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Data for an article "Hyperspace exploration using robotics for the discovery of mechanistically distinct transformations and complex functional products", Nature Synthesis, 2026

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Zenodo2026-05-18 更新2026-05-26 收录
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1. Quantum chemistry calculations Data related to quantum chemistry calculations is in quantum_chemical_calculations.tar.7z (7-zip, 13.5 GB when uncompressed). The contents of this archive are as follows: 1.1. Structure of a complex of two host molecules with Zn(II) cation Input and output files of quantum chemical calculations of solution ensemble of homodimer of 8a in complex with Zn2+ are located in subfolder 18_B_ome_dimer_homo_Zn_acetone. If you are only interested in a summary of conformer energies and their geometries, see subfolder 18_B_ome_dimer_homo_Zn_acetone/thermochemistry_summary, which contains the free energy and its components for every conformer in .csv and .json formats. The geometries and free energies of the conformers of the final sorted ensemble can be found in in 18_B_ome_dimer_homo_Zn_acetone/thermochemistry_summary/cregen/298.15/crest_ensemble.xyz file. The grouping of conformers into clusters, as described in the Supplementary Information of the accompanying research article, can be found in the 18_B_ome_dimer_homo_Zn_acetone/thermochemistry_summary/conf_clusters folder. The contents of respective subfolders are as follows: /crest subfolder contains CREST ensembles of conformers generated from different initial guesses. The /crest/combined folder contains the merged and sorted ensemble at the CREST/GFN-2/xTB level. /orca_opt_low contains input configurations for ORCA DFT calculations and the respective outputs for the geometry optimization of each conformer (subfolders named like /orca_opt_low/conf_0, /orca_opt_low/conf_1, /orca_opt_low/conf_2, and so on). /orca_freq_low contains input configurations for ORCA DFT calculations and the respective outputs for the thermostatistical corrections to enthalpy, entropy, and free energy -- primarily based on the Hessian estimation for vibrational modes -- for each conformer (subfolders named like /orca_freq_low/conf_0, /orca_freq_low/conf_1, /orca_freq_low/conf_2, and so on). /orca_solv contains the calculations of solvation free energy (openCOSMO-RS calculations performed by ORCA) for each conformer (subfolders named like /orca_solv/conf_0, /orca_solv/conf_1, /orca_solv/conf_2, and so on). /orca_sp contains input configurations for ORCA DFT calculations and the respective outputs for the single-point electronic energy calculations (and Boys-Bernardi counterpoise correction components) at ωB97X-3c level of theory for each conformer (subfolders named like /orca_sp/conf_0, /orca_sp/conf_1, /orca_sp/conf_2, and so on). For each conformer's folder, subfolders named like "E_subABC_supABC_parABC" follow the notation in the Section 2.11.1 of the ORCA 6.1 manual, "sub" meaning subscript, "sup" -- superscript, and "par" -- the expression in the parentheses. 1.2. Stability of diastereomers The folder /diastereomers of the archive root contains the calculations of free energies of various diastereomers of 8a, as discussed in the Sections 1.6 and 3.1 of Supplementary Information. Species are named as shown in the image located in /diastereomers/names_for_structures_here.png. The corresponding ChemDraw file can be found in the same folder as well. The folder structure has the form /diastereomers/{solvent}_{temperature}/{species}/, where the {solvent} is either "chloroform" or "acetonitrile", {temperature} is either "rt" for room temperature or "100c" for 100 degrees Celcius, and {species} are shown in the scheme /diastereomers/names_for_structures_here.png. A folder for each species has the following subfolders: /crest subfolder contains CREST ensembles of conformers. /conformers contains subfolders conf_0, conf_1, conf_2 with DFT calculations for individual conformers: /orca_opt contains input configurations for ORCA DFT calculations and the respective outputs for the geometry optimization of each conformer (subfolders named like /orca_opt_low/conf_0, /orca_opt_low/conf_1, /orca_opt_low/conf_2, and so on). /orca_freq contains input configurations for ORCA DFT calculations and the respective outputs for the thermostatistical corrections to enthalpy, entropy, and free energy -- primarily based on the Hessian estimation for vibrational modes. /solv contains the calculations of solvation free energy (openCOSMO-RS calculations performed by ORCA). It also contains the cosmors_dgsolvation.csv table listing the free energy of solvation at the relevant temperature. /orca_sp1 contains input configurations for ORCA DFT calculations and the respective outputs for the single-point electronic energy calculations at ωB97X-3c level of theory. /thermochemistry_summary contains the CSV tables conformer_thermochemistry*.csv with free energies and energy components for each conformer, as well as the file net_free_energies.csv containing the net free energy of the species in question. For geometries of conformers of the sorted ensemble, see the file subfolder /cregen/{T_kelvin}/crest_ensemble.xyz, where {T_Kelvin} is the folder named by a numerical value of the absolute temperature. 1.3. Circular dichroism measurements and theoretical calculations The folder /cd of the archive root contains the calculations of circular dichroism spectra, as discussed in the Section 3.3 of Supplementary Information. Experimental data of circular dichroism measurements is located in the /measurements subfolder; theoretical calculations -- in two subfolders that correspond to certain species: /1_b for the species 8a, and /2_h for species 20a. Calculation for 20a is used as theoretical prediction for 20b, as well. A folder for each species has the following subfolders: /crest subfolder contains CREST ensembles of conformers. /conformers contains subfolders conf_0, conf_1, conf_2 with DFT calculations for individual conformers: /orca_opt contains input configurations for ORCA DFT calculations and the respective outputs for the geometry optimization of each conformer (subfolders named like /orca_opt_low/conf_0, /orca_opt_low/conf_1, /orca_opt_low/conf_2, and so on). /orca_freq contains input configurations for ORCA DFT calculations and the respective outputs for the thermostatistical corrections to enthalpy, entropy, and free energy -- primarily based on the Hessian estimation for vibrational modes. /solv contains the calculations of solvation free energy (openCOSMO-RS calculations performed by ORCA). It also contains the cosmors_dgsolvation.csv table listing the free energy of solvation at the relevant temperature. /orca_sp1 contains input configurations for ORCA DFT calculations and the respective outputs for the single-point electronic energy calculations at ωB97X-3c level of theory. /thermochemistry_summary contains the CSV tables conformer_thermochemistry*.csv with free energies and energy components for each conformer, For geometries of conformers of the sorted ensemble, see the file subfolder /cregen/{T_kelvin}/crest_ensemble.xyz, where {T_Kelvin} is the folder named by a numerical value of the absolute temperature. /tddft contains the Gaussian16 (Revision C.01) job files .gjf and output files .log for several lowest-lying conformers. 2. Raw data and visualisation The folder UV-Vis.tar (814 MB when uncompressed) contains data accuired with NanoDrop spectrophotometer and fitted spectra after spectral unmixing procedure. The UV-Vis\2024-02-05-run01 folder contains spectra of pure components used for calibration curves and remaining files contain spreadsheets with reaction conditions executed by robotic pipetter and UV-Vis spectra of crude reaction mixtures as well as fitted spectra. The folder HPLC_maps.tar (21.3 MB when uncompressed) contains data related to analytical HPLC experiments (reaction conditions and chromatograms). The CSV file average_results_HPLCa.csv contains final data (yields, molar concentrations and mass efficiency values) calculated for three selected products. This file might be used to visualise reaction maps using HyperspaceViewer software available in the link: https://gitlab.com/az-steak/hyperspace_viewer/-/tree/main/Packages?ref_type=heads

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