From 9b3f0c8d5b2f7f74e41331d9f7944b5a3fe64e77 Mon Sep 17 00:00:00 2001 From: Belinda Slakman Date: Mon, 30 Mar 2015 17:24:46 -0400 Subject: [PATCH 1/3] Started a database for radical solvation thermo. These groups are radical corrections to the H bonding 'A' value. We use them after we calculate solvation thermo for a saturated structure that we made by saturating radicals with hydrogens. --- input/solvation/groups/radical.py | 119 ++++++++++++++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 input/solvation/groups/radical.py diff --git a/input/solvation/groups/radical.py b/input/solvation/groups/radical.py new file mode 100644 index 0000000000..892134f047 --- /dev/null +++ b/input/solvation/groups/radical.py @@ -0,0 +1,119 @@ +#!/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""" + +""", +) + +tree( +""" +L1: R_rad + L2: O_rad + L3: ROJ + L4: RC(O)OJ + L4: ROOJ +""" +) + From e3cfda4eeeb56a6a53b0aa9377c8d1ff5709f2ae Mon Sep 17 00:00:00 2001 From: Belinda Slakman Date: Tue, 31 Mar 2015 16:22:09 -0400 Subject: [PATCH 2/3] Additions to the solvation thermo radical groups. Radical groups were added for all Platts groups that have an A value, if they'd come about by saturating with H. --- input/solvation/groups/radical.py | 259 ++++++++++++++++++++++++++++++ 1 file changed, 259 insertions(+) diff --git a/input/solvation/groups/radical.py b/input/solvation/groups/radical.py index 892134f047..8ba08f4064 100644 --- a/input/solvation/groups/radical.py +++ b/input/solvation/groups/radical.py @@ -107,6 +107,254 @@ """, ) +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 @@ -114,6 +362,17 @@ 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 """ ) From abb6027a124b3d72e230f812a35055e7deb73793 Mon Sep 17 00:00:00 2001 From: Belinda Slakman Date: Wed, 1 Apr 2015 11:30:25 -0400 Subject: [PATCH 3/3] Added data for N3sH2 group. For some reason, there was no data for this group despite there being a Platts group. Allows ammonia unit test to pass. --- input/solvation/groups/abraham.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/input/solvation/groups/abraham.py b/input/solvation/groups/abraham.py index adef864a14..1f42e5befd 100644 --- 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"""