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Jonathan
Youngs
,
Nicholas M.
Provine
,
Nicholas
Lim
,
Hannah R.
Sharpe
,
Ali
Amini
,
Yi-Ling
Chen
,
Jian
Luo
,
Matthew D.
Edmans
,
Panagiota
Zacharopoulou
,
Wentao
Chen
,
Oliver
Sampson
,
Robert
Paton
,
William J.
Hurt
,
David A.
Duncan
,
Anna L.
Mcnaughton
,
Vincent N.
Miao
,
Susannah
Leaver
,
Duncan L. A.
Wyncoll
,
Jonathan
Ball
,
Philip
Hopkins
,
Donal T.
Skelly
,
Eleanor
Barnes
,
Susanna
Dunachie
,
Graham
Ogg
,
Teresa
Lambe
,
Ian
Pavord
,
Alex K.
Shalek
,
Craig P.
Thompson
,
Luzheng
Xue
,
Derek C.
Macallan
,
Philip
Goulder
,
Paul
Klenerman
,
Tihana
Bicanic
Open Access
Abstract: Prior studies have demonstrated that immunologic dysfunction underpins severe illness in COVID-19 patients, but have lacked an in-depth analysis of the immunologic drivers of death in the most critically ill patients. We performed immunophenotyping of viral antigen-specific and unconventional T cell responses, neutralizing antibodies, and serum proteins in critically ill patients with SARS-CoV-2 infection, using influenza infection, SARS-CoV-2-convalescent health care workers, and healthy adults as controls. We identify mucosal-associated invariant T (MAIT) cell activation as an independent and significant predictor of death in COVID-19 (HR = 5.92, 95% CI = 2.49–14.1). MAIT cell activation correlates with several other mortality-associated immunologic measures including broad activation of CD8+ T cells and non-Vδ2 γδT cells, and elevated levels of cytokines and chemokines, including GM-CSF, CXCL10, CCL2, and IL-6. MAIT cell activation is also a predictor of disease severity in influenza (ECMO/death HR = 4.43, 95% CI = 1.08–18.2). Single-cell RNA-sequencing reveals a shift from focused IFNα-driven signals in COVID-19 ICU patients who survive to broad pro-inflammatory responses in fatal COVID-19 –a feature not observed in severe influenza. We conclude that fatal COVID-19 infection is driven by uncoordinated inflammatory responses that drive a hierarchy of T cell activation, elements of which can serve as prognostic indicators and potential targets for immune intervention.
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Sep 2021
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I09-Surface and Interface Structural Analysis
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Samuel P.
Jarvis
,
Hongqian
Sang
,
Filipe
Junqueira
,
Oliver
Gordon
,
Joe E. A.
Hodgkinson
,
Alex
Saywell
,
Philipp
Rahe
,
Salvatore
Mamone
,
Simon
Taylor
,
Adam
Sweetman
,
Jeremy
Leaf
,
David A.
Duncan
,
Tien-Lin
Lee
,
Pardeep K.
Thakur
,
Gabriella
Hoffman
,
Richard J.
Whitby
,
Malcolm H.
Levitt
,
Georg
Held
,
Lev
Kantorovich
,
Philip
Moriarty
,
Robert G.
Jones
Diamond Proposal Number(s):
[12979, 15022]
Open Access
Abstract: Molecular surgery provides the opportunity to study relatively large molecules encapsulated within a fullerene cage. Here we determine the location of an H2O molecule isolated within an adsorbed buckminsterfullerene cage, and compare this to the intrafullerene position of HF. Using normal incidence X-ray standing wave (NIXSW) analysis, coupled with density functional theory and molecular dynamics simulations, we show that both H2O and HF are located at an off-centre position within the fullerene cage, caused by substantial intra-cage electrostatic fields generated by surface adsorption of the fullerene. The atomistic and electronic structure simulations also reveal significant internal rotational motion consistent with the NIXSW data. Despite this substantial intra-cage interaction, we find that neither HF or H2O contribute to the endofullerene frontier orbitals, confirming the chemical isolation of the encapsulated molecules. We also show that our experimental NIXSW measurements and theoretical data are best described by a mixed adsorption site model.
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Sep 2021
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B07-C-Versatile Soft X-ray beamline: Ambient Pressure XPS and NEXAFS
I09-Surface and Interface Structural Analysis
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Jake
Seymour
,
Ekaterina
Gousseva
,
Alex
Large
,
Coby J.
Clarke
,
Peter
Licence
,
Richard M.
Fogarty
,
David A.
Duncan
,
Pilar
Ferrer
,
Federica
Venturini
,
Roger A.
Bennett
,
Robert G.
Palgrave
,
Kevin R. J.
Lovelock
Diamond Proposal Number(s):
[20463, 24304, 25929]
Open Access
Abstract: Ionic liquid (IL) valence electronic structure provides key descriptors for understanding and predicting IL properties. The ionisation energies of 60 ILs are measured and the most readily ionised valence state of each IL (the highest occupied molecular orbital, HOMO) is identified using a combination of X-ray photoelectron spectroscopy (XPS) and synchrotron resonant XPS. A structurally diverse range of cations and anions were studied. The cation gave rise to the HOMO for nine of the 60 ILs presented here, meaning it is energetically more favourable to remove an electron from the cation than the anion. The influence of the cation on the anion electronic structure (and vice versa) were established; the electrostatic effects are well understood and demonstrated to be consistently predictable. We used this knowledge to make predictions of both ionisation energy and HOMO identity for a further 516 ILs, providing a very valuable dataset for benchmarking electronic structure calculations and enabling the development of models linking experimental valence electronic structure descriptors to other IL properties, e.g. electrochemical stability. Furthermore, we provide design rules for the prediction of the electronic structure of ILs.
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Sep 2021
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Open Access
Abstract: Background: A significant portion of COVID-19 sufferers have asthma. The impacts of asthma on COVID-19 progression are still unclear but a modifying effect is plausible as respiratory viruses are acknowledged to be an important trigger for asthma exacerbations and a different, potentially type-2 biased, immune response might occur. In this study, we compared the blood circulating cytokine response to COVID-19 infection in patients with and without asthma. Methods: Plasma samples and clinical information were collected from 80 patients with mild (25), severe (36) or critical (19) COVID-19 and 29 healthy subjects at the John Radcliffe Hospital, Oxford, UK. The concentrations of 51 circulating proteins in the plasma samples were measured with Luminex and compared between groups. Results: Total 16 pre-existing asthma patients were found (3 in mild, 10 in severe, and 3 in critical COVID-19). The prevalence of asthma in COVID-19 severity groups did not suggest a clear correlation between asthma and COVID-19 severity. Within the same COVID-19 severity group, no differences were observed between patients with or without asthma on oxygen saturation, CRP, neutrophil counts, and length of hospital stay. The mortality in the COVID-19 patients with asthma (12.5%) was not higher than that in patients without asthma (17.2%). No significant difference was found between asthmatic and non-asthmatic in circulating cytokine response in different COVID-19 severity groups, including the cytokines strongly implicated in COVID-19 such as CXCL10, IL-6, CCL2, and IL-8. Conclusions: Pre-existing asthma was not associated with an enhanced cytokine response after COVID-19 infection, disease severity or mortality.
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Jul 2021
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I09-Surface and Interface Structural Analysis
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Peter
Knecht
,
Joachim
Reichert
,
Peter S.
Deimel
,
Peter
Feulner
,
Felix
Haag
,
Francesco
Allegretti
,
Manuela
Garnica
,
Martin
Schwarz
,
Willi
Auwärter
,
Paul T. P.
Ryan
,
Tien-Lin
Lee
,
David A.
Duncan
,
Ari Paavo
Seitsonen
,
Johannes V.
Barth
,
Anthoula Chrysa
Papageorgiou
Diamond Proposal Number(s):
[24320]
Open Access
Abstract: We assess the crucial role of tetrapyrrole flexibility in the CO ligation to distinct Ru‐porphyrins supported on an atomistically well‐defined Ag(111) substrate. Our systematic real space visualisation and manipulation experiments with scanning tunnelling microscopy directly probe the ligation, while bond‐resolving atomic force microscopy and X‐ray standing waves measurements characterise the geometry, X‐ray and ultraviolet photoelectron spectroscopy the electronic structure, and temperature programmed desorption the binding strength. Density functional theory calculations provide additional insight into the functional interface. We unambiguously demonstrate that the substituents regulate the interfacial conformational adaptability, either promoting or obstructing the uptake of axial CO adducts.
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May 2021
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I09-Surface and Interface Structural Analysis
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Peter
Knecht
,
Bodong
Zhang
,
Joachim
Reichert
,
David A.
Duncan
,
Martin
Schwarz
,
Felix
Haag
,
Paul
Ryan
,
Tien-Lin
Lee
,
Peter S.
Deimel
,
Peter
Feulner
,
Francesco
Allegretti
,
Willi
Auwärter
,
Guillaume
Médard
,
Ari Paavo
Seitsonen
,
Johannes V.
Barth
,
Anthoula C.
Papageorgiou
Diamond Proposal Number(s):
[24320]
Abstract: The controlled arrangement of N-heterocyclic carbenes (NHCs) on solid surfaces is a current challenge of surface functionalization. We introduce a strategy of using Ru porphyrins in order to control both the orientation and lateral arrangement of NHCs on a planar surface. The coupling of the NHC to the Ru porphyrin is a facile process which takes place on the interface: we apply NHCs as functional, robust pillars on well-defined, preassembled Ru porphyrin monolayers on silver and characterize these interfaces with atomic precision via a battery of experimental techniques and theoretical considerations. The NHCs assemble at room temperature modularly and reversibly on the Ru porphyrin arrays. We demonstrate a selective and complete functionalization of the Ru centers. With its binding, the NHC modifies the interaction of the Ru porphyrin with the Ag surface, displacing the Ru atom by 1 Å away from the surface. This arrangement of NHCs allows us to address individual ligands by controlled manipulation with the tip of a scanning tunneling microscope, creating patterned structures on the nanometer scale.
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Mar 2021
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|
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Open Access
Abstract: The adsorption configurations of a technologically relevant model organic adsorbate on the silicon (001) surface were studied using energy scanned X-ray photoelectron diffraction (PhD). Previous work has established the existence of an interesting vertically-aligned ("flagpole") configuration, where the acetophenone attaches to Si(001) via the acetyl group carbon and oxygen atoms. DFT calculations have predicted two energetically similar variants of this structure, where the phenyl ring is orientated parallel or perpendicular to the rows of silicon dimers on this reconstructed surface. However, previously published experimental measurements, including scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure investigations were unable to distinguish between these two configurations. Here, we apply the unique experimental capabilities of the PhD technique to this system and demonstrate that the dominant adsorption configuration has the phenyl ring parallel to the dimer rows (the end-bridge structure). This information in turn facilitates the determination of the dominant reaction pathway for acetophenone on Si(001), which has remained elusive until now. Information about subtle preferences in reaction pathways that affect the alignment and orientation of organic adsorbates such as acetophenone on technologically-relevant semiconductor surfaces such as Si(001) is critical for the fabrication of future atomically-precise atomic and molecular-scale electronic devices utilising the organic-silicon interface, and this work demonstrates the unique and complementary capabilities of PhD for providing this information.
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Feb 2021
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I09-Surface and Interface Structural Analysis
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Peter
Knecht
,
Paul T. P.
Ryan
,
David A.
Duncan
,
Li
Jiang
,
Joachim
Reichert
,
Peter S.
Deimel
,
Felix
Haag
,
Johannes T.
Kuchle
,
Francesco
Allegretti
,
Tien-Lin
Lee
,
Martin
Schwarz
,
Manuela
Garnica
,
Willi
Auwärter
,
Ari Paavo
Seitsonen
,
Johannes V.
Barth
,
Anthoula C.
Papageorgiou
Diamond Proposal Number(s):
[24320, 17634]
Abstract: The adsorption and monolayer self-assembly of functional metal–organic blocks on solid surfaces are critical for the physicochemical properties of these low-dimensional materials. Although modern microscopy tools are very sensitive to the lateral arrangement of such blocks, they are still unable to offer directly the complete structural analysis especially for nonplanar molecules containing different atoms. Here, we apply a combinatorial approach for the characterization of such interfaces, which enables unexpected insights. An archetypal metalloporphyrin on a catalytically active surface as a function of its molecular coverage and substituent arrangement is characterized by low-energy electron diffraction, scanning probe microscopy, X-ray photoelectron spectroscopy, normal-incidence X-ray standing waves, and density functional theory. We look into Ru tetraphenyl porphyrin (Ru-TPP) on Ag(111), which is also converted into its planarized derivates via surface-assisted cyclodehydrogenation reactions. Depending on the arrangement of the phenyl substituents, the Ru atoms have distinct electronic structures and the porphyrin macrocycles adapt differently to the surface: saddle shape (pristine Ru-TPP) or bowl shape (planarized Ru-TPP derivates). In all cases, the Ru atom resides close to the surface (2.59/2.45 Å), preferably located at hollow sites and in the interface between the plane of the porphyrin macrocycle and the Ag surface. For the more flexible pristine Ru-TPP, we identify an additional self-assembled structure, allowing the molecular density of the self-assembled monolayer to be tuned within ∼20%. This precise analysis is central to harnessing the potential of metalloporphyrin/metal interfaces in functional systems.
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Jan 2021
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Zishu
Wang
,
Kai
Qian
,
Murat Anil
Öner
,
Peter S.
Deimel
,
Yan
Wang
,
Shuai
Zhang
,
Xiaoxi
Zhang
,
Vishal
Gupta
,
Juan
Li
,
Hong-Jun
Gao
,
David A.
Duncan
,
Johannes V.
Barth
,
Xiao
Lin
,
Francesco
Allegretti
,
Shixuan
Du
,
Carlos-Andres
Palma
Abstract: Precisely layered molecular heterostructures are promising but still largely unexplored materials, with the potential to complement and enhance the scope of two-dimensional heterostructures. The controlled epitaxial growth of vertically stacked molecular layers connected through tailored linkers, can lead to significant development in the field. Here, we demonstrate that sequential assembly of prototypical iron porphyrins and axial ligands can be steered via temperature-programmed desorption, and monitored by mass spectrometry and by high-resolution atomic force microscopy under ultrahigh vacuum conditions. Complementary photoelectron spectroscopy analysis delivers chemical insight into the formation of layer-by-layer nanoarchitectures. Our temperature-directed methodology outlines a promising strategy for the in vacuo fabrication of precisely stacked, multicomponent (metal–organic) molecular heterostructures.
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Nov 2020
|
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I09-Surface and Interface Structural Analysis
|
Diamond Proposal Number(s):
[18752]
Open Access
Abstract: The on-surface synthesis of covalently bonded materials differs from solution-phase synthesis in several respects. The transition from a three-dimensional reaction volume to quasi-two-dimensional confinement, as is the case for on-surface synthesis, has the potential to facilitate alternative reaction pathways to those available in solution. Ullmann-type reactions, where the surface plays a role in the coupling of aryl-halide functionalised species, has been shown to facilitate extended one- and two-dimensional structures. Here we employ a combination of scanning tunnelling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and X-ray standing wave (XSW) analysis to perform a chemical and structural characterisation of the Ullmann-type coupling of two iodine functionalised species on a Ag(111) surface held under ultra-high vacuum (UHV) conditions. Our results allow characterisation of molecular conformations and adsorption geometries within an on-surface reaction and provide insight into the incorporation of metal adatoms within the intermediate structures of the reaction.
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Nov 2020
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