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231 results for “dye”
Dataset of "Thermal Truncation of Heptamethine Cyanine Dyes"
<p>Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. Unlike phototruncation, the thermal truncation (chain-shortening) reaction is a phenomenon that has rarely been described for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3′ and C4′ positions of the chain and different heterocyclic end groups, the presence of different bases, nucleophiles and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, demonstrating the need to model catalytic reactions by highly correlated wavefunction-based methods. We show that entropic effects control the course of this process. The study provides a critical insight into the reactivity of the polyene chains of cyanines and offers new approaches to the synthesis of meso-substituted symmetrical and unsymmetrical pentamethine cyanines from Cy7 derivatives.</p>
Growth of Merocyanine Dye J-Aggregate Nanosheets by Living Supramolecular Polymerization
<p>Data to report <a href="https://doi.org/10.1002/ange.202314667">https://doi.org/10.1002/ange.202314667</a>:</p><p>J-aggregates are highly desired dye aggregates but so far there has been no general concept how to accomplish the required slip-stacked packing arrangement for dipolar merocyanine (MC) dyes whose aggregation commonly affords one-dimensional aggregates composed of antiparallel, co-facially stacked MCs with H-type coupling. Herein we describe a strategy for MC J-aggregates based on our results for an amphiphilic MC dye bearing alkyl and oligo(ethylene glycol) side chains. In an aqueous solvent mixture, we observe the formation of two supramolecular polymorphs for this MC dye, a metastable off-pathway nanoparticle showing H-type coupling and a thermodynamically favored nanosheet showing J-type coupling. Detailed studies concerning the self-assembly mechanism by UV-Vis spectroscopy and the packing structure by atomic force microscopy and wide-angle X-ray scattering show how the packing arrangement of such amphiphilic MC dyes can afford slip-stacked two-dimensional nanosheets whose macrodipole is compensated by the formation of a bilayer structure. As an additional feature we demonstrate how the size of the nanosheets can be controlled by seeded living supramolecular polymerization.</p>
Regulation of Dye-decolorizing Peroxidases Gene Expression in Pleurotus ostreatus Grown on Glycerol as the Carbon Source
<p>This dataset contains the raw data and code necessary to reproduce the results of: Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source.</p> <p> </p> <p>These data are also available at github: <a href="https://github.com/JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources">JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources: Data and scripts to reproduce the analysis performed at Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source (github.com)</a></p>
Panchromatic Light-Harvesting Antenna by Supramolecular Exciton Band Engineering for Heteromeric Dye Foldamer
<p>Data to report <a href="https://doi.org/10.1016/j.chempr.2024.05.023">https://doi.org/10.1016/j.chempr.2024.05.023</a>:</p> <p>Natural photosystems accomplish panchromatic light absorption by different chromophores that are non-covalently embedded in protein matrices and mostly lack close dye-dye interactions. In this article, we introduce a light-harvesting (LH) system established by four different merocyanine dyes that are co-facially stacked by dipole-dipole interactions and a peptide-like backbone in a folded heteromer architecture to afford a panchromatic absorption band consisting of several strongly coupled exciton states. This exciton manifold allows for ultrafast and efficient energy transport in the artificial antenna. Furthermore, due to the tight stacking of the dyes in their folded state, non-radiative processes are slowed down, thereby increasing the lifetime of the excited state and the fluorescence quantum yield from <3% for the individual dyes up to 38% for the folda-heteromer. Together with the panchromatic absorption, this leads to a substantial improvement of the fluorescence brightness upon broadband excitation in comparison with its constituent chromophores.</p>
Dataset: Utilization of Novel (KNbO3)1-x(Ba2FeNbO6)x (x = 0.1, 0.2, 0.3) Solid Solutions for Efficient Photo-assisted Fenton Degradation of Methylene Blue Dye
<p>Supplemental information containing the inputs and outputs of all DFT calculations performed as part of this work.</p> <p>This archive contains the following scripts:</p> <ul> <li>defects_workup.py: a Python script for processing all calculations in a given folder. It extracts the total energy, estimated SCF accuracy (for non-converged results), and convergence status (true/false) for all cases found in each subfolder. For converged calculations, the mean Ba-Ba distance and its standard deviation as well as the mean Ba-Fe distance and its standard deviation is calculated. </li> <li>bands_plotter.ipynb: a Jupyter notebook for band structure analysis.</li> <li>ase_rdf.ipynb: a Jupyter notebook for bond distance vs energy analysis</li> </ul> <p>Furthermore, the following data is included:</p> <ul> <li>3x2x2.json: the output json file generated for the 3x2x2 dataset using defect_workup.py</li> <li>3x2x2.7z: a compressed folder containing the 3x2x2 dataset with QE input and output files.</li> <li>3x2x2-v2.7z: a compressed dataset containing some supplementary calculations used in band plotting.</li> </ul>
Controlling the Supramolecular Polymerization of Squaraine Dyes by a Molecular Chaperone Analogue
<p>ABSTRACT: Molecular chaperones are proteins that assist in the (un)folding and (dis)assembly of other macromolecular structures toward their biologically functional state in a non-covalent manner. Transferring this concept from nature to artificial self-assembly processes, here, we show a new strategy to control supramolecular polymerization via a chaperone-like two-component system. A new kinetic trapping method was developed that enables efficient retardation of the spontaneous self-assembly of a squaraine dye monomer. The suppression of supramolecular polymerization could be regulated with a cofactor, which precisely initiates self-assembly. The presented system was investigated and characterized by ultraviolet–visible, Fourier transform infrared, and nuclear magnetic resonance spectroscopy, atomic force microscopy, isothermal titration calorimetry, and single-crystal X-ray diffraction. With these results, living supramolecular polymerization and block copolymer fabrication could be realized, demonstrating a new possibility for effective control over supramolecular polymerization processes.</p>
Generation of Random laser from Dye-Derived Red-Emitting Carbon Dots
<p>Carbon dots are carbon-based nanoparticles renowned for their intense light-emitting capabilities covering the whole visible light range. Here, we overcome these problems by solvothermally synthesizing carbon dots starting from Neutral Red, a common red-emitting dye, as a molecular precursor. The obtained nanoparticles are highly luminescent in the red region, with a quantum yield comparable to that of the starting dye. Most importantly, the nanoparticle carbogenic matrix protects the Neutral Red molecules from photobleaching under ultraviolet excitation while preventing aggregation-induced quenching, thus allowing solid-state emission inside PVA. Finally, the dye-based carbon dots demonstrate stable and efficient random lasing emission in the red region.</p>
Absorption and Emission Spectral Data of Room-temperature Rhodamine 6G Dye Solution and some typical Dye Microcavity parameters
<p>The repository contains spectral absorption and emission data [absorption cross section and Einstein coefficients] of rhodamine 6G dye solved in ethylene glycol at room temperature over the visible spectral range from 400.25nm to 619.85nm. In addition, typical values for the cavity loss rate are given for the same wavelength range. The data can be used e.g. for studies of two-dimensional thermalized photon gases and Bose-Einstein condensates of photons inside dye-filled optical microcavities.</p> <p><strong>Methodology</strong></p> <p>The absorption data has been obtained by white-light absorption spectroscopy of dye solutions with increasing concentration {0.01,0.1,1} mMol/Litre. The combined spectra have been calibrated with the rhodamine absorption cross section at 532nm wavelength, which we have independently determined in transmission measurements with a 532nm laser. The absorption cross section in this data repository constitutes a universal material property that is generally valid for rhodamine 6G solved in ethylene glycol at room temperature.</p> <p>The Einstein coefficient for absorption B_12 has been obtained specifically for the volume of the transverse ground mode in an optical microcavity formed by two curved mirrors with radius of curvature R = 1 and cavity length D = 1.5µm; see e.g. Klaers et al., <em>Nature</em> <strong>468</strong>, 545–548 (2010), Schmitt, <em>Phys. B: At. Mol. Opt. Phys.</em> <strong>51</strong>, 173001 (2018) and related work by the authors. For typical dye concentrations near 1mMol/Litre, approximately 10^8 molecules are contained in the ground mode volume. The Einstein coefficient for emission B_21 is deduced from B_12 assuming the Kennard Stepanov relation: B_21/B_12 = Exp[-h*c*(1/lambda - 1/lambda_zpl)/(k_B T)], where lambda_zpl = 545nm denotes the zero-phonon line of rhodamine 6G dye (h: Planck's constant, c: speed of light, lambda: wavelength, k_B: Boltzmann's constant, T: temperature). We have verified that the resulting B_21 spectrum agrees well with reference fluorescence spectra of rhodamine 6G. </p> <p>The spectral cavity loss rate c/(n0*D)*(1-R-A) with refractive index n0 = 1.43 and mirror absorption loss A = 1ppm is deduced from the wavelength-dependent mirror reflectivity R, which we have measured in cavity ring-down measurements at more than 10 wavelengths in the interval between 530nm to 605nm. For this, a tuneable dye laser was resonantly coupled into a 3.3cm-long cavity formed by the corresponding highly-reflecting dielectric mirrors. Note that the reciprocal values of the loss rates give the 1/e lifetime of the photons in the cavity.</p> <p><strong>Data format</strong></p> <p>The file 'data.dat' contains all data sorted by columns: wavelength (in units of nm), absorption cross section (in units of m^2), Einstein coefficients for absorption and emission (both in units of Hz), cavity loss rate (in units of Hz).</p>
Charge-Selective Photocatalytic Degradation of Organic Dyes using Halloysite Nanotubes
<p>This study explores the use of Halloysite NanoTubes (HNTs) as photocatalysts capable of<br>decomposing organic dyes under exposure to visible or ultraviolet light. We observe that the extent of RhB<br>photocatalytic degradation in 100 min in the presence of the HNTs is ~4 times higher compared to<br>that of bare RhB. Moreover, under optimized conditions, the as-extracted photodegradation rate of<br>RhB (~0.0022 /min) is comparable to that of the previously reported work on the photodegradation<br>of RhB in the presence of tubular nanostructures. A parallel effect is observed for anionic Coumarin<br>photodegradation, albeit less efficiently. By leveraging the unique properties of HNTs, a family of naturally occurring<br>nanotube structures, this research offers valuable insights for optimizing photocatalytic systems in<br>the pursuit of effective and eco-friendly solutions for environmental remediation.</p>
Raw data for the article "Organic Dye Photocatalyzed Synthesis of Functionalized Lactones and Lactams via a Cyclization-Alkynylation Cascade"
<p>Raw NMR and MS data for the article "Organic Dye Photocatalyzed Synthesis of Functionalized Lactones and Lactams via a Cyclization-Alkynylation Cascade" published in Organic Letters, DOI: </p> <p><a title="DOI URL" href="https://doi.org/10.1021/acs.orglett.3c03603">https://doi.org/10.1021/acs.orglett.4c01078</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Fig 1A in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Fig 1A: Section passing through gill of fresh water bivalve Lamellidensmarginalisfrom control group (400X). B: Effect of 40 ppm (LC0) of Basic Blue 3 on gill of fresh water bivalve Lamellidensmarginalis after 96 hours exposure (400X) C: Effect of 70 ppm (LC50) of Basic Blue 3 on gill of fresh water bivalve Lamellidenmarginalis after 96 hours exposure (400X)
Fig 2A in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Fig 2A: Section passing through hepatopancreas of fresh water bivalve Lamellidens marginalis from control group (400X). B: Effect of 40 ppm (LC0) of Basic Blue 3 on hepatopancreas of fresh water bivalve Lamellidens marginalis after 96 hours exposure (400X) C: Effect of 70 ppm (LC50) of Basic Blue 3 on hepatopancreas of fresh water bivalve Lamellidens marginalis after 96 hours exposure (400X)
Fig 4A in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Fig 4A: Photomicrogragh of gill cell of Lamellidens marginalis for 96 hours exposure; degree of damage class 0 B: Photomicrogragh of gill cell of Lamellidens marginalis for 96 hours exposure to 40 ppm concentration of Basic blue 3; degree of damage class 0 C: Photomicrogragh of gill cell of Lamellidens marginalis for 96 hours exposure to 70 ppm concentration of Basic blue 3; degree of damage class I
Fig 3A in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Fig 3A: Section passing through gonad of fresh water bivalve Lamellidens marginalis from control group (400X). B: Effect of 40 ppm (LC0) of Basic Blue 3 on gonad of fresh water bivalve Lamellidens marginalis after 96 hours exposure (400X) C: Effect of 70 ppm (LC50) of Basic Blue 3 on gonad of fresh water bivalve Lamellidens marginalis after 96 hours exposure (400X)
Graph 1 in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Graph 1: Changes in SODactivity in different tissues of fresh water bivalve, Lamellidens marginalis after acute exposure to basic blue 3(values are expressed in unit/mg protein/hour)
Graph 4 in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Graph 4: DNA strand breaks in gill cells of Lamellidens marginalis after acute exposure to Basic blue 3.
Graph 2 in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Graph 2: Changes in CAT activity in different tissues of fresh water bivalve, Lamellidens marginalis after acute exposure to basic blue 3 (values are inmmolH2O2/min/mg protein)
Graph 3 in Toxicological assessments of basic blue 3 dye in fresh water bivalve Lamellidens marginalis
Graph 3: Changes in GPx activityin different tissues of fresh water bivalve, Lamellidens marginalis after acute exposure to basic blue 3 (values are in mmol NADPH/min/mg protein)
Figure 1 in Applicability of the vital dyes neutral red and fluorescein diacetate to differentiate between alive and dead non-copepod zooplankton
Figure 1. Intensity of staining of the Black Sea zooplankton with neutral red (NR) and fluorescein diacetate (FDA). 1 (FDA), 2 (NR) – Penilia avirostris; 3, 4 (FDA), 5, 6 (NR) – Pleopis polyphemoides; 7, 8 (FDA), 9 (NR) – Evadne spinifera; 10 (FDA), 11 (NR) – Pseudevadne tergestina; 12, 13 (FDA), 14, 15 (NR) – Cirripedia nauplii; 16 (NR), 17 (FDA) – Rotifera; 18, 19 (FDA), 20, 21 (NR) – Polychaeta larvae; 22, 23 (FDA), 24 (NR) – Decapoda larvae; 25 (NR), 26 (FDA) – Pisces ova; 27 (NR) – Pisces larvae; 28 (FDA), 29 (NR) – Parasagitta setosa; 30 (FDA), 31 (NR) – Oikopleura dioica; 32, 33 (FDA), 34 (NR) – Noctiluca sсintillans; 35 (NR) – Hydromedusae; 36 (NR), 37 (FDA) – Bivalvia larvae; 38, 41 (NR), 39, 40 (FDA) – Gastropoda larvae.
Figure 1 in Decolorization of the benzidine-based azo dye Congo red by the new strain Shewanella xiamenensis G5-03
Figure 1. Neighbor-joining phylogenetic tree based on 16S rDNA gene sequences showing the relationships of strain G5-03 with other Shewanella species found in the GenBank. Numbers at nod shows the percentage of 1000 bootstrap replicates. The bar indicates 0.005 substitutions per nucleotide position.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.