Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

Hydrogen–deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Highly Tin‐Selective Stille Coupling: Synthesis of a Polymer Containing a Stannole in the Main Chain

The incorporation of heavier Group 14 element heteroles into semiconducting polymers leads to unusual optoelectronic properties. However, polymers containing stannoles have not been accessible to date. We report a synthetic route to a well‐defined, stannole‐containing polymer, the first example of this class of π‐conjugated polymers. This route was made possible by developing difunctionalized stannole monomers and highly tin‐selective Stille coupling reactions that leave the tin in the stannole untouched. Compared to poly(3‐n‐hexylthiophene), the resulting polymer displays a remarkable bathochromic shift in its absorption.     

Synthetic and Biological Studies on New Urea and Triazole Containing Cystobactamid Derivatives

Cystobactamids belong to the group of arene-based oligoamides that effectively inhibit bacterial type IIa topoisomerases. Cystobactamid 861-2 is the most active member of these antibiotics. Most amide bonds present in the cystobactamids link benzoic acids with anilines and it was found that some of these amide bonds undergo chemical and enzymatic hydrolysis, especially the one linking ring C with ring D. This work reports on the chemical synthesis and biological evaluation of thirteen new cystobactamids that still contain the methoxyaspartate hinge. However, we exchanged selected amide bonds either by the urea or the triazole groups and modified ring A in the latter case. While hydrolytic stability could be improved with these structural substitutes, the high antibacterial potency of cystobactamid 861-2 could only be preserved in selected cases. This includes derivatives, in which the urea group is positioned between rings A and B and where the triazole is found between rings C and D.     

Photochemical Transformations with Iodine Azide after Release from an Ion‐Exchange Resin

This report discloses the photochemical homolytic cleavage of iodine azide after its formation following release from polymer‐bound bisazido iodate(I) anions. A series of radical reactions are reported including the 1,2‐functionlization of alkenes and the unprecedented chemoselective oxidation of secondary alcohols in the presence of primary alcohols.     

Comparison of electron spin resonance probe and dielectric relaxation in physically and chemically crosslinked polymers

Dielectric relaxation spectroscopy in the frequency range from 10⁻² Hz to 10⁶ Hz and electron spin resonance (ESR) experiments are employed to study the dynamics in chemically and physically crosslinked networks. As examples for physically crosslinked networks ortho- and para-cresol novolacs were investigated. Dielectrically these materials show low-temperature β- and high-temperature α-relaxation. Both relaxation regions differ for both types of novolacs. This is also reflected by the ESR measurements and is discussed in terms of different hydrogen bonds found to be stronger in para-cresol novolac. For the chemically crosslinked poly(triallyl isocyanurate) only a β-peak is found by the dielectric measurements. Also in the ESR experiment the slow motion regime is characterized up to high temperatures. This means that the segmental motion is strongly suppressed by chemical crosslinking. Nevertheless the obtained change in the formal T_50G value can be used to characterize the glass transition in highly crosslinked systems by the ESR method.     

Dynamic mechanical investigations of different substituted cellulose o-silyl ethers

In contrast to many cellulose derivatives, the cellulose O-silyl ethers with bulky side groups exhibit scarcely a change in glass transition temperature by a variation of the degree of substitution (DS) or degree of polymerization (DP) or by introducing phenyl carbamate groups for the remaining hydroxyls along the main chain. However, a substitution of these hydroxyls by flexible acetate groups lowers the glass transition temperature considerably. The secondary dispersion (relaxation) behavior is strongly influenced by the various substituents and can be correlated to specific motions of the molecules. The dynamic mechanical properties are also dependent on the kind of preconditioning of the samples.