Search Results

You searched for all publications:

with publication states 'Published (Approved)'
published in journal 'Nature Chemistry'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

60 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Efficient and selective energy transfer photoenzymes powered by visible light Rebecca Crawshaw , Ross Smithson , Johannes Hofer , Florence J. Hardy , George W. Roberts , Jonathan S. Trimble , Anna R. Kohn , Colin W. Levy , Deborah A. Drost , Christian Merten , Derren J. Heyes , Richard Obexer , Thorsten Bach , Anthony P. Green Nature Chemistry 357 DOI: 10.1038/s41557-025-01820-0 Diamond Proposal Number(s): [31850] Open Access Show Abstract ▼ Abstract: The development of [2 + 2] cyclases containing benzophenone triplet sensitizers highlights the potential of engineered enzymes as a platform for stereocontrolled energy transfer photocatalysis. However, the suboptimal photophysical features of benzophenone necessitates the use of ultraviolet light, limits photochemical efficiency and restricts the range of chemistries accessible. Here we engineer an orthogonal Methanococcus jannaschii tyrosyl-tRNA synthetase/tRNA pair for encoding thioxanthone triplet sensitizers into proteins, which can efficiently harness visible light to drive photochemical conversions. Initially, we developed an enantioselective [2 + 2] cyclase that is orders of magnitude more efficient than our previously developed photoenzymes (kcat = 13 s−1, >1,300 turnovers). To demonstrate that thioxanthone-containing enzymes can enable more challenging photochemical conversions, we developed a second oxygen-tolerant enzyme that can steer selective C–H insertions of excited quinolone substrates to afford spirocyclic β-lactams with high selectivity (99% e.e., 22:1 d.r.). This photoenzyme also suppresses a competing substrate decomposition pathway observed with small-molecule sensitizers, underscoring the ability of engineered enzymes to control the fate of excited-state intermediates.	May 2025
B22-Multimode InfraRed imaging And Microspectroscopy	Flue gas desulfurization and SO2 recovery within a flexible hydrogen-bonded organic framework Lin Li , Xuan Zhang , Xin Lian , Laiyu Zhang , Zhiyuan Zhang , Xiongli Liu , Tengfei He , Baiyan Li , Banglin Chen , Xian-He Bu Nature Chemistry 325 DOI: 10.1038/s41557-025-01744-9 Show Abstract ▼ Abstract: The removal of SO2 from flue gas remains a challenge. Adsorption-based separation of SO2 using porous materials has been proposed as a more energy-efficient and cost-effective alternative to more traditional methods such as cryogenic distillations. Here we report a flexible hydrogen-bonded organic framework (HOF-NKU-1) that enables the sieving of SO2 through the guest-adaptive response and shape-memory effect of the material. HOF-NKU-1 exhibits a high selectivity of 7,331 for the separation of SO2/CO2 and a high SO2 storage density of 3.27 g cm−3 within the pore space at ambient conditions. The hydrophobic nature of HOF-NKU-1 enables high dynamic SO2 uptake and SO2 recovery, even in conditions of 95% humidity. The SO2/CO2 separation mechanism is studied through combinatorial gas sorption isotherms, breakthrough experiments and single-crystal diffraction studies, paving the way for the development of multifunctional shape-memory porous materials in the future.	Feb 2025
I19-Small Molecule Single Crystal Diffraction	A pseudo-cubic metal–organic cage with conformationally switchable faces for dynamically adaptive guest encapsulation Houyang Xu , Tanya K. Ronson , Andrew W. Heard , Paula C. P. Teeuwen , Laura Schneider , Philipp Pracht , John D. Thoburn , David J. Wales , Jonathan R. Nitschke Nature Chemistry 8 DOI: 10.1038/s41557-024-01708-5 Diamond Proposal Number(s): [29890] Open Access Show Abstract ▼ Abstract: The creation of hosts capable of accommodating different guest molecules may enable these hosts to play useful roles in chemical purifications, among other applications. Metal–organic cages are excellent hosts for various guests, but they generally incorporate rigid structural units that hinder dynamic adaptation to specific guests. Here we report a conformationally adaptable pseudo-cubic cage that can dynamically increase its cavity volume to fit guests with differing sizes. This pseudo-cube incorporates a tetramine subcomponent with 2,6-naphthalene arms that cooperatively adopt a non-planar conformation, enabling the cage faces to switch between endo and exo states. A wide range of guest molecules were observed to bind within the cavity of this cage, spanning a range of sizes from 46% to 154% of the cavity volume of the empty cage. Experimental and computational evidence characterizes the flipping of cage faces from endo to exo, expanding the cavity upon binding of larger guests.	Jan 2025
I04-1-Macromolecular Crystallography (fixed wavelength)	Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks K.-Y. M. Chen , J. K. Lai , L. S. P. Rudden , J. Wang , A. M. Russell , K. Conners , M. E. Rutter , B. Condon , F. Tung , L. Kodandapani , B. Chau , X. Zhao , J. Benach , K. Baker , E. J. Hembre , P. Barth Nature Chemistry 166 DOI: 10.1038/s41557-024-01719-2 Diamond Proposal Number(s): [14323] Open Access Show Abstract ▼ Abstract: Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein–solvent cooperative interactions has not yet been demonstrated. Here we report the design of 14 membrane receptors that catalyse G protein nucleotide exchange through diverse engineered allosteric pathways mediated by cooperative networks of intraprotein, protein–ligand and –solvent molecule interactions. Consistent with predictions, the designed protein activities correlated well with the level of plasticity of the networks at flexible transmembrane helical interfaces. Several designs displayed considerably enhanced thermostability and activity compared with related natural receptors. The most stable and active variant crystallized in an unforeseen signalling-active conformation, in excellent agreement with the design models. The allosteric network topologies of the best designs bear limited similarity to those of natural receptors and reveal an allosteric interaction space larger than previously inferred from natural proteins. The approach should prove useful for engineering proteins with novel complex protein binding, catalytic and signalling activities.	Jan 2025
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond	Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria Alexander T. Bakker , Ioli Kotsogianni , Mariana Avalos , Jeroen M. Punt , Bing Liu , Diana Piermarini , Berend Gagestein , Cornelis J. Slingerland , Le Zhang , Joost J. Willemse , Leela B. Ghimire , Richard J. H. B. N. Van Den Berg , Antonius P. A. Janssen , Tom H. M. Ottenhoff , Constant A. A. Van Boeckel , Gilles P. Van Wezel , Dmitry Ghilarov , Nathaniel I. Martin , Mario Van Der Stelt Nature Chemistry 399 DOI: 10.1038/s41557-024-01516-x Diamond Proposal Number(s): [33054] Open Access Show Abstract ▼ Abstract: Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase–LEI-800–DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.	Jun 2024
B07-B1-Versatile Soft X-ray beamline: High Throughput ES1	Upcycling of polyethylene to gasoline through a self-supplied hydrogen strategy in a layered self-pillared zeolite Ziyu Cen , Xue Han , Longfei Lin , Sihai Yang , Wanying Han , Weilong Wen , Wenli Yuan , Minghua Dong , Zhiye Ma , Fang Li , Yubin Ke , Juncai Dong , Jin Zhang , Shuhu Liu , Jialiang Li , Qian Li , Ningning Wu , Junfeng Xiang , Hao Wu , Lile Cai , Yanbo Hou , Yongqiang Chen , Luke L. Daemen , Anibal J. Ramirez-Cuesta , Pilar Ferrer , David C. Grinter , Georg Held , Yueming Liu , Buxing Han Nature Chemistry 3 DOI: 10.1038/s41557-024-01506-z Diamond Proposal Number(s): [33962] Open Access Show Abstract ▼ Abstract: Conversion of plastic wastes to valuable carbon resources without using noble metal catalysts or external hydrogen remains a challenging task. Here we report a layered self-pillared zeolite that enables the conversion of polyethylene to gasoline with a remarkable selectivity of 99% and yields of >80% in 4 h at 240 °C. The liquid product is primarily composed of branched alkanes (selectivity of 72%), affording a high research octane number of 88.0 that is comparable to commercial gasoline (86.6). In situ inelastic neutron scattering, small-angle neutron scattering, solid-state nuclear magnetic resonance, X-ray absorption spectroscopy and isotope-labelling experiments reveal that the activation of polyethylene is promoted by the open framework tri-coordinated Al sites of the zeolite, followed by β-scission and isomerization on Brönsted acids sites, accompanied by hydride transfer over open framework tri-coordinated Al sites through a self-supplied hydrogen pathway to yield selectivity to branched alkanes. This study shows the potential of layered zeolite materials in enabling the upcycling of plastic wastes.	Apr 2024
I19-Small Molecule Single Crystal Diffraction	Masked alkynes for synthesis of threaded carbon chains Connor W. Patrick , Yueze Gao , Prakhar Gupta , Amber L. Thompson , Anthony W. Parker , Harry L. Anderson Nature Chemistry 369 DOI: 10.1038/s41557-023-01374-z Diamond Proposal Number(s): [20876] Open Access Show Abstract ▼ Abstract: Polyynes are chains of sp1 carbon atoms with alternating single and triple bonds. As they become longer, they evolve towards carbyne, the 1D allotrope of carbon, and they become increasingly unstable. It has been anticipated that long polyynes could be stabilized by supramolecular encapsulation, by threading them through macrocycles to form polyrotaxanes—but, until now, polyyne polyrotaxanes with many threaded macrocycles have been synthetically inaccessible. Here we show that masked alkynes, in which the C≡C triple bond is temporarily coordinated to cobalt, can be used to synthesize polyrotaxanes, up to the C68 [5]rotaxane with 34 contiguous triple bonds and four threaded macrocycles. This is the length regime at which the electronic properties of polyynes converge to those of carbyne. Cyclocarbons constitute a related family of molecular carbon allotropes, and cobalt-masked alkynes also provide a route to [3]catenanes and [5]catenanes built around cobalt complexes of cyclo[40]carbon and cyclo[80]carbon, respectively.	Nov 2023
I03-Macromolecular Crystallography	Optical control of ultrafast structural dynamics in a fluorescent protein Christopher D. M. Hutchison , James Baxter , Ann Fitzpatrick , Gabriel Dorlhiac , Alisia Fadini , Samuel Perrett , Karim Maghlaoui , Salomé Bodet Lefèvre , Violeta Cordon-Preciado , Josie L. Ferreira , Volha U. Chukhutsina , Douglas Garratt , Jonathan Barnard , Gediminas Galinis , Flo Glencross , Rhodri M. Morgan , Sian Stockton , Ben Taylor , Letong Yuan , Matthew G. Romei , Chi-Yun Lin , Jon P. Marangos , Marius Schmidt , Viktoria Chatrchyan , Tiago Buckup , Dmitry Morozov , Jaehyun Park , Sehan Park , Intae Eom , Minseok Kim , Dogeun Jang , Hyeongi Choi , Hyojung Hyun , Gisu Park , Eriko Nango , Rie Tanaka , Shigeki Owada , Kensuke Tono , Daniel P. Deponte , Sergio Carbajo , Matt Seaberg , Andrew Aquila , Sebastien Boutet , Anton Barty , So Iwata , Steven G. Boxer , Gerrit Groenhof , Jasper J. Van Thor Nature Chemistry 4 DOI: 10.1038/s41557-023-01275-1 Diamond Proposal Number(s): [22819, 17221] Open Access Show Abstract ▼ Abstract: The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump–probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.	Aug 2023
I03-Macromolecular Crystallography	In vitro selection of macrocyclic peptide inhibitors containing cyclic γ2,4-amino acids targeting the SARS-CoV-2 main protease Takashi Miura , Tika R. Malla , C. David Owen , Anthony Tumber , Lennart Brewitz , Michael A. Mcdonough , Eidarus Salah , Naohiro Terasaka , Takayuki Katoh , Petra Lukacik , Claire Strain-Damerell , Halina Mikolajek , Martin A. Walsh , Akane Kawamura , Christopher J. Schofield , Hiroaki Suga Nature Chemistry 81 DOI: 10.1038/s41557-023-01205-1 Diamond Proposal Number(s): [27088] Open Access Show Abstract ▼ Abstract: γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1′ catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.	May 2023
I19-Small Molecule Single Crystal Diffraction	Growth of single-crystal imine-linked covalent organic frameworks using amphiphilic amino-acid derivatives in water Zhipeng Zhou , Lei Zhang , Yonghang Yang , Inigo J. Vitórica-Yrezábal , Honglei Wang , Fanglin Tan , Li Gong , Yuyao Li , Pohua Chen , Xin Dong , Zihao Liang , Jing Yang , Chao Wang , Yuexian Hong , Yi Qiu , Armin Gölzhäuser , Xudong Chen , Haoyuan Qi , Sihai Yang , Wei Liu , Junliang Sun , Zhikun Zheng Nature Chemistry 355 DOI: 10.1038/s41557-023-01181-6 Diamond Proposal Number(s): [31627] Show Abstract ▼ Abstract: A core feature of covalent organic frameworks (COFs) is crystallinity, but current crystallization processes rely substantially on trial and error, chemical intuition and large-scale screening, which typically require harsh conditions and low levels of supersaturation, hampering the controlled synthesis of single-crystal COFs, particularly on large scales. Here we report a strategy to produce single-crystal imine-linked COFs in aqueous solutions under ambient conditions using amphiphilic amino-acid derivatives with long hydrophobic chains. We propose that these amphiphilic molecules self-assemble into micelles that serve as dynamic barriers to separate monomers in aqueous solution (nodes) and hydrophobic compartments of the micelles (linkers), thereby regulating the polymerization and crystallization processes. Disordered polyimines were obtained in the micelle, which were then converted into crystals in a step-by-step fashion. Five different three-dimensional COFs and a two-dimensional COF were obtained as single crystals on the gram scale, with yields of 92% and above.	Apr 2023

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User