Add rates to 1+2_cycloaddition and 1,2_insertion

nyee · nyee · commit abee4d8773a7 · 2013-09-09T17:24:59.000-04:00
Rates taken from Polino et al. Paper not available to public yet
so comment about its methods will be added later.

Also these the1+2_cycloaddition family does not really work
correctly without additional hard-coded changes. These are
still being tested.
diff --git a/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/dictionary.txt b/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/dictionary.txt
@@ -15,24 +15,27 @@
 //
 // 2/3/2003
 
+// Changed carbene definitions to be singlet, as far as I know triplet carbene cannot react this way without intersystem conversion.
+// At least all the rates from Polino are for singlet carbene only. -nyee
+
 elec_def
 Union {carbene, me_carbene, dime_carbene, ph_carbene, o_atom}
 
 carbene
-1 *3 C 2 {2,S} {3,S}
+1 *3 C 2S {2,S} {3,S}
 2 H 0 {1,S}
 3 H 0 {1,S}
 
 me_carbene
-1 *3 C 2 {2,S} {3,S}
+1 *3 C 2S {2,S} {3,S}
 2 Cs 0 {1,S} {4,S} {5,S} {6,S}
 3 H 0 {1,S}
 4 H 0 {2,S}
 5 H 0 {2,S}
 6 H 0 {2,S}
 
 dime_carbene
-1 *3 C 2 {2,S} {3,S}
+1 *3 C 2S {2,S} {3,S}
 2 Cs 0 {1,S} {4,S} {5,S} {6,S}
 3 Cs 0 {1,S} {7,S} {8,S} {9,S}
 4 H 0 {2,S}
@@ -43,7 +46,7 @@ dime_carbene
 9 H 0 {3,S}
 
 ph_carbene
-1 *3 C 2 {2,S} {3,S}
+1 *3 C 2S {2,S} {3,S}
 2 Cb 0 {1,S} {4,B} {5,B}
 3 H 0 {1,S}
 4 Cb 0 {2,B} {6,B}
@@ -56,11 +59,11 @@ o_atom
 1 *3 O 2 
 
 multiplebond
-1 *1 {Cd,CO} 0 {2,D}
-2 *2 {Cd,O} 0 {1,D}
+//Union {mb_carbonyl, mb_db, mb_tb, mb_benzb}
+Union {mb_carbonyl, mb_db, mb_tb}
 
 mb_carbonyl
-1 *1 CO 0 {2,D}
+1 *1 {CO,Cdd} 0 {2,D}
 2 *2 O 0 {1,D}
 
 mb_carbonyl_2H
@@ -100,8 +103,8 @@ mb_carbonyl_DeDe
 4 {Cd,Ct,Cb,CO} 0 {1,S}
 
 mb_db
-1 *1 Cd 0 {2,D}
-2 *2 Cd 0 {1,D}
+1 *1 {Cd,Cdd} 0 {2,D}
+2 *2 {Cd,Cdd} 0 {1,D}
 
 mb_db_unsub
 1 *1 Cd 0 {2,D} {3,S} {4,S}
@@ -310,3 +313,43 @@ mb_db_tetrasub_fourDe
 4 {Cd,Ct,Cb,CO} 0 {1,S}
 5 {Cd,Ct,Cb,CO} 0 {2,S}
 6 {Cd,Ct,Cb,CO} 0 {2,S}
+
+mb_db_dbSub
+1 *1 Cdd 0 {2,D} {3,D}
+2 *2 Cd 0 {1,D}
+3 {Cd,Cdd} 0 {1,D}
+
+mb_tb
+1 *1 Ct 0 {2,T}
+2 *2 Ct 0 {1,T}
+
+mb_tb_unsub
+1 *1 Ct 0 {2,T} {3,S}
+2 *2 Ct 0 {1,T} {4,S}
+3 H 0 {1,S}
+4 H 0 {2,S}
+
+mb_tb_monosub
+1 *1 Ct 0 {2,T} {3,S}
+2 *2 Ct 0 {1,T} {4,S}
+3 R!H 0 {1,S}
+4 H 0 {2,S}
+
+mb_tb_monosub_Nd
+1 *1 Ct 0 {2,T} {3,S}
+2 *2 Ct 0 {1,T} {4,S}
+3 {Cs,Os} 0 {1,S}
+4 H 0 {2,S}
+
+mb_tb_disub
+1 *1 Ct 0 {2,T} {3,S}
+2 *2 Ct 0 {1,T} {4,S}
+3 R!H 0 {1,S}
+4 R!H 0 {2,S}
+
+mb_tb_disub_twoNd
+1 *1 Ct 0 {2,T} {3,S}
+2 *2 Ct 0 {1,T} {4,S}
+3 {Cs,Os} 0 {1,S}
+4 {Cs,Os} 0 {2,S}
+
diff --git a/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/rateLibrary.txt b/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/rateLibrary.txt
@@ -12,6 +12,9 @@ Arrhenius_EP
 // [195] Herbrechtsmeier, P. Reactions of O(3P) Atoms with Unsaturated C3 Hydrocarbons. In Combust. Inst. European Symp., 1973; pp13.
 // [196] Smith, I.W.M. Trans. Faraday Soc. 1968, 64, 378.
 // [197] Cvetanovic, R. J. Chem. Phys. 1959, 30, 19.
+// reminder to self to estimate errors add more to citation when that info becomes available -nyee
+// Polino D., J. Phys. Chem. A, 2013
+
 
 // rate constants from rate_library_4.txt, Cath, 03/07/28
 
@@ -26,3 +29,11 @@ Arrhenius_EP
 583.		o_atom		mb_db_onecdisub_Nd	298-410		7.6E+12		0		0		0.10	*1.2	0		0		0.40	4		Smith [196]
 584.		o_atom		mb_db_twocdisub_Nd	298			1.54E+13	0		0		0		0		0		0		0		4		Cvetanovic [197] 
 585.		o_atom		mb_db_tetrasub_Nd	298			3.18E+13	0		0		0		*1.2	0		0		0		4		Cvetanovic [197] 
+586.		carbene		mb_tb_unsub			200-2000	1.77E+15	-0.662	0		3.77E-2	0		0		0		0		2		Polino [carbene,acetylene]
+587.		carbene		mb_db_unsub			200-2000	1.24E+15	-0.684	0		-8.05E-2	0	0		0		0		2		Polino [carbene,ethene]
+588.		carbene		mb_tb_monosub_Nd	200-2000	4.50E+15	-0.708	0		-2.67E-2	0	0		0		0		2		Polino [carbene,propyne]
+589.		carbene		mb_db_monosub_Nd	200-2000	5.00E+15	-0.826	0		-0.09	0		0		0		0		2		Polino [carbene,propene]
+590.		carbene		mb_db_dbSub			200-2000	6.38E+14	-0.562	0		-0.133	0		0		0		0		2		Polino [carbene,propadiene]
+591.		carbene		mb_tb_disub_twoNd	200-2000	4.70E+15	-0.823	0		2.3E-2	0		0		0		0		2		Polino [carbene,2-butyne]
+592.		carbene		mb_db_monosub_De	200-2000	1.85E+15	-0.700	0		-6.72E-2	0	0		0		0		2		Polino [carbene,1,3-butadiene]
+	
diff --git a/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/tree.txt b/databases/RMG_database/kinetics_groups/1+2_Cycloaddition/tree.txt
@@ -21,7 +21,7 @@ L1: multiplebond
            L3: mb_db_unsub
            L3: mb_db_monosub
                L4: mb_db_monosub_Nd
-               L4: mb_db_monosub_De
+               L4: mb_db_monosub_De	
            L3: mb_db_onecdisub
                L4: mb_db_onecdisub_Nd
                L4: mb_db_onecdisub_oneDe
@@ -31,7 +31,7 @@ L1: multiplebond
                L4: mb_db_twocdisub_oneDe
                L4: mb_db_twocdisub_twoDe
            L3: mb_db_trisub
-	       L4: mb_db_trisub_Nd
+			   L4: mb_db_trisub_Nd
                L4: mb_db_trisub_oneMDe
                L4: mb_db_trisub_oneDDe
                L4: mb_db_trisub_onectwoDe
@@ -44,4 +44,12 @@ L1: multiplebond
                L4: mb_db_tetrasub_twoctwoDe
                L4: mb_db_tetrasub_threeDe
                L4: mb_db_tetrasub_fourDe
+			L3: mb_db_dbSub
+	 L2: mb_tb
+		   L3: mb_tb_unsub
+		   L3: mb_tb_monosub
+			   L4: mb_tb_monosub_Nd
+		   L3: mb_tb_disub
+			   L4: mb_tb_disub_twoNd
+	
  
diff --git a/databases/RMG_database/kinetics_groups/1,2_Insertion/dictionary.txt b/databases/RMG_database/kinetics_groups/1,2_Insertion/dictionary.txt
@@ -1,5 +1,13 @@
 //f11 : carbon monoxide insertion reaction (1,2-insertion) C.D.W. 01/29/03
 
+Y_birad
+Union{carbene,CO_birad}
+
+carbene
+1 *1 C 2S {2,S}, {3,S}
+2 H 0 {1,S}
+3 H 0 {1,S}
+
 CO_birad
 1 *1 C 2 {2,D}
 2    O 0 {1,D}
@@ -8,7 +16,7 @@ RR'
 Union {R_H,R_R'}
 
 R_H
-1 *2 {H,Cs,Cd,Cb,O,Sis,Sid} 0 {2,S}
+1 *2 {H,Cs,Cd,Cb,Ct,O,Sis,Sid} 0 {2,S}
 2 *3 H 0 {1,S}
 
 H2
@@ -57,6 +65,20 @@ C_pri/De
 4 H 0 {1,S}
 5 {Cd,Ct,Cb,CO} 0 {1,S}
 
+C_pri/Ct
+1 *2 C 0 {2,S}, {3,S}, {4,S}, {5,S}
+2 *3 H 0 {1,S}
+3 H 0 {1,S}
+4 H 0 {1,S}
+5 Ct 0 {1,S}
+
+C_pri/Cd
+1 *2 C 0 {2,S}, {3,S}, {4,S}, {5,S}
+2 *3 H 0 {1,S}
+3 H 0 {1,S}
+4 H 0 {1,S}
+5 Cd 0 {1,S}
+
 C_sec
 1 *2 C 0 {2,S}, {3,S}, {4,S}, {5,S}
 2 *3 H 0 {1,S}
@@ -209,6 +231,14 @@ Cd_pri
 3 *3 H 0 {1,S}
 4 H 0 {1,S}
 
+ethene
+1 *2 C 0 {2,D}, {3,S}, {4,S}
+2 C 0 {1,D} {5,S} {6,S}
+3 *3 H 0 {1,S}
+4 H 0 {1,S}
+5 H 0 {2,S}
+6 H 0 {2,S}
+
 Cd_sec
 1 *2 C 0 {2,D}, {3,S}, {4,S}
 2 C 0 {1,D}
@@ -239,9 +269,19 @@ Cb_H
 3 {Cb,Cbf} 0 {1,B}
 4 *3 H 0 {1,S} 
 
+Ct_H
+1 *2 Ct 0 {2,S}
+2 *3 H 0 {1,S}
+
+acetylene
+1 *2 Ct 0 {2,S} {3,T}
+2 *3 H 0 {1,S}
+3 Ct 0 {1,T} {4,S}
+4 H 0 {3,S}
+
 R_R'
 1 *2 {Cs,Sis} 0 {2,S}, {3,S}, {4,S}, {5,S}
-2 *3 {Cs,Cd,Cb,Sis,Sid} 0 {1,S}
+2 *3 {Cs,Cd,Cb,Ct,Sis,Sid} 0 {1,S}
 3 H 0 {1,S}
 4 H 0 {1,S}
 5 H 0 {1,S}
diff --git a/databases/RMG_database/kinetics_groups/1,2_Insertion/rateLibrary.txt b/databases/RMG_database/kinetics_groups/1,2_Insertion/rateLibrary.txt
@@ -7,6 +7,7 @@ Arrhenius_EP
 // Catherina Wijaya Thesis pg 130
 // [87] Sumathi et al (2003) - CBS-QB3 calculations. 
 // rate constants from rate_library_4.txt, Cath, 03/07/28
+// Polino, D. JPCA 2013 -Note to self, add error and better citation when info available -nyee
 
 //No.	CO_birad	RR'					Temp.		A			N		a		E0		DA		Dn		Da		DE0		Rank	Comments
 553.	CO_birad	RR'					300-1500	1E+05		2		0		80		0		0		0		0		0 		Default
@@ -16,5 +17,12 @@ Arrhenius_EP
 557.	CO_birad	C_pri/NonDeC		300-1500	9.14E+04	2.53	0		85.5	0		0		0		0		2		[87]CBS-QB3 calculations from Sumathi 2003.
 558.	CO_birad	C/H2/NonDeC			300-1500	7.66E+05	2.07	0		82.2	0		0		0		0		2		[87]CBS-QB3 calculations from Sumathi 2003.
 559.	CO_birad	C/H/Cs3				300-1500	8.89E+07	1.51	0		79.2	0		0		0		0		2		[87]CBS-QB3 calculations from Sumathi 2003.
-5600.	CO_birad	CsO_H	300-2000	0.127	3.7	0.0	53.36	0.0	0.0	0.0	0.0	2	CBS-QB3 calculations by Franklin, 2010	
-
+560.	CO_birad	CsO_H				300-2000	0.127		3.7		0.0		53.36	0.0		0.0		0.0		0.0		2		CBS-QB3 calculations by Franklin, 2010	
+561.	carbene		ethene				250-2000	6.63E+11	0.0073	0		-1.045	0		0		0		0		2		Polino
+562.	carbene		Cd_pri				250-2000	3.50E+10	0.465	0		-1.742	0		0		0		0		2		Polino, [carbene,propadiene] as model reaction
+563.	carbene		acetylene			250-2000	1.65E+7		1.475	0		-1.651	0		0		0		0		2		Polino
+564.	carbene		Ct_H				250-2000	1.02E+8		1.249	0		-2.214	0		0		0		0		2		Polino [carbene, propyne] as model reaction
+565.	carbene		C_pri/Cd			250-2000	6.62E+12	0.324	0		-0.935	0		0		0		0		2		Polino [carbene,propene]
+566.	carbene		C_pri/Ct			250-2000	2.47E+9		0.797	0		-1.174	0		0		0		0		2		Polino [carbene,2-butyne]
+567.	carbene		Cd/H/NonDeC			250-2000	1.07E+13	-0.274	0		-0.686	0		0		0		0		2		Polino [carbene,propene]
+568.	carbene		Cd/H/OneDe			250-200		1.84E+10	0.498	0		-1.758	0		0		0		0		2		Polino [carbene,1,3-butadiene]
diff --git a/databases/RMG_database/kinetics_groups/1,2_Insertion/reactionAdjList.txt b/databases/RMG_database/kinetics_groups/1,2_Insertion/reactionAdjList.txt
@@ -9,7 +9,7 @@
 
 // f11 1,2_insertion
 
-CO_birad + RR' -> R_CO_R'
+Y_birad + RR' -> R_CO_R'
 
 forward
 reverse(f12): 1,1_Elimination
diff --git a/databases/RMG_database/kinetics_groups/1,2_Insertion/tree.txt b/databases/RMG_database/kinetics_groups/1,2_Insertion/tree.txt
@@ -6,8 +6,12 @@
 // "Ketone" for this reaction family.  The other reactions seem not to be
 // favourable.Especially with CH2T and Oat it is not possible.  It has to be
 // singlet. I now feel it is not necessary.
+// note from nyee: I'm reinstating at least CH2(singlet) seeing as I have a paper with some of the rates. See rateLib for reference
 
-L1: CO_birad
+
+L1: Y_birad
+	L2: CO_birad
+	L2: carbene
 
 L1: RR'
 	L2: R_H
@@ -18,6 +22,8 @@ L1: RR'
 				L5: C_pri/NonDeC
 				L5: C_pri/NonDeO
 				L5: C_pri/De
+					L6: C_pri/Cd
+					L6: C_pri/Ct
 			L4: C_sec
 				L5: C/H2/NonDeC
 				L5: C/H2/NonDeO
@@ -40,13 +46,16 @@ L1: RR'
 				L5: C/H/ThreeDe
 	    L3: Cd_H
 			L4: Cd_pri
+				L5: ethene
 			L4: Cd_sec
 				L5: Cd/H/NonDeC
 				L5: Cd/H/NonDeO
 				L5: Cd/H/OneDe
 	    L3: Cb_H
 	    L3: RO_H
                    L4: CsO_H	
+		L3: Ct_H
+			L4: acetylene
 	L2 : R_R'
 		L3: Cs_Cs
 			L4: C_methyl_C_methyl
