A method for the generation of glycoprotein mimetics

A general method for preparing glycoprotein mimetics with defined glycan structure using the Z domain protein as an example is reported. An unnatural amino acid containing the keto group was site-specifically incorporated into a target protein, Z domain, in response to the amber nonsense codon with high translational fidelity and efficiency. An aminooxy saccharide derivative was then selectively coupled to this genetically encoded keto group. The resulting saccharide core was elaborated to a glycan complex with glycosyltransferases. Alternatively, aminooxy analogues of more complicated glycans were prepared and directly attached to the keto group. Homogeneous glycoprotein mimetics thus prepared should prove useful for the study of carbohydrate effects on glycoprotein structure and function. This method may also lead to the production of glycoprotein therapeutics from Escherichia coli.     

Experimental charge density of octafluoro-1,2-dimethylenecyclobutane: atomic volumes and charges in a perfluorinated hydrocarbon

Octafluoro-1,2-dimethylenecyclobutane, mp. 238 K, was crystallized in situ on a SMART 1000-CCD diffractometer, and high order X-ray diffraction data were collected at 100 K for a charge density determination. A topological analysis was applied and a partitioning of the molecule into atomic regions making use of Bader's zero flux surfaces yielded atomic volumes and charges. Corresponding atomic properties were also derived theoretically from B3LYP/6-311++G(3df,3pd) wavefunctions. While for carbon the volumes and charges are largely dependent on their bonding environment, fluorine has an almost constant atomic volume around 16-17 A3 and a charge between -0.6 and -0.7e, not only in the title compound, but also in two further perfluorinated hydrocarbons, of which the charge densities were determined earlier.     

η-Alkynyl and vinylidene transition metal complexes: 10. Reaction of the metal-acetylide [(η-C5H5)(CO)(NO)W---CC---C(CH3)3]Li with 1,2-diiodoethane as electrophile and with various nucleophiles

Treatment of the η¹-acetylide complex [(η⁵-C₅H₅)(CO)(NO)W---CC---C(CH₃)₃]Li (4) with 1,2-diiodoethane in THF at −78 °C, followed by the addition of Li---CC---R [R=C(CH₃)₃, C₆H₅, Si(CH₃)₃, 6a–6c] or n-C₄H₉Li and protonation with H₂O, afforded the corresponding oxametallacyclopentadienyl complexes (η⁵-C₅H₅)W(I)(NO)[η²-O=C(CC---R)CH=CC(CH₃)₃] (7a–7c), 8c and (η⁵-C₅H₅)W(I)(NO)[η²-O=C(n-C₄H₉)CH=CC(CH₃)₃] (9). The formation of these metallafuran derivatives is rationalized by the electrophilic attack of 1,2-diiodoethane onto the metal center of 4 to form first the neutral complex [(η⁵-C₅H₅)(I)(CO)(NO)W---CC---C(CH₃)₃] (5). Subsequent nucleophilic addition of Li---CC---R 6a–6c or n-C₄H₉Li and a reductive elimination step followed by protonation leads to the products 7a–7c and 9. One reaction intermediate could be trapped with CF₃SO₃CH₃ and characterized by a crystal structure analysis. The identity of another intermediate was established by infrared spectroscopic data. The oxametallacyclopentadienyl complex 10 forms in the presence of excess 1,2-diiodoethane through an alternative pathway and crystallizes as a clathrate containing iodine.     

A finite‐volume scheme for a spinorial matrix drift‐diffusion model for semiconductors

An implicit Euler finite‐volume scheme for a spinorial matrix drift‐diffusion model for semiconductors is analyzed. The model consists of strongly coupled parabolic equations for the electron density matrix or, alternatively, of weakly coupled equations for the charge and spin‐vector densities, coupled to the Poisson equation for the electric potential. The equations are solved in a bounded domain with mixed Dirichlet–Neumann boundary conditions. The charge and spin‐vector fluxes are approximated by a Scharfetter–Gummel discretization. The main features of the numerical scheme are the preservation of nonnegativity and bounds of the densities and the dissipation of the discrete free energy. The existence of a bounded discrete solution and the monotonicity of the discrete free energy are proved. For undoped semiconductor materials, the numerical scheme is unconditionally stable. The fundamental ideas are reformulations using spin‐up and spin‐down densities and certain projections of the spin‐vector density, free energy estimates, and a discrete Moser iteration. Furthermore, numerical simulations of a simple ferromagnetic‐layer field‐effect transistor in two space dimensions are presented. © 2015 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 32: 819–846, 2016     

Prediction of Propagation Rate Coefficients in Free Radical Solution Polymerization Based on Accurate Quantum Chemical Methods: Vinylic and Related Monomers,Including Acrylates and Acrylic Acid

The simulation of polymerization processes is of enormous industrial importance. A quantum chemical method based on density functional theory is developed and validated that provides almost chemical accuracy for radical polymerization propagation of industrially relevant monomers in aqueous solution. The necessary corrections are computed using the CC level of theory. Solvent effects are accounted for by the solvation model COSMO‐RS. The method is capable of reproducing and rationalizing, for example, monomer concentration effects on the propagation rate for NVP. A comparison is performed with recent PLP experimental data. The method does not rely on error compensation effects or empiric corrections and is suitable for industrially relevant systems.

     

The relaxation-time limit in the quantum hydrodynamic equations for semiconductors

The relaxation-time limit from the quantum hydrodynamic model to the quantum drift-diffusion equations in R³ is shown for solutions which are small perturbations of the steady state. The quantum hydrodynamic equations consist of the isentropic Euler equations for the particle density and current density including the quantum Bohm potential and a momentum relaxation term. The momentum equation is highly nonlinear and contains a dispersive term with third-order derivatives. The equations are self-consistently coupled to the Poisson equation for the electrostatic potential. The relaxation-time limit is performed both in the stationary and the transient model. The main assumptions are that the steady-state velocity is irrotational, that the variations of the doping profile and the velocity at infinity are sufficiently small and, in the transient case, that the initial data are sufficiently close to the steady state. As a by-product, the existence of global-in-time solutions to the quantum drift-diffusion model in R³ close to the steady-state is obtained.     

A Degenerate Fourth-Order Parabolic Equation Modeling Bose-Einstein Condensation Part II: Finite-Time Blow-Up

A degenerate fourth-order parabolic equation modeling condensation phenomena related to Bose-Einstein particles is analyzed. The model can be motivated from the spatially homogeneous and isotropic Boltzmann-Nordheim equation by a formal Taylor expansion of the collision integral. It maintains some of the main features of the kinetic model, namely mass and energy conservation and condensation at zero energy. The existence of local-in-time weak solutions satisfying a certain entropy inequality is proven. The main result asserts that if a weighted L ¹ norm of the initial data is sufficiently large and the initial data satisfies some integrability conditions, the solution blows up with respect to the L ^∞ norm in finite time. Furthermore, the set of all such blow-up enforcing initial functions is shown to be dense in the set of all admissible initial data. The proofs are based on approximation arguments and interpolation inequalities in weighted Sobolev spaces. By exploiting the entropy inequality, a nonlinear integral inequality is proved which implies the finite-time blow-up property.     

The free boundary problem of a semiconductor in thermal equilibrium

The quasi-hydrodynamic model for semiconductor devices in thermal equilibrium admits in general solutions for which the electron or hole density vanish. These sets are called vacuum sets. In this paper estimates on the vacuum sets and a first step in the regularity of the free boundary of these sets are presented. Numerical examples, including error estimates for linear finite elements, for the devices diode, bipolar transistor and thyristor indicate that the free boundary is more regular than theoretically predicted.