reaction.pbtxt

identifiers {
  type: NAME
  value: "deoxyfluorination"
}
inputs {
  key: "alcohol in THF"
  value {
    components {
      identifiers {
        type: SMILES
        value: "C"
      }
      amount {
        moles {
          value: 0.1
          units: MILLIMOLE
        }
      }
      reaction_role: REACTANT
      is_limiting: true
    }
    components {
      identifiers {
        type: SMILES
        value: "C1CCOC1"
      }
      amount {
        volume {
          value: 125.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: SOLVENT
      preparations {
        type: DRIED
      }
    }
    addition_order: 1
  }
}
inputs {
  key: "base"
  value {
    components {
      identifiers {
        type: SMILES
        value: "C"
      }
      amount {
        moles {
          value: 0.15
          units: MILLIMOLE
        }
      }
      reaction_role: REAGENT
    }
    addition_order: 3
  }
}
inputs {
  key: "sulfonyl fluoride solution"
  value {
    components {
      identifiers {
        type: SMILES
        value: "C"
      }
      amount {
        moles {
          value: 0.11
          units: MILLIMOLE
        }
      }
      reaction_role: REACTANT
      is_limiting: false
    }
    components {
      identifiers {
        type: SMILES
        value: "C1CCOC1"
      }
      amount {
        volume {
          value: 125.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: SOLVENT
      preparations {
        type: DRIED
      }
    }
    addition_order: 2
  }
}
setup {
  vessel {
    type {
      type: VIAL
    }
    material {
      type: GLASS
    }
    attachments {
      type: CAP
    }
    volume {
      value: 1.0
      units: MILLILITER
    }
  }
  is_automated: false
}
conditions {
  temperature {
    control {
      type: AMBIENT
    }
  }
  pressure {
    control {
      type: SEALED
    }
    atmosphere {
      type: AIR
    }
  }
  stirring {
    method {
      type: STIR_BAR
    }
    rate {
      type: HIGH
      details: "600"
    }
  }
}
workups {
  type: ADDITION
  input {
    components {
      identifiers {
        type: NAME
        value: "1-fluoronaphthalene"
      }
      identifiers {
        type: SMILES
        value: "C1=CC=C2C(=C1)C=CC=C2F"
      }
      amount {
        moles {
          value: 0.1
          units: MILLIMOLE
        }
      }
      reaction_role: INTERNAL_STANDARD
    }
    components {
      identifiers {
        type: NAME
        value: "CDCl3"
      }
      identifiers {
        type: SMILES
        value: "[2H]C(Cl)(Cl)Cl"
      }
      amount {
        volume {
          value: 250.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: WORKUP
    }
  }
}
outcomes {
  reaction_time {
    value: 48.0
    units: HOUR
  }
  products {
    identifiers {
      type: SMILES
      value: "C"
    }
    is_desired_product: true
    measurements {
      analysis_key: "19f NMR of crude"
      type: YIELD
      uses_internal_standard: true
      percentage {
        value: 50.0
        precision: 4.8
      }
    }
    measurements {
      analysis_key: "19f NMR of crude"
      type: IDENTITY
      uses_internal_standard: true
    }
    reaction_role: PRODUCT
  }
  analyses {
    key: "19f NMR of crude"
    value {
      type: NMR_OTHER
      details: "19F NMR using 1 equiv 1-fluoronaphthalene in chloroform as internal standard"
      is_of_isolated_species: false
      instrument_manufacturer: "Bruker"
    }
  }
}
provenance {
  city: "Princeton, NJ"
  doi: "10.1021/jacs.8b01523"
  publication_url: "https://pubs.acs.org/doi/10.1021/jacs.8b01523"
  record_created {
    time {
      value: "8/8/2020, 3:01:25 PM"
    }
    person {
      name: "Connor W. Coley"
      orcid: "0000-0002-8271-8723"
      organization: "MIT"
      email: "ccoley@mit.edu"
    }
  }
}

reaction_template.pbtxt

identifiers {
  type: NAME
  value: "deoxyfluorination"
}
inputs {
  key: "alcohol in THF"
  value {
    components {
      identifiers {
        type: SMILES
        value: "$alcohol_smiles$"
      }
      amount {
        moles {
          value: 0.1
          units: MILLIMOLE
        }
      }
      reaction_role: REACTANT
      is_limiting: true
    }
    components {
      identifiers {
        type: SMILES
        value: "C1CCOC1"
      }
      amount {
        volume {
          value: 125.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: SOLVENT
      preparations {
        type: DRIED
      }
    }
    addition_order: 1
  }
}
inputs {
  key: "base"
  value {
    components {
      identifiers {
        type: SMILES
        value: "$base_smiles$"
      }
      amount {
        moles {
          value: 0.15
          units: MILLIMOLE
        }
      }
      reaction_role: REAGENT
    }
    addition_order: 3
  }
}
inputs {
  key: "sulfonyl fluoride solution"
  value {
    components {
      identifiers {
        type: SMILES
        value: "$sulfonyl_fluoride_smiles$"
      }
      amount {
        moles {
          value: 0.11
          units: MILLIMOLE
        }
      }
      reaction_role: REACTANT
      is_limiting: false
    }
    components {
      identifiers {
        type: SMILES
        value: "C1CCOC1"
      }
      amount {
        volume {
          value: 125.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: SOLVENT
      preparations {
        type: DRIED
      }
    }
    addition_order: 2
  }
}
setup {
  vessel {
    type {
      type: VIAL
    }
    material {
      type: GLASS
    }
    attachments {
      type: CAP
    }
    volume {
      value: 1.0
      units: MILLILITER
    }
  }
  is_automated: false
}
conditions {
  temperature {
    control {
      type: AMBIENT
    }
  }
  pressure {
    control {
      type: SEALED
    }
    atmosphere {
      type: AIR
    }
  }
  stirring {
    method {
      type: STIR_BAR
    }
    rate {
      type: HIGH
      details: "600"
    }
  }
}
workups {
  type: ADDITION
  input {
    components {
      identifiers {
        type: NAME
        value: "1-fluoronaphthalene"
      }
      identifiers {
        type: SMILES
        value: "C1=CC=C2C(=C1)C=CC=C2F"
      }
      amount {
        moles {
          value: 0.1
          units: MILLIMOLE
        }
      }
      reaction_role: INTERNAL_STANDARD
    }
    components {
      identifiers {
        type: NAME
        value: "CDCl3"
      }
      identifiers {
        type: SMILES
        value: "[2H]C(Cl)(Cl)Cl"
      }
      amount {
        volume {
          value: 250.0
          units: MICROLITER
        }
        volume_includes_solutes: true
      }
      reaction_role: WORKUP
    }
  }
}
outcomes {
  reaction_time {
    value: 48.0
    units: HOUR
  }
  products {
    identifiers {
      type: SMILES
      value: "$product_smiles$"
    }
    is_desired_product: true
    measurements {
      analysis_key: "19f NMR of crude"
      type: YIELD
      uses_internal_standard: true
      percentage {
        value: $product_yield$
        precision: 4.8
      }
    }
    measurements {
      analysis_key: "19f NMR of crude"
      type: IDENTITY
      uses_internal_standard: true
    }
    reaction_role: PRODUCT
  }
  analyses {
    key: "19f NMR of crude"
    value {
      type: NMR_OTHER
      details: "19F NMR using 1 equiv 1-fluoronaphthalene in chloroform as internal standard"
      is_of_isolated_species: false
      instrument_manufacturer: "Bruker"
    }
  }
}
provenance {
  city: "Princeton, NJ"
  doi: "10.1021/jacs.8b01523"
  publication_url: "https://pubs.acs.org/doi/10.1021/jacs.8b01523"
  record_created {
    time {
      value: "8/8/2020, 3:01:25 PM"
    }
    person {
      name: "Connor W. Coley"
      orcid: "0000-0002-8271-8723"
      organization: "MIT"
      email: "ccoley@mit.edu"
    }
  }
}

spreadsheet.csv