B21-High Throughput SAXS
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Diamond Proposal Number(s):
[23750]
Open Access
Abstract: Histatin 5 (Hst5) is a histidine-rich intrinsically disordered protein (IDP) whose biological function arises from a highly heterogeneous conformational ensemble and environmental sensitivity. Unlike structured antimicrobial peptides that rely on persistent secondary motifs, Hst5 remains disordered across a wide range of conditions, enabling continuous adaptation to changes in pH, ionic strength, metal-ion concentration, macromolecular crowding, and interfaces such as membranes and mineral surfaces. Recent advances in small-angle X-ray scattering (SAXS), neutron-based methods, and surface-sensitive techniques, combined with computer simulations, have allowed quantitative characterization of Hst5′s ensemble structure, thermodynamics, and interactions. This work synthesizes current understanding of how intrinsic disorder, charge regulation, histidine chemistry, and multiscale interactions govern Hst5 behavior. Beyond its biological relevance, Hst5 has emerged as a benchmark system for elucidating general physicochemical principles of IDPs and for testing integrative and machine-learning approaches that map sequence features to ensemble architecture.
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Mar 2026
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[35585]
Open Access
Abstract: The self-assembly in aqueous solution and conformation of lipopeptides C16-WKK, C16-KWK, C16-YKK and C16-KYK is compared and examined. Remarkable differences are observed among the systems despite the small sequence changes comparing C16-XKK with the C16-KXK homologue (X = W or Y), depending on pH. These are rationalized using a molecular theory for amphiphile self-assembly (MOLT) to predict the morphology along with atomistic molecular dynamics simulations to probe local conformation and packing, along with new experimental data from small-angle X-ray scattering (SAXS) and FTIR spectroscopy. MOLT correctly describes the high-pH morphology behavior, i.e., fibrils for C16-XKK, and lamellar nanotapes for C16-KXK, although it predicts micelles for all systems at low pH, whereas experiments indicate that this only occurs for the C16-XKK lipopeptides, not the C16-KXK, which form lamellar nanotapes stable over an extended range of pH 2–12. Atomistic MD reveals β-sheet conformation is more favored for the C16-XKK lipopeptides which also have enhanced aggregation propensity compared to C16-KXK analogues. The extent of π-stacking was higher for the latter lamellar nanotape structures. The extent of hydrogen bonding is higher for the tyrosine-containing molecules than the tryptophan-based ones. The combination of a molecular theory and atomistic MD provides a comprehensive insight into the remarkable sequence- and pH-dependent molecular ordering within these model lipopeptides which will enable the rational design of future peptide amphiphiles with targeted nanostructures for desired applications.
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Dec 2025
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Jackson
Lederer
,
Martin
Centurion
,
Lauren
Bertram
,
Lisa
Huang
,
Surjendu
Bhattacharyya
,
Sebastien
Boutet
,
Xinxin
Cheng
,
Stuart W.
Crane
,
Robert J.
England
,
Martin
Graßl
,
Lauren
Heald
,
Fuhao
Ji
,
Patrick
Kramer
,
Huynh
Van Sa Lam
,
Kirk
Larsen
,
Cuong
Le
,
Ming-Fu
Li
,
Yusong
Liu
,
Kenneth
Lopata
,
Mike
Minitti
,
Sri
Bhavya Muvva
,
J. Pedro F.
Nunes
,
Zane
Phelps
,
Sharon
Santhamma Philip
,
Krishna
Khakurel
,
Alexander
Hume Reid
,
Daniel
Rolles
,
Artem
Rudenko
,
Sajib
Kumar Saha
,
John
Searles
,
Xiaozhe
Shen
,
Jiayue
Wang
,
Stephen P.
Weathersby
,
Peter M.
Weber
,
Thomas J. A.
Wolf
,
Yanwei
Xiong
,
Tianzhe
Xu
,
Longteng
Yun
,
Haoran
Zhao
,
Adam
Kirrander
,
Jie
Yang
Abstract: Conjugated cyclic organic molecules are common across many fields such as pharmaceuticals, are naturally occurring in biological systems, and are used in synthetic materials. One particular area of interest from a photochemical point of view is the formation of highly strained cyclic organics. We investigate the photoinduced reaction of cyclopentadiene, a five-membered organic ring molecule, which can form strained three and four carbon rings after photoexcitation with UV light, with the gas-phase ultrafast electron diffraction instrument at the SLAC MeV-UED facility. Electron diffraction offers a direct probe sensitive to the nuclear geometry during the reaction, allowing for the determination of the distribution of products formed following photoexcitation. We observe the simultaneous formation of the highly strained ring-closed bicyclo[2.1.0]pentene and vibrationally hot cyclopentadiene within the temporal resolution of the experiment and determine the relative yield of all reaction products. The experimental results are in good agreement with the predictions of trajectory simulations.
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Nov 2025
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[28022]
Open Access
Abstract: The mixing of Guanosine (Gua) and Guanosine 5′-monophosphate (GMP) in water in selected compositions yields highly hydrated, transparent, and self-healing self-assembled supramolecular G-hydrogels, attractive for biomedical applications. This work investigates how hydrogel composition affects solute transport, including diffusion, binding, loading, and release properties, using a set of fluorescent probes with varying size and polarity. Although small/wide-angle X-ray scattering techniques showed that no structural changes are induced by probe addition, even when intercalation into G-quadruplexes is expected, the internal mesh structure of the hydrogel, modulated by the Gua:GMP ratio, directly impacts probe diffusivity and loading. Tighter networks (e.g., 1:1) slow diffusion and enhance retention compared to looser configurations (e.g., 1:4). Moreover, UV–visible titrations revealed markedly different binding affinities (Kb ≈ 5.7 × 104 M–1 for DAPI, 8.0 × 103 M–1 for ThT, and 1.4 × 102 M–1 for RhB), which are expected to result in lower diffusion coefficients and slower release, especially for DAPI and ThT. Indeed, diffusion coefficients, obtained via fluorescence recovery after photobleaching and time-resolved fluorescence spectroscopy, reach 90, 20, and 60 μm2/s for FITC-dextran, ThT, and RhB, respectively. Probe release kinetics, modeled via Weibull fitting, indicated sustained release with characteristic times (τ) between 9.6 and 23.2 h and β ≈ 1 in 1× PBS, consistent with predominantly Fickian diffusion. Remarkably, switching to 10× PBS significantly accelerated release (τ reduced by ≈ 40–50%), suggesting that ionic strength and/or pH changes critically affect not only probe-hydrogel interactions but also the internal gel architecture, altering porosity, mesh size, and network tortuosity, thus enhancing molecular mobility. Overall, the G-hydrogel system offers a structurally tunable and composition-dependent platform capable of finely regulating molecular transport and release profiles, making it highly suitable for controlled drug delivery and adaptive biomaterial applications.
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May 2025
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Open Access
Abstract: Combined density functional theory (DFT) and X-ray standing wave (XSW) studies have previously provided evidence for the preferential adoption of an inverted conformation of 2H-TPP on Cu(111) in contrast to the saddle conformation usually favored by porphyrin molecules adsorbed on metals. We experimentally demonstrate, via X-ray photoelectron spectroscopy (XPS) analysis, that the binding energies of the aminic and iminic nitrogen species provide a spectral fingerprint for both inverted and saddle conformations, as predicted by DFT studies. Our complementary scanning tunneling microscopy (STM) characterization also reveals conversion from the saddle to inverted conformation at an elevated temperature for an analogous porphyrin species (Br2TPP).
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May 2025
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I06-Nanoscience (XPEEM)
I09-Surface and Interface Structural Analysis
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Yiru
Zhu
,
Zhepeng
Zhang
,
Ye
Wang
,
Soumya
Sarkar
,
Yang
Li
,
Han
Yan
,
Larissa
Ishibe-Veiga
,
Anita
Bagri
,
Ziwei J.
Yang
,
Hugh
Ramsden
,
Goki
Eda
,
Robert L. Z.
Hoye
,
Yan
Wang
,
Manish
Chhowalla
Diamond Proposal Number(s):
[36685, 33391]
Open Access
Abstract: Chalcogen vacancy defects in monolayer transition metal dichalcogenides form in-gap states that can trap excitons, leading to defect-mediated photoluminescence (PL) emission. Here, we show that room-temperature (RT, 300 K) PL from sulfur vacancies in defective monolayer MoS2 is sensitive to doping from dielectric substrates such as SiO2 and HfO2. The defect-mediated PL is observed for monolayer MoS2 on untreated HfO2 but is quenched on untreated SiO2, which is attributed to electron doping of MoS2 on SiO2. Electron doping of MoS2 is confirmed by Raman and synchrotron X-ray photoelectron spectroscopy. Annealing of the SiO2 substrate modifies its surface states, which is reflected in the recovery of the defect-mediated PL emission. The role of substrate-induced doping on sulfur vacancy-mediated PL is further supported by gate-dependent PL measurements. Our results suggest that excess electrons fill the defect energy states from sulfur vacancies in MoS2, reducing the probability of photoexcited carrier occupation and subsequent defect-mediated emission.
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Apr 2025
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I09-Surface and Interface Structural Analysis
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Jake M.
Seymour
,
Ekaterina
Gousseva
,
Lewis G.
Parker
,
Frances K.
Towers Tompkins
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Richard M.
Fogarty
,
Lennart
Frankemoelle
,
Rebecca
Rowe
,
Coby J.
Clarke
,
David A.
Duncan
,
Robert G.
Palgrave
,
Roger A.
Bennett
,
Patricia A.
Hunt
,
Kevin R. J.
Lovelock
Diamond Proposal Number(s):
[20463]
Open Access
Abstract: Liquid-phase d10s2 post-transition metal anions, such as [SnCl3]−, appear in a range of applications with a focus on catalysis and material preparation. However, little is known about their electronic structure and how it relates to reactivity. Using X-ray photoelectron spectroscopy and ab initio calculations, we demonstrate that liquid-phase d10s2 post-transition metal anions can act as dual-mode Lewis bases, interacting through the metal center and/or the ligands, with the interaction mode depending on the identity of the Lewis acid/electron acceptor. The Lewis basicity of the metal donor atom is controlled mainly by the metal identity; the ligand can be used for fine-tuning. Changing the metal center has a strong effect on the ligand basicity. These findings provide insight into d10s2 post-transition metal anion electronic structure, which will enable better molecular-level design of catalytic systems.
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Mar 2025
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[34748]
Abstract: We present a structural characterization of a low-transition-temperature mixture (LTTM), consisting of thymol and carvacrol, at an equimolar ratio. Carvacrol and thymol are natural regioisomers of terpenes. When combined at an equimolar ratio, they form a liquid mixture at room temperature, with supercooling capability and glass transition at ca. 210 K. Using small- and wide-angle X-ray scattering and molecular dynamics, we describe the structural complexity within this system. X-ray scattering reveals a low-Q peak at around 0.6 Å–1, indicating the existence of mesoscale structural heterogeneities, likely related to the segregation of polar moieties engaged in hydrogen bond (HB) interactions within an aromatic, apolar matrix. These polar interactions are predominantly a result of HBs involving thymol as the HB donor species. The liquid structure is also driven by O–H···π interactions, prevalently due to the ability of the carvacrol π-site to engage in this type of weak interaction as a HB acceptor. Besides, dispersive interactions affect the local arrangement of molecules, with a propensity of carvacrol rings to orient their first neighbors with a perpendicular orientation, while thymol tends to induce a closer approach of other thymol molecules with a preferential parallel alignment. Overall, we observed a complex structural arrangement driven by the interplay of both conventional and weak hydrogen bond interactions, with the aromatic nature of the compounds playing a pivotal role in shaping the system’s architecture. Carvacrol and thymol, despite being very similar compounds, are characterized by distinctly different behavior in terms of the interactions they engage in with their neighbors, likely due to the different steric hindrance experienced by their hydroxyl groups, which are close to either a small methyl or a bulky isopropyl group, respectively. Such observations can provide useful hints to develop new solvents with tailored properties.
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Mar 2025
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I11-High Resolution Powder Diffraction
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Rachael
Hamp
,
Christoph G.
Salzmann
,
Zachary
Amato
,
Milz L.
Beaumont
,
Hannah E.
Chinnery
,
Peter
Fawdon
,
Thomas F.
Headen
,
Paul F.
Henry
,
Liam
Perera
,
Stephen P.
Thompson
,
Mark G.
Fox-Powell
Diamond Proposal Number(s):
[36314]
Open Access
Abstract: Sodium chloride (NaCl) plays an important role in geochemistry, biology, industry, and food production, and it is among the most common salts in the solar system. Here, we report the discovery of a metastable NaCl dihydrate formed through rapid freezing (101–102 K s–1) of a NaCl solution at ambient pressure. Using synchrotron X-ray and neutron powder diffraction, we show that it transforms irreversibly to hydrohalite and ice Ih above 190 K upon heating and propose it is structurally related to hydrohalite with a 3 × 1 × 3 supercell as its unit cell. Calorimetric analyses reveal that the new hydrate transforms to hydrohalite with a heat release of −3.47 ± 0.55 kJ mol–1. The identification of this new NaCl dihydrate on the surfaces of icy worlds such as the moons of Jupiter and Saturn could indicate regions of recent activity where subsurface brines have frozen rapidly, priority targets for upcoming planetary missions.
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Dec 2024
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I09-Surface and Interface Structural Analysis
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Dennis
Meier
,
Peter
Knecht
,
Pablo
Vezzoni Vicente
,
Fulden
Eratam
,
Hongxiang
Xu
,
Tien-Lin
Lee
,
Alexander
Generalov
,
Alexander
Riss
,
Biao
Yang
,
Francesco
Allegretti
,
Peter
Feulner
,
Joachim
Reichert
,
Johannes V.
Barth
,
Ari Paavo
Seitsonen
,
David A.
Duncan
,
Anthoula C.
Papageorgiou
Diamond Proposal Number(s):
[30095]
Open Access
Abstract: Metalloporphyrins on interfaces offer a rich playground for functional materials and hence have been subjected to intense scrutiny over the past decades. As the same porphyrin macrocycle on the same surface may exhibit vastly different physicochemical properties depending on the metal center and its substituents, it is vital to have a thorough structural and chemical characterization of such systems. Here, we explore the distinctions arising from coverage and macrocycle substituents on the closely related ruthenium octaethyl porphyrin and ruthenium tetrabenzo porphyrin on Ag(111). Our investigation employs a multitechnique approach in ultrahigh vacuum, combining scanning tunneling microscopy, low-energy electron diffraction, photoelectron spectroscopy, normal incidence X-ray standing wave, and near-edge X-ray absorption fine structure, supported by density functional theory. This methodology allows for a thorough examination of the nuanced differences in the self-assembly, substrate modification, molecular conformation and adsorption height.
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Dec 2024
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