shell NLO supermolecular systems composed of phenalenyl radical building blocks.