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Jennifer A Clark

Jennifer A Clark

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Driver

Jennifer A Clark

Approver

Lily Wang

Contributors

Other stakeholders

Genetech, Chodera Lab

Objective

Provide Chodera lab and Genetech group with QM data necessary for training a machine learned forcefield.

Time frame

12/01/2024 - 12/01/2025

Key outcomes

A dataset that covers:

  • Relevant levels of theory

  • Support for metal centers of interest

  • Coverage of ligand chemical space

  • QM output with new OpenFF dataset type including properties such as: electronic and dispersion energies, forces, atomic spin density, partial charges, dipole moment, orbital energies, electronic structure of complexes (NBO? coefficients require too much storage), HOMO and LUMO energies

Key metrics

  • ?properties of interest

Key metrics

Forcefield goals

  • RMSE of relative conformational energies of DFT complexes

  • RMSD of energy minimized complexes at different spin states

Dataset Goals:

  • Provide opt and off-optimum geometries for primary targets with different spin states, sufficient to achieve forcefield goals.

Status

Status
colourYellow
titleIn progress

GitHub repo

Slack channel

https://openforcefieldgroup.slack.com/archives/C085GQ8BCNB

Designated meeting

TM FF Meeting

Released datasets

Publication

\uD83E\uDD14 Problem Statement and Objective

🎯 Scope

Organometallic complexes with multiple metal centers

Must have:

  • Dataset at agreed upon model chemistry (suggest BP86 / def2-TZVP for primary and B3LYP-d3bj)Support for metal covering:

    Coverage of charged

    • 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

  • Coverage of ligand chemical space

    • Charged molecules {+1, 0, −1}e

    (Check that these are all required)

    • QM output with

    new OpenFF dataset type including

    • properties such as:

    electronic and dispersion

    • energies, forces,

    atomic spin density,

    • partial charges,

    dipole moment, orbital energies, electronic structure of complexes (NBO? coefficients require too much storage), HOMO and LUMO energies

    • multipole moments, spin states

    • High-spin Fe complexes (e.g. up to 5/2)

    • Optimized and off-optimum structures

Nice to have:

  • Dataset with model chemistry overlapping with SPICE (i.e., ωB97M-D3BJ/def2-TZVPPD) and OpenFF (i.e., B3LYP-D3BJ/DZVP) standards.

  • Support for metal centers Dataset covering chemical space of secondary interest : Rh, Ir, Pt, Ni, Cr, Ag
    Better: Make it element agnosticCoverage of charged (in order of importance):

    • 2. Bi- and Tri- metal centers

    • 3. Charged molecules {+3, +2, +1, 0, −1, −2, −3}e

    etc.

  • Desiderata: High-spin Fe complexes (e.g. up to 5/2)

  • Desiderd: higher charge states

  • (Only include nice to haves, not listed above) QM output with new OpenFF dataset type including properties such as: electronic and dispersion energies, forces, atomic spin density, partial charges, dipole moment,

    • 4. Metal centers of secondary interest: Rh, Ir, Pt, Ni, Cr, Ag
      Better: Make it element agnostic

    • 5. Transition states

  • QM output with properties such as: atomic spin density, orbital energies, electronic structure of complexes (NBO? coefficients require too much storage), HOMO and LUMO energies

Not in scope:

⚙️ Project Approaches

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📖 References