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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 and those of secondary interest. 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.and single-point calculations for structures of primary interest. Only datasets of primary interest will be produced, containing:
The final model chemistry (level of theory + basis set) must be determined for production. These datasets will be run with the following workflow:
To achieve this the standard OpenFF QCA dataset submission pipeline must be adapted in multiple ways. Address incompatibility withto address incompatibility of existing OpenFF infrastructure with Organometallic CMILES Add ability for conformers to be imported into qc-submitCreate new dataset type with relevant properties. | ||||||||||||||||||||||
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\uD83D\uDEA9Â Milestones and metrics
Datasets will be labeled as DS#-XXX-1, e.g. DS1-CCD-1, which denotes dataset 1, taken from the CCD database, with the chemical space of primary interest defined above. 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 one of the secondary chemical space expansions that are outside of the scope of this approach:
Stage | Milestone/Benchmark | Contributors | Deadline | Status | ||||||
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Add ability for conformers to be imported into qc-submit | Assess ability for conformers to be added into qc-submit |
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Resolve qc-submit CMILES incompatibility with organometallic complexes | Determine if RDKit functionality will perform adequately |
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If RDKit will not handle CMILES, skip for cif to qca interaction |
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If RDKit will handle CMILES, assess work around for OpenEye, or implement error handling |
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Curate opt training dataset | Filter PDB Chemical Component Dictionary (CCD) and submit DS1-CCD-1 and DS1-CCD-2 at BP86 / def2-TZVP (split metal centers of primary and secondary interest) | Jennifer A Clark, Brent Westbrook | Jan. 15, 2025 |
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Submit DS1-CCD-1 and DS1-CCD-2 at alternative model chemistries for assessment |
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Choose model chemistry based off of DS1-CCD-1 and DS1-CCD-2 |
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Filter Crystallography Open Database (COD) and submit OPT DS2-COD-1 and DS2-COD-2 at GFN2-XTB |
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Filter CSD (cambridge strucural database) and submit OPT DS3-CSD-1 and DS3-CSD-2 at GFN2-XTB with structures neglected by tmQM |
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Filter MPtrj: Materials Project Trajectory Dataset and submit OPT DS4-MPT-1 and DS4-MPT-2 at GFN2-XTB |
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Submit DS2-COD-1 OPT at target model chemistry |
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Submit DS3-CSD-1 OPT at target model chemistry |
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Submit DS4-MPT-1 OPT at target model chemistry |
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Curate electronic properties training dataset | Define primary and secondary properties of interest | Jennifer A Clark , Chris Iacovella |
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Determine output protocol of primary properties of interest and implement |
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Determine output protocol of secondary properties of interest and implement |
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Submit DS1-CCD-1 Electronic Property calculation at target model chemistry |
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Submit DS2-COD-1 Electronic Property calculation at target model chemistry |
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Submit DS3-CSD-1 Electronic Property calculation at target model chemistry |
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Submit DS4-MPT-1 Electronic Property calculation at target model chemistry |
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