The gas-phase dipeptide analogue acetyl-phenylalanyl-amide: a model for the study of side chain/backbone interactions in proteins

The issue of the influence of the side chain/backbone interaction on the local conformational preferences of a phenylalanine residue in a peptide chain is addressed. A synergetic approach is used, which combines gas-phase UV spectroscopy as well as gas-phase IR/UV double-resonance experiments with DFT and post Hartree-Fock calculations. N-Acetyl-Phe-amide was chosen as a model system for which three different conformers were observed. The most stable conformer has been identified as an extended beta(L) conformation of the peptide backbone. It is stabilized by a weak but significant NH-pi interaction bridging the aromatic ring on the residue (i) with the NH group on residue (i+1), with the aromatic side chain being in an anti conformation. This stable conformation corresponds to the common NH(i+1)-aromatic(i) interaction encountered in proteins for the three aromatic residues (phenylalanine, tyrosine, and tryptophan), which illustrates the relevance of gas-phase investigations to structural biology issues. The two other less abundant conformers have been assigned to two gamma-folded backbone conformations that differ by the orientation of the side chain. In all cases, the IR data provided spectroscopic fingerprints of these interactions. Finally, the strong conformational dependence of the fluorescence yield found for N-acetyl-Phe-amide illustrates the role of the environment on the excited-state dynamics of these species, which is often exploited by biochemists to monitor protein structural changes from tryptophan lifetime measurements.     

Ion-beam analysis of CuInSe<Subscript>2</Subscript> solar cells deposited on polyimide foil

CuInSe₂ (CIS) solar cells deposited on polyimide foil by the Solarion company in a web-coater-based process using sputter and evaporation techniques were investigated in the ion beam laboratory LIPSION of the University of Leipzig by means of Rutherford backscattering spectrometry (RBS) and particle-induced X-ray emission (PIXE) using high-energy broad ion beams and microbeams. From these measurements the composition of the absorber and the lateral homogeneity and film thicknesses of the individual layers could be determined on the basis of some reasonable assumptions. For the first time, quantitative depth profiling of the individual elements was performed by microPIXE measurements on a beveled section prepared by ion-beam etching of a CIS solar cell. Within the CIS absorber layer no significant concentration–depth gradients were found for Cu, In, and Se, in contrast with results from secondary neutral mass spectrometry (SNMS) depth profiling, which was applied to the same samples for comparison. Furthermore, both PIXE and SNMS showed the presence of a remarkable amount of Cd from the CdS buffer layer in the underlying absorber.     

Hg-coordination studies of oligopeptides containing cysteine,histidine and tyrosine by 199mHg-TDPAC

In order to study the interaction of histidine- and tyrosine-containing peptide chains with Hg(II), the nuclear quadrupole interaction (NQI) of ^199mHg in the Hg complexes of the oligopeptides Alanyl–Alanyl–Histidyl–Alanyl–Alanine-amid (AAHAA–NH₂) and Alanyl–Alanyl–Tyrosyl–Alanyl–Alanine-amid (AAYAA–NH₂) was determined by time differential perturbed angular correlation and is compared with previous data on Alanyl–Alanyl–Cysteyl–Alanyl–Alanyl (AACAA–OH). The ^199mHg–NQIs depend on the oligopeptide to Hg(II) stoichiometry and indicate that two-fold and four-fold coordinations occur for the bound Hg(II). This revised version was published online in August 2006 with corrections to the Cover Date.     

A topological completeness theorem

We prove a topological completeness theorem for infinitary geometric theories with respect to sheaf models. The theorem extends a classical result of Makkai and Reyes, stating that any topos with enough points has an open spatial cover. We show that one can achieve in addition that the cover is connected and locally connected. Received: 27 September 1996 / Revised version: 15 January 1998     

Rough support vector regression

This paper describes the relationship between support vector regression (SVR) and rough (or interval) patterns. SVR is the prediction component of the support vector techniques. Rough patterns are based on the notion of rough values, which consist of upper and lower bounds, and are used to effectively represent a range of variable values. Predictions of rough values in a variety of different forms within the context of interval algebra and fuzzy theory are attracting research interest. An extension of SVR, called rough support vector regression   (RSVR), is proposed to improve the modeling of rough patterns. In particular, it is argued that the upper and lower bounds should be modeled separately. The proposal is shown to be a more flexible version of lower possibilistic regression model using ?$?$-insensitivity. Experimental results on the Dow Jones Industrial Average demonstrate the suggested RSVR modeling technique.     

The Role of Nuclear Nanoprobes in Inducing Magnetic Ordering in Graphite

In this article several aspects concerning the induction of magnetic ordering in graphite via proton bombardment using nuclear nanoprobes are addressed such as proton range and lateral straggling, defect densities, heat load, and simultaneous impurity analysis via particle induced X-ray emission.     

Highly Intact and Pure Oxo‐Functionalized Graphene: Synthesis and Electron‐Beam‐Induced Reduction

Controlling the chemistry of graphene is necessary to enable applications in materials and life sciences. Research beyond graphene oxide is targeted to avoid the highly defective character of the carbon framework. Herein, we show how to optimize the synthesis of oxo‐functionalized graphene (oxo‐G) to prepare high‐quality monolayer flakes that even allow for direct transmission electron microscopy investigation at atomic resolution (HRTEM). The role of undesired residuals is addressed and sources are eliminated. HRTEM provides clear evidence for the exceptional integrity of the carbon framework of such oxo‐G sheets. The patchy distribution of oxo‐functionality on the nm‐scale, observed on our highly clean oxo‐G sheets, corroborates theoretical predictions. Moreover, defined electron‐beam irradiation facilitates gentle de‐functionalization of oxo‐G sheets, a new route towards clean graphene, which is a breakthrough for localized graphene chemistry.     

Join tree propagation utilizing both arc reversal and variable elimination

In this paper, we put forth the first join tree propagation algorithm that selectively applies either arc reversal (AR) or variable elimination (VE) to build the propagated messages. Our approach utilizes a recent method for identifying the propagated join tree messages à priori. When it is determined that a join tree node will construct a single distribution to be sent to a neighbouring node, VE is utilized as it builds a single distribution in the most direct fashion; otherwise, AR is applied as it maintains a factorization of distributions allowing for barren variables to be exploited during propagation later on in the join tree. Experimental results, involving evidence processing in four benchmark Bayesian networks, empirically demonstrate that selectively applying VE and AR is faster than applying one of these methods exclusively on the entire network.     

Magnetic order in graphite: Experimental evidence,intrinsic and extrinsic difficulties

We discuss recently obtained data using different experimental methods including magnetoresistance measurements that indicate the existence of metal-free high-temperature magnetic order in graphite. Intrinsic as well as extrinsic difficulties to trigger magnetic order by irradiation of graphite are discussed in view of recently published theoretical work.