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NASA NTRS2005

Generalized Maximum Entropy

A long standing mystery in using Maximum Entropy (MaxEnt) is how to deal with constraints whose values are uncertain. This situation arises when constraint values are estimated from data, because of finite sample sizes. One approach to this problem, advocated by E.T. Jaynes [1], is to ignore this uncertainty, and treat the empirically observed values as exact. We refer to this as the classic MaxEnt approach. Classic MaxEnt gives point probabilities (subject to the given constraints), rather than probability densities. We develop an alternative approach that assumes that the uncertain constraint values are represented by a probability density {e.g: a Gaussian), and this uncertainty yields a MaxEnt posterior probability density. That is, the classic MaxEnt point probabilities are regarded as a multidimensional function of the given constraint values, and uncertainty on these values is transmitted through the MaxEnt function to give uncertainty over the MaXEnt probabilities. We illustrate this approach by explicitly calculating the generalized MaxEnt density for a simple but common case, then show how this can be extended numerically to the general case. This paper expands the generalized MaxEnt concept introduced in a previous paper [3].

Cheeseman, Peter↗

NASA NTRS2012

Calculation of the Frequency Distribution of the Energy Deposition in DNA Volumes by Heavy Ions

Radiation quality effects are largely determined by energy deposition in small volumes of characteristic sizes less than 10 nm representative of short-segments of DNA, the DNA nucleosome, or molecules initiating oxidative stress in the nucleus, mitochondria, or extra-cellular matrix. On this scale, qualitatively distinct types of molecular damage are possible for high linear energy transfer (LET) radiation such as heavy ions compared to low LET radiation. Unique types of DNA lesions or oxidative damages are the likely outcome of the energy deposition. The frequency distribution for energy imparted to 1-20 nm targets per unit dose or particle fluence is a useful descriptor and can be evaluated as a function of impact parameter from an ions track. In this work, the simulation of 1-Gy irradiation of a cubic volume of 5 micron by: 1) 450 (1)H(+) ions, 300 MeV; 2) 10 (12)C(6+) ions, 290 MeV/amu and 3) (56)Fe(26+) ions, 1000 MeV/amu was done with the Monte-Carlo simulation code RITRACKS. Cylindrical targets are generated in the irradiated volume, with random orientation. The frequency distribution curves of the energy deposited in the targets is obtained. For small targets (i.e. <25 nm size), the probability of an ion to hit a target is very small; therefore a large number of tracks and targets as well as a large number of histories are necessary to obtain statistically significant results. This simulation is very time-consuming and is difficult to perform by using the original version of RITRACKS. Consequently, the code RITRACKS was adapted to use multiple CPU on a workstation or on a computer cluster. To validate the simulation results, similar calculations were performed using targets with fixed position and orientation, for which experimental data are available [5]. Since the probability of single- and double-strand breaks in DNA as function of energy deposited is well know, the results that were obtained can be used to estimate the yield of DSB, and can be extended to include other targeted or non-target effects.

Plante, Ianik↗

NASA NTRS2018

Acoustic Radiation Pressure

The theoretical foundation of acoustic radiation pressure in plane wave beams is reexamined. It is shown from finite deformation theory and the Boltzmann-Ehrenfest Adiabatic Principle that the Brillouin stress tensor (BST) is the radiation stress in Lagrangian coordinates (not Eulerian coordinates) and that the terms in the BST are not the momentum flux density and mean excess Eulerian stress but are simply contributions to the variation in the wave oscillation period resulting from changes in path length and true wave velocity, respectively, from virtual variations in the strain. It is shown that the radiation stress in Eulerian coordinates is the mean Cauchy stress (not the momentum flux density, as commonly assumed) and that Langevin's second relation does not yield an assessment of the mean Eulerian pressure, since the enthalpy used in the traditional derivations is a function of the thermodynamic tensions - not the Eulerian pressure. It is shown that the transformation between Lagrangian and Eulerian quantities cannot be obtained from the commonly-used expansion of one of the quantities in terms of the particle displacement, since the expansion provides only the difference between the value of the quantity at two different points in Cartesian space separated by the displacement. The proper transformation is obtained only by employing the transformation coefficients of finite deformation theory, which are defined in terms of the displacement gradients. Finite deformation theory leads to the result that for laterally unconfined, plane waves the Lagrangian and Eulerian radiation pressures are equal with the value (1/4)(2K) along the direction of wave propagation, where (K) is the mean kinetic energy density, and zero in directions normal to the propagation direction. This is contrary to the Langevin result that the Lagrangian radiation pressure in the propagation direction is equal to (2K) and the BST result that the Eulerian radiation pressure in that direction is the momentum flux density.

Finite deformation theory↗

NASA NTRS2018

Materials International Space Station Experiment-9 (MISSE-9) Polymers and Composites Experiment

Spacecraft in low Earth orbit (LEO) are subjected to harsh environmental conditions, including radiation (cosmic rays, ultraviolet, x-ray, and charged particle radiation), micrometeoroids and orbital debris, temperature extremes, thermal cycling, and atomic oxygen (AO). These environmental exposures can result in erosion, embrittlement and optical property degradation, threatening spacecraft performance and durability. To increase our understanding of effects such as AO erosion and radiation induced embrittlement of spacecraft materials, NASA Glenn has developed a series of experiments flown as part of the Materials International Space Station Experiment (MISSE) missions on the exterior of the International Space Station (ISS). These experiments have provided critical LEO space environment durability data such as AO erosion data for many materials and mechanical properties changes after long term space exposure. In continuing these studies, a new experiment called the Polymers and Composites Experiment has been selected for flight on the MISSE-Flight Facility (MISSE-FF). The Polymers and Composites Experiment will be flown as part of the MISSE-9 mission, the inaugural mission of MISSE-FF manifested on SpaceX-14. This experiment includes 138 samples being flown in ram, wake or zenith orientations for space environmental durability assessment. The primary objective is to determine the LEO AO erosion yield, Ey (the volume loss per incident oxygen atom (cm3/atom)), of polymers, composites, and coated samples, as a function of solar irradiation and AO fluence. In addition, epoxy samples with varying levels of ZnO powder are included to study the effect of filler quantity on AO erosion. An AO Scattering Chamber is included to help improve the understanding of AO scattering mechanisms for improved AO undercutting modeling. Indium tin oxide (ITO) coated samples are included to validate the durability of ITO conductive coatings in LEO. Tensile samples of Teflon fluorinated ethylene propylene (FEP) of varying thicknesses and back-surface coatings will be flown in wake and zenith orientations to study radiation embrittlement versus thickness, and the effect of heating on FEP embrittlement. Finally, shape memory composite and cosmic ray shielding samples will be flown for LEO durability assessment. This paper presents an overview of the MISSE-9 Polymers and Composites Experiment.

Embrittlement↗

NASA NTRSDate not supplied

Coherent Mode Decomposition for Kolmogorov Optical Turbulence in a Finite Aperture

An analysis of the coherent mode decomposition of an optical field after propagation through atmospheric turbulence is presented. The coherent modes represent an ideal basis by which to decompose the field for design of mode-limited optical systems. Using the rotational symmetry of the Fredholm integral operator for Kolmogorov optical turbulence, it is shown that the coherent modes exhibit separable solutions classified by radial and azimuthal quantum numbers. The study of the coherent modes is then reduced that of the radial functions determined by the aperture-coherence diameter ratio and obscuration ratio. Analysis of the spectrum of eigenvalues yields sharp bounds on the efficiency of receivers using incoherent or coherent combining with mode-limited photonic devices in the presence of Kolmogorov turbulence. The effective number of modes needed to represent Kolmogorov optical turbulence is studied via the von Neumann entropy, purity, and largest eigenvalue, and the differences in the different definitions is discussed. The similarity of the coherent modes to linearly polarized (LP) fiber modes is quantified yielding a precise characterization of the maximum gain that can be achieved in mode-limited systems via mode shaping techniques. As a final application, a mode sorting technique is presented for optimally splitting power from atmospherically degraded light into a finite number of modes simultaneously maximizing total coupling efficiency and minimizing the average and instantaneous power ratio between channels.

free-space optical communication↗

DOE OSTI2023

Enhancing the accuracy of density functional tight binding models through ChIMES many-body interaction potentials

Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. In conclusion, our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Surface Phase Stability of Fe 2 O 3 (001) in Hydrogen Reducing Environments: A DFT and XPS Analysis

Here, this study combines density functional theory (DFT) and ab initio thermodynamics calculations with X-ray photoelectron spectroscopy (XPS) investigations to identify the reduction properties of the Fe 2 O 3 (001) surface with implications for corrosion resistance, hydrogen transport, and energy safety. Ab initio thermodynamics modeling predicts fully hydroxylated surface stability across a broad range of pressures (1 × 10 –23 to 1 × 10 5 mbar) and temperatures below 700 K, consistent with previous experimental studies. Above 800 K, exposures to 1 × 10 –4 mbar H 2 , 1 × 10 –4 mbar O 2 , or 1 × 10 –4 mbar H 2 + 1 × 10 –4 mbar O 2 each yield unique XPS signals indicating a loss of −OH coverage, aligning with DFT predictions. Insight into the mechanism of reduction as a function of H 2 exposure is provided, as well as conditions that promote further reduction toward Fe 3 O 4 . Theoretical and experimental investigations indicate the ability to maintain the Fe 2 O 3 protective layer of iron oxides that have been exposed to H 2 environments by including trace amounts of aqueous O2.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Advanced Modeling and Simulation Methods for Evaluation of Thermal Neutron Scattering Materials

With the rise of interest in thermal neutron scattering data for advanced reactor, criticality safety, and shielding applications, new experimental data are required for evaluation of new materials or for re-evaluation (or validations) of previously evaluated materials. New experimental data are evaluated in a three-step process: (1) computing the phonon characteristics, (2) computing the dynamic structure factor (DSF) from the data, and (3) using the experimental setup to simulate the experimental data. All three steps have challenges, ranging from the need for a sufficiently general material simulation code—a processing code that can compute the corresponding DSF—to having a detailed layout of the instrument/beamline/facility where the data were measured. Whereas phonon characteristics of materials can be computed using various methods (molecular dynamics, density functional theory, etc.), a high-fidelity computation of the DSF and the simulation of the experiment based on the DSF is vital to the accuracy of the evaluation. The latter two steps can be achieved by using the two corresponding code systems developed by instrument scientists at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory: (1) OCLIMAX, a program that calculates the dynamic structure factor from DFT and MD simulation results, and (2) MCViNE, a Monte Carlo neutron ray-tracing program designed to simulate neutron scattering experiments. Recently, polyethylene and yttrium hydride were measured at the Wide Angular-Range Chopper (ARCS) and SEQUOIA instrument stations of the SNS. These experiments are simulated using the density functional theory code, the Cambridge Serial Total Energy Package (CASTEP), to compute its phonon characteristics (eigenvalues/vectors and PDOS), which is then processed using OCLIMAX to yield the DSF, and finally the data at each instrument station are simulated by the MCViNE for comparison to the measured data for evaluation. For comparison to conventional evaluation methods, the scattering data processed from OCLIMAX are compared against those processed from the LEAPR module of NJOY, and the results from MCViNE simulations are compared against previously used simplified beamline models implemented in the Monte Carlo N-Particle (MCNP) code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2016

Tholins as Coloring Agents on Pluto and Other Icy Solar System Bodies

Tholins are refractory organic solids of complex structure and high molecular weight, with a wide range of color ranging from yellow and orange to dark red, and through tan to black. They are made in the laboratory by energy deposition (photons or charged particles) in gases and ices containing the simple molecules (e.g., N2, CH4, CO) found in planetary atmospheres or condensed on planetary surfaces. They are widely implicated in providing the colors and albedos, particularly in the region 0.3-1.0 microns, of several outer Solar System bodies, including Pluto, as well as aerosols in planetary atmospheres such as Titan. Recent color images of Pluto with the New Horizons spacecraft show concentrations of coloring agent(s) in some regions of the surface, and apparent near-absence in other regions. Tholins that may to some degree represent surface chemistry on Pluto have been synthesized in the laboratory by energetic processing of mixtures of the ices (N2, CH4, CO) known on Pluto's surface, or the same molecules in the gas phase. Details of the composition and yield vary with experimental conditions. Chemical analysis of Pluto ice tholins shows evidence of amides, carboxylic acids, urea, carbodiimides, and nitriles. Aromatic/olefinic, amide, and other functional groups are identified in XANES analysis. The ice tholins produced by e- irradiation have a higher concentration of N than UV ice tholins, with N/C approx. 0.9 (versus approx. 0.5 for UV tholins) and O/C approx.0.2. Raman spectra of the electron tholin show a high degree of structural disorder, while strong UV fluorescence indicates a large aromatic content. EUV photolysis of a Pluto gaseous atmosphere analog yields pale yellow solids relatively transparent in the visual, and with aliphatic CH bonds prominent in IR spectra. This or similar material may be responsible for Pluto's hazes.

Tholins↗

NASA NTRS1977

Gaseous hydrogen embrittlement of high strength steels

The effects of temperature, hydrogen pressure, stress intensity, and yield strength on the kinetics of gaseous hydrogen assisted crack propagation in 18Ni maraging steels were investigated experimentally. It was found that crack growth rate as a function of stress intensity was characterized by an apparent threshold for crack growth, a stage where the growth rate increased sharply, and a stage where the growth rate was unchanged over a significant range of stress intensity. Cracking proceeded on load application with little or no detectable incubation period. Gaseous hydrogen embrittlement susceptibility increased with increasing yield strength.

Gangloff, R. P.↗

DOE OSTI2020

Effects of graphene surface functionalities towards controlled reinforcement of a lignin based renewable thermoplastic rubber

In this report, we describe methods to enhance mechanical properties of a renewable thermoplastic rubber by incorporating functional graphene platelets into an equal-mass mixture of lignin, a feedstock from plant biomass, and a nitrile-butadiene rubber having 41 mol % acrylonitrile content (NBR41) that form a nanocomposite. Not all lignins yield mechanically strong material when they are combined with NBR41, and thus, limit its use for such rubbery products. Here, we evaluate different graphene oxides (GO) and reduced graphene oxides (rGO) dry-powders with different surface areas, functionality, and wettability in the synthesis of performance-enhanced nanocomposites of soft lignin/NBR41 matrix via a solvent-free, high shear reactive process. High surface area GO (HSGO) platelets with strong hydrophilicity exhibit good dispersion in the multiphase lignin/NBR41 composites with lignin dispersion varying from 200 to 2000 nm, resulting in superior reinforcement over other graphene derivatives. The addition of 1–4 wt % HSGO increased the tensile stress of the lignin/NBR41 thermoplastic rubber matrix by 60–160% (15–24 MPa) and the modulus by 200–700% (60–140 MPa). Scanning electron microscopy and small angle X-ray scattering results show that the well-dispersed HSGO platelets effectively disrupt the lignin-rich aggregates in NBR41 matrix, resulting in both strength and stiffness enhancements in the formed nanocomposites. This report on performance enhancement of lignin-based renewable polymers via the production of nanocomposite would increase potential for ‘finding the value of lignin’—a grand challenge associated with modern biorefineries.

36 MATERIALS SCIENCE↗

NASA NTRS1999

Effective Elastic Modulus as a Function of Angular Leaf Span for Curved Leaves of Pyrolytic Boron Nitride

A theoretical equation was derived to predict the spring constant (load/deflection) for a simply supported cylindrical section with a line force applied at the center. Curved leaves of PBN were mechanically deformed and the force versus deflection data was recorded and compared to the derived theoretical equation to yield an effective modulus for each leaf. The effective modulus was found to vary from the pure shear modulus for a flat plate to a mixed mode for a half cylinder as a function of the sine of one half the angular leaf span. The spring constants of individual PBN leaves were usually predicted to within 30%.

Kaforey, M. L.↗

DOE OSTI2022

A critical comparison of CH∙∙∙π versus π∙∙∙π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods

In this study, we have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π∙∙∙π (parallel displaced or PD(C 2h ), minimum) and CH∙∙∙π (T-shaped or T(C 2v ), transition state) and tilted T-shaped (or TT(Cs), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol -1 (TT). To this end, the CH∙∙∙π is ~0.2 kcal mol -1 stronger than the π∙∙∙π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol -1 . As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ~0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH∙∙∙π and π∙∙∙π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C 2h ) and T(C 2v ) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH∙∙∙π and π∙∙∙π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Efficient machine-learning model for fast assessment of elastic properties of high-entropy alloys

We combined descriptor-based analytical models for stiffness-matrix and elastic-moduli with mean-field methods to accelerate assessment of technologically useful properties of high-entropy alloys, such as strength and ductility. Model training for elastic properties uses Sure-Independence Screening (SIS) and Sparsifying Operator (SO) method yielding an optimal analytical model, constructed with meaningful atomic features to predict target properties. Computationally inexpensive analytical descriptors were trained using a database of elastic properties determined from density functional theory for binary and ternary subsets of Nb-Mo-Ta-W-V refractory alloys. The optimal Elastic-SISSO models, extracted from an exponentially large feature space, give an extremely accurate prediction of target properties, similar to or better than other models, with some verified from existing experiments. Here we also show that electronegativity variance and elastic-moduli can directly predict trends in ductility and yield strength of refractory HEAs, and reveals promising alloy concentration regions.

36 MATERIALS SCIENCE↗

DOE OSTI2022

From Petroleum to Biobased Crude: A Thermoplastic Polyurethane from Lignin-Oil Without Isocyanates

The movement to transfer from petroleum-based products and materials to renewables does not necessarily have to bypass the use of oil. A new type of "black-gold" is readily abundant from the earth's most abundant source of aromatic carbon: lignin. While fractionation of petroleum yields fuels and chemicals for a diverse set of industries, lignin fractionation using targeted catalysts has demonstrated the ability to generate monomers and oligomers rich in functional groups for polymer synthesis. This study explores the use of lignin-oil, generated from reductive catalytic fractionation of popular wood, to a hydroxyl-rich mixture of aromatics that is used to synthesize a thermoplastic non-isocyanate polyurethane. The lignin-oil is first converted to a cyclocarbonated derivative using a benign synthetic sequence and further polymerized with a diamine to yield the non-isocyanate TPU. While more work is underway to optimize the reaction conditions and meet typical mechanical properties of commercial materials, initial analysis shows thermoplastic behavior and flexible properties consistent with traditional thermoplastic polyurethanes.

BIOMASS FUELS↗

DOE OSTI2017

Modulating Hole Transport in Multilayered Photocathodes with Derivatized p-Type Nickel Oxide and Molecular Assemblies for Solar-Driven Water Splitting

We report here a new photocathode composed of a bi-layered doped NiO film topped by a macro-mesoporous ITO (ioITO) layer with molecular assemblies attached to the ioITO surface. The NiO film containing a 2% K+ doped NiO inner layer and a 2% Cu2+ doped NiO outer layer provides sufficient driving force for hole transport after injection to NiO by the molecular assembly. The tri-layered oxide, NiK0.02O | NiCu0.02O | ioITO, sensitized by a ruthenium polypyridyl dye and functionalized with a nickel-based hydrogen evolution catalyst, outperforms its counterpart, NiO | NiO | ioITO, in photocatalytic hydrogen evolution from water over a period of several hours with a Faradaic yield of ~90%.

Shan, Bing↗

DOE OSTI2025

Identifying High Ionic Conductivity Compositions of Ionic Liquid Electrolytes Using Features of the Solvation Environment

Binary mixtures of ionic liquids with molecular solvents are gaining interest in electrochemical applications due to the improvement in their performance over neat ionic liquids. Dilution with suitable molecular solvents can reduce the viscosity and facilitate faster diffusion of ions, thereby yielding substantially higher ionic conductivity than that for a pure ionic liquid. Although viscosity and diffusion coefficients typically behave as monotonic functions of concentration, ionic conductivity often passes through a peak value at an optimum molar ratio of the molecular solvent to the ionic liquid. The ionic conductivity maximum is generally explained in terms of a balance between the ease of charge transport and the concentration of the charge carriers. In this work, fluctuation in the local environment surrounding an ion is invoked as a plausible explanation for the ionic conductivity mechanism with a binary mixture of 1-ethyl-3-methylimidazolium tetrafluoroborate and ethylene glycol as an example. The magnitude of the dynamism in the local environment is captured by measuring the spatial and temporal features of the solvation environment. Standard deviation in the number of ions in the solvation environment serves as a spatial feature, while the cage correlation lifetimes for oppositely charged ions within the first solvation shell serve as a temporal feature. Large standard deviations in the cluster ion population and short cage correlation lifetimes are indicators of highly dynamic ionic environment at the molecular level and consequently yield high ionic conductivity. Such compositions were found to be in good agreement with the optimum ionic liquid mole fractions obtained through experimental measurement. Short cage correlation lifetimes enable the identification of optimum mixture compositions using simulation trajectories significantly shorter than those required to implement the Nernst–Einstein or Einstein formalisms for calculating ionic conductivity. We validated the applicability of this approach across force fields and in six ionic liquid-molecular solvent electrolytes formed with combination of cations, anions, and solvents. We offer a computationally efficient approach of screening ionic liquid-molecular solvent binary mixture electrolytes to identify molar ratios that yield high ionic conductivity.

25 ENERGY STORAGE↗

DOE OSTI2019

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer

Here, several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson–Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.

59 BASIC BIOLOGICAL SCIENCES↗