Ring-closing reaction of allenic/propargylic anions generated by base treatment of sulfonylallenes

The intramolecular trapping of allenyl/propargyl anions generated by base treatment of sulfonylallenes was investigated. Treatment of 1-(omega-iodoalkyl)-1-(phenylsulfonyl)allenes with TBAF or NaH in DMF efficiently produced three- to seven-membered 1-ethynyl-1-(phenylsulfonyl) substituted carbocycles. The allenyl/propargyl anions could also be intramolecularly trapped using a terminal aldehyde or alpha,beta-unsaturated ester. The phenylsulfonyl group was found to be replaced by other electron-withdrawing functionalities like ketone and ester groups but not by an alkyl group for this novel ring-closing reaction.     

Supervised consensus scoring for docking and virtual screening

Docking programs are widely used to discover novel ligands efficiently and can predict protein-ligand complex structures with reasonable accuracy and speed. However, there is an emerging demand for better performance from the scoring methods. Consensus scoring (CS) methods improve the performance by compensating for the deficiencies of each scoring function. However, conventional CS and existing scoring functions have the same problems, such as a lack of protein flexibility, inadequate treatment of salvation, and the simplistic nature of the energy function used. Although there are many problems in current scoring functions, we focus our attention on the incorporation of unbound ligand conformations. To address this problem, we propose supervised consensus scoring (SCS), which takes into account protein-ligand binding process using unbound ligand conformations with supervised learning. An evaluation of docking accuracy for 100 diverse protein-ligand complexes shows that SCS outperforms both CS and 11 scoring functions (PLP, F-Score, LigScore, DrugScore, LUDI, X-Score, AutoDock, PMF, G-Score, ChemScore, and D-score). The success rates of SCS range from 89% to 91% in the range of rmsd < 2 A, while those of CS range from 80% to 85%, and those of the scoring functions range from 26% to 76%. Moreover, we also introduce a method for judging whether a compound is active or inactive with the appropriate criterion for virtual screening. SCS performs quite well in docking accuracy and is presumably useful for screening large-scale compound databases before predicting binding affinity.     

Modulation of homogeneous shear turbulence laden with finite-size particles

The dynamics of homogeneous shear turbulence laden with spherical finite-size particles is investigated using fully resolved numerical simulations to understand how the presence of particles modulates turbulent shear flows. We focus on a dilute flow laden with non-sedimenting particles whose diameter is slightly smaller than or comparable with those of vortex cores in turbulence. An immersed boundary method is adopted to represent a spherical finite-size particle. Numerical results show that the presence of particles augments the viscous dissipation of turbulence kinetic energy, which leads to a slower increase in the turbulence energy. Although the augmentation of energy dissipation occurs predominantly inside viscous layers surrounding particles in an initial period, the contribution from their outside becomes more significant due to the modification of turbulence structures as turbulence develops. It is found that the particles exhibit weak tendency to accumulate in vortex layers. The particles approaching and colliding with vortex layers induce large velocity fluctuations, which leads to the generation and shedding of thin vortex tubes. Newly generated vortex tubes interact with developed vortex tubes and layers, and modify the entire structure of the vorticity field.     

Crystallographic orientation-dependent optical properties of GaInSb mid-infrared quantum well laser

The optical properties of compressively strained GaInSb/GaInAlSb quantum well (QW) laser are numerically studied in different crystal orientations solving envelope function equation using finite difference method. The simulation results demonstrate that there is a strong correlation between the optical gain and its emission wavelength with crystal orientation of the QW. The maximum and minimum optical gains are evaluated in the (1 1 3) and (1 1 1) crystal orientations, respectively, due to band mixing effects. The peak emission wavelength can be tuned from 2.4 μm to 2.25 μm by changing the crystal orientation from (1 1 0) to (1 1 1). Typical optical gains are evaluated 3115, 3080, 2790, 3415, and 2940 cm^?1 in (0 0 1), (1 1 0), (1 1 1), (1 1 3), and (1 3 1) crystal orientations, respectively, when the injection carrier density is 3.5 × 10¹⁸ cm^?3. The highest optical power and lower threshold current are obtained in (1 1 3) orientation for the number of quantum wells three.     

Computational Design of Single-Peptide Nanocages with Nanoparticle Templating

Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.     

Plasma Catalysis for Environmental Treatment and Energy Applications

The current status of plasma-catalysis research and the associated possible applications are outlined. A basic explanation of plasma chemistry is given, which is then used as a foundation to indicate the research vector for the ongoing development of various applications. As an example of an environmental application, volatile organic compound decomposition using plasma-catalysis is discussed in depth, from the fundamental concept to the current industrial application status. As a potential application of plasma-catalysis towards the realization of a future “hydrogen society”, ammonia synthesis is discussed in terms of current social attitudes and regulations, along with historical developments. Additionally, up-to-date information on the fundamentals of the nonthermal plasma interaction with a catalyst is provided.     

Die Dimensionen und Dipolmomente von Polypropylenglycol-Ketten

Ohne Zusammenfassung     

Studies of the micro-brownian motion of a polymer chain by the fluorescence polarization method. III. Fluorescent conjugates of polyethyleneimine

Fluorescent conjugates of polyethyleneimine (PEI) were prepared by conjugation of fluorescent dyes, fluorescein isocyanate (FIC), and 1-dimethylaminonaphthalene-5-sulfonyl chloride (DNS), to PEI. The degree of polarization of the fluorescence was measured as a function of temperature and solvent viscosity on aqueous solutions of the conjugates and the data thus obtained were analyzed in terms of an equation of the Perrin type to calculate the mean relaxation time of the conjugate. The mean relaxation times obtained for the two types of the conjugates, which differ in the excited lifetime by a factor of about three, practically agree with one another and are about 2.5 X 10^?8 sec. The relaxation time of the DNS conjugate increases with increasing molecular weight of the conjugate from 2 X 10^?8 to 4 X 10^?8 sec. These values are much larger than those of the PAA conjugates reported in Part I of this series. The relaxation time of this order may correspond to that for the cooperative rotary motion of about ten monomeric residues on the PEI chain, that is, for the motion of an intermediate segment of the PEI molecule in solution. Finally, relaxation time–molecular weight relationships for various types of fluorescent conjugates are compared. It is suggested that these data may serve as a basis for elucidating the mode of motion of a given molecule in solution from the polarization data.