Nature Chemistry Contents January 2014 Volume 6 Number 1 pp 1-82

TABLE OF CONTENTS January 2014 Volume 6, Issue 1 Thesis Research Highlights Blogroll News and Views Articles Erratum In Your Element Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement NatureJournals app for ipad The NatureJournals app for iPad now boasts over 25 Nature-branded titles. Subscribe to any journal in the app for $35.99* and gain access to world class research on the move. www.nature.com/content/app/anytitleoffer *Apple exchange rates apply. Limited time offer available on all journals except Scientific Reports. iPad is a trademark of Apple Inc.   Thesis Top Laughing matter   pp1 - 2 Michelle Francl doi:10.1038/nchem.1827 Michelle Francl takes a serious look at whether we should indulge in scientific humour. Research Highlights Top Sandwich complexes: Metals in the middle | Amorphous solids: Cage calculations | Photocycloadditions: Asymmetric at last | Nanoreactors: Catalysis in compartments Blogroll Top Blogroll: New thinking   p5 Joshua Howgego doi:10.1038/nchem.1824 News and Views Top Molecular dynamics: A stitch in time   pp7 - 8 Xavier Deupi doi:10.1038/nchem.1832 Lengthy molecular dynamics simulations of complex systems at the atomic scale usually require supercomputers. Now, by stitching together many shorter independent simulations run 'in the cloud', this requirement has been circumvented, allowing two milliseconds of the dynamics of a G-protein-coupled receptor to be simulated. See also: Article by Kohlhoff et al. Single-molecule chemistry: Knowing your neighbours   pp8 - 10 Peter Liljeroth doi:10.1038/nchem.1823 Quantitatively studying how the rate of a chemical reaction is affected by a reactant's atomic-scale environment is extremely challenging. This has now been achieved at the single-molecule level using scanning tunnelling microscopy to monitor tautomerization in an atomically well-defined environment. See also: Article by Kumagai et al. Biosynthesis: Non-stick natural products   pp10 - 12 Peter A. Jordan and Bradley S. Moore doi:10.1038/nchem.1828 Fluorine imparts many drugs with beneficial properties, however, the synthesis of fluorinated complex natural products is challenging. Biosynthetic strategies and recent experimental precedents have paved the way for bioengineered fluorinated polyketides. Separated tandem catalysis: It's about time   pp12 - 13 Sarah Abou-Shehada and Jonathan M. J. Williams doi:10.1038/nchem.1826 One-pot processes in which a single catalyst carries out several reactions are attractive, but typically promote the formation of by-products as well as the desired ones, and are not amenable to optimization of the individual transformations. Now, these issues have been overcome by separating the catalytic processes in time. See also: Article by Li & Herzon Biophysical chemistry: Strength in numbers   pp13 - 14 Graeme A. King and Gijs J. L. Wuite doi:10.1038/nchem.1831 Replication of the HIV-1 viral genome can be inhibited by a protein known as APOBEC3G, via two seemingly contradictory mechanisms. Now, the molecular conundrum behind these two processes has been resolved. See also: Article by Chaurasiya et al. Chemistry JOBS of the week Tenure-Track Faculty Positions in Chemical Biology University of Utah Postdoctoral Associate in Molecular Biology University of Minnesota - Twin Cities Technical Assistant Virology (m / f) Boehringer Ingelheim 4 PhD student positions on ?Dynamics of coagulation Factor VIII, von Willebrand factor and endothelial cells? at Sanquin Research, Amsterdam, The Netherlands Sanquin Research Associate Scientist Sanford-Burnham Medical Research Institute More Science jobs from Chemistry EVENT Modern Synthetic Methods in Organofluorine Chemistry 06.03.14 London, UK More science events from Articles Top Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways   pp15 - 21 Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding et al. doi:10.1038/nchem.1821 Two milliseconds of molecular dynamics simulations of a major drug-target G-protein-coupled receptor (GPCR) has been carried out using Google's Exacycle cloud computing platform. Markov state models were used to aggregate independent simulations into a statistical model that provides an atomistic description of GPCR ligand-modulated activation pathways. Chemical compounds See also: News and Views by Deupi Temporal separation of catalytic activities allows anti-Markovnikov reductive functionalization of terminal alkynes   pp22 - 27 Le Li and Seth B. Herzon doi:10.1038/nchem.1799 Multifunctional catalysts typically process substrates and intermediates concurrently. Here, a strategy is described to separate catalytic activities in the time domain (temporal separation). Application of this strategy has led to the development of a method to effect the anti-Markovnikov reductive functionalization of terminal alkynes; such an approach may facilitate the development of other synthetic reaction cascades. Chemical compounds See also: News and Views by Abou-Shehada & Williams Oligomerization transforms human APOBEC3G from an efficient enzyme to a slowly dissociating nucleic acid-binding protein   pp28 - 33 Kathy R. Chaurasiya, Micah J. McCauley, Wei Wang, Dominic F. Qualley, Tiyun Wu et al. doi:10.1038/nchem.1795 HIV-1 replication is inhibited by the enzyme APOBEC3G via two separate mechanisms. A deamination mechanism requires rapid binding and release of single-stranded DNA (ssDNA), whereas a roadblock mechanism requires slow binding. Now APOBEC3G has been shown to initially bind ssDNA with rapid on–off rates. The enzyme subsequently converts via oligomerization to a slowly dissociating binding mode, which, it is proposed, inhibits reverse transcription. See also: News and Views by King & Wuite The aromatic ene reaction   pp34 - 40 Dawen Niu and Thomas R. Hoye doi:10.1038/nchem.1797 An aryne intermediate produced by a hexadehydro-Diels–Alder reaction is shown to engage in an unusual — and before this work rare and inefficient — aromatic ene reaction to produce an isotoluene. This second reactive intermediate can then engage an external enophile resulting in a conjunctive cascade in which four C–C bonds and three rings are created without involvement of reagents or generation of by-products. Chemical compounds Controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby   pp41 - 46 Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis et al. doi:10.1038/nchem.1804 The rate of an intramolecular hydrogen transfer reaction in a single porphycene molecule resting on a copper surface can be controlled by placing a copper adatom close to it. Cooperativity effects are also observed in rows of porphycene molecules, where the reaction rate of each individual molecule depends on the precise tautomer state of its neighbours. See also: News and Views by Liljeroth Ligand-enabled multiple absolute stereocontrol in metal-catalysed cycloaddition for construction of contiguous all-carbon quaternary stereocentres   pp47 - 51 Kohsuke Ohmatsu, Naomichi Imagawa and Takashi Ooi doi:10.1038/nchem.1796 A palladium-catalysed, highly enantio- and diastereoselective [3 + 2] cycloaddition reaction to produce densely functionalized pyrrolidine frameworks is developed by exploiting a new phosphine ligand with a chiral ammonium salt component. Rigorous control of the individual absolute stereochemistry of three contiguous stereocentres, including vicinal all-carbon quaternary stereocentres, is possible using this methodology. Chemical compounds Calculations predict a stable molecular crystal of N8   pp52 - 56 Barak Hirshberg, R. Benny Gerber and Anna I. Krylov doi:10.1038/nchem.1818 Polynitrogen compounds are of interest on a fundamental level and as potential high-energy-density materials. A crystalline solid that consists of two isomeric forms of N8 molecules held together by weak van der Waals interactions has now been predicted to exist, and to be stable even at low pressures. Biogenetically inspired synthesis and skeletal diversification of indole alkaloids   pp57 - 64 Haruki Mizoguchi, Hideaki Oikawa and Hiroki Oguri doi:10.1038/nchem.1798 Emulating the biogenesis of natural products, a synthetic strategy is described in which an achiral multipotent intermediate reacts through three distinct [4 + 2] cyclizations and two types of redox-mediated annulation. This results in divergent access to natural product-like scaffolds in 6–9 steps. The efficiency of this approach is highlighted in the total syntheses of three natural products. Chemical compounds Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing   pp65 - 74 P. Both, A. P. Green, C. J. Gray, R. ?ardzík, J. Voglmeir et al. doi:10.1038/nchem.1817 Identification of glycosylation patterns is complicated by the lack of sensitive analytical techniques that can distinguish between epimeric carbohydrates. It has now been shown that ion-mobility tandem mass spectrometry of ions derived from glycopeptides and oligosaccharides enables glycan stereochemistry to be determined, highlighting the potential of this technique for sequencing complex carbohydrates on cell surfaces. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells   pp75 - 80 Giulia Biffi, Marco Di Antonio, David Tannahill and Shankar Balasubramanian doi:10.1038/nchem.1805 The presence of RNA G-quadruplex structures in human cells using a structure-specific antibody is demonstrated. Using small molecules, the selective stabilization of cytoplasmic RNA G-quadruplexes versus nuclear DNA G-quadruplexes is demonstrated. These findings validate the existence of RNA G-quadruplexes and their specific targeting by small molecules within a cellular context. Chemical compounds Erratum Top Erratum: Singlet exciton fission in solution   p81 Brian J. Walker, Andrew J. Musser, David Beljonne and Richard H. Friend doi:10.1038/nchem.1829 In Your Element Top Argon out of thin air   p82 Markku Räsänen doi:10.1038/nchem.1825 Markku Rasanen remembers making a neutral compound featuring argon, and ponders on the reactivity of this inert element. Top Advertisement Polymer Journal Invited Reviews Collection  Polymer Journal is proud to present the Invited Reviews Collection, which gathers the key invited reviews published in 2012 and 2013. 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