Experimental and Computational Models for Side Chain Discrimination in Peptide–Protein Interactions

A bis(18-crown-6) Tröger's base receptor and 4-substituted hepta-1,7-diyl bisammonium salt ligands have been used as a model system to study the interactions between non-polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all-anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor-ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl- and a phenyl group to an aromatic cavity, via CH-π, and combined aromatic CH-π and π-π interactions to be −1.7 and −3.3 kJ mol⁻¹, respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.     

Urine profiling using capillary electrophoresis-mass spectrometry and multivariate data analysis

This work presents the development of a general and fast method for metabolic profiling of urine, using capillary electrophoresis-electrospray ionisation mass spectrometry (CE-ESIMS) and multivariate data analysis (DA). Human urine samples collected before and after ingestion of paracetamol were analysed at acidic and basic CE conditions, using both positive and negative ESI-MS detection. Analysis of the entire resulting data set, with no prior knowledge of the target compounds, using pair-wise 'fuzzy' correlation and eigenvalue analysis enabled the samples to be discriminated between on the basis of blank urine and urine collected after drug intake. By generating two-dimensional loadings plots, it was also possible to identify the m/z values of the substances responsible for the differentiation between control and dosed samples.     

Expanding the scope of Lewis acid catalysis in water: remarkable ligand acceleration of aqueous ytterbium triflate catalyzed Michael addition reactions

[reaction: see text] Significant rate acceleration of metal-catalyzed Michael addition reactions in water was observed upon addition of small, dibasic ligands. Ytterbium triflate and TMEDA was the most effective combination leading to a nearly 20-fold faster reaction than in the absence of ligand.     

Sample pretreatment on a microchip with an integrated electrospray emitter

This study presents a microbead-packed PDMS microchip with an integrated electrospray emitter for sample pretreatment prior to sheathless ESI-MS. We prove the concept of analytical functions integrated onto a cm-sized area of a single bulk material. The microchip consists of two PDMS substrates replicated from SU-8 fabricated silicon wafer masters, bonded together after oxidation by corona discharge treatment. The channel within the microchip contains a grid structure that was used to trap 5 microm hypercross-linked polystyrene beads. The beads acted as a medium for sample desalting and enrichment. Electrical contact for the sheathless ESI process was achieved by coating the integrated emitter with conductive graphite powder after applying a thin layer of PDMS as glue. The coating as well as the bond of the PDMS structures showed excellent durability. A continuous spray was obtained from the microchip for over 800 h in a long-term electrospray stability experiment. Desalting and enrichment of neuropeptides from a physiological salt solution was successful by loading the sample onto the packed beads, followed by a washing and an eluting step. The results were obtained and evaluated using a TOF MS. An LOD of approximately 20 fmol (loaded onto the beads) for angiotensin II was obtained from a sample of neuropeptides dissolved in physiological salt solution.     

The synthesis and characterization of all diastereomers of a linear symmetrically fused Tris-Tröger's base analogue: new chiral cleft compounds

The synthesis and characterization of all diastereomers of a linear symmetrically fused tris-Tr?ger's base analogue are described. The diastereomers are unambiguously assigned as syn-anti 1 a, anti-anti 1 b, and syn-syn 1 c isomers, by using X-ray diffraction analysis and NMR spectroscopy. For the first time, the anti-anti and the syn-syn diastereomers of a linear symmetrically fused tris-Tr?ger's base analogue have been synthesized. Molecules 1 a and 1 c are new cleft compounds and analysis of compound 1 a in the solid state shows inclusion of one molecule of CH(2)Cl(2) in the larger aromatic cleft, whereas in isomer 1 c disordered solvent molecules are trapped in the extended aromatic cleft. Furthermore, in the solid state, isomer 1 c forms infinite open channels along one of the crystallographic axes and perpendicular to this axis there are infinitely extending "wedged-ravines". Importantly, each of the diastereomers 1 a-c is resistant to inversion at the stereogenic nitrogen atoms under strongly and weakly acidic conditions in the range from room temperature (RT) to 95 degrees C. This observed configurational stability at the stereogenic nitrogens of 1 a-c is unique for analogues of Tr?ger's base in general to date. Finally, the ratio of cleft compounds 1 a and 1 c significantly increased relative to cavity compound 1 b when ammonium chloride was used as an additive in the Tr?ger's base condensation to 1 a-c suggesting a templating effect of the ammonium ion.