[ { "id": "1", "category": "smiles_lookup", "query": "Provide the SMILES string corresponding to this molecule: sulfur dioxide", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "sulfur dioxide" } } ], "result": { "name": "sulfur dioxide", "smiles": "O=S=O" }, "structured_output": { "smiles": [ "O=S=O" ], "scalar_answer": null, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "2", "category": "smiles_lookup", "query": "Provide the SMILES string corresponding to this molecule: Nitrogen Dioxide", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Nitrogen Dioxide" } } ], "result": { "name": "Nitrogen Dioxide", "smiles": "N(=O)[O]" }, "structured_output": { "smiles": [ "N(=O)[O]" ], "scalar_answer": null, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "3", "category": "smiles_lookup", "query": "Provide the SMILES string corresponding to this molecule: water", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "water" } } ], "result": { "name": "water", "smiles": "O" }, "structured_output": { "smiles": [ "O" ], "scalar_answer": null, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "4", "category": "smiles_lookup", "query": "Provide the SMILES string corresponding to this molecule: carbon dioxide", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "carbon dioxide" } } ], "result": { "name": "carbon dioxide", "smiles": "C(=O)=O" }, "structured_output": { "smiles": [ "C(=O)=O" ], "scalar_answer": null, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "5", "category": "optimization_from_name", "query": "Run geometry optimization for sulfur dioxide and report its energy using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "sulfur dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=S=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_5/output.json", "single_point_energy": -16.815808019358535, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019358535, "property": "optimized energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "6", "category": "vibrations_from_name", "query": "Report the vibrational frequencies of water using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "vib", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "result": { "vibrational_frequencies": { "energies": [ "5.278838012595982i", "0.04764407633090353i", "0.005321020506525112i", "0.06055744294822688", "4.520458491661813", "5.344478380954939", "207.53984955909357", "461.6946537572708", "484.0428021965612" ], "energy_unit": "meV", "frequencies": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ], "frequency_unit": "cm-1" } }, "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_6/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ] }, "ir_spectrum": null, "atoms_data": null } } }, { "id": "7", "category": "thermochemistry_from_name", "query": "Report the thermochemical properties (Gibbs free energy) of carbon dioxide at 800 K using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 800 } } } ], "result": { "status": "success", "result": { "thermochemistry": { "enthalpy": -279.8479687871829, "entropy": 0.00267553279139694, "gibbs_free_energy": -281.98839502030046, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_7/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -281.98839502030046, "property": "Gibbs free energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "8", "category": "dipole_from_name", "query": "Report the dipole moment of carbon monoxide using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "carbon monoxide" } }, { "smiles_to_coordinate_file": { "smiles": "[C-]#[O+]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "dipole", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_8/output.json", "dipole_moment": [ -0.1278, -0.0, -0.0 ] }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": { "value": [ -0.1278, -0.0, -0.0 ], "unit": "e * Angstrom" }, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "9", "category": "energy_from_name", "query": "Report the single-point energy of nitrogen using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "nitrogen" } }, { "smiles_to_coordinate_file": { "smiles": "N#N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_9/output.json", "single_point_energy": -16.42796020021993, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "10", "category": "optimization_from_name", "query": "Run geometry optimization for ethene and report its energy using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethene" } }, { "smiles_to_coordinate_file": { "smiles": "C=C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_10/output.json", "single_point_energy": -170.64969292571732, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -170.64969292571732, "property": "optimized energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "11", "category": "vibrations_from_name", "query": "Report the vibrational frequencies of ethanol using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethanol" } }, { "smiles_to_coordinate_file": { "smiles": "CCO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "vib", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "result": { "vibrational_frequencies": { "energies": [ "2.8487477679839643i", "1.3603132350517313i", "0.21983103123530795i", "0.008847334847696479i", "0.14881363935060374", "1.1251489861100825", "27.798397380880044", "42.20918825555526", "52.10585749803683", "103.03144226048379", "115.54432766433835", "129.56743496749917", "135.15038253526848", "140.11576517953577", "153.1473372364278", "162.9209544186835", "167.31662813377304", "174.18841138098222", "183.86516633114854", "184.71269264793713", "185.60849327672528", "355.65983750781385", "369.881948660016", "374.1891849590732", "377.5211675990388", "377.9664145403596", "439.2993477525492" ], "energy_unit": "meV", "frequencies": [ "22.976700481238225i", "10.97166625761575i", "1.7730568560479967i", "0.07135856853925851i", "1.2002629566960932", "9.074938659422148", "224.20919733828583", "340.44006528188726", "420.2620865580306", "831.0046314295005", "931.9278592812555", "1045.0318483188712", "1090.0613576031817", "1130.1098698211686", "1235.2165876976974", "1314.046127167208", "1349.4996269469866", "1404.92429711877", "1482.9725899929615", "1489.8083507962422", "1497.0334701872569", "2868.590070157765", "2983.299133496947", "3018.0393374060463", "3044.9135900119045", "3048.504748810128", "3543.1882205762395" ], "frequency_unit": "cm-1" } }, "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_11/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "22.976700481238225i", "10.97166625761575i", "1.7730568560479967i", "0.07135856853925851i", "1.2002629566960932", "9.074938659422148", "224.20919733828583", "340.44006528188726", "420.2620865580306", "831.0046314295005", "931.9278592812555", "1045.0318483188712", "1090.0613576031817", "1130.1098698211686", "1235.2165876976974", "1314.046127167208", "1349.4996269469866", "1404.92429711877", "1482.9725899929615", "1489.8083507962422", "1497.0334701872569", "2868.590070157765", "2983.299133496947", "3018.0393374060463", "3044.9135900119045", "3048.504748810128", "3543.1882205762395" ] }, "ir_spectrum": null, "atoms_data": null } } }, { "id": "12", "category": "thermochemistry_from_name", "query": "Report the thermochemical properties (Gibbs free energy) of methane at 500 K using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "methane" } }, { "smiles_to_coordinate_file": { "smiles": "C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500 } } } ], "result": { "status": "success", "result": { "thermochemistry": { "enthalpy": -21.793386183692945, "entropy": 0.0021505247570400435, "gibbs_free_energy": -22.868648562212968, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_12/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -22.868648562212968, "property": "Gibbs free energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "13", "category": "dipole_from_name", "query": "Report the dipole moment of ammonia using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ammonia" } }, { "smiles_to_coordinate_file": { "smiles": "N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "dipole", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_13/output.json", "dipole_moment": [ -0.0051, -0.002, -0.3835 ] }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": { "value": [ -0.0051, -0.002, -0.3835 ], "unit": "e * Angstrom" }, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "14", "category": "energy_from_name", "query": "Report the single-point energy of methane using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "methane" } }, { "smiles_to_coordinate_file": { "smiles": "C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_14/output.json", "single_point_energy": -113.5639578693412, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -113.5639578693412, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "15", "category": "energy_from_name", "query": "Report the single-point energy of nitrogen using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "nitrogen" } }, { "smiles_to_coordinate_file": { "smiles": "N#N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 7, 7 ], "positions": [ [ 0.56000414, 0.0, 0.0 ], [ -0.56000414, 0.0, 0.0 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "energy", "optimizer": "bfgs", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0", "device": "cpu", "default_dtype": "float64", "dispersion": false, "damping": "bj", "dispersion_xc": "pbe", "dispersion_cutoff": 21.167088422553647 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -16.42796020021993, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.09377384185791016 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "16", "category": "optimization_from_name", "query": "Run geometry optimization for propane and report its energy using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "propane" } }, { "smiles_to_coordinate_file": { "smiles": "CCC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1 ], "positions": [ [ 1.1836990220404637, -0.44581775611645075, -0.21608217898758877 ], [ 0.013755939163535107, 0.5231870496938728, -0.33502779706029595 ], [ -1.193998971070771, 0.054076155230239634, 0.46693744811254595 ], [ 1.4921405564582122, -0.5456000103085392, 0.8224939842948522 ], [ 2.0343314895638045, -0.09291512805474228, -0.7950762275075864 ], [ 0.9022153167897163, -1.430444486069934, -0.583519605884765 ], [ -0.26707932569687626, 0.6232475369384911, -1.3858926897307564 ], [ 0.3231291409794439, 1.5085162554994638, 0.020798142197863384 ], [ -2.0168236556709362, 0.7588112197659447, 0.36866240378291826 ], [ -0.9407222264084549, -0.03410841244112956, 1.521360301361399 ], [ -1.5306472961481372, -0.9189524341372168, 0.11534622942141458 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "opt", "optimizer": "bfgs", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB", "charge": null, "multiplicity": null, "accuracy": 1.0, "electronic_temperature": 300.0, "max_iterations": 250, "initial_guess": "sad", "mixer_damping": 0.4, "electric_field": null, "spin_polarization": null, "cache_api": true, "verbosity": 0 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -285.74204449105804, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.12470197677612305 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -285.74204449105804, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "17", "category": "thermochemistry_from_name", "query": "Report the thermochemical properties (Gibbs free energy) of ammonia at 500 K using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ammonia" } }, { "smiles_to_coordinate_file": { "smiles": "N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500 } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 7, 1, 1, 1 ], "positions": [ [ 0.003690286031697614, 0.0014517023245638478, 0.2782984081375093 ], [ -0.5243290899394131, -0.7867688603042043, -0.08172821051080162 ], [ -0.42060408841591523, 0.8457563471952523, -0.09161946537099143 ], [ 0.9412428923236309, -0.06043919921561174, -0.10495074225571631 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "thermo", "optimizer": "bfgs", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0", "device": "cpu", "default_dtype": "float64", "dispersion": false, "damping": "bj", "dispersion_xc": "pbe", "dispersion_cutoff": 21.167088422553647 }, "fmax": 0.01, "steps": 1000, "temperature": 500.0, "pressure": 101325.0 }, "single_point_energy": -18.996991017234492, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "0.24294906810791458i", "0.1307692365477951i", "0.00405509797098614i", "2.3596437712477236", "3.781055210110371", "4.865268074396271", "114.75574227402079", "203.81605514250245", "203.87526854502778", "421.0187350418408", "432.0811779216365", "432.1695468268274" ], "energy_unit": "meV", "frequencies": [ "1.9595163997484952i", "1.054725031849781i", "0.03270657112874651i", "19.031810672640617", "30.496267181707292", "39.24103374917082", "925.5674891141101", "1643.8873616357228", "1644.3649499394644", "3395.745134323393", "3484.969754170924", "3485.682497464397" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -17.908497948341136, "entropy": 0.0022003386308278253, "gibbs_free_energy": -19.008667263755047, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.7565829753875732 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -18.996991017234492, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "18", "category": "energy_from_name", "query": "Report the single-point energy of ethane using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethane" } }, { "smiles_to_coordinate_file": { "smiles": "CC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 6, 1, 1, 1, 1, 1, 1 ], "positions": [ [ 0.75817634, -0.00414207, 0.04613654 ], [ -0.75817615, 0.00414192, -0.04613682 ], [ 1.08728759, -0.78406587, 0.76471975 ], [ 1.1947984, -0.22109989, -0.95148439 ], [ 1.11953509, 0.986582, 0.3937618 ], [ -1.1195354, -0.98658189, -0.39376044 ], [ -1.1947983, 0.22110085, 0.95148386 ], [ -1.08728755, 0.78406493, -0.76472029 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "energy", "optimizer": "bfgs", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB", "charge": null, "multiplicity": null, "accuracy": 1.0, "electronic_temperature": 300.0, "max_iterations": 250, "initial_guess": "sad", "mixer_damping": 0.4, "electric_field": null, "spin_polarization": null, "cache_api": true, "verbosity": 0 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -199.5763243283148, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.018312931060791016 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.5763243283148, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "19", "category": "optimization_from_name", "query": "Run geometry optimization for ethanol and report its energy using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethanol" } }, { "smiles_to_coordinate_file": { "smiles": "CCO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 6, 8, 1, 1, 1, 1, 1, 1 ], "positions": [ [ -0.8794906755245444, -0.12517653079525462, 0.13049741585746044 ], [ 0.5213304505800801, 0.48341392630125873, -0.007283766986061524 ], [ 1.4108996978379476, -0.4187880795329846, -0.7019155658145357 ], [ -1.2985557068327698, -0.35485212462745636, -0.8592997997501077 ], [ -1.529212856302033, 0.5967248507727829, 0.6403442234257548 ], [ -0.8515944623695518, -1.0522427941799235, 0.7242420708541866 ], [ 0.4903838833697194, 1.4242401579727364, -0.576471284495241 ], [ 0.9344039971315186, 0.7411951613000017, 0.9872610025235883 ], [ 1.2018356621096296, -1.2945145472112138, -0.33737429561505033 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "opt", "optimizer": "bfgs", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0", "device": "cpu", "default_dtype": "float64", "dispersion": false, "damping": "bj", "dispersion_xc": "pbe", "dispersion_cutoff": 21.167088422553647 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -46.24649506270806, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 2.1446499824523926 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -46.24649506270806, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "20", "category": "thermochemistry_from_name", "query": "Report the thermochemical properties (Gibbs free energy) of propane at 300 K using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "propane" } }, { "smiles_to_coordinate_file": { "smiles": "CCC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300 } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1 ], "positions": [ [ 1.1836990220404628, -0.44581775611645147, -0.2160821789875885 ], [ 0.013755939163534276, 0.5231870496938733, -0.33502779706029623 ], [ -1.193998971070771, 0.05407615523023995, 0.46693744811254556 ], [ 1.492140556458212, -0.5456000103085393, 0.822493984294853 ], [ 2.0343314895638027, -0.09291512805474231, -0.795076227507588 ], [ 0.9022153167897163, -1.4304444860699344, -0.5835196058847648 ], [ -0.26707932569687637, 0.6232475369384916, -1.3858926897307566 ], [ 0.3231291409794436, 1.508516255499464, 0.020798142197863363 ], [ -2.0168236556709376, 0.7588112197659452, 0.368662403782918 ], [ -0.9407222264084546, -0.03410841244112965, 1.5213603013613985 ], [ -1.5306472961481374, -0.918952434137217, 0.1153462294214143 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "thermo", "optimizer": "bfgs", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB", "charge": null, "multiplicity": null, "accuracy": 1.0, "electronic_temperature": 300.0, "max_iterations": 250, "initial_guess": "sad", "mixer_damping": 0.4, "electric_field": null, "spin_polarization": null, "cache_api": true, "verbosity": 0 }, "fmax": 0.01, "steps": 1000, "temperature": 300.0, "pressure": 101325.0 }, "single_point_energy": -285.74204449105787, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "1.931067548399899i", "0.40143578151796544i", "0.025482004618278688i", "0.02556789981728872", "0.07130391207346522", "0.9938585405067819", "25.67274838589215", "31.767145002949444", "46.2997190011046", "98.28573698682204", "115.0812838269354", "115.92647077262458", "118.10590256734419", "138.50928706465058", "144.78589979833498", "149.6723061008795", "157.82018744744772", "166.80551805921186", "175.164942519351", "176.13314007842516", "185.7740864672644", "185.92993424466613", "186.5205580971117", "187.10444134946425", "187.34686647797471", "368.00681863751544", "369.7634973112492", "375.3253945728249", "375.3839656494236", "375.95836359593585", "376.21105767328004", "376.53909735137523", "376.6671915401498" ], "energy_unit": "meV", "frequencies": [ "15.575110287852356i", "3.2377979609327068i", "0.2055262295791343i", "0.2062190210865504", "0.5751048405426179", "8.01600979299949", "207.0646818304612", "256.21930592801493", "373.4324210130853", "792.7279367109905", "928.1931588345325", "935.0100513372674", "952.5883543830292", "1117.1527498928206", "1167.7770460974132", "1207.1885711558973", "1272.9056667024972", "1345.377246149319", "1412.8005519873368", "1420.6095920053851", "1498.3690693524445", "1499.6260664591277", "1504.3897691313093", "1509.0991051968222", "1511.0543957386915", "2968.1751897857553", "2982.343758931041", "3027.203486044433", "3027.675893640148", "3032.3087255540067", "3034.3468407545774", "3036.9926592135735", "3038.0258085298933" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -282.7983244265669, "entropy": 0.0027898633321232586, "gibbs_free_energy": -283.6352834262039, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.9115989208221436 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -285.74204449105787, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "21", "category": "optimization_from_smiles", "query": "Run geometry optimization using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: O=S=O and report its energy.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "O=S=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_21/output.json", "single_point_energy": -16.815808019358535, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019358535, "property": "optimized energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "22", "category": "vibrations_from_smiles", "query": "Report the vibrational frequencies using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: O.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "vib", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "result": { "vibrational_frequencies": { "energies": [ "5.278838012595982i", "0.04764407633090353i", "0.005321020506525112i", "0.06055744294822688", "4.520458491661813", "5.344478380954939", "207.53984955909357", "461.6946537572708", "484.0428021965612" ], "energy_unit": "meV", "frequencies": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ], "frequency_unit": "cm-1" } }, "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_22/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ] }, "ir_spectrum": null, "atoms_data": null } } }, { "id": "23", "category": "thermochemistry_from_smiles", "query": "Report the thermochemical properties (Gibbs free energy) at 800 K using GFN2-xTB for the molecule with SMILES: O=C=O.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 800 } } } ], "result": { "status": "success", "result": { "thermochemistry": { "enthalpy": -279.8479687871829, "entropy": 0.002675532791396937, "gibbs_free_energy": -281.9883950203004, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_23/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -281.9883950203004, "property": "Gibbs free energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "24", "category": "dipole_from_smiles", "query": "Report the dipole moment using GFN2-xTB for the molecule with SMILES: [C-]#[O+].", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "[C-]#[O+]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "dipole", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_24/output.json", "dipole_moment": [ -0.1278, -0.0, -0.0 ] }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": { "value": [ -0.1278, -0.0, -0.0 ], "unit": "e * Angstrom" }, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "25", "category": "energy_from_smiles", "query": "Report the single-point energy using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: N#N.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "N#N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_25/output.json", "single_point_energy": -16.42796020021993, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "26", "category": "energy_from_smiles", "query": "Report the single-point energy using GFN2-xTB for the molecule with SMILES: CC.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "CC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_26/output.json", "single_point_energy": -199.57632432831485, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.57632432831485, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "27", "category": "dipole_from_smiles", "query": "Report the dipole moment using GFN2-xTB for the molecule with SMILES: O=CO.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "O=CO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "dipole", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_frvn7mte/entry_27/output.json", "dipole_moment": [ 0.2982, -0.3036, -0.0806 ] }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": { "value": [ 0.2982, -0.3036, -0.0806 ], "unit": "e * Angstrom" }, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "28", "category": "optimization_from_smiles", "query": "Run geometry optimization using GFN2-xTB for the molecule with SMILES: [C-]#[O+] and report its energy.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "[C-]#[O+]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 8 ], "positions": [ [ 0.5636640099849505, 1.1833012223432164e-17, 7.385689453225058e-17 ], [ -0.5636640099849506, -1.1655577734965483e-17, -7.366045646342532e-17 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "opt", "optimizer": "bfgs", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB", "charge": null, "multiplicity": null, "accuracy": 1.0, "electronic_temperature": 300.0, "max_iterations": 250, "initial_guess": "sad", "mixer_damping": 0.4, "electric_field": null, "spin_polarization": null, "cache_api": true, "verbosity": 0 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -166.58403031419738, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.027287960052490234 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -166.58403031419738, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "29", "category": "vibrations_from_smiles", "query": "Report the vibrational frequencies using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: OO.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "OO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "vib", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 8, 8, 1, 1 ], "positions": [ [ 0.7173313648954498, -0.3035068172317547, 0.14914178551688717 ], [ -0.7100699595038744, -0.30792042922766866, -0.17294367023482538 ], [ 1.0401875068657742, 0.3386440627911562, -0.5155796228581969 ], [ -1.0474489122573503, 0.2727831936682675, 0.5393814975761353 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "vib", "optimizer": "bfgs", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0", "device": "cpu", "default_dtype": "float64", "dispersion": false, "damping": "bj", "dispersion_xc": "pbe", "dispersion_cutoff": 21.167088422553647 }, "fmax": 0.01, "steps": 1000, "temperature": null, "pressure": 101325.0 }, "single_point_energy": -17.680770798599116, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "5.839866667656922i", "1.4593731001068235i", "0.12933134375735306i", "0.021255179803343262i", "0.006931986696477268", "1.2933954804428005", "3.035423994928984", "139.88888051204034", "158.52951837598707", "166.69219033890974", "458.14470997922837", "461.2410654321238" ], "energy_unit": "meV", "frequencies": [ "47.1017015901266i", "11.770637958326722i", "1.0431276442742923i", "0.17143458803371012i", "0.05591024374109585", "10.431938163115298", "24.482345804312516", "1128.2799215514706", "1278.6268065205938", "1344.463196434259", "3695.186318901835", "3720.160110061652" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.7819240093231201 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -17.680770798599116, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "30", "category": "thermochemistry_from_smiles", "query": "Report the thermochemical properties (Gibbs free energy) at 300 K using GFN2-xTB for the molecule with SMILES: CC(=O)N.", "answer": { "tool_calls": [ { "smiles_to_coordinate_file": { "smiles": "CC(=O)N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300 } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 6, 6, 8, 7, 1, 1, 1, 1, 1 ], "positions": [ [ -1.056197052819564, -0.29427917323260705, -0.10865006030204115 ], [ 0.15120762277362923, 0.4475440756642257, 0.423702209993113 ], [ 0.09946629579008916, 1.3108985551165295, 1.2673611991673102 ], [ 1.3218771277009658, 0.06376164005303474, -0.14325991602950205 ], [ -0.8664475987536145, -1.3639862268532048, -0.1418768992517026 ], [ -1.2781731740170454, 0.054741661454086724, -1.1152321135384529 ], [ -1.9126973076975242, -0.09409818431064752, 0.5276432529424482 ], [ 2.171753061414853, 0.5195445728223168, 0.14342031785194848 ], [ 1.3692110256082166, -0.644126910713731, -0.8531079808331217 ] ], "cell": [ [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ], [ 0.0, 0.0, 0.0 ] ], "pbc": [ false, false, false ] }, "simulation_input": { "input_structure_file": "molecule.xyz", "output_results_file": "output.json", "driver": "thermo", "optimizer": "bfgs", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB", "charge": null, "multiplicity": null, "accuracy": 1.0, "electronic_temperature": 300.0, "max_iterations": 250, "initial_guess": "sad", "mixer_damping": 0.4, "electric_field": null, "spin_polarization": null, "cache_api": true, "verbosity": 0 }, "fmax": 0.01, "steps": 1000, "temperature": 300.0, "pressure": 101325.0 }, "single_point_energy": -376.0460382004621, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "1.8374182752127235i", "0.7827634083130622i", "0.10481322114325074i", "0.01592822322360591i", "0.033909646202633335", "0.4575280525646818", "7.960397334373665", "33.507031377539285", "50.06796322791693", "63.016812205745744", "64.70915396877372", "74.29366203655434", "108.15210519403058", "121.2116510669512", "124.39232585131407", "131.93424204094543", "160.02346532294717", "170.0584466346726", "180.01130699457204", "181.35416218304644", "182.17233066570594", "219.95760938838342", "375.209529506445", "376.7361457797078", "380.7567614073637", "431.0057289929026", "440.29519369252074" ], "energy_unit": "meV", "frequencies": [ "14.819777953944058i", "6.313412715092876i", "0.845375647415273i", "0.12846978532820247i", "0.27349974363439294", "3.6902126413889267", "64.20493499604927", "270.25243604561376", "403.8253606452575", "508.2648718873898", "521.9145288482455", "599.2188004332496", "872.3055636537484", "977.637905574438", "1003.2917780126608", "1064.1214349206139", "1290.676301362131", "1371.6138847191548", "1451.8891179255108", "1462.7199755402194", "1469.3189494404464", "1774.0777777116725", "3026.268971252927", "3038.581961983365", "3071.0104142545933", "3476.2956735113107", "3551.220259827077" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -373.93910995845215, "entropy": 0.003089780455416954, "gibbs_free_energy": -374.86604409507726, "unit": "eV" }, "success": true, "error": "", "wall_time": 1.0386459827423096 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -376.0460382004621, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "31", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Methane Combustion at 300 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Methane + 2 Oxygen -> Carbon dioxide + 2 Water", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Methane" } }, { "smiles_to_coordinate_file": { "smiles": "C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Oxygen" } }, { "smiles_to_coordinate_file": { "smiles": "O=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "calculator": { "expression": "(1*(-22.794740964867238) + 2*(-13.693940906998133)) - (1*(-22.459430469602392) + 2*(-9.806576011384493))" } } ], "result": "-8.110040286492122", "structured_output": { "smiles": null, "scalar_answer": { "value": -8.110040286492122, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "32", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Ammonia Synthesis at 400 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Nitrogen gas + 3 Hydrogen gas -> 2 Ammonia", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Nitrogen gas" } }, { "smiles_to_coordinate_file": { "smiles": "N#N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Hydrogen gas" } }, { "smiles_to_coordinate_file": { "smiles": "[H][H]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Ammonia" } }, { "smiles_to_coordinate_file": { "smiles": "N" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "calculator": { "expression": "(2*(-120.23055652416785)) - (1*(-157.40205733763415) + 3*(-26.96535305958073))" } } ], "result": "-2.1629965319593794", "structured_output": { "smiles": null, "scalar_answer": { "value": -2.1629965319593794, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "33", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Water Gas Shift Reaction at 500 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Carbon monoxide + Water -> Carbon dioxide + Hydrogen gas", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Carbon monoxide" } }, { "smiles_to_coordinate_file": { "smiles": "[C-]#[O+]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Hydrogen gas" } }, { "smiles_to_coordinate_file": { "smiles": "[H][H]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "calculator": { "expression": "(1*(-23.2591982904147) + 1*(-6.8498115746834465)) - (1*(-15.11017325836859) + 1*(-14.10531608852551))" } } ], "result": "-0.8935205182040455", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.8935205182040455, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "34", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Ethene Hydrogenation at 300 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Ethene + Hydrogen gas -> Ethane", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Ethene" } }, { "smiles_to_coordinate_file": { "smiles": "C=C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Hydrogen gas" } }, { "smiles_to_coordinate_file": { "smiles": "[H][H]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Ethane" } }, { "smiles_to_coordinate_file": { "smiles": "CC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "calculator": { "expression": "(1*(-198.20004456643923)) - (1*(-169.86383043609288) + 1*(-26.82484537010822))" } } ], "result": "-1.5113687602381276", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.5113687602381276, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "35", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Ethanol Combustion at 400 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Ethanol + 3 Oxygen -> 2 Carbon dioxide + 3 Water", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Ethanol" } }, { "smiles_to_coordinate_file": { "smiles": "CCO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Oxygen" } }, { "smiles_to_coordinate_file": { "smiles": "O=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 400.0 } } }, { "calculator": { "expression": "(2*(-23.021725044406743) + 3*(-13.895177604585536)) - (1*(-45.20633988290186) + 3*(-10.014758620390138))" } } ], "result": "-12.478367158497832", "structured_output": { "smiles": null, "scalar_answer": { "value": -12.478367158497832, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "36", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Hydration of Alkene at 500 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Ethene + Water -> Ethanol", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Ethene" } }, { "smiles_to_coordinate_file": { "smiles": "C=C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Ethanol" } }, { "smiles_to_coordinate_file": { "smiles": "CCO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 500.0 } } }, { "calculator": { "expression": "(1*(-309.2281660435373)) - (1*(-170.34623039985362) + 1*(-138.32288268386057))" } } ], "result": "-0.5590529598231342", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.5590529598231342, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "37", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Hydrogen Peroxide Decomposition at 300 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: 2 Hydrogen peroxide -> 2 Water + Oxygen", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Hydrogen peroxide" } }, { "smiles_to_coordinate_file": { "smiles": "OO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Oxygen" } }, { "smiles_to_coordinate_file": { "smiles": "O=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 300.0 } } }, { "calculator": { "expression": "(2*(-13.693940906998133) + 1*(-9.806576011384493)) - (2*(-17.63331235114692))" } } ], "result": "-1.92783312308692", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.92783312308692, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "38", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Carbonic Acid Formation at 400 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Carbon dioxide + Water -> Carbonic acid", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "molecule_name_to_smiles": { "name": "Carbonic acid" } }, { "smiles_to_coordinate_file": { "smiles": "OC(=O)O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 400.0 } } }, { "calculator": { "expression": "(1*(-418.4893834047748)) - (1*(-280.9793530752565) + 1*(-138.11305167531472))" } } ], "result": "0.6030213457963782", "structured_output": { "smiles": null, "scalar_answer": { "value": 0.6030213457963782, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "39", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Propane Combustion at 500 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Propane + 5 Oxygen -> 3 Carbon dioxide + 4 Water", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Propane" } }, { "smiles_to_coordinate_file": { "smiles": "CCC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Oxygen" } }, { "smiles_to_coordinate_file": { "smiles": "O=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "molecule_name_to_smiles": { "name": "Water" } }, { "smiles_to_coordinate_file": { "smiles": "O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500.0 } } }, { "calculator": { "expression": "(3*(-23.2591982904147) + 4*(-14.10531608852551)) - (1*(-54.76195168042118) + 5*(-10.230824769847466))" } } ], "result": "-20.28278369568764", "structured_output": { "smiles": null, "scalar_answer": { "value": -20.28278369568764, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "40", "category": "reaction_energy", "query": "Report the Gibbs free energy of reaction for Formic Acid Decomposition at 300 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Formic acid -> Carbon dioxide + Hydrogen gas", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "Formic acid" } }, { "smiles_to_coordinate_file": { "smiles": "O=CO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Carbon dioxide" } }, { "smiles_to_coordinate_file": { "smiles": "O=C=O" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "molecule_name_to_smiles": { "name": "Hydrogen gas" } }, { "smiles_to_coordinate_file": { "smiles": "[H][H]" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "thermo", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" }, "temperature": 300.0 } } }, { "calculator": { "expression": "(1*(-280.75091473772557) + 1*(-26.82484537010822)) - (1*(-306.8161777456497))" } } ], "result": "-0.7595823621840623", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.7595823621840623, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } } ]