Avoidance of boxed mesh patterns on permutations

We introduce the notion of a boxed mesh pattern and study avoidance of these patterns on permutations. We prove that the celebrated former Stanley–Wilf conjecture is not true for all but eleven boxed mesh patterns; for seven out of the eleven patterns the former conjecture is true, while we do not know the answer for the remaining four (length-four) patterns. Moreover, we prove that an analogue of a well-known theorem of Erd?s and Szekeres does not hold for boxed mesh patterns of lengths larger than 2. Finally, we discuss enumeration of permutations avoiding simultaneously two or more length-three boxed mesh patterns, where we meet generalized Catalan numbers.     

Selection of aptamers for a non-DNA binding protein in the context of cell lysate

Aptamer-facilitated Protein Isolation from Cells (AptaPIC) is a recently introduced method that allows, in particular, generation of aptamers for a protein target in a context of a crude cell lysate. The approach enables efficient, tag-free, affinity purification of target proteins which are not available in a pure form a priori, and for which no affinity ligands are available. In the proof-of-principle work, AptaPIC was used to develop aptamers for and purify MutS, a DNA mismatch repair protein. The DNA-binding nature of MutS raised concerns that AptaPIC was not a generic technique and could be inapplicable to protein targets that do not possess native nucleic acid-binding properties. Here we prove that these concerns are invalid. We used AptaPIC to generate pools of aptamers for human Platelet-Derived Growth Factor chain B (PDGF-B) protein, a non-DNA binding protein, in the context of a bacterial cell lysate, and subsequently purify it from the same lysate. Within a small number of rounds, the efficiencies of aptamer selection were similar in conventional Systematic Evolution of Ligands by Exponential Enrichment (SELEX) for pure protein and in AptaPIC for protein in the cell lysate. The conventional selection approach resulted in an aptamer pool with an EC(50) value of 2.0±0.1 μM, while the AptaPIC selection approach resulted in a pool with an EC(50) value of 3.9±0.4 μM. Our results clearly demonstrate that selection of aptamers for proteins in the cell lysate is not only realistic but also efficient.     

Trivinylphosphine and trivinylphosphine chalcogenides: stereochemical trends of ³¹P-¹H spin-spin coupling constants

A combined theoretical and experimental study of the stereochemical behavior of (31)P-(1)H spin-spin coupling constants has been performed in the series of trivinylphosphine and related trivinylphosphine oxide, sulfide and selenide. Theoretical energy-based conformational analysis of the title compounds performed at the MP2/6-311G** level reveals that each of the four compounds of this series exists in the equilibrium mixture of five true-minimum conformers, namely s-cis-s-cis-s-cis, s-cis-s-cis-gauche, syn-s-cis-gauche-gauche, anti-s-cis-gauche-gauche and gauche-gauche-gauche, which were taken into account in the conformational averaging of (31)P-(1)H spin-spin couplings calculated at the second-order polarization propagator approach/aug-cc-pVTZ-J level of theory. All (31)P-(1)H spin-spin coupling constants involving phosphorus and either of the vinyl protons are found to demonstrate a marked stereochemical dependences with respect to the geometry of the coupling pathway and internal rotation of the vinyl group around the P-C bond which is of major importance in the stereochemical studies of the unsaturated phosphines and phosphine chalcogenides.     

Development of the custom polymeric materials specific for aflatoxin B1 and ochratoxin A for application with the ToxiQuant T1 sensor tool

Two polymers were computationally designed with affinity to two of the most abundant mycotoxins aflatoxin B1 (AFB1) and ochratoxin A (OTA) for application in the ToxiQuant T1 System. The principle of quantification of AFB1 and OTA using the ToxiQuant T1 instrument comprised of a fluorimetric analysis of mycotoxins adsorbed on the polymer upon exposure to UV light. High affinity of the developed resins allowed the adsorption of both toxins as discrete bands on the top of the cartridge with detection limit as low as 1 ng quantity of mycotoxins.     

The remarkable chemistry of trannulenes: green fluorinated fullerenes with unconventional aromaticity

We report the first reaction of trannulenes involving their thermal isomerization to a new class of compounds termed "triumphenes". The thermodynamically controlled conversion of trannulenes into triumphenes is accompanied by an unprecedented migration of three organic addends from one hemisphere of the fullerene cage to another. The reaction products, bearing aliphatic substituents, might find applications in materials science as strong electron acceptors due to the presence of fifteen electron-withdrawing fluorine atoms in their molecular framework. It was revealed that the isomerization of trannulenes can be affected by the presence of unsaturated compounds in the reaction mixture. Heating of trannulenes C(60)F(15)R(3) with C(60), C(70), anthracene, or pentacene at reflux in 1,2-dichlorobenzene yields fluorinated derivatives C(60)F(14)R(2)A, which possess a fused cyclic addend A. The products of this reaction have "triumphene-type" addition patterns and seem to be formed through an unprecedented sequence of elimination, addition, and isomerization steps. The molecular structure of a representative triumphene was proven unambiguously by X-ray single-crystal diffraction analysis and by NMR spectroscopy. The reactions revealed here open up numerous opportunities for chemical derivatization of fluorinated fullerenes. This method promises to provide a new path towards valuable photoactive materials and a new generation of fullerene-based compounds that are suitable for biomedical applications.     

Laccase–gold nanoparticle assisted bioelectrocatalytic reduction of oxygen

It was found that homogeneous activity of Trametes hirsuta laccase is considerably diminished in the presence of gold nanoparticles (Au-NPs). Heterogeneous electron transfer studies revealed that Au-NPs facilitate direct electron transfer (DET) between the T1 copper site of the laccase and the surface of Au-NP modified electrodes. DET was characterized by the standard heterogeneous ET constant of 0.5 ± 0.6 s^?1 at Au-NPs with an average diameter of 50 nm. As a consequence of this a well pronounced DET based bioelectrocatalytic oxygen reduction with current densities of 5–30 µA cm^?2 has been achieved at the laccase–Au-NP modified electrodes.     

Electrochemical and spectroscopic properties of poly-4,4′-dialkoxy-2,2′-bipyrroles

The structure and the electrochemical and spectral properties of two conductive electrochemically polymerized substituted bipyrroles 4,4′-methoxy-2,2′-bipyrrole and 4,4′-buthoxy-2,2′-bipyrrole were studied and compared. The polymers were characterized by cyclic voltammetry, FT-Raman spectroscopy, scanning electron microscopy, and in situ conductivity measurements at different pH and redox state.     

Thermochemistry of imidazolium-based ionic liquids: experiment and first-principles calculations

In this work the molar enthalpy of formation of the ionic liquid 1-ethyl-3-methylimidazolium dicyanoamide in the gaseous phase [C(2)MIM][N(CN)(2)] was measured by means of combustion calorimetry and enthalpy of vaporization using transpiration. Available, but scarce, primary experimental results on enthalpies of formation of imidazolium based ionic liquids with the cation [C(n)MIM] (where n = 2 and 4) and anions [N(CN)(2)], [NO(3)] and [NTf(2)] were collected and checked for consistency using a group additivity procedure. First-principles calculations of the enthalpies of formation in the gaseous phase for the ionic liquids with the common cation [C(n)MIM] (where n = 2 and 4) and with the anions [N(CN)(2)], [NO(3)], [NTf(2)], [Cl], [BF(4)] and [PF(6)] have been performed using the G3MP2 theory. It has been established that the gaseous phase enthalpies of formation of these ionic liquids obey the group additivity rules.