Transition Metal Forcefield Approach 1: Initial plan

Initial approach as suggested stakeholder consensus.

Overview

Summary

Create a QM dataset from an existing chemical structure databases running optimization and single-point calculations for structures of primary interest. Only datasets of primary interest will be produced, containing:

Metal centers of primary interest: Pd, Fe, Zn, Mg, Cu, Li
Single metal centers
Ligand chemical space with organic compound elements: C, H, P, S, O, N, F, Cl, Br
Charged molecules {+1, 0, −1}e
QM output with properties such as: energies, forces, partial charges, multipole moments, spin states
High-spin Fe complexes (e.g. up to 5/2)

The final model chemistry (level of theory + basis set) must be determined for production.

These datasets will be run with the following workflow:

Run with OPT calculation with GFN2-XTB
Run SP at GFN2-xTB
Run Opt at final level of theory
Run SP at final level of theory

To achieve this the standard OpenFF QCA dataset submission pipeline must be adapted to address incompatibility of existing OpenFF infrastructure with Organometallic CMILES

GitHub link

Status

status:NOT STARTED status:IN PROGRESS status:COMPLETED status:WON'T PROGRESS

1 Overview
2 Milestones and metrics
3 Progress and findings
- 3.1 Curated data (or similar title)

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

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		status:Not started
Resolve qc-submit CMILES incompatibility with organometallic complexes	Determine if RDKit functionality will perform adequately	@Jennifer A Clark		status:Not started
	If RDKit will not handle CMILES, skip for cif to qca interaction	@Jennifer A Clark		status:Not started
	If RDKit will handle CMILES, assess work around for OpenEye, or implement error handling	@Jennifer A Clark		status: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	status:In progress
	Submit DS1-CCD-1 and DS1-CCD-2 at alternative model chemistries for assessment	@Jennifer A Clark		status:Not started
	Choose model chemistry based off of DS1-CCD-1 and DS1-CCD-2	@Jennifer A Clark ,@Lily Wang		status:Not started
	Filter Crystallography Open Database (COD) and submit OPT DS2-COD-1 and DS2-COD-2 at GFN2-XTB	@Jennifer A Clark		status: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		status:Not started
	Filter MPtrj: Materials Project Trajectory Dataset and submit OPT DS4-MPT-1 and DS4-MPT-2 at GFN2-XTB	@Jennifer A Clark		status:Not started
	Submit DS2-COD-1 OPT at target model chemistry	@Jennifer A Clark		status:Not started
	Submit DS3-CSD-1 OPT at target model chemistry	@Jennifer A Clark		status:Not started
	Submit DS4-MPT-1 OPT at target model chemistry	@Jennifer A Clark		status:Not started
Curate electronic properties training dataset	Define primary and secondary properties of interest	@Jennifer A Clark , Chris Iacovella		status:COMPLETED
	Determine output protocol of primary properties of interest and implement	@Jennifer A Clark		status:IN PROGRESS
	Determine output protocol of secondary properties of interest and implement	@Jennifer A Clark		status:IN PROGRESS
	Submit DS1-CCD-1 Electronic Property calculation at target model chemistry	@Jennifer A Clark		status:Not started
	Submit DS2-COD-1 Electronic Property calculation at target model chemistry	@Jennifer A Clark		status:Not started
	Submit DS3-CSD-1 Electronic Property calculation at target model chemistry	@Jennifer A Clark		status:Not started
	Submit DS4-MPT-1 Electronic Property calculation at target model chemistry	@Jennifer A Clark		status:Not started

Transition Metal Forcefield Approach 1: Initial plan

Overview

Milestones and metrics

Progress and findings

Curated data (or similar title)

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