I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[21497]
Abstract: Organic semiconductors are promising for efficient, printable optoelectronics. Yet, strong excited-state quenching due to uncontrolled aggregation limits their use in devices. We report on the self-assembly of a supramolecular pseudo-cube formed from six perylene diimides (PDIs). The rigid, shape-persistent cage sets the distance and orientation of the PDIs and suppresses intramolecular rotations and vibrations, leading to non-aggregated, monomer-like properties in solution and the solid state, in contrast to the fast fluorescence quenching in the free ligand. The stabilized excited state and electronic purity in the cage enables the observation of delayed fluorescence due to a bright excited multimer, acting as excited-state reservoir in a rare case of benign inter-chromophore interactions in the cage. We show that self-assembly provides a powerful tool for retaining and controlling the electronic properties of chromophores, and to bring molecular electronics devices within reach.
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Jan 2023
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[25787, 27541, 29157]
Open Access
Abstract: Single-atom catalysts (SACs) on hematite photoanodes are efficient cocatalysts to boost photoelectrochemical performance. They feature high atom utilization, remarkable activity, and distinct active sites. However, the specific role of SACs on hematite photoanodes is not fully understood yet: Do SACs behave as a catalytic site or as a spectator? By combining spectroscopic experiments and computer simulations, we demonstrate that single-atom iridium (sIr) catalysts on hematite (α-Fe2O3/sIr) photoanodes act as a true catalyst by trapping holes from hematite and providing active sites for the water oxidation reaction. In situ transient absorption spectroscopy showed a reduced number of holes and shortened hole lifetime in the presence of sIr. This was particularly evident on the second timescale, indicative of fast hole transfer and depletion toward water oxidation. Intensity-modulated photocurrent spectroscopy evidenced a faster hole transfer at the α-Fe2O3/sIr/electrolyte interface compared to that at bare α-Fe2O3. Density functional theory calculations revealed the mechanism for water oxidation using sIr as a catalytic center to be the preferred pathway as it displayed a lower onset potential than the Fe sites. X-ray photoelectron spectroscopy demonstrated that sIr introduced a mid-gap of 4d state, key to the fast hole transfer and hole depletion. These combined results provide new insights into the processes controlling solar water oxidation and the role of SACs in enhancing the catalytic performance of semiconductors in photo-assisted reactions.
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Jan 2023
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B16-Test Beamline
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Abstract: Intense research activities have been made in the development of high-Z and wide-bandgap compound semiconductor pixel detectors for the next generation X-ray and gamma ray spectroscopic imagers. Cadmium telluride (CdTe) and cadmium–zinc–telluride (CdZnTe or CZT) pixel detectors have shown impressive performance in X-ray and gamma ray detection from energies of few keV up to 1 MeV. Charge sharing and cross-talk phenomena represent the typical drawbacks in sub-millimeter pixel detectors, with severe distortions in both energy and spatial resolution. In this chapter, we review the effects of these phenomena on the response of CZT/CdTe pixel detectors, with particular emphasis on the current state of the art of the discrimination/correction techniques. The results from original energy-recovery procedures of multiple charge sharing events, recently developed by our group, are also shown.
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Jan 2023
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B23-Circular Dichroism
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Abstract: High-resolution calorimetry has played a significant role in providing detailed information on phase transitions in liquid crystals. In particular, adiabatic scanning calorimetry (ASC), capable of providing simultaneous information on the temperature dependence of the specific enthalpy
h
(
T
)
and on the specific heat capacity
c
p
(
T
)
, has proven to be an important tool to determine the order of transitions and render high-resolution information on pretransitional thermal behavior. Here we report on ASC results on the compound 2,3′,4′,5′-tetrafluoro[1,1′-biphenyl]-4-yl 2,6-difluoro-4-(5-propyl-1,3-dioxan-2-yl) benzoate (DIO) and on mixtures with 4-[(4-nitrophenoxy)carbonyl]phenyl 2,4-dimethoxybenzoate (RM734). Both compounds exhibit a low-temperature ferroelectric nematic phase (
N
F
) and a high-temperature paraelectric nematic phase
(
N
)
. However, in DIO these two phases are separated by an intermediate phase (
N
x
). From the detailed data of
h
(
T
)
and
c
p
(
T
)
, we found that the intermediate phase was present in all the mixtures over the complete composition range, albeit with strongly decreasing temperature width for that phase with decreasing mole fraction of DIO (
x
DIO
). The
x
DIO
dependence on the transition temperatures for both transitions could be well described by a quadratic function. Both these transitions were weakly first order. The true latent heat of the
N
x
−
N
transition of DIO was as low as
L
=
0.0075
±
0.0005
J
/
g
and
L
=
0.23
±
0.03
J
/
g
for the
N
F
−
N
x
transition, which is about twice the previously reported value of 0.115 J/g for the
N
F
−
N
transition in RM734. In the mixtures both transition latent heats decrease gradually with decreasing
x
DIO
. At all the
N
x
−
N
transitions pretransition fluctuation effects are absent and these transitions are purely but very weakly first order. As in RM734 the transition from the
N
F
to the higher-temperature phase exhibits substantial pretransitional behavior, in particular, in the high-temperature phase. Power-law analysis of
c
p
(
T
)
resulted in an effective critical exponent
α
=
0.88
±
0.1
for DIO and this value decreased in the mixtures with decreasing
x
DIO
toward
α
=
0.50
±
0.05
reported for RM734. Ideal mixture analysis of the phase diagram was consistent with ideal mixture behavior provided the total transition enthalpy change was used in the analysis.
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Jan 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[14435, 15580, 15836, 15897]
Abstract: In meiosis, a supramolecular protein structure, the synaptonemal complex (SC), assembles between homologous chromosomes to facilitate their recombination. Mammalian SC formation is thought to involve hierarchical zipper-like assembly of an SYCP1 protein lattice that recruits stabilizing central element (CE) proteins as it extends. Here we combine biochemical approaches with separation-of-function mutagenesis in mice to show that, rather than stabilizing the SYCP1 lattice, the CE protein SYCE3 actively remodels this structure during synapsis. We find that SYCP1 tetramers undergo conformational change into 2:1 heterotrimers on SYCE3 binding, removing their assembly interfaces and disrupting the SYCP1 lattice. SYCE3 then establishes a new lattice by its self-assembly mimicking the role of the disrupted interface in tethering together SYCP1 dimers. SYCE3 also interacts with CE complexes SYCE1–SIX6OS1 and SYCE2–TEX12, providing a mechanism for their recruitment. Thus, SYCE3 remodels the SYCP1 lattice into a CE-binding integrated SYCP1–SYCE3 lattice to achieve long-range synapsis by a mature SC.
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Jan 2023
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B07-B-Versatile Soft X-ray beamline: High Throughput
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Abstract: We present a new beamline for Versatile Soft X-ray Spectroscopy at Diamond Light Source, VerSoX B07-B, with a medium X-rays flux in the photon energy range 45-2200 eV. B07-B has two endstations permitting studies of a wide range of interfaces and materials. ES-2 enables high-throughput NEXAFS (Near-Edge X-ray Absorption Fine Spectroscopy) under ambient-pressure conditions, ES-1 is dedicated to high-throughput X-ray Photoelectron Spectroscopy (XPS) and in ultra-high vacuum (UHV). ES-1 is fully motorised and automated; it is equipped with fast entry lock, rotary distribution, sample storage and two sample preparation chambers for standard UHV sample preparation and characterisation.
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Jan 2023
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I05-ARPES
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Kate
Reidy
,
Paulina Ewa
Majchrzak
,
Benedikt
Haas
,
Joachim Dahl
Thomsen
,
Andrea
Konečná
,
Eugene
Park
,
Julian
Klein
,
Alfred J. H.
Jones
,
Klara
Volckaert
,
Deepnarayan
Biswas
,
Matthew D.
Watson
,
Cephise
Cacho
,
Prineha
Narang
,
Christoph T.
Koch
,
Soeren
Ulstrup
,
Frances M.
Ross
,
Juan Carlos
Idrobo
Diamond Proposal Number(s):
[25368, 29607]
Abstract: The integration of metallic contacts with two-dimensional (2D) semiconductors is routinely required for the fabrication of nanoscale devices. However, nanometer-scale variations in the 2D/metal interface can drastically alter the local optoelectronic properties. Here, we map local excitonic changes of the 2D semiconductor MoS2 in contact with Au. We utilize a suspended and epitaxially grown 2D/metal platform that allows correlated electron energy-loss spectroscopy (EELS) and angle resolved photoelectron spectroscopy (nanoARPES) mapping. Spatial localization of MoS2 excitons uncovers an additional EELS peak related to the MoS2/Au interface. NanoARPES measurements indicate that Au–S hybridization decreases substantially with distance from the 2D/metal interface, suggesting that the observed EELS peak arises due to dielectric screening of the excitonic Coulomb interaction. Our results suggest that increasing the van der Waals distance could optimize excitonic spectra of mixed-dimensional 2D/3D interfaces and highlight opportunities for Coulomb engineering of exciton energies by the local dielectric environment or moiré engineering.
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Jan 2023
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B21-High Throughput SAXS
I03-Macromolecular Crystallography
I23-Long wavelength MX
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Eugene
Kuatsjah
,
Michael
Zahn
,
Xiangyang
Chen
,
Ryo
Kato
,
Daniel J.
Hinchen
,
Mikhail O.
Konev
,
Rui
Katahira
,
Christian
Orr
,
Armin
Wagner
,
Yike
Zou
,
Stefan J.
Haugen
,
Kelsey J.
Ramirez
,
Joshua K.
Michener
,
Andrew R.
Pickford
,
Naofumi
Kamimura
,
Eiji
Masai
,
Kendall N.
Houk
,
John
Mcgeehan
,
Gregg T.
Beckham
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
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Jan 2023
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[26794]
Open Access
Abstract: Hyperactive mutation V617F in the JAK2 regulatory pseudokinase domain (JH2) is prevalent in patients with myeloproliferative neoplasms. Here, we identified novel small molecules that target JH2 of JAK2 V617F and characterized binding via biochemical and structural approaches. Screening of 107,600 small molecules resulted in identification of 55 binders to the ATP-binding pocket of recombinant JAK2 JH2 V617F protein at a low hit rate of 0.05%, which indicates unique structural characteristics of the JAK2 JH2 ATP-binding pocket. Selected hits and structural analogs were further assessed for binding to JH2 and JH1 (kinase) domains of JAK family members (JAK1-3, TYK2) and for effects on MPN model cell viability. Crystal structures were determined with JAK2 JH2 wild-type and V617F. The JH2-selective binders were identified in diaminotriazole, diaminotriazine, and phenylpyrazolo-pyrimidone chemical entities, but they showed low-affinity, and no inhibition of MPN cells was detected, while compounds binding to both JAK2 JH1 and JH2 domains inhibited MPN cell viability. X-ray crystal structures of protein-ligand complexes indicated generally similar binding modes between the ligands and V617F or wild-type JAK2. Ligands of JAK2 JH2 V617F are applicable as probes in JAK-STAT research, and SAR optimization combined with structural insights may yield higher-affinity inhibitors with biological activity.
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Jan 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Andrej Emanuel
Cotman
,
Martina
Durcik
,
Davide
Benedetto Tiz
,
Federica
Fulgheri
,
Daniela
Secci
,
Maša
Sterle
,
Štefan
Možina
,
Žiga
Skok
,
Nace
Zidar
,
Anamarija
Zega
,
Janez
Ilaš
,
Lucija
Peterlin Mašič
,
Tihomir
Tomašič
,
Diarmaid
Hughes
,
Douglas L.
Huseby
,
Sha
Cao
,
Linnéa
Garoff
,
Talía
Berruga Fernández
,
Paraskevi
Giachou
,
Lisa
Crone
,
Ivailo
Simoff
,
Richard
Svensson
,
Bryndis
Birnir
,
Sergiy V.
Korol
,
Zhe
Jin
,
Francisca
Vicente
,
Maria C.
Ramos
,
Mercedes
De La Cruz
,
Björn
Glinghammar
,
Lena
Lenhammar
,
Sara R.
Henderson
,
Julia E. A.
Mundy
,
Anthony
Maxwell
,
Claren E. M.
Stevenson
,
David M.
Lawson
,
Guido V.
Janssen
,
Geert Jan
Sterk
,
Danijel
Kikelj
Diamond Proposal Number(s):
[18565, 25108]
Open Access
Abstract: We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.
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Jan 2023
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