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Radical solvation thermo groups #62

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merged 3 commits into from
Apr 1, 2015
Merged

Radical solvation thermo groups #62

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9b3f0c8
Started a database for radical solvation thermo.
bslakman Mar 30, 2015
e3cfda4
Additions to the solvation thermo radical groups.
bslakman Mar 31, 2015
abb6027
Added data for N3sH2 group.
bslakman Apr 1, 2015
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10 changes: 8 additions & 2 deletions input/solvation/groups/abraham.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"""

Expand Down
378 changes: 378 additions & 0 deletions input/solvation/groups/radical.py
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Original file line number Diff line number Diff line change
@@ -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
"""
)