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60 results for “Density functional theory”
Fig. 2 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer
Fig. 2. Optimized geometries for diferuloylputrescine, the diferuloylputrescine radical (with spin densities) and homo-coupled diferuloylputrescine dimers.
Fig. 7 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer
Fig. 7. Gibbs free energy of reaction for dehydrogenation and bond dissociation of cross-coupled diferuloylputrescine-coniferyl alcohol dimers.
Fig. 6 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer
Fig. 6. Gibbs free energy of reaction for dehydrogenation and bond dissociation of homo-coupled diferuloylputrescine dimers.
Density Functional Theory and Machine Learning for Electrochemical Square-Scheme Prediction: An Application to Quinone-type Molecules Relevant to Redox Flow Batteries
<p>The uploaded data contains (i) "<strong>01_Data</strong>" optimized molecular structure in XYZ format and the primary attributes and SMILES, (ii) "<strong>02_Datasets</strong>" datasets used in the publication, and (iv) "<strong>03_pynb_script</strong>" a Jupyter-Notebook. The <strong>01_Data </strong>directory contains more than 8000 subdirectories. Each is for a molecule that undergoes a two-proton two-electron transfer reaction. In each subdirectory, one finds the following files:</p> <p>(1) directories named corresponding to the ones in Figure 1 of the paper. Inside each, there are geometries and properties in XYZ and CSV format, respectively.</p> <p>(2)<strong> "freeEnergy.dat" </strong>contains the free energy of different states.</p> <p>(3) <strong>"schemesquare.dat" </strong>has the parameters of the electrochemical scheme of square representation.</p> <p>├── A<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── A1-<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── A2-<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH1+<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH1-<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH2<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH21+<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── AH22+<br> │ ├── info.csv<br> │ └── pos.xyz<br> ├── <strong>freeEnergy.dat</strong><br> └── <strong>schemesquare.dat</strong><br> ******************************************************<br> The new version (v1.1) contains some updates around:<br> (i) The DFT calculations workflow in a folder called "<strong>04_workflow_of_DFT</strong>"</p> <p> The Gaussian input files have been explained in the "README" file.</p> <p>(ii) The Python scripts for data extraction have been added and can be found in "<strong>05_how_to_extracted_data</strong>"</p> <p>(iii) We explained how to compute the Purbaix diagram in great detail "<strong>06_how_to_compute_Pourbaix_diagram</strong>/"</p> <p>All these changes/improvements were applied/made following the Referee of Digital Discovery Journal. Here, we would like to thank him/her.</p>
Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation
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Figure 6 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 6 Molecular dynamics of Tigogenin and Gitogenin bound to aldose reductase: (a) RMSD, (b) RMSF, (c) Hydrogen bond profile; green-Tigogenin, red-Gitogenin, black-apoprotein.
Supplementary material 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
List of molecular weight matched decoys retrieved from DEKOIS 2.0
Figure 5 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 5 HOMO and LUMO distribution plots: (a) HOMO (b) LUMO of Tigogenin (c) HOMO (d) LUMO of Gitogenin.
Figure 4 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 4 Intermolecular interactions of (a) Tigogenin, (b) Gitogenin, (c) Epalrestat with active-site amino acids of the enzyme aldose reductase. All the ligands are shown in all atoms' green-coloured ball and stick-type representations. The names of amino acids with ID numbers are mentioned under each circle around each ligand. On the 2D figures analysis, green-coloured dotted lines indicate hydrogen bonding interactions involving electronegative elements like nitrogen and oxygen atoms; light purple-coloured dotted lines indicate π-alkyl interactions; violet-coloured dotted lines indicate π-sigma interactions. Light green colour amino acids without bonding represent van der Waals interactions, whereas, orange-red colour amino acids indicate unfavourable interactions. The light-blue halo surrounding the interacting residues represents the solvent-accessible surface that is proportional to its diameter.
Figure 1 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 1 The binding site of aldose reductase was predicted using CASTp. The residues highlighted in blue boxes constitute the binding site.
Figure 3 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 3 Analysis and comparison of the predictive power of AutoDock and AutoDock Vina: (a) Receiver operating characteristic curves, (b) Predictiveness curves, (c) Enrichment curves, red is ADock and green is Avina.
Unraveling the impact of nuclear quantum effects on proton affinity using nuclear electronic orbital-density functional theory: A Comprehensive Benchmark Study
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Data Set For Projection-Based Density Matrix Renormalization Group in Density Functional Theory Embedding
<p><span>Funded by the National Science Center grant no 2021/43/I/ST4/02250 </span></p>
Data from: BNPd single-atom catalysts for selective hydrogenation of acetylene to ethylene: a density functional theory study
The mechanisms of selective hydrogenation of acetylene to ethylene on B11N12Pd single-atom catalyst (SAC) was investigated through the density functional theory by using 6-31++G basis set. We studied the adsorption characteristics of H2 and C2H2, and simulated the reaction mechanism. We have discovered that H2 absolutely dissociative chemisorption on single atom Pd and formed the B11N12Pd(2H) dihydride complex and then proceed the hydrogenation reaction with C2H2. The hydrogenation reaction of acetylene onto the B11N12Pd complies with the Horiuti-Polanyi mechanism, and the energy barrier as low as 26.55 kcal mol-1. The low desorption energy of ethylene, high ethylene hydrogenation activation energy can ensure the B11N12Pd SAC has high selectivity. Meanwhile it also has a higher selectivity than many bimetallic alloy single-atom catalyst.
Density functional theory study of Mobius boroncarbon-nitride as potential CH4, H2S, NH3, COCl2 and CH3OH gas sensor
<p>The interesting properties of Mobius structure and Boron-Carbon-Nitride inspired this research to study different characteristics of Mobius Boron-Carbon-Nitride (MBCN) nanoribbon. The structural stability, vibrational, electrical, and optical properties are analyzed using the density functional theory. The gas sensing ability of the modeled MBCN structure was also studied for CH<sub>4</sub>, H<sub>2</sub>S, NH<sub>3</sub>, COCl<sub>2</sub>, and CH<sub>3</sub>OH gases. The negative adsorption energy and alteration of electronic bandgap verified that MBCN is very sensitive toward the selected gases. The complex structures showed a high absorption coefficient with strong chemical potential and 7 ps- 0.3 ms recovery time. The negative change in entropy signifies that all the complex structures were thermodynamically stable. Among the selected gases, the MBCN showed the strongest interaction with CH<sub>3</sub>OH gas.</p>
Fig. 5 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer
Fig. 5. Optimized geometries for cross-coupled diferuloylputrescine-coniferyl alcohol dimers.
Fig. 1 in Density functional theory study on the coupling and reactions of diferuloylputrescine as a lignin monomer
Fig. 1. Diferuloylputrescine and resonance structures from dehydrogenation.
Data from: BNPd single-atom catalysts for selective hydrogenation of acetylene to ethylene: a density functional theory study
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Density functional theory study of Mobius boroncarbon-nitride as potential CH4, H2S, NH3, COCl2 and CH3OH gas sensor
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Figure 2 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 2 Benchmarking docking binding energy scores distribution: (a) AutoDock, (b) AutoDock Vina.
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