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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Diffusional Dynamics of Tetraalkylphosphonium Ionic Liquid Films Measured by Fluorescence Correlation Spectroscopy

Fluorescence correlation spectroscopy (FCS) is enacted to investigate the diffusional dynamics of hydrophilic (Atto 590) and amphiphilic (DiD) fluorophores in a series of alkylphosphonium ionic liquid (IL) films ([P4448][Cl], [P6668][Cl], [P66614][Cl], and [P66614][NTf2]) in order to determine diffusional parameters and to elucidate nanoscale structural heterogeneities within the IL. From the measured correlation functions, the diffusion coefficients of the fluorescent molecules are estimated, rendering values that span from 0.39-1.2 and 0.146-5.2 µm2/s, for Atto 590 and DiD, respectively. A decrease in the diffusion coefficients is measured as the alkyl chain increases, coincident with a decrease in their viscosity. Interestingly, deviations from the Brownian diffusion behavior of the fluorescent probes in the ILs are observed, showing a time-dependent diffusion coefficient in most of the cases. These deviations can be attributed to the presence of nanoscale structural heterogeneities in the tetraalkylphosphonium ILs. These conclusions validate experimentally the presence of nanosegregation in tetraalkylphosphonium ILs, which has previously been observed in molecular dynamics (MD) studies.

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

Synthesis and Characterization of Amorphous Lawsone Polymer Dots for Fluorescent Applications

In this work, a two-step hydrothermal/solvothermal process was developed to generate highly fluorescent lawsone polymer dots (LPDs) utilizing an inexpensive and abundant starting material, 2-hydroxy-1,4-napththoquinone (lawsone). This hydrothermal/solvothermal process produces LPDs that have excitation independent emission with well-defined electronic transitions. This two-step protocol provides a straightforward approach to remove unwanted small molecular fluorescence, which has plagued carbon dot systems, without the need for advanced chromatographic purification methods or steps. A series of spectroscopic, electrochemical, and theoretical experiments suggest that this process proceeds via a sequential dehydration and dehydrogenation pathway to cross-link the lawsone into a carbon dot structure. This polymerization process helps to stabilize and favor certain electronic transitions inherently present in the lawsone monomer. The generation of the LPDs results in a 2 order of magnitude increase in the emission intensity and a quantum yield of 37%. This behavior is likely the result of the cross-linked structure shielding these electronic states from deactivation caused by nonradiative processes such as vibrational coupling and excited state quenching from thermal deactivation and solvent collisions. This finding is consistent with a cross-linked enhanced emission (CEE) mechanism, as previously observed for other similar systems. The LPDs were then incorporated into a TiO2 photoanode and utilized as a photosensitizer in a dye-sensitized solar cell (DSSC) which showed an enhancement in photocurrent density over pure TiO2. We also prepared a derivative of the LPDs utilizing a diethylene triamine additive (nitrogen-doped lawsone polymer dots (N-LPDs)) using the same two-step protocol and demonstrated its potential as a fluorescence microscopy dye for imaging MDA-MB-231 cancer cells.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins

Red fluorescent protein (RFP) variants are highly sought after for in-vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pre-twisted chromophore conformation which provides easier access to conical intersections. Notably, the main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

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

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Optical Control of Fluorescence through plasmonic eigenmode extinction

We introduce the concept of optical control of the fluorescence yield of CdSe quantum dots through plasmon-induced structural changes in random semicontinuous nanostructured gold films. We demonstrate that the wavelength- and polarization dependent coupling between quantum dots and the semicontinuous films, and thus the fluorescent emission spectrum, can be controlled and significantly increased through the optical extinction of a selective band of eigenmodes in the films. This optical method of effecting controlled changes in the metal nanostructure allows for versatile functionality in a single sample and opens a pathway to in situ control over the fluorescence spectrum.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Mitochondria-targeting fluorescent molecules for high efficiency cancer growth inhibition and imaging

Fluorescent mitochondria-accumulating delocalized lipophilic cations (DLCs) for cancer therapy have drawn significant attention in the field of cancer theranostics. One of the most promising fluorescent DLCs, F16, can selectively trigger the apoptosis and necrosis of cancer cells, making it an attractive targeted theranostic drug candidate. However, it suffers from low clinical translation potential, largely due to its inefficient anti-cancer activity (IC 50 in the μM range) and poorly understood structure–activity relationship (SAR). In this report, eleven indole-ring substituted F16 derivatives (F16s) were synthesized. Among these derivatives, 5BMF was identified as a highly effective theranostic agent, with in vitro studies showing a low IC 50 of ~50 nM (to H2228 cells) and high cancer to normal cell selectivity index of 225. In vivo studies revealed that tumors treated with 5BMF were significantly suppressed (almost no growth over the treatment period) compared to the PBS treated control group, and also no obvious toxicity to mice was found. In addition, the tumor imaging capability of 5BMF was demonstrated by in vivo fluorescence imaging. Finally, we report for the first time a proposed SAR for F16 DLCs. Our work lays down a solid foundation for translating 5BMF into a novel and highly promising DLC for cancer theranostics.

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

Simultaneous quantification of uranium( VI ), samarium, nitric acid, and temperature with combined ensemble learning, laser fluorescence, and Raman scattering for real-time monitoring

In this work, laser-induced fluorescence spectroscopy (LIFS), Raman spectroscopy, and a stacked regression ensemble was developed for near real-time quantification of uranium(VI) (1–100 μg mL –1 ), samarium (0–200 μg mL –1 ) and nitric acid (0.1–4 M) with varying temperature (20 °C–45 °C). LIFS applications range from fundamental lab-scale studies to real-time process monitoring at industrial levels, such as nuclear reprocessing applications, provided the phenomena affecting the fluorescence spectrum are accounted for (e.g., absorption, quenching, complexation). Multiple chemometric models were examined and compared to a more traditional multivariate regression approach called partial least squares (PLS). Results obtained on synthetic samples selected using D-optimal experimental design indicated that a stacked regression method, which included ridge regression, random forest, PLS, and an eXtreme gradient boost algorithm, successfully measured uranium(VI) concentrations directly in nitric acid without measuring luminescence lifetimes or standard addition. The top model resulted in percent root-mean-square error of prediction values of 5.2, 1.9, 3.0, and 2.3% for U(VI), Sm 3+ , HNO 3 , and temperature, respectively. The approach may be useful for quantifying fluorescent fission products (e.g., Sm 3+ ) to provide information on burnup of irradiated nuclear fuel. This novel framework reinforces the applicability of LIFS for real-time applications in nuclear fuel cycle applications.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Fluorescent, phosphorescent, magnetic resonance contrast and radioactive tracer labelling of extracellular vesicles

This review focusses on the significance of fluorescent, phosphorescent labelling and tracking of extracellular vesicles (EVs) for unravelling their biology, pathophysiology, and potential diagnostic and therapeutic uses. Various labeling strategies, such as lipid membrane, surface protein, luminal, nucleic acid, radionuclide, quantum dot labels, and metal complex-based stains, are evaluated for visualizing and characterizing EVs. Direct labelling with fluorescent lipophilic dyes is simple but generally lacks specificity, while surface protein labelling offers selectivity but may affect EV-cell interactions. Luminal and nucleic acid labelling strategies have their own advantages and challenges. Here, each labelling approach has strengths and weaknesses, which require a suitable probe and technique based on research goals, but new tetranuclear polypyridylruthenium(II) complexes as phosphorescent probes have strong phosphorescence, selective staining, and stability. Future research should prioritize the design of novel fluorescent probes and labelling platforms that can significantly enhance the efficiency, accuracy, and specificity of EV labeling, while preserving their composition and functionality. It is crucial to reduce false positive signals and explore the potential of multimodal imaging techniques to gain comprehensive insights into EVs.

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

Fluorescence intensity correlation imaging with high spatial resolution and elemental contrast using intense x-ray pulses

We theoretically investigate the fluorescence intensity correlation (FIC) of Ar clusters and Mo-doped iron oxide nanoparticles subjected to intense, femtosecond, and sub-femtosecond x-ray free-electron laser pulses for high-resolution and elemental contrast imaging. We present the FIC of Kα and Kαh emission in Ar clusters and discuss the impact of sample damage on retrieving high-resolution structural information and compare the obtained structural information with those from the coherent diffractive imaging (CDI) approach. We found that, while sub-femtosecond pulses will substantially benefit the CDI approach, few-femtosecond pulses may be sufficient for achieving high-resolution information with the FIC. Furthermore, we show that the fluorescence intensity correlation computed from the fluorescence of the Mo atoms in Mo-doped iron oxide nanoparticles can be used to image dopant distributions in the nonresonant regime.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Quantifying cellulose accessibility during enzyme-mediated deconstruction using 2 fluorescence-tagged carbohydrate-binding modules

Two fluorescence-tagged carbohydrate-binding modules (CBMs), which specifically bind to crystalline (CBM2a-RRedX) and paracrystalline (CBM17-FITC) cellulose, were used to differentiate the supramolecular cellulose structures in bleached softwood Kraft fibers during enzyme-mediated hydrolysis. Differences in CBM adsorption were elucidated using confocal laser scanning microscopy (CLSM), and the structural changes occurring during enzyme-mediated deconstruction were quantified via the relative fluorescence intensities of the respective probes. It was apparent that a high degree of order (i.e., crystalline cellulose) occurred at the cellulose fiber surface, which was interspersed by zones of lower structural organization and increased cellulose accessibility. Quantitative image analysis, supported by 13 C NMR, scanning electron microscopy (SEM) imaging, and fiber length distribution analysis, showed that enzymatic degradation predominates at these zones during the initial phase of the reaction, resulting in rapid fiber fragmentation and an increase in cellulose surface crystallinity. By applying this method to elucidate the differences in the enzyme-mediated deconstruction mechanisms, this work further demonstrated that drying decreased the accessibility of enzymes to these disorganized zones, resulting in a delayed onset of degradation and fragmentation. The use of fluorescence-tagged CBMs with specific recognition sites provided a quantitative way to elucidate supramolecular substructures of cellulose and their impact on enzyme accessibility. By designing a quantitative method to analyze the cellulose ultrastructure and accessibility, this study gives insights into the degradation mechanism of cellulosic substrates.

09 BIOMASS FUELS↗
DOE OSTI2025

Low-cost production method for fluorescent particles for liquid flow velocimetry applications

Abstract In this Technical Note, we present a simple and low-cost production method for fluorescent particles perfectly suitable for velocimetry applications. We leverage the unique ability of Nile Red (NR) fluorophores to adsorb on the polymer surface and/or embed itself in between polymeric chains. The laboratory procedure to dye polyamide particles with NR and monetary advantages over commercially available fluorescent particles is outlined. Subsequently, the fluorescence behavior of the dyed particles is tested under a laser illumination source in polar and non-polar liquids. The distinct advantage of the emission spectrum of NR-dyed particles is demonstrated with sample test results.

42 ENGINEERING↗
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↗
DOE OSTI2024

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum ( X max ) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence dataset, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio X max resolution as a function of energy and demonstrate the ability to make competitive high-resolution X max measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments. Published by the American Physical Society 2024

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Utilization of PARAFAC ‐Modeled Excitation‐Emission Matrix ( EEM ) Fluorescence Spectroscopy to Identify Biogeochemical Processing of Dissolved Organic Matter in a Northern Peatland

Abstract In this study, we contrast the fluorescent properties of dissolved organic matter ( DOM ) in fens and bogs in a Northern Minnesota peatland using excitation emission matrix fluorescence spectroscopy with parallel factor analysis ( EEM ‐ PARAFAC ). EEM ‐ PARAFAC identified four humic‐like components and one protein‐like component and the dynamics of each were evaluated based on their distribution with depth as well as across sites differing in hydrology and major biological species. The PARAFAC ‐ EEM experiments were supported by dissolved organic carbon measurements ( DOC ), optical spectroscopy ( UV ‐Vis), and compositional characterization by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectroscopy ( FT ‐ ICR MS ). The FT ‐ ICR MS data indicate that metabolism in peatlands reduces the molecular weights of individual components of DOM , and oxygen‐rich less aromatic molecules are selectively biodegraded. Our data suggest that different hydrologic and biological conditions within the larger peat ecosystem drive molecular changes in DOM , resulting in distinctly different chemical compositions and unique fluorescent fingerprints. PARAFAC modeling of EEM data coupled with ultrahigh resolution FT ‐ ICR MS has the potential to provide significant molecular‐based information on DOM composition that will support efforts to better understand the composition, sources, and diagenetic status of DOM from different terrestrial and aquatic systems.

Tfaily, Malak M.↗
DOE OSTI2021

Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts

Abstract Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial‐microbial holobiont (termed HT‐58‐2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a , complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH 2 Cl 2 /2‐propanol, 1:1) of HT‐58‐2 cultures with NaBH 4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17‐dioxobacteriochlorins) exhibit a bathochromic shift ( λ abs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 13 1 ‐oxochlorin) exhibits a hypsochromic shift ( λ abs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λ em 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non‐axenic cultures at microscale quantities (2 mL, 2 μ m ), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT‐58‐2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.

Nguyen, Kathy‐Uyen↗
DOE OSTI2025

Substituent effect on napthodithiophene-fused porphyrins: Understanding the unusual trend of fluorescence quantum yield quenching

A series of π-extended porphyrins containing thiophene units was prepared to investigate an unusual trend observed in the fluorescence quantum yield of naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins. Monobenzoporphyrins carrying 2-thiophenyl (vinyl thiophene porphyrin) groups (2VTP, 2VTBr and Br2VTP) (numbering 2 and 3 refers to the position of sulfur on the thiophene ring) were synthesized through a Heck-based cascade reaction followed by a newly developed bromination method. These were converted to naphtho[2,1-b:3,4-b']dithiophene-fused porphyrin derivatives (FBr2VTP and F2VTBr) via ring closure with an intramolecular Scholl reaction. Increasingly larger Stokes shifts with a higher number of bromo groups were observed in the unfused π-extended molecular systems, reflecting the heavy atom effect. Fluorescence spectroscopy further confirmed the unusual trend seen in the previous work: structural rigidification in naphtho[2,1-b:3,4-b']dithiophene-fused porphyrins leads to longer fluorescence lifetimes but unexpectedly lowers the quantum yield. Adding one bromo group to the naphtho[2,1-b:3,4-b']dithiophene unit does not change this trend. Furthermore, the presence of two bromo groups prevents the quantum yield from dropping. DFT, TDDFT, and NICS analyses suggest a drastic change in aromaticity in the pyrrole ring where the naphtho[2,1-b:3,4-b']dithiophene is fused in FBr2VTP, which might contribute to the quantum yield reductions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Fluorescent Amplification of Next Generation Sequencing Libraries Tools (FA-NGS tools) v1

This is a software utility for calculating pooling volumes and graphing quality control data of next generation sequencing libraries amplified with fluorescent intercalating agents and monitored by real-time quantitative PCR (qPCR). The tool is used to calculate pooling volumes of individual next generation sequencing libraries based on experimentally determined fluorescence values. To do this, fluorescent values are used as a proxy for relative concentration to determine the ratio of transfer volumes. The output is a "transfer file" that specifies the transfer volume and destination well of a given library. The tool can also be used to assess the quality of individual next generation sequencing libraries by melting curve analysis. The output are small-multiples graphs of the melting curves of individual sequencing libraries according to the specified plate layout.

Garber, Megan↗
DOE OSTI2022

Computational microscopy for fast widefield deep-tissue fluorescence imaging using a commercial dual-cannula probe

A solid-glass cannula serves as a micro-endoscope that can deliver excitation light deep inside tissue while also collecting emitted fluorescence. Then, we utilize deep neural networks to reconstruct images from the collected intensity distributions. By using a commercially available dual-cannula probe, and training a separate deep neural network for each cannula, we effectively double the field of view compared to prior work. We demonstrated ex vivo imaging of fluorescent beads and brain slices and in vivo imaging from whole brains. We clearly resolved 4 µm beads, with FOV from each cannula of 0.2 mm (diameter), and produced images from a depth of ∼1.2 mm in the whole brain, currently limited primarily by the labeling. Since no scanning is required, fast widefield fluorescence imaging limited primarily by the brightness of the fluorophores, collection efficiency of our system, and the frame rate of the camera becomes possible.

42 ENGINEERING↗