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Abstract: Chiral materials formed by aggregated organic compounds play a fundamental role in chiral optoelectronics, photo- and spin-tronics. Nonetheless, a precise understanding of the molecular interactions involved remains an open problem. Here we introduce magnetic circular dichroism (MCD) as a new tool to elucidate molecular interactions and structural parameters of a supramolecular system. A detailed analysis of MCD together with electronic circular dichroism spectra combined to ab initio calculations unveils essential information on the geometry and energy levels of a self-assembled thin film made of a carbazole di-bithiophene chiral molecule. This approach can be extended to a generality of chiral organic materials and can help rationalizing the fundamental interactions leading to supramolecular order. This in turn could enable a better understanding of structure-property relationships, resulting in a more efficient material design.
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Nov 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[20221]
Open Access
Abstract: Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable insights into the structure and dynamics of biomolecules in solution, complementing a wide range of structural techniques, including molecular dynamics simulations. As contrast-based methods, they are sensitive not only to structural properties but also to solvent–solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. In this work, we demonstrate the feasibility of calculating SAXS and SANS intensities using a coarse-grained representation consisting of one bead per amino acid and three beads per nucleic acid, with form factors that can be corrected on the fly to account for solvation effects at no additional computational cost. By coupling this forward model with molecular dynamics simulations restrained with SAS data, it is possible to determine conformational ensembles or refine the structure and dynamics of proteins and nucleic acids in agreement with the experimental results. To assess the robustness of this approach, we applied it to gelsolin, for which we acquired SAXS data on its closed state, and to a UP1-microRNA complex, for which we used previously collected measurements. Our hybrid-resolution small-angle scattering (hySAS) implementation, being distributed in PLUMED, can be used with atomistic and coarse-grained simulations using diverse restraining strategies.
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Nov 2023
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[15723]
Open Access
Abstract: Calcium carbonate is a compound that is well-recognized and very prevalent in daily life e.g., chalk, mussel shells and limescale. However, scientists still have many questions about its formation mechanisms, the different crystal forms it takes, and how we can control and direct this formation to produce this material with different properties. Project M was a chemistry citizen science project for UK secondary schools exploring the synthesis of samples of calcium carbonate under different reaction conditions and analyzing them at Beamline I11, an X-ray diffraction laboratory at the Diamond Light Source synchrotron. Science communication played a crucial role in the success of the project, connecting different communities to the science and creating unique opportunities to center and empower the Project M Scientists.
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Nov 2023
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V.
Mangini
,
E.
Rosini
,
R.
Caliandro
,
G. F.
Mangiatordi
,
P.
Delre
,
A. G.
Sciancalepore
,
L.
Pollegioni
,
M.
Haidukowski
,
M.
Mazzorana
,
M.w.
Sumarah
,
J. B,
Renaud
,
R.
Flaig
,
G.
Mulè
,
Benny D.
Belviso
,
M.
Loi
Abstract: Aflatoxin B1 (AFB1) is one of the most potent carcinogens and a widespread food and feed contaminant. As for other toxins, many efforts are devoted to find efficient and environmentally-friendly methods to degrade AFB1, such as enzymatic treatments, thus improving the safety of food and feed products. In this regard, the dye decolorizing peroxidase of type B (DypB) can efficiently degrade AFB1. The molecular mechanism, which is required to drive protein optimization in view of the usage of DypB as a mycotoxin reduction agent in large scale application, is unknown. Here, we focused on the role of four DypB residues in the degradation of AFB1 by alanine-scanning (residues 156, 215, 239 and 246), which were identified from biochemical assays to be kinetically relevant for the degradation. As a result of DypB degradation, AFB1 converts into four products. Interestingly, the relative abundancy of these products depends on the replaced residues. Molecular dynamics simulations were used to investigate the role of these residues in the binding step between protein and manganese, a metal ion which is expected to be involved in the degradation process. We found that the size of the haem pocket as well as conformational changes in the protein structure could play a role in determining the kinetics of AFB1 removal and, consequently, guide the process towards specific degradation products.
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Nov 2023
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Abstract: Advanced applications of hardmetal (HM) in chemically aggressive ambients call for the improvement of their corrosion resistance, combined with optimal abrasion and toughness properties. This goal is chiefly achieved with binder alloying. In particular, Cr and Mo additions to Co-Ni matrices have proved effective in many cases, but the physico-chemical mechanisms underlying this functional improvement are poorly understood. This situation, on the one hand does not enable the fine-tuning of the composition, and, on the other hand, does not allow to reliably extrapolate the performance of these grades to new ambients. The aim of this work is to propose a molecular-level approach to the understanding of the electrochemical corrosion of HM, based on space-resolved compositional and chemical-state analysis of the surface of HM subjected to controlled electrochemical corrosion. This type of analysis is enabled by synchrotron-based scanning photoelectron microscopy (SPEM) and photoelectron microspectroscopy (μ-XPS). Specifically, we studied a WC-based grade with 15 w% binder with 4.67 Co/Ni ratio, alloyed with 0.78 w% Cr and 0.94 w% Mo, corroded potentiostatically in neutral sulphate aqueous solution in the pseudopassive and transpassive ranges. SPEM and μ-XPS allowed to locate and distinguish the chemical state of the binder and carbide elements in the respective phases and to distinguish the surface stoichiometry brought about by corrosion in different conditions. In particular, we found that pseudopassive conditions lead to the formation of surface films, enriched in W(VI) and Cr(III). Transpassive conditions cause notable surface enrichment in Cr(III) as well as to the formation of mixed Cr-W oxides in the WC regions. Mo is leached from the binder at all potentials investigated, while Mo(0) is present in the WC region under pseudopassive conditions, while transpassivity leads to its oxidative removal. Chloride in the electrolyte favours dissolution of oxidized metals, in particular causing the leaching of Cr(III), while Mo(III) is found at the surface of WC grains.
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Nov 2023
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I19-Small Molecule Single Crystal Diffraction
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Zi
Wang
,
Alena M.
Sheveleva
,
Jiangnan
Li
,
Zhengyang
Zhou
,
Sergei
Sapchenko
,
George
Whitehead
,
Mark R.
Warren
,
David
Collison
,
Junliang
Sun
,
Martin
Schroeder
,
Eric J. L.
Mcinnes
,
Sihai
Yang
,
Floriana
Tuna
Diamond Proposal Number(s):
[31627]
Open Access
Abstract: MFM-520(Zn) confines dimers of NO2 with a high adsorption of 4.52 mmol g−1 at 1 bar at 298 K. The synthesis and the incommensurate structure of Cu-doped MFM-520(Zn) are reported. The introduction of paramagnetic Cu2+ sites allows investigation of the electronic and geometric structure of metal site by in situ electron paramagnetic resonance (EPR) spectroscopy upon adsorption of NO2. By combining continuous wave and electron-nuclear double resonance spectroscopy, an unusual reverse Berry distorted coordination geometry of the Cu2+ centers is observed. Interestingly, Cu-doped MFM-520(Zn0.95Cu0.05) shows enhanced adsorption of NO2 of 5.02 mmol g−1 at 1 bar at 298 K. Whereas MFM-520(Zn) confines adsorbed NO2 as N2O4, the presence of monomeric NO2 at low temperature suggests that doping with Cu2+ centers into the framework plays an important role in tuning the dimerization of NO2 molecules in the pore via the formation of specific host-guest interactions.
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Nov 2023
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[19880]
Open Access
Abstract: The bile acid sodium symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM. The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. We observe that the pantoate binds, specifically, between the N-termini of two of the opposing helices in this cross-over region. During molecular dynamics simulations the pantoate remains in this position when sodium ions are present but is more mobile in their absence. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.
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Nov 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[22563]
Open Access
Abstract: The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as Methanothermus fervidus, Methanopyrus kandleri, and Methanothermobacter thermoautotrophicus. Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent SN2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.
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Nov 2023
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B18-Core EXAFS
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Renier Arabolla
Rodríguez
,
Manuel Avila
Santos
,
Abil E.
Aliev
,
Richard I.
Walton
,
Luis A. Tavera
Carrasco
,
Eduardo L. Perez
Cappe
,
Marlene González
Montiel
,
Edgar O. Pérez
Reyex
,
Nelcy Della Santina
Mohallem
,
Reza J.
Kashtiban
,
Yodalgis Mosqueda
Laffita
,
Carolina Leyva
Insunza
,
Paul R.
Shearing
,
Dan J. L.
Brett
Diamond Proposal Number(s):
[14239]
Abstract: The current work reports an unprecedented multifunctional material with optical activity and a modified magnetic response by a unique combination of doping with P and Fe into the spinel LiMn2O4. Through inductively coupled plasma – optical emission spectroscopy, X-ray absorption near-edge spectroscopy, X-ray diffraction and scanning transmission electron microscopy, the chemical composition, oxidation state and the crystalline structure are determined. Solid-state UV-Vis spectroscopy, magnetic susceptibility and electronic conductivity reveal the critical importance of the interaction between iron and phosphorus when simultaneously doping the crystalline structure of LiMn2O4. The presence of Fe and P considerably increases charge carrier concentration as a mechanism for enhancing electronic conductivity. Fe and P doping also creates Fe-Fe spin interactions that allow double electron optical excitations. This opens a pathway to create multifunctional materials for light-assisted charging lithium-ion batteries. P doping also induces the formation of magnetic clusters arising from the Fe-O-Fe, Fe-O-Mn and Mn-O-Mn spin exchange interactions. The magnetic response of the materials is strongly influenced by the relative amount of Fe in octahedral or tetrahedral sites of the spinel structure. Such ferrimagnetic behaviour has not been reported before LiMn2O4 doped with Fe or P separately. The potential applicability of this newly identified magnetic feature was demonstrated by a significant capacity gain when a lithium-ion cell is exposed to a static external magnetic field.
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Nov 2023
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B21-High Throughput SAXS
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Francesco
Rinaldi
,
Fabrizio
Schipani
,
Beatrice
Balboni
,
Federico
Catalano
,
Roberto
Marotta
,
Samuel H.
Myers
,
Viola
Previtali
,
Marina
Veronesi
,
Luigi
Scietti
,
Valentina
Cecatiello
,
Sebastiano
Pasqualato
,
Jose Antonio
Ortega
,
Stefania
Girotto
,
Andrea
Cavalli
Diamond Proposal Number(s):
[30465]
Abstract: RAD51 is a key player in the homologous recombination pathway. Upon DNA damage, RAD51 is transported into the nucleus by BRCA2, where it can repair DNA double-strand breaks. Due to the structural complexity and dynamics, researchers have not yet clarified the mechanistic details of every step of RAD51 recruitment and DNA repair. RAD51 possesses an intrinsic tendency to form oligomeric structures, which make it challenging to conduct biochemical and biophysical investigations. Here, for the first time, we report on the isolation and characterization of a human monomeric RAD51 recombinant form, obtained through a double mutation, which preserves the protein’s integrity and functionality. We investigated different buffers to identify the most suitable condition needed to definitively stabilize the monomer. The monomer of human RAD51 provides the community with a unique biological tool for investigating RAD51-mediated homologous recombination, and paves the way for more reliable structural, mechanistic, and drug discovery studies.
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Nov 2023
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