Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Isolation of phenolic compounds from hop extracts using polyvinylpolypyrrolidone: Characterization by high-performance liquid chromatography–diode array detection–electrospray tandem mass spectrometry

The aim of the present work was the development of a suitable methodology for the separation and determination of phenolic compounds in the hop plant. The developed methodology was based on the sample purification by adsorption of phenolic compounds from the matrix to polyvinylpolypyrrolidone (PVPP) and subsequent desorption of the adsorbed polyphenols with acetone/water (70:30, v/v). At last, the extract was analyzed by HPLC–DAD and HPLC–ESI-MS/MS. The first phase of this work consisted of the study of the adsorption behavior of several classes of phenolic compounds (e.g. phenolic acids, flavonols, and flavanols) by PVPP in model solutions. It has been observed that the process of adsorption of the different phenolic compounds to PVPP (at low concentrations) is differentiated, depending on the structure of the compound (number of OH groups, aromatic rings, and stereochemistry hindrance). For example, within the phenolic acids class (benzoic, p-hydroxybenzoic, protocatechuic and gallic acids) the PVPP adsorption increases with the number of OH groups of the phenolic compound. On the other hand, the derivatization of OH groups (methylation and glycosylation) resulted in a greatly diminished binding. The use of PVPP revealed to be very efficient for adsorption of several phenolic compounds such as catechin, epicatechin, xanthohumol and quercetin, since high adsorption and recovery values were obtained. The methodology was further applied for the extraction and isolation of phenolic compounds from hops. With this methodology, it was possible to obtain high adsorption values (≥80%) and recovery yield values (≥70%) for the most important phenolic compounds from hops such as xanthohumol, catechin, epicatechin, quercetin and kaempferol glycosides, and in addition it allows the identification of about 30 phenolic compounds by HPLC–DAD and HPLC–ESI-MS/MS.     

Breather Solutions in Periodic Media

For nonlinear wave equations existence proofs for breathers are very rare. In the spatially homogeneous case up to rescaling the sine-Gordon equation \({\partial^2_t u = \partial^2_x u - \sin (u)}\) is the only nonlinear wave equation which is known to possess breather solutions. For nonlinear wave equations in periodic media no examples of breather solutions have been known so far. Using spatial dynamics, center manifold theory and bifurcation theory for periodic systems we construct for the first time such time periodic solutions of finite energy for a nonlinear wave equation

$ s(x) \partial^2_t u(x,t) = \partial^2_x u(x,t) - q(x) u(x,t)+ r(x)u(x,t)^3, $

with spatially periodic coefficients s, q, and r on the real axis. Such breather solutions play an important role in theoretical scenarios where photonic crystals are used as optical storage.

     

Disorder-mediated electron valley resonance in carbon nanotube quantum dots

We propose a scheme for coherent rotation of the valley isospin of a single electron confined in a carbon nanotube quantum dot. The scheme exploits the ubiquitous atomic disorder of the nanotube crystal lattice, which induces time-dependent valley mixing as the confined electron is pushed back and forth along the nanotube axis by an applied ac electric field. Using experimentally determined values for the disorder strength we estimate that valley Rabi oscillations with a period on the nanosecond time scale are feasible. The valley resonance effect can be detected in the electric current through a double quantum dot in the single-electron transport regime.     

Probing the out-of-plane distortion of single point defects in atomically thin hexagonal boron nitride at the picometer scale

Crystalline systems often lower their energy by atom displacements from regular high-symmetry lattice sites. We demonstrate that such symmetry lowering distortions can be visualized by ultrahigh resolution transmission electron microscopy even at single point defects. Experimental investigation of structural distortions at the monovacancy defects in suspended bilayers of hexagonal boron nitride (h-BN) accompanied by first-principles calculations reveals a characteristic charge-induced pm symmetry configuration of boron vacancies. This symmetry breaking is caused by interlayer bond reconstruction across the bilayer h-BN at the negatively charged boron vacancy defects and results in local membrane bending at the defect site. This study confirms that boron vacancies are dominantly present in the h-BN membrane.     

Validity of the KdV equation for the modulation of periodic traveling waves in the NLS equation

Bethuel et al.  and  and Chiron and Rousset [3] gave very nice proofs of the fact that slow modulations in time and space of periodic wave trains of the NLS equation can approximately be described via solutions of the KdV equation associated with the wave train. Here we give a much shorter proof of a slightly weaker result avoiding the very detailed and fine analysis of ,  and . Our error estimates are based on a suitable choice of polar coordinates, a Cauchy–Kowalevskaya-like method, and energy estimates.     

The Existence of Bifurcating Invariant Tori in a Spatially Extended Reaction-Diffusion-Convection System with Spatially Localized Amplification

We consider a spatially extended reaction-diffusion-convection system with a marginally stable ground state and a spatially localized amplification. We are interested in solutions bifurcating from the spatially homogeneous ground state in the case when pairs of imaginary eigenvalues simultaneously cross the imaginary axis. For this system we prove the bifurcation of a family of invariant tori which may contain quasiperiodic solutions. There is a serious difficulty in obtaining this result, because the linearization at the ground state possesses an essential spectrum up to the imaginary axis for all values of the bifurcation parameter. To construct the invariant tori, we use their invariance under the flow which manifests in a condition in PDE form. The nonlinear terms of this resulting PDE exhibit a loss of regularity. Since the linear part of this PDE is not smoothing, an adaption of the hard implicit function theorem (or Nash-Moser scheme) and energy estimates will be used to prove our result.     

In situ PM‐IRRAS studies of organothiols and organosilane monolayers–ZnO interfaces at high water activities

In situ photoelastic‐modulated Fourier transform infrared reflection absorption spectroscopy has been applied for the investigation of interfacial stability of organothiol and organosilane monolayer films on nanocrystalline zinc oxide thin films. It has been shown that for octadecyltriethoxysilane films, exposure to high water activities results in physisorption of water in the cross‐linked film. This high water activity at the interface leads to a reversible wet de‐adhesion of the interfacial silanol groups from the ZnO surface. However, the organothiol seems to form a denser monolayer and a stable by S–Zn bond that is resistant to the competition with adsorbed water. The reversible attachment for cross‐linked organosilanol films has been demonstrated for the first time by means of an in situ spectroscopic method on model ZnO surfaces. Copyright © 2016 John Wiley & Sons, Ltd.     

Structure elucidation and 1H/13C NMR spectral assignments of four trabectedin related compounds

This article presents the structure elucidation of four new compounds, formed during the hemisynthetic preparation of trabectedin, an anti-tumor natural product from Ecteinascidia turbinata. We report herein on the use of UV, MS and NMR spectroscopic data along with (1)H and (13)C spectral assignments obtained by means of 1D and 2D homo- and heteronuclear NMR techniques.     

Synthesis of 3-amino-4-fluoropyrazoles

Fluorinated pyrazoles bearing additional functional groups that allow further functionalization are of considerable interest as building blocks in medicinal chemistry. The developed synthetic strategy for new 3-amino-4-fluoropyrazoles consists of a monofluorination of β-methylthio-β-enaminoketones using 1-(chloromethyl)-4-fluoro-1,4-diazoniabicyclo[2.2.2]octane bis(tetrafluoroborate) (Selectfluor) toward the corresponding monofluorinated enaminoketones, followed by condensation with different hydrazines.