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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Constraining Flexibility in the MIL-88 Topology through Integration of 3-Dimensional Linkers

Metal–organic frameworks (MOFs) are a class of crystalline, nanoporous materials that are recognized for their tunability. While some MOFs demonstrate flexibility, this characteristic can pose challenges in achieving precise pore control or establishing permanent porosity. Specifically, MIL-88B, is notable for its high flexibility, as it is constructed from metal trimer clusters and 2-dimensional linkers (2DLs) featuring planar, aromatic cores, allowing significant structural changes. In this study, we synthesized two new MOFs, NU-2010 and NU-2011, which are structurally analogous to MIL-88B but incorporate ditopic 3-dimensional linkers (3DLs) with sterically bulky cores and higher symmetry. Our aim was to investigate whether the introduction of 3DLs could mitigate the flexibility observed in MIL-88B. We employed a combination of single crystal and powder X-ray diffraction techniques to assess the flexibility of MIL-88B, NU-2010, and NU-2011 under various conditions including thermal activation, solvent exchange, and temperature changes. Furthermore, our findings indicate that incorporating 3DLs significantly reduces framework flexibility in NU-2010 and NU-2011 relative to MIL-88B.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Confinement-controlled selective CO 2 insertion into a dicopper dihydride core: A multiscale mechanistic study

CO 2 is an abundant C 1 feedstock for fuel and chemical synthesis. We have previously demonstrated experimentally a stepwise insertion of CO 2 into a [Cu 2 H 2 ] core via a solid–gas in crystallo reaction, forming formate species that are unstable and inaccessible under solution-phase conditions. This work elucidates how structural confinement within the crystal lattice enables such selective reactivity. In particular, co-crystallized tetrahydrofuran molecules induce site asymmetry around the [Cu 2 H 2 ] unit, modulating both the local electronic environment and CO 2 diffusion pathways. Using a multiscale computational approach that combines classical molecular mechanics, hybrid quantum mechanics/molecular mechanics molecular dynamics, and enhanced-sampling free energy calculations, we demonstrate how site asymmetry affects CO 2 binding affinities and reaction pathways. These results provide detailed mechanistic insight into CO 2 insertion and hydride transfer, highlighting key differences between crystal- and solution-phase pathways and offering a general framework for understanding how lattice confinement shapes chemical reactivity.

Chemical bonding↗
DOE OSTI2022

Application of the core shell model for strengthening polymer filament interfaces

While surface segregation has been intensively studied in thin films, relatively little has been investigated in filament geometries. In contrast to thin films, the filament surface forms a continuum, with interactions both at the free air and internal filament interface, which makes it difficult to achieve an equilibrium configuration. This asymmetry has become particularly apparent with the increasing use of additive manufacturing where entire structures are constructed via layered deposition of filamentous layers from a moving thermal nozzle. In addition, this process is highly non-equilibrated with poor thermal retention and is responsible for insufficient filament–filament interfacial fusion and internal pore formation along the printing direction. These features all contribute to poor mechanical and structural properties, which are exacerbated in semi-crystalline polymers, such as Polylactic Acid (PLA), where the melting point, T m , is much higher than the glass transition, T g . Even though system is liquid the molecules become ordered within the crystal structure and this ordering interferes with interdiffusion, which in turn prevents proper interfacial fusion. Capitalizing on the differential in surface tension, we show that addition of less than 1%, or trace amounts, of longer chain polymers, an oriented core shell structure, will be formed with a self-limiting thickness of three time the radius of gyration, R g , of the tracer chains. The lower T g of the tracers and their orientation makes them poised for interdiffusion when subsequent layers are deposited producing structures with significant improvement of the mechanical properties and internal structural integrity.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Y-shaped tricatenar azobenzenes – functional liquid crystals with synclinic–anticlinic transitions and spontaneous helix formation

A series of achiral tricatenar rod-like molecules with a 3,5-disubstitution pattern at one end and a single alkyl chain at the other end of a rod-like azobenzene derived core is reported. Depending on temperature and alkyl chain length, these Y-shaped compounds self-assemble into different types of liquid crystalline (LC) phases, ranging from non-tilted and synclinic tilted hexatic, via non-tilted and anticlinic tilted smectic and bicontinuous cubic LC phases, to a spontaneous mirror symmetry broken isotropic liquid (Iso 1 [*]) or a related achiral liquid network phase (Iso 1 ). An additional tilted, but uniaxial smectic phase was observed at the transition between anticlinic and synclinic tilt correlation and was investigated by soft resonant X-ray scattering with respect to possible helix formation. This work provides a new concept for the design of technological interesting azobenzene based LC materials with anticlinic tilted smectic C phases (SmC a ) and with azobenzene units organized in the long range or short range helical network structures of bicontinuous cubic and chiral isotropic liquid phases, respectively. Core fluorination removes all lamellar phases, leaving only the cubic phase over wide temperature ranges, even at ambient temperature.

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

Molecular dynamics simulations of radiation cascade evolution near cellular dislocation structures in additively manufactured stainless steels

The dislocation dense cellular structures observed in additively manufactured (AM) stainless steels can allow these materials to have enhanced strength and ductility compared to conventionally manufactured materials. Effective design of radiation resistant materials often necessitates creating microstructures containing of a high density of dislocations that act as sinks for radiation induced defects. This work uses molecular dynamics simulations to study the impact of pre-existing defects on radiation damage in stainless steel 316L fabricated by the laser powder bed fusion process. The evolution of synthetically generated dislocations in a crystal system in response to multiple radiation collision cascades suggest that dislocation dense regions reduce the probability of surviving point defects forming clusters. This finding seems to result from the dislocation cores’ ability to absorb point defects, thereby limiting the formation of clusters during the recombination phase. However, after successive cascades, the ability of the dislocation entanglement to prevent defect formation is diminished and defect cluster formation trends to an equilibrium. Accordingly, it is hypothesized that in an experimental setting the dislocation cells will initially act as neutral sinks for point defects, potentially delaying the onset of radiation damage effects; but, these structures will be degraded due to radiation-enhanced diffusion and lose their effectiveness at doses above 1.5–2 displacements per atom. Nevertheless, the ability to produce complex and feature-specific microstructures suggests promise for the design of radiation tolerant materials using AM methods.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Magnetic and dielectric property control in the multivalent nanoscale perovskite Eu 0.5 Ba 0.5 TiO 3

We report nanoscale Eu 0.5 Ba 0.5 TiO 3 , a multiferroic in the bulk and candidate in the search to quantify the electric dipole moment of the electron. Eu 0.5 Ba 0.5 TiO 3 , in the form of nanoparticles and other nanostructures is interesting for nanocomposite integration, biomedical imaging and fundamental research, based upon the prospect of polarizability, f-orbital magnetism and tunable optical/radio luminescence. We developed a [non-hydrolytic]sol–[H 2 O-activated]gel route, derived from in-house metallic Ba (s) /Eu (s) alkoxide precursors and Ti{(OCH(CH 3 ) 2 } 4 . Two distinct nanoscale compounds of Ba:Ti:Eu with the parent perovskite crystal structure were produced, with variable dielectric, magnetic and optical properties, based on altering the oxidizing/reducing conditions. Eu 0.5 Ba 0.5 TiO 3 prepared under air/O 2 atmospheres produced a spherical core–shell nanostructure (30–35 nm), with perovskite Eu 0.5 Ba 0.5 TiO 3 nanocrystal core-insulating oxide shell layer (~3 nm), presumed a pre-pyrochlore layer abundant with Eu 3+ . Fluorescence spectroscopy shows a high intensity 5 D 0 → 7 F 2 transition at 622 nm and strong red fluorescence. The core/shell structure demonstrated excellent capacitive properties: assembly into dielectric thin films gave low conductivity (2133 GΩ mm -1 ) and an extremely stable, low loss permittivity of ε eff ~25 over a wide frequency range (tan δ < 0.01, 100 kHz–2 MHz). Eu 0.5 Ba 0.5 TiO 3 prepared under H 2 /argon produced more irregular shaped nanocrystals (20–25) nm, with a thin film permittivity around 4 times greater ( ε eff 101, tan δ < 0.05, 10 kHz–2 MHz, σ ~59.54 kΩ mm -1 ). Field-cooled magnetization values of 0.025 emu g -1 for EBTO-Air and 0.84 emu g -1 for EBTO-Argon were observed. X-ray photoelectron spectroscopy analysis reveals a complex interplay of Eu II/III /Ti III/IV configurations which contribute to the observed ferroic and fluorescence behavior.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Oxygen isotope ratios in zircon and garnet: A record of assimilation and fractional crystallization in the Dinkey Dome peraluminous granite, Sierra Nevada, California

Abstract The 119 Ma Dinkey Dome pluton in the central Sierra Nevada Batholith is a peraluminous granite and contains magmatic garnet and zircon that are complexly zoned with respect to oxygen isotope ratios. Intracrystalline SIMS analysis tests the relative importance of magmatic differentiation processes vs. partial melting of metasedimentary rocks. Whereas δ18O values of bulk zircon concentrates are uniform across the entire pluton (7.7‰ VSMOW), zircon crystals are zoned in δ18O by up to 1.8‰, and when compared to late garnet, show evidence of changing magma chemistry during multiple interactions of the magma with wall rock during crustal transit. The evolution from an early high-δ18O magma [δ18O(WR) = 9.8‰] toward lower values is shown by high-δ18O zircon cores (7.8‰) and lower δ 18O rims (6.8‰). Garnets from the northwest side of the pluton show a final increase in δ18O with rims reaching 8.1‰. In situ REE measurements show zircon is magmatic and grew before garnets. Additionally, δ18O in garnets from the western side of the pluton are consistently higher (avg = 7.3‰) relative to the west (avg = 5.9‰). These δ18O variations in zircon and garnet record different stages of assimilation and fractional crystallization whereby an initially high-δ18O magma partially melted low-δ18O wallrock and was subsequently contaminated near the current level of emplacement by higher δ18O melts. Collectively, the comparison of δ18O zoning in garnet and zircon shows how a peraluminous pluton can be constructed from multiple batches of variably contaminated melts, especially in early stages of arc magmatism where magmas encounter significant heterogeneity of wall-rock assemblages. Collectively, peraluminous magmas in the Sierran arc are limited to small <100 km2 plutons that are intimately associated with metasedimentary wall rocks and often surrounded by later and larger metaluminous tonalite and granodiorite plutons. The general associations suggest that early-stage arc magmas sample crustal heterogeneities in small melt batches, but that with progressive invigoration of the arc, such compositions are more effectively blended with mantle melts in source regions. Thus, peraluminous magmas provide important details of the nascent Sierran arc and pre-batholithic crustal structure.

Geochemistry & Geophysics↗
DOE OSTI2025

Soft x-ray high-harmonic generation in an anti-resonant hollow core fiber driven by a 3 μ m ultrafast laser

High-harmonic upconversion driven by a mid-infrared femtosecond laser can generate coherent soft x-ray beams in a tabletop-scale setup. Here, we report on a compact ytterbium-pumped optical parametric chirped pulse amplifier (OPCPA) laser system seeded by an all-fiber front-end and employing periodically poled lithium niobate (PPLN) nonlinear media operated near the pulse fluence limits of current commercially available PPLN crystals. The OPCPA delivers 3 µm wavelength pulses with 775 µJ energy at 1 kHz repetition rate, with transform-limited 120 fs pulse duration, diffraction-limited beam quality, and ultrahigh 0.33% rms energy stability over >18 h. Using this laser, we generate soft x-ray high harmonics (HHG) in argon gas by focusing into a low-loss, high-pressure gas-filled anti-resonant hollow core fiber (ARHCF), generating coherent light at photon energies up to the argon L-edge (250 eV) and carbon K-edge (284 eV), with high beam quality and ∼1% rms energy stability. This work demonstrates soft x-ray HHG in a high-efficiency guided-wave phase matched geometry, overcoming the high losses inherent to mid-IR propagation in unstructured waveguides, or the short interaction lengths of gas cells or jets. The ARHCF can operate in the long term without damage and with the repetition rate, stability, and robustness required for demanding applications in spectromicroscopy and imaging. Finally, we discuss routes for further optimizing the soft x-ray HHG flux by driving He at higher laser intensities using either the signal (1.5 μm) or idler wavelengths (3 μm).

Femtosecond lasers↗
DOE OSTI2023

Organo‐Functionalized Lacunary Double Cubane‐Type Oxometallates: Synthesis, Structure, and Properties of [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (M=Co, Zn)

Abstract Organofunctionalized tetranuclear clusters [(M II Cl) 2 (V IV O) 2 {((HOCH 2 CH 2 )(H)N(CH 2 CH 2 O))(HN(CH 2 CH 2 O) 2 )} 2 ] (1, M=Co,2: M=Zn) containing an unprecedented oxometallacyclic {M 2 V 2 Cl 2 N 4 O 8 } (M=Co, Zn) framework have been prepared by solvothermal reactions. The new oxo‐alkoxide compounds were fully characterized by spectroscopic methods, magnetic susceptibility measurement, DFT and ab initio computational methods, and complete single‐crystal X‐ray diffraction structure analysis. The isostructural clusters are formed of edge‐sharing octahedral {VO 5 N} and trigonal bipyramidal {MO 3 NCl} units. Diethanolamine ligates the bimetallic lacunary double cubane core of1and2in an unusual two‐mode fashion, unobserved previously. In the crystalline state, the clusters of1and2are joined by hydrogen bonds to form a three‐dimensional network structure. Magnetic susceptibility data indicate weakly antiferromagnetic interactions between the vanadium centers [J iso (V IV −V IV )=−5.4(1); −3.9(2) cm −1 ], and inequivalent antiferromagnetic interactions between the cobalt and vanadium centers [J iso (V IV −Co II )=−12.6 and −7.5 cm −1 ] contained in1.

Chemistry↗
DOE OSTI2022

Twisted A-D-A Type Acceptors with Thermally-Activated Delayed Crystallization Behavior for Efficient Nonfullerene Organic Solar Cells

We report that molecular aggregation and crystallization during film coating play a crucial role in the realization of high-performing organic photovoltaics. Strong intermolecular interactions and high solid-state crystallinity are beneficial for charge transport. However, fast crystallization during thin-film drying often limits the formation of the finely phase-separated morphology required for efficient charge generation. Herein, the authors show that twisted acceptor-donor-acceptor (A-D-A) type compounds, containing an indacenodithiophene (IDT) electron-rich core and two naphthalenediimide (NDI) electron-poor units, leads to formation of mostly amorphous phases in the as-cast film, which can be readily converted into more crystalline domains by means of thermal annealing. This design strategy solves the aforementioned conundrum, leading to an optimal morphology in terms of reduced donor/acceptor domain-separation sizes (ca. 13 nm) and increased packing order. Solar cells based on these acceptors with a PBDB-T polymer donor show a power conversion efficiency over 10% and stable morphology, which results from the combined properties of desirable excited-state dynamics, high charge mobility, and optimal aggregation/crystallization characteristics. These results demonstrate that the twisted A-D-A motif featuring thermally-induced crystallization behavior is indeed a promising alternative design approach toward more morphologically robust materials for efficient organic photovoltaics.

14 SOLAR ENERGY↗
DOE OSTI2021

Nanoscale microstructure and chemistry of transparent gahnite glass-ceramics revealed by atom probe tomography

The nanoscale microstructure and chemistry of a transparent gahnite glass-ceramic and its precursor glass were investigated using atom probe tomography, transmission electron microscopy, and nuclear magnetic resonance spectroscopy. In the annealed precursor glass, statistically significant ZrO clustering was observed along with Si depletion within 2 nm of the ZrO clusters. This clustering is expected to be the first step in the nucleation and crystallization of the nucleating agent, ZrO 2 . In the glass-ceramic, gahnite (ZnAl 2 O 4 ) crystallites were found to exist in proximal locations to ZrO 2 and not in a core-shell arrangement. The residual glass composition was directly measured by atom probe, showing higher concentrations of Al, Zn, and Zr than previously expected. At the interfaces between the crystallites and residual glass, no enrichment or depletion zones were found. Our findings provide answers to outstanding questions surrounding the nucleation and elemental partitioning, microstructure, and the residual glass composition of transparent gahnite glass-ceramics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Multi-scale investigation on mechanical behavior and microstructural alteration of C-S-H in carbonated Alite paste

Carbonation treatment is a promising option to enhance recycled concrete aggregate (RCA) quality and eventually improve concrete performance. This study investigated the multi-scale mechanical properties of calcium silicate hydrates (C-S-H) in a mature alite paste subjected to accelerated carbonation treatment by testing macro compressive strength, microhardness and nanoindentation. The results show that, carbonation treatment resulted in a heterogeneous distribution of carbonation products in the alite sample. Reinforcement of C-S-H by the randomly precipitated calcite and vaterite crystals prevailed over the nano-structural and compositional alteration of C-S-H induced by carbonation, leading to an increase of nano-indentation modulus at the edge of the sample. Also, the microhardness at the edge zone was markedly higher than that at the core of the carbonated sample. The carbonated peripheral zone with improved nano-scale modulus and microhardness was likely serving as a “hard shell”, contributing to the improved macro compressive strength. The new insights into the multi-scale mechanical properties of carbonated C-S-H contribute to further understanding of the enhanced properties of RCA after carbonation treatment.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Fatty acid capped, metal oxo clusters as the smallest conceivable nanocrystal prototypes

Metal oxo clusters of the type M 6 O 4 (OH) 4 (OOCR) 12 (M = Zr or Hf) are valuable building blocks for materials science. Here, we synthesize a series of zirconium and hafnium oxo clusters with ligands that are typically used to stabilize oxide nanocrystals (fatty acids with long and/or branched chains). The fatty acid capped oxo clusters have a high solubility but do not crystallize, precluding traditional purification and single-crystal XRD analysis. We thus develop alternative purification strategies and we use X-ray total scattering and Pair Distribution Function (PDF) analysis as our main method to elucidate the structure of the cluster core. We identify the correct structure from a series of possible clusters (Zr3, Zr4, Zr6, Zr12, Zr10, and Zr26). Excellent refinements are only obtained when the ligands are part of the structure model. Further evidence for the cluster composition is provided by nuclear magnetic resonance (NMR), infrared spectroscopy (FTIR), thermogravimetry analysis (TGA), and mass spectrometry (MS). We find that hydrogen bonded carboxylic acid is an intrinsic part of the oxo cluster. Using our analytical tools, we elucidate the conversion from a Zr6 monomer to a Zr12 dimer (and vice versa), induced by carboxylate ligand exchange. Finally, we compare the catalytic performance of Zr12-oleate clusters with oleate capped, 5.5 nm zirconium oxide nanocrystals in the esterification of oleic acid with ethanol. The oxo clusters present a five times higher reaction rate, due to their higher surface area. Since the oxo clusters are the lower limit of downscaling oxide nanocrystals, we present them as appealing catalytic materials, and as atomically precise model systems. In addition, the lessons learned regarding PDF analysis are applicable to other areas of cluster science as well, from semiconductor and metal clusters, to polyoxometalates.

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

Isoreticular Linker Substitution in Conductive Metal–Organic Frameworks with Through‐Space Transport Pathways

Abstract The extension of reticular chemistry concepts to electrically conductive three‐dimensional metal–organic frameworks (MOFs) has been challenging, particularly for cases in which strong interactions between electroactive linkers create the charge transport pathways. Here, we report the successful replacement of tetrathiafulvalene (TTF) with a nickel glyoximate core in a family of isostructural conductive MOFs with Mn 2+ , Zn 2+ , and Cd 2+ . Different coordination environments of the framework metals lead to variations in the linker stacking geometries and optical properties. Single‐crystal conductivity data are consistent with charge transport along the linker stacking direction, with conductivity values only slightly lower than those reported for the analogous TTF materials. These results serve as a case study demonstrating how reticular chemistry design principles can be extended to conductive frameworks with significant intermolecular contacts.

Xie, Lilia S.↗
DOE OSTI2022

Materials under high pressure: a chemical perspective

At high pressure, the typical behavior of elements dictated by the periodic table, including oxidation numbers, stoichiometries in compounds, and reactivity, to name but a few, is altered dramatically. As pressure is applied, the energetic ordering of atomic orbitals shifts, allowing core orbitals to become chemically active, atypical electron congurations to occur, and in some cases,non-atom-centered orbitals to form in the interstices of solid structures. Strange stoichiometries, structures, and bonding motifs result. Crystal structure prediction tools, not burdened by preconceived notions about structural chemistry learned at atmospheric pressure, have been applied to great success to explore phase diagrams at high pressure, identifying novel structures in diverse chemical systems. Several of these phases have been subsequently synthesized. Experimentally, access to high-pressure regimes has been bolstered by advances in diamond anvil cell and dynamic com- pression techniques. Here, the joint efforts of experiment and theory have led to startling success stories in the realm of high-temperature superconductivity, identifying many novel phases (some of which have been synthesized) whose superconducting transition approaches room temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Atypical phase-change alloy Ga 2 Te 3 : atomic structure, incipient nanotectonic nuclei, and multilevel writing

Emerging brain-inspired computing, including artificial optical synapses, photonic tensor cores, neuromorphic networks, etc., needs phase-change materials (PCMs) of the next generation with lower energy consumption and a wider temperature range for reliable long-term operation. Gallium tellurides with higher melting and crystallization temperatures appear to be promising candidates and enable achieving the necessary requirements. Here, using high energy X-ray diffraction and Raman spectroscopy supported by first-principles simulations, we show that vitreous g-Ga 2 Te 3 films essentially have a tetrahedral local structure and sp 3 hybridization, similar to those in the stable fcc Ga 2 Te 3 polymorph and in contrast to a vast majority of typical PCMs. Nevertheless, optical pump–probe laser experiments revealed high-contrast, fast and reversible multilevel SET-RESET transitions raising a question related to the phase change mechanism. A recently observed nanotectonic compression in bulk glassy Ga–Te alloys seems to be responsible for the PCM performance. Incipient nanotectonic nuclei, reminiscent of monoclinic high-pressure HP-Te II and rhombohedral HP-Ga 2 Te 3 , are present as minorities (2–4%) in g-Ga 2 Te 3 but are suggested to grow dramatically with increasing temperature while interacting with appropriate laser pulses. This leads to co-crystallization of HP-polymorphs amplified by a high internal local pressure reaching 4–8 GPa. The metallic HP-forms provide an increasing optical and electrical contrast, favorable for reliable PCM operations, and higher energy efficiency.

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

Isoreticular Linker Substitution in Conductive Metal–Organic Frameworks with Through–Space Transport Pathways

The extension of reticular chemistry concepts to electrically conductive three-dimensional metal–organic frameworks (MOFs) has been challenging, particularly for cases in which strong interactions between electroactive linkers create the charge transport pathways. Here, we report the successful replacement of tetrathiafulvalene (TTF) with a nickel glyoximate core in a family of isostructural conductive MOFs with Mn 2+ , Zn 2+ , and Cd 2+ . Different coordination environments of the framework metals lead to variations in the linker stacking geometries and optical properties. Single-crystal conductivity data are consistent with charge transport along the linker stacking direction, with conductivity values only slightly lower than those reported for the analogous TTF materials. Lastly, these results serve as a case study demonstrating how reticular chemistry design principles can be extended to conductive frameworks with significant intermolecular contacts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches.

Biochemistry & Molecular Biology↗