Gaussian QM Fragmentation and Torsion Scan

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

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

  • Task-based/Quantum Mechanics/Torsion Sampling

  • Role-based/Computational Chemist

  • Product-based/Quantum Mechanics/Gaussian

Description

This floe fragments molecules around each rotatable bond and then performs a 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 OESzybki TK at a specified resolution (in degrees). This function includes a force field minimization of all internal degrees of freedom except for the rotating torsion in each fragment. Then a QM optimization is performed with the torsion constrained while all other degrees of freedom are relaxed.

Finally, 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 multiconformer 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 Gaussian QM Conformer Ensemble Floe 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: gau_torsion_rule_output

Output Dataset (failure): Dataset to store records which fail during the floe.

  • Required

  • Type: dataset_out

  • Default: gaussian_fragmentation_failures

Output Dataset (fragment_output): Dataset to store fragment records with torsion scans. Each record is a multiconformer molecule with one conformer per angle sampled.

  • Required

  • Type: dataset_out

  • Default: gau_fragment_output

Gaussian Fragmentation Report Title (frag_floe_report_name):

  • Type: string

  • Default: Fragmentation_Report

Torsion Scan Parameters

Torsion Increment (resolution): Torsion increment angle in degrees for the scan.

  • Type: decimal

  • Default: 5

QM Switch (qm_switch): Controls QM calculation. When On, a QM optimization is run on each fragment for each torsion. When Off, the force field energies are used for rule generation (recommended only for testing).

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Gaussian Calculation Parameters

Gaussian Solvent Environment (solvent): Solvent environment used for this Gaussian calculation

  • Type: string

  • Default: Gas Phase

  • Choices: [‘Gas Phase’, ‘Water IEFPCM’, ‘Water CPCM’, ‘Water SMD’, ‘DMSO IEFPCM’, ‘DMSO CPCM’, ‘DMSO SMD’, ‘Octanol IEFPCM’, ‘Octanol CPCM’, ‘Octanol SMD’]

Gaussian Method (method): Method used for this Gaussian calculation

  • Type: string

  • Default: HF

  • Choices: [‘HF’, ‘B3LYP’, ‘B3LYP - GD3’, ‘B3LYP - GD3BJ’, ‘B2PLYP’, ‘B2PLYPD3’, ‘M06’, ‘M062X’, ‘M06L’, ‘MN15’, ‘MN15L’, ‘PW6B95D3’, ‘CAM-B3LYP’, ‘CAM-B3LYP - GD3’, ‘CAM-B3LYP - GD3BJ’, ‘WB97X’, ‘wB97XD’, ‘LC-wHPBE’, ‘PBE1PBE’, ‘MP2’, ‘PW91PW91’, ‘PM6’]

Gaussian Basis Set (basis): Basis set used for property calculation with Gaussian

  • Type: string

  • Default: 6-31G

  • Choices: [‘3-21G’, ‘6-31G’, ‘6-31G*’, ‘6-31+G*’, ‘6-31G**’, ‘6-31+G**’, ‘6-311G**’, ‘6-311+G**’, ‘6-311G(2d,2p)’, ‘def2SVP’, ‘def2TZVP’, ‘def2TZVPP’, ‘aug-cc-pvdz’, ‘aug-cc-pvtz’, ‘’]

Hardware Requirements for Gaussian Calculation

Gaussian # Threads (gaussian_nthreads): Number of CPUs for Gaussian calculation.

  • Type: integer

  • Default: 8

Gaussian Memory (gaussian_memory): Memory for Gaussian calculations in MBs.

  • Type: decimal

  • Default: 14400

Gaussian Disk Space (gaussian_disk_space): Temporary disk space (in MB) required for your calculation.

  • Type: decimal

  • Default: 25600

Advanced Parameters

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

  • Required

  • Type: field_parameter::float

  • Default: Gaussian Energy (kcal/mol)

Gaussian Strain Energy Field (gau_strain_energy): 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: Gaussian Strain Energy (kcal/mol)

Save Log files (store_log_file): Save output log files for all calculations, they are always saved for failed calculations.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Report Name for Log Files (gau_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: Gaussian Log File Report

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, for molecules 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 5 kcal is chosen based on the assumption that these rules will later be used to generate conformers in a 10 kcal/mol energy window. If you plan to generate a QM conformer ensemble in a larger energy window you may want to increase this cutoff accordingly.

  • Type: decimal

  • Default: 5

Timeout for Gaussian Calculation (Hours) (gau_timeout): Parallel Cubes have a strict time limit, this parameter stops the gaussian calculation before it reaches that limit. Note, this is a maximum only, the cube will finish when the calculation finishes if it is less than the time limit.

  • Type: decimal

  • Default: 10

Maximum number of retries (gau_retries): Maximum number of attempts to perform QM calculation

  • Type: integer

  • Default: 3

Advanced Force Field Parameters

Force Field (ff_type): Built-in force field model to be used.

  • Type: string

  • Default: mmff94s

  • Choices: [‘mmff94s’, ‘smirnoff99frost’, ‘parsley_openff100’, ‘parsley_openff111’, ‘parsley_openff121’, ‘parsley_openff131’, ‘sage_openff200’]

None (ff_solvent_model): Solvent model to be used

  • Type: string

  • Default: Sheffield

  • Choices: [‘Gas-phase’, ‘Sheffield’, ‘SheffieldPB’]

Penalty Force Constant (force_constant): Force constant used to apply the dihedral constraint.

  • Type: decimal

  • Default: 100000

Energy field (ff_en_field): Energy field for force field energies.

  • Type: field_parameter::float

  • Default: FF Energy (kcal/mol)

Conformer Strain Energy Field 2 (ff_strain_field):

  • Type: field_parameter::float

  • Default: Relative FF Energy (kcal/mol)