Publisher Correction: Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process Nat. Chem. (IF 26.201) Pub Date : 2018-07-10 Irina Yarulina, Kristof De Wispelaere, Simon Bailleul, Joris Goetze, Mike Radersma, Edy Abou-Hamad, Ina Vollmer, Maarten Goesten, Brahim Mezari, Emiel J. M. Hensen, Juan S. Martínez-Espín, Magnus Morten, Sharon Mitchell, Javier Perez-Ramirez, Unni Olsbye, Bert M. Weckhuysen, Veronique Van Speybroeck, Freek Kapteijn, Jorge Gascon
Publisher Correction: Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process Publisher Correction: Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process, Published online: 10 July 2018; doi:10.1038/s41557-018-0118-4 Publisher Correction: Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process
Author Correction: Foldamers wave to the ribosome Nat. Chem. (IF 26.201) Pub Date : 2018-07-10 Alanna Schepartz
Author Correction: Foldamers wave to the ribosome Author Correction: Foldamers wave to the ribosome, Published online: 10 July 2018; doi:10.1038/s41557-018-0101-0 Author Correction: Foldamers wave to the ribosome
Towards simple kinetic models of functional dynamics for a kinase subfamily Nat. Chem. (IF 26.201) Pub Date : 2018-07-09 Mohammad M. Sultan, Gert Kiss, Vijay S. Pande
Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways. However, in silico modelling of the conformational ensembles of these enzymes is difficult due to inherent limitations and the cost of computational approaches. Recent algorithmic advances combined with homology modelling and parallel simulations have enabled researchers to address this computational sampling bottleneck. Here, we present the results of molecular dynamics studies for seven Src family kinase (SFK) members: Fyn, Lyn, Lck, Hck, Fgr, Yes and Blk. We present a sequence invariant extension to Markov state models, which allows us to quantitatively compare the structural ensembles of the seven kinases. Our findings indicate that in the absence of their regulatory partners, SFK members have similar in silico dynamics with active state populations ranging from 4 to 40% and activation timescales in the hundreds of microseconds. Furthermore, we observe several potentially druggable intermediate states, including a pocket next to the adenosine triphosphate binding site that could potentially be targeted via a small-molecule inhibitor.
Approaching sub-ppm-level asymmetric organocatalysis of a highly challenging and scalable carbon–carbon bond forming reaction Nat. Chem. (IF 26.201) Pub Date : 2018-07-09 Han Yong Bae, Denis Höfler, Philip S. J. Kaib, Pinar Kasaplar, Chandra Kanta De, Arno Döhring, Sunggi Lee, Karl Kaupmees, Ivo Leito, Benjamin List
The chemical synthesis of organic molecules involves, at its very essence, the creation of carbon–carbon bonds. In this context, the aldol reaction is among the most important synthetic methods, and a wide variety of catalytic and stereoselective versions have been reported. However, aldolizations yielding tertiary aldols, which result from the reaction of an enolate with a ketone, are challenging and only a few catalytic asymmetric Mukaiyama aldol reactions with ketones as electrophiles have been described. These methods typically require relatively high catalyst loadings, deliver substandard enantioselectivity or need special reagents or additives. We now report extremely potent catalysts that readily enable the reaction of silyl ketene acetals with a diverse set of ketones to furnish the corresponding tertiary aldol products in excellent yields and enantioselectivities. Parts per million (ppm) levels of catalyst loadings can be routinely used and provide fast and quantitative product formation in high enantiopurity. In situ spectroscopic studies and acidity measurements suggest a silylium ion based, asymmetric counteranion-directed Lewis acid catalysis mechanism.
A designer enzyme for hydrazone and oxime formation featuring an unnatural catalytic aniline residue Nat. Chem. (IF 26.201) Pub Date : 2018-07-02 Ivana Drienovská, Clemens Mayer, Christopher Dulson, Gerard Roelfes
Creating designer enzymes with the ability to catalyse abiological transformations is a formidable challenge. Efforts toward this goal typically consider only canonical amino acids in the initial design process. However, incorporating unnatural amino acids that feature uniquely reactive side chains could significantly expand the catalytic repertoire of designer enzymes. To explore the potential of such artificial building blocks for enzyme design, here we selected p-aminophenylalanine as a potentially novel catalytic residue. We demonstrate that the catalytic activity of the aniline side chain for hydrazone and oxime formation reactions is increased by embedding p-aminophenylalanine into the hydrophobic pore of the multidrug transcriptional regulator from Lactococcus lactis. Both the recruitment of reactants by the promiscuous binding pocket and a judiciously placed aniline that functions as a catalytic residue contribute to the success of the identified artificial enzyme. We anticipate that our design strategy will prove rewarding to significantly expand the catalytic repertoire of designer enzymes in the future.
Polyyne formation via skeletal rearrangement induced by atomic manipulation Nat. Chem. (IF 26.201) Pub Date : 2018-07-02 Niko Pavliček, Przemyslaw Gawel, Daniel R. Kohn, Zsolt Majzik, Yaoyao Xiong, Gerhard Meyer, Harry L. Anderson, Leo Gross
Rearrangements that change the connectivity of a carbon skeleton are often useful in synthesis, but it can be difficult to follow their mechanisms. Scanning probe microscopy can be used to manipulate a skeletal rearrangement at the single-molecule level, while monitoring the geometry of reactants, intermediates and final products with atomic resolution. We studied the reductive rearrangement of 1,1-dibromo alkenes to polyynes on a NaCl surface at 5 K, a reaction that resembles the Fritsch–Buttenberg–Wiechell rearrangement. Voltage pulses were used to cleave one C–Br bond, forming a radical, then to cleave the remaining C•–Br bond, triggering the rearrangement. These experiments provide structural insight into the bromo-vinyl radical intermediates, showing that the C=C•–Br unit is nonlinear. Long polyynes, up to the octayne Ph–(C≡C)8–Ph, have been prepared in this way. The control of skeletal rearrangements opens a new window on carbon-rich materials and extends the toolbox for molecular synthesis by atom manipulation.
Author Correction: Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface Nat. Chem. (IF 26.201) Pub Date : 2018-06-28 Mijanur Rahaman Molla, Poornima Rangadurai, Lucas Antony, Subramani Swaminathan, Juan J. de Pablo, S. Thayumanavan
Author Correction: Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface Author Correction: Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface, Published online: 28 June 2018; doi:10.1038/s41557-018-0090-z Author Correction: Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface
Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process Nat. Chem. (IF 26.201) Pub Date : 2018-06-25 Irina Yarulina, Kristof De Wispelaere, Simon Bailleul, Joris Goetze, Mike Radersma, Edy Abou-Hamad, Ina Vollmer, Maarten Goesten, Brahim Mezari, Emiel J. M. Hensen, Juan S. Martínez-Espín, Magnus Morten, Sharon Mitchell, Javier Perez-Ramirez, Unni Olsbye, Bert M. Weckhuysen, Veronique Van Speybroeck, Freek Kapteijn, Jorge Gascon
The combination of well-defined acid sites, shape-selective properties and outstanding stability places zeolites among the most practically relevant heterogeneous catalysts. The development of structure–performance descriptors for processes that they catalyse has been a matter of intense debate, both in industry and academia, and the direct conversion of methanol to olefins is a prototypical system in which various catalytic functions contribute to the overall performance. Propylene selectivity and resistance to coking are the two most important parameters in developing new methanol-to-olefin catalysts. Here, we present a systematic investigation on the effect of acidity on the performance of the zeolite ‘ZSM-5’ for the production of propylene. Our results demonstrate that the isolation of Brønsted acid sites is key to the selective formation of propylene. Also, the introduction of Lewis acid sites prevents the formation of coke, hence drastically increasing catalyst lifetime.
Complementary site-selectivity in arene functionalization enabled by overcoming the ortho constraint in palladium/norbornene catalysis Nat. Chem. (IF 26.201) Pub Date : 2018-06-25 Jianchun Wang, Renhe Li, Zhe Dong, Peng Liu, Guangbin Dong
Achieving site-selectivity in arene functionalization that is complementary to the site-selectivity from electrophilic aromatic substitution reactions has been a long-standing quest in organic synthesis. Palladium/norbornene cooperative catalysis potentially offers a unique approach to this problem, but its use has been hampered by the ortho constraint, which is the requirement of an ortho substituent for mono ortho functionalization of haloarenes. Here, we show that such a challenge could be addressed using a new class of bridgehead-modified norbornenes, thereby enabling a broadly useful strategy for arene functionalization with complementary site-selectivity. A range of ortho-unsubstituted aryl iodides, previously problematic substrates, can now be employed to provide mono ortho-functionalized products effectively. This method is applicable for late-stage functionalization of complex bioactive molecules at positions that are difficult to reach by conventional approaches.
Non-aqueous homogenous biocatalytic conversion of polysaccharides in ionic liquids using chemically modified glucosidase Nat. Chem. (IF 26.201) Pub Date : 2018-06-25 Alex P. S. Brogan, Liem Bui-Le, Jason P. Hallett
The increasing requirement to produce platform chemicals and fuels from renewable sources means advances in biocatalysis are rapidly becoming a necessity. Biomass is widely used in nature as a source of energy and as chemical building blocks. However, recalcitrance towards traditional chemical processes and solvents provides a significant barrier to widespread utility. Here, by optimizing enzyme solubility in ionic liquids, we have discovered solvent-induced substrate promiscuity of glucosidase, demonstrating an unprecedented example of homogeneous enzyme bioprocessing of cellulose. Specifically, chemical modification of glucosidase for solubilization in ionic liquids can increase thermal stability to up to 137 °C, allowing for enzymatic activity 30 times greater than is possible in aqueous media. These results establish that through a synergistic combination of chemical biology (enzyme modification) and reaction engineering (solvent choice), the biocatalytic capability of enzymes can be intensified: a key step towards the full-scale deployment of industrial biocatalysis.
The oganesson odyssey Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Kit Chapman
The oganesson odyssey The oganesson odyssey, Published online: 21 June 2018; doi:10.1038/s41557-018-0098-4 Kit Chapman explores the voyage to the discovery of element 118, the pioneer chemist it is named after, and false claims made along the way.
2D materials worth their salt Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Artem R. Oganov
2D materials worth their salt 2D materials worth their salt, Published online: 21 June 2018; doi:10.1038/s41557-018-0096-6 Sodium chloride phases with unconventional non-1:1 stoichiometries are known to exist under high-pressure conditions. Now, Na2Cl and Na3Cl two-dimensional crystals have been obtained under ambient conditions, on graphene surfaces, from dilute solutions.
Ring binders Nat. Chem. (IF 26.201) Pub Date : 2018-06-21
Ring binders Ring binders, Published online: 21 June 2018; doi:10.1038/s41557-018-0103-y Encoded chemical libraries can be used to screen a vast array of compounds against a protein target to identify potent binders. A collection of articles in this issue discuss different methods to increase the chemical space sampled by encoded macrocycle libraries and the advantages that such libraries offer for discovering new drug leads.
Cyclometallated ruthenium catalyst enables late-stage directed arylation of pharmaceuticals Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Marco Simonetti, Diego M. Cannas, Xavier Just-Baringo, Iñigo J. Vitorica-Yrezabal, Igor Larrosa
Biaryls are ubiquitous core structures in drugs, agrochemicals and organic materials that have profoundly improved many aspects of our society. Although traditional cross-couplings have made practical the synthesis of many biaryls, C–H arylation represents a more attractive and cost-effective strategy for building these structural motifs. Furthermore, the ability to install biaryl units in complex molecules via late-stage C–H arylation would allow access to valuable structural diversity, novel chemical space and intellectual property in only one step. However, known C–H arylation protocols are not suitable for substrates decorated with polar and delicate functionalities, which are commonly found in molecules that possess biological activity. Here we introduce a class of ruthenium catalysts that display a unique efficacy towards late-stage arylation of heavily functionalized substrates. The design and development of this class of catalysts was enabled by a mechanistic breakthrough on the Ru(ii)-catalysed C–H arylation of N–chelating substrates with aryl (pseudo)halides, which has remained poorly understood for nearly two decades.
Talking to Pauling’s ghost Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Michelle Francl
Talking to Pauling’s ghost Talking to Pauling’s ghost, Published online: 21 June 2018; doi:10.1038/s41557-018-0099-3 Michelle Francl dusts off Pauling’s notes on bonding to explore the illusory link between electron promotion and hybridization.
Looking in the library Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Russell Johnson
Looking in the library Looking in the library, Published online: 21 June 2018; doi:10.1038/s41557-018-0094-8 Ghotas Evindar, Chemistry Group Leader at GlaxoSmithKline, talks with Nature Chemistry about the advantages of using encoded libraries in drug discovery and the challenges these technologies present.
Shaping molecular diversity Nat. Chem. (IF 26.201) Pub Date : 2018-06-21 Emil S. Iqbal, Matthew C. T. Hartman
Shaping molecular diversity Shaping molecular diversity, Published online: 21 June 2018; doi:10.1038/s41557-018-0095-7 Certain drug targets have been deemed undruggable because of the difficulty in finding pharmacologically useful inhibitors. Now, two teams have developed exciting technologies for the creation of diverse collections of macrocyclic molecules and have demonstrated their usefulness for discovering macrocyclic inhibitors.
A human MUTYH variant linking colonic polyposis to redox degradation of the [4Fe4S]2+ cluster Nat. Chem. (IF 26.201) Pub Date : 2018-06-18 Kevin J. McDonnell, Joseph A. Chemler, Phillip L. Bartels, Elizabeth O’Brien, Monica L. Marvin, Janice Ortega, Ralph H. Stern, Leon Raskin, Guo-Min Li, David H. Sherman, Jacqueline K. Barton, Stephen B. Gruber
The human DNA repair enzyme MUTYH excises mispaired adenine residues in oxidized DNA. Homozygous MUTYH mutations underlie the autosomal, recessive cancer syndrome MUTYH-associated polyposis. We report a MUTYH variant, p.C306W (c.918C>G), with a tryptophan residue in place of native cysteine, that ligates the [4Fe4S] cluster in a patient with colonic polyposis and family history of early age colon cancer. In bacterial MutY, the [4Fe4S] cluster is redox active, allowing rapid localization to target lesions by long-range, DNA-mediated signalling. In the current study, using DNA electrochemistry, we determine that wild-type MUTYH is similarly redox-active, but MUTYH C306W undergoes rapid oxidative degradation of its cluster to [3Fe4S]+, with loss of redox signalling. In MUTYH C306W, oxidative cluster degradation leads to decreased DNA binding and enzyme function. This study confirms redox activity in eukaryotic DNA repair proteins and establishes MUTYH C306W as a pathogenic variant, highlighting the essential role of redox signalling by the [4Fe4S] cluster.
Infrared spectroscopy reveals multi-step multi-timescale photoactivation in the photoconvertible protein archetype dronpa Nat. Chem. (IF 26.201) Pub Date : 2018-06-11 Sergey P. Laptenok, Agnieszka A. Gil, Christopher R. Hall, Andras Lukacs, James N. Iuliano, Garth A. Jones, Gregory M. Greetham, Paul Donaldson, Atsushi Miyawaki, Peter J. Tonge, Stephen R. Meech
Photochromic fluorescent proteins play key roles in super-resolution microscopy and optogenetics. The light-driven structural changes that modulate the fluorescence involve both trans-to-cis isomerization and proton transfer. The mechanism, timescale and relative contribution of chromophore and protein dynamics are currently not well understood. Here, the mechanism of off-to-on-state switching in dronpa is studied using femtosecond-to-millisecond time-resolved infrared spectroscopy and isotope labelling. Chromophore and protein dynamics are shown to occur on multiple timescales, from picoseconds to hundreds of microseconds. Following excitation of the trans chromophore, a ground-state primary product is formed within picoseconds. Surprisingly, the characteristic vibrational spectrum of the neutral cis isomer appears only after several tens of nanoseconds. Further fluctuations in protein structure around the neutral cis chromophore are required to form a new intermediate, which promotes the final proton-transfer reaction. These data illustrate the interplay between chromophore dynamics and the protein environment underlying fluorescent protein photochromism.
Catalytic promiscuity enabled by photoredox catalysis in nicotinamide-dependent oxidoreductases Nat. Chem. (IF 26.201) Pub Date : 2018-06-11 Kyle F. Biegasiewicz, Simon J. Cooper, Megan A. Emmanuel, David C. Miller, Todd K. Hyster
Strategies that provide enzymes with the ability to catalyse non-natural reactions are of considerable synthetic value. Photoredox catalysis has proved adept at expanding the synthetic repertoire of existing catalytic platforms, yet, in the realm of biocatalysis it has primarily been used for cofactor regeneration. Here we show that photoredox catalysts can be used to enable new catalytic function in nicotinamide-dependent enzymes. Under visible-light irradiation, xanthene-based photocatalysts enable a double-bond reductase to catalyse an enantioselective deacetoxylation. Mechanistic experiments support the intermediacy of an α-acyl radical, formed after the elimination of acetate. Isotopic labelling experiments support nicotinamide as the source of the hydrogen atom. Preliminary calculations and mechanistic experiments suggest that binding to the protein attenuates the reduction potential of the starting material, an important feature for localizing radical formation to the enzyme active site. The generality of this approach is highlighted with the radical dehalogenation of α-bromoamides catalysed by ketoreductases with Eosin Y as a photocatalyst.
Controlling Pd(iv) reductive elimination pathways enables Pd(ii)-catalysed enantioselective C(sp3)−H fluorination Nat. Chem. (IF 26.201) Pub Date : 2018-06-11 Hojoon Park, Pritha Verma, Kai Hong, Jin-Quan Yu
The development of a Pd(ii)-catalysed enantioselective fluorination of C(sp3)−H bonds would offer a new approach to making chiral organofluorines. However, such a strategy is particularly challenging because of the difficulty in differentiating prochiral C(sp3)−H bonds through Pd(ii)-insertion, as well as the sluggish reductive elimination involving Pd−F bonds. Here, we report the development of a Pd(ii)-catalysed enantioselective C(sp3)−H fluorination using a chiral transient directing group strategy. In this work, a bulky, amino amide transient directing group was developed to control the stereochemistry of the C−H insertion step and selectively promote the C(sp3)−F reductive elimination pathway from the Pd(iv)–F intermediate. Stereochemical analysis revealed that while the desired C(sp3)−F formation proceeds via an inner-sphere pathway with retention of configuration, the undesired C(sp3)−O formation occurs through an SN2-type mechanism. Elucidation of the dual mechanism allows us to rationalize the profound ligand effect on controlling reductive elimination selectivity from high-valent Pd species.
Shape-preserving transformation of carbonate minerals into lead halide perovskite semiconductors based on ion exchange/insertion reactions Nat. Chem. (IF 26.201) Pub Date : 2018-06-04 Tim Holtus, Lukas Helmbrecht, Hans C. Hendrikse, Iaroslav Baglai, Sophie Meuret, Gede W. P. Adhyaksa, Erik C. Garnett, Willem L. Noorduin
Biological and bio-inspired mineralization processes yield a variety of three-dimensional structures with relevance for fields such as photonics, electronics and photovoltaics. However, these processes are only compatible with specific material compositions, often carbonate salts, thereby hampering widespread applications. Here we present a strategy to convert a wide range of metal carbonate structures into lead halide perovskite semiconductors with tunable bandgaps, while preserving the 3D shape. First, we introduce lead ions by cation exchange. Second, we use carbonate as a leaving group, facilitating anion exchange with halide, which is followed rapidly by methylammonium insertion to form the perovskite. As proof of principle, pre-programmed carbonate salt shapes such as vases, coral-like forms and helices are transformed into perovskites while preserving the morphology and crystallinity of the initial micro-architectures. This approach also readily converts calcium carbonate biominerals into semiconductors, furnishing biological and programmable synthetic shapes with the performance of artificial compositions such as perovskite-based semiconductors.
Publisher Correction: Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids Nat. Chem. (IF 26.201) Pub Date : 2018-05-31 Joseph M. Rogers, Sunbum Kwon, Simon J. Dawson, Pradeep K. Mandal, Hiroaki Suga, Ivan Huc
Publisher Correction: Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids Publisher Correction: Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids, Published online: 31 May 2018; doi:10.1038/s41557-018-0086-8 Publisher Correction: Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids
Mutually orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs Nat. Chem. (IF 26.201) Pub Date : 2018-05-28 Julian C. W. Willis, Jason W. Chin
Genetically encoding distinct non-canonical amino acids (ncAAs) into proteins synthesized in cells requires mutually orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs. The pyrrolysyl-tRNA synthetase/PyltRNA pair from Methanosarcina mazei (Mm) has been engineered to incorporate diverse ncAAs and is commonly considered an ideal pair for genetic code expansion. However, finding new aaRS/tRNA pairs that share the advantages of the MmPylRS/MmPyltRNA pair and are orthogonal to both endogenous aaRS/tRNA pairs and the MmPylRS/MmPyltRNA pair has proved challenging. Here we demonstrate that several ΔNPylRS/PyltRNACUA pairs, in which PylRS lacks an N-terminal domain, are active, orthogonal and efficiently incorporate ncAAs in Escherichia coli. We create new PylRS/PyltRNA pairs that are mutually orthogonal to the MmPylRS/MmPyltRNA pair and show that transplanting mutations that reprogram the ncAA specificity of MmPylRS into the new PylRS reprograms its substrate specificity. Finally, we show that distinct PylRS/PyltRNA-derived pairs can function in the same cell, decode distinct codons and incorporate distinct ncAAs.
Solvents can control solute molecular identity Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Devon. R. Widmer, Benjamin J. Schwartz
For solution-phase chemical reactions, the solvent is often considered simply as a medium to allow the reactants to encounter each other by diffusion. Although examples of direct solvent effects on molecular solutes exist, such as the compression of solute bonding electrons due to Pauli repulsion interactions, the solvent is not usually considered a part of the chemical species of interest. We show, using quantum simulations of Na2, that when there are local specific interactions between a solute and solvent that are energetically on the same order as a hydrogen bond, the solvent controls not only the bond dynamics but also the chemical identity of the solute. In tetrahydrofuran, dative bonding interactions between the solvent and Na atoms lead to unique coordination states that must cross a free energy barrier of ~8 kBT—undergoing a chemical reaction—to interconvert. Each coordination state has its own dynamics and spectroscopic signatures, highlighting the importance of considering the solvent in the identity of condensed-phase chemical systems.
Hitting the sweet spot Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Lara R. Malins
Hitting the sweet spot Hitting the sweet spot, Published online: 21 May 2018; doi:10.1038/s41557-018-0071-2 As the most abundant class of biomolecules on Earth, carbohydrates are implicated in a multitude of biological functions. Now, a simple chemical transformation has enabled the direct and selective installation of carbohydrates onto a diverse range of small molecules and peptides.
A new fundamental type of conformational isomerism Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Peter J. Canfield, Iain M. Blake, Zheng-Li Cai, Ian J. Luck, Elmars Krausz, Rika Kobayashi, Jeffrey R. Reimers, Maxwell J. Crossley
Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol−1, which we term ‘akamptisomerization’. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.
Vibrations that live long and prosper Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Arthur L. Utz
Vibrations that live long and prosper Vibrations that live long and prosper, Published online: 21 May 2018; doi:10.1038/s41557-018-0072-1 Molecular vibrations can be highly effective promoters of gas-phase chemistry. Now, measurements show that excited vibrational states can survive on metal surfaces far longer than expected — reshaping our understanding of how vibrational excitation might also promote or modify heterogeneously catalysed chemistry on metals.
Identification and characterization of diverse coherences in the Fenna–Matthews–Olson complex Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Erling Thyrhaug, Roel Tempelaar, Marcelo J. P. Alcocer, Karel Žídek, David Bína, Jasper Knoester, Thomas L. C. Jansen, Donatas Zigmantas
The idea that excitonic (electronic) coherences are of fundamental importance to natural photosynthesis gained popularity when slowly dephasing quantum beats (QBs) were observed in the two-dimensional electronic spectra of the Fenna–Matthews–Olson (FMO) complex at 77 K. These were assigned to superpositions of excitonic states, a controversial interpretation, as the strong chromophore–environment interactions in the complex suggest fast dephasing. Although it has been pointed out that vibrational motion produces similar spectral signatures, a concrete assignment of these oscillatory signals to distinct physical processes is still lacking. Here we revisit the coherence dynamics of the FMO complex using polarization-controlled two-dimensional electronic spectroscopy, supported by theoretical modelling. We show that the long-lived QBs are exclusively vibrational in origin, whereas the dephasing of the electronic coherences is completed within 240 fs even at 77 K. We further find that specific vibrational coherences are produced via vibronically coupled excited states. The presence of such states suggests that vibronic coupling is relevant for photosynthetic energy transfer.
Communicating catalysts Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Bert M. Weckhuysen
Communicating catalysts Communicating catalysts, Published online: 21 May 2018; doi:10.1038/s41557-018-0069-9 The beauty and activity of enzymes inspire chemists to tailor new and better non-biological catalysts. Now, a study reveals that the active sites within heterogeneous catalysts actively cooperate in a fashion phenomenologically similar to, but mechanistically distinct, from enzymes.
Tritium trinkets Nat. Chem. (IF 26.201) Pub Date : 2018-05-21 Brett F. Thornton, Shawn C. Burdette
Tritium trinkets Tritium trinkets, Published online: 21 May 2018; doi:10.1038/s41557-018-0070-3 Scientists take nomenclature seriously, but tritium was named in a casual aside. Brett F. Thornton and Shawn C. Burdette discuss the heavy, radioactive hydrogen isotope that is available for purchase online.
Enrichment-triggered prodrug activation demonstrated through mitochondria-targeted delivery of doxorubicin and carbon monoxide Nat. Chem. (IF 26.201) Pub Date : 2018-05-14 Yueqin Zheng, Xingyue Ji, Bingchen Yu, Kaili Ji, David Gallo, Eva Csizmadia, Mengyuan Zhu, Manjusha Roy Choudhury, Ladie Kimberly C. De La Cruz, Vayou Chittavong, Zhixiang Pan, Zhengnan Yuan, Leo E. Otterbein, Binghe Wang
Controlled activation is a critical component in prodrug development. Here we report a concentration-sensitive platform approach for bioorthogonal prodrug activation by taking advantage of reaction kinetics. Using two ‘click and release’ systems, we demonstrate enrichment and prodrug activation specifically in mitochondria to demonstrate the principle of the approach. In both cases, the payload (doxorubicin or carbon monoxide) was released inside the mitochondrial matrix following the enrichment-initiated click reaction. Furthermore, mitochondria-targeted delivery yielded substantial augmentation of functional biological and therapeutic effects in vitro and in vivo when compared to controls, which did not result in enrichment. This method is thus a platform for targeted drug delivery that is amenable to conjugation with a variety of molecules and is not limited to cell-surface delivery. Taken together, these two 'click and release' pairs clearly demonstrate the concept of enrichment-triggered drug release and the critical feasibility of treating clinically relevant diseases such as acute liver injury and cancer.
Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus Nat. Chem. (IF 26.201) Pub Date : 2018-05-14 Aurélie Mousnier, Andrew S. Bell, Dawid P. Swieboda, Julia Morales-Sanfrutos, Inmaculada Pérez-Dorado, James A. Brannigan, Joseph Newman, Markus Ritzefeld, Jennie A. Hutton, Anabel Guedán, Amin S. Asfor, Sean W. Robinson, Iva Hopkins-Navratilova, Anthony J. Wilkinson, Sebastian L. Johnston, Robin J. Leatherbarrow, Tobias J. Tuthill, Roberto Solari, Edward W. Tate
Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dual inhibitor of the human N-myristoyltransferases NMT1 and NMT2, and use it to demonstrate that pharmacological inhibition of host-cell N-myristoylation rapidly and completely prevents rhinoviral replication without inducing cytotoxicity. The identification of cooperative binding between weak-binding fragments led to rapid inhibitor optimization through fragment reconstruction, structure-guided fragment linking and conformational control over linker geometry. We show that inhibition of the co-translational myristoylation of a specific virus-encoded protein (VP0) by IMP-1088 potently blocks a key step in viral capsid assembly, to deliver a low nanomolar antiviral activity against multiple RV strains, poliovirus and foot and-mouth disease virus, and protection of cells against virus-induced killing, highlighting the potential of host myristoylation as a drug target in picornaviral infections.
Harvesting multiple electron–hole pairs generated through plasmonic excitation of Au nanoparticles Nat. Chem. (IF 26.201) Pub Date : 2018-05-07 Youngsoo Kim, Jeremy G. Smith, Prashant K. Jain
Multi-electron redox reactions, although central to artificial photosynthesis, are kinetically sluggish. Amidst the search for synthetic catalysts for such processes, plasmonic nanoparticles have been found to catalyse multi-electron reduction of CO2 under visible light. This example motivates the need for a general, insight-driven framework for plasmonic catalysis of such multi-electron chemistry. Here, we elucidate the principles underlying the extraction of multiple redox equivalents from a plasmonic photocatalyst. We measure the kinetics of electron harvesting from a gold nanoparticle photocatalyst as a function of photon flux. Our measurements, supported by theoretical modelling, reveal a regime where two-electron transfer from the excited gold nanoparticle becomes prevalent. Multiple electron harvesting becomes possible under continuous-wave, visible-light excitation of moderate intensity due to strong interband transitions in gold and electron–hole separation accomplished using a hole scavenger. These insights will help expand the utility of plasmonic photocatalysis beyond CO2 reduction to other challenging multi-electron, multi-proton transformations such as N2 fixation.
Two-dimensional Na–Cl crystals of unconventional stoichiometries on graphene surface from dilute solution at ambient conditions Nat. Chem. (IF 26.201) Pub Date : 2018-05-07 Guosheng Shi, Liang Chen, Yizhou Yang, Deyuan Li, Zhe Qian, Shanshan Liang, Long Yan, Lu Hua Li, Minghong Wu, Haiping Fang
NaCl in a 1:1 stoichiometry is the only known stable form of the Na–Cl crystal under ambient conditions, and non-1:1 Na–Cl species can only form under extreme conditions, such as high pressures. Here we report the direct observation, under ambient conditions, of Na2Cl and Na3Cl as two-dimensional (2D) Na–Cl crystals, together with regular NaCl, on reduced graphene oxide membranes and on the surfaces of natural graphite powders from salt solutions far below the saturated concentration. Molecular dynamics and density functional theory calculations suggest that this unconventional crystallization process originates from the cation–π interaction between the ions and the π-conjugated system in the graphitic surface, which promotes the ion–surface adsorption. The strong Na+–π interaction and charge transfer lead to stoichiometries with an excess of Na+. With unique electron and spin distributions and bonding, the resulting 2D crystals may have unusual electronic, magnetic, optical and mechanical properties.
Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes Nat. Chem. (IF 26.201) Pub Date : 2018-05-07 Johnny Habchi, Sean Chia, Céline Galvagnion, Thomas C. T. Michaels, Mathias M. J. Bellaiche, Francesco Simone Ruggeri, Michele Sanguanini, Ilaria Idini, Janet R. Kumita, Emma Sparr, Sara Linse, Christopher M. Dobson, Tuomas P. J. Knowles, Michele Vendruscolo
Alzheimer’s disease is a neurodegenerative disorder associated with the aberrant aggregation of the amyloid-β peptide. Although increasing evidence implicates cholesterol in the pathogenesis of Alzheimer’s disease, the detailed mechanistic link between this lipid molecule and the disease process remains to be fully established. To address this problem, we adopt a kinetics-based strategy that reveals a specific catalytic role of cholesterol in the aggregation of Aβ42 (the 42-residue form of the amyloid-β peptide). More specifically, we demonstrate that lipid membranes containing cholesterol promote Aβ42 aggregation by enhancing its primary nucleation rate by up to 20-fold through a heterogeneous nucleation pathway. We further show that this process occurs as a result of cooperativity in the interaction of multiple cholesterol molecules with Aβ42. These results identify a specific microscopic pathway by which cholesterol dramatically enhances the onset of Aβ42 aggregation, thereby helping rationalize the link between Alzheimer’s disease and the impairment of cholesterol homeostasis.
Cyclization of peptides with two chemical bridges affords large scaffold diversities Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Sangram S. Kale, Camille Villequey, Xu-Dong Kong, Alessandro Zorzi, Kaycie Deyle, Christian Heinis
Successful screening campaigns depend on large and structurally diverse collections of compounds. In macrocycle screening, variation of the molecular scaffold is important for structural diversity, but so far it has been challenging to diversify this aspect in large combinatorial libraries. Here, we report the cyclization of peptides with two chemical bridges to provide rapid access to thousands of different macrocyclic scaffolds in libraries that are easy to synthesize, screen and decode. Application of this strategy to phage-encoded libraries allowed for the screening of an unprecedented structural diversity of macrocycles against plasma kallikrein, which is important in the swelling disorder hereditary angioedema. These libraries yielded inhibitors with remarkable binding properties (subnanomolar Ki, >1,000-fold selectivity) despite the small molecular mass (~1,200 Da). An interlaced bridge format characteristic of this strategy provided high proteolytic stability (t1/2 in plasma of >3 days), making double-bridged peptides potentially amenable to topical or oral delivery.
Manganese-catalysed benzylic C(sp3)–H amination for late-stage functionalization Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Joseph R. Clark, Kaibo Feng, Anasheh Sookezian, M. Christina White
Reactions that directly install nitrogen into C–H bonds of complex molecules are significant because of their potential to change the chemical and biological properties of a given compound. Although selective intramolecular C–H amination reactions are known, achieving high levels of reactivity while maintaining excellent site selectivity and functional-group tolerance remains a challenge for intermolecular C–H amination. Here, we report a manganese perchlorophthalocyanine catalyst [MnIII(ClPc)] for intermolecular benzylic C–H amination of bioactive molecules and natural products that proceeds with unprecedented levels of reactivity and site selectivity. In the presence of a Brønsted or Lewis acid, the [MnIII(ClPc)]-catalysed C–H amination demonstrates unique tolerance for tertiary amine, pyridine and benzimidazole functionalities. Mechanistic studies suggest that C–H amination likely proceeds through an electrophilic metallonitrene intermediate via a stepwise pathway where C–H cleavage is the rate-determining step of the reaction. Collectively, these mechanistic features contrast with previous base–metal-catalysed C–H aminations and provide new opportunities for tunable selectivities.
Ring-through-ring molecular shuttling in a saturated rotaxane Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Kelong Zhu, Giorgio Baggi, Stephen J. Loeb
Mechanically interlocked molecules such as rotaxanes and catenanes comprise two or more components whose motion relative to each other can be controlled. A rotaxane molecular shuttle, for example, consists of an axle bearing two recognition sites and a single macrocyclic wheel that can undergo a to-and-fro motion along the axle—shuttling between the recognition sites. The ability of mechanically interlocked molecules to undergo this type of large-amplitude change is the core mechanism behind almost every interlocked molecular switch or machine, including sophisticated mechanical systems such as a molecular elevator and a peptide synthesizer. Here, as a way to expand the scope of dynamics possible at the molecular level, we have developed a molecular shuttling mechanism involving the exchange of rings between two recognition sites in a saturated rotaxane (one with no empty recognition sites). This was accomplished by passing a smaller ring through a larger one, thus achieving ring-through-ring molecular shuttling.
Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Mijanur Rahaman Molla, Poornima Rangadurai, Lucas Antony, Subramani Swaminathan, Juan J. de Pablo, S. Thayumanavan
Nature has engineered exquisitely responsive systems where molecular-scale information is transferred across an interface and propagated over long length scales. Such systems rely on multiple interacting, signalling and adaptable molecular and supramolecular networks that are built on dynamic, non-equilibrium structures. Comparable synthetic systems are still in their infancy. Here, we demonstrate that the light-induced actuation of a molecularly thin interfacial layer, assembled from a hydrophilic- azobenzene -hydrophobic diblock copolymer, can result in a reversible, long-lived perturbation of a robust glassy membrane across a range of over 500 chemical bonds. We show that the out-of-equilibrium actuation is caused by the photochemical trans–cis isomerization of the azo group, a single chemical functionality, in the middle of the interfacial layer. The principles proposed here are implemented in water-dispersed nanocapsules, and have implications for on-demand release of embedded cargo molecules.
Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Robert Alberstein, Yuta Suzuki, Francesco Paesani, F. Akif Tezcan
De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.
Rapid phenolic O-glycosylation of small molecules and complex unprotected peptides in aqueous solvent Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Tyler J. Wadzinski, Angela Steinauer, Liana Hie, Guillaume Pelletier, Alanna Schepartz, Scott J. Miller
Glycosylated natural products and synthetic glycopeptides represent a significant and growing source of biochemical probes and therapeutic agents. However, methods that enable the aqueous glycosylation of endogenous amino acid functionality in peptides without the use of protecting groups are scarce. Here, we report a transformation that facilitates the efficient aqueous O-glycosylation of phenolic functionality in a wide range of small molecules, unprotected tyrosine, and tyrosine residues embedded within a range of complex, fully unprotected peptides. The transformation, which uses glycosyl fluoride donors and is promoted by Ca(OH)2, proceeds rapidly at room temperature in water, with good yields and selective formation of unique anomeric products depending on the stereochemistry of the glycosyl donor. High functional group tolerance is observed, and the phenol glycosylation occurs selectively in the presence of virtually all side chains of the proteinogenic amino acids with the singular exception of Cys. This method offers a highly selective, efficient, and operationally simple approach for the protecting-group-free synthesis of O-aryl glycosides and Tyr-O-glycosylated peptides in water.
A molecular multi-gene classifier for disease diagnostics Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Randolph Lopez, Ruofan Wang, Georg Seelig
Despite its early promise as a diagnostic and prognostic tool, gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Here, we introduce a molecular computation strategy for analysing the information contained in complex gene expression signatures without the need for costly instrumentation. Our workflow begins by training a computational classifier on labelled gene expression data. This in silico classifier is then realized at the molecular level to enable expression analysis and classification of previously uncharacterized samples. Classification occurs through a series of molecular interactions between RNA inputs and engineered DNA probes designed to differentially weigh each input according to its importance. We validate our technology with two applications: a classifier for early cancer diagnostics and a classifier for differentiating viral and bacterial respiratory infections based on host gene expression. Together, our results demonstrate a general and modular framework for low-cost gene expression analysis.
Amino-acid-encoded biocatalytic self-assembly enables the formation of transient conducting nanostructures Nat. Chem. (IF 26.201) Pub Date : 2018-04-30 Mohit Kumar, Nicole L. Ing, Vishal Narang, Nadeesha K. Wijerathne, Allon I. Hochbaum, Rein V. Ulijn
Aqueous compatible supramolecular materials hold promise for applications in environmental remediation, energy harvesting and biomedicine. One remaining challenge is to actively select a target structure from a multitude of possible options, in response to chemical signals, while maintaining constant, physiological conditions. Here, we demonstrate the use of amino acids to actively decorate a self-assembling core molecule in situ, thereby controlling its amphiphilicity and consequent mode of assembly. The core molecule is the organic semiconductor naphthalene diimide, functionalized with D- and L- tyrosine methyl esters as competing reactive sites. In the presence of α-chymotrypsin and a selected encoding amino acid, kinetic competition between ester hydrolysis and amidation results in covalent or non-covalent amino acid incorporation, and variable supramolecular self-assembly pathways. Taking advantage of the semiconducting nature of the naphthalene diimide core, electronic wires could be formed and subsequently degraded, giving rise to temporally regulated electro-conductivity.
Reversible calcium alloying enables a practical room-temperature rechargeable calcium-ion battery with a high discharge voltage Nat. Chem. (IF 26.201) Pub Date : 2018-04-23 Meng Wang, Chunlei Jiang, Songquan Zhang, Xiaohe Song, Yongbing Tang, Hui-Ming Cheng
Calcium-ion batteries (CIBs) are attractive candidates for energy storage because Ca2+ has low polarization and a reduction potential (−2.87 V versus standard hydrogen electrode, SHE) close to that of Li+ (−3.04 V versus SHE), promising a wide voltage window for a full battery. However, their development is limited by difficulties such as the lack of proper cathode/anode materials for reversible Ca2+ intercalation/de-intercalation, low working voltages (<2 V), low cycling stability, and especially poor room-temperature performance. Here, we report a CIB that can work stably at room temperature in a new cell configuration using graphite as the cathode and tin foils as the anode as well as the current collector. This CIB operates on a highly reversible electrochemical reaction that combines hexafluorophosphate intercalation/de-intercalation at the cathode and a Ca-involved alloying/de-alloying reaction at the anode. An optimized CIB exhibits a working voltage of up to 4.45 V with capacity retention of 95% after 350 cycles.
I-motif DNA structures are formed in the nuclei of human cells Nat. Chem. (IF 26.201) Pub Date : 2018-04-23 Mahdi Zeraati, David B. Langley, Peter Schofield, Aaron L. Moye, Romain Rouet, William E. Hughes, Tracy M. Bryan, Marcel E. Dinger, Daniel Christ
Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.
Direct observation of forward-scattering oscillations in the H+HD→H2+D reaction Nat. Chem. (IF 26.201) Pub Date : 2018-04-23 Daofu Yuan, Shengrui Yu, Wentao Chen, Jiwei Sang, Chang Luo, Tao Wang, Xin Xu, Piergiorgio Casavecchia, Xingan Wang, Zhigang Sun, Dong H. Zhang, Xueming Yang
Accurate measurements of product state-resolved angular distributions are central to fundamental studies of chemical reaction dynamics. Yet, fine quantum-mechanical structures in product angular distributions of a reactive scattering process, such as the fast oscillations in the forward-scattering direction, have never been observed experimentally and the nature of these oscillations has not been fully explored. Here we report the crossed-molecular-beam experimental observation of these fast forward-scattering oscillations in the product angular distribution of the benchmark chemical reaction, H + HD → H2 + D. Clear oscillatory structures are observed for the H2(v′ = 0, j′ = 1, 3) product states at a collision energy of 1.35 eV, in excellent agreement with the quantum-mechanical dynamics calculations. Our analysis reveals that the oscillatory forward-scattering components are mainly contributed by the total angular momentum J around 28. The partial waves and impact parameters responsible for the forward scatterings are also determined from these observed oscillations, providing crucial dynamics information on the transient reaction process.
Claim to FAME Nat. Chem. (IF 26.201) Pub Date : 2018-04-19 Alvaro Mata
Claim to FAME Claim to FAME, Published online: 19 April 2018; doi:10.1038/s41557-018-0049-0 Proteins are attractive material building blocks, yet their intrinsic functionality has remained largely untapped. Now, a protein-based material that exhibits controllable self-assembling behaviour has been prepared in a one-pot synthesis by simultaneous use of recombinant expression and post-translational modification.
Tweaking mechanosensors Nat. Chem. (IF 26.201) Pub Date : 2018-04-19 Bruce C. Gibb
Tweaking mechanosensors Tweaking mechanosensors, Published online: 19 April 2018; doi:10.1038/s41557-018-0051-6 Bruce C. Gibb discusses the biochemistry behind the sensory experiences associated with eating chillies and the lesser-known tingle-inducing ‘sanshools’.
Understanding the quantum nature of low-energy C(3P j ) + He inelastic collisions Nat. Chem. (IF 26.201) Pub Date : 2018-04-16 Astrid Bergeat, Simon Chefdeville, Michel Costes, Sébastien B. Morales, Christian Naulin, Uzi Even, Jacek Kłos, François Lique
Inelastic collisions that occur between open-shell atoms and other atoms or molecules, and that promote a spin–orbit transition, involve multiple interaction potentials. They are non-adiabatic by nature and cannot be described within the Born–Oppenheimer approximation; in particular, their theoretical modelling becomes very challenging when the collision energies have values comparable to the spin–orbit splitting. Here we study inelastic collisions between carbon in its ground state C(3Pj=0) and helium atoms—at collision energies in the vicinity of spin–orbit excitation thresholds (~0.2 and 0.5 kJ mol−1)—that result in spin–orbit excitation to C(3Pj=1) and C(3Pj=2). State-to-state integral cross-sections are obtained from crossed-beam experiments with a beam source that provides an almost pure beam of C(3Pj=0) . We observe very good agreement between experimental and theoretical results (acquired using newly calculated potential energy curves), which validates our characterization of the quantum dynamical resonances that are observed. Rate coefficients at very low temperatures suitable for chemical modelling of the interstellar medium are also calculated.
Tracing the ‘ninth sulfur’ of the nitrogenase cofactor via a semi-synthetic approach Nat. Chem. (IF 26.201) Pub Date : 2018-04-16 Kazuki Tanifuji, Chi Chung Lee, Nathaniel S. Sickerman, Kazuyuki Tatsumi, Yasuhiro Ohki, Yilin Hu, Markus W. Ribbe
The M-cluster is the [(homocitrate)MoFe7S9C] active site of nitrogenase that is derived from an 8Fe core assembled viacoupling and rearrangement of two [Fe4S4] clusters concomitant with the insertion of an interstitial carbon and a ‘ninth sulfur’. Combining synthetic [Fe4S4] clusters with an assembly protein template, here we show that sulfite can give rise to the ninth sulfur that is incorporated in the catalytically important belt region of the cofactor after the radical S-adenosyl-l-methionine-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe8S8C] cluster intermediate, the L*-cluster, which is similar to the [Fe8S9C] L-cluster, but lacks the ninth sulfur from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.
Cold quantum-controlled rotationally inelastic scattering of HD with H2 and D2 reveals collisional partner reorientation Nat. Chem. (IF 26.201) Pub Date : 2018-04-16 William E. Perreault, Nandini Mukherjee, Richard N. Zare
Molecular interactions are best probed by scattering experiments. Interpretation of these studies has been limited by lack of control over the quantum states of the incoming collision partners. We report here the rotationally inelastic collisions of quantum-state prepared deuterium hydride (HD) with H2 and D2 using a method that provides an improved control over the input states. HD was coexpanded with its partner in a single supersonic beam, which reduced the collision temperature to 0–5 K, and thereby restricted the involved incoming partial waves to s and p. By preparing HD with its bond axis preferentially aligned parallel and perpendicular to the relative velocity of the colliding partners, we observed that the rotational relaxation of HD depends strongly on the initial bond-axis orientation. We developed a partial-wave analysis that conclusively demonstrates that the scattering mechanism involves the exchange of internal angular momentum between the colliding partners. The striking differences between H2/HD and D2/HD scattering suggest the presence of anisotropically sensitive resonances.
Publisher Correction: O2−O2 and O2−N2 collision-induced absorption mechanisms unravelled Nat. Chem. (IF 26.201) Pub Date : 2018-04-13 Tijs Karman, Mark A. J. Koenis, Agniva Banerjee, David H. Parker, Iouli E. Gordon, Ad van der Avoird, Wim J. van der Zande, Gerrit C. Groenenboom
Publisher Correction: O2−O2 and O2−N2 collision-induced absorption mechanisms unravelled Publisher Correction: O2−O2 and O2−N2 collision-induced absorption mechanisms unravelled, Published online: 13 April 2018; doi:10.1038/s41557-018-0063-2 Publisher Correction: O2−O2 and O2−N2 collision-induced absorption mechanisms unravelled
Retraction Note: Catalytic living ring-opening metathesis polymerization Nat. Chem. (IF 26.201) Pub Date : 2018-04-11 Amit A. Nagarkar, Andreas F. M. Kilbinger
Retraction Note: Catalytic living ring-opening metathesis polymerization Retraction Note: Catalytic living ring-opening metathesis polymerization, Published online: 11 April 2018; doi:10.1038/s41557-018-0044-5 Retraction Note: Catalytic living ring-opening metathesis polymerization
O2−O2 and O2−N2 collision-induced absorption mechanisms unravelled Nat. Chem. (IF 26.201) Pub Date : 2018-04-09 Tijs Karman, Mark A. J. Koenis, Agniva Banerjee, David H. Parker, Iouli E. Gordon, Ad van der Avoird, Wim J. van der Zande, Gerrit C. Groenenboom
Collision-induced absorption is the phenomenon in which interactions between colliding molecules lead to absorption of light, even for transitions that are forbidden for the isolated molecules. Collision-induced absorption contributes to the atmospheric heat balance and is important for the electronic excitations of O2 that are used for remote sensing. Here, we present a theoretical study of five vibronic transitions in O2−O2 and O2−N2, using analytical models and numerical quantum scattering calculations. We unambiguously identify the underlying absorption mechanism, which is shown to depend explicitly on the collision partner—contrary to textbook knowledge. This explains experimentally observed qualitative differences between O2−O2 and O2−N2 collisions in the overall intensity, line shape and vibrational dependence of the absorption spectrum. It is shown that these results can be used to discriminate between conflicting experimental data and even to identify unphysical results, thus impacting future experimental studies and atmospheric applications.
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