diff --git a/input/forbiddenStructures.py b/input/forbiddenStructures.py index 9e9085555a..fe59266d12 100644 --- a/input/forbiddenStructures.py +++ b/input/forbiddenStructures.py @@ -319,22 +319,22 @@ """, ) -entry( - label = "cyclopropyne", - group = -""" -1 C u0 {2,T} {3,S} -2 C u0 {1,T} {3,S} -3 C u0 {1,S} {2,S} {4,S} {5,S} -4 H u0 {3,S} -5 H u0 {3,S} -""", - shortDesc = u"""""", - longDesc = -u""" - -""", -) +# entry( +# label = "cyclopropyne", +# group = +# """ +# 1 C u0 {2,T} {3,S} +# 2 C u0 {1,T} {3,S} +# 3 C u0 {1,S} {2,S} {4,S} {5,S} +# 4 H u0 {3,S} +# 5 H u0 {3,S} +# """, +# shortDesc = u"""""", +# longDesc = +# u""" +# +# """, +# ) entry( label = "3H-Pyrazol", @@ -443,3 +443,177 @@ """, ) +entry( + label = "cyclobutyne", + group = +""" +1 R!H ux {2,T} {4,[S,D,T]} +2 R!H ux {1,T} {3,[S,D,T]} +3 R!H ux {2,[S,D,T]} {4,[S,D,T]} +4 R!H ux {1,[S,D,T]} {3,[S,D,T]} +""", + shortDesc = u"""""", + longDesc = +u""" +""", +) + +entry( + label = "s2_3_4_yne_1", + group = +""" +1 R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {4,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} {5,[S,D,T,B]} +3 R!H ux {1,[S,D,T,B]} {2,[S,D,T,B]} +4 R!H ux {1,[S,D,T,B]} {5,T} +5 R!H ux {2,[S,D,T,B]} {4,T} +""", + shortDesc = u"""""", + longDesc = +u""" +""", +) + +entry( + label = "s2_4_4_yne_1", + group = +""" +1 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {5,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} {6,[S,D,T,B]} +3 R!H ux {2,[S,D,T,B]} {4,T} +4 R!H ux {1,[S,D,T,B]} {3,T} +5 R!H ux {1,[S,D,T,B]} {6,[S,D,T,B]} +6 R!H ux {2,[S,D,T,B]} {5,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +""", +) + +entry( + label = "s2_4_5_yne_5", + group = +""" +1 R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {5,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {6,[S,D,T,B]} +3 R!H ux {1,[S,D,T,B]} {4,T} +4 R!H ux {2,[S,D,T,B]} {3,T} +5 R!H ux {1,[S,D,T,B]} {7,[S,D,T,B]} +6 R!H ux {2,[S,D,T,B]} {7,[S,D,T,B]} +7 R!H ux {5,[S,D,T,B]} {6,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +""", +) + +entry( + label = "s2_4_6_yne_6", + group = +""" +1 R!H ux {2,[S,D,T,B]} {3,[S,D,T,B]} {6,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {5,[S,D,T,B]} +3 R!H ux {1,[S,D,T,B]} {4,T} +4 R!H ux {2,[S,D,T,B]} {3,T} +5 R!H ux {2,[S,D,T,B]} {8,[S,D,T,B]} +6 R!H ux {1,[S,D,T,B]} {7,[S,D,T,B]} +7 R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]} +8 R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +""", +) + +entry( + label = "strained_tetracyclic_1", + group = +""" +1 R!H ux {2,[S,D,T,B]} {9,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} +3 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {10,[S,D,T,B]} +4 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]} +5 R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} +6 R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} +7 R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]} {10,[S,D,T,B]} +8 R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]} {10,[S,D,T,B]} +9 R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {8,[S,D,T,B]} +10 R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]} {8,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +For certain unsaturated versions of this strained tetracyclic, RMG finds multiple reverse H-abstraction reactions, causing RMG +to crash. +""", +) + +entry( + label = "strained_tricyclic_1", + group = +""" +2 R!H ux {3,[S,D,T,B]} {10,[S,D,T,B]} +3 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} +4 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} +5 R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {9,[S,D,T,B]} +6 R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} {10,[S,D,T,B]} +7 R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]} +8 R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]} +9 R!H ux {5,[S,D,T,B]} {8,[S,D,T,B]} {10,[S,D,T,B]} +10 R!H ux {2,[S,D,T,B]} {6,[S,D,T,B]} {9,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +For certain unsaturated versions of this strained tricyclic, RMG's Clar optimization fails, causing RMG +to crash. +""", +) + +entry( + label = "strained_tricyclic_2", + group = +""" +1 R!H ux {2,[S,D,T,B]} {10,[S,D,T,B]} +2 R!H ux {1,[S,D,T,B]} {3,[S,D,T,B]} +3 R!H ux {2,[S,D,T,B]} {4,[S,D,T,B]} {8,[S,D,T,B]} +4 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} +5 R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {10,[S,D,T,B]} +6 R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} +7 R!H ux {6,[S,D,T,B]} {8,[S,D,T,B]} +8 R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]} {9,[S,D,T,B]} +9 R!H ux {8,[S,D,T,B]} {10,[S,D,T,B]} +10 R!H ux {1,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +Certain unsaturated versions of this strained tricyclic cause RMG +to crash. +""", +) + +entry( + label = "strained_tricyclic_3", + group = +""" +1 R!H ux {3,[S,D,T,B]} {7,[S,D,T,B]} +3 R!H ux {1,[S,D,T,B]} {4,[S,D,T,B]} {10,[S,D,T,B]} +4 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} +5 R!H ux {4,[S,D,T,B]} {6,[S,D,T,B]} {10,[S,D,T,B]} +6 R!H ux {5,[S,D,T,B]} {7,[S,D,T,B]} +7 R!H ux {1,[S,D,T,B]} {6,[S,D,T,B]} {8,[S,D,T,B]} +8 R!H ux {7,[S,D,T,B]} {9,[S,D,T,B]} +9 R!H ux {8,[S,D,T,B]} {10,[S,D,T,B]} +10 R!H ux {3,[S,D,T,B]} {5,[S,D,T,B]} {9,[S,D,T,B]} +""", + shortDesc = u"""""", + longDesc = +u""" +Certain unsaturated versions of this strained tricyclic cause RMG +to crash. +""", +) \ No newline at end of file diff --git a/input/thermo/groups/group.py b/input/thermo/groups/group.py index 496c67b6fc..b7298f1cee 100644 --- a/input/thermo/groups/group.py +++ b/input/thermo/groups/group.py @@ -44845,6 +44845,30 @@ """, ) +entry( + index = 1932, + label = "Cds-(Cds-Os)CbH", + group = +""" +1 * Cd u0 {2,D} {3,S} {4,S} +2 Cd u0 {1,D} {5,S} +3 Cb u0 {1,S} +4 H u0 {1,S} +5 Os u0 {2,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([5.28, 6.83, 7.245, 7.264, 8.226, 9.901, 10.176],'cal/(mol*K)'), + H298 = (10.329,'kcal/mol'), + S298 = (2.958,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculations for OC=Cc1ccccc1 +""", +) + tree( """ L1: R @@ -45053,6 +45077,7 @@ L5: Cds-CdsCtH L6: Cds-CdsH(CtN3t) L5: Cds-CdsCbH + L6: Cds-(Cds-Os)CbH L5: Cds-CddCsH L6: Cds-(Cdd-Od)CsH L6: Cds-(Cdd-Sd)CsH diff --git a/input/thermo/groups/polycyclic.py b/input/thermo/groups/polycyclic.py index c297b36aa8..244844c85f 100644 --- a/input/thermo/groups/polycyclic.py +++ b/input/thermo/groups/polycyclic.py @@ -2572,16 +2572,16 @@ S298 = (236.447,'J/(mol*K)'), ), shortDesc = u"""Fitted from thermo library values""", - longDesc = -u""" -Fitted from molecule s2_3_6_ane from Bicyclics_QM_190_isomorphic library. -""", + longDesc= + u""" + Fitted from molecule s2_3_6_ane from Bicyclics_QM_190_isomorphic library. + """, ) entry( index = 0, label = "s2_3_6_ene", - group = "OR{s2_3_6_ene_1, s2_3_6_ene_2}", + group = "OR{s2_3_6_ene_1, s2_3_6_ene_2, s2_3_6_ene_5}", thermo = None, shortDesc = u"""""", longDesc = @@ -2645,7 +2645,7 @@ entry( index = 0, label = "s2_3_6_diene", - group = "OR{s2_3_6_diene_0_2, s2_3_6_diene_0_3, s2_3_6_diene_1_3}", + group = "OR{s2_3_6_diene_0_2, s2_3_6_diene_0_3, s2_3_6_diene_1_3, s2_3_6_diene_2_5}", thermo = None, shortDesc = u"""""", longDesc = @@ -4976,7 +4976,7 @@ entry( index = 117, label = "s2_5_6_indene", - group = + group = """ 1 * R!H u0 {2,B} {3,S} {4,B} 2 R!H u0 {1,B} {5,S} {6,B} @@ -4995,7 +4995,7 @@ S298 = (33.08,'cal/(mol*K)'), ), shortDesc = u"""""", - longDesc = + longDesc = u""" Verevkin (2011), experimental, S and cp from PM7 """, @@ -7164,7 +7164,7 @@ entry( index = 0, label = "s3_5_5_diene", - group = "OR{s3_5_5_diene_1_4}", + group = "OR{s3_5_5_diene_1_4, s3_5_5_diene_0_4}", thermo = None, shortDesc = u"""""", longDesc = @@ -8035,7 +8035,7 @@ group = "OR{s4_6_8_ene_7}", thermo = None, shortDesc = u"""""", - longDesc = + longDesc = u""" """, @@ -8554,6 +8554,431 @@ """, ) +entry( + index = 76, + label = "s2_3_6_ene_5", + group = +""" +1 R!H u0 {2,S} {3,D} {4,S} +2 R!H u0 {1,S} {3,S} {5,S} +3 R!H u0 {1,D} {2,S} +4 R!H u0 {1,S} {7,S} +5 R!H u0 {2,S} {6,S} +6 * R!H u0 {5,S} {7,S} +7 R!H u0 {4,S} {6,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-33.0644, -30.4388, -27.9344, -25.2475, -19.6467, -15.2896, -10.1737], 'J/(mol*K)'), + H298=(262.495, 'kJ/mol'), + S298=(238.794, 'J/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + +entry( + index = 77, + label = "s2_3_6_diene_2_5", + group = +""" +1 R!H u0 {2,S} {3,D} {4,S} +2 R!H u0 {1,S} {3,S} {5,S} +3 R!H u0 {1,D} {2,S} +4 R!H u0 {1,S} {7,S} +5 R!H u0 {2,S} {6,S} +6 * R!H u0 {5,S} {7,D} +7 R!H u0 {4,S} {6,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-25.6671, -24.8396, -23.399, -21.6937, -17.9095, -14.865, -11.0665], 'J/(mol*K)'), + H298=(259.334, 'kJ/mol'), + S298=(242.952, 'J/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + +entry( + index = 0, + label = "s3_5_6_ben_ane", + group = "OR{s3_5_6_ben_ane_res1, s3_5_6_ben_ane_res2}", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 78, + label = "s3_5_6_ben_ane_res1", + group = +""" +1 R!H u0 {3,B} {5,S} {6,B} +2 R!H u0 {3,B} {4,S} {7,B} +3 R!H u0 {1,B} {2,B} +4 R!H u0 {2,S} {5,S} +5 R!H u0 {1,S} {4,S} +6 R!H u0 {1,B} {8,B} +7 R!H u0 {2,B} {8,B} +8 * R!H u0 {6,B} {7,B} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-0.469, -0.262, -0.442, -0.825, -0.747, 0.339, 0.354], 'cal/(mol*K)'), + H298=(166.291, 'kcal/mol'), + S298=(30.103, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + +entry( + index = 78, + label = "s3_5_6_ben_ane_res2", + group = +""" +1 R!H u0 {3,S} {5,S} {6,D} +2 R!H u0 {3,D} {4,S} {7,S} +3 R!H u0 {1,S} {2,D} +4 R!H u0 {2,S} {5,S} +5 R!H u0 {1,S} {4,S} +6 R!H u0 {1,D} {8,S} +7 R!H u0 {2,S} {8,D} +8 * R!H u0 {6,S} {7,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-7.466, -8.33, -8.73, -8.665, -6.596, -3.859, -3.506], 'cal/(mol*K)'), + H298=(145.431, 'kcal/mol'), + S298=(63.603, 'cal/(mol*K)'), + ), + shortDesc=u"""""", + longDesc= + u""" + Fitted to CBS-QB3 calculations + """, +) + +entry( + index = 0, + label = "s3_5_6_ben_ene", + group = "OR{s3_5_6_ben_ene_res1, s3_5_6_ben_ene_res2}", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 79, + label = "s3_5_6_ben_ene_res1", + group = +""" +1 R!H u0 {3,B} {5,S} {6,B} +2 R!H u0 {3,B} {4,S} {7,B} +3 R!H u0 {1,B} {2,B} +4 R!H u0 {2,S} {5,D} +5 R!H u0 {1,S} {4,D} +6 R!H u0 {1,B} {8,B} +7 R!H u0 {2,B} {8,B} +8 * R!H u0 {6,B} {7,B} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-7.96404, -8.74552, -8.7074, -8.03332, -5.94428, -4.49956, -4.93892], 'J/(mol*K)'), + H298=(708.321, 'kJ/mol'), + S298=(145.354, 'J/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + +entry( + index = 80, + label = "s3_5_6_ben_ene_res2", + group = +""" +1 R!H u0 {3,S} {5,S} {6,D} +2 R!H u0 {3,D} {4,S} {7,S} +3 R!H u0 {1,S} {2,D} +4 R!H u0 {2,S} {5,D} +5 R!H u0 {1,S} {4,D} +6 R!H u0 {1,D} {8,S} +7 R!H u0 {2,S} {8,D} +8 * R!H u0 {6,S} {7,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-14.24, -20.6281, -22.933, -23.0957, -21.9272, -19.2272, -22.6791], 'J/(mol*K)'), + H298=(600.625, 'kJ/mol'), + S298=(297.401, 'J/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + +entry( + index = 86, + label = "s1-2_5d1d3_3_5d1_triene", + group = +""" +1 * R!H u0 {2,S} {3,S} {4,S} {5,S} +2 R!H u0 {1,S} {3,S} {6,S} +3 R!H u0 {1,S} {2,S} {7,S} +4 R!H u0 {1,S} {9,D} +5 R!H u0 {1,S} {10,D} +6 R!H u0 {2,S} {8,D} +7 R!H u0 {3,S} {8,S} +8 R!H u0 {6,D} {7,S} +9 R!H u0 {4,D} {10,S} +10 R!H u0 {5,D} {9,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-7.108, -7.764, -7.893, -7.784, -7.495, -7.132, -5.2],'cal/(mol*K)'), + H298 = (38.553,'kcal/mol'), + S298 = (95.09,'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 87, + label = "s2-2_5d1_3_6d1d3_triene", + group = +""" +1 * R!H u0 {2,S} {3,S} {4,S} {5,S} +2 R!H u0 {1,S} {3,S} {7,S} +3 R!H u0 {1,S} {2,S} {6,S} +4 R!H u0 {1,S} {8,S} +5 R!H u0 {1,S} {10,D} +6 R!H u0 {3,S} {8,D} +7 R!H u0 {2,S} {9,D} +8 R!H u0 {4,S} {6,D} +9 R!H u0 {7,D} {10,S} +10 R!H u0 {5,D} {9,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-6.846, -7.913, -8.399, -8.495, -8.078, -7.325, -5.437],'cal/(mol*K)'), + H298 = (32.243,'kcal/mol'), + S298 = (93.33,'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 119, + label = "s3_5_5_diene_0_4", + group = +""" +1 R!H u0 {3,S} {6,S} {7,S} +2 R!H u0 {3,S} {4,D} {5,S} +3 R!H u0 {1,S} {2,S} +4 * R!H u0 {2,D} {6,S} +5 R!H u0 {2,S} {7,D} +6 R!H u0 {1,S} {4,S} +7 R!H u0 {1,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-7.117, -6.624, -6.352, -6.401, -5.37, -3.457, -3.059],'cal/(mol*K)'), + H298 = (86.425,'kcal/mol'), + S298 = (57.025,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted to CBS-QB3 calculation""", + longDesc = +u""" +Fitted to CBS-QB3 calculation. +""", +) + +entry( + index = 0, + label = "s4_6_6_ben_ben", + group = "OR{s4_6_6_ben_ben_res1, s4_6_6_ben_ben_res2, s4_6_6_ben_ben_res3}", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 180, + label = "s4_6_6_ben_ben_res1", + group = +""" +1 * R!H u0 {3,B} {6,B} {8,B} +2 R!H u0 {4,B} {5,B} {7,B} +3 R!H u0 {1,B} {4,B} +4 R!H u0 {2,B} {3,B} +5 R!H u0 {2,B} {6,B} +6 R!H u0 {1,B} {5,B} +7 R!H u0 {2,B} {8,B} +8 R!H u0 {1,B} {7,B} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([0.711, 2.163, 2.154, 1.273, 0.527, 0.897, -1.267],'cal/(mol*K)'), + H298 = (165.718,'kcal/mol'), + S298 = (12.735,'cal/(mol*K)'), + ), + shortDesc=u"""Fitted to CBS-QB3 calculation""", + longDesc= + u""" + Fitted to CBS-QB3 calculation. + """, +) + +entry( + index = 181, + label = "s4_6_6_ben_ben_res2", + group = +""" +1 * R!H u0 {3,S} {6,B} {8,B} +2 R!H u0 {4,S} {5,B} {7,B} +3 R!H u0 {1,S} {4,D} +4 R!H u0 {2,S} {3,D} +5 R!H u0 {2,B} {6,B} +6 R!H u0 {1,B} {5,B} +7 R!H u0 {2,B} {8,B} +8 R!H u0 {1,B} {7,B} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-2.829, -1.234, -0.797, -1.155, -1.114, -0.25, -0.824],'cal/(mol*K)'), + H298 = (156.978,'kcal/mol'), + S298 = (28.635,'cal/(mol*K)'), + ), + shortDesc=u"""Fitted to CBS-QB3 calculation""", + longDesc= + u""" + Fitted to CBS-QB3 calculation. + """, +) + +entry( + index = 182, + label = "s4_6_6_ben_ben_res3", + group = +""" +1 * R!H u0 {3,S} {6,D} {8,S} +2 R!H u0 {4,S} {5,D} {7,S} +3 R!H u0 {1,S} {4,D} +4 R!H u0 {2,S} {3,D} +5 R!H u0 {2,D} {6,S} +6 R!H u0 {1,D} {5,S} +7 R!H u0 {2,S} {8,D} +8 R!H u0 {1,S} {7,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([0.711, 2.163, 2.154, 1.273, 0.527, 0.897, -1.267], 'cal/(mol*K)'), + H298=(165.718, 'kcal/mol'), + S298=(12.735, 'cal/(mol*K)'), + ), + shortDesc=u"""""", + longDesc= + u""" + Copy of res 1 correction. + """, +) + +entry( + index = 0, + label = "s3_4_6_ben_ane", + group = "OR{s3_4_6_ben_ane_res1, s3_4_6_ben_ane_res2}", + thermo = None, + shortDesc = u"""""", + longDesc = +u""" + +""", +) + +entry( + index = 213, + label = "s3_4_6_ben_ane_res1", + group = +""" +1 R!H u0 {3,B} {4,S} {6,B} +2 R!H u0 {3,B} {4,S} {7,B} +3 R!H u0 {1,B} {2,B} +4 * R!H u0 {2,S} {1,S} +6 R!H u0 {1,B} {8,B} +7 R!H u0 {2,B} {8,B} +8 R!H u0 {6,B} {7,B} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([0.971, 1.615, 1.051, -0.042, -1.098, -0.849, -2.199], 'cal/(mol*K)'), + H298=(150.622, 'kcal/mol'), + S298=(34.822, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + +entry( + index = 214, + label = "s3_4_6_ben_ane_res2", + group = +""" +1 R!H u0 {3,S} {4,S} {6,D} +2 R!H u0 {3,D} {4,S} {7,S} +3 R!H u0 {1,S} {2,D} +4 * R!H u0 {2,S} {1,S} +6 R!H u0 {1,D} {8,S} +7 R!H u0 {2,S} {8,D} +8 R!H u0 {6,S} {7,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-6.57, -6.954, -7.598, -8.045, -6.641, -4.264, -4.149], 'cal/(mol*K)'), + H298=(129.962, 'kcal/mol'), + S298=(67.112, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + tree( """ L1: PolycyclicRing @@ -8571,6 +8996,8 @@ L2: s2-4f1_5_5_7_ane L2: s4-3f1_6_6_6_ane L2: s3-3f1_6_5_6_ane + L2: s1-2_5d1d3_3_5d1_triene + L2: s2-2_5d1_3_6d1d3_triene L2: s1_3_3 L3: s1_3_3_ane L3: s1_3_3_ene @@ -8682,10 +9109,12 @@ L3: s2_3_6_ene L4: s2_3_6_ene_1 L4: s2_3_6_ene_2 + L4: s2_3_6_ene_5 L3: s2_3_6_diene L4: s2_3_6_diene_0_2 L4: s2_3_6_diene_0_3 L4: s2_3_6_diene_1_3 + L4: s2_3_6_diene_2_5 L3: s2_3_6_ben L2: s2_3_7 L3: s2_3_7_ane @@ -8859,6 +9288,9 @@ L4: s3_4_6_diene_0_4 L4: s3_4_6_diene_1_4 L4: s3_4_6_diene_1_5 + L3: s3_4_6_ben_ane + L4: s3_4_6_ben_ane_res1 + L4: s3_4_6_ben_ane_res2 L2: s3_5_5 L3: s3_5_5_ene L4: s3_5_5_ene_0 @@ -8868,6 +9300,7 @@ L3: s3_5_5_ane L3: s3_5_5_diene L4: s3_5_5_diene_1_4 + L4: s3_5_5_diene_0_4 L2: s3_5_6 L3: s3_5_6_ane L3: s3_5_6_ene @@ -8875,6 +9308,12 @@ L4: s3_5_6_ene_5 L3: s3_5_6_diene L4: s3_5_6_diene_1_5 + L3: s3_5_6_ben_ane + L4: s3_5_6_ben_ane_res1 + L4: s3_5_6_ben_ane_res2 + L3: s3_5_6_ben_ene + L4: s3_5_6_ben_ene_res1 + L4: s3_5_6_ben_ene_res2 L2: s3_6_6 L3: s3_6_6_ane L3: s3_6_6_ene @@ -8900,6 +9339,10 @@ L4: s3_6_7_diene_6_9-0 L2: s4_6_6 L3: s4_6_6_ane + L3: s4_6_6_ben_ben + L4: s4_6_6_ben_ben_res1 + L4: s4_6_6_ben_ben_res2 + L4: s4_6_6_ben_ben_res3 L2: s4_6_8 L3: s4_6_8_ane L3: s4_6_8_ene diff --git a/input/thermo/groups/radical.py b/input/thermo/groups/radical.py index 26c0331123..b4d0e6b006 100644 --- a/input/thermo/groups/radical.py +++ b/input/thermo/groups/radical.py @@ -2676,7 +2676,7 @@ entry( index = 182, label = "1,3-cyclopentadiene-allyl", - group = + group = """ 1 * Cs u1 {2,S} {3,S} {6,S} 2 Cd u0 {1,S} {4,D} @@ -2687,14 +2687,15 @@ """, thermo = ThermoData( Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([-1.54,-1.82,-2.08,-2.32,-2.75,-3.14,-3.85],'cal/(mol*K)'), - H298 = (82.6,'kcal/mol'), - S298 = (-3.81,'cal/(mol*K)'), + Cpdata = ([2.157, 0.892, -0.937, -2.776, -4.931, -3.793, -4.855],'cal/(mol*K)'), + H298 = (84.912,'kcal/mol'), + S298 = (-2.047,'cal/(mol*K)'), ), - shortDesc = u"""Homolytic C-H and N-H bond dissociation energies of strained organic compounds Feng et al. 2004S, Cp copied from Cds_S""", - longDesc = + shortDesc = u"""Combined experimental and theoretical results of Tranter for 1,2-CPD'yl""", + longDesc = u""" - +Absolute Enthalpy of formation at 298 K from experiment (1998 Kern and Tranter). +All other values from theory (2001 Kiefer and Tranter). """, ) @@ -8351,6 +8352,29 @@ """, ) +entry( + index = 137, + label = "OC=CJCb", + group = +""" +1 * Cd u1 {2,D} {3,S} +2 C u0 {1,D} {4,S} +3 Cb u0 {1,S} +4 Os u0 {2,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([0.047, 0.607, 0.374, -0.3, -1.28, -1.972, -3.196],'cal/(mol*K)'), + H298 = (123.797,'kcal/mol'), + S298 = (2.661,'cal/(mol*K)'), + ), + shortDesc = u"""Fit to CCSD(T)-F12/cc-pVDZ-F12//M06/vtz calculations""", + longDesc = +u""" +Fit to CCSD(T)-F12/cc-pVDZ-F12//M06/vtz calculations for OC=[C]c1ccccc1 +""", +) + tree( """ L1: Radical @@ -8612,6 +8636,7 @@ L6: CCCJ=C=O L7: CC(C)CJ=C=O L7: C=C(C)CJ=C=O + L6: OC=CJCb L5: CdsJ-Ss L5: C=CJO L4: CtJ diff --git a/input/thermo/groups/ring.py b/input/thermo/groups/ring.py index 7856bd19de..d9a735f913 100644 --- a/input/thermo/groups/ring.py +++ b/input/thermo/groups/ring.py @@ -81,8 +81,8 @@ label = "ThreeMember", group = """ -1 * R!H u0 {2,[S,D]} {3,[S,D]} -2 R!H u0 {1,[S,D]} {3,[S,D]} +1 * R!H u0 {2,[S,D,T]} {3,[S,D]} +2 R!H u0 {1,[S,D,T]} {3,[S,D]} 3 R!H u0 {1,[S,D]} {2,[S,D]} """, thermo = u'Cyclopropane', @@ -660,60 +660,6 @@ """, ) -entry( - index = 14, - label = "Cyclobutene2", - group = -""" -1 [Cs,N3s] u0 {2,S} {4,S} -2 * [Cd,N3d] u0 {1,S} {3,D} -3 [Cd,N3d] u0 {2,D} {4,S} -4 [Cs,N3s] u0 {1,S} {3,S} -""", - thermo = u'Cyclobutene', - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 14, - label = "Cyclobutadiene2", - group = -""" -1 [Cs,N3s] u0 {2,S} {4,S} -2 * [Cd,N3d] u0 {1,S} {3,D} -3 Cdd u0 {2,D} {4,D} -4 [Cd,N3d] u0 {1,S} {3,D} -""", - thermo = u'Cyclobutene', - shortDesc = u"""""", - longDesc = -u""" - -""", -) - -entry( - index = 14, - label = "Cyclobutadiene3", - group = -""" -1 * [Cs,N3s] u0 {2,S} {4,S} -2 [Cd,N3d] u0 {1,S} {3,D} -3 Cdd u0 {2,D} {4,D} -4 [Cd,N3d] u0 {1,S} {3,D} -""", - thermo = u'Cyclobutene', - shortDesc = u"""""", - longDesc = -u""" - -""", -) - entry( index = 70, label = "Oxetane", @@ -854,7 +800,7 @@ entry( index = 19, - label = "cyclobutadiene", + label = "cyclobutadiene_13", group = """ 1 [Cd,N3d] u0 {2,D} {4,S} @@ -1115,11 +1061,11 @@ label = "FiveMember", group = """ -1 * R!H u0 {2,[S,D]} {5,[S,D]} -2 R!H u0 {1,[S,D]} {3,[S,D]} +1 * R!H u0 {2,[S,D,T]} {5,[S,D]} +2 R!H u0 {1,[S,D,T]} {3,[S,D]} 3 R!H u0 {2,[S,D]} {4,[S,D]} -4 R!H u0 {3,[S,D]} {5,[S,D]} -5 R!H u0 {1,[S,D]} {4,[S,D]} +4 R!H u0 {3,[S,D]} {5,[S,D,T]} +5 R!H u0 {1,[S,D]} {4,[S,D,T]} """, thermo = u'Cyclopentane', shortDesc = u"""""", @@ -1203,25 +1149,20 @@ entry( index = 152, - label = "Cyclopentatriene", + label = "five-inringthreedouble-124", group = """ -1 * [Cd,N3d] u0 {2,D} {5,S} +1 * R!H u0 {2,D} {5,[S,D]} 2 Cdd u0 {1,D} {3,D} -3 [Cd,N3d] u0 {2,D} {4,S} -4 [Cd,N3d] u0 {3,S} {5,D} -5 [Cd,N3d] u0 {1,S} {4,D} +3 R!H u0 {2,D} {4,[S,D]} +4 R!H u0 {3,[S,D]} {5,D} +5 R!H u0 {1,[S,D]} {4,D} """, - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([-4.08,-4.69,-4.58,-4.25,-3.54,-3.08,-2.47],'cal/(mol*K)'), - H298 = (70.16,'kcal/mol'), - S298 = (36.76,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 isodesmic reaction approach allene + 2-butene = cyclopentatriene + 2 CH4, DHr = 220.8 kJ mol-1, exp data from NIST""", + thermo = u'Cyclopentatriene', + shortDesc = u"""""", longDesc = u""" - +For now, any 5-membered ring that has at least 3 double-bonds in the 1,2,4 positions will use this general correction. """, ) @@ -1932,12 +1873,12 @@ label = "SixMember", group = """ -1 * R!H u0 {2,[S,D]} {6,[S,D]} -2 R!H u0 {1,[S,D]} {3,[S,D]} -3 R!H u0 {2,[S,D]} {4,[S,D]} -4 R!H u0 {3,[S,D]} {5,[S,D]} -5 R!H u0 {4,[S,D]} {6,[S,D]} -6 R!H u0 {1,[S,D]} {5,[S,D]} +1 * R!H u0 {2,[S,D,T]} {6,[S,D]} +2 R!H u0 {1,[S,D,T]} {3,[S,D]} +3 R!H u0 {2,[S,D]} {4,[S,D,T]} +4 R!H u0 {3,[S,D,T]} {5,[S,D]} +5 R!H u0 {4,[S,D]} {6,[S,D,T]} +6 R!H u0 {1,[S,D]} {5,[S,D,T]} """, thermo = u'Cyclohexane', shortDesc = u"""""", @@ -2736,26 +2677,22 @@ entry( index = 153, - label = "six-inringthreedouble", + label = "six-inringthreedouble_124", group = """ -1 Cd u0 {2,D} {6,S} +1 R!H u0 {2,D} {6,S} 2 * Cdd u0 {1,D} {3,D} -3 Cd u0 {2,D} {4,S} -4 [Cs,Os] u0 {3,S} {5,S} -5 Cd u0 {4,S} {6,D} -6 Cd u0 {1,S} {5,D} +3 R!H u0 {2,D} {4,S} +4 R!H u0 {3,S} {5,[S,D]} +5 R!H u0 {4,[S,D]} {6,D} +6 R!H u0 {1,S} {5,D} """, - thermo = ThermoData( - Tdata = ([300,400,500,600,800,1000,1500],'K'), - Cpdata = ([-4.21,-4.32,-3.9,-3.46,-2.71,-2.25,-1.38],'cal/(mol*K)'), - H298 = (36.04,'kcal/mol'), - S298 = (26.47,'cal/(mol*K)'), - ), - shortDesc = u"""CBS-QB3 isodesmic reaction approach C1=CC=CCC=1 + 3 ethane + ethene = allene + 2 2-butene + propane""", + thermo = u'124cyclohexatriene', + shortDesc = u"""""", longDesc = u""" - +Use 124cyclohexatriene correction for any 6-membered ring that contains at least 3 double bonds in the 1,2 and 4 p +positions. """, ) @@ -3128,8 +3065,8 @@ label = "SevenMember", group = """ -1 * R!H u0 {2,[S,D]} {7,[S,D]} -2 R!H u0 {1,[S,D]} {3,[S,D]} +1 * R!H u0 {2,[S,D,T]} {7,[S,D]} +2 R!H u0 {1,[S,D,T]} {3,[S,D]} 3 R!H u0 {2,[S,D]} {4,[S,D]} 4 R!H u0 {3,[S,D]} {5,[S,D]} 5 R!H u0 {4,[S,D]} {6,[S,D]} @@ -3164,7 +3101,7 @@ S298 = (15.9,'cal/(mol*K)'), ), shortDesc = u"""Cycloheptane ring BENSON""", - longDesc = + longDesc = u""" """, @@ -3819,6 +3756,654 @@ """, ) +entry( + index = 92, + label = "five-inringtwodouble-12", + group = +""" +1 * R!H u0 {2,[S,D]} {5,S} +2 R!H u0 {1,[S,D]} {3,D} +3 Cdd u0 {2,D} {4,D} +4 R!H u0 {3,D} {5,[S,D]} +5 R!H u0 {1,S} {4,[S,D]} +""", + thermo = u'1,2-Cyclopentadiene', + shortDesc = u"""""", + longDesc = +u""" +For now, any 5-membered ring that has at least 2 double-bonds in the 1,2 positions will use this general correction. +""", +) + +entry( + index = 93, + label = "Cyclopentyne", + group = +""" +1 * Ct u0 {2,T} {5,S} +2 Ct u0 {1,T} {3,S} +3 C u0 {2,S} {4,S} +4 C u0 {3,S} {5,S} +5 C u0 {1,S} {4,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-1.441, -1.573, -1.731, -1.812, -1.511, -1.194, -3.151],'cal/(mol*K)'), + H298 = (72.047,'kcal/mol'), + S298 = (28.96,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted to CBS-QB3 calculation""", + longDesc = +u""" + +""", +) + +entry( + index = 94, + label = "five-inringonetriple", + group = +""" +1 * R!H u0 {2,T} {5,S} +2 R!H u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,[S,D]} +4 R!H u0 {3,[S,D]} {5,[S,D,T]} +5 R!H u0 {1,S} {4,[S,D,T]} +""", + thermo = u'Cyclopentyne', + shortDesc = u"""""", + longDesc = +u""" +Use cyclopentyne ring correction for any five-membered ring containing a triple bond. +""", +) + +entry( + index = 95, + label = "six-inringonetriple", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,S} +4 R!H u0 {3,S} {5,S} +5 R!H u0 {4,S} {6,S} +6 R!H u0 {1,S} {5,S} +""", + thermo = u'cyclohexyne', + shortDesc = u"""""", + longDesc = +u""" +Use cyclohexyne correction for any 6-membered ring containing 1 triple bond +""", +) + +entry( + index = 96, + label = "six-inringonetripleonedouble-13", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,D} +4 R!H u0 {3,D} {5,S} +5 R!H u0 {4,S} {6,[S,D]} +6 R!H u0 {1,S} {5,[S,D]} +""", + thermo = u'cyclohex_1_yne_3_ene', + shortDesc = u"""""", + longDesc = +u""" +Use cyclohex_1_yne_3_ene correction for any 6-membered ring containing at least one triple bond +and one double bond in the 1,3-positions. +""", +) + +entry( + index = 171, + label = "six-inringonetripleonedouble-14", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,S} +4 R!H u0 {3,S} {5,D} +5 R!H u0 {4,D} {6,S} +6 R!H u0 {1,S} {5,S} +""", + thermo = u'cyclohex_1_yne_4_ene', + shortDesc = u"""""", + longDesc = +u""" +Use cyclohex_1_yne_4_ene correction for any 6-membered ring containing at least one triple bond +and one double bond in the 1,4-positions. +""", +) + +entry( + index = 172, + label = "six-inringonetripletwodouble-134", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,D} +4 R!H u0 {3,D} {5,D} +5 R!H u0 {4,D} {6,S} +6 R!H u0 {1,S} {5,S} +""", + thermo = u'cyclohex_1_yne_3_ene', + shortDesc = u"""""", + longDesc = +u""" +Use cyclohex_1_yne_3_ene correction for any 6-membered ring containing at least one triple bond +and two double bonds in the 1,3,4-positions. +""", +) + +entry( + index = 173, + label = "six-inringonetriplethreedouble-1345", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {2,S} {4,D} +4 R!H u0 {3,D} {5,D} +5 R!H u0 {4,D} {6,D} +6 R!H u0 {1,S} {5,D} +""", + thermo = u'cyclohex_1_yne_3_ene', + shortDesc = u"""""", + longDesc = +u""" +Use cyclohex_1_yne_3_ene correction for any 6-membered ring containing at least one triple bond +and three double bonds in the 1,3,4,5-positions. +""", +) + +entry( + index = 97, + label = "cyclohex_1_yne_3_ene", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 Cd u0 {2,S} {4,D} +4 Cd u0 {3,D} {5,S} +5 [C,Os] u0 {4,S} {6,S} +6 [C,Os] u0 {1,S} {5,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-2.292 ,-2.038, -2.856, -3.187, -2.814, -1.639,-2.564],'cal/(mol*K)'), + H298 = (48.034,'kcal/mol'), + S298 = (25.6327,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculation for cyclohex_1_yne_3_ene +""", +) + +entry( + index = 98, + label = "six-inringtwotriple-13", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 Ct u0 {2,S} {4,T} +4 Ct u0 {3,T} {5,S} +5 R!H u0 {4,S} {6,[S,D,T]} +6 R!H u0 {1,S} {5,[S,D,T]} +""", + thermo = u'1_3_cyclohexadiyne', + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Use 1_3_cyclohexadiyne correction for any six-membered ring with at least two triple bonds +""", +) + +entry( + index = 99, + label = "1,2-Cyclopentadiene", + group = +""" +1 * C u0 {2,S} {5,S} +2 Cd u0 {1,S} {3,D} +3 Cdd u0 {2,D} {4,D} +4 Cd u0 {3,D} {5,S} +5 C u0 {1,S} {4,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-3.610227533, -3.220365201, -2.9183174, -2.860732314, -2.503231358, -1.669783939, -1.310015296],'cal/(mol*K)'), + H298 = (65.85343212,'kcal/mol'), + S298 = (26.75230402,'cal/(mol*K)'), + ), + shortDesc = u"""Fitted to M06 calculation""", + longDesc = +u""" + +""", +) + +entry( + index = 153, + label = "Cyclopentatriene", + group = +""" +1 * Cd u0 {2,D} {5,S} +2 Cdd u0 {1,D} {3,D} +3 Cd u0 {2,D} {4,S} +4 Cd u0 {3,S} {5,D} +5 Cd u0 {1,S} {4,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-4.08,-4.69,-4.58,-4.25,-3.54,-3.08,-2.47],'cal/(mol*K)'), + H298 = (70.16,'kcal/mol'), + S298 = (36.76,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 isodesmic reaction approach allene + 2-butene = cyclopentatriene + 2 CH4, DHr = 220.8 kJ mol-1, exp data from NIST""", + longDesc = +u""" + +""", +) + +entry( + index = 154, + label = "cyclohexyne", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 [C,Os] u0 {2,S} {4,S} +4 [C,Os] u0 {3,S} {5,S} +5 [C,Os] u0 {4,S} {6,S} +6 [C,Os] u0 {1,S} {5,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-3.306, -2.849, -2.452, -2.229, -1.543, -0.932, -2.535],'cal/(mol*K)'), + H298 = (39.857,'kcal/mol'), + S298 = (21.862,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculation for cyclohexyne +""", +) + +entry( + index = 155, + label = "cyclohex_1_yne_4_ene", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 [C,Os] u0 {2,S} {4,S} +4 Cd u0 {3,S} {5,D} +5 Cd u0 {4,D} {6,S} +6 [C,Os] u0 {1,S} {5,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-1.431, -0.775, -1.308, -1.515, -1.294, -0.369, -1.036],'cal/(mol*K)'), + H298 = (38.484,'kcal/mol'), + S298 = (25.2137,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculation for cyclohex_1_yne_4_ene +""", +) + +entry( + index = 156, + label = "1_3_cyclohexadiyne", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 Ct u0 {2,S} {4,T} +4 Ct u0 {3,T} {5,S} +5 [C,Os] u0 {4,S} {6,S} +6 [C,Os] u0 {1,S} {5,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-1.086,-1.458,-1.692,-1.747,-1.465,-1.403,-3.712],'cal/(mol*K)'), + H298 = (103.484,'kcal/mol'), + S298 = (31.221,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculation for 1_3_cyclohexadiyne +""", +) + +entry( + index = 157, + label = "124cyclohexatriene", + group = +""" +1 Cd u0 {2,D} {6,S} +2 * Cdd u0 {1,D} {3,D} +3 Cd u0 {2,D} {4,S} +4 [Cs,Os] u0 {3,S} {5,S} +5 Cd u0 {4,S} {6,D} +6 Cd u0 {1,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-4.21,-4.32,-3.9,-3.46,-2.71,-2.25,-1.38],'cal/(mol*K)'), + H298 = (36.04,'kcal/mol'), + S298 = (26.47,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3 isodesmic reaction approach C1=CC=CCC=1 + 3 ethane + ethene = allene + 2 2-butene + propane""", + longDesc = +u""" + +""", +) + +entry( + index = 158, + label = "Cyclopropyne", + group = +""" +1 * Ct u0 {2,T} {3,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {1,S} {2,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([2.22, 1.515, 0.554, -0.319, -1.215, -1.31, -2.439],'cal/(mol*K)'), + H298 = (111.641,'kcal/mol'), + S298 = (37.345,'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + + +entry( + index = 159, + label = "six-inringthreedouble_123", + group = +""" +1 Cdd u0 {2,D} {6,D} +2 * Cdd u0 {1,D} {3,D} +3 R!H u0 {2,D} {4,[S,D]} +4 R!H u0 {3,[S,D]} {5,[S,D]} +5 R!H u0 {4,[S,D]} {6,[S,D]} +6 R!H u0 {1,D} {5,[S,D]} +""", + thermo = u'123cyclohexatriene', + shortDesc = u"""""", + longDesc = +u""" +Use 123cyclohexatriene correction for any 6-membered ring that contains at least 3 double bonds in the 1,2 and 3 +positions. +""", +) + +entry( + index = 160, + label = "123cyclohexatriene", + group = +""" +1 Cdd u0 {2,D} {6,D} +2 * Cdd u0 {1,D} {3,D} +3 Cd u0 {2,D} {4,S} +4 Cs u0 {3,S} {5,S} +5 Cs u0 {4,S} {6,S} +6 Cd u0 {1,D} {5,S} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-4.033, -4.022, -3.919, -3.755, -3.149 ,-2.312, -1.645],'cal/(mol*K)'), + H298 = (50.291,'kcal/mol'), + S298 = (27.334,'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to M06 calculations +""", +) + +entry( + index = 161, + label = "four-inringonedouble", + group = +""" +1 R!H u0 {2,D} {4,S} +2 R!H u0 {1,D} {3,S} +3 * R!H u0 {2,S} {4,S} +4 R!H u0 {1,S} {3,S} +""", + thermo = u'Cyclobutene', + shortDesc = u"""""", + longDesc = +u""" +Use cyclobutene correction for any four membered ring with one double bond +""", +) + +entry( + index = 162, + label = "four-inringtwodouble", + group = +""" +1 R!H u0 {2,D} {4,[S,D]} +2 * R!H u0 {1,D} {3,[S,D]} +3 R!H u0 {2,[S,D]} {4,D} +4 R!H u0 {1,[S,D]} {3,D} +""", + thermo = u'cyclobutadiene_13', + shortDesc = u"""""", + longDesc = +u""" +Use cyclobutadiene_13 correction for any four membered ring with at least two double bonds in the 1,3-positions +""", +) + +entry( + index = 163, + label = "cyclobutadiene_12", + group = +""" +1 R!H u0 {2,D} {4,S} +2 * R!H u0 {1,D} {3,D} +3 R!H u0 {2,D} {4,S} +4 R!H u0 {1,S} {3,S} +""", + thermo = u'cyclobutadiene_13', + shortDesc = u"""""", + longDesc = +u""" +Use cyclobutadiene_13 correction for 1,2_CBD +""", +) + +entry( + index = 164, + label = "o_benzyne", + group = +""" +1 * Ct u0 {2,T} {6,S} +2 Ct u0 {1,T} {3,S} +3 Cd u0 {2,S} {4,D} +4 Cd u0 {3,D} {5,S} +5 Cd u0 {4,S} {6,D} +6 Cd u0 {1,S} {5,D} +""", + thermo = ThermoData( + Tdata = ([300,400,500,600,800,1000,1500],'K'), + Cpdata = ([-4.003, -4.523, -5.242, -5.892, -5.423, -3.742, -3.198],'cal/(mol*K)'), + H298 = (26.527,'kcal/mol'), + S298 = (29.264,'cal/(mol*K)'), + ), + shortDesc = u"""CBS-QB3""", + longDesc = +u""" +Fitted to CBS-QB3 calculation for o_benzyne +""", +) + +entry( + index = 165, + label = "seven-inringtwodouble-12", + group = +""" +1 * Cd u0 {2,D} {7,S} +2 Cdd u0 {1,D} {3,D} +3 Cd u0 {4,S} {2,D} +4 R!H u0 {3,S} {5,[S,D]} +5 R!H u0 {6,[S,D]} {4,[S,D]} +6 R!H u0 {5,[S,D]} {7,[S,D]} +7 R!H u0 {1,S} {6,[S,D]} +""", + thermo = u'1_2_cycloheptadiene', + shortDesc = u"""""", + longDesc = +u""" +Use 1_2_cycloheptadiene correction for any seven membered ring with at least two double bonds in the 1,2-positions +""", +) + +entry( + index = 166, + label = "1_2_cycloheptadiene", + group = +""" +1 * Cd u0 {2,D} {7,S} +2 Cdd u0 {1,D} {3,D} +3 Cd u0 {4,S} {2,D} +4 C u0 {3,S} {5,S} +5 C u0 {6,S} {4,S} +6 C u0 {5,S} {7,S} +7 C u0 {1,S} {6,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-5.058, -4.616, -4.065, -3.549, -2.425, -1.185, -0.012], 'cal/(mol*K)'), + H298=(19.726, 'kcal/mol'), + S298=(17.979, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + +entry( + index = 167, + label = "seven-inringthreedouble-123", + group = +""" +1 * R!H u0 {2,D} {7,[S,D]} +2 Cdd u0 {1,D} {3,D} +3 Cdd u0 {4,D} {2,D} +4 R!H u0 {3,D} {5,[S,D]} +5 R!H u0 {6,[S,D]} {4,[S,D]} +6 R!H u0 {5,[S,D]} {7,[S,D]} +7 R!H u0 {1,[S,D]} {6,[S,D]} +""", + thermo = u'1_2_3_cycloheptatriene', + shortDesc = u"""""", + longDesc = +u""" +Use 1_2_3_cycloheptatriene correction for any seven membered ring with at least three double bonds in the 1,2 and 3-positions +""", +) + +entry( + index = 168, + label = "1_2_3_cycloheptatriene", + group = +""" +1 * Cd u0 {2,D} {7,S} +2 Cdd u0 {1,D} {3,D} +3 Cdd u0 {4,D} {2,D} +4 Cd u0 {3,D} {5,S} +5 C u0 {6,S} {4,S} +6 C u0 {5,S} {7,S} +7 C u0 {1,S} {6,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-4.854, -4.544, -4.148, -3.726, -2.801, -1.852, -0.8], 'cal/(mol*K)'), + H298=(25.76, 'kcal/mol'), + S298=(22.122, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + +entry( + index = 169, + label = "seven-inringonetriple", + group = +""" +1 * Ct u0 {2,T} {7,S} +2 Ct u0 {1,T} {3,S} +3 R!H u0 {4,[S,D]} {2,S} +4 R!H u0 {3,[S,D]} {5,[S,D]} +5 R!H u0 {6,[S,D]} {4,[S,D]} +6 R!H u0 {5,[S,D]} {7,[S,D]} +7 R!H u0 {1,S} {6,[S,D]} +""", + thermo = u'cycloheptyne', + shortDesc = u"""""", + longDesc = +u""" +Use cycloheptyne correction for any seven membered ring with at least one triple bond +""", +) + +entry( + index = 170, + label = "cycloheptyne", + group = +""" +1 * Ct u0 {2,T} {7,S} +2 Ct u0 {1,T} {3,S} +3 C u0 {4,S} {2,S} +4 C u0 {3,S} {5,S} +5 C u0 {6,S} {4,S} +6 C u0 {5,S} {7,S} +7 C u0 {1,S} {6,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-4, -3.568, -3.106, -2.646, -1.582, -0.695, -1.916], 'cal/(mol*K)'), + H298=(24.448, 'kcal/mol'), + S298=(17.688, 'cal/(mol*K)'), + ), + shortDesc = u"""""", + longDesc = +u""" +Fitted to CBS-QB3 calculations +""", +) + tree( """ L1: Ring @@ -3830,6 +4415,7 @@ L3: Cyclopropene2 L3: Cyclopropadiene L3: Cyclopropadiene2 + L3: Cyclopropyne L3: oxirene L3: Cyclopropatriene L3: Ethylene_oxide @@ -3850,18 +4436,18 @@ L3: 12Methylenecyclopropane L2: FourMember L3: Cyclobutane - L3: Cyclobutene - L3: Cyclobutene2 - L3: cyclobutadiene - L3: Cyclobutadiene2 - L3: Cyclobutadiene3 L3: 34methylenecyclobutene + L3: dioxerene + L3: Oxetene + L3: four-inringonedouble + L4: Cyclobutene L3: Oxetane - L3: Oxetene L3: Beta-Propiolactone L3: Cyclobutanone L3: 12dioxetane - L3: dioxerene + L3: four-inringtwodouble + L4: cyclobutadiene_13 + L3: cyclobutadiene_12 L3: thietane L3: 1,2-dithietane L3: 1,3-dithietane @@ -3876,6 +4462,12 @@ L3: Cyclopentane L3: Cyclopentene L3: Cyclopentadiene + L3: five-inringtwodouble-12 + L4: 1,2-Cyclopentadiene + L3: five-inringthreedouble-124 + L4: Cyclopentatriene + L3: five-inringonetriple + L4: Cyclopentyne L3: Tetrahydrofuran L3: 2,3-Dihydrofuran L3: 1,3-Dioxolane @@ -3905,7 +4497,6 @@ L3: 3-Methylenecyclopentene L3: 4-Methylenecyclopentene L3: 12methylenecyclopentane - L3: Cyclopentatriene L2: SixMember L3: sixnosidedouble L4: Cyclohexane @@ -3940,7 +4531,10 @@ L3: six-inringtwodouble-14 L4: 1,4-Cyclohexadiene L4: 14dioxin - L3: six-inringthreedouble + L3: six-inringthreedouble_124 + L4: 124cyclohexatriene + L3: six-inringthreedouble_123 + L4: 123cyclohexatriene L3: six-inringtwodouble-12 L3: six-oneside-twoindoubles-25 L4: 25cyclohexadienone @@ -3956,6 +4550,17 @@ L4: pbenzoquinone L4: pxylene L3: 3,4-dimethylenecyclohexene + L3: six-inringonetriple + L4: cyclohexyne + L3: six-inringonetripleonedouble-13 + L4: cyclohex_1_yne_3_ene + L4: o_benzyne + L3: six-inringonetripleonedouble-14 + L4: cyclohex_1_yne_4_ene + L3: six-inringonetripletwodouble-134 + L3: six-inringonetriplethreedouble-1345 + L3: six-inringtwotriple-13 + L4: 1_3_cyclohexadiyne L2: SevenMember L3: Cycloheptane L3: Cycloheptene @@ -3963,7 +4568,13 @@ L3: 1,3,5-Cycloheptatriene L3: Cycloheptanone L3: 1,4-Cycloheptadiene - L3: 1,2,4,6-Cycloheptatetraene + L3: seven-inringtwodouble-12 + L4: 1_2_cycloheptadiene + L4: 1,2,4,6-Cycloheptatetraene + L3: seven-inringthreedouble-123 + L4: 1_2_3_cycloheptatriene + L3: seven-inringonetriple + L4: cycloheptyne L3: heptasulfur L3: oxepane L2: EightMember