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While calculating the energy difference between two alkane conformers with RDKit via QCEngine, I encountered a spurious energy difference between several conformers with MMFF94.
Most relative energies are okay, but some conformer energies are several orders of magnitude off. conda listC12 conformer AOutput of {"id": null, "schema_name": "qcschema_output", "schema_version": 1, "molecule": {"schema_name": "qcschema_molecule", "schema_version": 2, "validated": true, "symbols": ["C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"], "geometry": [1.19109412, 0.80445624, 0.0, 3.62468289, -0.72565467, 0.0, 6.00687112, 0.88306882, 0.0, 8.43932605, -0.64779797, 0.0, 10.82453784, 0.95827991, 0.0, 13.23790655, -0.59564154, 0.0, 14.91673887, 0.59753127, 0.0, 13.34108557, -1.8126249, -1.66050198, 13.34108557, -1.8126249, 1.66050198, 10.80242805, 2.20549888, -1.64840774, 10.80242805, 2.20549888, 1.64840774, 8.46181379, -1.89652872, 1.64916363, 8.46181379, -1.89652872, -1.64916363, 5.98740694, 2.13123266, -1.6493526, 5.98740694, 2.13123266, 1.6493526, 3.6452809, -1.97400748, 1.64916363, 3.6452809, -1.97400748, -1.64916363, -1.19109412, -0.80445624, 0.0, -3.62468289, 0.72565467, 0.0, -6.00687112, -0.88306882, 0.0, -8.43932605, 0.64779797, 0.0, -10.82453784, -0.95827991, 0.0, -13.23790655, 0.59564154, 0.0, -14.91673887, -0.59753127, 0.0, -13.34108557, 1.8126249, 1.66050198, -13.34108557, 1.8126249, -1.66050198, -10.80242805, -2.20549888, -1.64840774, -10.80242805, -2.20549888, 1.64840774, -8.46181379, 1.89652872, 1.64916363, -8.46181379, 1.89652872, -1.64916363, -5.98740694, -2.13123266, -1.6493526, -5.98740694, -2.13123266, 1.6493526, -3.6452809, 1.97400748, -1.64916363, -3.6452809, 1.97400748, 1.64916363, -1.17068508, -2.05262007, 1.64916363, -1.17068508, -2.05262007, -1.64916363, 1.17068508, 2.05262007, -1.64916363, 1.17068508, 2.05262007, 1.64916363], "name": "C12H26", "molecular_charge": 0.0, "molecular_multiplicity": 1, "atomic_numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], "connectivity": [[0, 1, 1.0], [0, 17, 1.0], [0, 36, 1.0], [0, 37, 1.0], [1, 2, 1.0], [1, 15, 1.0], [1, 16, 1.0], [2, 3, 1.0], [2, 13, 1.0], [2, 14, 1.0], [3, 4, 1.0], [3, 11, 1.0], [3, 12, 1.0], [4, 5, 1.0], [4, 9, 1.0], [4, 10, 1.0], [5, 6, 1.0], [5, 7, 1.0], [5, 8, 1.0], [17, 18, 1.0], [17, 34, 1.0], [17, 35, 1.0], [18, 19, 1.0], [18, 32, 1.0], [18, 33, 1.0], [19, 20, 1.0], [19, 30, 1.0], [19, 31, 1.0], [20, 21, 1.0], [20, 28, 1.0], [20, 29, 1.0], [21, 22, 1.0], [21, 26, 1.0], [21, 27, 1.0], [22, 23, 1.0], [22, 24, 1.0], [22, 25, 1.0]], "fix_com": false, "fix_orientation": false, "provenance": {"creator": "QCElemental", "version": "v0.24.0", "routine": "qcelemental.molparse.from_schema"}}, "driver": "energy", "model": {"method": "MMFF94", "basis": null}, "keywords": {}, "protocols": {}, "extras": {}, "provenance": {"creator": "rdkit", "version": "2021.09.3", "routine": "rdkit.Chem.AllChem.UFFGetMoleculeForceField", "hostname": "saw3620", "cpu": "Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz", "qcengine_version": "v0.21.0", "wall_time": 1.3892173767089844, "username": "awvwgk"}, "properties": {"return_energy": -0.0018999033026132282}, "wavefunction": null, "return_result": -0.0018999033026132282, "stdout": null, "stderr": null, "native_files": null, "success": true, "error": null}C12 conformer BOutput of {"id": null, "schema_name": "qcschema_output", "schema_version": 1, "molecule": {"schema_name": "qcschema_molecule", "schema_version": 2, "validated": true, "symbols": ["C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "C", "C", "C", "C", "C", "C", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"], "geometry": [-1.29295033, 1.23947109, 4.68897641, -2.55207457, -1.30976889, 4.19349032, -2.98160923, -2.03391178, 1.44053791, -4.74056592, -0.27778968, 0.00472431, -5.06276415, -0.97661025, -2.76183413, -6.79809927, 0.81825123, -4.17950635, -8.68196683, 0.8501876, -3.3434917, -7.00200068, 0.28081324, -6.15672637, -6.07074385, 2.74633838, -4.12886171, -3.20591967, -1.00249949, -3.67117014, -5.78671807, -2.90696506, -2.90658712, -6.59022944, -0.2604042, 0.93182375, -4.04401302, 1.66144684, 0.11754094, -1.16822843, -2.14880711, 0.45958129, -3.75450704, -3.94990468, 1.38101155, -1.40047572, -2.77770782, 5.08392908, -4.36904584, -1.34642957, 5.18011612, 1.36268121, 1.54655152, 3.58594351, 1.48267879, 2.7013629, 0.95242176, 4.15966423, 3.07533962, -0.04781006, 5.69771199, 0.66952982, -0.44484143, 4.61905655, -1.13515823, -2.40354213, 6.24251991, -3.47085921, -2.79962864, 6.42506742, -4.5532941, -1.05484489, 5.43711882, -4.72053483, -4.2246708, 8.14490679, -2.96838115, -3.41341155, 2.72082708, -1.72380779, -1.84796277, 4.39474611, -0.13133594, -4.19726978, 7.60935852, 1.20602295, -1.01988497, 5.92617983, -0.33051303, 1.34869724, 4.05988672, 4.09843712, -1.84134873, 5.18729708, 4.31159818, 1.25213226, 0.54405203, 4.54233369, 1.00344435, 0.39514165, 1.57187385, -0.38285843, 2.3031977, -0.29252954, 3.59803775, 2.48404445, 2.74539351, 4.84166624, -1.19317281, 1.47360811, 6.73743908, -2.50105198, 2.77789679, 4.02492679], "name": "C12H26", "molecular_charge": 0.0, "molecular_multiplicity": 1, "atomic_numbers": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], "connectivity": [[0, 1, 1.0], [0, 17, 1.0], [0, 36, 1.0], [0, 37, 1.0], [1, 2, 1.0], [1, 15, 1.0], [1, 16, 1.0], [2, 3, 1.0], [2, 13, 1.0], [2, 14, 1.0], [3, 4, 1.0], [3, 11, 1.0], [3, 12, 1.0], [4, 5, 1.0], [4, 9, 1.0], [4, 10, 1.0], [5, 6, 1.0], [5, 7, 1.0], [5, 8, 1.0], [17, 18, 1.0], [17, 34, 1.0], [17, 35, 1.0], [18, 19, 1.0], [18, 32, 1.0], [18, 33, 1.0], [19, 20, 1.0], [19, 30, 1.0], [19, 31, 1.0], [20, 21, 1.0], [20, 28, 1.0], [20, 29, 1.0], [21, 22, 1.0], [21, 26, 1.0], [21, 27, 1.0], [22, 23, 1.0], [22, 24, 1.0], [22, 25, 1.0]], "fix_com": false, "fix_orientation": false, "provenance": {"creator": "QCElemental", "version": "v0.24.0", "routine": "qcelemental.molparse.from_schema"}}, "driver": "energy", "model": {"method": "MMFF94", "basis": null}, "keywords": {}, "protocols": {}, "extras": {}, "provenance": {"creator": "rdkit", "version": "2021.09.3", "routine": "rdkit.Chem.AllChem.UFFGetMoleculeForceField", "qcengine_version": "v0.21.0", "hostname": "saw3620", "cpu": "Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz", "username": "awvwgk", "wall_time": 1.3882358074188232}, "properties": {"return_energy": 2.9393960771040584e-05}, "wavefunction": null, "return_result": 2.9393960771040584e-05, "stdout": null, "stderr": null, "native_files": null, "success": true, "error": null} |
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Answered by
ptosco
Jan 7, 2022
Replies: 2 comments 1 reply
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Hi @awvwgk, The units of the energies are kcal/mol, so that delta seems within reason to me. |
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@awvwgk If I understand correctly the above table, for UFF you computed the energy delta between conformers by taking the difference between 0.005645484386974499 and 0.007951857342940268 (hartree) and converting to kcal/mol: When I repeat the same calculation with the MMFF94 conformers I get 1.21 kcal/mol: However, I do get 1.8457e03 kcal/mol if I omit the So I wonder if your parser omitted the |
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My bad, yes this seems to be an oversight on my side. |
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awvwgk
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@awvwgk If I understand correctly the above table, for UFF you computed the energy delta between conformers by taking the difference between 0.005645484386974499 and 0.007951857342940268 (hartree) and converting to kcal/mol:
When I repeat the same calculation with the MMFF94 conformers I get 1.21 kcal/mol:
However, I do get 1.8457e03 kcal/mol if I omit the
e-05from the first figure:So I wonder if your parser omitted the
e-05part.