Skip to content

SMARTS NOTES

Jump to bottom
Kate Fieseler edited this page Dec 8, 2023 · 5 revisions

As of 29 Nov 2023 these are the rxns encoded into SMARTS found here. NOTES are above the associated rxn name.

  1. "Amidation": "[#6:1](=[#8:2])-[#8;H1].[#7&X3;!$(NC=*);!$(NS):3]>>[#6:1](=[#8:2])-[#7X3:3]",

  2. "Amide_schotten-baumann": "[#7;H2,H1:3].[#6:1](=[#8:2])-[#17]>>[#6:1](=[#8:2])-[#7:3]",

  3. "Reductive_amination": "[#6:2](=[#8])(-[#6:1]).[#7;H2,H1:3]>>[#6:2](-[#6:1])-[#7:3]",

  4. "N-nucleophilic_aromatic_substitution": "[#6:3]-[#7;H3,H2,H1:2].[c:1]-[F,Cl,Br,I]>>[#6:3]-[#7:2]-[c:1]",

  5. "Sp2-sp2_Suzuki_coupling": "[#6X3:1]-[F,Cl,Br,I].[#6X3:2]-[B](-[O])(-[O])>>[#6X3:1]-[#6X3:2]",

  6. "Formation_of_urea_from_two_amines": "[N&X3;H2,H1;!$(NC=O);!$(NS):3].[N&X3;H2,H1;!$(NC=O);!$(NS):4]>>[#7&X3:3]-[#6](=[#8])-[#7&X3:4]",

  7. "Sulfonamide_Schotten-Baumann_with_amine_(intermolecular)": "[#16X4:1](=[OX1:2])(=[OX1:3])([#6,#7:4])[#17,#9].[#7&X3;H2,H1;!$(NC=O);!$(NS):5]>>[#16X4:1](=[OX1:2])(=[OX1:3])([#6,#7:4])-[#7:5]",

  8. "Buchwald-Hartwig_amination": "[ar:1]-[Cl,Br,I].[#7&X3;H2,H1;!$(NC=*);!$(NS);!$(NN):7]>>[ar:1]-[N:7]",

  9. "Nucleophilic_substitution_with_thiol": "[Cl,Br]-[C;H2,H1;+0:1].[SH;+0:2]>>[S&X2;H0;D2;+0:2]-[C&X4;D2;+0:1]",

  10. "Mitsunobu_reaction_with_amine_alcohol_and_thioalcohol": "[OH]-[#6&X4:1].[NX3;H2,H1;!$(NC=O):2]>>[NX3;!$(NC=O):2]-[#6&X4:1]",

  11. "Amide_Schotten-Baumann_with_amine": "[#6:2]-[#6:1](=[OX1])[#17,#9].[#7&X3;H2,H1;!$(NC=*);!$(NS):3]>>[#6:2]-[#6:1](=[OX1])-[#7:3]",

  12. "Ester_amidation": "C-O-[C;H0;D3;+0:1](-[#6:2])=[O;D1;H0:3].[N;H1,H2;+0:5]>>[N&X3;+0:5]-[C;H0;D3;+0:1](-[#6:2])=[O;D1;H0:3]",

  13. "Nucleophilic_substitution_with_amine": "[Cl,Br]-[C;H2,H1;+0:1].[#7&X3;H2,H1;+0:5]>>[#7&X3;+0:5]-[C&X4;+0:1]",

  14. "N-Boc_deprotection": "[#7&X3:2]-[#6](=[#8])-[#8]-[#6](-[#6])(-[#6])(-[#6])>>[#7&X3:2]",
    Only allows for halide leaving groups, does not allow for sulfonyl fluoro group which seems to be present in Manifold output.
  15. "Sp3-sp2_Suzuki_coupling": "[#6X3:1]-[F,Cl,Br,I].[CX4:2]-[B](-[O])(-[O])>>[#6X3:1]-[CX4:2]", 

  16. "Buchwald-Hartwig_amidation_with_amide-like_nucleophile": "[Cl,Br,I]-[ar:1].[CX3:7](-[NH2;D1;+0:8])=[O,S;D1;H0:9]>>[CX3:7](=[O,S;D1;H0:9])-[NH;D2;+0:8]-[ar:1]",

  17. "Steglich_esterification": "[OH]-[C;H0;D3;+0:1]=[O;D1;H0:3].[CX4;+0:7]-[OH;D1;+0:9]>>[CX4:7]-[O;H0;D2;+0:9]-[C;H0;D3;+0:1]=[O;D1;H0:3]",

  18. "N-Bn_deprotection": "[#7&X3:2]-[#6]-[cR1]1[cR1][cR1][cR1][cR1][cR1]1>>[#7&X3:2]",
    Does not allow for ammonia to be the 'amine' reactant.
  19. "Williamson_ether_synthesis": "[Cl,Br,I]-[#6:1].[#6;+0:2]-[OH;D1;+0:3]>>[#6X4:1]-[O;H0;D2;+0:3]-[#6X4+0:2]",

  20. "Epoxide_+_amine_coupling": "[#6:1]-[CH;D3;+0:2]1-[CH2;D2;+0:3]-[O;H0;D2;+0:4]-1.[N;H2,H1;+0:6]-[#6:7]>>[#6:1]-[C;+0:2](-[OH;D1;+0:4])-[C&X4;+0:3]-[N&X3;+0:6]-[#6:7]"
Clone this wiki locally