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1,294 results for “reactions”
Data for Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties
<p>Data for the manuscript "Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties". The data set contains all the generated mechanisms, DFT data used for the construction of the RMG library, a backup of the RMG-database, all results and scripts for the evaluation of the results. </p>
Mapping Catalyst–Solvent Interplay in Competing Carboamination/Cyclopropanation Reactions
<p>Selectivity and activity maps can be used to predict and rationalize reaction outcomes based on catalyst and solvent choice. Here, there utility is demonstrated by examining competing carboamination/cyclopropanation reactions catalyzed by Group 9 catalysts featuring cyclopentadienyl ligands, which reveals an interesting energetic interplay involving the role of the solvent and of the catalyst.</p>
Quantum Chemical Calculations for the Reaction of Methoxide with OTP and CL
<p>DFT calculations at the BP/def2-TZVPD level are executed with Turbomole 7.3 and COSMO-RS calculations with COSMOtherm 19.0.4.</p> <p> </p> <p>One folder is used for one molecule which take part in the following reactions.<br> Educt + Nu- -> Intermediate -> Product<br> Charged system:<br> CL + MeO- -> 2a- -> 3a-<br> OTP + MeO- -> 2b- -> 3b-<br> Neutral system:<br> CL + MeOH -> 2aH -> 3aH<br> OTP + MeOH -> 2bH -> 3bH</p> <p>Folderstructure:<br> opt: Geometric structure optimization with PBEh-3c, frequency analysis<br> sp-vac: Electronic Structure of the vacuum state<br> sp-sol: Electronic Structure of the solute as ideal conductor<br> sp-cosmors: Calculation of solvation enthalpy</p> <p>Quantum Chemical Data Collection (QCDC) creates data.json<br> Further information can be found here:<br> https://github.com/lucasteiner/qcdc<br> </p>
Dataset for "Reactivation strategies for nucleation-inhibited catalyst beds in continuously operated gas-release reactions from liquids."
<p>This dataset contains the measurements that were used to create the diagrams in the manuscript "Reactivation strategies for nucleation-inhibited catalyst beds in continuously operated gas-release reactions from liquids."</p>
Supporting Information from The Next Frontier of Environmental Unknowns: Substances of Unknown or Variable Composition, Complex Reaction Products, or Biological Materials (UVCBs)
<p>Supporting Information (Open Data) from The Next Frontier of Environmental Unknowns: Substances of Unknown or Variable Composition, Complex Reaction Products, or Biological Materials (UVCBs)</p>
Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
<p>The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikatis. The detailed description of the datafiles and scripts is provided in the accompanying README.rtf file.</p>
Why The Perfectly Symmetric Cobalt-Pentapyridyl Loses the H2 Production Challenge: Theoretical Insight into Reaction Mechanism and Reduction Free Energies
<p>Abstract</p> <p>Researchers have extensively investigated photo-catalytic water reduction utilizing Cobalt-based catalysts with poly-pyridyl ligands. While catalysts exhibiting distorted poly-pyridyl ligand demonstrate higher H2 production yields, those with ideal octahedral coordination display poor performance. This outcome suggests the crucial role of ligand framework in catalytic activity, yet reasons behind the disparity in H2 production rates for catalysts with octahedral geometries remain unclear. We theoretically examined the water reduction mechanism of Co-based poly-pyridyl catalyst, CoPy5, having perfect octahedral coordination. We clarified the effect of octahedral coordination by utilizing each intermediate step of ECEC mechanism. We determined spin states, solvent response, electronic structures, and reduction free energies. CoPy5 with perfect octahedral coordination, alongside its distorted counterparts, exhibit similar spin states as the reaction progresses through each intermediate step. However, the first reduction free energy obtained for the CoPy5 is slightly higher than that of its distorted counterparts. Following the second protonation, resulting H2 molecule experiences limited diffusion from the Co center due to the compact structure of the CoPy5, which blocks the Co center for the next H2 production cycle. Catalysts having distorted octahedral geometries facilitate fast removal of H2 into the solvent. Thus, the reaction center becomes immediately available for subsequent H2 production.</p> <p>Computational Details</p> <p>AIMD simulations have been performed for modeling intermediate states of the ECEC mechanisms of H2 production through water splitting. Open source CP2K simulation package have been used in all simulations. PBE density functional in general gradient approximation (GGA) formalism was employed for the AIMD simulations. Goedecker-Teter-Hutter (GTH) potentials were applied for the estimation of core electron interactions with the valence shell and nucleus. Valence electrons were modeled explicitly and valence shells of Co, N, C, O and H contain 17, 5, 4, 6 and 1 electrons, respectively. DZVP-MOLOPT basis set was used for all atomic kinds. For auxiliary plane wave basis set, a cutoff of 400 Ry was utilized. Dispersion interactions were taken into consideration by applying Vydrov and Van Voorhis vdW density functional, in the revised form (rVV10). Periodic boundary<br> conditions and spin polarization were always applied. For the CoPy5 complex, AIMD simulations were carried out in a box defined as cubic with explicit water environment. The CoPy5 catalyst was first solvated in 215 water molecules and the simulation volume was relaxed by performing AIMD simulations for approximately 20 ps in the isothermal-isobaric ensemble (NPT). Cubic simulation box volume was determined as 6163.28 ̊A3. Following the determination of the simulation box size, each intermediate step were modeled by applying AIMD simulations in the canonical ensemble (NVT) for approximately 20 ps. Time step was set to 0.5 fs. Canonical sampling through velocity rescaling (CSVR) thermostat with a time constant of 100 fs was applied in order to keep<br> the simulation temperature at 300 K.</p> <p>Please see the corresponding article for more details.</p>
Data for Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates
<p>Data and scripts for the preprint "Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates".</p>
Comparison of thermal developmental plasticity among seven recently sympatric <i>Anolis</i> species: insights into the evolution of reaction norms
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Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects
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Dataset for: Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR
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Data from: Constraints and demands interact to affect prey dietary reaction to predation
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Data for: Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
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Data from: A reaction norm for flowering time plasticity reveals physiological footprints of maize adaptation
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SN2 Reactions (QCArchive View Formatted)
<p>Data curated by the QCArchive team, originally sourced from quantum-machine.org.</p> <p>S<sub>N</sub>2 reactions of methyl halides with halide anions for the halides F, Cl, Br, and I. Structures are generated by high-temperature molecular dynamics evaluated at the DSD-BLYP-D3(BJ)/def2-TZVP level of theory, and include molecules of the following types: CH<sub>3</sub>X, CH<sub>3</sub>X + Y<sup>-</sup>, HX, CHX, CH<sub>2</sub>X<sup>-</sup>, H<sub>2</sub>, CH<sub>2</sub>, CH<sub>3</sub><sup>+</sup>, and XY where X and Y are halides. </p> <p>For more information, see http://qcarchive.molssi.org/apps/ml_datasets/.</p>
IscoKin database of rate constants for reaction of organic contaminants with the major oxidants relevant to In Situ Chemical Oxidation
<p>Database of second-order rate constants for aqueous phase reaction of organic contaminants with the major oxidants involved in groundwater remediation by In Situ Chemical Oxidation (ISCO)—including permanganate, hydroxyl radical (from activated peroxide), and sulfate radical (from activated persulfate)—plus other comparable oxidants of environmental interest (carbonate radical, chlorine dioxide, and ozone).</p> <p>The data were compiled between 2003 and 2005 by Rachel Waldemer, Jaimie Powell, and other students under the direction of Professor Paul G. Tratnyek at the Oregon Graduate Institute in Beaverton, Oregon, USA. In 2006, a script written by Kaylie Langley was used to make the data available online via an interface that allowed searching by chemical name, CAS-RN, etc. The result was named the “IscoKin” database and was available at http://cgr.ebs.ogi.edu/iscokin/search.php until the server was retired in 2019.</p> <p>In place of IscoKin, we have made all of the data available as a spreadsheet in .xlsx format. The file includes two sheets, the first contains one “recommended” rate constant for each combination of organic compound and oxidant (i.e., one row per compound). The second sheet contains all of the individual rate constants that were compiled (i.e., one row per experimental result).</p> <p>The "best" value is most often an average of the individual values listed in the "All_values_with_references" sheet; but occasionally this value represents a single value, usually the "best" value given in Buxton et al. (1988) “Critical review of rate constants for reactions of hydrated electrons. hydrogen atoms and hydroxyl radicals (•OH/•O-) in aqueous solution” J. Phys. Chem. Ref. Data. 17, 513-886.</p> <p>While the database was checked thoroughly, it still is unlikely to be completely accurate or complete. For critical applications, we recommend tracking down the primary sources (listed in the spreadsheet) and use them for data, conditions, and other caveats. Obviously, we do not accept any responsibility for what anyone does with information obtained from this document.</p> <p>The work was funded by the Strategic Environmental Research and Development Program (SERDP), under grant number ER-1289, titled “Improved Understanding of In Situ Chemical Oxidation”. More details on this work can be found in Part 1 of the final project report, which is located at https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminated-Groundwater/Persistent-Contamination/ER-1289/.</p>
Metasomatic reactions between Archean dunite and trondhjemite at the Seqi Olivine Mine in Greenland
<p>Supplementary materials relating to the paper: Metasomatic reactions between Archean dunite and trondhjemite at the Seqi Olivine Mine in Greenland by Wyatt et al.</p>
Simulation data for Modelling DNA-strand displacement reactions in the presence of base-pair mismatches
<p>Raw and processed simulation data from the paper Modelling DNA-strand displacement reactions in the presence of base-pair mismatches (J. Am. Chem. Soc.)</p>
Data for article "Triazene-Activated Donor–Acceptor Cyclopropanes: Ring-Opening and (3 + 2) Annulation Reactions"
<p>This upload contains raw data (NMR, X-Ray) files for the article: </p> <p>A. A. Suleymanov, E. Le Du, Z. Dong, B. Muriel, R. Scopelliti, F. Fadaei-Tirani, J. Waser, K. Severin, </p> <p>"Triazene-Activated Donor-Acceptor Cyclopropanes: Ring-Opening and (3 + 2) Annulation Reactions"</p> <p><em>Org. Lett. </em><strong>2020</strong>, DOI: 10.1021/acs.orglett.0c01527<em>.</em></p>
Supplementary data for "Molecular dynamics study of confined water in the periclase-brucite system under conditions of reaction-induced fracturing"
<p>In this dataset you can find sample data from periclase and brucite simulations and python scripts that can be used to confirm the plots in the paper.</p> <ul> <li>"bruciteSimualtions" and "periclaseSimualtions" contains the simulations where the mineral in contact with water is either brucite or periclase. Within each of these two folders, there are two subfolders, "waterProperties" and "waterThickness". <ul> <li>The data in "waterProperties" is used to calculate water properties. Each folder inside "simulations" represent one simulation.</li> <li>The data in "waterThickness" is used to calculate the change in water film thickness with time under different conditions. The simulations are run for either 3 ns or 10 ns. Each folder inside "simulations_Xns" represent one simulation.</li> </ul> </li> <li>For each folder containing one simulations, we provide: <ul> <li>NAME.run: The input script</li> <li>NAME.data: The input data</li> <li>job.sh: Script to run the simulation</li> <li>log.lammps: Thermodynamic output from the simulation</li> <li>Note that the pressures given in the folder names and in the simulations are in atm, not MPa.</li> </ul> </li> </ul> <p> </p> <ul> <li>"bruciteSimulations" and "periclaseSimualtions" are in zip containers. In order to use them, please unzip them and leave the resulting folders in the same directory as this README file. </li> </ul> <p> </p> <ul> <li>The python scripts shows how to extract the relevant data from the lammps log files, which enables reproduction of the figures in the paper. See instructions below to use the scripts.</li> </ul> <p><br> Installation instructions to make the python plot scripts working, assuming you already have numpy and matplotlib:</p> <p>> pip3 install git+https://github.com/henriasv/regex-file-collector.git</p> <p>> pip3 install git+https://github.com/henriasv/lammps-logfile.git<br> </p> <p>If this does not work, please contact Marthe Grønlie Guren, m.g.guren@geo.uio.no</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.