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Inspection of iodine containing molecules in 2nd gen. training set for valence parameter optimization

Inspection of iodine containing molecules in 2nd gen. training set for valence parameter optimization

Owned by Hyesu Jang
Last updated: Feb 08, 2022 by Karmen Condic-Jurkic
2 min read

 

  • In 2nd gen training set (used for Parsley version>=1.2.0), 40 optgeo, 5 td, 3 vibfreq targets have iodine. For optimized geometry, 10 unique molecules Cc1c(cnn1CC(=O)C)I,  c1cc(cc(c1)I)[C@@H]2CCN2, c1cc(ccc1N/N=C(/C#N)\\c2nnc3n2CCCCC3)I, CC(C)(C#N)C(=O)Nc1cc(ccc1Cl)I, c1cc(nc(c1)I)SC(F)(F)F, c1cc(c(c(c1)I)O)C(=O)O, c1cc(c(cc1Br)I)[N+](=O)[O-],  Cc1c(cn(n1)CC(=O)C)I,  Cc1cc(nc(n1)N/N=C/c2c(nc3n2cc(cc3)I)C)C,  Cc1c(cc(c(c1Cl)I)Cl)[N+](=O)[O-] were selected from eMolecules discrepancy set. All of them are molecules with an iodine attached to an aromatic ring.

  • All parameters assigned to substructures including an iodine

    • Bonds

      • ID: b73, smirks: [#6:1]-[#53:2]

    • Angles

      • ID: a10, smirks: [*:1]~[#6X3:2]~[*:3]

      • ID: a14, smirks: [*:1]~;!@[*;X3;r5:2]~;@[*;r5:3]

    • Torsions

      • ID: t43, smirks: [*:1]~[#6X3:2]-[#6X3:3]~[*:4]

      • ID: t44, smirks: [*:1]~[#6X3:2]:[#6X3:3]~[*:4]

      • ID: t45, smirks: [*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4]

      • ID: t47, smirks: [*:1]~[#6X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4]

      • ID: t75, smirks: [*:1]~[#7X2,#7X3$(*~[#8X1]):2]:[#6X3:3]~[*:4]

    • Angle and torsion terms assigned to the iodine-containing substructures are general terms, not specific for iodine containing substructures(terminal atoms are not specified to iodine). And the torsion terms are described by a 2-fold cosine function only(f(x)=k(1+cos(x-180))), forcing all MM optimized geometries to locate iodine and the connected aromatic ring on the same plane, regardless of the reference QM optimized geometries.

    • For bonds terms, specific rules are defined for bonds connecting iodine to another element. Therefore, the iodine-related bonds, fitted to the wrong QM geometries, need to be re-fitted. (initial guess on the equilibrium length of b73= 2.075 Å, v1.2.0=2.25 Å, bond lengths at QM optimized geometries= 2.19 ~ 2.33 Å)

  • For example,

    • targets/optgeo_OpenFF_Gen_2_Opt_Set_4_eMolecules_Discrepancy-01/52_C7H9IN2O

      • reference QM (DZVP) vs MM from v1.2.0 (transparent red)

      • QM w/ DZVP vs QM w/ def2-svp (diffuse blue)

    • targets/optgeo_OpenFF_Gen_2_Opt_Set_4_eMolecules_Discrepancy-15/778_C9H10IN

      • reference QM w/ DZVP vs MM from v1.2.0

         

TODO

  • Add iodine containing molecules to the theory benchmarking set

  •  

 

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