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10 results for “ion solvation”
Predictive simulations of ionization energies of solvated halide ions with relativistic embedded Equation of Motion Coupled-Cluster Theory: Figures
<p>This entry contains the sources for the figures included in the body of the paper titled "Predictive simulations of ionization energies of solvated halide ions with relativistic embedded Equation of Motion Coupled-Cluster Theory", by Yassine Bouchafra, Avijit Shee, Florent Réal, Valérie Vallet and André Severo Pereira Gomes, as well as those found in the supplementary information.</p> <p>It accompanies the dataset found at the DOI: 10.5281/zenodo.1477004</p> <p> </p> <p> </p>
Radiation damage hot spots formed by two-step electron transfer mediated decay of solvated ions - data
<p>Data set pertaining to the manuscript "Radiation damage hot spots formed by two-step electron transfer mediated decay of solvated ions", accepted for publication in Nature Chemistry.</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2022.07, see<br> https://www.nexusformat.org/<br> https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br> NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br> * nexpy (distributed with python)<br> * https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)</p> <p>In each NeXus file-entry, two types of spectra are shown:<br> 1. Sweep-averaged spectra, integrated over the non-dispersive coordinate of our detector ('data') if applicable.<br> 2. As-measured data ('raw').</p> <p>Files with extension .csv are comma-separated ascii-files, designed to be opened with a spreadsheet programme.</p> <p><br> The following files are provided:</p> <p>Photoemission data pertaining to ETMD measurements:<br> alcl3-K-etmd.h5 (ETMD after Al K-shell photoionization)<br> alcl3-L23-etmd.h5 (ETMD after Al L-shell photoionization)</p> <p>Calculated energies of the ETMD final states after 1s ionization. The energies were calculated at the CAS-CI/cc-pVDZ level. The states were shifted so that the lowest-energy state corresponds to the LC-ωPBE/aug-cc-pVTZ and aug-cc-pCVTZ value obtained in a polarizable continuum:<br> Dataset_ETMD_after_1s_ionization.csv<br> Dataset_ETMD_after_2p_ionization.csv</p> <p>Geometrical coordinates of the clusters that were used for energy calculation:<br> clusters.dat<br> clusters_small.dat</p> <p>Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .</p> <p> </p> <p>Version history:</p> <p>v3 - Al L2,3 data: Orientation of the analyser hemisphere corrected. Direction of the linear polarization vector added. All other data unchanged.<br> v2 - cluster coordinates added, all other data unchanged.<br> v1 - initial upload.</p>
The conception of a solvated electron: X-ray-induced attosecond electron dynamics of aqueous ions - data
<p>Data set pertaining to the article "Attosecond formation of charge-transfer-to-solvent states of aqueous ions probed using the core-hole-clock technique", published in <a href="https://doi.org/10.1038/s41467-024-52740-5" target="_blank" rel="noopener">Nature Communications</a>.</p> <p>Here we describe the time-evolution of core level excited electronic states of metal ions in aqueous solution on an ultrashort time scale. Extensive simulations towards this project were carried out. Simulated data include geometries for solvated metal ion complexes and their X-Ray absorption spectra. Experimental data were recorded by photoemission spectroscopy from a liquid jet source using synchrotron radiation. </p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2022.07, see<br>https://www.nexusformat.org/<br>https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br>NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br>* nexpy (distributed with python)<br>* https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)</p> <p>In each NeXus file-entry, two types of spectra are shown:<br>1. Sweep-averaged spectra, integrated over the non-dispersive coordinate of our detector ('data') if applicable.<br>2. As-measured data ('raw').</p> <p>Files with extension .csv or .txt are comma-separated ascii-files, designed to be opened with a spreadsheet programme.</p> <p><br>The following files are provided:</p> <table> <tbody> <tr> <td>Filename</td> <td>Content</td> </tr> <tr> <td> </td> <td>Experimental Data:</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/na_mg_al_1s-resonance_cfs.h5/content" target="_blank" rel="noopener noreferrer">na_mg_al_1s-resonance_cfs.h5</a></td> <td>Series of experimental photoemission spectra recorded over the 1s - val resonances, for NaCl, MgCl2 andAlCl3 metallic salt solutions</td> </tr> <tr> <td><span><a href="https://zenodo.org/api/records/13862194/draft/files/SI-Fig6.zip/content" target="_blank" rel="noopener noreferrer">SI-Fig6.zip</a></span></td> <td>Ascii representation of the data and fit curves used to determine in 1s lifetime broadening, shown in Fig. 6 of the Supplementary Information.</td> </tr> <tr> <td> </td> <td>Theoretical Data:</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.geometries.zip/content" target="_blank" rel="noopener noreferrer">th.geometries.zip</a></td> <td>Cartesian coordinates of the constituents of metal-water clusters containing 6 water molecules and containing 18 water molecules. Unit of length is Ångström.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.excitation_energy.zip/content" target="_blank" rel="noopener noreferrer">th.excitation_energy.zip</a></td> <td>Excitation energies for metal-water clusters containing 6 water molecules and containing 18 water molecule, at various levels of approximation. tddft-src2: at the SRC2-R2 level with a cc-pCVTZ basis set on the cations and a cc-pVTZ basis set on the water molecules in a polarizable continuum; eomccsd: at the EOM-EE-CCSD level with a cc-pCVTZ basis set on the cations and a cc-pVTZ basis set on the water molecules. For the purpose of spectra construction in Figure 1, each calculated spectral point was broadened by a phenomenological value of 0.2 eV. Energies are in eV, transition dipole moment components in e*bohr.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.spektrum.pade.zip/content" target="_blank" rel="noopener noreferrer">th.spektrum.pade.zip</a></td> <td>Excitation energies for metal-water clusters containing 6 water molecules calculated at the RT-TDDFT level with a cc-pVTZ basis set. For each cation, 3 trajectories were run. Energies are in eV.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/th.excitation_energy.zip/content" target="_blank" rel="noopener noreferrer">th.excitation_energy.zip</a></td> <td>Exciton analysis of the wave function (RMS electron size) for a set of 50 geometries of clusters containing 6 water molecules (small) or 18 water molecules (large) calculated at the SRC2-R2/cc-pVTZ level. The oscillator strengths are in a.u., the size of the electron is in Ångström.</td> </tr> <tr> <td><a href="../api/records/10600583/draft/files/description_zenodo.pdf/content" target="_blank" rel="noopener noreferrer">description_zenodo.pdf</a></td> <td>More detailed description of the theoretical data sets.</td> </tr> </tbody> </table> <p> </p> <p>Version history<br>v2: fixed incorrect choice of data file for Na scan. Data for lifetime-figure in SI added.<br>v1: initial upload</p> <p>If you use part or all of these data in your scientific work we kindly ask you to provide us a copy. Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .</p>
Predictive simulations of ionization energies of solvated halide ions with relativistic embedded Equation of Motion Coupled-Cluster Theory: Dataset
<p>This dataset collects the unprocessed (= outputs from calculations) and processed (= plots, average values for ionization energies) results discussed in the paper titled "Predictive simulations of ionization energies of solvated halide ions with relativistic embedded Equation of Motion Coupled-Cluster Theory", by Yassine Bouchafra, Avijit Shee, Florent Réal, Valérie Vallet and André Severo Pereira Gomes.</p> <p>In each archive file there is a README explaining how to use the bundled scripts to process the data.</p>
X-ray radiation damage cycle of solvated inorganic ions
<p>Data set pertaining to the manuscript "X-ray radiation damage cycle of solvated inorganic ions", accepted for publication at Nature Communication.</p> <p>The manuscript describes results on the low-energy electron emission in a cascade of the decay of core ionized states, explored experimentally by liquid jet multi-electron coincidence spectra compared to theoretical predictions. Here we provide the underlying experimental data including metadata.</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2024.02, see<br>https://www.nexusformat.org/<br>https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br>NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br>* nexpy (distributed with python)<br>* https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)<br>Additionally, some properties of our liquid jet sample environment are described by extensions to standard NeXus explained in a notes-section in each file.</p> <p> </p> <p>In each NeXus file-entry, two types of data are present:<br>1. An energy-calibrated single electron spectra as histogram of the single electron events in events/eV ('data').<br>2. Energy-calibrated single, double and triple electron events ('raw').</p> <p> </p> <p>The following files are provided: Electron emission coincidence data pertaining to Mg<sup>2+</sup> and Al<sup>3+</sup> measurements mg_ee_coinc.h5 (Mg<sup>2+</sup> data recorded at BESSY II) mg_petra_ee_coinc.h5 (Mg<sup>2+</sup> data recorded at PETRA III) al_ee_coinc.h5 (Al<sup>3+</sup> data recorded at PETRA III)</p> <p> </p> <p>Contact: Dana Bloß (dana.bloss@uni-kassel.de) Andreas Hans (hans@physik.uni-kassel.de) </p> <p> </p> <p> </p> <p> </p>
DFT data for "The Role of Ion Solvation in Lithium Mediated Nitrogen Reduction"
<p>Density Functional Theory data used in the paper "The Role of Ion Solvation in Lithium Mediated Nitrogen Reduction".</p>
Parameters for the solvated KcsA-LAB-TEA, when the LAB-TEA is placed inside the channel cavity without K+-ion
<p>Parameters for the solvated KcsA-LAB-TEA. These KcsA-LAB-TEA systems were solvated by truncated octahedron TIP3PBOX, using the leap program in AMBER20. The LAB-TEA is placed inside the channel cavity. The simulation is performed without K<sup>+</sup>-ion.</p>
Parameters for the solvated KcsA-K+-LAB-TEA, when both LAB-TEA and K+-ion placed inside the channel cavity
<p>Parameters for the solvated KcsA-K<sup>+</sup>-LAB-TEA. These KcsA-K<sup>+</sup>-LAB-TEA systems were solvated by truncated octahedron TIP3PBOX, using the leap program in AMBER20. Both LAB-TEA and K<sup>+</sup>-ion are placed inside the channel cavity.</p>
Inputs to calculate the solvation free energies of ECC ions in SPCE water
<p>Scripts and input files for the calculation of the solvation free energies of selected cations with the ECC model. The simulation box contains one cation and 800 water molecules. The ion topologies are from https://bitbucket.org/hseara/ions. Notably, before comparison with experimental values, the electronic solvation free energy contribution must be added to the result [1], as well as the correction due to the use of neutralizing charge density [2].</p> <p>In each folder, ./run.sh creates the folders representing different lambda values in the free energy perturbation approach and performs the respective calculation in each folder. There are a total of 31 windows (11 for electrostatics and 20 for Lennard-Jones). After running the script, the free energy can be extracted by</p> <p>gmx bar -f ?/md.xvg ??/md.xvg -temp 298 -o -b 100</p> <p>The results are reported in DOI: [ADD]</p> <p>[1] DOI: 10.1021/ct9005807</p> <p>[2] DOI: 10.1080/08927022.2015.1121544</p>
Parameters for the solvated KcsA-K+-LAB-TEA, when LAB-TEA place in cytoplasmic region and K+-ion inside the cavity
<p>Parameters for the solvated KcsA-K<sup>+</sup>-LAB-TEA. These KcsA-K<sup>+</sup>-LAB-TEA systems were solvated by truncated octahedron TIP3PBOX, using the leap program in AMBER20. The LAB-TEA is placed in the cytoplasmic region and K<sup>+</sup>-ion inside the channel cavity.</p>
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