I06-Nanoscience (XPEEM)
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Yang
Li
,
Yan
Wang
,
Andrew F.
May
,
Mauro
Fianchini
,
Chiara
Biz
,
Saeyoung
Oh
,
Yiru
Zhu
,
Hu Young
Jeong
,
Jieun
Yang
,
Jose
Gracia
,
Manish
Chhowalla
Diamond Proposal Number(s):
[33245]
Open Access
Abstract: Spin selective catalysis is an emerging approach for improving the thermodynamics and kinetics of reactions. The role of electron spins has been scarcely studied in catalytic reactions. One exception is the oxygen evolution reaction (OER) where strongly correlated metals and oxides are used as catalysts. In OER, spin alignment facilitates the transition of singlet state of the reactant to the triplet state of O2. However, the influence of strong correlations on spin exchange mechanism and spin selective thermodynamics of most catalytic reactions remain unclear. Here we decouple the strongly correlated catalyst from the electrolyte to study spin exchange in two-dimensional (2D) magnetic iron germanium telluride (FGT) heterostructure. We demonstrate that transmission of spin and electrochemical information between the catalyst and the reactant can occur through quantum exchange interaction despite the catalyst of FGT being completely encapsulated by graphene or hexagonal boron nitride (hBN). The strong correlations in FGT that lead to enhanced spin exchange in OER are observed in graphene or hBN layers with thicknesses of up to 6 nm. We demonstrate that spin alignment in FGT leads to a lowering of thermodynamic barrier for adsorption of hydroxide ion and electron transfer to the catalyst. This results in up to fivefold enhancement in OER performance and improved kinetics. Our results provide clear evidence that transmission of both quantum mechanical and electrochemical information through quantum spin exchange interaction in FGT leads to an enhancement in catalytic performance.
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Dec 2024
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B18-Core EXAFS
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Nivetha
Jeyachandran
,
Wangchao
Yuan
,
Xiang
Li
,
Akshayini
Muthuperiyanayagam
,
Stefania
Gardoni
,
Jiye
Feng
,
Qingsheng
Gao
,
Martin
Wilding
,
Peter
Wells
,
Devis
Di Tommaso
,
Cristina
Giordano
Diamond Proposal Number(s):
[29721]
Open Access
Abstract: The rising levels of CO2 have spurred growing concerns for our environment, and curbing CO2 emissions may not be practically viable with the expanding human population. One attractive strategy is the electrochemical CO2 reduction (CO2RR) into value added chemicals but because of the chemical inertness of the CO2 molecule, the electrochemical reduction requires a suitable catalyst. Cu-based catalysts have been largely investigated for CO2RR, however, the difficulty achieving a high selectivity and faradaic efficiency towards specific products, especially hydrocarbons, is still a challenge, alongside the concern over cost, stability and scarcity of the metal catalyst. The present research focuses on tuning the crystallinity of Cu nanoparticles via a green, cost-friendly, and facile method, called the urea glass route. Remarkably, the incorporation of a selected nitrogen-carbon rich source (namely, 4,5 dicyanoimidazole) at low temperatures allow the formation of an oxidized derived amorphous Cu system, whilst a second thermal treatment enables the transformation to crystalline Cu0. We found that the combination of surface Cu0 and Cu1+ (observed via XPS studies) present in our amorphous and crystalline Cu nanoparticles leads to interesting differences in the final catalytic activity when tested under CO2 reaction conditions. The combination of extended X-ray absorption fine structure (EXAFS) experiments and molecular dynamics simulations provides compelling evidence for the amorphous and metallic nature of Cu nanoparticles.
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Dec 2024
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[29651]
Open Access
Abstract: Degradation tests are a key step in the development of a bioresorbable stent. The present study focused on the degradation of bioresorbable stents made from PLLA filaments, and examined the variation of the physical, thermal, and mechanical properties of the material and the devices under both real-time and accelerated degradation conditions. Results showed that the undegraded filaments were highly crystalline and composed by both
and
crystalline phases, induced by both the melt spinning and heat treatment processes. The latter was shown to have an important influence on the further formation of
crystalline phase and therefore crystalline structure perfectioning. Real-time degradation tests showed that the devices maintained structural stability for up to a year, meeting the required 6-month degradation period for vascular stents. Degradation was shown to primarily affect the crystalline regions, and to cause a gradual loss of material ductility before any mass loss or decrease in crystallinity. In turn, a constant decrease of molecular weight was observed, with stent failure occurring around day 389 due to a drop in molecular weight below 10,000 g/mol. Accelerated degradation tests mirrored real-time results until mass loss began. Subsequently a slower molecular weight decrease was observed, with an increase and subsequent decrease of material crystallinity. The consistency of the data obtained between real-time and accelerated degradation before mass loss confirmed the possibility to gain insights into real-time degradation through an accelerated protocol. However, attention must be paid to the initial molecular weight of the material, which has been shown to highly influence the acceleration rate. This study provides a wide range of experimental data both on the real-time and thermally accelerated degradation behaviour of PLLA braided stents that can be used as benchmark for further studies in the field.
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Dec 2024
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I23-Long wavelength MX
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Open Access
Abstract: Analytical absorption corrections are employed in scaling diffraction data for highly absorbing samples, such as those used in long-wavelength crystallography, where empirical corrections pose a challenge. AnACor2.0 is an accelerated software package developed to calculate analytical absorption corrections. It accomplishes this by ray-tracing the paths of diffracted X-rays through a voxelized 3D model of the sample. Due to the computationally intensive nature of ray-tracing, the calculation of analytical absorption corrections for a given sample can be time consuming. Three experimental datasets (insulin at λ = 3.10 Å, thermolysin at λ = 3.53 Å and thaumatin at λ = 4.13 Å) were processed to investigate the effectiveness of the accelerated methods in AnACor2.0. These methods demonstrated a maximum reduction in execution time of up to 175× compared with previous methods. As a result, the absorption factor calculation for the insulin dataset can now be completed in less than 10 s. These acceleration methods combine sampling, which evaluates subsets of crystal voxels, with modifications to standard ray-tracing. The bisection method is used to find path lengths, reducing the complexity from O(n) to O(log2 n). The gridding method involves calculating a regular grid of diffraction paths and using interpolation to find an absorption correction for a specific reflection. Additionally, optimized and specifically designed CUDA implementations for NVIDIA GPUs are utilized to enhance performance. Evaluation of these methods using simulated and real datasets demonstrates that systematic sampling of the 3D model provides consistently accurate results with minimal variance across different sampling ratios. The mean difference of absorption factors from the full calculation (without sampling) is at most 2%. Additionally, the anomalous peak heights of sulfur atoms in the Fourier map show a mean difference of only 1% compared with the full calculation. This research refines and accelerates the process of analytical absorption corrections, introducing innovative sampling and computational techniques that significantly enhance efficiency while maintaining accurate results.
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Dec 2024
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Eugene
Kuatsjah
,
Alexa
Schwartz
,
Michael
Zahn
,
Konstantinos
Tornesakis
,
Zoe A.
Kellermyer
,
Morgan A.
Ingraham
,
Sean P.
Woodworth
,
Kelsey J.
Ramirez
,
Paul A.
Cox
,
Andrew R.
Pickford
,
Davinia
Salvachúa
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.
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Dec 2024
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I24-Microfocus Macromolecular Crystallography
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Maria Elena
Laugieri
,
Immacolata
Speciale
,
Ana
Gimeno
,
Sicheng
Lin
,
Brock W.
Byers
,
Ana
Poveda
,
Reyes
Núñez‐franco
,
Idoia
Iturrioz
,
María J.
Moure
,
Gonzalo
Jiménez-Osés
,
Irene
Russo‐krauss
,
Anna
Notaro
,
James L.
Van Etten
,
Todd L.
Lowary
,
Jesús
Jimenez-Barbero
,
Cristina
De Castro
,
Michela
Tonetti
,
Adriana L.
Rojas
Diamond Proposal Number(s):
[20113]
Open Access
Abstract: Protein A075L is a β-xylosyltransferase that participates in producing the core of the N-glycans found in VP54, the major viral capsid protein of Paramecium bursaria chlorella virus-1 (PBCV-1). In this study, we present an X-ray crystallographic analysis of the apo form of A075L, along with its complexes with the sugar donor and with a trisaccharide acceptor. The protein structure shows a typical GT-B folding, with two Rossmann-like fold domains, in which the acceptor substrate binds to the N-terminal region, and the nucleotide-sugar donor binds to the C-terminal region. We propose that the catalytic mechanism follows a direct displacement SN2-like reaction, where Asp73 serves as a catalytic base that deprotonates the incoming nucleophile of the acceptor, facilitating direct displacement of the UDP with the inversion of the anomeric configuration of the acceptor without metal ion dependence, while the interactions with side chains of Arg158 and Arg208 stabilize the developing negative charge. Using isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, high-performance liquid chromatography, and molecular dynamics simulations, the catalytic activity and specificity of this enzyme have been unraveled.
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Dec 2024
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[34808]
Open Access
Abstract: Tripartite ATP-independent periplasmic (TRAP) transporters are widespread in prokaryotes and are responsible for the transport of a variety of different ligands, primarily organic acids. TRAP transporters can be divided into two subclasses; DctP-type and TAXI type, which share the same overall architecture and substrate-binding protein requirement. DctP-type transporters are very well studied and have been shown to transport a range of compounds including dicarboxylates, keto acids, and sugar acids. However, TAXI-type transporters are relatively poorly understood. To address this gap in our understanding, we have structurally and biochemically characterized VC0430 from Vibrio cholerae. We show it is a monomeric, high affinity glutamate-binding protein, which we thus rename VcGluP. VcGluP is stereoselective, binding the L-isomer preferentially, and can also bind L-glutamine and L-pyroglutamate with lower affinity. Structural characterization of ligand-bound VcGluP revealed details of its binding site and biophysical characterization of binding site mutants revealed the substrate binding determinants, which differ substantially from those of DctP-type TRAPs. Finally, we have analyzed the interaction between VcGluP and its cognate membrane component, VcGluQM (formerly VC0429) in silico, revealing an architecture hitherto unseen. To our knowledge, this is the first transporter in V. cholerae to be identified as specific to glutamate, which plays a key role in the osmoadaptation of V. cholerae, making this transporter a potential therapeutic target.
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Dec 2024
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Abstract: Through a combination of magnetic susceptibility, specific heat, and neutron powder diffraction measurements we have revealed a sequence of four magnetic phase transitions in the columnar quadruple perovskite Er2CuMnMn4O12. A key feature of the quadruple perovskite structural framework is the complex interplay of multiple magnetic sublattices via frustrated exchange topologies and competing magnetic anisotropies. It is shown that in Er2CuMnMn4O12, this phenomenology gives rise to multiple spin-reorientation transitions driven by the competition of easy-axis single ion anisotropy and the Dzyaloshinskii–Moriya interaction; both within the manganese B-site sublattice. At low temperature, one Er sublattice orders due to a finite f-d exchange field aligned parallel to its Ising axis, while the other Er sublattice remains non-magnetic until a final, symmetry-breaking phase transition into the ground state. This non-trivial low-temperature interplay of transition metal and rare-earth sublattices, as well as an observed k = (0, 0, ½) periodicity in both manganese spin canting and Er ordering, raises future challenges to develop a complete understanding of the R2CuMnMn4O12 family.
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Dec 2024
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I19-Small Molecule Single Crystal Diffraction
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Mariya
Aleksich
,
Yeongsu
Cho
,
Daniel W.
Paley
,
Maggie C.
Willson
,
Hawi N.
Nyiera
,
Patience A.
Kotei
,
Vanessa
Oklejas
,
David W.
Mittan-Moreau
,
Elyse A.
Schriber
,
Kara
Christensen
,
Ichiro
Inoue
,
Shigeki
Owada
,
Kensuke
Tono
,
Michihiro
Sugahara
,
Satomi
Inaba-Inoue
,
Mohammad
Vakili
,
Christopher J.
Milne
,
Fabio
Dallantonia
,
Dmitry
Khakhulin
,
Fernando
Ardana-Lamas
,
Frederico
Lima
,
Joana
Valerio
,
Huijong
Han
,
Tamires
Gallo
,
Hazem
Yousef
,
Oleksii
Turkot
,
Ivette J. Bermudez
Macias
,
Thomas
Kluyver
,
Philipp
Schmidt
,
Luca
Gelisio
,
Adam R.
Round
,
Yifeng
Jiang
,
Doriana
Vinci
,
Yohei
Uemura
,
Marco
Kloos
,
Adrian P.
Mancuso
,
Mark
Warren
,
Nicholas K.
Sauter
,
Jing
Zhao
,
Tess
Smidt
,
Heather J.
Kulik
,
Sahar
Sharifzadeh
,
Aaron S.
Brewster
,
J. Nathan
Hohman
Diamond Proposal Number(s):
[35300]
Abstract: X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. The proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.
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Dec 2024
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Jaydeep
Patel
,
Adam
Round
,
Raphael
De Wijn
,
Mohammad
Vakili
,
Gabriele
Giovanetti
,
Diogo Filipe Monrroy Vilan E
Melo
,
Juncheng
E
,
Marcin
Sikorski
,
Jayanth
Koliyadu
,
Faisal H. M.
Koua
,
Tokushi
Sato
,
Adrian
Mancuso
,
Andrew
Peele
,
Brian
Abbey
Open Access
Abstract: Automated evaluation of optical microscopy images of liquid jets, commonly used for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as the proportion of XFEL pulses intersecting with the liquid jet. This method utilizes machine vision for preprocessing, feature extraction, segmentation and jet detection as well as tracking to extract key physical characteristics (such as the jet angle) from optical microscopy images captured during experiments. To determine the effectiveness of these tools in monitoring jet stability and enhancing sample delivery efficiency, we conducted XFEL experiments with various sample compositions (pure water, buffer and buffer with crystals), nozzle designs and jetting conditions. We integrated our real-time analysis algorithm into the Karabo control system at the European XFEL. The results indicate that the algorithm performs well in monitoring the jet angle and provides a quantitative characterization of liquid jet stability through optical image analysis conducted during experiments.
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Dec 2024
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