Wolfram Cloud Document

Organic Chemical Reactions in the Wolfram Language

Organic Synthesis Project

Reactions Completed So Far

[This, my second notebook, is a continuation of the research started in my first notebook, “Wolfram Summer School Project 2020”.]Reactions that Form Carbon-Carbon BondsNote that for chemical reactions that form new C-C, C-N, C-O, or C-S bonds, a third parameter “default_” specifies which of the two reactants will be passed through the function unchanged when the reaction does not apply. “Does not apply” means that at least one of the necesarry functional groups (structural patterns) is absent among the reactants.

Reaction 4: Alkylation of Alkynes

ChemAlkyneAlkylation[alkyne_,primaryalkylhalide_,default_]:=Module[{yne=alkyne,hal=primaryalkylhalide,def=default},termalkynepat=MoleculePattern[{"C","C","H","C"},{Bond[{1,2},"Triple"],Bond[{1,3},"Single"],Bond[{2,4},"Single"]}];ethynepat=MoleculePattern[{"C","C","H","H"},{Bond[{1,2},"Triple"],Bond[{1,3},"Single"],Bond[{2,4},"Single"]}];primalkylhalidepat=MoleculePattern[{"C","Br","H","H"},{Bond[{1,2},"Single"],Bond[{1,3},"Single"],Bond[{1,4},"Single"]}];methylhalidepat=MoleculePattern[{"C","Br","H","H","H"},{Bond[{1,2},"Single"],Bond[{1,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"]}];If[def==2,flask=hal,flask=yne];If[Length[hal]==0,start=yne,alist=Join[AtomList[yne],AtomList[hal]];f[x_]:=x+AtomCount[yne];primalkylhalidebondlist2=Map[f,BondList[hal],{-2}];blist=Join[BondList[yne],primalkylhalidebondlist2];start=Molecule[alist,blist];];If[MoleculeContainsQ[start,termalkynepat],termalkynefindlist=FindMoleculeSubstructure[start,termalkynepat];If[MoleculeContainsQ[start,primalkylhalidepat],primalkylhalidefindlist=FindMoleculeSubstructure[start,primalkylhalidepat];flask=MoleculeModify[start,{"ReplaceAtom",primalkylhalidefindlist[[1]][[2]]"H"}];flask=MoleculeModify[flask,{"AddBond",Bond[{termalkynefindlist[[1]][[1]],primalkylhalidefindlist[[1]][[1]]},"Single"]}];];If[MoleculeContainsQ[start,methylhalidepat],methylhalidefindlist=FindMoleculeSubstructure[start,methylhalidepat];flask=MoleculeModify[start,{"ReplaceAtom",methylhalidefindlist[[1]][[2]]"H"}];flask=MoleculeModify[flask,{"AddBond",Bond[{termalkynefindlist[[1]][[1]],methylhalidefindlist[[1]][[1]]},"Single"]}];];];If[MoleculeContainsQ[start,ethynepat],ethynefindlist=FindMoleculeSubstructure[start,ethynepat];If[MoleculeContainsQ[start,primalkylhalidepat],primalkylhalidefindlist=FindMoleculeSubstructure[start,primalkylhalidepat];flask=MoleculeModify[start,{"ReplaceAtom",primalkylhalidefindlist[[1]][[2]]"H"}];flask=MoleculeModify[flask,{"AddBond",Bond[{ethynefindlist[[1]][[1]],primalkylhalidefindlist[[1]][[1]]},"Single"]}];];If[MoleculeContainsQ[start,methylhalidepat],methylhalidefindlist=FindMoleculeSubstructure[start,methylhalidepat];flask=MoleculeModify[start,{"ReplaceAtom",methylhalidefindlist[[1]][[2]]"H"}];flask=MoleculeModify[flask,{"AddBond",Bond[{ethynefindlist[[1]][[1]],methylhalidefindlist[[1]][[1]]},"Single"]}];];];]alkyne=Molecule["1-octyne"];primaryalkylhalide=Molecule["benzyl bromide"];ChemAlkyneAlkylation[alkyne,primaryalkylhalide,1];MoleculePlot[start]MoleculePlot[flask]

Out[]=

The function above accepts either a primary halide or methyl halide, and performs both intermolecular and intramolecular versions of the reaction. The second molecule parameter can be left null if the first molecule contains both needed functional group patterns.

Reaction 7: Grignard Reaction of Aldehydes and Ketones [original version]

ChemGrignardAldKet[aldehydeketone_,organichalide_,default_]:=Module[{aldket=aldehydeketone,hal=organichalide,def=default},ketonepat=MoleculePattern[{"C","O","C","C"},{Bond[{1,2},"Double"],Bond[{1,3},"Single"],Bond[{1,4},"Single"]}];aldehydepat=MoleculePattern[{"C","O","H","C"},{Bond[{1,2},"Double"],Bond[{1,3},"Single"],Bond[{1,4},"Single"]}];formaldehydepat=MoleculePattern[{"C","O","H","H"},{Bond[{1,2},"Double"],Bond[{1,3},"Single"],Bond[{1,4},"Single"]}];organichalidepat=MoleculePattern[{"C","Br"},{Bond[{1,2},"Single"]}];secalcoholpat=MoleculePattern[{"C","O","H","C","C","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"],Bond[{1,6},"Single"]}];primalcoholpat=MoleculePattern[{"C","O","H","C","H","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"],Bond[{1,6},"Single"]}];methylalcoholpat=MoleculePattern[{"C","O","H","H","H","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"],Bond[{1,6},"Single"]}];If[def==2,flask=hal,flask=aldket];If[Length[hal]==0,start=aldket,alist=Join[AtomList[aldket],AtomList[hal]];f[x_]:=x+AtomCount[aldket];organichalidebondlist2=Map[f,BondList[hal],{-2}];blist=Join[BondList[aldket],organichalidebondlist2];start=Molecule[alist,blist];];If[MoleculeContainsQ[start,organichalidepat],organichalidefindlist=FindMoleculeSubstructure[start,organichalidepat];If[MoleculeContainsQ[start,ketonepat],ketonefindlist=FindMoleculeSubstructure[start,ketonepat];flask=MoleculeModify[start,{"DeleteBond",Bond[{ketonefindlist[[1]][[1]],ketonefindlist[[1]][[2]]},"Double"]}];flask=MoleculeModify[flask,{"AddBond",Bond[{ketonefindlist[[1]][[1]],ketonefindlist[[1]][[2]]},"Single"]}];flask=MoleculeModify[flask,{"ReplaceAtom",organichalidefindlist[[1]][[2]]"H"}];secalcoholfindlist=FindMoleculeSubstructure[flask,secalcoholpat];flask=MoleculeModify[flask,{"AddBond",Bond[{secalcoholfindlist[[1]][[1]],organichalidefindlist[[1]][[1]]},"Single"]}];];If[MoleculeContainsQ[start,aldehydepat],aldehydefindlist=FindMoleculeSubstructure[start,aldehydepat];flask=MoleculeModify[start,{"DeleteBond",Bond[{aldehydefindlist[[1]][[1]],aldehydefindlist[[1]][[2]]},"Double"]}];flask=MoleculeModify[flask,{"AddBond",Bond[{aldehydefindlist[[1]][[1]],aldehydefindlist[[1]][[2]]},"Single"]}];flask=MoleculeModify[flask,{"ReplaceAtom",organichalidefindlist[[1]][[2]]"H"}];primalcoholfindlist=FindMoleculeSubstructure[flask,primalcoholpat];flask=MoleculeModify[flask,{"AddBond",Bond[{primalcoholfindlist[[1]][[1]],organichalidefindlist[[1]][[1]]},"Single"]}];];If[MoleculeContainsQ[start,formaldehydepat],formaldehydefindlist=FindMoleculeSubstructure[start,formaldehydepat];flask=MoleculeModify[start,{"DeleteBond",Bond[{formaldehydefindlist[[1]][[1]],formaldehydefindlist[[1]][[2]]},"Double"]}];flask=MoleculeModify[flask,{"AddBond",Bond[{formaldehydefindlist[[1]][[1]],formaldehydefindlist[[1]][[2]]},"Single"]}];organichalidefindlist=FindMoleculeSubstructure[flask,organichalidepat];flask=MoleculeModify[flask,{"ReplaceAtom",organichalidefindlist[[1]][[2]]"H"}];methylalcoholfindlist=FindMoleculeSubstructure[flask,methylalcoholpat];flask=MoleculeModify[flask,{"AddBond",Bond[{methylalcoholfindlist[[1]][[1]],organichalidefindlist[[1]][[1]]},"Single"]}];];];]aldket=Molecule["p-(8,8-dimethyl-8-bromooctyl)benzaldehyde"];hal="";ChemGrignardAldKet[aldket,hal,1];MoleculePlot[start]MoleculePlot[flask]

Reaction 7: Grignard Reaction of Aldehydes and Ketones [alternate version]

Reaction 13: Carboxylation of Grignard Reagent (to Carboxylic Acid)

Reactions that Form C-O, C-N, and C-S Bonds

Reaction 8: Alkylation of Alcohols (Williamson Ether Synthesis)

Reaction 9: Mono-Alkylation of Ammonia (Gabriel Synthesis of Primary Amines)

Reaction 10: Fischer Ester Synthesis from Alcohols and Carboxylic Acids

Functional Group Interconversions

Reaction 1: H2 Reduction of Aldehydes/Ketones to Alcohols

Reaction 2: Bromination of Alcohols

Reaction 3: Oxidation of Alcohols to Aldehyde/Ketones

Reaction 5: H2 Reduction of Alkyne to Alkene

Reaction 6: H2 Reduction of Alkenes and Alkynes to Alkanes

Reaction 11: Alkene Hydration (to Alcohol)

Reaction 12: Alkene HydroHalogenation (to Alkyl Halide)