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269 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes

It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin’s role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Abbr. Final report: Self-assembled molecular containers as artificial water channels: towards biomimetic desalination membranes

Global water scarcity demands advances in desalination technologies that can deliver more fresh water with less energy. Current reverse osmosis membranes are fundamentally limited by a trade-off between how much water they can pass and how well they block salts. To address this challenge, we developed a bottom-up strategy to design and test artificial water channels that mimic the efficiency of biological proteins but are built from robust synthetic molecules. Over two years, we synthesized and evaluated more than twenty molecular channel candidates, including supramolecular macrocycles and nanographene pores with atomically precise structures. We showed that small chemical modifications allow direct control over pore size and chemistry, which in turn govern water permeability and salt rejection. In collaboration with university partners, we reported the first experimental demonstration of water transport through a nanographene pore, bridging a long-standing gap between simulation and experiment. Several of the artificial channels we developed achieved water–salt selectivity beyond conventional polymer membranes, highlighting their potential for next-generation desalination and precision separations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Competing Intermolecular and Molecule–Surface Interactions: Dipole–Dipole-Driven Patterns in Mixed Carborane Self-Assembled Monolayers

Carboranedithiol isomers adsorbing with opposite orientations of their dipoles on surfaces are self-assembled together to form mixed monolayers where both lateral dipole–dipole and lateral thiol–thiolate (S–H···S) interactions provide enhanced stability over single-component monolayers. Here, we demonstrate the first instance of the ability to map individual isomers in a mixed monolayer using the model system carboranedithiols on Au{111}. The addition of methyl groups to one isomer provides both an enhanced dipole moment and extra apparent height for differentiation via scanning tunneling microscopy (STM). Associated computational investigations rationalize favorable interactions of mixed pairs and the associated stability changes that arise from these interactions. Both STM images and Monte Carlo simulations yield similarly structured mixed monolayers, where approximately 10% of the molecules have reversed dipole moment orientations but no direct chemical attachment to the surface, leading to homogeneous monolayers with no apparent phase separation. Deprotonating the thiols by depositing the molecules under basic conditions eliminates the lateral S–H···S interactions while accentuating the dipole–dipole forces. The molecular system investigated is composed of isomeric molecules with opposite orientations of dipoles and identical surface packing, which enables the mapping of individual molecules within the mixed monolayers and enables analyses of the contributions of the relatively weak lateral interactions to the overall stability of the assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes

NLRP1 and CARD8 are related cytosolic sensors that upon activation form supramolecular signalling complexes known as canonical inflammasomes, resulting in caspase-1 activation, cytokine maturation and/or pyroptotic cell death. NLRP1 and CARD8 use their C-terminal (CT) fragments containing a caspase recruitment domain (CARD) and the UPA (conserved in UNC5, PIDD, and ankyrins) subdomain for self-oligomerization, which in turn form the platform to recruit the inflammasome adaptor ASC (apoptosis-associated speck-like protein containing a CARD) or caspase-1, respectively. Here, we report cryo-EM structures of NLRP1-CT and CARD8-CT assemblies, in which the respective CARDs form central helical filaments that are promoted by oligomerized, but flexibly linked, UPAs surrounding the filaments. Through biochemical and cellular approaches, we demonstrate that the UPA itself reduces the threshold needed for NLRP1-CT and CARD8-CT filament formation and signalling. Structural analyses provide insights on the mode of ASC recruitment by NLRP1-CT and the contrasting direct recruitment of caspase-1 by CARD8-CT. We also discover that subunits in the central NLRP1 CARD filament dimerize with additional exterior CARDs, which roughly doubles its thickness and is unique among all known CARD filaments. Finally, we engineer and determine the structure of an ASC CARD –caspase-1 CARD octamer, which suggests that ASC uses opposing surfaces for NLRP1, versus caspase-1, recruitment. Together these structures capture the architecture and specificity of the active NLRP1 and CARD8 inflammasomes in addition to key heteromeric CARD-CARD interactions governing inflammasome signalling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tubulin Double Helix: Lateral and Longitudinal Curvature Changes of Tubulin Protofilament

By virtue of their native structures, tubulin dimers are protein building blocks that are naturally pre-programmed to assemble into cytoskeletal polymers known as microtubules (MTs). Here we demonstrate polycation-directed (i.e. electrostatically tunable) assembly of tubulins through tubulin protofilament conformational changes in the longitudinal and lateral directions, creating novel tubulin double helices and various tubular architectures. Synchrotron small angle X-ray scattering and transmission electron microscopy reveal a remarkable range of nanoscale assembly structures: single- and double-layered double-helix tubulin tubules. The phase transitions from MTs into the new assemblies are dependent on the size and concentration of polycations. Two characteristic scales that determine the number of observed phases are the size of polycation compared to the size of tubulin (≈4 nm) and MT diameter (≈25 nm). This work suggests the feasibility of “programmable breakdown” of protein nanotubes, tearing MTs into double-stranded tubulins and building up previously undiscovered nanostructures, by using polycations with scissor- and glue-like properties. Importantly, we define a new role of tubulins as two-dimensionally shape-controllable building blocks for novel supramolecular architectures. Furthermore, these findings provide insight into the design of protein-based functional materials, for example, as metallization templates for nanoscale electronic devices, kinesin motor-driving molecular screws, and anticancer drug delivery vehicles.

2D shape‐control↗
DOE OSTI2025

Encapsulation Enhances the Quantum Coherence of a Solid‐State Molecular Spin Qubit

Spins within molecules benefit from the atomistic control of synthetic chemistry for the realization of qubits. One advantage is that the quantum superpositions of the spin states encoding the qubit can be coherently manipulated using electromagnetic radiation. The main challenge is the fragility of these superpositions when qubits are to partake of solid-state devices. We address this issue with a supramolecular approach for protecting molecular spin qubits against decoherence. The molecular qubit [Cr(ox)3]3- has been encapsulated inside the diamagnetic triple-stranded helicate [Zn2L3]4+ (L is a bis-pyrazolylpyridine ligand). The quantum coherence of the protected qubit is then analyzed with pulsed EPR spectroscopy and compared with the unprotected qubit, both in solution and in the solid state. Crucially, the spin-spin relaxation in the solid state has been examined within diamagnetic crystal lattices of the isostructural ([Al(ox)3]@[Zn2L3])+ or [Al(ox)3]3- assemblies, respectively, doped with the Cr3+ qubit in two different (<10%) concentrations. The study unveils a surprising increase of the phase memory time of the qubit upon encapsulation only in the solid. Spin-lattice relaxation times also exhibit a significant enhancement, as established from inversion recovery pulse sequences and from slow relaxation of the magnetization of the protected qubit, not featured by the free qubit.

Swain, Abinash↗
DOE OSTI2021

Investigation of Nucleation and Growth at a Liquid–Liquid Interface by Solvent Exchange and Synchrotron Small-Angle X-Ray Scattering

Hybrid nanomaterials possess complex architectures that are driven by a self-assembly process between an inorganic element and an organic ligand. The properties of these materials can often be tuned by organic ligand variation, or by swapping the inorganic element. This enables the flexible fabrication of tailored hybrid materials with a rich variety of properties for technological applications. Liquid-liquid interfaces are useful for synthesizing these compounds as precursors can be segregated and allowed to interact only at the interface. Although procedurally straightforward, this is a complex reaction in an environment that is not easy to probe. Here, we explore the interfacial crystallization of mithrene, a supramolecular multi-quantum well. This material sandwiches a well-defined silver-chalcogenide layer between layers of organic ligands. Controlling mithrene crystal size and morphology to be useful for applications requires understanding details of its crystal growth, but the specific mechanism for this reaction remain only lightly investigated. We performed a study of mithrene crystallization at an oil-water interfaces to elucidate how the interfacial free energy affects nucleation and growth. We exchanged the oil solvent on the basis of solvent viscosity and surface tension, modifying the dynamic contact angle and interfacial free energy. We isolated and characterized the reaction byproducts via scanning electron microscopy (SEM). We also developed a high-throughput small angle X-ray scattering (SAXS) technique to measure crystallization at short reaction timescales (minutes). Our results showed that modifying interfacial surface energy affects both the reaction kinetics and product size homogeneity and yield. Our SAXS measurements reveal the onset of crystallinity after only 15 min. These results provide a template for exploring directed synthesis of complex materials via experimental methods.

Schriber, Elyse A.↗
DOE OSTI2022

Assembling Phenothiazine into a Porous Coordination Cage to Improve Its Photocatalytic Efficiency for Organic Transformations

Abstract Photo‐catalysis by small‐molecules is often limited by catalyst degradation and low electron‐transfer efficiency. Herein we report a stable N‐phenyl‐phenothiazine (PTH)‐derived porous coordination cage (PCC) as a highly efficient photocatalyst. By the incorporation of the photocatalytic PTH moiety into a PCC, aggregation‐induced quenching (AIQ) was shown to be reduced. An improvement in catalyst stability was discovered, ascribed to the synergistic effects of the PTH moieties. The catalyst, operating through a photolytic single‐electron transfer, was utilized for photo‐catalyzed dehalogenation and borylation. Evaluation of the catalytic mechanism in the borylation reaction showed that the improved performance results from the more efficient formation of the electron donor‐acceptor (EDA) complex with the cage. This discovery provides a potential strategy to improve the photophysical properties and stabilities of small‐molecule organic photocatalysts via supramolecular chemistry.

Chemistry↗
DOE OSTI2025

Anion Binding by Macrocyclic Receptors: Computational Landscape of 1:1 and 2:1 Stoichiometries

Macrocyclic receptors play a crucial role in supramolecular chemistry, enabling the selective binding of guest molecules through non-covalent interactions. This study investigates the anion binding properties of three shape-persistent macrocycles, triazolophane, cyanostar, and tricarb, each featuring preorganized cavities with polarized CH hydrogen bond donors. In the 1:1 binding stoichiometries, the macrocycles preferentially bind anions that fit inside their two-dimensional cavities, with this preference being more pronounced in solution. Specifically, the triazolophane favors smaller anions like chloride and bromide, while the larger cavities offered by cyanostar and tricarb macrocycles preferentially bind the larger iodide. For large, polyatomic anions (SCN − , BF$^{−}_{4}$, ClO$^{−}_{4}$, and PF$^{−}_{6}$), the macrocycles self-assemble to form stable 2:1 sandwich complexes, exhibiting stronger binding. This shift in selectivity highlights the versatility of the macrocycles, making them promising candidates for anion sensing and regulation with various complexation stoichiometries.

Che, Minwei [Indiana University, Bloomington, IN (↗
DOE OSTI2025

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing the local conformation of the unit cell, which further impacts the dimensionality of hierarchical structures. Moreover, these fibers were readily functionalized with biological ligands to afford one-dimensional (1D) protein arrays. This approach for the high-precision bottom-up assembly of ultranarrow 1D nanostructures offers significant potential for developing novel biomimetic nanostructures.

Lee, Yen Jea↗
DOE OSTI2020

Supramolecular and Hybrid Bonding Polymers

Staudinger established a century ago the existence of covalent macromolecules, work that led to the development of transformative materials of great benefit to society and a “quantum leap” in our understanding of biological systems. Over the past few decades the concept of supramolecular polymers has emerged–chemical systems in which structural units bond strongly to each other non-covalently. Herein, we discuss how these dynamic systems actually exist in the natural world and can create soft materials with structures, properties, and functions beyond the ones we know in Staudinger polymers. We reflect here on the potential of novel systems in which covalent and supramolecular polymers are chemically integrated and describe them as hybrid bonding polymers. This paper describes the concept with recent examples from the Stupp laboratory, and discusses their potential functions as robotic materials that mimic living matter and structures that offer new ideas on how to recycle and reuse soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Direct-write orientation of charge-transfer liquid crystals enables polarization-based coding and encryption

Abstract Optical polarizers encompass a class of anisotropic materials that pass-through discrete orientations of light and are found in wide-ranging technologies, from windows and glasses to cameras, digital displays and photonic devices. The wire-grids, ordered surfaces, and aligned nanomaterials used to make polarized films cannot be easily reconfigured once aligned, limiting their use to stationary cross-polarizers in, for example, liquid crystal displays. Here we describe a supramolecular material set and patterning approach where the polarization angle in stand-alone films can be precisely defined at the single pixel level and reconfigured following initial alignment. This capability enables new routes for non-binary information storage, retrieval, and intrinsic encryption, and it suggests future technologies such as photonic chips that can be reconfigured using non-contact patterning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Supramolecular meso -Trick: Ambidextrous Mirror Symmetry Breaking in a Liquid Crystalline Network with Tetragonal Symmetry

Bicontinuous and multicontinuous network phases are among nature's most complex structures in soft matter systems. Here, a chiral bicontinuous tetragonal phase is reported as a new stable liquid crystalline intermediate phase at the transition between two cubic phases, the achiral double gyroid and the chiral triple network cubic phase with an I 23 space group, both formed by dynamic networks of helices. The mirror symmetry of the double gyroid, representing a meso -structure of two enantiomorphic networks, is broken at the transition to this tetragonal phase by retaining uniform helicity only along one network while losing it along the other one. This leads to a conglomerate of enantiomorphic tetragonal space groups, P 4 1 2 1 2 and P 4 3 2 1 2. Phase structures and chirality were analyzed by small-angle X-ray scattering (SAXS), grazing-incidence small-angle X-ray scattering (GISAXS), resonant soft X-ray scattering (RSoXS) at the carbon K-edge, and model-dependent SAXS/RSoXS simulation. In conclusion, our findings not only lead to a new bicontinuous network-type three-dimensional mesophase but also reveal a mechanism of mirror symmetry breaking in soft matter by partial meso -structure racemization at the transition from enantiophilic to enantiophobic interhelical self-assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Insights into water extraction and aggregation mechanisms of malonamide-alkane mixtures

Structure at the nanoscale in the organic phase of liquid–liquid extraction systems is often tied to separation performance. However, the weak interactions that drive extractant assembly lead to poorly defined structures that are challenging to identify. Here, in this work, we investigate the mechanism of water extraction for a malonamide extractant commonly applied to f-element separations. We measure extractant concentration fluctuations in the organic phase with small angle X-ray scattering (SAXS) before and after contact with water at fine increments of extractant concentration, finding no qualitative changes upon water uptake that might suggest significant nanoscopic reorganization of the solution. The critical composition for maximum fluctuation intensity is consistent with small water–extractant adducts. The extractant concentration dependence of water extraction is consistent with a power law close to unity in the low concentration regime, suggesting the formation of 1 : 1 water–extractant adducts as the primary extraction mechanism at low concentration. At higher extractant concentrations, the power law slope increases slightly, which we find is consistent with activity effects modeled using Flory–Huggins theory without introduction of additional extractant–water species. Molecular dynamics simulations are consistent with these findings. The decrease in interfacial tension with increasing extractant concentration shows a narrow plateau region, but it is not correlated with any change in fluctuation or water extraction trends, further suggesting no supramolecular organization such as reverse micellization. This study suggests that water extraction in this system is particularly simple: it relies on a single mechanism at all extractant concentrations, and only slightly enhances the concentration fluctuations characteristic of the dry binary extractant/diluent mixture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Spin-dependent charge transmission through chiral 2T3N self-assembled monolayer on Au

In this study, a gold surface is functionalized by chemisorption of the enantiopure N,N'-bis-[2,2';5',2"]tert-thiophene-5-yl methylcyclohexane-1,2-diamine (2T3N), a chiral oligothiophene derivative, via overnight incubation in a 2T3N ethanol solution. The Au|2T3N interface is characterized by x-ray photoelectron circular dichroism and comparing x-ray photoemission spectroscopy and electro-desorption results. Charge transmission at the Au|2T3N| solution interface is characterized by recording the cyclic voltammetry of the Fe(III)/Fe(II) reversible redox couple, finding a charge transfer rate constant, k°, variation from 1 × 10 -1 to 3.3 × 10 -2 cm s -1 , when comparing the bare Au and the Au|2T3N interfaces, respectively. The “anomalous” high value of k° found for the chiral Au|2T3N interface can be rationalized on the basis of the chiral-induced spin selectivity effect, as further proved by magnetic–conductive atomic force microscopy measurements at room temperature. A spin polarization of about 30% is found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Two-photon excited deep-red and near-infrared emissive organic co-crystals

Abstract Two-photon excited near-infrared fluorescence materials have garnered considerable attention because of their superior optical penetration, higher spatial resolution, and lower optical scattering compared with other optical materials. Herein, a convenient and efficient supramolecular approach is used to synthesize a two-photon excited near-infrared emissive co-crystalline material. A naphthalenediimide-based triangular macrocycle and coronene form selectively two co-crystals. The triangle-shaped co-crystal emits deep-red fluorescence, while the quadrangle-shaped co-crystal displays deep-red and near-infrared emission centered on 668 nm, which represents a 162 nm red-shift compared with its precursors. Benefiting from intermolecular charge transfer interactions, the two co-crystals possess higher calculated two-photon absorption cross-sections than those of their individual constituents. Their two-photon absorption bands reach into the NIR-II region of the electromagnetic spectrum. The quadrangle-shaped co-crystal constitutes a unique material that exhibits two-photon absorption and near-infrared emission simultaneously. This co-crystallization strategy holds considerable promise for the future design and synthesis of more advanced optical materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Plutonium Hybrid Materials: A Platform to Explore Assembly and Metal–Ligand Bonding

In this work, we report the synthesis of five new hybrid materials containing the [PuCl 6 ] 2- anion and charge balancing, non-covalent interaction donating 4-X-pyridinium (X = H, Cl, Br, I) cations. Single crystals of the title compounds were grown and harvested from acidic, chloride-rich, aqueous media and their structures were determined via X-ray diffraction. Compounds 1-4, (4XPyH) 2 [PuCl 6 ] and 5, (4IPyH) 4 [PuCl 6 ] · 2Cl, exhibit two distinct sheet-like structure types. Structurally relevant non-covalent interactions were tabulated from crystallographic data and verified computationally using electrostatic surface potential maps and the quantum theory of atoms in molecules (QTAIM) approach. The strength of the hydrogen and halogen bonds was quantified using Kohn-Sham density functional theory and a hierarchy of acceptor-donor pairings established. In turn, the PuIV-Cl bonds were studied using the QTAIM and natural localized molecular orbital (NLMO) approaches to delineate the underlying bond mechanism and hybrid atomic orbital contributions therein. Energy decomposition (ED) and natural ED analyses were also explored to probe the bond mechanism and, more broadly, explore the efficacy of these techniques in studying these anionic systems. The results of the PuIV-Cl bond analyses were compared across composition via analogous treatments of previously reported [PuO 2 Cl 4 ] 2- and [PuCl 3 (H 2 O) 5 ] molecular units. In summary, our study indicates that the Pu-Cl bonds are predominately ionic, yet exhibit small varying degrees of covalent character that increase from [PuCl 3 (H 2 O) 5 ], [PuO 2 Cl 4 ] 2- , to [PuCl 6 ] 2- , while the participation of the Pu based s/d and f orbitals concurrently decrease and increase, respectively.

transuranic↗