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135 results for “DFT”
Datasets for: Fullerene-based Single Molecule Diodes with Huge Rectification Ratios: A DFT-NEGF Study
<p>Input files and main output files for the study "Fullerene-based Single Molecule Diodes with Huge Rectification Ratios: A DFT-NEGF Study"</p>
TD-DFT of Diketopyrrolopyrrole (DPP) Annihilators
<p>Molecular geometry of the excited triplet and singlet state energies of DPP derivatives (DPP-S-Th, DPP-Th, DPP-S-2tb-Th, and DPP-2tb-Th) were modelled using the quantum chemistry software ORCA. Density functional theory (DFT) geometry optimization was performed using the B3LYP/6-31G(d) functional/basis set in a vacuum. The T1, T2 and S1 energies were obtained by employing time dependent DFT calculations with the same functional/basis set.</p>
Supporting data for "The Operando Nature of Isobutene in H–SSZ–13 Unraveled by Machine Learning Potentials Beyond DFT Accuracy"
<p>Supporting data for "The Operando Nature of Isobutene in H–SSZ–13 Unraveled by Machine Learning Potentials Beyond DFT Accuracy" by M. Bocus, S. Vandenhaute and V. Van Speybroeck.</p> <p>This dataset contains examples of input files, submission and analysis scripts, in addition to the molecular dynamics trajectories used to obtain the results reported in the main manuscript. A more detailed description of the dataset content is provided in the README files therein.</p>
CsSn(Cl/Br/I)3 Perovskite Alloy DFT Dataset for Machine Learning
<p>This upload contains density functional theory (DFT) calculations of CsSn(Cl/Br/I)3 perovskite alloy. The calculations were performed for a study, where the DFT data was used to train an energy predicting machine learning model for CsSn(Cl/Br/I)3. The code related to the study is available through GitLab (https://gitlab.com/cest-group/learnsolar-cssnclbri).</p> <p>The data is divided into four data sets. For each set, the atomic structure data with total energies and forces has been separated into an ASE (Atomic Simulation Environment) extended XYZ file. Additional information on the atomic structures (e.g. space groups) is provided in JSON format. The data sets are:</p> <p><strong>sp_train_set</strong><br>Single point DFT calculations of 16 000 algorithmically generated CsSn(Cl/Br/I)3 structures of four different space groups: Pm-3m, P4/mbm, I4/mcm, and Pnma. Lattice parameters and atomic positions are determined through Vegard's law, but random deviations have been added to the atom positions, tilting angles of the Sn coordination octahedra, cell volume, cell height-to-width ratio, and some lattice vector angles. Cl/Br/I configurations are randomized. This data set was used to fit an initial machine learning model. The atomic structures included were selected using a clustering algorithm to accelerate learning.</p> <p><strong>sp_test_set</strong><br>Single point DFT calculations of 2 600 atomic structures similar to sp_train_set. The Cl/Br/I compositions are uniformly represented, having two atomic structures per composition and space group. This data was used for testing the machine learning model. </p> <p><strong>al_data</strong><br>DFT relaxation structure snapshots from the active learning run that was performed to improve the machine learning model's structure relaxation accuracy. There are 4230 structure snapshots in total.</p> <p><strong>relax_test_set</strong><br>100 DFT relaxations used for testing the machine learning relaxation accuracy. There are 2881 structure snapshots in total. Both initial (relax_test_set_initial.xyz) and final (relax_test_set_relaxed.xyz) atomic geometries are included.</p>
Progeny Project DFT and NAMD data for periodic 2D surfactant
<p>Crystalline unit cell, band structure, and electron-hole recombination dynamics from non-adiabatic molecular dynamics for the periodic 2D surfactant of the Progeny.</p> <p>See Readme.txt for more details.</p>
Progeny Project DFT and TD-DFT data for MW1 and its variants with different side chain length
<p>DFT and TD-DFT data, i.e. geometries, electronic excited states for the MW1 and its variants in vacuum with different length of side chains.</p> <p>See Readme.txt for more details.</p>
Synchrotron bulk photoemission data from Au(111) and DFT calculations
<p>Extreme UV photoemission band mapping of Au(111) surface and bulk. Measurements were conducted at the SGM-3 beamline of the 3rd-generation ASTRID2 synchrotron radiation source in Aarhus, Denmark with a photon energy of 80 eV. The gold sample was purchased from MaTecK GmbH with a (111) surface. The sample temperature was maintained at 100 K during measurements.<br> <br> Experimental data are provided in ibw format (Igor Pro), HDF5, and TIFF format along with calibrated energy.</p> <p>Density functional theory calculations were carried out using GPAW 1.31 code using GLLBSC pseudopotentials. The valence electrons were described with plane-wave basis sets with a kinetic energy threshold of 600 eV and reciprocal space was sampled with a (12x12x1) mesh of k-points.</p>
Theoretical DFT calculation based output file of esters in water
<p>The presented theoretical DFT study resolves the question of why the hydrolysis of simple ester can occur in acidic as well as basic medium while that of S-naproxen ester in acidic medium only.</p>
Intrinsic Effects of Sulfidation on the Reactivity of Zero-Valent Iron With Trichloroethene: DFT Calculations
<p>This dataset contains the input and output files of density functional theory (DFT) calculations supporting the research published in the peer-reviewed article "Intrinsic Effects of Sulfidation on the Reactivity of Zero-Valent Iron With Trichloroethene: A DFT Study" by M. Brumovský and D. Tunega, available at DOI 10.1021/acs.jpcc.3c04459. Please cite this article when using the dataset.</p> <p>This dataset includes the following data:<br> * Structures and energies of various surface slab models, encompassing pristine and modified iron surfaces (Fe(110), Fe(111), S-in-Fe(110), S-on-Fe(110), S1/4ML-Fe(110), S1/2ML-Fe(110), O-on-Fe(110), OH-on-Fe(110), and H-on-Fe(110)).<br> * Structures and energies of isolated TCE, H2O, and H2 molecules.<br> * Adsorption configurations of TCE molecule and its dechlorination products at the mentioned surfaces, including transition state calculations using the CI-NEB method. <br> * Adsorption configurations of H2O and H species at Fe(110), S-in-Fe(110), and S-on-Fe(110) surfaces.<br> * In specific cases, data related to implicit solvation, charge analysis, and density of states calculations.</p> <p>Files are organized according to the respective modeled surfaces. The final geometry data can be found in the CONTCAR files, while energy data can be found in the OUTCAR files. Please note that the POTCAR files are not allowed to be made publicly accessible but are specified within the OUTCAR files. For additional details about input and output files, refer to the VASP manual. </p> <p>The fully relaxed unit cell of Fe is accessible in a previously published dataset, available at doi 10.5281/zenodo.6338412.</p> <p>Funding: This research received support from the Austrian Science Fund (FWF) under project M 2892-N. The Vienna Scientific Cluster (Project No. 70544) is gratefully acknowledged for providing computational resources. </p> <p>Terms of use: These data are provided "as is", without any warranty. This dataset is provided under the Creative Commons Attribution 4.0 International license.</p>
A dataset of DFT-computed oxygen vacancy formation energies of metal oxides
<p>This dataset contains DFT-computed oxygen vacancy formation energies of different oxygen sites in over 1000 metal oxides present on the Open Quantum Materials Database (OQMD). Entries in the Data.csv file are indexed using the OQMD entry ID of the pristine structure, and list, alongside the oxygen vacancy formation energy, a number of other properties used as features in machine learning models. An exemplary code allowing to test the performance of a random forest regressor using different sets of features to predict the vacancy formation energy, as a function of training set size, is provided in Test_Models.py. More details on the dataset and machine learning models can be found in: arXiv:2309.01160. </p><p> </p><p><strong>Acknowledgments</strong></p><p>The work was funded by the U.S. Department of Energy under Grant DE-EE0008089. S. G. acknowledges the Air Force Office of Scientific Research for support under Award No. FA9550-18-1-0136 (OQMD database). A. G. acknowledges the Center for Hierarchical Materials Design (ChiMaD) under Award No. 70NANB19H005 (ML models). A. J.A. S.-C. acknowledges the financial support to National Agency for Research and Development (ANID)/DOCTORADO BECAS CHILE/2018 - 56180024. A. J.A. S.-C. and T. L. acknowledge funding from the Toyota Research Institute through the Accelerated Materials Design and Discovery program (ML representations). The data was produced relying on the computing power provided by Quest high performance computing facility at Northwestern University.</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>
DFT Calculated xyz and log Files in Support of "Reaction Mechanism of Pd-catalyzed "CO-free" Carbonylation Reaction Uncovered by In situ Spectroscopy: The Formyl Mechanism"
<p>Theoretically calculated xyz and log files for hydrogen, carbon monoxide, carbon dioxide, methane, methanol, methyl formate, butene, methyl pentanoate and multiple Pd-dtbpx complexes (dtbpx = 1,2-Bis(di-<em>tert</em>-butylphosphino)xylene) which catalyze the addition of HCOOMe/CO onto butene to form methyl pentanoate.</p> <p>All quantum chemical simulations were performed using the Gaussian16 software. The ground state equilibrium structures and electronic properties were obtained at the density functional (DFT) level of theory utilizing the B3LYP XC functional.The def2-SVP basis set as well as the respective core potentials were applied for all atoms. A subsequent vibrational analysis was carried out for each optimized ground state structure to verify that a minimum on the potential energy (hyper‑)surface (PES) was obtained. All calculations were performed including D3 dispersion correction with Becke-Johnson damping.</p> <p>An analogous computational setup was applied for the optimization of transition states (TSs), while an initial guess in the vicinity of the saddle point was at first obtained via the Nudged Elastic Band (NEB) method as implemented in pysisyphus with xtb.<sup> </sup>Thereafter, the TSs were obtained in Gaussian16 via the Berny algorithm, followed by a vibrational analysis to verify that a first-order saddle point on the PES was obtained.</p>
Supporting data for: A linear response, DFT+U study of trends in the oxygen evolution activity of transition metal rutile dioxides
<p>This directory contains all of the finished calculations required for fully analysis of the paper "A linear response, DFT+U study of trends in the oxygen evolution activity of transition metal rutile dioxides" by Zhongnan Xu, Jan Rossmeisl, and John R Kitchin. To use this repository, download the supporting information file and run the scripts present in either 'supporting-information.pdf' or 'supporting-information.org'.</p> <p>The is the release of the supporting data before the first submission to the first journal.</p>
DFT Dilute Solute Diffusion Database in Mg
<p>This is a database of first-principles results for dilute solute diffusion in HCP magnesium. The diffusivities were computed using the eight-frequency HCP diffusion model, where all the frequencies have been calculated using density functional theory. All eight frequencies for all solutes are reported as well as the diffusion coefficient (D0) and diffusion activation energy (Q).</p>
Platinum pyridine cations: the DFT optimized geometries
<p>The geometries were optimized with the hybrid M06 functional, the mDZP all-electron basis set for platinum atom, and the def2-TZVP basis set for light atoms.</p> <p>Working material for the upcoming article.</p>
Dataset for "Effect of benzothiadiazole-based π-spacers on fine-tuning of optoelectronic properties of oligothiophene-core donor materials for efficient organic solar cells: a DFT study"
<p># Data and code for "Effect of benzothiadiazole-based π-spacers on fine-tuning of optoelectronic properties of oligothiophene-core donor materials for efficient organic solar cells: a DFT study."</p><p>## Contents</p><p>* data-{type}/*: reproducible data</p><p>* job.job : example slurm script</p><p> </p><p>## Description of the data</p><p>The data are organized in subdirectories *data-{type}/{system}/* corresponding to the considered molecules and simulation type:</p><p>* data-gs: Ground state calculations</p><p>* data-td: TD-DFT calculations</p><p>The contents of each subdirectory are:</p><p>* data-gs/{system}/structure.xyz: physical atomic structure</p><p>* data-td/{system}/td-dft/td_uvvis.txt: photoabsorption spectrum</p><p>The spectrum plots in the article correspond to the first (x values) and second (y values) columns of the spectrum files.</p><p> </p><p>## Reproduction of the data</p><p>The data were produced using Gaussian version g16.A.01</p><p>The calculation of the data of a system consists of the following steps:</p><p>1. Ground-state (gs) calculation:</p><p> * Prepare the input file for the gs by adjusting the parameters of the ground state calculations:</p><p> * "# opt b3lyp/6-311+g(d,p) scrf=(smd,solvent=chloroform) geom=connectivity empiricaldispersion=gd3bj out=wfn"</p><p> * out = wfn keyword to create a wfn file of the ground state that will be used for EDD and RDG investigations</p><p> * Submit the job.job file for the gs calculation as appropriate for the particular input file of the system</p><p> * The optimized sturctures are visualised using GaussView</p><p>2. Time-propagation calculation:</p><p> * Requires finished ground-state calculation</p><p> * Set up the TD-DFT calculation parameters as necessary:</p><p> * "# td=(nstates=6) wb97xd/6-311+g(d,p) scrf=(smd,solvent=chloroform) guess=read density out=wfn"</p><p> * density out = wfn keywords to create a wfn file of the excited state that will be used for EDD investigation</p><p> * Submit the job.job file for TD-DFT calculation as appropriate for the particular system</p><p> * The photoabsoption specta are visualised using GaussView</p><p>3. RDG calculation:</p><p> * Put the .wfn file of the gs calculation in the command window of the open source Multiwfn software and follow the sturcture in Section 3.23.1 in the manual</p><p>4. DOS calculation:</p><p> * The dos curves are plotted starting from the .fchk of the ground state geometry, select the atoms index corresponding to the diffrents subpart of the studied molecules (donor, acceptor, pi-spacer)</p><p> * Put the .fchk file of the gs calculation in the command window of the open source Multiwfn software and follow the structure in Section 4.10.1 in the manual</p><p> * the output generates .chk file which is transformed to .fchk file : formchk .chk .fch</p><p>5. TDM calculations:</p><p> * Requires finished ground-state calculation</p><p> * Set up the TD-DFT calculaton parameters as necessary</p><p> * "# td=(nstates=6) wb97xd/6-311+g(d,p) scrf=(smd,solvent=chloroform) guess=read density transition=1 iop(6/8=3) out=wfn"</p><p> * Put the .fchk file of the gs calculation in the command window of the open source Multiwfn software and follow the sturcture in Section 4.18.8 in the manual</p><p>6. EDD calculation:</p><p> * Edd plots are plotted based on the es.wfn and gs.wfn following Section 4.18.1 in the manual</p><p> </p>
DFT Calculation Data for "Stabilized tilted-octahedra halide perovskites inhibit local formation of performance-limiting phases"
<p>Initial and optimized structures that are used for DFT simulations associated with Fig 2A-G in <em>Science</em> <strong>374</strong>, 1598 (2021) (DOI: 10.1126/science.abl4890)</p>
Iron Nitride Nanoparticles for Enhanced Reductive Dechlorination of Trichloroethylene: DFT Calculations
<p>This dataset contains input and output files of density functional theory calculations on which the computational part of the peer-reviewed article "Iron Nitride Nanoparticles for Enhanced Reductive Dechlorination of Trichloroethylene" by M. Brumovský et al., doi 10.1021/acs.est.1c08282, is based. Please cite this article when using the dataset.</p> <p>The dataset includes:<br> * Fully relaxed unit cells of Fe, Fe4N, and FeS in the folder "Unit_cells"<br> * Structures and energies of adsorbed TCE and H2O molecules on the Fe(110), Fe4N(001), and FeS(001) surfaces in the folder "Adsorption_calculations"<br> * Transition state calculations of TCE chemisorption and the first dechlorination step on the Fe4N(001) surface, including frequency calculations of transitions states, in the folder "NEB_calculations_on_Fe4N"<br> * TCE homolytic bond dissociation energies calculated using VASP and TURBOMOLE in the folder "BDE_calculations"<br> * Energies of reactants, products, and transitions states calculated with the inclusion of the solvent effect in the folder "VASPsol_calculations"</p> <p>The final geometries and energies calculated using VASP are reported in the CONTCAR and OUTCAR files, respectively. Note that the POTCAR files are not allowed to be made publicly accessible. However, their description is given in the OUTCAR files. Please consult VASP/TURBOMOLE manual for more information regarding input and output files. </p> <p>Funding: This work was supported by the Austrian Science Fund (FWF) project M 2892-N and the University of Ostrava (IRP201826, SGS06/PrF/2021). The Vienna Scientific Cluster (Project No. 70544) and IT4 Innovations National Supercomputing Center (LM2015070) are gratefully acknowledged for providing computational resources. </p> <p>Terms of use: These data are provided "as is", without any warranty. The data are provided under the Creative Commons Attribution 4.0 International license.</p>
DFT investigation on the application of pure and doped X12N12 (X = B and Al) fullerene-like nano-cages towards the adsorption of temozolomide
<p>The sensitivity of pure and doped X<sub>12</sub> N<sup><sub>12</sub></sup> (X = B and Al) fullerene-like nano-cages (FLNs) toward the anticancer drug temozolomide (TMZ) is probed herein at DFT/M06-2X-D3/6-311G(d,p) theoretical level in both gas phase and water. A noticeable affinity of the FLNs toward TMZ was observed along with the negative gas-phase adsorption energies -1.37 and -2.09 eV for the most stable configurations of pure B12N12 and Al12N12 pristines, respectively. Considerable charge transfer from TMZ to the FLNs was also revealed via NBO analysis and the Hirshfeld atomic charges, making the dipole moment vector of the molecular complexes to be oriented from the nano-cages to the TMZ moiety. Furthermore, a percentage decrease in the HOMO-LUMO energy gap (ΔEg) of 38.09 and 17.72 % was obtained for the B12N12 and Al12N12 nano-cages, respectively. The percentage change in ΔEg was found to be reduced upon doping and solvation of the FLNs. Finally, a recovery time in vacuum ultraviolet light of 1.06 s is found for the complex with pure B12N12, which in addition to the above-mentioned parameters make this boron nitride cage the best sensor for TMZ, among the FLNs considered in the present work.</p>
DFT Calculated xyz Files in Support of "Bidentate Rh(I)-Phosphine Complexes for the C-H Activation of Alkanes: Computational Modelling and Mechanistic Insight"
<p>Theoretically calculated xyz files for propane, carbon monoxide, butyraldehyde and multiple Rh-phosphine complexes as well as transition states relevant for the C-H activation and subsequent carbonylation of alkanes.</p> <p>All quantum chemical simulations were performed using the Gaussian 16 software package. Closed-shell equilibrium structures, i.e., minima and transition states (TSs) as well as electronic properties of educts, intermediates, and products involved in the C-H activation of propane (methyl group activation) and subsequent steps mediated by the Rh complexes were obtained at the DFT level of theory. The range-separated B97XD functional was employed. The def2-SVP basis set and the respective effective core potential (ECP) were utilized for all atoms. TSs were fully optimized at the same level of theory using the rational function optimization (RFO) approach as well as nudged elastic band (NEB) method as implemented in the pysisyphus<sup> </sup>software suite. Subsequently, a vibrational analysis was carried out for each stationary point to verify that a minimum or first-order saddle point was obtained on the 3<em>N</em>-6-dimensional potential energy (hyper)surface (PES).</p>
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