The bond bundle in open systems

Much of modern chemistry is concerned with the properties and dynamics of chemical bonds. Although they have been described variously, the most familiar representation is that of a link connecting two atoms. However, no one has yet developed a scheme by which to partition a molecule into bond volumes with well‐defined properties. As a consequence, the chemical bond is left as nothing more than a heuristic devise. Here, we show molecules can be partitioned into bond‐bundles–volumes that share many of the properties associated with the conceptual bond. This partitioning follows naturally through an extension of Baders topological theory of molecular structure. Surprisingly, it also bounds regions of space containing nonbonding or lone‐pair electrons and leads to bond orders consistent with those expected from theories of directed valance. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Book Notices

Journal of Optimization Theory and Applications -     

Selenium-modified TiO2 and its impact on photocatalysis

This work describes the preparation of a selenium-modified TiO(2) photocatalyst and a preliminary evaluation of its photocatalytic activity. Se-TiO(2) displayed greater visible absorption than undoped TiO(2) and was still capable of degrading quinoline at a slightly faster rate than undoped TiO(2) under UV light. Se-TiO(2) was also able to degrade organic molecules under purely visible light by a single electron transfer pathway. Irradiation with >435 nm light showed no evidence of efficient production of HO?-like species. Se-TiO(2) was also examined under hypoxic conditions, where the Se atoms were capable of trapping photogenerated electrons as evidenced by XPS.     

Microfluidic device generating stable concentration gradients for long term cell culture: application to Wnt3a regulation of β-catenin signaling

In developing tissues, proteins and signaling molecules present themselves in the form of concentration gradients, which determine the fate specification and behavior of the sensing cells. To mimic these conditions in vitro, we developed a microfluidic device designed to generate stable concentration gradients at low hydrodynamic shear and allowing long term culture of adhering cells. The gradient forms in a culture space between two parallel laminar flow streams of culture medium at two different concentrations of a given morphogen. The exact algorithm for defining the concentration gradients was established with the aid of mathematical modeling of flow and mass transport. Wnt3a regulation of β-catenin signaling was chosen as a case study. The highly conserved Wnt-activated β-catenin pathway plays major roles in embryonic development, stem cell proliferation and differentiation. Wnt3a stimulates the activity of β-catenin pathway, leading to translocation of β-catenin to the nucleus where it activates a series of target genes. We cultured A375 cells stably expressing a Wnt/β-catenin reporter driving the expression of Venus, pBARVS, inside the microfluidic device. The extent to which the β-catenin pathway was activated in response to a gradient of Wnt3a was assessed in real time using the BARVS reporter gene. On a single cell level, the β-catenin signaling was proportionate to the concentration gradient of Wnt3a; we thus propose that the modulation of Wnt3a gradients in real time can provide new insights into the dynamics of β-catenin pathway, under conditions that replicate some aspects of the actual cell-tissue milieu. Our device thus offers a highly controllable platform for exploring the effects of concentration gradients on cultured cells.     

Incorporation of 2,3-Disubstituted-1,4-Naphthoquinones into the A1 Binding Site of Photosystem I Studied by EPR and ENDOR Spectroscopy

Transient electron paramagnetic resonance and pulsed electron-nuclear double resonance (ENDOR) spectra of the state $ P_{700}^{ \cdot + } A_{1}^{ \cdot - } $ in photosystem I containing a series of non-native naphthoquinones (NQs) are presented. Previous studies have shown that quinones bind to the A₁ site with only one of their carbonyl groups H-bonded to the protein and that the asymmetric H-bond produces an odd alternant distribution of the spin density within the quinone. It is known that the native phylloquinone binds with its methyl group meta and its phytyl tail ortho to the H-bonded carbonyl. Monosubstituted NQs with short alkyl chains have been found to bind preferentially with their alkyl side groups meta to the H-bonded carbonyl. The selectivity of the binding site toward methyl and short chain substituents is studied by incorporating disubstituted NQs that have a methyl group at the 2-position and a short chain at the 3-position of the quinone ring. The hyperfine couplings (hfcs) of the methyl group protons are sensitive to the spin density distribution on the quinone and are used to deduce the position of the methyl group relative to the H-bonded carbonyl. The measured methyl proton hfcs indicate that the disubstituted quinones bind exclusively with their methyl group in the meta position relative to the H-bonded carbonyl and no evidence for binding with the methyl group in the ortho position is found. The disubstituted quinones have also been chosen to study the effect of electron withdrawing substituents on the spin density distribution. When the short chain contains electronegative atoms such as sulfur or chlorine, the methyl proton hfcs of the quinone in the A₁ binding site are found to be significantly larger than those of 2-methyl-1,4-naphthoquinone and phylloquinone in the same environment. Solution ENDOR measurements of the quinone radical anions in isopropanol and density functional theory (DFT) calculations in vacuo show that this increase in the hfcs is mostly intrinsic to the quinones due to the electron-withdrawing ability of the short chain and is not a result of differences in the binding to the protein. The DFT calculations suggest that the main reason for the increased methyl proton hfcs is delocalization of the singly occupied molecular orbital onto the side chain, which leads to an increase of the spin density on the neighboring carbon, which carries methyl group.     

Efficient catalysis of ammonia borane dehydrogenation

In the presence of an iridium pincer complex, dehydrogenation of ammonia borane (H3NBH3) occurs rapidly at room temperature in tetrahydrofuran to generate 1.0 equivalent of H2 and [NH2BH2]5. A metal borohydride complex has been isolated as a dormant form of the catalyst which can be reactivated by reaction with H2.     

Structural polarity induced by cooperative hydrogen bonding and lone-pair alignment in the molecular uranyl iodate Na2[UO2(IO3)4(H2O)

Na2[UO2(IO3)4(H2O)] has been synthesized under mild hydrothermal conditions. Its structure consists of Na+ cations and [UO2(IO3)4(H2O)](2-) anions. The [UO2(IO3)4(H2O)](2-) anions are formed from the coordination of a nearly linear uranyl, UO2(2+), cation by four monodentate IO(3-) anions and a coordinating water molecule to yield a pentagonal bipyramidal environment around the uranium center. The water molecules form intermolecular hydrogen bonds with the terminal oxo atoms of neighboring [UO2(IO3)4(H2O)](2-) anions to yield one-dimensional chains that extend down the b axis. There are two crystallographically unique iodate anions in the structure of Na2[UO2(IO3)4(H2O)]. One of these anions is aligned so that the lone-pair of electrons is also directed along the b axis. The overall structure is therefore polar, owing to the cooperative alignment of both the hydrogen bonds and the lone-pair of electrons on iodate. The polarity of the monoclinic space group C2 (a = 11.3810(12) A, b = 8.0547(8) A, c = 7.6515(8) A, beta = 90.102(2) degrees , Z = 2, T = 193 K) found for this compound is consistent with the structure. Second-harmonic generation of 532 nm light from a 1064 nm laser source yields a response of approximately 16x alpha-SiO2.