Detecting coupled collective motions in protein by independent subspace analysis

Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.     

PIDA-mediated synthesis of oxazoles through oxidative cycloisomerization of propargylamides

PIDA [phenyliodine(III) diacetate] in AcOH or AcOH-HFIP (hexafluoroisopropanol) efficiently promotes the formation of 2,5-disubstituted oxazoles via the oxidative cycloisomerization of propargylamide derivatives.     

Density functional theory investigation of novel Eu(III) complexes with asymmetric bis(phosphine) oxides

Recently, we have developed novel Eu(III) complexes with three beta-diketonates and one asymmetric bis(phosphine) oxide whose light emission intensity is drastically increased. In this paper, one of these complexes is investigated by the density functional theory calculation. Sixteen isomers of this complex have been considered. The ratio of the existence for the most stable isomer (B1_1a) is found to be about 51%, and the sum of the ratio of the existence for the six most stable isomers (B1_1a, B1_3a, B1_8a, B1_2a, B1_1b, and B1_5a) is about 100%, assuming the Boltzmann distribution (T = 300 K). The coordination structures of the six most stable isomers in the ground states are similar, and we can expect asymmetric ligand fields for them, favorable for the efficient light emission. Vertical excitation energies and oscillator strengths for each isomer have been obtained by the time-dependent density functional theory. With the red-shift of the wavelength and the interpolation by Gaussian convolution, both the calculated absorption spectra for the most stable isomer B1_1a and the calculated absorption spectra for the ensemble average of the isomers are found to be similar to the experimental fluorescence excitation spectra. The efficiency of energy transfer from the triplet excited state to the Eu(III) ion is considered by calculating DeltaEET (difference between the adiabatic excitation energy of the complex for the lowest triplet state and the emission energy of the Eu(III) ion for 5D0 to 7F2). The characters for the lowest triplet states for the isomers are investigated by the spin density distributions of the triplet states.     

Infrared spectroscopy of ozone-water complex in a neon matrix

Matrix isolation infrared spectroscopy has been applied to study an ozone-water complex of atmospheric interest. The complex was identified in the spectral region of three normal modes of ozone and water. Ab initio calculation at MP4(SDQ), QCISD, and CCSD(T) levels indicates the existence of only one stable conformer, which accords with the present experimental result. This conformer belongs to the Cs symmetry group where two molecular planes of ozone and water are perpendicular to the Cs symmetry plane. The binding energy was calculated to be 1.89 kcal/mol at the CCSD(T)/6-311++G(3df,3pd)//CCSD(T)/6-311++G(d,p) level of theory. The formation constant and atmospheric abundance of the ozone-water complex are estimated using the thermodynamic and spectroscopic data obtained.     

Spontaneous vesicle formation of single chain and double chain cationic surfactant mixtures

The concentration vs composition diagram of aggregate formation of the dodecyltrimethylammonium bromide (DTAB) and didodecyldimethylammonium bromide (DDAB) mixture in aqueous solution at rather dilute region was constructed by analyzing the surface tension, turbidity, and electrical conductivity data and inspected by cryo-TEM images and dynamic light scattering data. Although the aqueous solution of DTAB forms only micelles, the transition from monomer to small aggregates and then to vesicle was found at 0.1 < X2 相似文献   

Thermal change of Alq3, tris(8-hydroxyquinolinato) aluminum(III) studied by TG and XRD-DSC

The thermal change of the tris(8-hydroxyquinolinato)aluminum (Alq₃) is currently investigated by XRD-DSC and TG. The phase transition of Alq₃ from α-phase to γ-phase takes place at 643–669 K. A very sharp peak with the peak temperature at approx. 709 K is ascribed to the melting of the Alq₃. The decomposition of the Alq₃ was observed accompanied with the melting and evaporation at >703K. The effect of the atmospheres on the mass loss procedure was studied by TG. It was found that thermal process of Alq₃ was strongly influenced by the partial pressure of water vapor in the atmosphere instead of oxygen.     

Pictet-Spengler reactions catalyzed by Brønsted acid-surfactant-combined catalyst in water or aqueous media

Perfluorooctanesulfonic acid (PFOSA), Brønsted acid-surfactant-combined catalyst, efficiently catalyzes the Pictet-Spengler reactions of β-arylethyl carbamate derivatives with aldehydes in water. The present reaction is accelerated by the addition of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP).     

Catalytic transformation of methane over in-loaded ZSM-5 zeolite in the presence of ethene

Methane is shown to react with ethene over In-loaded ZSM-5 to higher hydrocarbons such as propene and toluene at around 673 K. Such methane conversion is not catalyzed by proton-exchanged ZSM-5 (H-ZSM-5) under the same conditions, only C2H4 being converted to higher hydrocarbons. By using 13C-labeled methane (13CH4) as a reactant, the reaction paths for the formation of propene, benzene and toluene were examined. 13C-labeled propene (13CC2H6) is formed by the reaction of 13CH4 with C2H4. The lack of 13C-labeled benzene revealed that propene is not transformed to benzene, which instead originates entirely from C2H4. The 13C atom is inserted both into the methyl group and benzene ring in the toluene formed. This indicates that toluene is formed by two reaction paths; the reaction of 13CC2H6 with butenes formed by the dimerization of C2H4 and the reaction of benzene with 13CH4. The existence of the latter path was proved by the direct reaction of 13CH4 with benzene. The reaction of methane with benzene was also carried out in a continuous flow system over In-loaded ZSM-5. The reaction afforded 7.6% and 0.9% yields of toluene and xylenes, respectively, at 623 K.     

Synthesis of the common left-half part of pectenotoxins

The common left-half [C31-C33(OC1-C7)-C40] part of pectenotoxins has been synthesized convergently from the C31-C35, C36-C40, and C1-C7 parts. The C31-C35 part, prepared via a new route shorter than our previous route, was coupled with the C36-C40 part through reductive lithiation and addition reactions to give an adduct stereoselectively, which was converted to a cyclic acetal corresponding to the C31-C40 part. The left-half was synthesized by a three-step process including esterification of the C31-C40 part with the C1-C7 part.