[ { "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 using the mace_mp calculator with the medium-mpa-0 model. Report the optimized energy in eV.", "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": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_5/output.json", "driver": "opt", "potential_energy": -16.815808019299542, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_5/output.json", "converged": true, "optimization_steps": 7, "single_point_energy": -16.815808019299542, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019299542, "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. Report the frequencies in cm-1.", "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", "driver": "vib", "potential_energy": -13.786081737592212, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_6/output.json", "converged": true, "optimization_steps": 5, "result": { "vibrational_frequencies": { "energies": [ "207.53984955905088", "461.69465375900324", "484.0428021982815" ], "energy_unit": "meV", "frequencies": [ "1673.9217893672067", "3723.81854667216", "3904.0685213348656" ], "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_d4so2zji/entry_6/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "1673.9217893672067", "3723.81854667216", "3904.0685213348656" ] }, "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. Report the Gibbs free energy in eV.", "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", "driver": "thermo", "potential_energy": -280.5072746974306, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_7/output.json", "converged": true, "optimization_steps": 4, "result": { "thermochemistry": { "enthalpy": -279.8479687871831, "entropy": 0.0026755327913969397, "gibbs_free_energy": -281.9883950203007, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_7/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -281.9883950203007, "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. Report the unit in e * Angstrom.", "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": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_8/output.json", "driver": "dipole", "potential_energy": -166.583990551454, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_8/output.json", "dipole_moment": [ -0.1278, -0.0, -0.0 ], "dipole_unit": "e * Angstrom" }, "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. Report the energy in eV.", "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": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_9/output.json", "driver": "energy", "potential_energy": -16.42796019351169, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_9/output.json", "single_point_energy": -16.42796019351169, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796019351169, "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 using GFN2-xTB. Report the optimized energy in eV.", "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": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_10/output.json", "driver": "opt", "potential_energy": -170.6496929174168, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_10/output.json", "converged": true, "optimization_steps": 7, "single_point_energy": -170.6496929174168, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -170.6496929174168, "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. Report the frequencies in cm-1.", "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", "driver": "vib", "potential_energy": -310.05574173057624, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_11/output.json", "converged": true, "optimization_steps": 42, "result": { "vibrational_frequencies": { "energies": [ "27.79839738085244", "42.20918825556391", "52.10585749803795", "103.03144226048957", "115.54432766434203", "129.5674349675032", "135.1503825352714", "140.1157651795237", "153.1473372364309", "162.92095441870595", "167.31662813378034", "174.18841138098236", "183.86516633113928", "184.71269264793014", "185.6084932767352", "355.6598375077792", "369.8819486599839", "374.1891849590782", "377.5211675990512", "377.96641454036194", "439.2993477525251" ], "energy_unit": "meV", "frequencies": [ "224.20919733806318", "340.44006528195706", "420.26208655803964", "831.0046314295472", "931.9278592812851", "1045.0318483189035", "1090.0613576032051", "1130.109869821071", "1235.2165876977222", "1314.046127167389", "1349.4996269470455", "1404.9242971187714", "1482.9725899928867", "1489.8083507961858", "1497.0334701873367", "2868.590070157485", "2983.2991334966882", "3018.039337406087", "3044.913590012004", "3048.504748810147", "3543.1882205760453" ], "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_d4so2zji/entry_11/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "224.20919733806318", "340.44006528195706", "420.26208655803964", "831.0046314295472", "931.9278592812851", "1045.0318483189035", "1090.0613576032051", "1130.109869821071", "1235.2165876977222", "1314.046127167389", "1349.4996269470455", "1404.9242971187714", "1482.9725899928867", "1489.8083507961858", "1497.0334701873367", "2868.590070157485", "2983.2991334966882", "3018.039337406087", "3044.913590012004", "3048.504748810147", "3543.1882205760453" ] }, "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. Report the Gibbs free energy in eV.", "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", "driver": "thermo", "potential_energy": -23.166948941922847, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_12/output.json", "converged": true, "optimization_steps": 3, "result": { "thermochemistry": { "enthalpy": -21.793386183692945, "entropy": 0.002150524757040044, "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_d4so2zji/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. Report the unit in e * Angstrom.", "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": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_13/output.json", "driver": "dipole", "potential_energy": -120.3884877975335, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_13/output.json", "dipole_moment": [ -0.0051, -0.002, -0.3835 ], "dipole_unit": "e * Angstrom" }, "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. Report the energy in eV.", "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": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_14/output.json", "driver": "energy", "potential_energy": -113.5639578693412, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/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. Report the energy in eV.", "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 }, "potential_energy": -16.42796019351169, "single_point_energy": -16.42796019351169, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.07802295684814453 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796019351169, "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 using GFN2-xTB. Report the optimized energy in eV.", "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": [ [ 1.1836990220404633, -0.44581775611645097, -0.21608217898758883 ], [ 0.01375593916353461, 0.5231870496938736, -0.33502779706029545 ], [ -1.1939989710707712, 0.05407615523023968, 0.4669374481125458 ], [ 1.492140556458213, -0.5456000103085398, 0.8224939842948521 ], [ 2.034331489563803, -0.09291512805474225, -0.7950762275075874 ], [ 0.9022153167897162, -1.430444486069934, -0.583519605884764 ], [ -0.2670793256968763, 0.6232475369384919, -1.3858926897307557 ], [ 0.3231291409794443, 1.5085162554994647, 0.020798142197863304 ], [ -2.016823655670937, 0.7588112197659447, 0.36866240378291837 ], [ -0.9407222264084546, -0.03410841244112963, 1.5213603013613983 ], [ -1.5306472961481357, -0.9189524341372162, 0.11534622942141484 ] ], "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 }, "potential_energy": -285.7420444910579, "single_point_energy": -285.7420444910579, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.11945223808288574 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -285.7420444910579, "property": "optimized 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. Report the Gibbs free energy in eV.", "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": [ [ 0.0036902860317103415, 0.0014517023245687634, 0.2782984081384455 ], [ -0.5243290899394365, -0.786768860304234, -0.08172821051111336 ], [ -0.4206040884159343, 0.8457563471952805, -0.09161946537130351 ], [ 0.9412428923236599, -0.06043919921561554, -0.10495074225602877 ] ], "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 }, "potential_energy": -18.99699101723432, "single_point_energy": -18.99699101723432, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "114.75574227469036", "203.81605514196224", "203.87526854494172", "421.0187351052851", "432.0811779867121", "432.1695468939" ], "energy_unit": "meV", "frequencies": [ "925.5674891195106", "1643.8873616313656", "1644.3649499387705", "3395.7451348351055", "3484.969754695794", "3485.6824980053743" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -17.9084979482433, "entropy": 0.0022003386308275287, "gibbs_free_energy": -19.008667263657067, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.5119638442993164 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -19.008667263657067, "property": "Gibbs free 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. Report the energy in eV.", "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 }, "potential_energy": -199.5763243283149, "single_point_energy": -199.5763243283149, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.02064800262451172 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.5763243283149, "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 using the mace_mp calculator with the medium-mpa-0 model. Report the optimized energy in eV.", "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": [ [ -0.8794906755245355, -0.12517653079523533, 0.13049741585759014 ], [ 0.5213304505801076, 0.4834139263013097, -0.007283766985899955 ], [ 1.410899697837937, -0.4187880795328392, -0.701915565814603 ], [ -1.2985557068321445, -0.35485212462812854, -0.8592997997500754 ], [ -1.5292128563023695, 0.5967248507729708, 0.6403442234252554 ], [ -0.8515944623694992, -1.052242794179637, 0.7242420708547302 ], [ 0.4903838833697525, 1.4242401579728698, -0.5764712844949716 ], [ 0.934403997131652, 0.7411951612999549, 0.9872610025237544 ], [ 1.201835662109114, -1.2945145472113064, -0.3373742956158028 ] ], "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 }, "potential_energy": -46.24649506270807, "single_point_energy": -46.24649506270807, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 1.2704977989196777 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -46.24649506270807, "property": "optimized 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. Report the Gibbs free energy in eV.", "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": [ [ 1.1836990220404633, -0.44581775611645064, -0.21608217898758916 ], [ 0.013755939163534655, 0.523187049693874, -0.3350277970602955 ], [ -1.193998971070771, 0.054076155230239294, 0.4669374481125455 ], [ 1.4921405564582126, -0.5456000103085404, 0.822493984294852 ], [ 2.034331489563804, -0.09291512805474317, -0.7950762275075877 ], [ 0.9022153167897164, -1.4304444860699346, -0.5835196058847643 ], [ -0.2670793256968761, 0.6232475369384919, -1.3858926897307557 ], [ 0.3231291409794435, 1.5085162554994642, 0.020798142197863034 ], [ -2.0168236556709362, 0.7588112197659449, 0.36866240378291865 ], [ -0.9407222264084554, -0.03410841244112987, 1.5213603013613988 ], [ -1.530647296148136, -0.9189524341372167, 0.1153462294214153 ] ], "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 }, "potential_energy": -285.74204449105764, "single_point_energy": -285.74204449105764, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "25.672748385887864", "31.767145002963083", "46.29971900110429", "98.28573698682752", "115.0812838269321", "115.92647077262373", "118.10590256733789", "138.50928706464754", "144.7858997983338", "149.67230610087833", "157.82018744745008", "166.80551805921144", "175.16494251935248", "176.13314007842217", "185.77408646726374", "185.9299342446661", "186.5205580971136", "187.104441349465", "187.34686647797358", "368.00681863751487", "369.7634973112615", "375.3253945728226", "375.38396564942155", "375.9583635959367", "376.2110576732755", "376.53909735137614", "376.66719154015556" ], "energy_unit": "meV", "frequencies": [ "207.06468183042665", "256.2193059281249", "373.4324210130828", "792.7279367110348", "928.1931588345058", "935.0100513372606", "952.5883543829785", "1117.1527498927962", "1167.7770460974036", "1207.1885711558878", "1272.9056667025163", "1345.3772461493154", "1412.8005519873486", "1420.6095920053613", "1498.369069352439", "1499.6260664591275", "1504.3897691313248", "1509.099105196828", "1511.0543957386824", "2968.1751897857507", "2982.34375893114", "3027.203486044414", "3027.675893640131", "3032.3087255540136", "3034.3468407545406", "3036.9926592135803", "3038.0258085299392" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -282.7983244265667, "entropy": 0.00278986333212324, "gibbs_free_energy": -283.63528342620367, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.7957310676574707 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -283.63528342620367, "property": "Gibbs free 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. Report the optimized energy in eV.", "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": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_21/output.json", "driver": "opt", "potential_energy": -16.815808019299542, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_21/output.json", "converged": true, "optimization_steps": 7, "single_point_energy": -16.815808019299542, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019299542, "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. Report the frequencies in cm-1.", "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", "driver": "vib", "potential_energy": -13.786081737592212, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_22/output.json", "converged": true, "optimization_steps": 5, "result": { "vibrational_frequencies": { "energies": [ "207.53984955905088", "461.69465375900324", "484.0428021982815" ], "energy_unit": "meV", "frequencies": [ "1673.9217893672067", "3723.81854667216", "3904.0685213348656" ], "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_d4so2zji/entry_22/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "1673.9217893672067", "3723.81854667216", "3904.0685213348656" ] }, "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. Report the Gibbs free energy in eV.", "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", "driver": "thermo", "potential_energy": -280.5072746974304, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_23/output.json", "converged": true, "optimization_steps": 4, "result": { "thermochemistry": { "enthalpy": -279.8479687871829, "entropy": 0.002675532791396939, "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_d4so2zji/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+]. Report the unit in e * Angstrom.", "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": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_24/output.json", "driver": "dipole", "potential_energy": -166.58399055145404, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_24/output.json", "dipole_moment": [ -0.1278, -0.0, -0.0 ], "dipole_unit": "e * Angstrom" }, "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. Report the energy in eV.", "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": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_25/output.json", "driver": "energy", "potential_energy": -16.42796019351169, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_25/output.json", "single_point_energy": -16.42796019351169, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796019351169, "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. Report the energy in eV.", "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": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_26/output.json", "driver": "energy", "potential_energy": -199.57632432831494, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_26/output.json", "single_point_energy": -199.57632432831494, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.57632432831494, "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. Report the unit in e * Angstrom.", "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": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_27/output.json", "driver": "dipole", "potential_energy": -306.5615867600617, "energy_unit": "eV", "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_27/output.json", "dipole_moment": [ 0.2982, -0.3036, -0.0806 ], "dipole_unit": "e * Angstrom" }, "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+]. Report the optimized energy in eV.", "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, 1.1808251099592349e-17, 7.38756240636133e-17 ], [ -0.5636640099849506, -1.1655577734965465e-17, -7.36604564634253e-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 }, "potential_energy": -166.58403031419724, "single_point_energy": -166.58403031419724, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.024730205535888672 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -166.58403031419724, "property": "optimized 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. Report the frequencies in cm-1.", "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": [ [ 0.7173313648954506, -0.30350681723175466, 0.1491417855168849 ], [ -0.7100699595038746, -0.3079204292276688, -0.172943670234823 ], [ 1.0401875068657729, 0.3386440627911561, -0.5155796228581963 ], [ -1.0474489122573492, 0.2727831936682675, 0.5393814975761345 ] ], "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 }, "potential_energy": -17.680770798599116, "single_point_energy": -17.680770798599116, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "3.0354239948576773", "139.888880512038", "158.52951837598616", "166.69219033890997", "458.14470997922865", "461.2410654321233" ], "energy_unit": "meV", "frequencies": [ "24.482345803737388", "1128.2799215514517", "1278.6268065205868", "1344.463196434261", "3695.1863189018372", "3720.1601100616485" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.4964940547943115 }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "24.482345803737388", "1128.2799215514517", "1278.6268065205868", "1344.463196434261", "3695.1863189018372", "3720.1601100616485" ] }, "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. Report the Gibbs free energy in eV.", "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": [ [ -1.0561970528195654, -0.2942791732326082, -0.10865006030204082 ], [ 0.15120762277362695, 0.44754407566422527, 0.42370220999311276 ], [ 0.09946629579008696, 1.3108985551165295, 1.2673611991673097 ], [ 1.321877127700965, 0.06376164005303514, -0.14325991602950267 ], [ -0.8664475987536161, -1.363986226853206, -0.14187689925170305 ], [ -1.2781731740170457, 0.05474166145408574, -1.1152321135384529 ], [ -1.912697307697526, -0.09409818431064794, 0.527643252942447 ], [ 2.171753061414852, 0.5195445728223171, 0.14342031785194903 ], [ 1.3692110256082155, -0.6441269107137323, -0.8531079808331195 ] ], "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 }, "potential_energy": -376.04603820046225, "single_point_energy": -376.04603820046225, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "7.96039733434048", "33.507031377538226", "50.06796322791752", "63.01681220574526", "64.70915396876808", "74.29366203654509", "108.15210519403792", "121.21165106695638", "124.3923258513124", "131.9342420409418", "160.0234653229489", "170.05844663467028", "180.0113069945646", "181.35416218304755", "182.1723306657076", "219.9576093883842", "375.20952950644755", "376.7361457797097", "380.7567614073652", "431.0057289929032", "440.2951936925229" ], "energy_unit": "meV", "frequencies": [ "64.20493499578161", "270.25243604560524", "403.82536064526226", "508.2648718873859", "521.9145288481999", "599.2188004331749", "872.3055636538076", "977.6379055744796", "1003.2917780126473", "1064.1214349205843", "1290.676301362145", "1371.6138847191362", "1451.8891179254506", "1462.7199755402282", "1469.3189494404598", "1774.0777777116791", "3026.2689712529473", "3038.5819619833806", "3071.010414254605", "3476.2956735113153", "3551.2202598270947" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -373.9391099584523, "entropy": 0.003089780455417321, "gibbs_free_energy": -374.86604409507754, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.9351739883422852 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -374.86604409507754, "property": "Gibbs free 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*(-22.79474096690007) + 2*(-13.693940906996428)) - (1*(-22.459430469602392) + 2*(-9.806576011375233))" } } ], "result": "-8.11004028854007", "structured_output": { "smiles": null, "scalar_answer": { "value": -8.11004028854007, "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*(-120.23055652416788)) - (1*(-157.40205733754945) + 3*(-26.96535305958073))" } } ], "result": "-2.162996532044133", "structured_output": { "smiles": null, "scalar_answer": { "value": -2.162996532044133, "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*(-23.259198292438935) + 1*(-6.8498115746834465)) - (1*(-15.110173260039074) + 1*(-14.105316088523805))" } } ], "result": "-0.8935205185595017", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.8935205185595017, "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*(-198.20004456643926)) - (1*(-169.86383082086292) + 1*(-26.82484537010822))" } } ], "result": "-1.5113683754681233", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.5113683754681233, "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*(-23.02172504643544) + 3*(-13.89517760458383)) - (1*(-45.206339882899954) + 3*(-10.014758620380904))" } } ], "result": "-12.478367162579701", "structured_output": { "smiles": null, "scalar_answer": { "value": -12.478367162579701, "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*(-309.22816604353767)) - (1*(-170.34623079585663) + 1*(-138.32288268386057))" } } ], "result": "-0.559052563820444", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.559052563820444, "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*(-13.693940906996428) + 1*(-9.806576011375233)) - (2*(-17.633312351147527))" } } ], "result": "-1.927833123073036", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.927833123073036, "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*(-280.9793530752564) + 1*(-138.11305167531467))" } } ], "result": "0.6030213457962645", "structured_output": { "smiles": null, "scalar_answer": { "value": 0.6030213457962645, "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*(-23.259198292438935) + 4*(-14.105316088523805)) - (1*(-54.761951680421184) + 5*(-10.230824769838229))" } } ], "result": "-20.2827837017997", "structured_output": { "smiles": null, "scalar_answer": { "value": -20.2827837017997, "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*(-280.75091473772534) + 1*(-26.82484537010822)) - (1*(-306.8161777456493))" } } ], "result": "-0.7595823621842328", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.7595823621842328, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } } ]