High-resolution liquid chromatography/electrospray ionization time-of-flight mass spectrometry combined with liquid chromatography/electrospray ionization tandem mass spectrometry to identify polyphenols from grape antioxidant dietary fiber

Grape antioxidant dietary fiber (GADF) is a dietary supplement that combines the benefits of both fiber and antioxidants that help prevent cancer and cardiovascular diseases. The antioxidant polyphenolic components in GADF probably help prevent cancer in the digestive tract, where they are bioavailable. Mass spectrometry coupled to liquid chromatography is a powerful tool for the analysis of complex plant derivatives such as GADF. We use a combination of MS techniques, namely liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF-MS) and liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) on a triple quadrupole, for the identification of the polyphenolic constituents of the soluble fraction of GADF. First, we separated the mixture into four fractions which were tested for phenolic constituents using the TOF system in the full scan mode. The high sensitivity and resolution of the TOF detector over the triple quadrupole facilitate the preliminary characterization of the fractions. Then we used LC/ESI-MS/MS to identify the individual phenols through MS/MS experiments (product ion scan, neutral loss scan, precursor ion scan). Finally, most of the identities were unequivocally confirmed by accurate mass measurements on the TOF spectrometer. LC/ESI-TOF-MS combined with MS/MS correctly identifies the bioactive polyphenolic components from the soluble fraction of GADF. High-resolution TOF-MS is particularly useful for identifying the structure of compounds with the same LC/ESI-MS/MS fragmentation patterns.     

First examples of the cocrystallization of diastereomers of chiral phosphorus compounds

The first three examples of the cocrystallization of covalent diastereomers of phosphorus compounds containing different chiral elements (centres of chirality on carbon and phosphorus, and an axis of chirality) are reported. The phenomenon can be attributed to the complementarity of the molecular shapes of the diastereomers. The X-ray data of all the crystals exhibit centrosymmetric statistics regardless of their very different natures. Dedicated to the memory of Professor Viktor Naumov (1932–2007).     

Nanomolar CFTR inhibition by pore-occluding divalent polyethylene glycol-malonic acid hydrazides

Inhibitors of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel have potential application as antisecretory therapy in cholera. We synthesized mono- and divalent CFTR inhibitors consisting of a malonic acid hydrazide (MalH) coupled via a disulfonic stilbene linker to polyethylene glycols (PEGs; 0.2-100 kDa). IC50 values for CFTR inhibition were 10-15 microM for the monovalent MalH-PEGs, but substantially lower for divalent MalH-PEG-MalH compounds, decreasing from 1.5 to 0.3 microM with increasing PEG size and showing positive cooperativity. Whole-cell patch-clamp showed voltage-dependent CFTR block with inward rectification. Outside-out patch-clamp showed shortened single-channel openings, indicating CFTR pore block from the extracellular side. Luminally added MalH-PEG-MalH blocked by >90% cholera toxin-induced fluid secretion in mouse intestinal loops (IC50 approximately 10 pmol/loop), and greatly reduced mortality in a suckling mouse cholera model. These conjugates may provide safe, inexpensive antisecretory therapy.     

Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.     

Water interaction with hydrophobic and hydrophilic soot particles

The interaction of water with laboratory soots possessing a range of properties relevant for atmospheric studies is examined by two complementary methods: gravimetrical measurement of water uptake coupled with chemical composition and porosity analysis and HTDMA (humidified tandem differential mobility analyzer) inference of water uptake accompanied by separate TEM (transmission electron microscopy) analysis of single particles. The first method clarifies the mechanism of water uptake for bulk soot and allows the classification of soot with respect to its hygroscopicity. The second method highlights the dependence of the soot aerosol growth factor on relative humidity (RH) for quasi-monodisperse particles. Hydrophobic and hydrophilic soot are qualitatively defined by their water uptake and surface polarity: laboratory soot particles are thus classified from very hydrophobic to very hydrophilic. Thermal soot particles produced from natural gas combustion are classified as hydrophobic with a surface of low polarity since water is found to cover only half of the surface. Graphitized thermal soot particles are proposed for comparison as extremely hydrophobic and of very low surface polarity. Soot particles produced from laboratory flame of TC1 aviation kerosene are less hydrophobic, with their entire surface being available for statistical monolayer water coverage at RH approximately 10%. Porosity measurements suggest that, initially, much of this surface water resides within micropores. Consequently, the growth factor increase of these particles to 1.07 at RH > 80% is attributed to irreversible swelling that accompanies water uptake. Hysteresis of adsorption/desorption cycles strongly supports this conclusion. In contrast, aircraft engine soot, produced from burning TC1 kerosene in a gas turbine engine combustor, has an extremely hydrophilic surface of high polarity. Due to the presence of water soluble organic and inorganic material it can be covered by many water layers even below water saturation conditions. This soot demonstrates a gradual diameter growth factor (D(wet)/D(dry)) increase up to 1.22 at 93% relative humidity, most likely due to the presence of single particles with water soluble material heterogeneously distributed over their surface.     

Oxygen Microscopy by Two‐Photon‐Excited Phosphorescence

High‐resolution images of oxygen distributions in microheterogeneous samples are obtained by two‐photon laser scanning microscopy (2P LSM), using a newly developed dendritic nanoprobe with internally enhanced two‐photon absorption (2PA) cross‐section. In this probe, energy is harvested by a 2PA antenna, which passes excitation onto a phosphorescent metalloporphyrin via intramolecular energy transfer. The 2P LSM allows sectioning of oxygen gradients with near diffraction‐limited resolution, and lifetime‐based acquisition eliminates dependence on the local probe concentration. The technique is validated on objects with a priori known oxygen distributions and applied to imaging of pO₂ in cells.     

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules

The folding and unfolding kinetics of single molecules, such as proteins or nucleic acids, can be explored by mechanical pulling experiments. Determining intrinsic kinetic information, at zero stretching force, usually requires an extrapolation by fitting a theoretical model. Here, we apply a recent theoretical approach describing molecular rupture in the presence of force to unfolding kinetic data obtained from coarse-grained simulations of ubiquitin. Unfolding rates calculated from simulations over a broad range of stretching forces, for different pulling directions, reveal a remarkable "turnover" from a force-independent process at low force to a force-dependent process at high force, akin to the "roll-over" in unfolding rates sometimes seen in studies using chemical denaturant. While such a turnover in rates is unexpected in one dimension, we demonstrate that it can occur for dynamics in just two dimensions. We relate the turnover to the quality of the pulling direction as a reaction coordinate for the intrinsic folding mechanism. A novel pulling direction, designed to be the most relevant to the intrinsic folding pathway, results in the smallest turnover. Our results are in accord with protein engineering experiments and simulations which indicate that the unfolding mechanism at high force can differ from the intrinsic mechanism. The apparent similarity between extrapolated and intrinsic rates in experiments, unexpected for different unfolding barriers, can be explained if the turnover occurs at low forces.     

Quantum-chemical modeling of polypyrrole structure in neutral complexes with electron density acceptors

Quantum chemical approach has been applied for modeling the change in the conformation of the polypyrrole (PPy) chain both in its neutral and positively charged (doped) states due to its interaction with incorporated counterions. Polymer has been modeled by oligopyrrole molecule of 9–15 monomer units. It is shown that it is energetically favorable to reorient the pyrrole rings closest to the anion from trans to cis position. This reorientation leads to the formation of meanders which include 3–5 pyrrole rings per loop. Reduction in the loop size decreases the energy of interaction with the ion while an increase in the loop size reduces the number of attached ionic species accompanied by a slight change in their interaction energy with the PPy chain. The observed effect of polymer chain structuring in the presence of anions is proposed as a possible reason explaining the experimentally recorded broadening of the electroactivity potential region and the conductive state of the polypyrrole film on the electrode surface as a result of multiple repetitions of charge/discharge cycles of the polymer chain. Vibrational spectra of oligopyrrole complexes have been calculated, and prospects for experimental detection of predicted conformational states by IR spectroscopy are assessed.