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48 results for “Porphyrins”
Research Data supporting "Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization"
<p>Raw research data supporting the article E. Weyandt, L. Leanza, R. Capelli, G. M. Pavan, G. Vantomme, and E.W. Meijer, "Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization".</p>
Raw data for 'Increasing the Modulation Depth of Gd(III)-based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-GdIII Laser Induced Magnetic Dipole Spectroscopy'
<p>Raw data for 'Increasing the Modulation Depth of Gd(III)-based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-GdIII Laser Induced Magnetic Dipole Spectroscopy'</p>
BIR-MicroED: selected area electron diffraction tilt series datasets used to determine representative structures of biotin, Cu(II)-serine, Zn(II)-methionine, Zn(II)-histidine, and Co(II)-porphyrin
<div> <div> </div> </div> <div> <p>This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format (except for the data collected from Co(II) porphyrin, which are 300 kV data in .tvips file format). Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature), where the reduced data from each were merged to determine a single representative structure of the compound by microED. Zip files are named according to the format: <em>"CompoundName</em>_<em>AcceleratingVoltage</em>_<em>Temperature_</em>structuredatasets.zip"</p> <p>Diffraction datasets within each folder are named according to the format: <em>CompoundName</em>_structuretiltseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>_crystal#.mrc (or .tvips).</p> <p>All 200 kV datasets were collected with a rotation speed of 1 degree/second and an effective frame rate of 1 frame/second, with the exception of two Zn(II) methionine datasets collected with a frame rate of 3 frames/second. These are noted by the presence of "3fps" in the file name.</p> <p>All 300 kV datasets were collected with a rotation speed of 0.03 degrees/second and a frame rate of 0.5 frames/second.</p> </div>
Data for: Charge Delocalization and Global Aromaticity in a Partially Fused 12-Porphyrin Nanoring
<p><span>The xyz coordinates for the calculated geometries (B3LYP/6-31G*) of <strong><em>c</em>-P12[b<sub>6</sub>f<sub>6</sub>]•(T6<sub>A</sub>)<sub>2</sub></strong>, <strong><em>c</em>-P12[b<sub>6</sub>f<sub>6</sub>]</strong></span><strong><span>•</span><span>(T6<sub>B</sub>)<sub>2</sub> </span></strong><span>and <strong><em>c</em>-P12[b<sub>6</sub>f<sub>6</sub>]</strong></span><strong><span>•</span><span>T6<sub>A</sub></span><span>•</span><span>T6<sub>B</sub></span></strong><span> (shown in Figure 3) and of <strong><em>c</em>-P12[b<sub>6</sub>f<sub>6</sub>]</strong> (BLYP35/def2-SVP or 6-31+G*) in its neutral, 2+, 4+, 6+, 8+, 2–, 4– and 6– oxidation states.</span></p>
Data for: Cationic Polaron Delocalization in Porphyrin Nanoribbons
<p>The xyz coordinates for the calculated geometries (B3LYP/6-31G*) of radical cations <strong>P<em>N</em></strong><strong><sup>·+</sup></strong> for <em>N</em> = 1, 2, 3, 4, 6, 10, 14 and 18.</p>
Data for: Bimolecular Sandwich Aggregates of Porphyrin Nanorings
<p><em><span>Supporting data files for "Bimolecular Sandwich Aggregates of Porphyrin Nanorings”</span></em></p> <p><span><span>(a) <strong>PALES_structures</strong></span>. Files for analyzing RDCs: input text file (1 txt file), input geometries (61 pdb files) and output (61 txt files).</span></p> <p><span>(b) <strong>XTB_optimized_structures</strong></span>. Geometries of bimolecular aggregates of <strong><em>c-</em>P8</strong> and <strong><em>c-</em>P12</strong> with different substituents (4 xyz files).</p> <p><span><span>(c) <strong>TS_trajectory_structures</strong></span>. Calculated geometries along the transition state trajectory for intramolecular rotation of the <strong>(<em>c-</em>P12_t-Bu)2</strong> aggregate (9 xyz files).</span></p> <p><span><span>(d) <strong>Planarization_calculations</strong></span>. DFT calculated geometries of <strong><em>c-</em>P6</strong>, <strong><em>c-</em>P8</strong>, <strong><em>c-</em>P10</strong>, <strong><em>c-</em>P12</strong> and <strong><em>c-</em>P14</strong> when 2D planar (optimized in xy-plane) or 3D cylindrical (10 xyz files).</span></p> <p><span><span>(e) <strong>Molecular_Dynamics_GROMACS_input_files</strong></span>. Molecular dynamics input files for <strong>(<em>c-</em>P8_OOct)2</strong> and <strong>(<em>c-</em>P12_tBu)2</strong> (2x gro+top+itp+4xmdp).</span></p> <p><span><span>(f) <strong>cP12_tBu_2_structure</strong></span>. Idealized structure for the <strong>(<em>c-</em>P12_t-Bu)2</strong> aggregate as shown in Figure 3 of the manuscript (1 xyz file).</span></p>
Polymorphism and flexibility of six-porphyrin nanorings in the solid state
<p>Computational output files and optimized geometries for our research paper.</p>
BIR-MicroED: TEM image series revealing bend contour motion in static microcrystals (biotin, Zn(II)-methionine, Co(II)-porphyrin, AVAAGA) and diffraction patterns acquired from the same crystals at 200 kV
<p>This deposition contains a series zip files each containing TEM image series and electron diffraction images in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: <em>"CompoundName</em>_bendcontour_imageseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>.zip"</p> <p>Data is further divided into sub-directories according to the particular crystal studied (crystal1, crystal2, crystal3), each containing a TEM image series (name format: "<em>CompoundName</em>_static_imageseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>_crystal#.mrc") and 10 diffraction snapshots (2 frames each, each convering 1 second of electron beam exposure) acquired at equally spaced time intervals throughout the image series. These are named according to the format:</p> <p>"CompoundName_bendcontour_crystal#_diffraction_snap#.mrc"</p>
Data for: Molecular Aharonov-Bohm Interferometers Based on Porphyrin Nanorings
<p>The directories in this dataset contain:</p> <p>./cpn<br>xyz files: Optimized geometries of the c-PN porphyrin nanorings using the GFN1-xTB method in the absence of a magnetic field. <br>txt files: Orbital energies of the c-PN porphyrin nanorings relative to its HOMO-LUMO gap center in the absence of a magnetic field calculated using the GFN1-xTB-M1 method where first number in each line is the magnetic field strength (Tesla) and the remaining numbers are the orbital energies (eV).</p> <p>./cpn_flat<br>xyz files: Optimized geometries of the flattened c-PN porphyrin nanorings using the GFN1-xTB method in the absence of a magnetic field. <br>txt files: Orbital energies of the flattened c-PN porphyrin nanorings relative to its HOMO-LUMO gap center in the absence of a magnetic field calculated using the GFN1-xTB-M1 method where the first number in each line is the magnetic field strength (Tesla) and the remaining numbers are the orbital energies (eV).</p> <p>./current<br>txt files: The calculated current as a function of the external magnetic field for the specified Fermi transport windows and electronic temperatures where the first number in each line is the magnetic field strength (Tesla) and the second number is the current (micro Amps).</p> <p>./finite_junction<br>xyz files: Optimized geometries of the finite junction model using the GFN1-xTB method in the absence of a magnetic field. <br>txt files: Orbital energies of the finite junction model relative to the HOMO-LUMO gap center of the c-P10 nanoring in the absence of a magnetic field calculated using the GFN1-xTB-M1 method where the first number in each line is the magnetic field strength (Tesla) and the remaining numbers are the orbital energies (eV).</p> <p>./fpn<br>xyz files: Optimized geometries of the f-PN porphyrin nanobelts using the GFN1-xTB method in the absence of a magnetic field. <br>txt files: Orbital energies of the f-PN porphyrin nanobelts relative to its HOMO-LUMO gap center in the absence of a magnetic field calculated using the GFN1-xTB-M1 method where the first number in each line is the magnetic field strength (Tesla) and the remaining numbers are the orbital energies (eV).</p> <p>./transmission<br>txt files: The transmission function calculation results using the NEGF+GFN1-xTB-M1 method for a number of field strengths and biased electron densities where the 1st, 2nd and 3rd numbers in each line are the energy (Hartree) relative to the HOMO-LUMO gap center of the c-P10 nanoring in the absence of a magnetic field, transmission probability, and density of states.</p> <p>./transmission_homo-1<br>txt files: The transmission function calculation results using the NEGF+GFN1-xTB-M1 method for energies around the HOMO-1 and HOMO-2 peaks for a number of field strengths where the 1st, 2nd and 3rd numbers in each line are the energy (Hartree) relative to the HOMO-LUMO gap center of the c-P10 nanoring in the absence of a magnetic field, transmission probability, and density of states.</p>
Dataset - Removal of diclofenac by adsorption process studied in free-base porphyrins Zr-metal organic frameworks (Zr-MOFs)
<p>Dataset for the paper entitled "Removal of diclofenac by adsorption process studied in free-base porphyrins Zr-metal organic frameworks (Zr-MOFs) "</p>
Numerical data for systemic effects of photoactivated 5,10,15,20-tetrakis(N-methylpyridinium-3-yl) porphyrin on healthy Drosophila melanogaster
Open the record for dataset details and reuse information.
Ferrocene Appended Porphyrin Based Bipolar Electrode Material for High Performance Energy Storage -Data for publication
<p>All combined datasets</p>
Data for: Template-Directed Synthesis of Strained meso-meso-Linked Porphyrin Nanorings
<p>Calculated molecular xyz coordinates from molecular dynamics simulations, StrainViz calculations and screening of ligand designs.</p>
DLS measurements of WS2 flakes, AuNP@WS2 and porphyrin-functionalized AuNP@WS2
<p>This dataset contains DLS (dynamic light scattering) investigations on WS2 nanoflakes decorated with Au NP and THPP (<span>5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin</span>).</p>
Exploring the chemical and structural change of copper porphyrins upon charging by means of synchrotron X-ray absorption spectroscopy
<h2><span>Abstract</span></h2> <p><span>In response to the growing demand for battery materials, researchers explore alternative resources with a focus on sustainability. Among these, organic electrode materials—including porphyrins—have emerged as promising candidates due to their advantageous properties, such as rapid charging capabilities and high energy densities. However, despite their potential, the precise charging mechanism of these alternatives remains elusive. To address this gap, our study delved into copper porphyrins, with a primary focus on [5,15-bis(ethynyl)-10,20-diphenylporphinato] copper(II) (CuDEPP). Employing synchrotron X-ray absorption spectroscopy in <em>operando</em> mode, we probed the evolution in chemical and electronic structure of Cu in CuDEPP. Our findings unequivocally demonstrate the participation of copper as a redox center during reversible charge storage, shedding light on its superior electrochemical performance. Furthermore, a combined approach involving extended X-ray absorption fine structure (EXAFS) studies and theoretical calculations provided deeper insights into the observed structural distortion during the charge storage process. Notably, our results support the hypothesis that redox processes, specifically those involving the aromatic porphyrin ring, drive the electrochemical activity of CuDEPP. In summary, our investigation offers important insights into the charging mechanism of copper porphyrins—an essential step toward advancing sustainable organic materials for batteries. </span></p>
Influence of Keto-Enol Tautomerism in Regulating CO2 Photoreduction Activity in Porous Organic Porphyrinic Photopolymer
<p><span>This folder contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</span></p> <p><span>"Influence of Keto-Enol Tautomerism in Regulating CO2 Photoreduction Activity in Porous Organic Porphyrinic Photopolymer"</span></p> <p><span>In the naming of the structures, suffix "m" denotes model, e.g., POP-1m is model system for POP-1 and so on; suffix "n" denotes the enone form of the POP, e.g., POP-1n is the enone form of POP-1m and so on. "rc" denotes radical cation and "ra" denotes radical anion.</span></p>
Publication data for "Symmetry breaking fluctuations split the porphyrin Q bands"
<p>This directory contains all files necessary to reproduce the data presented in "Symmetry breaking fluctuations split the porphyrin Q bands" by Z. R Wiethorn, K. E. Hunter, A. Montoya-Castillo and T. J. Zuehlsdorff.<span> </span></p> <p>The folder "Frequency_analysis" contains input and output files for Gaussian ground-state frequency calculations of porphine, TPP, and TPPL.</p> <p>The folder "MD_simulations" contains raw trajectory files, as well as all input data necessary to reproduce QM/MM simulations of porphine, TPP and TPPL in CS2 solvent. Calculations are run using an interface between the classical MD code AMBER and thequantum chemistry code TeraChem. AMBER .paramtop and restart files, as well as Terachem files for the QM region are provided. Additionally, example terachem files for computing vertical excitation energies for individual snapshots are provided.</p> <p>The folder spectra_generation contains raw data of transition dipole and energy gap fluctuationsalong the MD trajectory, after the appropriate Eckart rotation and determination of the correct sign of the dipole moment. It also contains input files for the MolSpeckPy code, that can beused to generate spectra in the GCT and GNCT schemes. Finished spectra, energy gap and dipole spectral densities that are analysed in the main text are also provided. Additionally, we provide input and output files to compute optical spectra for TPPL and TPPL without its phenol rings in the FCHT scheme implemented in Gaussian.</p>
Data for publication: Encapsulation of an Au25 Nanocluster inside a Porphyrin Nanoring Enhances Singlet Oxygen Generation and Photo-Electrocatalytic CO2 Reduction (Angewandte Chemie 2024)
<p>Original data of the paper Encapsulation of an Au25 Nanocluster inside a Porphyrin Nanoring Enhances Singlet Oxygen Generation and Photo-Electrocatalytic CO2 Reduction (Angewandte Chemie 2024)</p>
Type-I Hemins and Free Porphyrins from a Western Australian Sponge Isabela sp.
<p>Supporting information</p> <p> </p> <p>NMR (1H, 1H-1H-COSY, HSQC, HMBC, NOESY) <br> Single crystal X-ray diffraction data of 1a (CIF)<br> Single crystal X-ray diffraction data of 1b (CIF)</p>
Sputum Labeling Utilizing Synthetic Meso-Tetra (4-Carboxyphenyl) Porphyrin (TCPP) for Detection of Lung Cancer
ClinicalTrials.gov study NCT03837600. IPD Sharing: NO. Countries: 1. Publications: 1.
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