Merge pull request #23 from wsprague-nu/dev

Update to version 0.5.6a1

doranet/modules/synthetic/Reaction_Smarts_Forward.py

@@ -726,6 +726,25 @@ class OperatorSmarts:
         (1, 1),
         (1,),
     ),
+    # Enolate Alkylation
+    # From James Gerken: it doesn't really form HX as a product but rather MX
+    # and the protonated form of whatever base was used to deprotonate alpha to the carbonyl.
+    # Estimated difference in DMSO pKa between RC(=O)C-H and H-Br, should be about -33 kcal/mol
+    OperatorSmarts(
+        "Enolate Alkylation",
+        "[C+0:2](=[O+0:3])[C+0!H0:4].[CX4;+0:5][F,Cl,Br,I;+0:6]>>[*:2](=[*:3])[*:4][*:5].[*:6]",
+        (1, 1),
+        (1, 1),
+        enthalpy_correction=-33,
+    ),
+    OperatorSmarts(
+        "Enolate Alkylation, Intramolecular",
+        "([C+0:2](=[O+0:3])[C+0!H0:4].[CX4;+0:5][F,Cl,Br,I;+0:6])>>[*:2](=[*:3])[*:4][*:5].[*:6]",
+        (1,),
+        (1, 1),
+        enthalpy_correction=-33,
+        ring_issue=True,
+    ),
     # Alcohols #############################################################
     # Glycol Cleavage by Oxidation
     OperatorSmarts(
@@ -1133,6 +1152,26 @@ class OperatorSmarts:
         (1, 1),
         (1, 1),
     ),
+    OperatorSmarts(
+        "Synthesis of Enol Ethers from Aldehyde and Alcohol, Intramolecular",
+        "([CX4+0;H2,H3:1][O+0H:2].[CX4+0!H0:3][CX3+0H:4]=[O+0:5])>>[*:1][*:2][*:4]=[*:3].[*:5]",
+        (1,),
+        (1, 1),
+    ),
+    # Pinacol Coupling
+    OperatorSmarts(
+        "Pinacol Coupling",
+        "[C+0X3;!$(*-O):2](=[O+0:3]).[C+0X3;!$(*-O):6](=[O+0:7]).[H][H]>>[*:2](-[*:3])-[*:6]-[*:7]",
+        (1, 1, 1),
+        (1,),
+    ),
+    OperatorSmarts(
+        "Pinacol Coupling, Intramolecular",
+        "([C+0X3;!$(*-O):2](=[O+0:3]).[C+0X3;!$(*-O):6](=[O+0:7])).[H][H]>>[*:2](-[*:3])-[*:6]-[*:7]",
+        (1, 1),
+        (1,),
+        ring_issue=True,
+    ),
     # Carboxylic Acids ####################################################
     # Carboxylic Acids Decarboxylation
     OperatorSmarts(

doranet/modules/synthetic/Reaction_Smarts_Retro.py

@@ -748,6 +748,24 @@ class OperatorSmarts:
         (1,),
         (1, 1),
     ),
+    # Enolate Alkylation
+    # From James Gerken: it doesn't really form HX as a product but rather MX
+    # and the protonated form of whatever base was used to deprotonate alpha to the carbonyl.
+    # Estimated difference in DMSO pKa between RC(=O)C-H and H-Br, should be about -33 kcal/mol
+    OperatorSmarts(
+        "Enolate Alkylation",
+        "[C+0:2](=[O+0:3])[C+0:4]!@[CX4;+0:5].[F,Cl,Br,I;+0H:6]>>[*:2](=[*:3])[*:4].[*:5][*:6]",
+        (1, 1),
+        (1, 1),
+        enthalpy_correction=-33,
+    ),
+    OperatorSmarts(
+        "Enolate Alkylation, Intramolecular",
+        "[C+0:2](=[O+0:3])[C+0:4]@[CX4;+0:5].[F,Cl,Br,I;+0H:6]>>([*:2](=[*:3])[*:4].[*:5][*:6])",
+        (1, 1),
+        (1,),
+        enthalpy_correction=-33,
+    ),
     # Alcohols #############################################################
     # Glycol Cleavage by Oxidation
     OperatorSmarts(
@@ -1180,6 +1198,25 @@ class OperatorSmarts:
         (1, 1),
         (1, 1),
     ),
+    OperatorSmarts(
+        "Synthesis of Enol Ethers from Aldehyde and Alcohol, Intramolecular",
+        "[CX4+0;H2,H3:1][O+0:2]-@[C+0H:4]=[CX3+0:3].[O+0H2:5]>>([*:1][*:2].[*:3][*:4]=[*:5])",
+        (1, 1),
+        (1,),
+    ),
+    # Pinacol Coupling
+    OperatorSmarts(
+        "Pinacol Coupling",
+        "[C+0X4;!$(*(-O)-O):2](-[O+0H:3])-!@[C+0X4;!$(*(-O)-O):6]-[O+0H:7]>>[*:2](=[*:3]).[*:6](=[*:7]).[H][H]",
+        (1,),
+        (1, 1, 1),
+    ),
+    OperatorSmarts(
+        "Pinacol Coupling, Intramolecular",
+        "[C+0X4;!$(*(-O)-O):2](-[O+0H:3])-@[C+0X4;!$(*(-O)-O):6]-[O+0H:7]>>([*:2](=[*:3]).[*:6](=[*:7])).[H][H]",
+        (1,),
+        (1, 1),
+    ),
     # Carboxylic Acids ####################################################
     # Carboxylic Acids Decarboxylation
     OperatorSmarts(

doranet/modules/synthetic/generate_network.py

@@ -68,12 +68,13 @@ def __call__(
             if rea_Hf is None:
                 return float("nan")
             dH = dH - rea_Hf * data.operator.meta["reactants_stoi"][idx]
-        if data.operator.meta["enthalpy_correction"] is not None:
-            dH = dH + data.operator.meta["enthalpy_correction"]
+        correction = data.operator.meta["enthalpy_correction"]
+        if correction is None:
+            correction = 0
         if self.direction == "forward":
-            dH = dH / data.operator.meta["number_of_steps"]
+            dH = (dH + correction) / data.operator.meta["number_of_steps"]
         if self.direction == "retro":
-            dH = -dH / data.operator.meta["number_of_steps"]
+            dH = (-dH + correction) / data.operator.meta["number_of_steps"]
         return round(dH, 4)
 
     @property

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = 'doranet'
-version = '0.5.5a1'
+version = '0.5.6a1'
 authors = [
     { name='William Sprague', email='[email protected]' },
     { name='Quan Zhang', email='[email protected]' },