Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed via Photoreaction between a Thymine and a Toluene Residue in the Dinucleotide Framework

Written by Degang Liu, Yan Zhou, Jingzhi Pu, Lei Li on May 15, 2012 – 8:10 pm -

Abstract

Substituted toluenyl groups are considered as close isosteres of the thymine residue. They can be recognized by DNA polymerases as if they were thymine. These toluene derivatives are generally inert toward radical additions, including the [2+2] photo-cycloadditions, due to the stable structure of the aromatic ring and are usually used as solvents for radical reactions. Surprisingly, after incorporating toluene into the dinucleotide framework, we found that the UV excited thymine residue readily dimerizes with the toluenyl moiety through a [2+2] photo-addition reaction. Furthermore, the reaction site on the toluenyl moiety is not the C5C6 bond, as commonly observed in cyclobutane pyrimidine dimers, but the C4C5 or C3C4 instead. Such a reaction pattern suggests that in the stacked structure, it is one of these bonds, not the C5C6, that is close to the thymine C5C6 bond. A similar structural feature is found in DNA duplex with a thymine replaced by a 2,4-difluorotoluene. Our results argue that although the substituted toluenyl moieties closely mimic the size and shape of the thymine residue, their more hydrophobic nature determines that they stack on DNA bases differently from the natural thymine residue and likely cause local conformational changes in duplex DNA.

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Can you spare a dimer? We have synthesized the dinucleotide TpTo and studied its photoreaction under UV irradiation. The UV excited thymine residue readily dimerized with the toluenyl moiety through a [2+2] photo-addition reaction (see scheme). Our data suggest that although the substituted toluene closely mimics the size and shape of thymine, its stronger hydrophobic nature might result in a subtle DNA conformational change.


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Dynamic Mixtures: Challenges and Opportunities for the Amplification and Sensing of Scents

Written by Andreas Herrmann on May 15, 2012 – 8:10 pm -

Abstract

Nature generates compounds as complicated mixtures, but surprisingly little is known about the synergies or inhibitory effects of compound mixtures, which is likely to become an important research area in life sciences in the near future. Some recently developed concepts in dynamic combinatorial/covalent chemistry (DCC) have been applied to amplify (increase the intensity and long-lastingness of perception) and sense (selectively detect and discriminate) individual bioactive volatile molecules in compound mixtures. This Concept article focuses on the potential of DCC to impact and modulate the biological and chemical properties of mixtures of bioactive volatile compounds to gain a more fundamental understanding of the properties of compound mixtures in molecular recognition.

An der Natur fanne mir Moleküllen als komplizéiert Mëschungen, mä iwwerraschend wéineg ass bekannt iwwert d’Synergien oder d’Inhibitiounseffekter vun esou Mëschungen, een Thema waat emmer méi u Bedeitung an der Naturwëssenschaft wäert gewannen. Nei entwéckelt Konzepter an der “dynamic combinatorial/covalent” Chimie (DCC) goufen ugewannt fir d‘Perceptioun (daat heescht souwuel d’Intensivitéit wéi och d’Dauer vun der Perceptioun) vun individuellen, bioaktiven, volatile Moleküllen a Mëschungen ze verstäerken a selektiv ze erkennen. Dësen Artikel konzentréiert sech op d’Méiglechkeet datt DCC biologesch a chemesch Propriétéiten vu Mëschungen vu volatilen, bioaktive Moleküllen beaflosse kéint, an datt mer doduerch eist fundamentalt Wëssen vun de Propriétéiten vu Mëschungen kéinten erweideren.

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Mixtures are annoying, but nevertheless the distinction of odorant mixtures is an important task in the everyday life of most species. Dynamic combinatorial/covalent chemistry impacts the emission and reception of bioactive volatile compounds at the air–water interface and might thus become a key concept in gaining fundamental insight into the molecular recognition of bioactive compound mixtures.


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Gold(I)-Catalysed Cycloisomerisation of 1,6-Cyclopropene-enes

Written by Frédéric Miege, Christophe Meyer, Janine Cossy on May 15, 2012 – 8:10 pm -

Abstract

The gold(I)-catalysed cycloisomerisation of appropriately substituted 1,6-cyclopropene-enes proceeds through regioselective electrophilic ring opening of the three-membered ring to generate an alkenyl gold carbenoid that achieves the intramolecular cyclopropanation of the remote olefin. This strategy allows straightforward, highly efficient and diastereoselective access to a variety of substituted 3-oxa- and 3-azabicyclo[4.1.0]heptanes, as well as to bicyclo[4.1.0]heptan-3-ol derivatives. Since the isopropylidene group in the resulting cycloisomerisation products can be subjected to ozonolysis, 3,3-dimethylcyclopropenes behave as interesting surrogates for α-diazoketones.

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Worth its weight in gold: The gold(I)-catalysed cycloisomerisation of appropriately substituted 1,6-cyclopropene-enes allows efficient and highly diastereoselective access to substituted 3-oxa- and 3-azabicyclo[4.1.0]heptanes, as well as to bicyclo[4.1.0]heptan-3-ol derivatives (see scheme). Since the isopropylidene group in the resulting products can be subjected to ozonolysis, 3,3-dimethylcyclopropenes behave as interesting surrogates of α-diazoketones.


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Synthesis of an Enlarged Library of Dynamic DNA Activators with Oxime, Disulfide and Hydrazone Bridges

Written by Javier Montenegro, Eun-Kyoung Bang, Naomi Sakai, Stefan Matile on May 15, 2012 – 8:10 pm -

Abstract

Dynamic amphiphiles have a “bridge” between their charged head and their hydrophobic tails. The presence of dynamic covalent bonds is of interest for differential and biosensing applications as well as for rapid access to the libraries needed to screen for gene delivery or cellular uptake of siRNA. However, efforts to develop libraries have so far concentrated on hydrazone bridges to monocationic heads. Here, we report synthesis efforts to enlarge this focused library with oxime and disulfide bridges and dynamic amphiphiles with more than one positive charge. Evaluation in fluorogenic vesicles reveals best activation of DNA as ion transporters by dynamic amphiphiles with dendritic scaffolds, doubly charged heads and four tails. Moreover, oximes, contrary to hydrazones, remain active under acidic conditions. Linear elongation of dendritic head-groups seems to cause increasing detergent effects and should therefore be avoided.

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Head on: Design, synthesis and evaluation of dynamic amphiphiles with singly or doubly charged peptide dendrons as head-groups, hydrazones, oximes and disulfides as bridges, and with fragrant tails are reported. Amphiphiles with two charges and four tails (see figure) are identified as the most powerful activators of DNA as ion transporters and thus as the most promising family to screen for gene and siRNA delivery.


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Magnetic Nanoparticles Entrapped in Siliceous Mesocellular Foam: A New Catalyst Support

Written by Su Seong Lee, Siti Nurhanna Riduan, Nandanan Erathodiyil, Jaehong Lim, Jian Liang Cheong, Junhoe Cha, Yu Han, Jackie Y. Ying on May 15, 2012 – 7:51 pm -

Abstract

γ-Fe2O3 nanoparticles were formed inside the cage-like pores of mesocellular foam (MCF). These magnetic nanoparticles showed a uniform size distribution that could be easily controlled by the MCF pore size, as well as by the hydrocarbon chain length used for MCF surface modification. Throughout the entrapment process, the pore structure and surface area of the MCF remained intact. The resulting magnetic MCF facilitated the immobilization of biocatalysts, homogeneous catalysts, and nanoclusters. Moreover, the MCF allowed for facile catalyst recovery by using a simple magnet. The supported catalysts exhibited excellent catalytic efficiencies that were comparable to their homogeneous counterparts.

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Foam party: γ-Fe2O3 nanoparticles were grown inside siliceous mesocellular foams (MCFs), which retained a high surface area and a large pore size. The MCFs facilitated the recovery of enzyme catalysts, Pd nanoclusters, and Ru-based catalysts (see figure).


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Can Commonly Used Hydrazine Produce n-Type Graphene?

Written by Surajit Some, Prasenjit Bhunia, EunHee Hwang, Keunsik Lee, Yeoheung Yoon, Sohyeon Seo, Hyoyoung Lee on May 15, 2012 – 7:51 pm -

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A simple chemical method to obtain bulk quantities of N-doped, reduced graphene oxide (rGO) sheets (see figure) as an n-type semiconductor through the treatment of as-prepared GO sheets with the commonly used reducing reagent hydrazine, followed by rapid thermal annealing (RTA) is described.


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Ionic-Liquid-Mediated Active-Site Control of MoS2 for the Electrocatalytic Hydrogen Evolution Reaction

Written by Vincent Wing-hei Lau, Anthony F. Masters, Alan M. Bond, Thomas Maschmeyer on May 15, 2012 – 7:50 pm -

Abstract

The layered crystal MoS2 has been proposed as an alternative to noble metals as the electrocatalyst for the hydrogen evolution reaction (HER). However, the activity of this catalyst is limited by the number of available edge sites. It was previously shown that, by using an imidazolium ionic liquid as synthesis medium, nanometre-size crystal layers of MoS2 can be prepared which exhibit a very high number of active edge sites as well as a de-layered morphology, both of which contribute to HER electrocatalytic activity. Herein, it is examined how to control these features synthetically by using a range of ionic liquids as synthesis media. Non-coordinating ILs with a planar heterocyclic cation produced MoS2 with the de-layered morphology, which was subsequently shown to be highly advantageous for HER electrocatalytic activity. The results furthermore suggest that the crystallinity, and in turn the catalytic activity, of the MoS2 layers can be improved by employing an IL with specific solvation properties. These results provide the basis for a synthetic strategy for increasing the HER electrocatalytic activity of MoS2 by tuning its crystal properties, and thus improving its potential for use in hydrogen production technologies.

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Peeling sheets away for HER: The morphology and crystallinity of MoS2 nanocrystals synthesised by an ionic-liquid-mediated procedure are shown to be controllable by employing ionic liquids with specific intermolecular interactions. The MoS2 sample with the best electrocatalytic activity for the hydrogen evolution reaction (HER) is found to be highly crystalline and has a de-layered morphology (see figure).


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Mesoporous Nickel Oxide Nanowires: Hydrothermal Synthesis, Characterisation and Applications for Lithium-Ion Batteries and Supercapacitors with Superior Performance

Written by Dawei Su, Hyun-Soo Kim, Woo-Seong Kim, Guoxiu Wang on May 15, 2012 – 7:50 pm -

Abstract

Mesoporous nickel oxide nanowires were synthesized by a hydrothermal reaction and subsequent annealing at 400 °C. The porous one-dimensional nanostructures were analysed by field-emission SEM, high-resolution TEM and N2 adsorption/desorption isotherm measurements. When applied as the anode material in lithium-ion batteries, the as-prepared mesoporous nickel oxide nanowires demonstrated outstanding electrochemical performance with high lithium storage capacity, satisfactory cyclability and an excellent rate capacity. They also exhibited a high specific capacitance of 348 F g−1 as electrodes in supercapacitors.

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Outstanding electrochemical performance for lithium storage in lithium-ion batteries and a high specific capacitance as electrode materials in supercapacitors are exhibited by mesoporous nickel oxide nanowires (see figure) that were synthesised by a hydrothermal reaction and subsequent annealing.


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Ligand Conformation Dictates Membrane and Endosomal Trafficking of Arginine-Glycine-Aspartate (RGD)-Functionalized Mesoporous Silica Nanoparticles

Written by I-Ju Fang, Igor I. Slowing, Kevin C.-W. Wu, Victor S.-Y. Lin, Brian G. Trewyn on May 15, 2012 – 7:50 pm -

Abstract

Recent breakthrough research on mesoporous silica nanoparticle (MSN) materials has illustrated their significant potential in biological applications due to their excellent drug delivery and endocytotic behavior. We set out to determine if MSN, covalently functionalized with conformation specific bioactive molecules (either linear or cyclic RGD ligands), behave towards mammalian cells in a similar manner as the free ligands. We discovered that RGD immobilized on the MSN surface did not influence the integrity of the porous matrix and improved the endocytosis efficiency of the MSN materials. Through competition experiments with free RGD ligands, we also discovered a conformation specific receptor–integrin association. The interaction between RGD immobilized on the MSN surface and integrins plays an important role in endosome trafficking, specifically dictating the kinetics of endosomal escape. Thus, covalent functionalization of biomolecules on MSN assists in the design of a system for controlling the interface with cancer cells.

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Borne this way: Arginine-glycine-aspartate (RGD) ligand was covalently attached to mesoporous silica nanoparticle (MSN) surface. Upon exposure to cells, the nanoparticles were internalized through the integrin mediated endocytosis pathway by way of RGD–integrin interaction (see illustration).


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Click Ionic Liquids: A Family of Promising Tunable Solvents and Application in Suzuki–Miyaura Cross-Coupling

Written by Liuyi Li, Jinyun Wang, Tao Wu, Ruihu Wang on May 15, 2012 – 7:50 pm -

Abstract

A series of click ionic salts 4 a4 n was prepared through click reaction of organic azides with alkyne-functionalized imidazolium or 2-methylimidazolium salts, followed by metathesis with lithium bis(trifluoromethanesulfonyl)amide or potassium hexafluorophosphate. All salts were characterized by IR, NMR, TGA, and DSC, and most of them can be classified as ionic liquids. Their steric and electronic properties can be easily tuned and modified through variation of the aromatic or aliphatic substituents at the imidazolium and/or triazolyl rings. The effect of anions and substituents at the two rings on the physicochemical properties was investigated. The charge and orbital distributions based on the optimized structures of cations in the salts were calculated. Reaction of 4 a with PdCl2 produced mononuclear click complex 4 a-Pd, the structure of which was confirmed by single-crystal X-ray diffraction analysis. Suzuki–Miyaura cross-coupling shows good catalytic stability and high recyclability in the presence of PdCl2 in 4 a. TEM and XPS analyses show formation of palladium nanoparticles after the reaction. The palladium NPs in 4 a are immobilized by the synergetic effect of coordination and electrostatic interactions with 1,2,3-triazolyl and imidazolium, respectively.

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Triazolyl-functionalized ionic liquids (ILs) were obtained by click reaction between organic azides and alkyne-functionalized imidazolium salts. Their steric and electronic properties can be flexibly tuned through variation of the substituents at the imidazolium and/or 1,2,3-triazolyl rings (see figure). These ILs serve as efficient protective agents for immobilization of catalytic palladium nanoparticles in Suzuki–Miyaura cross-coupling reactions.


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