Psi4 QM Tautomer Floe

Category Paths

  • Solution-based/Small Molecule Lead-opt/QM Analysis/Tautomer Analysis

  • Task-based/Quantum Mechanics/Energetic Analysis

  • Role-based/Computational Chemist

  • Product-based/Quantum Mechanics/Psi4

Description

Begins by enumerating all reasonable tautomers of the input molecules. Then, performs a local minimum search by (1) generating conformers, (2) performing a geometry optimization, and then (3) de-duplicating local minima. The last step is an optional single point energy calculation at a higher level of theory. The final results are output as one record for each enumerated tautomer as a multi-conformer molecule. The minimum energy for each tautomer is saved on the primary molecule record and a report is created summarizing the energy distributions for each tautomer.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): The dataset(s) to read records from

  • Required

  • Type: data_source

Outputs

Intermediate Optimization Output (confs_out): Dataset to store QM optimized conformers before deduplication. If a job is cancelled early (either by the user or hitting a cost threshold is reached), these intermediate optimized conformers, will still be saved.

  • Required

  • Type: dataset_out

  • Default: psi4_all_conf_gopt

Optimized Tautomer Output (out): Dataset to store optimized conformers of each tautomer. There is one multi-conformer record for each enumerated tautomer.

  • Required

  • Type: dataset_out

  • Default: psi4_tautomer_opt_out

Failures (failure): Dataset to store records which fail during this Floe.

  • Required

  • Type: dataset_out

  • Default: psi4_tautomer_failures

Tautomer Floe Report Title (taut_floe_report_name):

  • Type: string

  • Default: Psi4 Tautomer Floe Report

Tautomer and Conformer Parameters

RMSD Threshold for conformer generation (confgen_rmsd_threshold): RMSD threshold for conformer duplicate removal

  • Type: decimal

  • Default: 0.5

Maximum Conformers for Geometry Optimization (limit_confs): This parameter limits the number of conformers optimized, to prevent accidentally spending more than expected on a single Floe. If more than this number of conformers are generated, then only one conformer will be optimized to learn about the cost of this floe/conformer. If the max number of conformers is set to 0, then ALL generated conformers are optimized.

  • Type: integer

  • Default: 100

Include Single Point Energy (spe_switch): Optionally perform an additional single point energy calculation (On). Otherwise (Off), only the final energy for the geometry optimization is stored. If On, make sure that the single point energy method and basis set are different from the geometry optimization.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Generate Reasonable Tautomers Only (reasonable_tautomers): Choice of rather to generate reasonable tautomers (On) or all possible tautomers (Off).

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Strict Stereo (strict_stereo): Flag indicating if all chiral atoms and bonds must have specified stereo during conformer generation. If your molecule has stereo specified, that stereochemistry will remain fixed during tautomer enumeration. However, depending on the molecule, generated tautomers may have unspecified stereochemistry. Those tautomers will fail if this is set to On.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Psi4 Calculation Parameters

Psi4 Hamiltonian (Geometry Optimization) (psi4_gopt_method): Method used for Psi4 geometry optimization.

  • Type: string

  • Default: HF3c

  • Choices: [‘HF3c’, ‘PBEh3c’, ‘HF’, ‘HF-D3’, ‘B3LYP’, ‘B3LYP-D3BJ’, ‘B3LYP-D3MBJ’, ‘B2PLYP-D3BJ’, ‘M06’, ‘M06-2X’, ‘M06-L’, ‘MN15-D3BJ’, ‘MN15-L’, ‘PW6B95-D3BJ’, ‘CAM-B3LYP’, ‘CAM-B3LYP-D3BJ’, ‘WB97X’, ‘WB97X-D’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Geometry Optimization) (psi4_gopt_basis): Basis set for Psi4 geometry optimization.

  • Type: string

  • Default:

  • Choices: [‘’, ‘minix’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2-SVP’, ‘def2-SVPD’, ‘def2-TZVP’, ‘def2-TZVPD’, ‘def2-TZVPP’, ‘def2-TZVPPD’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]

Psi4 Hamiltonian (Single Point Energy) (psi4_spe_method): Method used for optional single point energy calculation.

  • Type: string

  • Default: B3LYP-D3MBJ

  • Choices: [‘HF3c’, ‘PBEh3c’, ‘HF’, ‘HF-D3’, ‘B3LYP’, ‘B3LYP-D3BJ’, ‘B3LYP-D3MBJ’, ‘B2PLYP-D3BJ’, ‘M06’, ‘M06-2X’, ‘M06-L’, ‘MN15-D3BJ’, ‘MN15-L’, ‘PW6B95-D3BJ’, ‘CAM-B3LYP’, ‘CAM-B3LYP-D3BJ’, ‘WB97X’, ‘WB97X-D’, ‘PBE’, ‘PBE0’]

Psi4 Basis Set (Single Point Energy) (psi4_spe_basis): Basis set used for optional single point energy calculation.

  • Type: string

  • Default: 6-31G*

  • Choices: [‘’, ‘minix’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2-SVP’, ‘def2-SVPD’, ‘def2-TZVP’, ‘def2-TZVPD’, ‘def2-TZVPP’, ‘def2-TZVPPD’, ‘cc-pVDZ’, ‘aug-cc-pVDZ’, ‘cc-pVTZ’, ‘aug-cc-pVTZ’, ‘LanL2DZ’]

Psi4 Memory (psi4_memory): Memory for Psi4 calculations in MBs

  • Type: decimal

  • Default: 14400

Psi4 #Threads (psi4_nthreads): Number of CPUs for Psi4 calculations

  • Type: integer

  • Default: 8

Advanced Parameters

Save Psi4 Log Files (store_log_file): The log file generated from Psi4 is saved. It will be available as a Floe Report when the Floe is complete.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Report name for log files (qm_log_report_name): Floe Report to store QM Log files. This report is only created if the calculation log files were stored.

  • Type: string

  • Default: Psi4 Log File Report