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29 results for “DFT calculations”
DFT Calculated xyz and log Files as well as csv Files for Machine Learning in Support of "Tailoring Phosphine Ligands for Improved C H Activation: Insights from Δ-Machine Learning"
<p>Transition metal complexes have played crucial roles in various homogeneous catalytic processes due to their exceptional versatility. This adaptability stems not only from the central metal ions but also from the vast array of choices of the ligand spheres, which form an enormously large chemical space. For example, Rh complexes, with a well-designed ligand sphere, are known to be efficient in catalyzing the C-H activation process in alkanes. To investigate the structure-property relation of the Rh complex and identify the optimal ligand that minimizes the calculated reaction energy ΔE of an alkane C-H activation, we have applied a Δ-Machine Learning method trained on various features to study 1,743 pairs of reactants (Rh(PLP)(Cl)(CO)) and intermediates (Rh(PLP)(Cl)(CO)(H)(propyl)). Our findings demonstrate that the models exhibit robust predictive performance when trained on features derived from electron density (R<sup>2 </sup>= 0.816), and SOAPs (R<sup>2 </sup>= 0.819), a set of position-based descriptors. Leveraging the model trained on xTB-SOAPs that only depend on the xTB-equilibrium structures, we propose an efficient and accurate screening procedure to explore the extensive chemical space of bisphosphine ligands. By applying this screening procedure, <a>we identify ten newly selected reactant-intermediate pairs with an average ΔE </a>of 33.2 kJ mol<sup>-1</sup>, remarkably lower than the average ΔE of the original data set of 68.0 kJ mol<sup>-1</sup>. This underscores the efficacy of our screening procedure in pinpointing structures with significantly lower energy levels.</p> <p>_______________________________________________________________________</p> <p>The dataset contains three file types:</p> <p>Version 1.0:</p> <ol> <li>xyz files of the final optimized Rh-phosphine complexes; one set for the starting materials denoted as "molecule-XXXX_4-times" and one set for the intermediates after C-H activation denoted as "molecule-XXXX_6-times"</li> <li>Gaussian16 log files for the optimization process; one set for the starting materials denoted as "molecule-XXXX_4-times" and one set for the intermediates after C-H activation denoted as "molecule-XXXX_6-times"</li> <li>csv files containing the per molecule features used for training the different machine learning models. The name of the csv files indicates which property was predicted and which model was used</li> </ol> <p>New in version 1.1 (other data is unchanged):</p> <ol> <li>Gaussian16 log files for the ten newly identified bisphosphine ligands; one set for the product material denoted as "LXX_6-times-axial" and one set for the transition state for the C-H activation denoted as "LXX_C-H-activation_TS"</li> </ol>
Iron Nitride Nanoparticles for Rapid Dechlorination of Mixed Chlorinated Ethene Contamination: 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 rapid dechlorination of mixed chlorinated ethene contamination" by M. Brumovský et al., doi 10.1016/j.jhazmat.2022.129988, is based. Please cite this article when using the dataset.</p> <p>The dataset includes:<br> * Structures and energies of adsorbed cis-DCE and PCE molecules on the Fe(110), Fe4N(001), and FeS(001) surfaces in the folder "Adsorption_calculations", including structures and energies of adsorbed TCE on the FeS(001) surface<br> * cis-DCE and PCE homolytic bond dissociation energies calculated using VASP and TURBOMOLE in the folder "BDE_calculations"<br> * Relaxed structures of dechlorinated intermediates on the Fe(110), Fe4N(001), and FeS(001) surfaces in the folder "Intermediates"<br> * Transition state calculations of chloroethene dechlorination reactions, including frequency calculations of transitions states, in the folder "NEB_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>The fully relaxed unit cells of Fe, Fe4N, and FeS, as well as adsorption calculations of TCE, and transition state calculations of TCE chemisorption and its first dechlorination step on the Fe4N(001) surface are accessible in a previously published dataset, doi 10.5281/zenodo.6338412.</p> <p>Funding: This work was supported by the Austrian Science Fund (FWF) 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. The data are provided under the Creative Commons Attribution 4.0 International license.</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>
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>
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 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>
Strong toxic gas detection on Penta-BCP monolayers: insights from DFT calculations
<p>Rapid and accurate detection of toxic gases remains important for industrial safety and environmental well-being. This study examines the potential of <em>penta</em>-BCP monolayer as a high-performance toxic gas sensor utilizing the robust framework of density functional theory (DFT). <em>Penta</em>-BCP exhibits strong and selective interactions with specific toxic gas molecules, including CO, NO, and NO<sub>2</sub>. This results in the remarkable ability to readily capture these harmful gases while demonstrating minimal interaction with non-toxic counterparts such as H<sub>2</sub>, N<sub>2</sub>, CO<sub>2</sub>, and CH<sub>4</sub>, underlining its exceptional selectivity. Furthermore, <em>penta</em>-BCP has a significantly shorter recovery time for NO and NO<sub>2</sub> gases compared to <em>penta</em>-BCN, which has a similar structure. These findings collectively position <em>penta</em>-BCP as a frontrunner for the next generation of toxic gas sensors, paving the way for enhanced environmental monitoring and improved public health protection.</p>
Measurement Results of Single-Bit Sigma-Delta Modulator and Simulation Data for DFT Based RSSI Calculation
<p>Measurement of single-bit output data stream of an low-IF receiver with sigma-delta ADC. Inphase and Quadraturephase signals can be found in raw_rx_*.csv files. Simulation results of DFT based RSSI calculation are found in sim_RSSI_*.csv. Measurement results of the RSSI dynamic range are located in meas_RSSI_dynamicRange.csv.</p>
DFT calculated dielectric tensor Sb2S3
<p>Dielectric tensor of Sb2S3.</p> <p>Files generated for imaginary and real parts.</p> <p>Structure of the file: eV // dielectric function</p> <p>Details on the calculations are available at https://doi.org/10.1016/j.isci.2022.104377</p>
Decoratype-based materials informatics: Polaritype identification, convex hull DFT calculations, training data, and predicted compounds data
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Strong toxic gas detection on Penta-BCP monolayers: insights from DFT calculations
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Calculating bond dissociation energies of X-H (X = C, N, O, S) bonds of aromatic systems via DFT: A detailed comparison of methods
<p>In this study, the bond dissociation energy (BDE) values of X-H (X = C, N, O, S) bonds of aromatic compounds were computed by using 17 different DFT functionals, namely M08-HX, M06-2X, M05-2X, M06, M05, BMK, MPW1B95, B1B95, B98, B97-2, LC-wPBE, B3LYP, cam-B3LYP, B2PLYP, MPWB1K, BB1K, BB95, within the basis set range 6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-311G(d,p) and 6-311++G(d,p). The results show that the 6-31G(d) is the most convenient basis set to perform the BDE calculations with sufficient accuracy compared to the relevant experimental BDEs. The M06-2X, M05-2X, and M08-HX functionals gave highly accurate BDE values (with the average mean unsigned error MUE = 1.2-1.5 kcal/mol), performing better than the other functionals. The results suggest that the M06-2X, M05-2X, and M08-HX density functionals in the combined DFT/6-311+G(3df,2p)//B3LYP/6-31G(d) model chemistry offer the best method for calculating BDEs of ArX-H (X = C, N, O, S) bonds.</p>
Supplementary Data for "Comprehensive Phase Diagrams of MoS2 Edge Sites Using Dispersion-Corrected DFT Free Energy Calculations"
<p>MoS2 Phase Diagrams to accompany DOI: 10.1021/acs.jpcc.8b02524</p>
The hydrous mechanism changes in enstatite with Al incorporation studied by DFT calculations
<p>The data are crystallographic information files used in submitted paper "The hydrous mechanism changes in enstatite with Al incorporation studied by DFT calculations" by Sakurai et al..</p>
Fig. 4 in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments
Fig. 4. The four most relevant global-minimum energy conformations of 1 modeled in CHCl3 solution accounting for the 78% of the total population.
Fig. 3. Chemical correlations between 5,6 in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments
Fig. 3. Chemical correlations between 5,6-dihydro-2H-pyran-2-ones and 2(5H)-furanones. A possible biogenetic correlation is indicated by a dotter arrow.
Fig. 1. 1H in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments
Fig. 1. 1H NMR spectral sections of peracetylated montecofuranolide (2). (A) Simulated spectrum using DFT 3J of peracetyl-5′-epi-synrotolide (5) in gas H,H phase with chemical shifts of the experimental spectrum of compound 2 and coupling constants of monticolide A (6) for J ′ ′ 3 -4 proS = 8.7 Hz, J ′ ′ 3 -4 proR = 4 Hz to simulate the multiplicity for H-4′. (B) Fully simulated spectrum obtained by iteration of chemical shifts, 3J, and linewidths of compound 2. (C) ExperiH,H mental spectrum in CDCl3 (400 MHz).
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