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.     

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.     

Overcrowded naphthologs of mono-bridged tetraarylethylenes: analogs of bistricyclic aromatic enes

The naphthalogous mono-bridged tetraarylethylenes 9,9′-di-(1-naphthylmethylene)-9H-fluorene (5) and 9,9′-di-(1-naphthylmethylene)-9H-xanthene (6), analogs of bifluorenylidene (1) and bixanthenylidene (2), have been synthesized and their molecular and crystal structures have been determined. Ene 5 has been prepared by two alternative synthetic routes. The molecular structures of 5 and 6 show that each of these enes has very small twist around the central double bond, but the two naphthalene rings in both 5 and 6 are highly twisted. According to the NMR study, 5 and 6 in solution adopt conformations which are similar to those found by X-ray crystal structure analysis. The notable upfield shifts of H¹ and H⁸ (6.11 and 6.83 ppm, respectively) and H² and H⁷ (6.70 and 6.44 ppm, respectively) in 5 and 6 are due to the shielding caused by the nearly orthogonally twisted naphthalene rings. The B3LYP/6-31G(d) calculations of 5, 6, and their 2-naphthyl and phenyl analogs have been performed. In the 1-naphthyl series, the more efficient conjugation between the naphthyl substituents and the central C=C and the overcrowding due to the peri-hydrogen atoms lead to higher twists of the naphthyl groups and to lower twists of the central C=C. In the 2-naphthyl series, the opposite effects are noted. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Nanostructured Macromolecular Metal Containing Materials in Catalysis

Summary: Nanostructured regular materials based on cross-linked polypropylene imine (PPI) dendrimers and silica-gel polyamine composites were used as a support for the synthesis of Pd nanoparticles. The materials were tested as catalysts and displayed a high activity and selectivity for the hydrogenation of conjugated double bonds.     

Consistent approach to adsorption thermodynamics on heterogeneous surfaces using different empirical energy distribution models

Adsorption on heterogeneous surfaces with three basic energy distribution models (uniform model, exponential model, and normal-like model) is studied. Exact analytical solutions of the adsorption isotherms and the heats of adsorption are derived for the uniform and exponential models, and, with these solutions including a numerical solution for the normal-like model, the behavior of the differential heat of adsorption and the "apparent" standard adsorption entropy concerning the overall surface is described as a function of coverage and temperature. The approximations underlying the isotherms and heats of adsorption in the Temkin, Freundlich, and Langmuir-Freundlich types of adsorption are rationalized. By comparing these empirical formulas to the exact solutions, the level of these approximations is found to be identical, which is similar to the "condensation approximation". Their preconditions are that either the temperature is low enough, or the surface is strongly heterogeneous. Generally, they are suitable for the middle coverage range. The exact solutions provide a method to obtain more information on the heats, entropy, and heterogeneity of the catalyst surface from the calorimetric measurement of the heat of adsorption.     

Attachment of motile bacterial cells to prealigned holed microarrays

Construction of biomotors is an exciting area of scientific research that holds great promise for the development of new technologies with broad potential applications in areas such as the energy industry and medicine. Herein, we demonstrate the fabrication of prealigned microarrays of motile Escherichia coli bacterial cells on SiOx substrates. To prepare these arrays, holed surfaces with a gold layer on the bottom of the holes were utilized. The attachment of bacteria to the holes was achieved via nonspecific interactions using poly-l-lysine hydrobromide (PLL). Our data suggest that a single motile bacterial cell can be selectively attached to an individual hole on a surface and bacterial cell binding can be controlled by altering the pH, with the greatest occupancy occurring at pH 7.8. Cells attached to hole arrays remained motile for at least 4 h. These data indicate that holed surface structures provide a promising footprint for the attachment of motile bacterial cells to form high-density site-specific functional bacterial microarrays.