Vibrational spectra and quantum chemical calculations of uracilyl–pyridinium mesomeric betaine

Modified nucleobases (MNs) are promising molecules with potential application in non‐linear optic (NLO) and drug design against a wide number of diseases. In the present paper we report studies on a cross‐conjugated mesomeric betaine, which can act as a MN, formed by the covalent union of a 4‐dimethylamino pyridinium and a uracilyl groups. The molecule thus formed must be presented by a dipolar canonical formulae in which positive and negative charges are delocalized within separated moieties. Quantum chemistry density functional theory (DFT) calculations, at the B3PW91/6‐31G** level, and Fourier transform (FT) infrared and Raman spectra of this molecule and its N‐deuterated derivative were performed. The calculated structural properties over the ground state optimized structure evidenced a strong separation between the two conjugated systems. Comparison with previous results obtained for the cationic species indicated that N‐protonation clearly affects the degree of conjugation. Assignments of the FT‐IR and FT‐Raman spectra were supported by the DFT wavenumbers, intensities and normal modes, which also evidenced the separation of the two conjugated systems. Significant deviations were found for the stretching force constants of the inter‐ring and the uracilyl skeletal bonds when comparing this molecule with its N‐protonated species. Copyright © 2007 John Wiley & Sons, Ltd.     

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.

Enhancement of inhomogeneities in gels upon swelling and stretching

In this paper, it is shown how a percolation process can be used to describe the inhomogeneities of polymer concentration, appearing in gels prepared by random crosslinking of a semi-dilute solution, and how they are modified by swelling or stretching of the network. Neutron scattering experimental data are compared to the predictions of this model in the isotropic and anisotropic cases. A good agreement is found. In particular, “abnormal” butterfly patterns in the iso-intensity curves have been detected, as expected from the model.     

Enantioselective liquid-solid extraction for screening of structurally related chiral stationary phases

Summary An enantioselective liquid-solid batch extraction method is described for the screening of novel chiral stationary phases (CSPs) during optimization studies of chiral selectors derived form a common lead structure. Extraction enantioselectivity (α) values can be calculated from the enantiomeric excess ee-values of the selectand, which are measured in the liquid phase by enantioselective HPLC. Extraction α-values have been correlated with chromatographic α-values. The influence was studied of several experimental parameters of the assay (pH_a, buffer concentration, temperature, selector/selectand and phase ratio) on the enantiomeric excess (ee) values of the selectands and the enantioselectivity of the CSPs, respectively. The derived statistically significant model has then been implemented to predict chromatographic α-values of novel CSPs. For example, an ee of 89.3% for DNB-Leu as selectand could be achieved in batch extraction for a novel synthesized but mechanistically similarly-acting CSP derived form quinine. This corresponds to a calculated extraction α-value of 17.7. Based on this α_extraction a chromatographic α-value of 28.8 was predicted by the linear correlation model; the experimental HPLC α-value of 31.7 was in good agreement and demonstrated the validity of the proposed screening method. The method is particularly helpful in SO optimization studies.     

Highly phosphorylated core oligosaccharide structures from cold-adapted Psychromonas arctica

Many cold habitats contain plenty of microorganisms that represent the most abundant cold-adapted life forms on earth. These organisms have developed a wide range of adaptations that involve the cell wall of the microorganism. In particular, bacteria enhance the synthesis of unsaturated fatty acids of membrane lipids to maintain the membrane fluidity, but very little is known about the adaptational changes in the structure of the lipopolysaccharides (LPSs), the main constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. The aim of this study was to investigate the chemical structure of these LPSs for insight into the temperature-adaptation mechanism. For this objective, the cold-adapted Psychromonas arctica bacterium, which lives in the arctic sea-water near Spitzbergen (Svalbard islands, Arctic) was cultivated at 4 degrees C. The lipooligosaccharides (LOSs) were isolated and analysed by means of chemical analysis and electrospray ionisation high-resolution Fourier transform mass spectrometry. The LOS was then degraded either by mild hydrazinolysis (O-deacylation) or with hot 4 M KOH (N-deacylation). Both products were investigated in detail by using 1H and 13C NMR spectroscopy and mass spectrometry. The core consists of a mixture of species that differ because of the presence of nonstoichiometric D-fructose and/or D-galacturonic acid units.     

New open-chain tetrapyrroles as chromophores in the plant photoreceptor phytochrome

A series of six open-chain tetrapyrroles has been synthesized and used as chromophores for the plant photoreceptor protein phytochrome. The novel chromophores vary in the size of substituents 17 and 18 at ring D. This ring undergoes maximal conformational change upon light excitation ( Z --> E photoisomerization of the 15,16-double bond). Instead of methyl and vinyl substituents (positions 17, 18) as present in the native chromophore phytochromobilin, dimethyl, methyl and isopropyl, methyl and tert-butyl, ethyl and methyl, vinyl and methyl, and isopropyl and methyl substituents have been generated. All novel chromophores assemble with the apoprotein. The obtained chromoproteins show hypsochromic shifts of the absorbance maxima by 10 nm maximally, compared to the native pigment, except for the 17-isopropyl-18-methyl-substituted compound which showed a 100 nm hypsochromic shift of selectively the P r form. The assembly kinetics were slowed down in correlation to the increasing size of the substituents, with stronger effects for modified substituents at position 17. The thermal stability of the photoinduced P fr form for the 18-isopropyl and the 18- tert butyl substituents was even greater than that of the native pigments. Those chromophores carrying substituents at position 17 larger than the methyl group (ethyl and isopropyl) showed a very low stability of the respective P fr forms. Time-resolved detection of the P r to P fr conversion (laser-induced flash photolysis) revealed a slower formation of the P fr form for those chromophores carrying larger substituents at position 18, whereas the rise and decay kinetics of the early intermediates are only moderately changed. Introduction of larger substituents at position 17 (ethyl, vinyl, and isopropyl) causes drastic changes in the kinetics; in particular the formation of the first thermally stable intermediate, I 700, is significantly slowed, making a detection of its rise possible.     

Malondialdehyde tagging improves the analysis of arginine oligomers and arginine-containing dendrimers by HPLC-MS

The selective modification of arginine residues by malondialdehyde (MDA) was used to improve the mass spectrometric analysis of arginine oligomers (Arg(x), x = 4, 6, 7, 8, 9) and an arginine-containing dendrimeric peptide. MDA tagging significantly increased the hydrophobicity of the arginine side-chain and resulted in improved retention in RP HPLC of the oligoarginines using formic acid as mobile phase additive. This avoided the use of TFA to generate sufficient retention, as TFA was shown to lead to a dramatically reduced sensitivity (up to ten-fold for Arg(8) and Arg(9)) as a result of the strong signal suppression by ion pairing with multiple basic residues. MDA modification of Arg oligomers not only resulted in improved detection sensitivity for most of the peptides studied (e. g., more than six-fold for Arg(7)), but also greatly enhanced the quality of MS/MS spectra, in line with previous results for other peptides. Furthermore, MDA modification helped to identify major side products in a sample of a dendrimeric peptide, a class of peptides that is typically difficult to analyze by MS.