Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides

Solvent and temperature can affect the structural properties of cyclic peptides by controlling their flexibility. Here, we investigate two cyclic peptides, featuring beta turns. Using temperature-dependent NMR and FT-IR, we observed a pronounced temperature effect on the conformation of the cyclic peptide D-1 in CHCl₃ but a much smaller effect in CH₃CN. Almost no effect was observed for its diastereomer L-1 within a similar temperature range and using the same solvents. With the aid of Replica Exchange Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we were able to explain this behavior based on the increased flexibility of D-1 (in CHCl₃) in terms of intramolecular hydrogen bonding. The largest temperature dependence is observed for D - 1 in CHCl₃, while the temperature effect is less pronounced for L-1 in CHCl₃ and for both peptides in CH₃CN. This work provides new insights into the role of the environment and temperature on the conformations of cyclic peptides.     

The Effect of Air Plasma Activated Liquid on Uropathogenic Bacteria

Plasma Chemistry and Plasma Processing - Urinary tract infections (UTI) are often caused by resistant uropathogenic bacteria and can lead to sepsis or chronic renal failure. Cold plasma activated...     

Free Massive Fermions¶Inside the Quantum Discrete sine-Gordon Model

We extend the notion of space shifts introduced in [FV3] for certain quantum light cone lattice equations of sine-Gordon type at root of unity (e.g. [FV1,FV2,BKP,BBR]). As a result, we obtain a compatibility equation for the roots of central elements within the algebra of observables (also called current algebra). The equation, which is obtained by exponentiating these roots, is exactly the evolution equation for the?“classical background” as described in [BBR]. As an application for the introduced constructions, we derive a one to one correspondence between a special case of the quantum light cone lattice equations of sine-Gordon type and free massive fermions on a lattice, as a special case of the lattice Thirring model constructed in [DV]. Received: 2 December 1996 / Accepted: 19 January 1999     

Beyond Kozeny–Carman: Predicting the Permeability in Porous Media

Transport in Porous Media - Various processes such as heterogeneous reactions or biofilm growth alter a porous medium’s underlying geometric structure. This significantly affects its...     

Time-resolved photoelectron spectroscopy of solvated electrons in aqueous NaI solution

Time-resolved photoelectron spectroscopy was used to study the energetics and dynamics of solvated electrons in aqueous solution. Solvated electrons are generated by ultrafast photodetachment in a 100 mM aqueous NaI solution. Initially, an ensemble of strongly bound ("cold") solvated electrons and an ensemble of weakly bound ("hot") electrons in an unequilibrated solvent environment are observed. We report an ultrafast recombination channel for the "hot" electrons with a rate of (800 fs)(-1) which is in competition with thermalization occurring with a rate of (1.1 ps)(-1). The thermalized electrons recombine with the iodide radical with a rate of (22 ps)(-1). About 35% of the thermalized electrons escape geminate recombination and form free, solvated electrons. The vertical detachment energy for the solvated electron is determined to be 3.40 eV. No indication for a surface-bound electron at lower binding energies was observed.     

Colorimetric quantification of mRNA expression in rare tumour cells amplified by multiple ligation-dependent probe amplification

An enzyme-linked oligonucleotide assay (ELONA) for quantification of mRNA expression of five genes involved in breast cancer, extracted from isolated rare tumour cells and amplified by multiplex ligation-dependent probe amplification (MLPA) is presented. In MLPA, a multiplex oligonucleotide ligation assay is combined with a PCR reaction in which all ligation products are amplified by use of a single primer pair. Biotinylated probes complementary to each of the target sequences were immobilised on the surface of a streptavidin-coated microtitre plate and exposed to single-stranded MLPA products. A universal reporting probe sequence modified with horseradish peroxidase (URP–HRP) and complementary to a universal primer used during the MLPA step was further added to the surface-bound duplex as a reporter probe. Simultaneous addition of anchoring probe and target, followed by addition of reporter probe, rather than sequential addition, was achieved with no significant effect on sensitivity and limits of detection, but considerably reduced the required assay time. Detection limits as low as 20 pmol L⁻¹, with an overall assay time of 95 min could be achieved with negligible cross-reactivity between probes and non-specific targets present in the MLPA-PCR product. The same MLPA-PCR product was analysed using capillary electrophoresis, the technique typically used for analysis of MLPA products, and good correlation was observed. The assay presented is easy to carry out, relatively inexpensive, rapid, does not require sophisticated instrumentation, and enables quantitative analysis, making it very promising for the analysis of MLPA products.     

Hyperconjugation and the increasing bulk of OCOCX3 substituents in trans-1,4-disubstituted cyclohexanes destabilize the diequatorial conformer

The trans diesters of 1,4-cyclohexanediol with a number of acetic acid analogues, CX3COOH, of varying steric hindrance and polarity (CX3 = Me, Et, iso-Pr, tert-Bu, CF3, CH2Cl, CHCl2, CCl3, CH2Br, CHBr2, CBr3) were synthesized, and the axial,axial/equatorial,equatorial conformational equilibria were studied by low-temperature 1H NMR spectroscopy in CD2Cl2. The structures and relative energies of the axial,axial and equatorial,equatorial conformers were calculated at both the MP2/6-311G* and the MP2/6-311+G* levels of theory, and it was only by including diffuse functions that a good correlation of deltaG(o)calcd vs deltaG(o)exptl could be obtained. Both the structures and the energy differences of the axial,axial and equatorial,equatorial conformers are discussed with respect to the established models of conformational analysis, viz., steric 1,3-diaxial and hyperconjugative interactions. Interestingly, the hyperconjugative interactions sigma(C-C)/sigma(C-H) --> sigma*(C-O), together with a steric effect which also destabilizes the equatorial,equatorial conformers on increasing bulk of the substituents, proved to dominate the position of the conformational equilibria. In addition, the preference of the axial,axial conformers with respect to their equatorial,equatorial analogues was greater than expected from the conformational energies of the corresponding substituents in the monosubstituted cyclohexyl esters. The reason for this very interesting and unexpected result is also discussed.