Add nitrogen BEP rules

input/kinetics/families/Surface_Abstraction/groups.py

@@ -614,3 +614,26 @@
         L3: *-O-N
 """
 )
+
+forbidden(
+    label = "Surf_Atom",
+    group =
+"""
+1 *4 R   ux px c0 {2,S} {4,[S,D,T]}
+2 *3 R!H ux px c0 {1,S} {3,[S,D,T]}
+3 *5 Xo  u0 p0 c0 {2,[S,D,T]}
+4 Xo u0 {1,[S,D,T]}
+""",
+)
+
+forbidden(
+    label = "beta_Surf_Atom",
+    group =
+"""
+1 *4 R   ux px c0 {2,S} {4,[S,D,T]}
+2 *3 R!H ux px c0 {1,S} {3,[S,D,T]}
+3 *5 Xo  u0 p0 c0 {2,[S,D,T]}
+4 R u0 {1,[S,D,T]} {5,[S,D,T]} 
+5 Xo u0 c0 {4,[S,D,T]} 
+""",
+)

input/kinetics/families/Surface_Abstraction/rules.py

@@ -26,7 +26,7 @@
 )
 
 entry(
-    index = 1,
+    index = 2,
     label = "Abstracting;*R-H",
     kinetics = SurfaceArrheniusBEP(
         A = (4.18e17, 'm^2/(mol*s)'),
@@ -91,7 +91,7 @@
     kinetics = SurfaceArrheniusBEP(
         A = (4.18e17, 'm^2/(mol*s)'),
         n = 0,
-        alpha =0.37,
+        alpha = 0.37,
         E0 = (99.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
@@ -103,4 +103,50 @@
 BEP values from "Quantifying the Impact of Parametric Uncertainty on Automatic Mechanism Generation for CO2 Hydrogenation on Ni(111)", Kreitz et al., JACS Au, 2021, 1, 10, 1656-1673 DOI:10.1021/jacsau.1c00276
 Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
+)
+
+entry(
+    index = 6,
+    label = "Abstracting;*N-H",
+    kinetics = SurfaceArrheniusBEP(
+        A = (3.06e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.93,
+        E0 = (101, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data from Ma and Schneider: 
+
+https://doi.org/10.1021/acscatal.8b04251
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)
+
+entry(
+    index = 7,
+    label = "N=*;*R-H",
+    kinetics = SurfaceArrheniusBEP(
+        A = (3.06e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.0768,
+        E0 = (101, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data from Ma and Schneider: 
+
+https://doi.org/10.1021/acscatal.8b04251
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)

input/kinetics/families/Surface_Abstraction_Beta/groups.py

@@ -61,7 +61,7 @@
     group =
 """
 1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
-2 *2 C u0 px c0 {1,S} {3,S}
+2 *2 C u0 p0 c0 {1,S} {3,S}
 3 *3 H   u0 {2,S}
 4 *5 Xo  u0 {1,[D,T]}
 """,
@@ -131,7 +131,7 @@
     group =
 """
 1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
-2 *2 R!H u0 px c0 {1,S} {3,S}
+2 *2 R!H u0 p[0,2] c0 {1,S} {3,S}
 3 *3 H   u0 {2,S}
 4 *5 Xo  u0 {1,[D,T]}
 """,
@@ -164,6 +164,33 @@
     kinetics = None,
 )
 
+entry(
+    index = 12,
+    label = "R-R-N",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
+2 *2 R!H u0 p[0,2] c0 {1,S} {3,S}
+3 *3 N   u0 p1 {2,S}
+4 *5 Xo  u0 {1,[D,T]}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 13,
+    label = "R-N-R",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
+2 *2 N u0 p1 c0 {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,[D,T]}
+""",
+    kinetics = None,
+)
+
+
 tree(
 """
 L1: Abstracting
@@ -175,8 +202,47 @@
 L1: Donating
     L2: R-R-H
         L3: R-C-H
-	   L4: R-CH3
+	        L4: R-CH3
         L3: R-O-H
+    L2: R-R-N
+    L2: R-N-R
 """
 )
 
+forbidden(
+    label = "Surf_Atom1",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
+2 *2 R!H u0 px c0 {1,S} {3,S}
+3 *3 R   u0 {2,S} {5,[S,D,T]}
+4 *5 Xo  u0 {1,[D,T]}
+5 Xo u0 {3,[S,D,T]}
+""",
+)
+
+forbidden(
+    label = "Surf_Atom2",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
+2 *2 R!H u0 px c0 {1,S} {3,S} {5,[S,D]}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,[D,T]}
+5 Xo u0 {2,[S,D]}
+""",
+)
+
+forbidden(
+    label = "Surf_beta",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,[D,T]}
+2 *2 R!H u0 px c0 {1,S} {3,S}
+3 *3 R   u0 {2,S} {5,[S,D,T]}
+4 *5 Xo  u0 {1,[D,T]}
+5 R u0 {3,[S,D,T]} {6,[S,D,T]}
+6 Xo u0 {5,[S,D,T]}
+""",
+)
+

input/kinetics/families/Surface_Abstraction_Beta/rules.py

@@ -12,7 +12,7 @@
     kinetics = SurfaceArrheniusBEP(
         A = (4.18e17, 'm^2/(mol*s)'),
         n = 0.,
-        alpha =0.94,
+        alpha = 0.94,
         E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
@@ -32,7 +32,7 @@
     kinetics = SurfaceArrheniusBEP(
         A = (4.18e17, 'm^2/(mol*s)'),
         n = 0.,
-        alpha =0.94,
+        alpha = 0.94,
         E0 = (129.3, 'kJ/mol'),
         Tmin = (200, 'K'),
         Tmax = (3000, 'K'),
@@ -62,4 +62,70 @@
 BEP values from "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt", Sutton et al., The Journal of Physical Chemistry C, 2013, 117, 4691-4706, DOI:10.1021/jp312593u
 From Table 7 includes beta and alpha position. Pre-exponential coefficient is calculated from 1e13 s^-1 (standard guess from transition state theory) divided by 2.39e-9 mol cm^-2 (surface site density of Pt(111)
 """
-)
+)
+
+entry(
+    index = 4,
+    label = "Abstracting;R-R-N",
+    kinetics = SurfaceArrheniusBEP(
+        A = (2.20e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)
+
+entry(
+    index = 5,
+    label = "Abstracting;R-N-R",
+    kinetics = SurfaceArrheniusBEP(
+        A = (2.20e21, 'cm^2/(mol*s)'),
+        n = 0,
+        alpha = 0.52,
+        E0 = (126, 'kJ/mol'),
+        Tmin = (200, 'K'),
+        Tmax = (3000, 'K'),
+    ),
+    rank = 0,
+    shortDesc = u"""Default""",
+    longDesc = u"""
+This BEP is created from a mixture of data in literature taken from the following papers: 
+
+Ma and Schneider
+https://doi.org/10.1021/acscatal.8b04251
+
+Gomez-Díaz and Lopez
+https://pubs.acs.org/doi/10.1021/jp1093349
+
+Farberow et al.
+https://doi.org/10.1021/cs500668k
+
+Deng et al.
+https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f
+
+and the current manuscript in progress by Badger et al. looking at the effects
+of NO on the light out curves for hydrocarbons.
+"""
+)

input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py

@@ -107,6 +107,32 @@
     kinetics = None,
 )
 
+entry(
+    index = 7,
+    label = "R-N-R",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,S}
+2 *2 N u0 p1 c0 {1,S} {3,S}
+3 *3 R   u0 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
+entry(
+    index = 8,
+    label = "R-R-N",
+    group =
+"""
+1 *1 R!H u0 px c0 {2,S} {4,S}
+2 *2 R!H u0 px c0 {1,S} {3,S}
+3 *3 N   u0 p1 {2,S}
+4 *5 Xo  u0 {1,S}
+""",
+    kinetics = None,
+)
+
 tree(
 """
 L1: Abstracting
@@ -115,28 +141,45 @@
     L2: R-C-H
 	L3: R-CH3
     L2: R-O-H
+    L2: R-R-N
+    L2: R-N-R
 """
 )
 
 forbidden(
-    label = "Donating_Bidentate",
+    label = "Surface_atom1",
     group =
 """
 1 *1 R!H u0 px cx {2,S} {4,S}
 2 *2 R   u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S} {5,[S,D,T]}
+4 *5 Xo  u0 {1,S}
+5    Xo  u0 {3,[S,D,T]} 
+"""
+)
+
+forbidden(
+    label = "Surface_atom2",
+    group =
+"""
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R   u0 px cx {1,S} {3,S} {5,[S,D,T]}
 3 *3 R   u0 {2,S}
 4 *5 Xo  u0 {1,S}
-5    Xo  u0 
+5    Xo  u0 {2,[S,D,T]}
 """
 )
 
 forbidden(
-    label="Abstracting_Bidentate",
+    label = "Surface_beta",
     group =
 """
-1 *6 Xo  u0 {2,D}
-2 *4 R!H u0 px cx {1,D}	
-3    Xo  u0 
+1 *1 R!H u0 px cx {2,S} {4,S}
+2 *2 R   u0 px cx {1,S} {3,S}
+3 *3 R   u0 {2,S} {5,[S,D,T]}
+4 *5 Xo  u0 {1,S}
+5 R!H u0 {3,[S,D,T]} [6,[S,D,T]}
+6 Xo u0 {5,[S,D,T]}
 """
 )