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Jack
Scantlebury
,
Lucy
Vost
,
Anna
Carbery
,
Thomas E.
Hadfield
,
Oliver M.
Turnbull
,
Nathan
Brown
,
Vijil
Chenthamarakshan
,
Payel
Das
,
Harold
Grosjean
,
Frank
Von Delft
,
Charlotte M.
Deane
Open Access
Abstract: Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs the energy of their interaction. Only a scoring function that accounts for the interatomic interactions involved in binding can accurately predict binding affinity on unseen molecules. However, many scoring functions make predictions based on data set biases rather than an understanding of the physics of binding. These scoring functions perform well when tested on similar targets to those in the training set but fail to generalize to dissimilar targets. To test what a machine learning-based scoring function has learned, input attribution, a technique for learning which features are important to a model when making a prediction on a particular data point, can be applied. If a model successfully learns something beyond data set biases, attribution should give insight into the important binding interactions that are taking place. We built a machine learning-based scoring function that aimed to avoid the influence of bias via thorough train and test data set filtering and show that it achieves comparable performance on the Comparative Assessment of Scoring Functions, 2016 (CASF-2016) benchmark to other leading methods. We then use the CASF-2016 test set to perform attribution and find that the bonds identified as important by PointVS, unlike those extracted from other scoring functions, have a high correlation with those found by a distance-based interaction profiler. We then show that attribution can be used to extract important binding pharmacophores from a given protein target when supplied with a number of bound structures. We use this information to perform fragment elaboration and see improvements in docking scores compared to using structural information from a traditional, data-based approach. This not only provides definitive proof that the scoring function has learned to identify some important binding interactions but also constitutes the first deep learning-based method for extracting structural information from a target for molecule design.
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May 2023
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I07-Surface & interface diffraction
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Daniel T. W.
Toolan
,
Michael P.
Weir
,
Shuangqing
Wang
,
Simon A.
Dowland
,
Zhilong
Zhang
,
James
Xiao
,
Jonathan
Rawle
,
Neil
Greenham
,
Richard
Friend
,
Akshay
Rao
,
Richard A. L.
Jones
,
Anthony J.
Ryan
Diamond Proposal Number(s):
[23587]
Open Access
Abstract: Hybrid small-molecule organic semiconductor / quantum dot blend films are attractive for high efficiency low-cost solar energy harvesting devices. Understanding and controlling the self-assembly of the organic semiconductor and quantum dots is crucial in optimising device performance, not only at a lab-scale but for large-scale high-throughput printing and coating methods. Here, in situ grazing incidence X-ray scattering (GIXS) is employed in order to gain direct insights into how small-molecule organic semiconductor / quantum dot blends self-assemble during blade coating. Results show that for two different archetypal organic small molecule:quantum dot blends, small-molecule crystallisation may either occur spontaneously or be mediated by the formation of quantum dot aggregates. Irrespective of the initial crystallisation route, the small-molecule crystallisation acts to exclude the quantum dot impurities from the growing crystalline matrix phase. These results provide important fundamental understanding of structure formation of small organic molecule:quantum dot films prepared via solution processing routes, compatible with large scale deposition manufacturing.
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May 2023
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Qi
Xue
,
Ching Kit Tommy
Wun
,
Tianxiang
Chen
,
Shogo
Kawaguchi
,
Sarah
Day
,
Chiu C.
Tang
,
Tai-Sing
Wu
,
Yun-Liang
Soo
,
Cong
Lin
,
Yung-Kang
Peng
,
Jun
Yin
,
Tsz Woon Benedict
Lo
Abstract: Supported bimetallic dual-atom catalysts (DACs) have been regarded as a promising class of materials for small molecule activation, but their syntheses remain challenging. Here, we report the controlled synthesis of supported Cu,Fe DACs on the ZrO6O4 secondary building units of UiO-66-NH2 which allows the efficient activation of O2. Remarkably high product selectivity (>92%) towards benzaldehyde over our model photocatalytic styrene oxidation reaction has been achieved. The superior reactivity has been attributed to the well-balanced synergy between the electronic and steric characteristics, which enables efficient O2 activation by the sterically restrained Cu and Fe sites in proximity for the formation of the bridging peroxy group. This bridging peroxy group facilitates the selective oxidation of styrene akin to many peroxide-based oxidants. The confined microporous environment allows the control of the electronic and geometric properties of the DACs, which subsequently sheds light towards more precise atomistic engineering that approaches the conventional inorganic metal(s)-complex counterparts.
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May 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[21871]
Open Access
Abstract: β-NaYF4 nanocrystals are a popular class of optical materials. They can be doped with optically active lanthanide ions and shaped into core–multi-shell geometries with controlled dopant distributions. Here, we follow the synthesis of β-NaYF4 nanocrystals from α-NaYF4 precursor particles using in situ small-angle and wide-angle X-ray scattering and ex-situ electron microscopy. We observe an evolution from a monomodal particle size distribution to bimodal, and eventually back to monomodal. The final size distribution is narrower in absolute numbers than the initial distribution. These peculiar growth dynamics happen in large part before the α-to-β phase transformation. We propose that the splitting of the size distribution is caused by variations in the reactivity of α-NaYF4 precursor particles, potentially due to inter-particle differences in stoichiometry. Rate equation modeling confirms that a continuous distribution of reactivities can result in the observed particle growth dynamics.
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May 2023
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[25756]
Open Access
Abstract: Caries is a chronic disease that causes the alteration of the structure of dental tissues by acid dissolution (in enamel, dentine and cementum) and proteolytic degradation (dentine and cementum) and generates an important cost of care. There is a need to visualise and characterise the acid dissolution process on enamel due to its hierarchical structure leading to complex structural modifications. The process starts at the enamel surface and progresses into depth, which necessitates the study of the internal enamel structure. Artificial demineralisation is usually employed to simulate the process experimentally. In the present study, the demineralisation of human enamel was studied using surface analysis carried out with atomic force microscopy as well as 3D internal analysis using synchrotron X-ray tomography during acid exposure with repeated scans to generate a time-lapse visualisation sequence. Two-dimensional analysis from projections and virtual slices and 3D analysis of the enamel mass provided details of tissue changes at the level of the rods and inter-rod substance. In addition to the visualisation of structural modifications, the rate of dissolution was determined, which demonstrated the feasibility and usefulness of these techniques. The temporal analysis of enamel demineralisation is not limited to dissolution and can be applied to other experimental conditions for the analysis of treated enamel or remineralisation.
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May 2023
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I22-Small angle scattering & Diffraction
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Abstract: In this thesis, we report the ability to fabricate hydrogels using low molecular weight gelators (LMWGs) and the subsequent characterisation of their mechanical properties over a variety of different length scales. These materials have been investigated due to their potential use in a wide range of biomedical applications including drug delivery, tissue engineering, cell culture and wound healing.
We describe the localised gelation of LMWGs on electrode surfaces via electrochemically generated pH gradients. The electrofabrication of hydrogels on electrode surfaces has shown great potential in the field of biomedicine, with applications ranging from antimicrobial wound dressings, tissue engineering scaffolds and biomimetic materials.
First, we describe the largest reported di- and tri-peptide-based hydrogels on electrode surfaces via the electrochemical oxidation of hydroquinone. Expanding upon previous work which focuses on the fabrication of hydrogels on the nanometre to millimetre scale, we deposit hydrogels around 3 cm3 in size. Furthermore, we demonstrate that there is an upper limit to how large the hydrogels can grow which is determined by the size of the pH gradient from the electrode surface. To grow hydrogels of this size, much longer deposition times of two to five hours are required than in previous reports. When the gelator/hydroquinone solution is left exposed to the open atmosphere for this amount of time, the hydroquinone in solution oxidises to benzoquinone/quinhydrone before it can be consumed electrochemically. This inhibits the electrochemical reaction and reduces gelation efficiency. To prevent this, we build a system that can perform the fabrication process under an inert nitrogen atmosphere. Using this system, we show how the choice of gelator affects the mechanical properties of the hydrogel and the resulting material phenomena that cause these changes. As well as this, we show how this approach can be used to grow multi-layered hydrogels, with each layer presenting different chemical and mechanical properties.
Secondly, we report the first known example of electrodeposition for a LMWG molecule using an electrochemically generated basic pH gradient at electrode surfaces. This approach has previously been used to fabricate hydrogels of the biopolymer chitosan using the galvanostatic reduction of hydrogen peroxide. During the electrochemical reduction of hydrogen peroxide, hydroxide ions are produced. As a result, a basic pH zone is generated at the electrode, triggering solutions of chitosan to form immobilised hydrogels on the electrode surface. Using this approach, we show how electrodeposition at high pH can be applied to our LMWG system.
We then show that we can electrochemically form hydrogels at high pH, with the gel properties being greatly improved by the addition and increased concentration of hydrogen peroxide. Following from this, we then show the simultaneous formation of two low molecular weight hydrogels at acidic and basic pH extremes. To achieve this, we couple the electrochemical reduction of hydrogen peroxide and the electrochemical oxidation of hydroquinone described in the previous chapter.
Finally, we report the electrodeposition of five carbazole-protected amino acid hydrogels on electrode surfaces via the electrochemical oxidation of hydroquinone. As well as this, we report the full to partial electropolymerisation of the pre-assembled hydrogels in perchloric acid. For the less bulky carbazole-protected amino acids, the full collapse of the hydrogel to form electrochromic polymers on the electrode surface is achieved. However, for the bulkier gelators, little to no evidence of polymerisation occurs. We believe this is due to the bulky side chain on the gelator backbone preventing the molecular reorganization required for polymerization to occur.
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May 2023
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[24447]
Open Access
Abstract: The β-glucans are structurally varied, naturally occurring components of the cell walls and storage materials of a variety of plant and microbial species. In the human diet, mixed-linkage glucans [MLG - β-(1,3/4)-glucans] influence the gut microbiome and the host immune system. Although consumed daily, the molecular mechanism by which human gut Gram-positive bacteria utilize MLG largely remains unknown. In this study, we used Blautia producta ATCC 27340 as a model organism to develop understanding of MLG utilization. B. producta encodes a gene locus comprising a multi-modular cell-anchored endo-glucanase (BpGH16MLG), an ABC transporter, and a glycoside phosphorylase (BpGH94MLG) for utilizing MLG, as evidenced by the up-regulation of expression of the enzyme- and solute binding protein (SBP)-encoding genes in this cluster when the organism is grown on MLG. We determined that recombinant BpGH16MLG cleaved various types of β-glucan, generating oligosaccharides suitable for cellular uptake by B. producta. Cytoplasmic digestion of these oligosaccharides is then performed by recombinant BpGH94MLG and β-glucosidases (BpGH3-AR8MLG and BpGH3-X62MLG). Using targeted deletion, we demonstrated BpSBPMLG is essential for B. producta growth on barley β-glucan. Furthermore, we revealed that beneficial bacteria, such as Roseburia faecis JCM 17581T, Bifidobacterium pseudocatenulatum JCM 1200T, Bifidobacterium adolescentis JCM 1275T, and Bifidobacterium bifidum JCM 1254, can also utilize oligosaccharides resulting from the action of BpGH16MLG. Disentangling the β-glucan utilizing capability of B. producta provides a rational basis on which to consider the probiotic potential of this class of organism.
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May 2023
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Yue
Pang
,
Nils
Nöthling
,
Markus
Leutzsch
,
Liqun
Kang
,
Eckhard
Bill
,
Maurice
Van Gastel
,
Edward
Reijerse
,
Richard
Goddard
,
Lucas
Wagner
,
Daniel
Santalucia
,
Serena
Debeer
,
Frank
Neese
,
Josep
Cornella
Diamond Proposal Number(s):
[30449]
Abstract: Large Spin-Orbit Coupling (SOC) is an intrinsic property of the heavy-elements that directly affects the electronic structures of the compounds. Herein we report the synthesis and characterization of a mono-coordinate bismuthinidene featuring a rigid and bulky ligand. All magnetic measurements (SQUID, NMR) point to a diamagnetic compound. However, multiconfigurational quantum chemical calculations predict the ground state of the compound to be dominated (76%) by a spin-triplet. The apparent diamagnetism is explained by an extremely large SOC induced positive zero-field-splitting of more than 4500 cm−1 that leaves the MS = 0 magnetic sublevel thermally isolated in the electronic ground state.
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May 2023
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Open Access
Abstract: Calcium dialuminate, CaAl4O7, nanopowders with a grossite-type structure, doped with chromium ions, were synthesized via the combined sol–gel solution combustion method. The evolution of phase composition, crystal structure, and microstructural parameters of the nanocrystalline materials depending on the temperature of the thermal treatment was investigated via X-ray powder diffraction and applying the Rietveld refinement technique. The photoluminescent properties of CaAl4O7 nanophosphors activated with Cr3+ ions were studied over the temperature range of 4.5–325 K. The samples show deep red and near-infrared luminescence due to the 2E → 4A2 and 4T2 → 4A2 energy level transitions of Cr3+ ions under excitation in the two broad emission bands in the visible spectral region. The R lines emission reveals a strong temperature dependence. The feasibility of the material for non-contact luminescence sensing is investigated, and good sensitivity is obtained based on the (R2/R1) luminescence intensity ratio and the lifetime of the emission.
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May 2023
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Abstract: The epitaxial growth of anatase (001) films deposited by pulsed laser deposition (PLD) and molecular beam epitaxy (MBE) on SrTiO3 (001) (STO) single crystals has been studied using X-ray diffraction and surface sensitivity UHV techniques. The evolution of the strain represented by the microstrain and the change of the in-plane and out-of-plane lattice parameters with film growth temperature, the effect of the annealing temperature and the influence of the oxygen content of the film have been investigated.
The out-of-plane lattice strain shows a compressive (-0.2%) or expansive (+0.3%) behavior, in the range 600 - 900°C, for temperatures below or above 700°C, respectively. The in-plane lattice parameters, as well as the cell volume of the film, remain under compression over the entire temperature range explored.
PLD films grow into square islands that align with the surface lattice directions of the STO substrate. The maximum size of these islands is reached at growth temperatures close to 875-925°C. Film annealing at temperatures of 800°C or higher melts the islands into flat terraces. Larger terraces are reached at high annealing temperatures of 925°C for extended periods of 12 hours. This procedure allows flat surface terrace sizes of up to 650 nm to be achieved.
The crystalline quality achieved in anatase films prepared by PLD or MBE growth methods is similar. The two-step anatase growth process used during the synthesis of the films with both methods: film growth and post-annealing treatment in oxygen or air at ambient pressure, using temperature and time as key parameters, allows to control the surface terrace size and stoichiometry of the films, as well as the anatase/rutile intermixing rates at sufficiently high temperatures. This growth process could allow the substitution of their equivalent single crystals. The range of applicability of these films would include their use as structural and electronic model systems, or in harsh experimental conditions due to their low production cost.
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May 2023
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