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74 results for “Hydroxyl”
Supplementary Data to Kinetic oxygen isotope fractionation between water and aqueous OH- during hydroxylation of CO2
<p>In this dataset, we provide analytical data to <strong>Kinetic oxygen isotope fractionation between water and aqueous OH<sup>-</sup> during hydroxylation of CO<sub>2</sub></strong> by Bajnai and Herwartz (2021). Also deposited here is the R code that was used to generate the figures in the manuscript.</p>
Dataset for: Exploring the Possibility of Identifying Hydride and Hydroxyl Cations of Noble Gas Species in the Crab Nebula Filament.
<p>The repository contains the spectroscopic information of ArOH+, NeOH+, and HeOH+ described in Appendix B of the accepted manuscript, "<em>Exploring the Possibility of Identifying Hydride and Hydroxyl Cations of Noble Gas Species in the Crab Nebula Filament</em>."</p> <p>The values given in the files are provided for both the ground vibrational and equilibrium values of rotational constants calculated by Theis & Fortenberry (2016) in case of ArOH+ and NeOH+, whereas, in the case of HeOH+, calculated parameters in this work are used (Please see Table B1). Ground and equilibrium values are stored in separate subdirectories. The files are provided in the <a href="http://spec.jpl.nasa.gov/ftp/pub/catalog/README">JPL spectral line catalog format</a>. </p> <p>More information is found in the documentation, ReadMe.md.</p>
(DATASET) (10,0) carbon nanotubes functionalized with carboxyl and hydroxyl organic groups
<p>Starting from a (10,0) carbon nanotube, 10 000 structures where randomly generated for both functionalizations (carboxyl, -COOH, and hydroxyl, -OH) and for 5 concentrations of the surface being funcionalized (5%, 10%, 15%, 20% and 25%). Then, the entropy of all system was calculated. The structures with highest entropy on each group/percentage where selected as representative of each functionalization.</p> <p>Here are the structures of functionalized (10,0) carbon nanotubes in MOL2 and XYZ formats.</p> <p>These systems were used in the following publications:</p> <ul> <li>M.S. Ribeiro, A.L. Pascoini, W.G. Knupp, I. Camps. <em>Effects of surface functionalization on the electronic and structural properties of carbon nanotubes: A computational approach</em>. Applied Surface Science 426 (2017) 781–787. DOI: <a href="http://dx.doi.org/10.1016/j.apsusc.2017.07.162">10.1016/j.apsusc.2017.07.162</a></li> <li>W.G. Knupp, M.S. Ribeiro, M. Mir, I. Camps. <em>Dynamics of hydroxyapatite and carbon nanotubes interaction</em>. Applied Surface Science 495 (2019) 143493. DOI: <a href="https://doi.org/10.1016/j.apsusc.2019.07.235">10.1016/j.apsusc.2019.07.235</a></li> </ul>
Direct assessment of the acidity of individual surface hydroxyls_experimental dadaset
<p>This dataset contains the raw experimental data for the article "Direct assessment of the acidity of individual surface hydroxyls" by Margareta Wagner, Bernd Meyer, Martin Setvin, Michael Schmid & Ulrike Diebold in <a href="https://www.nature.com/"><em>Nature</em></a> <strong>volume 592</strong>, pages722–725 (2021). </p>
Dataset for Hydrogen Atom Abstraction from Methane by Hydroxyl Radical
<p>Data for the reaction OH + CH4 −−→ CH3 + H2O. Contains 167196 geometries and corresponding {omega}B97X/6-31G(D) energies, 12416 geometries and corresponding CCSD(T)/aug-cc-pvtz energies.</p>
Atmospheric hydroxyl distribution from the EMAC model (MOM kinetic chemistry mechanism)
<p>This dataset contains the output from the simulations with the EMAC model implementing the MOM kinetic chemistry mechanism presented in <a href="https://doi.org/10.5194/acp-16-12477-2016">Lelieveld et al. (2016)</a> study. In addition to the computed atmospheric hydroxyl (OH) and hydroperoxyl (HO2) radicals abundance distributions, we add related model fields facilitating usage/comparison of these results with other estimates.</p><p>The data containers format is netCDF v.4 (compressed); please refer to the container variables/attributes for the extended information. We present here the actual model output (weekly averages for the 2013−2014 period, in EMAC-MOM__*.nc) and the monthly "climatology" fields (average, SD, minima and maxima of the time steps falling in particular month, in EMAC-MOM__*--clim.nc, respectively).</p><p>See the .README.pdf file for additional notes.</p><p>Changes w.r.t. initial version from 2020/09/22:</p><p>2020/10/30: Updated attributes and DOIs in .nc/.jnl files, added OH "climatology", updated README.</p><p>2020/10/31: Updated description and "climatology" (SD fields were missing).</p><p>2022/06/19: Added hydroperoxyl (HO2) fields, updated species average concentration plot sample script.</p><p>2023/10/26: Dataset title adjusted for clarity</p>
Data for Estimate of water and hydroxyl abundance on asteroid (16) Psyche from JWST data
<p>The data as ASCII files used to produce the figures in the manuscript, " Estimate of water and hydroxyl abundance on asteroid (16) Psyche from JWST data". Almost all the files are ECSV files created from astropy Table. These files have complete metadata headers. Otherwise, the data, where appropriate, include s3d fits IFU data cubes used to produce 1D spectra, the solar spectra output by the Planetary Spectrum Generator, a thermophysical model output, asteroid reflectance measurements, and chondrite reflectance measurements all of which are described in further detail below. </p> <p>The Figures folder contains data behind the figures where data were used.</p> <p>For Figure 2 this corresponds to the NIRSpec and MIRI flux observations with a column for wavelength (in microns), flux (in Jansky), and error (in Jansky). </p> <p>For Figure 3 this corresponds to the normalized reflectance for the NIRSpec observations. The first column in each dataset corresponds to the wavelength in microns, the second column to the normalized reflectance (unitless), the third column to the error (unitless), and in the case of the .txt files the fourth column corresponds to the gaussian fit to the normalized reflectance. </p> <p>For Figure 4 these are the normalized reflectance divided by the continuum of the groups of data along wavelength ranges described in the manuscript for Figure 4. The first column corresponds to the wavelength in microns, the second column to the reflectance, the third column to the continuum fit to the data, the fourth column is the normalized reflectance divided by the continuum, and the error. </p> <p>For Figure 5 these are the data used to produce the 3-micron feature plot with the gaussian fit for each NIRSpec observation. The first column corresponds to the wavelength in microns, second column to the normalized reflectance divided by the continuum (unitless) and subtracted from the mean of the continuum between 3.6 and 3.7 microns such that the average of the continuum would be 0, the fourth column the error (unitless), and the fifth column the gaussian fit to the data. </p> <p>For Figure 6 the only additional data needed to produce this plot beyond what is provided for Figure 5 is the IRTF data which is provided as a text file. The first column corresponds to the wavelength in microns, the second column to the normalized reflectance divided by the continuum (unitless), and the third column to the error (unitless). </p> <p>For Figure 7 the additional data used to produce this plot beyond what is provided for Figure 5 includes laboratory reflectance measurements of various chondrites. The .scl files are the original laboratory measurements where the first column corresponds to the wavelength in microns, the second column to the normalized reflectance (unitless) and the third column to the error to 1 significant digit (unitless). The scaled_lab_reflectance.txt file has all the laboratory reflectance data used to produce the Figure 7 plot that includes the wavelength in microns, the normalized scaled reflectance for the CM chondrite, the normalized scaled reflectance for the CH/CBb chondrite, and the normalized scaled reflectance for the CY chondrite. </p> <p>For Figure 8 the additional data include original normalized reflectance data for asteroids interamnia, themis, bamberga, and europa as .trim files. The columns for these files correspond to wavelength in microns, normalized reflectance (unitless), and the error (unitless). The 'continuumremoved' .txt files correspond to the wavelength in microns and the normalized reflectance divided by the continuum (unitless). </p> <p>For Figure 9 these are the MIRI emissivity data for the two sets of observations. The first column corresponds to the wavelength in microns, the second column to the normalized emission by taking the flux subtracting the solar flux and dividing by a thermophysical model (unitless), the error (unitless), and the gaussian fit to the normalized emission. </p> <p>For the supplemental figures these are the additional fit absorption features that are located in the appendix of the manuscript. For the 1.25 - 4.8 micron text files the columns correspond to the wavelength in microns, the continuum divided normalized reflectance (unitless), the error (unitless), and the gaussian fit. For the 5.74 - 5.98 micron text files the columns correspond to wavelength in microns, normalized emission divided by a linear fit to a region outside any potential features (unitless), the error (unitless), and the gaussian fit to the feature. </p> <p>The MIRI 1D spectra folder contains the ASCII files corresponding to the 1 arcsec aperture summed spectra from the MIRI observations. The columns correspond to wavelength in microns, flux in Jansky, and error in Jansky. </p> <p>The NIRSpec 1D spectra folder contains the ASCII files corresponding to the 1 arcsec aperture summed spectra from the NIRSpec observations. The columns correspond to wavelength in microns, flux in Jansky, and error in Jansky. </p> <p>The Solar Spectra folder contains the solar spectra flux used to reduce the data to produce the reflectance and emission spectra. The lbl text files are equivalent to the files with the same name without the lbl but also include the column information. The first column corresponds to the wavelength in microns, the second column to the total spectral irradiance in Jansky, the third column to the flux from the object in Jansky, the fourth column to the reflected sunlight in Jansky, and the fifth column to the thermal contribution in Jansky. The only column used for the solar reflectance used in the analysis corresponds to the fourth column. </p> <p>The ThermalModel folder contains the ASCII files with the data corresponding to the thermophysical model used to produce the reflectance (by subtracting the thermal contribution) and the emission (by dividing by the thermal contribution). The first column corresponds to the wavelength in microns, the second to the thermal flux in Jansky, the third to the smoothed thermal flux in Jansky, and the fourth column to the normalized thermal flux. Only column two corresponding to the thermal flux in Jansky was used in the analysis associated with the manuscript. </p>
Dataset: Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates
<p>The derived data is part of a manuscript submitted to the journal Green Chemistry, entitled "Catalytic pyrolysis mechanism of lignin moieties driven by aldehyde, hydroxyl, methoxy, and allyl functionalization: the role of reactive quinone methide and ketene intermediates". [DOI https://doi.org/10.1039/d4gc03143a. This work is supported by the Swiss National Science Foundation (project number 200021_178952)</p> <p>Raw data can be found: https://doi.org/10.16907/1ac46f03-6e1b-4230-b5c0-3df2cec87b5e</p> <p>The raw Photoelectron Photoion Coincidence (PEPICO) data were obtained during catalytic fast pyrolysis of eugenol, vanillin, syringol over H-ZSM-5 and HFAU. The analysis software can be obtained from: https://www.psi.ch/en/sls/vuv/pepico. The folders contain mass spectra and threshold photoelectron raw data at different reactor temperatures.</p>
Measuring the Variability of Hydroxyl Emissions in Infrared Sky Spectra using SPIRou: Dataset
<p>Abstract</p> <p>Subtracting the changing sky contribution from the near-infrared (NIR) spectra of faint astronomical<br>objects is challenging and crucial to a wide range of science cases such as estimating the velocity<br>dispersions of dwarf galaxies, studying the gas dynamics in faint galaxies, and accurate redshifts, and<br>any spectroscopic studies of faint targets. Since the sky background varies with time and location, NIR<br>spectral observations, especially those employing fiber spectrometers and targeting extended sources,<br>require frequent sky-only observations for calibration. However, sky subtraction can be optimized<br>with sufficient a priori knowledge of the sky’s variability. In this work, we explore how to optimize sky<br>subtraction by analyzing 1075 high-resolution NIR spectra from the CFHT’s SPIRou on Maunakea,<br>and we estimate the variability of 481 hydroxyl (OH) lines. These spectra were collected during two<br>sets of three nights dedicated to obtaining sky observations every five and a half minutes. During<br>the first set, we observed how the Moon affects the NIR, which has not been accurately measured at<br>these wavelengths. We suggest that if one uses a principal component analysis reconstruction of the<br>sky spectrum and attempts to observe targets at Y JHK mags fainter than ∼15 and attempts a sky<br>subtraction better than 1%, then the Moon contribution must be accounted for at Moon separation<br>distances of at least 10◦. We also identified 126 spectral doublet, or OH lines that split into at least two<br>components, at SPIRou’s resolution. In addition, we used Lomb-Scargle Periodograms and Gaussian<br>process regression to estimate most OH lines vary on similar timescales, which provides a valuable<br>input for IR spectroscopic survey strategies. The data and code developed for this study are publicly<br>available here.</p> <p>Dataset description</p> <p>In total, we collected 1075 sky observations, which spanned from July 28th, 2018 to January 10th, 2022, or approximately 3.5 years. These observations included two sets of three days dedicated to sky measurement where each day, a sky spectrum was observed approximately every 5.5 minutes for 12 hours. These days occurred on December 14th, 15th, and 16th of 2019 and January 22nd, 23rd, and 25th 2020. These 1D extracted and flat fielded sky spectra have a wavelength range of 0.965 − 2.500μm containing 285,377 wavelength bins resampled on a uniform wavelength grid with a step of 1 km/s/pixel. Since the pixels were constant in velocity, the change in wavelength increased from 3x10^−6 − 8x10^−6 μm per pixel. All observations were affected by a steep black body curve starting at 2.1μm, which was caused by thermal emission.</p> <p>We also present a table of doublets identified during this study with the transition, the measured singlet line from Rousselot 2000 (mu0), the doublet lines (mu1 and mu2), and if the line was identified as a doublet (Y/N).</p>
Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water
<p>The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H<sub>3</sub>O<sup>+</sup>) that was formed within 140 femtoseconds through a direct oxygen-oxygen bond contraction and proton transfer, followed by the radical-cation pair dissociation and the subsequent structural relaxation of water within 250 femtoseconds. These measurements provide direct evidence of capturing this metastable radical-cation complex before separation, thereby improving our fundamental understanding of elementary reaction dynamics in ionized liquid water.</p>
Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign
<p>To make it consistent with our manuscript, in this version of Zenodo dataset, all "conformers" have been changed to "poses" in the file names and the contents of the Perl scripts (in Scripts.zip). </p>
Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water
Open the record for dataset details and reuse information.
Supplementary data as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)
<p>Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered 2 Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)</p>
Morphology of the excited hydroxyl in the Martian atmosphere: A model study. Where to search for airglow on Mars?
<p>The data for Remote Sensing article figures.</p>
Analytical approximations of the characteristics of the nighttime hydroxyl on Mars and intra-annual variations
<p>The data for Solar System Research article figures.</p>
Intramolecular Hydroxyl Nucleophilic Attack Pathway by a Polymeric Water Oxidation Catalyst with Single Cobalt Sites
<p>Exploring efficient water oxidation catalysts (WOCs) is the primary challenge in converting renewable energy into fuels. Here we report a molecularly well-defined heterogeneous WOC with Aza-fused-π-conjugated-microporous-polymer (Aza-CMP) coordinated single cobalt sites (Aza-CMP-Co). The single cobalt sites in Aza-CMP-Co exhibited superior activity under alkaline and near-neutral conditions. Moreover, the molecular nature of the isolated catalytic sites makes Aza-CMP-Co a reliable model for studying the heterogeneous water oxidation mechanism. By combining the experimental and theoretical results, a pH-dependent nucleophilic attack pathway for O-O bond formation was proposed. Under alkaline conditions, the intramolecular hydroxyl nucleophilic attack (IHNA) process that the adjacent -OH group nucleophilically attacks Co<sup>4+</sup>=O was identified as the rate-determining step. The process leads to lower activation energy and boosted kinetics than that of the intermolecular water nucleophilic attack pathway. This study provides significant insights into the crucial function of electrolyte pH in water oxidation catalysis and enhancement of the water oxidation activity by regulating the IHNA pathway.</p>
Research Data for "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface"
<p>This folder contains data used in the paper "Molecular Dynamics Study of Structure and Reactions at the Hydroxylated Mg(0001)/Bulk Water Interface" (Title subject to change). Some details on the structure are as follows:</p> <p>The folder "figures" contains data to create various figures in the main paper. Each file contains a json object, where keys "0", "1", etc. refer to the 1st/2nd subplot for a figure. The values are then another json object with the data used to create the relevant plot; the most useful of which is the "data" key which contains the plot data.</p> <p>The folder "md_traj" contains the molecular dynamics trajectory. The file "traj.exyz" is a standard format which can be opened with various software. "traj.json" contains the same information in an in-house format used by the author. The "thermo_data.json" contains various thermodynamics properties over the simulation, such as temperatures and kinetic energies. Units are femtoseconds, Angstrom, electron-volts and Kelvin.</p> <p>The folder "react_traj" contains trajectories in the same formats as "md_traj", but each are limited to time-windows where reactions occurred (so each trajectory will only be hundreds of femtoseconds long at most). The subfolder "full_traj" contains the trajectories with all atoms present, whilst "trimmed_traj" contains trajectories with most atoms removed (the atoms included are those nearest the reaction).We include these "trimmed_traj" files as it is difficult to find the reacting molecules when visualising all atoms in the simulation.</p> <p>The folder "opt_geoms" contains geometries for various structures used in the paper (in *.exyz format). These also contain *.json files; these contain information on how the calculations were carried out in a format used by the author (they are small files primarily included for the benefit of the author).</p> <p> </p> <p> </p>
IQ recording of W3OH hydroxyl spectral line at 1665.4 MHz
<p>This dataset contains a recording of the -OH radical spectral line (rest frequency 1665.4018 MHz) of the W3OH complex done with one of the 6.2 meter antennas of the Allen Telescope Array. The recording lasts approximately 500 seconds and is in IQ (raw voltage mode) format.</p> <p>The hardware configuration was as follows: antenna 1a was connected to RFCB LO d, which was tuned to a frequency of 1665.4 MHz and used an output IF of 512 MHz. A USRP N321 was connected to the IF output of the RFCB. The USRP N321 digitized both linear polarizations of the antenna. An external 10 MHz reference and PPS coming from the observatory distribution system was used, and LO sharing was set up among the two channels channels. The IQ sample rate of the USRP was 1.92 Msps. A GNU Radio flowgraph was used to record IQ data to disk.</p> <p>The antenna was pointed to J2000 right ascension 02h 27m 04.1s, declination +61d 52m 22s.</p> <p>The GNU Radio flowgraph stored the IQ data for each channel as 16-bin integers in the <a href="https://wiki.gnuradio.org/index.php/Metadata_Information">GNU Radio metatata file format</a>, with detached headers. After recording, the data was converted to <a href="https://github.com/gnuradio/SigMF">SigMF</a> format.</p>
Raw spectroscopic data for "Cage effects control the mechanism of methane hydroxylation in zeolites"
<p>This Excel spreadsheet contains all Mössbauer and resonance Raman data presented in the main text of Snyder et al., Science 2021.</p>
Enantioselective Hydroxylation of Benzylic C(sp3)–H Bonds by an Artificial Iron Hydroxylase Based on the Biotin–Streptavidin Technology
<p>Data underlying the figures in the publication “Enantioselective Hydroxylation of Benzylic C(sp<sup>3</sup>)–H Bonds by an Artificial Iron Hydroxylase Based on the Biotin–Streptavidin Technology”, published in <em>J. Am. Chem. Soc.,</em> <strong>2020</strong>, 142, 24, 10617–10623.</p> <p><a href="https://pubs.acs.org/doi/10.1021/jacs.0c02788">https://pubs.acs.org/doi/10.1021/jacs.0c02788</a></p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Excel file containing the numerical data for <em>Scheme 3b)</em> and <em>3c).</em></p> <p> </p> <p> </p>
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International Brain Laboratory public data
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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.