Psi4 QM Fragmentation and Torsion Scanning

Category Paths

  • Solution-based/Small Molecule Lead-opt/QM Analysis/Torsions & Strain

  • Task-based/Quantum Mechanics/Torsion Sampling

  • Role-based/Computational Chemist

  • Product-based/Quantum Mechanics/Psi4

Description

This Floe fragments molecules around each rotatable bond and then performs torsion scan on each fragment. Fragments are created around rotatable bonds to allow torsion scans to mimic the energetics of that torsion in the original molecule.

Torsion scanning is performed with the OETorsionScan function from the OESzybki Toolkit at a specified resolution (in degrees). This function includes a force field minimization of all internal degrees of freedom except for rotatable torsion in each fragment. Then, a QM optimization is performed with the torsion constrained while all other degrees of freedom are relaxed.

Lastly, these torsion scans are used to determine the torsion rules that should be used for each rotatable bond in future conformer generation. There are two outputs from this Floe: First, the fragments as multi-conformer molecules where each conformer represents one angle from the torsion scan. Second, the input (parent) molecules with the torsion rules for conformer generation. The parent output can be used as input for the Psi4 QM Conformer Ensemble or Psi4 QM Local Minima Search Floes and the custom torsion rules will be used in the conformer generation step.

Promoted Parameters

Title in user interface (promoted name)

Inputs

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

  • Required

  • Type: data_source

Outputs

Torsion Rules Output (out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: psi4_torsion_rule_output

Fragment Output (frag_out): Dataset to store fragment records with torsion scans.

  • Required

  • Type: dataset_out

  • Default: psi4_fragment_output

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

  • Required

  • Type: dataset_out

  • Default: psi4_fragmentation_failures

Fragmentation Report Title (frag_floe_report_name):

  • Type: string

  • Default: Psi4 Fragmentation Report

Torsion Parameters

Torsion Increment (resolution): Torsion angle increment in degrees

  • Type: decimal

  • Default: 5.0

Psi4 Calculation Parameters

Psi4 Hamiltonian (Torsion Scan) (torsion_method): Method used for geometry optimizations in torsion scans.

  • 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 (Torsion Scan) (torsion_basis): Basis set used for geometry optimizations in torsion scans.

  • 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 Memory (Torsion Scan) (torsion_memory): Memory for Psi4 calculations in MBs

  • Type: decimal

  • Default: 14400

Psi4 #Threads (Torsion Scan) (torsion_nthreads): Number of CPUs for Psi4 calculations.

  • Type: integer

  • Default: 8

Advanced Parameters

Remove Extended Ring Atoms (remove_extended): When On, heuristics are used to reduce the size of the fragments by removing atoms from extended ring systems where possible. Turn Off to keep all atoms in complex ring systems. In very rare cases, (with obscure chemistries) turning this Off may reduce problems in fragmentation

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Energy Cutoff (max_sample_energy): Energy cutoff for choosing angles in custom torsion rules. Default value of 5kcal is chosen based on the assumption that these rules will later be used to generate conformers in a 10kcal/mol energy window. If you plan to generate a QM conformer ensemble in a larger energy window you may want to increase this cut off accordingly.

  • Type: decimal

  • Default: 5

Psi4 Energy Field (frag_energy_field): New field created on torsion scan output to store QM energy at each torsion angle.

  • Type: field_parameter::float

  • Default: Psi4 Energy (kcal/mol)

Psi4 Strain Energy Field (frag_strain_energy_field): New field created on torsion scan output to store relative QM energies at each torsion angle, for each fragment.

  • Required

  • Type: field_parameter::float

  • Default: Psi4 Strain Energy (kcal/mol)

Save Psi4 Log File (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