Positivity for cluster algebras from surfaces

We give combinatorial formulas for the Laurent expansion of any cluster variable in any cluster algebra coming from a triangulated surface (with or without punctures), with respect to an arbitrary seed. Moreover, we work in the generality of principal coefficients. An immediate corollary of our formulas is a proof of the positivity conjecture of Fomin and Zelevinsky for cluster algebras from surfaces, in geometric type.     

Metastable Linkage Isomerism in [Ni(Et(4) dien)(NO(2) )(2) ]: A Combined Thermal and Photocrystallographic Structural Investigation of a Nitro/Nitrito Interconversion

One way or another: The N-bound NO(2) group in [Ni(Et(4) dien)(η(2) -O,ON)(η(1) -NO(2) )] (see structure Ni turquoise, N blue, O red) has been shown to undergo reversible conversion into the O-bound nitrito linkage isomer under both thermal and photoactivation of a single crystal. Et(4) dien=N,N,N',N'-tetraethyldiethylenetriamine.     

Rapid synthesis and zebrafish evaluation of a phenanthridine-based small molecule library

A Heck cyclisation approach is described for the rapid synthesis of a library of natural product-like small molecules, based on the phenanthridine core. The synthesis of a range of substituted benzylamine building blocks and their incorporation into the library is reported, together with a highly selective cis-dihydroxylation protocol that enables access to the target compounds in an efficient manner. Biological evaluation of the library using zebrafish phenotyping has led to the discovery of compound 20c, a novel inhibitor of early-stage zebrafish embryo development.     

Versatile synthesis of functionalised dibenzothiophenes via Suzuki coupling and microwave-assisted ring closure

Amino-substituted biphenyls were obtained by Suzuki cross-coupling of 2,6-dibromoaniline with a phenylboronic acid (substituted with Me, NO(2), OH, OMe or Cl) preferably assisted by microwave irradiation. Conversion of the amino group into a thiol preceded a base-induced intramolecular substitution, also facilitated by microwave heating, to generate the second C-S bond of the target dibenzothiophene. The 1-, 2-, 3- or 4-substituted 6-halodibenzothiophenes obtained were subjected to a palladium-mediated coupling with 2-morpholin-4-yl-8-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-4H-chromen-4-one to give the respective 6-, 7-, 8- or 9-substituted dibenzothiophen-4-ylchromenones. These compounds were evaluated as inhibitors of DNA-dependent protein kinase (DNA-PK) and compared to the parent 8-(dibenzo[b,d]thiophen-4-yl)-2-morpholin-4-yl-4H-chromen-4-one. Notably, derivatives bearing hydroxy or methoxy substituents at C-8 or C-9 retained activity, whereas substitution at C-7 lowered activity. Substitution with chloro at C-6 was not detrimental to activity, but a chloro group at C-7 or C-8 reduced potency. The data indicate permissive elaboration of hydroxyl at C-8 or C-9, enabling the possibility of improved pharmaceutical properties, whilst retaining potency against DNA-PK.     

Structures, host-guest chemistry and mechanism of stepwise self-assembly of M4L6 tetrahedral cage complexes

The ligand L(bip), containing two bidentate pyrazolyl-pyridine termini separated by a 3,3'-biphenyl spacer, has been used to prepare tetrahedral cage complexes of the form [M(4)(L(bip))(6)]X(8), in which a bridging ligand spans each of the six edges of the M(4) tetrahedron. Several new examples have been structurally characterized with a variety of metal cation and different anions in order to examine interactions between the cationic cage and various anions. Small anions such as BF(4)(-) and NO(3)(-) can occupy the central cavity where they are anchored by an array of CH···F or CH···O hydrogen-bonding interactions with the interior surface of the cage, but larger anions such as naphthyl-1-sulfonate or tetraphenylborate lie outside the cavity and interact with the external surface of the cage via CH···π interactions or CH···O hydrogen bonds. The cages with M = Co and M = Cd have been examined in detail by NMR spectroscopy. For [Co(4)(L(bip))(6)](BF(4))(8) the (1)H NMR spectrum is paramagnetically shifted over the range -85 to +110 ppm, but the spectrum has been completely assigned by correlation of measured T(1) relaxation times of each peak with Co···H distances. (19)F DOSY measurements on the anions show that at low temperature a [BF(4)](-) anion diffuses at a similar rate to the cage superstructure surrounding it, indicating that it is trapped inside the central cage cavity. Furthermore, the equilibrium step-by-step self-assembly of the cage superstructure has been elucidated by detailed modeling of spectroscopic titrations at multiple temperatures of an acetonitrile solution of L(bip) into an acetonitrile solution of Co(BF(4))(2). Six species have been identified: [Co(2)L(bip)](4+), [Co(2)(L(bip))(2)](4+), [Co(4)(L(bip))(6)](8+), [Co(4)(L(bip))(8)](8+), [Co(2)(L(bip))(5)](4+), and [Co(L(bip))(3)](2+). Overall the assembly of the cage is entropy, and not enthalpy, driven. Once assembled, the cages show remarkable kinetic inertness due to their mechanically entangled nature: scrambling of metal cations between the sites of pure Co(4) and Cd(4) cages to give a statistical mixture of Co(4), Co(3)Cd, Co(2)Cd(2), CoCd(3) and Cd(4) cages takes months in solution at room temperature.     

Disrupted cortical connectivity theory as an explanatory model for autism spectrum disorders

Recent findings of neurological functioning in autism spectrum disorder (ASD) point to altered brain connectivity as a key feature of its pathophysiology. The cortical underconnectivity theory of ASD (Just et al., 2004) provides an integrated framework for addressing these new findings. This theory suggests that weaker functional connections among brain areas in those with ASD hamper their ability to accomplish complex cognitive and social tasks successfully. We will discuss this theory, but will modify the term underconnectivity to ‘disrupted cortical connectivity’ to capture patterns of both under- and over-connectivity in the brain. In this paper, we will review the existing literature on ASD to marshal supporting evidence for hypotheses formulated on the disrupted cortical connectivity theory. These hypotheses are: 1) underconnectivity in ASD is manifested mainly in long-distance cortical as well as subcortical connections rather than in short-distance cortical connections; 2) underconnectivity in ASD is manifested only in complex cognitive and social functions and not in low-level sensory and perceptual tasks; 3) functional underconnectivity in ASD may be the result of underlying anatomical abnormalities, such as problems in the integrity of white matter; 4) the ASD brain adapts to underconnectivity through compensatory strategies such as overconnectivity mainly in frontal and in posterior brain areas. This may be manifested as deficits in tasks that require frontal–parietal integration. While overconnectivity can be tested by examining the cortical minicolumn organization, long-distance underconnectivity can be tested by cognitively demanding tasks; and 5) functional underconnectivity in brain areas in ASD will be seen not only during complex tasks but also during task-free resting states. We will also discuss some empirical predictions that can be tested in future studies, such as: 1) how disrupted connectivity relates to cognitive impairments in skills such as Theory-of-Mind, cognitive flexibility, and information processing; and 2) how connection abnormalities relate to, and may determine, behavioral symptoms hallmarked by the triad of Impairments in ASD. Furthermore, we will relate the disrupted cortical connectivity model to existing cognitive and neural models of ASD.     

Comprehensive chemical characterization of complexes involving lead-amino acid interactions

Complexes of lead with L-phenylalanine, L-isoleucine, L-valine, or L-arginine have been isolated from reaction mixtures containing lead nitrate and the respective amino acid in acidic aqueous solution. The compounds have been comprehensively characterized using X-ray crystallography, solid state NMR spectroscopy and solution state NMR spectroscopy, IR and Raman spectroscopies, and electrospray ionization mass-spectrometry. The solid state structures of lead-phenylalanine, lead-valine, and lead-valine-isoleucine complexes show a lead center coordinated by two amino acid ligands, while the lead-arginine complex is a cluster involving two lead centers and three arginine molecules. The structural, spectroscopic, and spectrometric characterization of the complexes provides a basis to establish a fundamental understanding of heavy metal-amino acid interactions.     

Signal Enhancement of Abiotically-Synthesized RNA Oligonucleotides and other Biopolymers using Unmodified Fused Silica in MALDI-MS

Metal is the standard desorption platform for MALDI-MS but other surfaces have been shown to offer advantages for particular types of analytes or applications. One such substrate is fused silica, which has been employed for matrix-free detection of low mass analytes and for affinity MALDI-MS in which binding ligands are immobilized at the fused silica surface. The present work reports improved MALDI-MS detection of RNA oligonucleotides, including polyA, polyU, and polyA/U, at the high end of the mass range when unmodified fused silica is used instead of stainless steel as the MALDI target. The RNA oligonucleotides were abiotically synthesized from activated monomers on catalytic clay surfaces. Further investigation found enhanced signals as well for other anionic biopolymers, including DNA oligonucleotides and heparin. Enhancement also was observed for dextran, which is neutral, indicating that the effect is not restricted to anionic biopolymers. Among more general analytical applications, the results are particularly relevant to rapid screening of abiotic RNA polymerization toward elucidating pathways to life on Earth.