B21-High Throughput SAXS
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Diamond Proposal Number(s):
[20161]
Open Access
Abstract: Iron is a fundamental element for virtually all forms of life. Despite its abundance, its bioavailability is limited, and thus, microbes developed siderophores, small molecules, which are synthesized inside the cell and then released outside for iron scavenging. Once inside the cell, iron removal does not occur spontaneously, instead this process is mediated by siderophore-interacting proteins (SIP) and/or by ferric-siderophore reductases (FSR). In the past two decades, representatives of the SIP subfamily have been structurally and biochemically characterized; however, the same was not achieved for the FSR subfamily. Here, we initiate the structural and functional characterization of FhuF, the first and only FSR ever isolated. FhuF is a globular monomeric protein mainly composed by α-helices sheltering internal cavities in a fold resembling the “palm” domain found in siderophore biosynthetic enzymes. Paramagnetic NMR spectroscopy revealed that the core of the cluster has electronic properties in line with those of previously characterized 2Fe–2S ferredoxins and differences appear to be confined to the coordination of Fe(III) in the reduced protein. In particular, the two cysteines coordinating this iron appear to have substantially different bond strengths. In similarity with the proteins from the SIP subfamily, FhuF binds both the iron-loaded and the apo forms of ferrichrome in the micromolar range and cyclic voltammetry reveals the presence of redox-Bohr effect, which broadens the range of ferric-siderophore substrates that can be thermodynamically accessible for reduction. This study suggests that despite the structural differences between FSR and SIP proteins, mechanistic similarities exist between the two classes of proteins.
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Feb 2021
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[22264]
Abstract: The high-voltage (4.7 V vs Li+/Li) spinel lithium nickel manganese oxide (LiNi0.5Mn1.5O4, LNMO) is a promising candidate for the next generation of lithium-ion batteries due to its high energy density, low cost, and low environmental impact. However, poor cycling performance at high cutoff potentials limits its commercialization. Herein, hollow-structured LNMO is synergistically paired with an ionic liquid electrolyte, 1 M lithium bis(fluorosulfonyl)imide (LiFSI) in N-propyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide (Pyr1,3FSI), to achieve stable cycling performance and improve the rate capability. The optimized cathode–electrolyte system exhibits extended cycling performance (>85% capacity retention after 300 cycles) and high rate performance (106.2 mAh g–1 at 5C) even at an elevated temperature of 65 °C. X-ray photoelectron spectroscopy and spatially resolved X-ray fluorescence analyses confirm the formation of a robust, LiF-rich cathode–electrolyte interphase. This study presents a comprehensive design strategy to improve the electrochemical performance of high-voltage cathode materials.
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Feb 2021
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[19823]
Abstract: Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo–electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1–like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery.
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Feb 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[16420]
Abstract: Simple n-alcohols, such as 1-dodecanol, show anomalous film-forming and friction behaviors under elastohydrodynamic lubrication (EHL) conditions, as found inside bearings and gears. Using tribometer, diamond anvil cell (DAC), and differential scanning calorimetry (DSC) experiments, we show that liquid 1-dodecanol undergoes a pressure-induced solidification when entrained into EHL contacts. Different solid polymorphs are formed inside the contact depending on the temperature and pressure conditions. Surprisingly, at a moderate temperature and pressure, 1-dodecanol forms a polymorph that exhibits robust macroscale superlubricity. The DAC and DSC experiments show that superlubricity is facilitated by the formation of lamellar, hydrogen-bonded structures of hexagonally close-packed molecules, which promote interlayer sliding. This novel superlubricity mechanism is similar to that proposed for the two-dimensional materials commonly employed as solid lubricants, but it also enables the practical advantages of liquid lubricants to be maintained. When the pressure is increased, 1-dodecanol undergoes a polymorphic transformation into a phase that gives a higher friction. The DAC and DSC experiments indicate that the high-friction polymorph is an orthorhombic crystal. The polymorphic transformation pressure coincides with the onset of a dimple formation in the EHL films, revealing that the anomalous film shapes are caused by the formation of rigid orthorhombic crystals inside the contact. This is the first demonstration of a macroscale superlubricity in an EHL contact lubricated by a nonaqueous liquid that arises from bulk effects rather than tribochemical transformations at the surfaces. Since the superlubricity observed here results from phase transformations, it is continuously self-replenishing and is insensitive to surface chemistry and topology. This discovery creates the possibility of implementing superlubricity in a wide range of machine components, which would result in enormous improvements in efficiency and durability.
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Feb 2021
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Open Access
Abstract: The utilization of operando spectroscopy has allowed us to watch the dynamic nature of supported metal nanoparticles. However, the realization that subtle changes to environmental conditions affect the form of the catalyst necessitates that we assess the structure of the catalyst across the reactant/product gradient that exists across a fixed bed reactor. In this study, we have performed spatial profiling of a Pd/Al2O3 catalyst during NH3 oxidation, simultaneously collecting mass spectrometry and X-ray absorption spectroscopy data at discrete axial positions along the length of the catalyst bed. The spatial analysis has provided unique insights into the structure–activity relationships that govern selective NH3 oxidation—(i) our data is consistent with the presence of PdNx after the spectroscopic signatures for bulk PdNx disappear and that there is a direct correlation to the presence of this structure and the selectivity toward N2; (ii) at high temperatures, ≥400 °C, we propose that there are two simultaneous reaction pathways—the oxidation of NH3 to NOx by PdO and the subsequent catalytic reduction of NOx by NH3 to produce N2. The results in this study confirm the structural and catalytic diversity that exists during catalysis and the need for such an understanding if improvements to important emission control technologies, such as the selective catalytic oxidation of NH3, are to be made.
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Feb 2021
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B22-Multimode InfraRed imaging And Microspectroscopy
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Xue
Han
,
Wanpeng
Lu
,
Yinlin
Chen
,
Ivan
Da Silva
,
Jiangnan
Li
,
Longfei
Lin
,
Weiyao
Li
,
Alena M.
Sheveleva
,
Harry G. W.
Godfrey
,
Zhenzhong
Lu
,
Floriana
Tuna
,
Eric J. L.
Mcinnes
,
Yongqiang
Cheng
,
Luke L.
Daemen
,
Laura J.
Mccormick Mcpherson
,
Simon J.
Teat
,
Mark D.
Frogley
,
Svemir
Rudic
,
Pascal
Manuel
,
Anibal J.
Ramirez-cuesta
,
Sihai
Yang
,
Martin
Schroeder
Diamond Proposal Number(s):
[23782]
Abstract: Ammonia (NH3) is a promising energy resource owing to its high hydrogen density. However, its widespread application is restricted by the lack of efficient and corrosion-resistant storage materials. Here, we report high NH3 adsorption in a series of robust metal–organic framework (MOF) materials, MFM-300(M) (M = Fe, V, Cr, In). MFM-300(M) (M = Fe, VIII, Cr) show fully reversible capacity for >20 cycles, reaching capacities of 16.1, 15.6, and 14.0 mmol g–1, respectively, at 273 K and 1 bar. Under the same conditions, MFM-300(VIV) exhibits the highest uptake among this series of MOFs of 17.3 mmol g–1. In situ neutron powder diffraction, single-crystal X-ray diffraction, and electron paramagnetic resonance spectroscopy confirm that the redox-active V center enables host–guest charge transfer, with VIV being reduced to VIII and NH3 being oxidized to hydrazine (N2H4). A combination of in situ inelastic neutron scattering and DFT modeling has revealed the binding dynamics of adsorbed NH3 within these MOFs to afford a comprehensive insight into the application of MOF materials to the adsorption and conversion of NH3.
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Feb 2021
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[20757]
Open Access
Abstract: Understanding the kinetics of the crystallization process for organometal halide perovskite formation is critical in determining the crystalline, nanoscale morphology and therefore the electronic properties of the films produced during thin film formation from solution. In this work, in situ grazing incidence small-angle X-ray scattering (GISAXS) and optical microscopy measurements are used to investigate the processes of nucleation and growth of pristine mixed halide perovskite (MAPbI3–xClx) crystalline films deposited by bar coating at 60 °C, with and without additives in the solution. A small amount of 1,8-diiodooctane (DIO) and hydriodic acid (HI) added to MAPbI3–xClx is shown to increase the numbers of nucleation centers promoting heterogeneous nucleation and accelerate and modify the size of nuclei during nucleation and growth. A generalized formation mechanism is derived from the overlapping parameters obtained from real-time GISAXS and optical microscopy, which revealed that during nucleation, perovskite precursors cluster before becoming the nuclei that function as elemental units for subsequent formation of perovskite crystals. Additive-free MAPbI3–xClx follows reaction-controlled growth, in contrast with when DIO and HI are present, and it is highly possible that the growth then follows a hindered diffusion-controlled mechanism. These results provide important details of the crystallization mechanisms occurring and will help to develop greater control over perovskite films produced.
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Feb 2021
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13587]
Open Access
Abstract: Isoelectronic metal fluoride transition state analogue (TSA) complexes, MgF3– and AlF4–, have proven to be immensely useful in understanding mechanisms of biological motors utilizing phosphoryl transfer. Here we report a previously unobserved octahedral TSA complex, MgF3(H2O)−, in a 1.5 Å resolution Zika virus NS3 helicase crystal structure. 19F NMR provided independent validation and also the direct observation of conformational tightening resulting from ssRNA binding in solution. The TSA stabilizes the two conformations of motif V of the helicase that link ATP hydrolysis with mechanical work. DFT analysis further validated the MgF3(H2O)− species, indicating the significance of this TSA for studies of biological motors.
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Feb 2021
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[22322]
Abstract: The lithium-exchanged form of a merlinoite zeolite (MER) with Si/Al = 4.2 (unit cell composition Li6.2Al6.2Si25.8O64) possesses a strongly contracted framework when dehydrated (the unit cell volume decreases by 12.9% from the hydrated “wide-pore” form to the dehydrated “narrow-pore” form). It shows cooperative adsorption behavior for CO2, leading to two-step isotherms with the second step at elevated pressure (>2.5 bar at 298 K). Partially exchanging Na and K cations to give single-phase Li,Na- and Li,K-MER materials reduces the pressure of this second adsorption step because the transition from narrow- to wide-pore forms upon CO2 adsorption occurs at lower partial pressures compared to that in Li-MER: partial exchange with Cs does not reduce the pressure of this transition. Exsolution effects are also seen at K cation contents >2.2 per unit cell. The phase transitions proceed via intermediate structures by complex phase behavior rarely seen for zeolitic materials. The strongly distorted narrow-pore structures adopted upon dehydration give one-dimensional channel structures in which the percolation of CO2 through the material requires cation migration from their locations in ste sites. This is slow in Li3.4Cs2.8-MER where Cs cations occupy these critical ste cavities in the channels, causing very slow adsorption kinetics. As the partial pressure of CO2 increases, a threshold pressure is reached where cooperative adsorption and Cs cation migration occur and the wide-pore form results, with a three-dimensionally connected pore system, leading to a sharp increase in uptake. This is far in excess of the increase of unit cell volume because more of the pore space becomes accessible. Strong hysteretic effects occur upon desorption, leading to CO2 encapsulation. CO2 remaining within the material after repeated adsorption/desorption cycles without heated activation improves sorption kinetics and modifies the stepped isotherms.
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Feb 2021
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I02-Macromolecular Crystallography
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Open Access
Abstract: Structure-guided vaccine design provides a route to elicit a focused immune response against the most functionally important regions of a pathogen surface. This can be achieved by identifying epitopes for neutralizing antibodies through structural methods and recapitulating these epitopes by grafting their core structural features onto smaller scaffolds. In this study, we conducted a modified version of this protocol. We focused on the PfEMP1 protein family found on the surfaces of erythrocytes infected with Plasmodium falciparum. A subset of PfEMP1 proteins bind to endothelial protein C receptor (EPCR), and their expression correlates with development of the symptoms of severe malaria. Structural studies revealed that PfEMP1 molecules present a helix-kinked-helix motif that forms the core of the EPCR-binding site. Using Rosetta-based design, we successfully grafted this motif onto a three-helical bundle scaffold. We show that this synthetic binder interacts with EPCR with nanomolar affinity and adopts the expected structure. We also assessed its ability to bind to antibodies found in immunized animals and in humans from malaria-endemic regions. Finally, we tested the capacity of the synthetic binder to effectively elicit antibodies that prevent EPCR binding and analyzed the degree of cross-reactivity of these antibodies across a diverse repertoire of EPCR-binding PfEMP1 proteins. Despite our synthetic binder adopting the correct structure, we find that it is not as effective as the CIDRα domain on which it is based for inducing adhesion-inhibitory antibodies. This cautions against the rational design of focused immunogens that contain the core features of a ligand-binding site of a protein family, rather than those of a neutralizing antibody epitope.
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Feb 2021
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