I09-Surface and Interface Structural Analysis
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Open Access
Abstract: Understanding a material’s electronic structure is crucial to the development of many functional devices from semiconductors to solar cells and Li-ion batteries. A material’s properties, including electronic structure, are dependent on the arrangement of its atoms. However, structure determination (the process of uncovering the atomic arrangement), is impeded, both experimentally and computationally, by disorder. The lack of a verifiable atomic model presents a huge challenge when designing functional amorphous materials. Such materials may be characterised through their local atomic environments using, for example, solid-state NMR and XAS. By using these two spectroscopy methods to inform the sampling of configurations from ab initio molecular dynamics we devise and validate an amorphous model, choosing amorphous alumina to illustrate the approach due to its wide range of technological uses. Our model predicts two distinct geometric environments of AlO5 coordination polyhedra and determines the origin of the pre-edge features in the Al K-edge XAS. From our model we construct an average electronic density of states for amorphous alumina, and identify localized states at the conduction band minimum (CBM). We show that the presence of a pre-edge peak in the XAS is a result of transitions from the Al 1s to Al 3s states at the CBM. Deconvoluting this XAS by coordination geometry reveals contributions from both AlO4 and AlO5 geometries at the CBM give rise to the pre-edge, which provides insight into the role of AlO5 in the electronic structure of alumina. This work represents an important advance within the field of solid-state amorphous modelling, providing a method for developing amorphous models through the comparison of experimental and computationally derived spectra, which may then be used to determine the electronic structure of amorphous materials.
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Dec 2022
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[21755, 28766]
Open Access
Abstract: Previously inaccessible large S8-corona[n]arene macrocycles (n = 8-12) with alternating aryl and 1,4-C6F4 subunits are easily prepared on up to gram scales, without the need for chromatography (up to 45% yield, 10 different examples) through new high acceleration SNAr subsitution protocols (catalytic NR4F in pyridine, R = H, Me, Bu). Macrocycle size and functionality are tunable by precursor and catalyst selection. Equivalent simple NR4F catalysis allows facile late-stage SNAr difunctionalisation of the ring C6F4 units with thiols (8 derivatives, typically 95+% yields) providing two-step access to highly functionalised fluoromacrocycle libraries. Macrocycle host binding supports fluoroaryl catalytic activation through contact ion pair binding of NR4F and solvent inclusion. In the solid-state, solvent inclusion also intimately controls macrocycle conformation and fluorine-fluorine interactions leading to spontaneous self-assembly into infinite columns with honeycomb-like lattices.
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Nov 2022
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[23480]
Open Access
Abstract: Ethylene-bridged oligoureas are dynamic foldamers in which the polarity of a coherent chain of intramolecular hydrogen bonds may be controlled by intra- or intermolecular interactions with hydrogen-bond donors or acceptors. In this paper, we describe the way that supramolecular interactions between ethylene-bridged oligoureas bearing a 3,5-bis(trifluoromethyl)phenylurea (BTMP) terminus leads to higher-order structures both in the crystalline state and in solution. The oligoureas self-assemble by head-to-tail hydrogen bonding interactions to form either supramolecular ‘nanorings’ with cyclic hydrogen bond chain directionality, or supramolecular helical chains of hydrogen bonds. The self-assembly process features a cascade of cooperative positive allostery, in which each intermolecular hydrogen bond formation at the BTMP terminus switches the native hydrogen bond chain directionality of monomers, favouring further assembly. Monomers with a benzyl urea terminus self-assemble into nanorings, whereas monomers with a N-ethyl urea terminus form helical chains. In the crystal state, parallel helices have identical handedness and polarity, whereas antiparallel helices have opposite handedness. The overall dipole moment of crystals is zero due to the antiparallel arrangements of local dipoles in the crystal packing. Supramolecular interactions in solution were also examined by VT and DOSY NMR spectroscopy, up to the point of crystal formation. The size of higher aggregates in dichloromethane was estimated by their hydrodynamic radius. The relative orientation of the monomers within the aggregates, determined by 2D ROESY NMR, was the same as in the crystals, where syn-orientations lead to the formation of rings and anti-orientations result in chains. Overall, the switch of hydrogen bond polarity propagates intermolecularly in crystal and solution states, constituting an example of intermolecular communication within supramolecular polymers.
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Nov 2022
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[2373]
Open Access
Abstract: The design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein–structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein–protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design.
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Sep 2022
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[28349]
Open Access
Abstract: Metal–organic frameworks (MOFs) are among the most promising materials for next-generation energy storage systems. However, the impact of particle morphology on the energy storage performances of these frameworks is poorly understood. To address this, here we use coordination modulation to synthesise three samples of the conductive MOF Cu3(HHTP)2 (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene) with distinct microstructures. Supercapacitors assembled with these samples conclusively demonstrate that sample microstructure and particle morphology have a significant impact on the energy storage performances of MOFs. Samples with ‘flake-like’ particles, with a pore network comprised of many short pores, display superior capacitive performances than samples with either ‘rod-like’ or strongly agglomerated particles. The results of this study provide a target microstructure for conductive MOFs for energy storage applications.
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Aug 2022
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Open Access
Abstract: Phosphides are interesting candidates for hole transport materials and p-type transparent conducting applications, capable of achieving greater valence band dispersion than their oxide counterparts due to the higher lying energy and increased size of the P 3p orbital. After computational identification of the indirect-gap semiconductor CaCuP as a promising candidate, we now report reactive sputter deposition of phase-pure p-type CaCuP thin films. Their intrinsic hole concentration and hole mobility exceed 1 × 1020 cm−3 and 35 cm2 V−1 s−1 at room temperature, respectively. Transport calculations indicate potential for even higher mobilities. Copper vacancies are identified as the main source of conductivity, displaying markedly different behaviour compared to typical p-type transparent conductors, leading to improved electronic properties. The optical transparency of CaCuP films is lower than expected from first principles calculations of phonon-mediated indirect transitions. This discrepancy could be partly attributed to crystalline imperfections within the films, increasing the strength of indirect transitions. We determine the transparent conductor figure of merit of CaCuP films as a function of composition, revealing links between stoichiometry, crystalline quality, and opto-electronic properties. These findings provide a promising initial assessment of the viability of CaCuP as a p-type transparent contact.
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May 2022
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B07-C-Versatile Soft X-ray beamline: Ambient Pressure XPS and NEXAFS
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Diamond Proposal Number(s):
[25766]
Open Access
Abstract: Conductometric gas sensors (CGS) provide a reproducible gas response at a low cost but their operation mechanisms are still not fully understood. In this paper, we elucidate the nature of interactions between SnO2, a common gas-sensitive material, and O2, a ubiquitous gas central to the detection mechanisms of CGS. Using synchrotron radiation, we investigated a working SnO2 sensor under operando conditions via near-ambient pressure (NAP) XPS with simultaneous resistance measurements, and created a depth profile of the variable near-surface stoichiometry of SnO2−x as a function of O2 pressure. Our results reveal a correlation between the dynamically changing surface oxygen vacancies and the resistance response in SnO2-based CGS. While oxygen adsorbates were observed in this study we conclude that these are an intermediary in oxygen transport between the gas phase and the lattice, and that surface oxygen vacancies, not the observed oxygen adsorbates, are central to response generation in SnO2-based gas sensors.
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May 2022
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I19-Small Molecule Single Crystal Diffraction
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Lei
Ji
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Stefan
Riese
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Alexander
Schmiedel
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Marco
Holzapfel
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Maximillian
Fest
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Jörn
Nitsch
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Basile F. E.
Curchod
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Alexandra
Friedrich
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Lin
Wu
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Hamad H.
Al Mamari
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Sebastian
Hammer
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Jens
Pflaum
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Mark A.
Fox
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David J.
Tozer
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Maik
Finze
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Christoph
Lambert
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Todd B.
Marder
Diamond Proposal Number(s):
[18456]
Open Access
Abstract: Reversible conversion between excited-states plays an important role in many photophysical phenomena. Using 1-(pyren-2′-yl)-o-carborane as a model, we studied the photoinduced reversible charge-transfer (CT) process and the thermodynamic equilibrium between the locally-excited (LE) state and CT state, by combining steady state, time-resolved, and temperature-dependent fluorescence spectroscopy, fs- and ns-transient absorption, and DFT and LR-TDDFT calculations. Our results show that the energy gaps and energy barriers between the LE, CT, and a non-emissive ‘mixed’ state of 1-(pyren-2′-yl)-o-carborane are very small, and all three excited states are accessible at room temperature. The internal-conversion and reverse internal-conversion between LE and CT states are significantly faster than the radiative decay, and the two states have the same lifetimes and are in thermodynamic equilibrium.
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Apr 2022
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Thomas M.
Wood
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Matthieu R.
Zeronian
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Ned
Buijs
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Kristine
Bertheussen
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Hanieh K.
Abedian
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Aidan V.
Johnson
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Nicholas M.
Pearce
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Martin
Lutz
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Johan
Kemmink
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Tjalling
Seirsma
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Leendert W.
Hamoen
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Bert J. C.
Janssen
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Nathaniel I.
Martin
Diamond Proposal Number(s):
[19800]
Open Access
Abstract: The continued rise of antibiotic resistance is a global concern that threatens to undermine many aspects of modern medical practice. Key to addressing this threat is the discovery and development of new antibiotics that operate by unexploited modes of action. The so-called calcium-dependent lipopeptide antibiotics (CDAs) are an important emerging class of natural products that provides a source of new antibiotic agents rich in structural and mechanistic diversity. Notable in this regard is the subset of CDAs comprising the laspartomycins and amphomycins/friulimicins that specifically target the bacterial cell wall precursor undecaprenyl phosphate (C55-P). In this study we describe the design and synthesis of new C55-P-targeting CDAs with structural features drawn from both the laspartomycin and amphomycin/friulimicin classes. Assessment of these lipopeptides revealed previously unknown and surprisingly subtle structural features that are required for antibacterial activity. High-resolution crystal structures further indicate that the amphomycin/friulimicin-like lipopeptides adopt a unique crystal packing that governs their interaction with C55-P and provides an explanation for their antibacterial effect. In addition, live-cell microscopy studies provide further insights into the biological activity of the C55-P targeting CDAs highlighting their unique mechanism of action relative to the clinically used CDA daptomycin.
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Feb 2022
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[20038]
Open Access
Abstract: Four novel dicyanamide-containing hybrid organic-inorganic ABX3 structures are reported, and the thermal behaviour of a series of nine perovskite and non-perovskite [AB(N(CN)2)3] (A = (C3H7)4N, (C4H9)4N, (C5H11)4N; B = Co, Fe, Mn). Structure-property relationships are investigated by varying both A-site organic and B-site transition metal cations. In particular, increasing the size of the A-site cation from (C3H7)4N → (C4H9)4N → (C5H11)4N was observed to result in a decrease in Tm through an increase in ΔSf. Consistent trends in Tm with metal replacement are observed with each A-site cation, with Co < Fe < Mn. The majority of the melts formed were found to recrystallise partially upon cooling, though glasses could be formed through a small degree of organic linker decomposition. Total scattering methods are used to provide a greater understanding of the melting mechanism
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Jan 2022
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