From 7c9719da1c798a1e49350fd0071139fbd4256da1 Mon Sep 17 00:00:00 2001 From: Max Liu Date: Mon, 14 Oct 2019 12:08:29 -0400 Subject: [PATCH 1/6] Add polycyclic corrections for strained bi- and tri-cyclics --- input/thermo/groups/polycyclic.py | 123 ++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) diff --git a/input/thermo/groups/polycyclic.py b/input/thermo/groups/polycyclic.py index d95f918827..fe050ba73f 100644 --- a/input/thermo/groups/polycyclic.py +++ b/input/thermo/groups/polycyclic.py @@ -9321,6 +9321,125 @@ """, ) +entry( + index = 219, + label = "s3_5_5_triene", + group = +""" +1 * R!H u0 p0 c0 {2,S} {5,D} +2 R!H u0 p0 c0 {1,S} {6,D} +3 R!H u0 p0 c0 {4,D} {6,S} +4 R!H u0 p0 c0 {3,D} {5,S} +5 R!H u0 p0 c0 {1,D} {4,S} {7,S} +6 R!H u0 p0 c0 {2,D} {3,S} {7,S} +7 R!H u0 p0 c0 {5,S} {6,S} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-7.643, -8.911, -8.948, -8.325, -6.710, -5.427, -4.153],'cal/(mol*K)'), + H298 = (103.170,'kcal/mol'), + S298 = (67.392,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C12=CC=C(C1)C=C2. Mengjie Liu 10/14/18. +Symmetry correction removed from calculated entropy using RMG estimated +symmetry number of 4 to give correct GAV entropy estimate. +""", +) + +entry( + index = 220, + label = "s2_s2_s3_6_6_6_ben_triene", + group = +""" +1 R!H u0 p0 c0 {2,B} {3,B} {5,S} +2 R!H u0 p0 c0 {1,B} {6,B} {11,S} +3 R!H u0 p0 c0 {1,B} {8,S} {9,B} +4 R!H u0 p0 c0 {5,D} {7,S} {10,S} +5 R!H u0 p0 c0 {1,S} {4,D} +6 R!H u0 p0 c0 {2,B} {12,B} +7 R!H u0 p0 c0 {4,S} {8,D} +8 R!H u0 p0 c0 {3,S} {7,D} +9 R!H u0 p0 c0 {3,B} {12,B} +10 R!H u0 p0 c0 {4,S} {11,D} +11 R!H u0 p0 c0 {2,S} {10,D} +12 * R!H u0 p0 c0 {6,B} {9,B} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-7.245, -7.052, -6.442, -5.661, -4.296, -3.190, -3.003],'cal/(mol*K)'), + H298 = (105.475,'kcal/mol'), + S298 = (58.725,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=C3C=C(C=CC3=C1)C=C2. Mengjie Liu 10/14/19. +""", +) + +entry( + index = 221, + label = "s2_s2_s2_6_5_5_ben_diene1", + group = +""" +1 R!H u0 p0 c0 {2,S} {5,S} {6,S} +2 * R!H u0 p0 c0 {1,S} {3,B} {4,B} +3 R!H u0 p0 c0 {2,B} {8,S} {9,B} +4 R!H u0 p0 c0 {2,B} {7,S} {10,B} +5 R!H u0 p0 c0 {1,S} {7,D} +6 R!H u0 p0 c0 {1,S} {8,D} +7 R!H u0 p0 c0 {4,S} {5,D} +8 R!H u0 p0 c0 {3,S} {6,D} +9 R!H u0 p0 c0 {3,B} {11,B} +10 R!H u0 p0 c0 {4,B} {11,B} +11 R!H u0 p0 c0 {9,B} {10,B} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-7.094, -6.439, -6.029, -5.410, -4.401, -3.268, -1.804],'cal/(mol*K)'), + H298 = (31.613,'kcal/mol'), + S298 = (54.952,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=C3C(=C1)C=CC3C=C2. Mengjie Liu 10/14/19. +""", +) + +entry( + index = 222, + label = "s2_s2_s2_6_5_5_ben_diene2", + group = +""" +1 R!H u0 p0 c0 {2,S} {6,S} +2 R!H u0 p0 c0 {1,S} {3,B} {7,B} +3 * R!H u0 p0 c0 {2,B} {4,S} {5,B} +4 R!H u0 p0 c0 {3,S} {6,D} {10,S} +5 R!H u0 p0 c0 {3,B} {8,B} {9,S} +6 R!H u0 p0 c0 {1,S} {4,D} +7 R!H u0 p0 c0 {2,B} {11,B} +8 R!H u0 p0 c0 {5,B} {11,B} +9 R!H u0 p0 c0 {5,S} {10,D} +10 R!H u0 p0 c0 {4,S} {9,D} +11 R!H u0 p0 c0 {7,B} {8,B} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-7.726, -7.742, -7.568, -7.171, -6.048, -4.988, -3.887],'cal/(mol*K)'), + H298 = (27.606,'kcal/mol'), + S298 = (67.124,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=C3C(=C1)C=CC3=CC2. Mengjie Liu 10/14/19. +""", +) + tree( """ L1: PolycyclicRing @@ -9550,6 +9669,8 @@ L4: s2_5_6_tetraene_1_3_5_8 L3: s2_5_6_ben L3: s2_5_6_indene + L4: s2_s2_s2_6_5_5_ben_diene1 + L4: s2_s2_s2_6_5_5_ben_diene2 L2: s2_5_7 L3: s2_5_7_triene L4: s2_5_7_triene_0_2_8 @@ -9601,6 +9722,7 @@ L4: s2_6_6_ben_ene_1 L4: s2_6_6_ben_ene_2 L3: s2_6_6_naphthalene + L3: s2_s2_s3_6_6_6_ben_triene L2: s2_6_7 L3: s2_6_7_diene L4: s2_6_7_diene_0_2 @@ -9650,6 +9772,7 @@ L3: s3_5_5_diene L4: s3_5_5_diene_1_4 L4: s3_5_5_diene_0_4 + L3: s3_5_5_triene L2: s3_5_6 L3: s3_5_6_ane L3: s3_5_6_ene From 3772e94949a0fea7eb01b4b15a3e57cacee9c0dd Mon Sep 17 00:00:00 2001 From: Max Liu Date: Mon, 14 Oct 2019 12:08:30 -0400 Subject: [PATCH 2/6] Add polycyclic corrections for some unsaturated bicyclo C6 species --- input/thermo/groups/polycyclic.py | 153 +++++++++++++++++++++++++++++- 1 file changed, 151 insertions(+), 2 deletions(-) diff --git a/input/thermo/groups/polycyclic.py b/input/thermo/groups/polycyclic.py index fe050ba73f..cfd593ea7d 100644 --- a/input/thermo/groups/polycyclic.py +++ b/input/thermo/groups/polycyclic.py @@ -2978,7 +2978,7 @@ entry( index = 0, label = "s2_4_4_ene", - group = "OR{s2_4_4_ene_1, s2_4_4_ene_m}", + group = "OR{s2_4_4_ene_1, s2_4_4_ene_2, s2_4_4_ene_m}", thermo = None, shortDesc = u"""""", longDesc = @@ -8669,7 +8669,7 @@ entry( index = 0, label = "s2_4_4_diene", - group = "OR{s2_4_4_diene_1_m}", + group = "OR{s2_4_4_diene_1_3, s2_4_4_diene_1_4, s2_4_4_diene_1_m, s2_4_4_diene_2_5}", thermo = None, shortDesc = u"""""", longDesc = @@ -9440,6 +9440,149 @@ """, ) +entry( + index = 223, + label = "s2_4_4_ene_2", + group = +""" +1 R!H u0 p0 c0 {2,S} {4,S} {5,S} +2 R!H u0 p0 c0 {1,S} {3,S} +3 * R!H u0 p0 c0 {2,S} {5,S} +4 R!H u0 p0 c0 {1,S} {6,S} +5 R!H u0 p0 c0 {1,S} {3,S} {6,D} +6 R!H u0 p0 c0 {4,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-5.463, -5.577, -5.448, -4.796, -4.053, -3.693, -2.850],'cal/(mol*K)'), + H298 = (80.045,'kcal/mol'), + S298 = (60.555,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1CC2CCC=12. Mengjie Liu 10/14/19. +""", +) + +entry( + index = 224, + label = "s2_4_4_diene_1_3", + group = +""" +1 R!H u0 p0 c0 {2,S} {3,S} {5,S} +2 R!H u0 p0 c0 {1,S} {4,S} +3 R!H u0 p0 c0 {1,S} {4,D} {6,S} +4 * R!H u0 p0 c0 {2,S} {3,D} +5 R!H u0 p0 c0 {1,S} {6,D} +6 R!H u0 p0 c0 {3,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-6.387, -6.461, -6.218, -5.581, -4.592, -4.193, -3.443],'cal/(mol*K)'), + H298 = (96.567,'kcal/mol'), + S298 = (67.309,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2CC=C12. Mengjie Liu 10/14/19. +""", +) + +entry( + index = 225, + label = "s2_4_4_diene_1_4", + group = +""" +1 R!H u0 p0 c0 {2,S} {4,S} {5,S} +2 R!H u0 p0 c0 {1,S} {3,S} {6,S} +3 * R!H u0 p0 c0 {2,S} {4,D} +4 R!H u0 p0 c0 {1,S} {3,D} +5 R!H u0 p0 c0 {1,S} {6,D} +6 R!H u0 p0 c0 {2,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-6.490, -5.314, -4.653, -4.048, -3.323, -3.248, -2.934],'cal/(mol*K)'), + H298 = (65.133,'kcal/mol'), + S298 = (65.027,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2C=CC12. Mengjie Liu 10/14/19. +Symmetry correction removed from calculated entropy using RMG estimated +symmetry number of 4 to give correct GAV entropy estimate. +""", +) + +entry( + index = 226, + label = "s2_4_4_diene_2_5", + group = +""" +1 R!H u0 p0 c0 {3,S} {5,S} +2 * R!H u0 p0 c0 {4,S} {6,S} +3 R!H u0 p0 c0 {1,S} {4,S} {6,D} +4 R!H u0 p0 c0 {2,S} {3,S} {5,D} +5 R!H u0 p0 c0 {1,S} {4,D} +6 R!H u0 p0 c0 {2,S} {3,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-4.942, -6.178, -6.329, -5.779, -4.891, -4.528, -3.455],'cal/(mol*K)'), + H298 = (106.085,'kcal/mol'), + S298 = (65.391,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1CC2=CCC=12. Mengjie Liu 10/14/19. +Symmetry correction removed from calculated entropy using RMG estimated +symmetry number of 2 to give correct GAV entropy estimate. +""", +) + +entry( + index = 227, + label = "s2_4_4_triene", + group = "OR{s2_4_4_triene_1_4_m}", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 228, + label = "s2_4_4_triene_1_4_m", + group = +""" +1 R!H u0 p0 c0 {2,D} {4,S} {5,S} +2 R!H u0 p0 c0 {1,D} {3,S} {6,S} +3 * R!H u0 p0 c0 {2,S} {4,D} +4 R!H u0 p0 c0 {1,S} {3,D} +5 R!H u0 p0 c0 {1,S} {6,D} +6 R!H u0 p0 c0 {2,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-1.380, -3.176, -4.085, -4.386, -4.685, -4.712, -5.913],'cal/(mol*K)'), + H298 = (118.453,'kcal/mol'), + S298 = (76.077,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2C=CC=21. Mengjie Liu 10/14/19. +Symmetry correction removed from calculated entropy using RMG estimated +symmetry number of 4 to give correct GAV entropy estimate. +""", +) + tree( """ L1: PolycyclicRing @@ -9585,9 +9728,15 @@ L3: s2_4_4_ane L3: s2_4_4_ene L4: s2_4_4_ene_1 + L4: s2_4_4_ene_2 L4: s2_4_4_ene_m L3: s2_4_4_diene + L4: s2_4_4_diene_1_3 + L4: s2_4_4_diene_1_4 L4: s2_4_4_diene_1_m + L4: s2_4_4_diene_2_5 + L3: s2_4_4_triene + L4: s2_4_4_triene_1_4_m L2: s2_4_5 L3: s2_4_5_ane L3: s2_4_5_ene From 67de8935fd0f1484942ff4b7a9a2d8db77367761 Mon Sep 17 00:00:00 2001 From: Max Liu Date: Mon, 14 Oct 2019 12:08:30 -0400 Subject: [PATCH 3/6] Add polycyclic correction for barrelene --- input/thermo/groups/polycyclic.py | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/input/thermo/groups/polycyclic.py b/input/thermo/groups/polycyclic.py index cfd593ea7d..292087f15b 100644 --- a/input/thermo/groups/polycyclic.py +++ b/input/thermo/groups/polycyclic.py @@ -9583,6 +9583,35 @@ """, ) +entry( + index = 229, + label = "s4_6_6_barrelene", + group = +""" +1 * R!H u0 p0 c0 {3,S} {5,S} {8,S} +2 R!H u0 p0 c0 {4,S} {6,S} {7,S} +3 R!H u0 p0 c0 {1,S} {4,D} +4 R!H u0 p0 c0 {2,S} {3,D} +5 R!H u0 p0 c0 {1,S} {6,D} +6 R!H u0 p0 c0 {2,S} {5,D} +7 R!H u0 p0 c0 {2,S} {8,D} +8 R!H u0 p0 c0 {1,S} {7,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-6.525, -4.619, -3.437, -2.596, -1.814, -1.708, -1.904],'cal/(mol*K)'), + H298 = (19.066,'kcal/mol'), + S298 = (49.625,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1(C=C2)C=CC2C=C1. Mengjie Liu 10/14/19. +Symmetry correction removed from calculated entropy using RMG estimated +symmetry number of 4 to give correct GAV entropy estimate. +""", +) + tree( """ L1: PolycyclicRing @@ -9960,6 +9989,7 @@ L4: s3_6_7_diene_6_9-0 L2: s4_6_6 L3: s4_6_6_ane + L3: s4_6_6_barrelene L3: s4_6_6_ben_ben L4: s4_6_6_ben_ben_res1 L4: s4_6_6_ben_ben_res2 From 5bccedcdf831ad300a653cc894413360918e3b90 Mon Sep 17 00:00:00 2001 From: Max Liu Date: Mon, 14 Oct 2019 12:08:30 -0400 Subject: [PATCH 4/6] Recalculate ring correction for methylenecyclobutane --- input/thermo/groups/ring.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/input/thermo/groups/ring.py b/input/thermo/groups/ring.py index 2da054b1a5..0180335694 100644 --- a/input/thermo/groups/ring.py +++ b/input/thermo/groups/ring.py @@ -996,15 +996,15 @@ 5 [Cd,N] u0 {2,D} """, thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([-3.91,-3.339,-2.739,-2.2,-1.51,-1.051,-62.52],'cal/(mol*K)'), - H298 = (26.9,'kcal/mol'), - S298 = (28.8887,'cal/(mol*K)'), + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-3.862, -3.896, -3.629, -3.244, -2.480, -1.836, -1.085],'cal/(mol*K)'), + H298 = (29.371,'kcal/mol'), + S298 = (30.511,'cal/(mol*K)'), ), - shortDesc = u"""""", - longDesc = -u""" - + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C=C1CCC1. Mengjie Liu 9/9/19. """, ) From 7c461075f979a7ca85af7efdb8501032e8098946 Mon Sep 17 00:00:00 2001 From: Max Liu Date: Tue, 22 Oct 2019 15:31:45 -0400 Subject: [PATCH 5/6] Add polycyclic corrections for more strained tricyclics --- input/thermo/groups/polycyclic.py | 186 ++++++++++++++++++++++++++++++ 1 file changed, 186 insertions(+) diff --git a/input/thermo/groups/polycyclic.py b/input/thermo/groups/polycyclic.py index 292087f15b..aa05e69a21 100644 --- a/input/thermo/groups/polycyclic.py +++ b/input/thermo/groups/polycyclic.py @@ -9612,6 +9612,186 @@ """, ) +entry( + index = 230, + label = "s2_s2_s3_6_6_5_ben_ene", + group = +""" +1 R!H u0 p0 c0 {2,S} {4,S} +2 R!H u0 p0 c0 {1,S} {5,S} +3 R!H u0 p0 c0 {4,S} {6,S} +4 * R!H u0 p0 c0 {1,S} {3,S} {8,D} +5 R!H u0 p0 c0 {2,S} {7,B} {9,B} +6 R!H u0 p0 c0 {3,S} {7,B} {10,B} +7 R!H u0 p0 c0 {5,B} {6,B} {8,S} +8 R!H u0 p0 c0 {4,D} {7,S} +9 R!H u0 p0 c0 {5,B} {11,B} +10 R!H u0 p0 c0 {6,B} {11,B} +11 R!H u0 p0 c0 {9,B} {10,B} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-6.450, -5.745, -5.424, -5.174, -4.423, -3.607, -2.536],'cal/(mol*K)'), + H298 = (132.105,'kcal/mol'), + S298 = (58.708,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=C3C=C(CC2)CC3=C1. Mengjie Liu 10/22/19. +""", +) + +entry( + index = 231, + label = "s2_s2_s3_6_6_5_diene_diene", + group = +""" +1 R!H u0 p0 c0 {4,S} {6,S} {7,S} +2 R!H u0 p0 c0 {4,S} {5,S} +3 * R!H u0 p0 c0 {5,S} {8,S} +4 R!H u0 p0 c0 {1,S} {2,S} {9,D} +5 R!H u0 p0 c0 {2,S} {3,S} {7,D} +6 R!H u0 p0 c0 {1,S} {8,D} {10,S} +7 R!H u0 p0 c0 {1,S} {5,D} +8 R!H u0 p0 c0 {3,S} {6,D} +9 R!H u0 p0 c0 {4,D} {11,S} +10 R!H u0 p0 c0 {6,S} {11,D} +11 R!H u0 p0 c0 {9,S} {10,D} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-11.166, -12.168, -11.642, -10.223, -7.567, -5.820, -4.412],'cal/(mol*K)'), + H298 = (117.332,'kcal/mol'), + S298 = (83.403,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=CCC3=CC2C(=C1)C3. Mengjie Liu 10/22/19. +""", +) + +entry( + index = 232, + label = "s2_s2_s2_6_5_5_diene_ene_ene1", + group = +""" +1 * R!H u0 p0 c0 {2,S} {3,S} {4,S} +2 R!H u0 p0 c0 {1,S} {5,S} {7,S} +3 R!H u0 p0 c0 {1,S} {6,S} {8,S} +4 R!H u0 p0 c0 {1,S} {9,S} {10,D} +5 R!H u0 p0 c0 {2,S} {6,D} +6 R!H u0 p0 c0 {3,S} {5,D} +7 R!H u0 p0 c0 {2,S} {11,D} +8 R!H u0 p0 c0 {3,S} {9,D} +9 R!H u0 p0 c0 {4,S} {8,D} +10 R!H u0 p0 c0 {4,D} {11,S} +11 R!H u0 p0 c0 {7,D} {10,S} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-13.880, -13.484, -12.673, -11.404, -8.898, -6.838, -4.917],'cal/(mol*K)'), + H298 = (15.048,'kcal/mol'), + S298 = (90.457,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2C=CC3C=CC(=C1)C23. Mengjie Liu 10/22/19. +""", +) + +entry( + index = 233, + label = "s2_s2_s2_6_5_5_diene_ene_ene2", + group = +""" +1 R!H u0 p0 c0 {2,S} {3,S} {7,S} +2 * R!H u0 p0 c0 {1,S} {4,S} {5,S} +3 R!H u0 p0 c0 {1,S} {6,S} +4 R!H u0 p0 c0 {2,S} {6,D} {9,S} +5 R!H u0 p0 c0 {2,S} {8,S} {10,D} +6 R!H u0 p0 c0 {3,S} {4,D} +7 R!H u0 p0 c0 {1,S} {8,D} +8 R!H u0 p0 c0 {5,S} {7,D} +9 R!H u0 p0 c0 {4,S} {11,D} +10 R!H u0 p0 c0 {5,D} {11,S} +11 R!H u0 p0 c0 {9,D} {10,S} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-14.117, -14.900, -14.467, -13.113, -10.292, -7.892, -5.481],'cal/(mol*K)'), + H298 = (20.095,'kcal/mol'), + S298 = (90.893,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=CCC3C=CC(=C1)C23. Mengjie Liu 10/22/19. +""", +) + +entry( + index = 234, + label = "s2_s2_6_6_3_ben_ene", + group = +""" +1 R!H u0 p0 c0 {2,S} {3,S} {4,S} +2 R!H u0 p0 c0 {1,S} {4,S} +3 R!H u0 p0 c0 {1,S} {5,S} +4 * R!H u0 p0 c0 {1,S} {2,S} {7,D} +5 R!H u0 p0 c0 {3,S} {6,B} {8,B} +6 R!H u0 p0 c0 {5,B} {7,S} {9,B} +7 R!H u0 p0 c0 {4,D} {6,S} +8 R!H u0 p0 c0 {5,B} {11,B} +9 R!H u0 p0 c0 {6,B} {10,B} +10 R!H u0 p0 c0 {9,B} {11,B} +11 R!H u0 p0 c0 {8,B} {10,B} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-6.078, -6.636, -6.774, -6.170, -4.869, -3.677, -2.520],'cal/(mol*K)'), + H298 = (49.858,'kcal/mol'), + S298 = (57.209,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=C(C=C1)CC1CC1=C2. Mengjie Liu 10/22/19. +""", +) + +entry( + index = 235, + label = "s2_s2_s4_6_6_6_5ene", + group = +""" +1 R!H u0 p0 c0 {2,S} {3,S} {5,S} +2 R!H u0 p0 c0 {1,S} {6,D} {8,S} +3 R!H u0 p0 c0 {1,S} {7,S} {9,D} +4 * R!H u0 p0 c0 {6,S} {7,D} {10,S} +5 R!H u0 p0 c0 {1,S} {10,D} +6 R!H u0 p0 c0 {2,D} {4,S} +7 R!H u0 p0 c0 {3,S} {4,D} +8 R!H u0 p0 c0 {2,S} {11,D} +9 R!H u0 p0 c0 {3,D} {11,S} +10 R!H u0 p0 c0 {4,S} {5,D} +11 R!H u0 p0 c0 {8,D} {9,S} +""", + thermo = ThermoData( + Tdata = ([300, 400, 500, 600, 800, 1000, 1500],'K'), + Cpdata = ([-11.327, -11.768, -11.530, -10.808, -8.938, -7.248, -6.477],'cal/(mol*K)'), + H298 = (118.078,'kcal/mol'), + S298 = (93.217,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted from CBS-QB3 calculation""", + longDesc = +u"""" +Fitted from CBS-QB3 calculation for C1=CC2=CC3=CC(=C1)C2C=C3. Mengjie Liu 11/6/19. +""", +) + tree( """ L1: PolycyclicRing @@ -9835,6 +10015,8 @@ L3: s2_5_6_triene L4: s2_5_6_triene_0_2_6 L4: s2_5_6_triene_0_2_7 + L5: s2_s2_s2_6_5_5_diene_ene_ene1 + L5: s2_s2_s2_6_5_5_diene_ene_ene2 L4: s2_5_6_triene_0_3_7 L4: s2_5_6_triene_1_3_5 L4: s2_5_6_triene_1_3_6 @@ -9894,10 +10076,14 @@ L4: s2_6_6_tetraene_0_2_5_7 L4: s2_6_6_tetraene_0_2_6_8 L4: s2_6_6_tetraene_0_3_6_8 + L5: s2_s2_s3_6_6_5_diene_diene + L5: s2_s2_s4_6_6_6_5ene L4: s2_6_6_tetraene_1_3_6_8 L3: s2_6_6_ben L3: s2_6_6_ben_ene L4: s2_6_6_ben_ene_1 + L5: s2_s2_6_6_3_ben_ene + L5: s2_s2_s3_6_6_5_ben_ene L4: s2_6_6_ben_ene_2 L3: s2_6_6_naphthalene L3: s2_s2_s3_6_6_6_ben_triene From f21a9bb393ca41de082c89e656b8db32049cd874 Mon Sep 17 00:00:00 2001 From: Max Liu Date: Tue, 22 Oct 2019 15:32:36 -0400 Subject: [PATCH 6/6] Fix HBI value for dihydronaphthalene radical Species matching this group seemed to have incorrect enthalpies After comparing with the calculated enthalpy for the species used to fit the HBI value, it seemed that the value was off by exactly the enthalpy of an H atom. Also fix SMILES for the model species used to fit the Benzyl_S_dihydronaphthalene and Benzyl_T_dihydronaphthalene group values since they seem to have been swapped. --- input/thermo/groups/radical.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/input/thermo/groups/radical.py b/input/thermo/groups/radical.py index 876397ac31..0f428202fc 100644 --- a/input/thermo/groups/radical.py +++ b/input/thermo/groups/radical.py @@ -9036,7 +9036,7 @@ thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), Cpdata = ([-0.762975,-1.091932,-1.454467,-1.908359,-2.748445,-3.446538,-4.576528],'cal/(mol*K)','+|-',[0.226952,0.226952,0.226952,0.226952,0.226952,0.226952,0.226952]), - H298 = (31.565243,'kcal/mol','+|-',0.869131), + H298 = (83.668243,'kcal/mol','+|-',0.869131), S298 = (1.433096,'cal/(mol*K)','+|-',0.350884), ), shortDesc = u"""Calculations from Hexylbenzene Library, Lawrence Lai""", @@ -9049,8 +9049,11 @@ Model Species used include: C1=CC=C2C=CC[CH]C2=C1 -C[C]1CC=CC2=CC=CC=C12 -CC[C]1CC=CC2=CC=CC=C12 +CC1=CC[CH]C2=CC=CC=C12 +CCC1=CC[CH]C2=CC=CC=C12 + +Modified 10/2019 by Max Liu. Added enthalpy of H atom so that GAV predicted +enthalpy for C1=CC=C2C=CC[CH]C2=C1 matches calculated value. """, ) @@ -9082,8 +9085,8 @@ http://pubs.acs.org/doi/abs/10.1021/acs.jpca.5b05448 Model Species used include: -CC1=CC[CH]C2=CC=CC=C12 -CCC1=CC[CH]C2=CC=CC=C12 +C[C]1CC=CC2=CC=CC=C12 +CC[C]1CC=CC2=CC=CC=C12 """, )