Transition Metal Forcefield Approach 1: Initial plan
- Jennifer A Clark
Initial approach as suggested stakeholder consensus.
Overview
Summary | Create a QM dataset from an existing chemical structure databases running optimization, torsion-drive, and *new* electronic property calculation types. Datasets will be split into two sets, those with metal centers of primary interest (i.e., Pd, Fe, Zn, Mg, Cu, Li) and those of secondary interest (i.e., Rh, Ir, Pt, Ni, Cr, Ag). Those of secondary interest will only be run with OPT calculation with GFN2-XTB. Those of primary interest will be run with a target level of theory, to be determined in this work, and have the target electronic properties evaluated. These dataset will be accompanied by organic compound elements: C, H, P, S, O, N, F, Cl, Br. To achieve this the standard OpenFF QCA dataset submission pipeline must be adapted in multiple ways.
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GitHub link |
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Status | NOT STARTED IN PROGRESS COMPLETED WON'T PROGRESS |
Milestones and metrics
Datasets will be labeled as DS#-XXX-{1,2}, e.g. DS1-CCD-2, which denotes dataset 1, taken from the CCD database, with the metal centers of secondary interest. The first number and the middle three letter code are always paired to avoid confusion between similar database abbreviations, e.g. CCD vs COD vs CSD. The last number denotes inclusion of metal centers of primary and secondary interest:
1: primary interest: {Pd, Fe, Zn, Mg, Cu, Li}
2: secondary interest: {Rh, Ir, Pt, Ni, Cr, Ag}
Stage | Milestone/Benchmark | Contributors | Deadline | Status |
|---|---|---|---|---|
Add ability for conformers to be imported into qc-submit | Assess ability for conformers to be added into qc-submit | @Jennifer A Clark |
| Not started |
Resolve qc-submit CMILES incompatibility with organometallic complexes | Determine if RDKit functionality will perform adequately | @Jennifer A Clark |
| Not started |
| If RDKit will not handle CMILES, skip for cif to qca interaction | @Jennifer A Clark |
| Not started |
| If RDKit will handle CMILES, assess work around for OpenEye, or implement error handling | @Jennifer A Clark |
| Not started |
Curate opt training dataset | Filter PDB Chemical Component Dictionary (CCD) and submit DS1-CCD-1 and DS1-CCD-2 at BP86 / def2-TZVP | @Jennifer A Clark, Brent Westbrook | Jan. 15, 2025 | In progress |
| Submit DS1-CCD-1 and DS1-CCD-2 at alternative model chemistries for assessment | @Jennifer A Clark |
| Not started |
| Choose model chemistry based off of DS1-CCD-1 and DS1-CCD-2 | @Jennifer A Clark ,@Lily Wang |
| Not started |
| Filter Crystallography Open Database (COD) and submit OPT DS2-COD-1 and DS2-COD-2 at GFN2-XTB | @Jennifer A Clark |
| Not started |
| Filter CSD (cambridge strucural database) and submit OPT DS3-CSD-1 and DS3-CSD-2 at GFN2-XTB with structures neglected by tmQM | @Jennifer A Clark |
| Not started |
| Filter MPtrj: Materials Project Trajectory Dataset and submit OPT DS4-MPT-1 and DS4-MPT-2 at GFN2-XTB | @Jennifer A Clark |
| Not started |
| Submit DS2-COD-1 OPT at target model chemistry | @Jennifer A Clark |
| Not started |
| Submit DS3-CSD-1 OPT at target model chemistry | @Jennifer A Clark |
| Not started |
| Submit DS4-MPT-1 OPT at target model chemistry | @Jennifer A Clark |
| Not started |
Curate electronic properties training dataset | Define primary and secondary properties of interest | @Jennifer A Clark , Chris Iacovella |
| COMPLETED |
| Determine output protocol of primary properties of interest and implement | @Jennifer A Clark |
| IN PROGRESS |
| Determine output protocol of secondary properties of interest and implement | @Jennifer A Clark |
| IN PROGRESS |
| Submit DS1-CCD-1 Electronic Property calculation at target model chemistry | @Jennifer A Clark |
| Not started |
| Submit DS2-COD-1 Electronic Property calculation at target model chemistry | @Jennifer A Clark |
| Not started |
| Submit DS3-CSD-1 Electronic Property calculation at target model chemistry | @Jennifer A Clark |
| Not started |
| Submit DS4-MPT-1 Electronic Property calculation at target model chemistry | @Jennifer A Clark |
| Not started |
Progress and findings
Curated data (or similar title)