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20 results for “DFT structures”
Supplementary Material Containing DFT Structure Files and Convergence Tests for our μSR study on Fe2O3
<p>Supplemental material for <em>Local Electronic Structure and Dynamics of Muon-Polaron Complexes in Fe<sub>2</sub>O<sub>3</sub></em></p> <p>M. H. Dehn,<sup>1,2,3</sup> J. K. Shenton,<sup>4,*</sup> D. J. Arseneau,<sup>3</sup> W. A. MacFarlane,<sup>2,3,5</sup> G. D. Morris,<sup>3</sup> A. Maigné,<sup>2</sup> N. A. Spaldin<sup>4</sup> and R. F. Kiefl<sup>1,2,3</sup></p> <p><sup>1</sup>Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z1, Canada<br> <sup>2</sup>Stewart Blusson Quantum Matter Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada<br> <sup>3</sup>Triumf, Vancouver, BC V6T 2A3, Canada<br> <sup>4</sup>Department of Materials, ETH Zurich, CH-8093 Zürich, Switzerland<br> <sup>5</sup>Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada<br> <sup>*</sup> For queries about the supplemental material in this repository contact <a href="mailto:john.shenton@mat.ethz.ch">J. Kane Shenton</a>.</p> <p>In these notebooks we provide supplemental material for our work on understanding the behaviour of muon-polaron complexes in Fe<sub>2</sub>O<sub>3</sub>.</p> <p>We provide VASP input and output files for each of the candidate muon stopping sites and states identified in the paper (also labelled as in the paper). We summarise the muon stopping sites and provide the code for analysing hyperfine tensors in the jupyter notebook: <a href="https://nbviewer.jupyter.org/github/Shenton-supplemental/Muons_in_Fe2O3/blob/master/Muon-site-summary.ipynb"><code>Muon-site-summary.ipynb</code></a>. There one can also find a summary of the <strong>computational details</strong> for the paper.</p> <p>We further provide <code>vasprun.xml</code> files for some of the tests of convergence with respect to plane-wave cutoff energy and k-point sampling density. These tests are summarised in the jupyter notebook: <a href="https://nbviewer.jupyter.org/github/Shenton-supplemental/Muons_in_Fe2O3/blob/master/Convergence_tests-ENCUT-KPOINTS.ipynb"><code>Convergence_tests-ENCUT-KPOINTS.ipynb</code></a>.</p> <p>A major source of uncertainty stems from the choice of Hubbard U<sub>eff</sub> correction. We varied U<sub>eff</sub> in the range 3 − 6 eV to gauge the impact of this parameter on the predicted energies and precession frequencies of the four charge-neutral muon-polaron complex states. This analysis is available in the notebook: <code><a href="https://nbviewer.jupyter.org/github/Shenton-supplemental/Muons_in_Fe2O3/blob/master/muons_wrt_U.ipynb">muons_wrt_U.ipynb</a>.</code> Although the numerical values do vary as a function of U<sub>eff</sub>, the qualitative behaviour as well as the ordering of frequencies and energy differences presented in the paper (corresponding to U<sub>eff</sub> = 4 eV) remain robust throughout the range: 3 − 5 eV which is the range typically employed for Fe <em>d</em> states.</p> <p>Finally, in the notebook: <a href="https://nbviewer.jupyter.org/github/Shenton-supplemental/Muons_in_Fe2O3/blob/master/Separating_the_muon-polaron_complex.ipynb"><code>Separating_the_muon-polaron_complex.ipynb</code></a>, we analyse the separation of muon from the polaron in different configurations. Here again we provide the VASP input and output files as well as the code used to analyse these results.</p> <p>These jupyter notebooks may be previewed on <a href="https://github.com/Shenton-supplemental/Muons_in_Fe2O3">github</a> or via the <a href="https://nbviewer.jupyter.org/github/Shenton-supplemental/Muons_in_Fe2O3">jupyter notebook viewer</a>. The latter does a better job of rendering the inline LaTeX and is therefore preferred.</p> <p>Note that all of files are currently compressed to save space. These must be uncompressed before the notebooks will run. In each notebook there is a cell one can run to decompress the files needed for that particular notebook.</p>
DFT optimised structure used for the paper "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst"
<p>DFT optimised structures used to calculate the OER activities in "Cation Insertion to Break the Activity/Stability Relationship for Highly Active Oxygen Evolution Reaction Catalyst". The structures are bundled in two databases, LiIrO3.db which contains all structures for alpha-LiIrO<sub>3</sub> and KLiIrO3-disordered.db which contains all the structures for the disordered Li<sub>0.75</sub>K<sub>0.25</sub>(H<sub>2</sub>O)<sub>0.50</sub>IrO<sub>3 </sub>structure. The structures can be retrieved using the Atomic Simulation Environment (ASE, https://wiki.fysik.dtu.dk/ase/index.html). The keywords 'ads' and 'surface' can be used to search the structure, e.g. surface='Z-step' and ads='*OOH' will give the structure with OOH adsorbed on the Z-step surface (see paper for details on the different surfaces).</p>
Dataset for DFT and one-step model results used in publication "Persistence of Structural Distortion and Bulk Band Rashba Splitting in SnTe above Its Ferroelectric Critical Temperature" in Nano Letters, 2024, 24, 1, 82–88
<p>Dataset for DFT and one-step model results used in publication DOI 10.1021/acs.nanolett.3c03280, "Persistence of Structural Distortion and Bulk Band Rashba Splitting in SnTe above Its Ferroelectric Critical Temperature" in Nano Letters, 2024, 24, 1, 82–88.</p> <p>Description of dataset is in the ReadMe.txt file in subdirectories.</p>
Experimental and DFT structural data for OPE3-Ph - Au molecular junctions
<p>Experimental crystal structures (CIF), plane wave DFT relaxed structures (Quantum ESPRESSO) and DFTB transport geometries (CIF, GEN) for OPE3-Ph - Au molecular junctions.</p> <p>Data for article: "Electronic Conductance and Thermopower of Single-molecule<br> Junctions of Oligo(phenyleneethynylene) Derivatives" by Hervé Dekkiche, Andrea Gemma, Fatemeh Tabatabatai, Andrei S. Batsanov, Thomas Niehaus, Bernd Gotsmann, and Martin R. Bryce to appear in Nanoscale</p> <p> </p> <p> </p>
Data for "Structure, short-range order, and phase stability of the Al$_x$CrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis"
<p>Data associated with "Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis", published in npj Comput. Mater. <strong>10</strong>, 271 (2024).</p>
XYZ files of geometry optimized structures of TTM-TTM by DFT
<p>XYZ files of calculated geometry optimized structures of <strong>TTM-TTM </strong>by DFT methods ((U)B3LYP-D3/def-SVP).</p> <p>For unconstrained (uncon) geometry optimizations the initial structures were extracted from a single crystal structure.</p> <p>For the constrained geometry opimizations (XCH23065 and XCH23116) only the positions of the hydrogen atoms were optimized within the crystal structure.</p>
DFT-NMR-Validated Full Structure Elucidation of Theionbrunonine C, An Unstable N-Oxide Theionbrunonine from Mostuea brunonis
<p>The structure elucidation of theionbrunonine C, a thioether-bridged dimeric monoterpene indole alkaloid (MIA), and more generally, one of the very few Sulfur-containing MIA, is reported after its isolation from Mostuea brunonis (Gelsemiaceae). This unstable structure had already been targeted for isolation in our former, molecular network-guided, investigation of this plant but this compound had degraded before sufficient spectroscopic data could have been acquired for a complete structure assignment. With this constraint in mind, the rapid acquisition of NMR data enabled retrieving sufficient spectroscopic information for full structure elucidation, although from a partial set of spectroscopic information (1H and 13C NMR; COSY, HSQC, and HMBC). In conjunction with biosynthetic considerations, the cursory examination of 13C NMR data unambiguously defined the complete stereostructure of 1, as further supported by DFT-NMR calculations and subsequent DP4 probability score.</p>
Crystal structure, PXRD, FTIR-ATR, thermal analysis, DFT and ESP data
<p>The zip file contains folder with selected PXRD, FTIR-ATR, thermal analysis, single crystal structure (CIF) data, as well as calculated ESP data, as well as data relevant for periodic DFT calculations.</p>
DFT optimised structures of Ru(II)-based photocatalysts
<p>DFT optimised xyz structures of a series of [(N,N)<sub>2</sub>Ru(tpphz)RhCp<sup>*</sup>Cl]<sup>n+/-</sup> complexes, where the (N,N) ligand is varied ((N,N)= tbbpy, prbim, prbimOMe2, dmabim, bim). The optimised geometries of the singlet electronic ground state (S0), the triplet metal-to-ligand charge transfer (3MLCT) to the bridging ligand and the triplet metal centred state on the Ru centre (3MC) are provided, as well as the linear interpolated geometries connecting the 3MLCT and 3MC states.</p>
Fig. 4 in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 4. NOE correlations and comparison between experimental and calculated ECD spectra for compound 1.
Optimized DFT structures for the queous microsolvation of Cu2+ , Zn2+ and Cd2+
<p>Optimized DFT structures for the queous microsolvation of Cu2+ , Zn2+ and Cd2+</p>
Fig. 5 in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 5. NOE correlations of compounds 2–7.
Fig. 1. Hypothetical biosynthetic pathway for 1–7 in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 1. Hypothetical biosynthetic pathway for 1–7.
Fig. 3. 1H–1H in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 3. 1H–1H COSY and HMBC correlations of compounds 1–7.
Fig. 2 in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 2. Structures of Structures of ganorbifates C–I (1–7).
DFT-predicted equilibrium structures of Ir(III) complexes for halogen bond-assisted chemo-sensors
<p>Fully relaxed equilibrium structures of <strong>IrF-XB</strong> (without chloride anion coordinated by halogen bonding) as well as <strong>IrF-XBCl</strong> (with chloride anion coordinated by halogen bonding), <strong>IrF-XBBr</strong>, <strong>IrF-XB-Acetate</strong> and <strong>(IrF-XB)2-Acetate</strong> as predicted at the DFT level of theory (B3LYP/def2-SVP) including D3BJ dispersion correction and implicit solvent effects (acetonitrile). All investigated Ir(III)-based molecular sensors were optimized in singlet and triplet multiplicity in order to (subsequently) evaluate the Franck-Condon photophysics as well as the properties of the emissive triplet state. The multiplicity is indicated in the filename.</p>
DFT optimised structures of a series of bichromophoric photosensitisers
<p>This dataset contains the DFT optimised xyz geometries of a series of bichromophoric photosensitisers where the metal corresponds to a Re(I)CO3Cl or a Pt(4-pentylphenylacetylide)2 core and the organic ligand is comprised of a 1,10-phenanthroline (phen) acceptor connected to a triphenylamine (TPA) donor via a variable bridging moiety (B). The bridging units explored are thiophene (thio), ethynyl (CC) and 1,2,3-triazole (trz). In the case of the thio and trz complexes, rotation of the bridging group means that rotamers are possible. Four rotamers were identified in both the ground state (S0) and the lowest triplet state (T1) and their structures provided. They are labelled A through D, where A corresponds to the lowest energy structure. The S0 rotamers of the thio-TPA ligand are also given. All structures were confirmed to be energetic minima via frequency calculations.</p>
DFT-predicted equilibrium structures and electron transfer coordinate: CuPYBCP, CoPYN5, and CuPYBCP-CoPYN5
<p>Fully relaxed equilibrium structures of <strong>CuPYBCP</strong>, <strong>CoPYN5</strong>, and <strong>CuPYBCP</strong>-<strong>CoPYN5</strong> as predicted at the DFT level of theory (PBE0/def2-SVP) including D3BJ dispersion correction and implicit solvent effects (acetonitrile). The total charge as well as the multiplicity are indicated in the filename of the respective structure, e.g., “CuPYBCP-1.1-FC.xyz” being the ground state structure of <strong>CuPYBCP</strong> with a charge of “1” and with a multiplicity of “1” (singlet), while “CuPYBCP-0.2-FC.xyz” is the structure of its singly reduced “0” (uncharged) doublet “2” ground state. In case of the triplet intermediates, the labels “IL” (intraligand) and “MLCT” (metal-to-ligand charge transfer) indicate the electronic nature of the respective open-shell species.</p> <p>Structures along the electron transfer coordinate (<em>R</em><sub>ET</sub>) in <strong>CuPYBCP-CoPYN5</strong>, approximated by means of a linear-interpolated internal coordinate (LIIC) that connects the equilibrium structure of the electron donor state “D” and electron acceptor state “A”, are summarized in one trajectory file “CuPYBCP-CoPYN5-LIIC-2.3.trj”.</p>
DFT and TDDFT-predicted equilibrium structures of bipyridine-annulated perylene tetracarboxylic ester photocatalysts with PdCl2 and PtCl2
<p>Fully relaxed equilibrium structures of <strong>P-Pd</strong> and <strong>P-Pt</strong> as predicted at the DFT and TDDFT levels of theory (B3LYP/def2-SVP) including D3BJ dispersion correction and implicit solvent effects (CH<sub>2</sub>Cl<sub>2</sub>). Both photocatalysts were optimized in singlet (S0) and triplet multiplicity in order to evaluate the Franck-Condon photophysics as well as the prominent triplet species involved in the photphysical and photochemical properties, i.e. triplet intra-ligand (3IL) and triplet metal-to-ligand charge transfer (MLCT) states. The multiplicity is indicated in the filename.</p>
Fig. 6. Photoinitiated n in Structures of ganorbifates C-I, seven previously undescribed lanostanoids from the mushroom Ganoderma orbiforme, and insights of computed biosynthesis with DFT
Fig. 6. Photoinitiated n→π* excitation and the subsequent hydrogen abstraction in 1–3.
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