Merge pull request #62 from bslakman/master

Radical solvation thermo groups
ReactionMechanismGenerator · Apr 1, 2015 · c602f61 · c602f61
2 parents 89841fc + abb6027
commit c602f61
Show file tree

Hide file tree

Showing 2 changed files with 386 additions and 2 deletions.
diff --git a/input/solvation/groups/abraham.py b/input/solvation/groups/abraham.py
@@ -595,8 +595,14 @@
 2   H   u0 {1,S}
 3   H   u0 {1,S}
 """,
-    solute = None,
-    shortDesc = u"""""",
+    solute = SoluteData(
+        S = 0.175,
+        B = 0.481,
+        E = 0.085,
+        L = 0.781,
+        A = 0.0,
+    ),
+    shortDesc = u"""Platts fragment 10 -NH2-aliphatic""",
     longDesc = 
 u"""
 

diff --git a/input/solvation/groups/radical.py b/input/solvation/groups/radical.py
@@ -0,0 +1,378 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "Radical Groups"
+shortDesc = u"Radical corrections to A"
+longDesc = u"""
+H-bonding parameter A should be modified for when we saturate 
+radical molecules with hydrogens and look up the saturated
+structure.
+"""
+entry(
+    index = 0,
+    label = "R_rad",
+    group = 
+"""
+1 * R u1
+""",
+    solute = None,
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 1,
+    label = "O_rad",
+    group = 
+"""
+1 * O u1 p2
+""",
+    solute = None,
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 2,
+    label = "ROJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   R u0 {1,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.345,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 3,
+    label = "ROOJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   O u0 p2 {1,S} {3,S}
+3   R u0 {2,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.345,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 4,
+    label = "RC(O)OJ",
+    group = 
+"""
+1 * O u1 p2 c0 {2,S}
+2   C u0 p0 {1,S} {3,D} {4,S}
+3   O u0 p2 {2,D}
+4   R u0 {2,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.243,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 5,
+    label = "N3s_rad",
+    group = 
+"""
+1 * N3s u1 p1 
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.087,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 6,
+    label = "N3_pyrrole",
+    group = 
+"""
+1 * N3s u1 p1 {2,S} {3,S}
+2   Cb  u0 {1,S} {4,B}
+3   Cb  u0 {1,S} {5,B}
+4   Cb  u0 {2,B} {5,B}
+5   Cb  u0 {3,B} {4,B}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.371,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 7,
+    label = "phenoxy",
+    group = 
+"""
+1 * O  u1 p2 c0 {2,S}
+2   Cb u0 {1,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.543,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 8,
+    label = "N3_aniline",
+    group = 
+"""
+1 * N3s u1 p1 c0 {2,S} {3,S}
+2   H   u0 p0 c0 {1,S}
+3   Cb  u0 {1,S} {4,B} {5,B}
+4   Cb  u0 {3,B} {6,B}
+5   Cb  u0 {3,B} {7,B}
+6   Cb  u0 {4,B} {8,B}
+7   Cb  u0 {5,B} {8,B}
+8   Cb  u0 {6,B} {7,B}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.247,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 9,
+    label = "N3_amide_pri",
+    group = 
+"""
+1 * N3s u1 p1 c0 {2,S} {3,S}
+2   H   u0 p0 c0 {1,S}
+3   CO  u0 {1,S} {4,D}
+4   O   u0 p2 {3,D}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.275,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 10,
+    label = "N3_amide_sec",
+    group = 
+"""
+1 * N3s u1 p1 c0 {2,S} {3,S}
+2   R!H u0 {1,S}
+3   CO  u0 {1,S} {4,D}
+4   O   u0 p2 {3,D}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.281,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 11,
+    label = "N3_amide_aromatic",
+    group = 
+"""
+1 * N3s      u1 p1 c0 {2,S} {3,S}
+2   [Cb,N3b] u0 {1,S}
+3   CO       u0 {1,S} {4,D}
+4   O        u0 p2 {3,D}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = 0.091,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 12,
+    label = "N3_urea_pri",
+    group = 
+"""
+1 * N3s u1 p1 c0 {2,S} {3,S}
+2   R!H u0 p0 c0 {1,S}
+3   CO  u0 {1,S} {4,D} {5,S}
+4   O   u0 p2 {3,D}
+5   N3s u0 p1 {3,S} {6,S}
+6   H   u0 p0 c0 {5,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = 0.0825,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 13,
+    label = "N3_urea_sec",
+    group = 
+"""
+1 * N3s u1 p1 c0 {2,S} {3,S}
+2   R!H u0 p0 c0 {1,S}
+3   CO  u0 {1,S} {4,D} {5,S}
+4   O   u0 p2 {3,D}
+5   N3s u0 p1 {3,S} {6,S} {7,S}
+6   R!H u0 {5,S}
+7   R!H u0 {5,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = 0.119,
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+
+entry(
+    index = 14,
+    label = "N3d_guanidine",
+    group = 
+"""
+1   Cd  u0 {2,D} {3,S} {4,S}
+2 * N3d u1 {1,D}
+3   N3s u0 {1,S} {5,S} {6,S}
+4   N3s u0 {1,S} {7,S} {8,S}
+5   H   u0 {3,S}
+6   H   u0 {3,S}
+7   H   u0 {4,S}
+8   H   u0 {4,S}
+""",
+    solute = SoluteData(
+        S = 0.0,
+        B = 0.0,
+        E = 0.0,
+        L = 0.0,
+        A = -0.17
+    ),
+    shortDesc = u"""""",
+    longDesc = 
+u"""
+
+""",
+)
+tree(
+"""
+L1: R_rad
+    L2: O_rad
+        L3: ROJ
+            L4: RC(O)OJ
+            L4: ROOJ
+            L4: phenoxy
+    L2: N3s_rad
+        L3: N3_pyrrole
+        L3: N3_aniline
+        L3: N3_amide_pri
+            L4: N3_urea_pri
+        L3: N3_amide_sec
+            L4: N3_urea_pri
+            L4: N3_urea_sec
+            L4: N3_amide_aromatic
+    L2: N3d_guanidine
+"""
+)
+