Constituents of Holothuroidea, 15. Isolation of ante-iso type regio-isomer on long chain base moiety of glucocerebroside from the sea cucumber Holothuria leucospilota

An ante-iso type regio-isomer on the long chain base moiety of a glucocerebroside, HLC-2-A, has been isolated from its parent glucocerebroside molecular species HLC-2 composed of iso and ante-iso isomers, from the less polar lipid fraction of a chloroform/methanol extract of the sea cucumber Holothuria leucospilota. Reverse-phase HPLC that included a recycling system was effective in separating the regio-isomer from its counterpart, revealing a very close resemblance in structure. Other typical glucocerebroside molecular species HLC-1 and HLC-3 were obtained together with HLC-2. The structures of these glucocerebrosides were determined on the basis of chemical and spectroscopic evidence.     

A tris(2,2'-bipyridine)ruthenium(II) derivative tethered to a cis-PtCl2(amine)2 moiety: syntheses, spectroscopic properties, and visible-light-induced scission of DNA

A tris(2,2'-bipyridine)ruthenium(II) derivative having two N-(3-ammoniopropyl)carbamoyl pendant units has been prepared and reacted with cis-PtCl2(DMSO)2 (DMSO = dimethyl sulfoxide) to give a heteronuclear Ru(II)Pt(II) dimer having a cis-Pt(II)Cl2(aliphatic amine)2 unit, [Ru(bpy)2(mu-bridge)PtCl2](PF6)2 (bpy = 2,2'-bipyridine, bridge = 4,4'-bis(N-(3-aminopropyl)carbamoyl)-2,2'-bipyridine). The ESI-TOF mass spectrum of the Ru(II)Pt(II) dimer shows a set of signals corresponding to {[Ru(bpy)2(mu-bridge)PtCl2](PF6)}(+) (m/z 1181.1). The MLCT (metal-to-ligand charge transfer) luminescence intensity is enhanced upon the platination of two amine units, presumably due to the formation of a relatively rigid metallocycle. More interestingly, the luminescence intensity is further enhanced by the complexation of the Ru(II)Pt(II) dimer with either 5'-GMP (guanosine 5'-monophosphate disodium salt) or calf thymus DNA. Visible-light-induced scission of supercoiled pBR322 DNA is found to be efficiently enhanced in the presence of the title Ru(II)Pt(II) dimer.     

Designer variable repeat length polypeptides as scaffolds for surface immobilization of quantum dots

We demonstrate the use of a series of engineered, variable-length de novo polypeptides to discretely immobilize luminescent semiconductor nanocrystals or quantum dots (QDs) onto functional surfaces. The polypeptides express N-terminal dicysteine and C-terminal hexahistidine residues that flank a variable number (1, 3, 5, 7, 14, 21, 28, or 35) of core beta-strand repeats, with tyrosine, glutamic acid, histidine, and lysine residues located at the turns. Polypeptides have molecular weights ranging from 4 to 83 kDa and retain a rigid structure based on the antiparallel beta-sheet motif. We first use a series of dye-labeled polypeptides to test and characterize their self-assembly onto hydrophilic CdSe-ZnS QDs using fluorescence resonance energy transfer (FRET). Results indicate that peptides maintain their beta-sheet conformation after self-assembly onto the QD surfaces, regardless of their length. We then immobilize biotinylated derivatives of these polypeptides on a NeutrAvidin-functionalized substrate and use them to capture QDs via specific interactions between the peptides' polyhistidine residues and the nanocrystal surface. We found that each of the polypeptides was able to efficiently capture QDs, with a clear correlation between the density of the surface-tethered peptide and the capacity for nanocrystal capture. The versatility of this capture strategy is highlighted by the creation of a variety of one- and two-dimensional polypeptide-QD structures as well as a self-assembled surface-immobilized FRET-based nutrient sensor.     

Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model

The heterogeneous dielectric generalized Born (HDGB) methodology is an the extension of the GBMV model for the simulation of integral membrane proteins with an implicit membrane environment. Three large integral membrane proteins, the bacteriorhodopsin monomer and trimer and the BtuCD protein, were simulated with the HDGB model in order to evaluate how well thermodynamic and dynamic properties are reproduced. Effects of the truncation of electrostatic interactions were examined. For all proteins, the HDGB model was able to generate stable trajectories that remained close to the starting experimental structures, in excellent agreement with explicit membrane simulations. Dynamic properties evaluated through a comparison of B-factors are also in good agreement with experiment and explicit membrane simulations. However, overall flexibility was slightly underestimated with the HDGB model unless a very large electrostatic cutoff is employed. Results with the HDGB model are further compared with equivalent simulations in implicit aqueous solvent, demonstrating that the membrane environment leads to more realistic simulations.     

Observation of B(s)(0) → D(s)(*)+ D(s)(*)- using e+ e- collisions and a determination of the B(s)-B(s) width difference ΔΓ(s)

We have made the first observation of B(s)(0)→D(s)(*)+ D(s)(*)- decays using 23.6 fb(-1) of data recorded by the Belle experiment running on the Υ(5S) resonance. The branching fractions are measured to be B(B(s)(0)→D(s)+ D(s)-)=(1.03(-0.32-0.25)(+0.39+0.26))%, B(B(s)(0)→D(s)(*±) D(s)(?))=(2.75(-0.71)(+0.83)±0.69)%, and B(B(s)(0)→D(s)*+ D(s)*-)=(3.08(-1.04-0.86)(+1.22+0.85))%; the sum is B[B(s)(0)→D(s)(*)+ D(s)(*)-]=(6.85(-1.30-1.80)(+1.53+1.79))%. Assuming B(s)(0)→D(s)(*)+ D(s)(*)- saturates decays to CP-even final states, the branching fraction determines the ratio ΔΓ(s)/cosφ, where ΔΓ(s) is the difference in widths between the two B(s)-B(s) mass eigenstates, and φ is a CP-violating weak phase. Taking CP violation to be negligibly small, we obtain ΔΓ(s)/Γ(s)=0.147(-0.030)(+0.036)(stat)(-0.041)(+0.042)(syst), where Γ(s) is the mean decay width.     

Existence of densities of solutions of stochastic differential equations by Malliavin calculus

I considered if solutions of stochastic differential equations have their density or not when the coefficients are not Lipschitz continuous. However, when stochastic differential equations whose coefficients are not Lipschitz continuous, the solutions would not belong to Sobolev space in general. So, I prepared the class Vh which is larger than Sobolev space, and considered the relation between absolute continuity of random variables and the class Vh. The relation is associated to a theorem of N. Bouleau and F. Hirsch. Moreover, I got a sufficient condition for a solution of stochastic differential equation to belong to the class Vh, and showed that solutions of stochastic differential equations have their densities in a special case by using the class Vh.     

Raman Scattering Intensities of the NO2 Symmetric Stretching Vibration Band of Some Aromatic Nitrocompounds

Raman scattering intensities of the NO₂ symmetric stretching vibration band were measured for some aromatic nitrocompounds. It was shown that in the case of ortho alkyl-substituted nitrobenzenes, the intensities decrease in an orderly fashion with the increase of the degrees of twisting of NO₂ group from the plane of benzene ring. From this result, it was assumed that the factor determining the intensities in question is the conjugation effect between NO₂ group and benzene ring. Then, the intensities for some para substituted nitrobenzenes were examined, and the influence of substituents was discussed in terms of the conjugation effect. It was shown that when the electron donating character of substituents becomes stronger, the intensities intensity change among the compounds. The more experimental data and the detailed theoretical analysis of them are necessary not only for the elucidation of spectroscopic aspects of the intensity in question, but also for establishing the criterion for the application of it to the group type analysis and the microanalysis. Therefore, further experimental and theoretical examinations are required and now proceeding in our laboratory.     

Molecular understanding of the adhesive interactions between silica surface and epoxy resin: Effects of interfacial water

The molecular mechanism of the adhesion between silica surface and epoxy resin under atmospheric conditions is investigated by periodic density-functional-theory (DFT) calculations. Slab models of the adhesion interface were built by integrating a fragment of epoxy resin and hydroxylated (0 0 1) surface of α-cristobalite in the presence of adsorbed water molecules. Effects of adsorbed water on the adhesion interaction are evaluated on the basis of geometry-optimized structures, adhesion energies, and forces. Calculated results demonstrate that adsorbed water molecules significantly reduce both the adhesion energies and forces of the silica surface–epoxy resin interface. The reduction of adhesion properties can be associated with structural deformation of water molecules confined in the tight space between the adhesive and adherend as well as structural flexibility of the hydrogen-bonding network in the interfacial region during detachment of the epoxy resin from the hydrophilic silica surface. © 2018 Wiley Periodicals, Inc.     

Extending spin-symmetry projected coupled-cluster to large model spaces using an iterative null-space projection technique

Recently, we introduced an orbital-invariant approximate coupled-cluster (CC) method in the spin-projection manifold. The multi-determinantal property of spin-projection means that the parametrization in the spin-extended CC (ECC) ansatz is nonorthogonal and overcomplete. Therefore, the linear dependencies must be removed by an orthogonalization procedure to obtain meaningful solutions. Multi-reference methods often achieve this by diagonalizing a metric of the equation system, but this is not feasible with ECC because of the enormous size of the metric, a consequence of the incomplete active space of the spin-projected Hartree–Fock reference. As a result, the applicability of ECC has been limited to small benchmark systems, for which the ansatz was shown to be superior to the configuration interaction and linearized approximations. In this article, we provide a solution to this problem that completely avoids the metric diagonalization by iteratively projecting out its null-space from the working equations. As the additional computational cost required for this iterative projection is only marginal, it greatly expands the application range of ECC. We demonstrate the potential of approximate ECC by studying the complete basis set limit of F₂ and transition metal complexes such as NiO, Mn₂, and [Cu₂O₂]²⁺ , which have all been hindered by the prohibitively large metric size. We also identify the potential inadequacy of the molecular orbitals given by spin-projected Hartree–Fock in some cases, and propose possible solutions. © 2018 Wiley Periodicals, Inc.