diff --git a/input/kinetics/families/Surface_Abstraction/groups.py b/input/kinetics/families/Surface_Abstraction/groups.py index f78b040d28..d7183c0d97 100644 --- a/input/kinetics/families/Surface_Abstraction/groups.py +++ b/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]} +""", +) diff --git a/input/kinetics/families/Surface_Abstraction/rules.py b/input/kinetics/families/Surface_Abstraction/rules.py index e14329048d..0b36319871 100644 --- a/input/kinetics/families/Surface_Abstraction/rules.py +++ b/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) """ -) \ No newline at end of file +) + +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. +""" +) diff --git a/input/kinetics/families/Surface_Abstraction_Beta/groups.py b/input/kinetics/families/Surface_Abstraction_Beta/groups.py index c49b8b72cf..fd188534a6 100755 --- a/input/kinetics/families/Surface_Abstraction_Beta/groups.py +++ b/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]} +""", +) + diff --git a/input/kinetics/families/Surface_Abstraction_Beta/rules.py b/input/kinetics/families/Surface_Abstraction_Beta/rules.py index c2cfcf8b4f..9d22e8104b 100644 --- a/input/kinetics/families/Surface_Abstraction_Beta/rules.py +++ b/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) """ -) \ No newline at end of file +) + +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. +""" +) diff --git a/input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py b/input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py index 09b2237ed7..b9fede30e8 100755 --- a/input/kinetics/families/Surface_Abstraction_Beta_vdW/groups.py +++ b/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]} """ ) diff --git a/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py index 09444ba85d..83a4107778 100755 --- a/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py +++ b/input/kinetics/families/Surface_Abstraction_Beta_vdW/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'), @@ -31,7 +31,7 @@ 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'), @@ -50,8 +50,27 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.65, - E0 = (15.4, 'kJ/mol'), + alpha = 0.94, + E0 = (129.3, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +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 +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-CH3", + kinetics = SurfaceArrheniusBEP( + A = (1.393e17, 'm^2/(mol*s)'), + n = 0., + alpha = 0.94, + E0 = (129.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), @@ -60,5 +79,92 @@ longDesc = u""" 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 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) +Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) +""" +) + +entry( + index = 5, + label = "O;R-CH3", + kinetics = SurfaceArrheniusBEP( + A = (1.393e17, 'm^2/(mol*s)'), + n = 0., + alpha = 0.94, + E0 = (129.3, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +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 +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) +Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) +""" +) + +entry( + index = 6, + label = "Abstracting;R-R-N", + kinetics = SurfaceArrheniusBEP( + A = (5.20e21, '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 = 7, + label = "Abstracting;R-N-R", + kinetics = SurfaceArrheniusBEP( + A = (5.20e21, '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. """ -) \ No newline at end of file +) diff --git a/input/kinetics/families/Surface_Abstraction_vdW/groups.py b/input/kinetics/families/Surface_Abstraction_vdW/groups.py index f56834a142..6c70396540 100644 --- a/input/kinetics/families/Surface_Abstraction_vdW/groups.py +++ b/input/kinetics/families/Surface_Abstraction_vdW/groups.py @@ -548,3 +548,13 @@ L3: *#N """ ) + +forbidden( + label = "surf", + group = +""" +1 *1 Xv u0 p0 c0 +2 *2 R!H u0 px c0 {3,S} +3 *3 Xo u0 p0 c0 {2,S} +""", +) diff --git a/input/kinetics/families/Surface_Abstraction_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_vdW/rules.py index 0002685b56..2623d09e6d 100644 --- a/input/kinetics/families/Surface_Abstraction_vdW/rules.py +++ b/input/kinetics/families/Surface_Abstraction_vdW/rules.py @@ -14,7 +14,7 @@ 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'), @@ -26,4 +26,56 @@ 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) """ -) \ No newline at end of file +) + +entry( + index = 2, + label = "AdsorbateVdW;*N", + kinetics = SurfaceArrheniusBEP( + A = (5.20e21, '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 = 3, + label = "O-R;*N", + kinetics = SurfaceArrheniusBEP( + A = (5.09e21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.305, + E0 = (48.5, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +This BEP is created from data from Ma and Schneider: +https://doi.org/10.1021/acscatal.8b04251 +""" +) diff --git a/input/kinetics/families/Surface_Bidentate_Dissociation/groups.py b/input/kinetics/families/Surface_Bidentate_Dissociation/groups.py index 1e89f93285..25af8faa3b 100644 --- a/input/kinetics/families/Surface_Bidentate_Dissociation/groups.py +++ b/input/kinetics/families/Surface_Bidentate_Dissociation/groups.py @@ -30,18 +30,72 @@ label = "Combined", group = """ -1 *1 R!H u0 {2,[S]} {3,[S,D,T]} -2 *2 R!H u0 {1,[S]} {4,[S,D,T]} +1 *1 R!H u0 c0 {2,[S]} {3,[S,D,T]} +2 *2 R!H u0 c0 {1,[S]} {4,[S,D,T]} 3 *3 Xo u0 {1,[S,D,T]} 4 *4 Xo u0 {2,[S,D,T]} """, kinetics = None, ) +entry( + index = 2, + label = "N-C", + group = +""" +1 *1 N u0 p1 c0 {2,S} {3,[S,D,T]} +2 *2 C u0 p0 c0 {1,S} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 *4 Xo u0 {2,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 3, + label = "C-N", + group = +""" +1 *1 C u0 p0 c0 {2,S} {3,[S,D,T]} +2 *2 N u0 p1 c0 {1,S} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 *4 Xo u0 {2,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 4, + label = "R-N", + group = +""" +1 *1 R!H u0 c0 {2,[S]} {3,[S,D,T]} +2 *2 N u0 p1 c0 {1,[S]} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 *4 Xo u0 {2,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 5, + label = "N-R", + group = +""" +1 *1 N u0 p1 c0 {2,[S]} {3,[S,D,T]} +2 *2 R!H u0 c0 {1,[S]} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 *4 Xo u0 {2,[S,D,T]} +""", + kinetics = None, +) tree( """ L1: Combined + L2: R-N + L3: C-N + L2: N-R + L3: N-C """ ) - diff --git a/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py b/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py index e646edb87d..e2216f48ac 100644 --- a/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py +++ b/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py @@ -9,21 +9,108 @@ index = 1, label = "Combined", kinetics = SurfaceArrheniusBEP( - A = (1.187E12, '1/s'), + A = (4.55E13, '1/s'), n = 0.0, - alpha = 0.842, - E0 = (145.69, 'kJ/mol'), + alpha = 1.17, + E0 = (167, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", longDesc = u""" -A factors are averages of training reactions 1-4 and the reverse direction of training reactions 5-7, -and alpha and E0 are BEP parameters from training reactions 1-4 and the reverse of training reactions 5-7. +This BEP is created from a mixture of data in literature taken from: -Details on the computational method to derive the rate constants for the BEP relation are provided in "Automatic mechanism generation involving -kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173 -doi:10.1039/d3dd00184a +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = 2, + label = "C-N", + kinetics = SurfaceArrheniusBEP( + A = (1e13, '1/s'), + n = 0, + alpha = 0.967, + E0 = (194, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +This BEP is created from data in literature taken from: +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 +""" +) +entry( + index = 3, + label = "N-C", + kinetics = SurfaceArrheniusBEP( + A = (1e13, '1/s'), + n = 0, + alpha = 0.967, + E0 = (194, 'kJ/mol'), + Tmin = (200, 'K'), + Tmax = (3000, 'K'), + ), + rank = 0, + shortDesc = u"""Default""", + longDesc = u""" +This BEP is created from data in literature taken from: +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 +""" +) +entry( + index = 4, + label = "N-R", + kinetics = SurfaceArrheniusBEP( + A = (4.55E13, '1/s'), + n = 0.0, + alpha = 1.17, + E0 = (167, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = "R-N", + kinetics = SurfaceArrheniusBEP( + A = (4.55E13, '1/s'), + n = 0.0, + alpha = 1.17, + E0 = (167, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +and the current manuscript in progress by Badger et al. looking at the effects +of NO on the light out curves for hydrocarbons. """ ) diff --git a/input/kinetics/families/Surface_Dissociation/groups.py b/input/kinetics/families/Surface_Dissociation/groups.py index 0fd579b26b..aa7caafa92 100644 --- a/input/kinetics/families/Surface_Dissociation/groups.py +++ b/input/kinetics/families/Surface_Dissociation/groups.py @@ -316,6 +316,41 @@ kinetics = None, ) +entry( + index = 24, + label = "C-N", + group = +""" +1 *1 C u0 {2,S} {3,[S,D,T]} +2 *2 N u0 {1,S} +3 *3 Xo u0 {1,[S,D,T]} +""", + kinetics = None, +) + +entry( + index = 25, + label = "N-O", + group = +""" +1 *1 N u0 {2,S} {3,[S,D]} +2 *2 O u0 {1,S} +3 *3 Xo u0 {1,[S,D]} +""", + kinetics = None, +) + +entry( + index = 26, + label = "N-C", + group = +""" +1 *1 N u0 {2,S} {3,[S,D]} +2 *2 C u0 {1,S} +3 *3 Xo u0 {1,[S,D]} +""", + kinetics = None, +) tree( """ @@ -331,6 +366,7 @@ L3: C-O L4: C-OH L3: C-C + L3: C-N L2: O L3: O-H L3: O-C @@ -341,6 +377,31 @@ L3: N-H2 L3: N-H L3: N-N + L3: N-O + L3: N-C L1: VacantSite """ ) + +forbidden( + label = "Surf_Atom", + group = +""" +1 *1 R!H u0 c0 {2,S} {3,[S,D,T]} +2 *2 R u0 c0 {1,S} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 Xo u0 {2,[S,D,T]} +""", +) + +forbidden( + label = "beta_Surf_Atom", + group = +""" +1 *1 R!H u0 c0 {2,S} {3,[S,D,T]} +2 *2 R u0 c0 {1,S} {4,[S,D,T]} +3 *3 Xo u0 {1,[S,D,T]} +4 R!H u0 {2,[S,D,T]} {5,[S,D,T]} +5 Xo u0 {4,[S,D,T]} +""", +) diff --git a/input/kinetics/families/Surface_Dissociation/rules.py b/input/kinetics/families/Surface_Dissociation/rules.py index b84ec00e45..fdc3eba495 100644 --- a/input/kinetics/families/Surface_Dissociation/rules.py +++ b/input/kinetics/families/Surface_Dissociation/rules.py @@ -30,19 +30,27 @@ index = 2, label = "C-H_Bidentate;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (1.36e18, 'm^2/(mol*s)'), + A = (2.29e22, 'cm^2/(mol*s)'), n = 0.0, - alpha = 0.85, - E0 = (65.61, 'kJ/mol'), + alpha = 0.778, + E0 = (79.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", longDesc = u""" -A and n factors are from the average rate constant of training reactions 60-63, and alpha and E0 are BEP -parameters from training reactions 60-63. The A factor has been divided by 2 here to account for the degeneracies of the training reactions. - """ +This BEP is created from a mixture of data in literature taken from the following papers: + +Kreitz et al. +https://doi.org/10.1021/acscatal.2c03378 + +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( @@ -51,7 +59,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.77, + alpha = 0.77, E0 = (142.8, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -70,7 +78,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.57, + alpha = 0.57, E0 = (75.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -90,7 +98,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.26, + alpha = 0.26, E0 = (73.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -109,7 +117,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.58, + alpha = 0.58, E0 = (117.7, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -128,7 +136,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.72, + alpha = 0.72, E0 = (126.4, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -139,4 +147,152 @@ E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374. 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) """ -) \ No newline at end of file +) + +entry( + index = 8, + label = "C-N;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (6.72E21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.883, + E0 = (162, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = 9, + label = "N-C;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (6.72E21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.883, + E0 = (162, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = 10, + label = "N-H;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (1.63e22, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.379, + E0 = (94.7, '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 = 11, + label = "N-O;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (2.08e21, 'cm^2/(mol*s)'), + n = 0, + alpha = 1.09, + E0 = (162, '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 + +Farberow et al. +https://doi.org/10.1021/cs500668k + +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 = 12, + label = "N;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (9.88e21, '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. +""" +) + diff --git a/input/kinetics/families/Surface_Dissociation_Beta/groups.py b/input/kinetics/families/Surface_Dissociation_Beta/groups.py index bcbb85efda..2be6b6459d 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta/groups.py +++ b/input/kinetics/families/Surface_Dissociation_Beta/groups.py @@ -33,8 +33,8 @@ label = "Combined", group = """ -1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 R!H u0 {1,S} {3,S} +1 *1 R!H u0 {2,[S,D,T]} {4,[D,T]} +2 *2 R!H u0 {1,[S,D,T]} {3,S} 3 *3 R u0 {2,S} 4 *4 Xo u0 {1,[D,T]} """, @@ -57,7 +57,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 C u0 {1,S} {3,S} +2 *2 C u0 p0 c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,[D,T]} """, @@ -70,7 +70,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 O u0 {1,S} {3,S} +2 *2 O u0 p2 c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,[D,T]} """, @@ -83,7 +83,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 R!H u0 {1,S} {3,S} +2 *2 R!H u0 p[0,2] c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,[D,T]} """, @@ -111,7 +111,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,D} -2 *2 C u0 {1,S} {3,S} {5,S} +2 *2 C u0 p0 c0 {1,S} {3,S} {5,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,D} 5 R!H u0 {2,S} @@ -119,37 +119,137 @@ kinetics = None, ) +entry( + index = 8, + label = "N-R", + group = +""" +1 *1 R!H u0 {2,[S,D]} {4,[D,T]} +2 *2 N u0 p1 c0 {1,[S,D]} {3,S} +3 *3 R u0 px c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 9, + label = "R-N", + group = +""" +1 *1 R!H u0 {2,[S,D,T]} {4,[D,T]} +2 *2 R!H u0 px c0 {1,[S,D,T]} {3,S} +3 *3 N u0 p1 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 10, + label = "C-N", + group = +""" +1 *1 R!H u0 {2,[S,D,T]} {4,[D,T]} +2 *2 C u0 p0 c0 {1,[S,D,T]} {3,S} +3 *3 N u0 p1 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 11, + label = "O-N", + group = +""" +1 *1 R!H u0 {2,[S,D,T]} {4,[D,T]} +2 *2 O u0 p2 c0 {1,[S,D,T]} {3,S} +3 *3 N u0 p1 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 12, + label = "N-H", + group = +""" +1 *1 R!H u0 {2,[S,D]} {4,[D,T]} +2 *2 N u0 p1 c0 {1,[S,D]} {3,S} +3 *3 H u0 p0 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 13, + label = "N-C", + group = +""" +1 *1 R!H u0 {2,[S,D]} {4,[D,T]} +2 *2 N u0 p1 c0 {1,[S,D]} {3,S} +3 *3 C u0 p0 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + +entry( + index = 14, + label = "N-O", + group = +""" +1 *1 R!H u0 {2,[S,D]} {4,[D,T]} +2 *2 N u0 p1 c0 {1,[S,D]} {3,S} +3 *3 O u0 p2 c0 {2,S} +4 *4 Xo u0 {1,[D,T]} +""", + kinetics = None, +) + + tree( """ L1: Combined L2: R-H L3: CR-H L3: C-H - L4: CH3 + L4: CH3 L3: O-H + L2: R-N + L3: C-N + L3: O-N + L2: N-R + L3: N-C + L3: N-O + L3: N-H L1: VacantSite """ ) forbidden( - label = "R-C", + label = "surf1", group = """ -1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 R!H u0 {1,S} {3,S} -3 *3 C u0 px cx {2,S} +1 *1 R!H u0 c0 {2,S} {4,[D,T]} +2 *2 R!H u0 c0 {1,S} {3,S} {5,[S,D,T]} +3 *3 R u0 c0 {2,S} 4 *4 Xo u0 {1,[D,T]} -""", +5 Xo u0 p0 c0 {2,[S,D,T]} +""" ) forbidden( - label = "Bidentate", + label = "surf2", group = """ -1 *1 R!H u0 {2,S} {4,[D,T]} -2 *2 R!H u0 {1,S} {3,S} -3 *3 R u0 {2,S} +1 *1 R!H u0 c0 {2,S} {4,[D,T]} +2 *2 R!H u0 c0 {1,S} {3,S} +3 *3 R u0 c0 {2,S} {5,[S,D,T]} 4 *4 Xo u0 {1,[D,T]} -5 Xo u0 +5 Xo u0 p0 c0 {3,[S,D,T]} """ ) diff --git a/input/kinetics/families/Surface_Dissociation_Beta/rules.py b/input/kinetics/families/Surface_Dissociation_Beta/rules.py index 21fa41d8de..c741a24d98 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta/rules.py +++ b/input/kinetics/families/Surface_Dissociation_Beta/rules.py @@ -12,7 +12,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.84, + alpha = 0.84, E0 = (185.1, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -33,7 +33,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.58, + alpha = 0.58, E0 = (112.9, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -52,7 +52,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.26, + alpha = 0.26, E0 = (73.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -63,4 +63,184 @@ E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374. 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) """ -) \ No newline at end of file +) + +entry( + index = 4, + label = "C-N;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (6.72E21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.883, + E0 = (162, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = "N-C;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (6.72E21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.884, + E0 = (162, '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: + +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +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 = 6, + label = "N-H;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (4.03e21, 'cm^2/(mol*s)'), + n = 0, + alpha = 0.379, + E0 = (94.7, '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 = 7, + label = "N-O;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (2.08e21, 'cm^2/(mol*s)'), + n = 0, + alpha = 1.09, + E0 = (162, '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 + +Farberow et al. +https://doi.org/10.1021/cs500668k + +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 = 8, + label = "N-R;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (9.88e21, '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 = 9, + label = "R-N;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (9.88e21, '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. +""" +) diff --git a/input/kinetics/families/Surface_Dissociation_Beta_vdW/groups.py b/input/kinetics/families/Surface_Dissociation_Beta_vdW/groups.py index 586e86d219..de3d161d2e 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta_vdW/groups.py +++ b/input/kinetics/families/Surface_Dissociation_Beta_vdW/groups.py @@ -58,7 +58,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,S} -2 *2 R!H u0 {1,S} {3,S} +2 *2 R!H u0 p[0,2] c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,S} """, @@ -71,7 +71,7 @@ group = """ 1 *1 R!H u0 {2,S} {4,S} -2 *2 C u0 {1,S} {3,S} +2 *2 C u0 p0 c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,S} """, @@ -99,13 +99,38 @@ group = """ 1 *1 R!H u0 {2,S} {4,S} -2 *2 O u0 px {1,S} {3,S} +2 *2 O u0 p2 c0 {1,S} {3,S} 3 *3 H u0 {2,S} 4 *4 Xo u0 {1,S} """, kinetics = None, ) +entry( + index = 7, + label = "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 c0 {2,S} +4 *4 Xo u0 {1,S} +""", + kinetics = None, +) + +entry( + index = 8, + label = "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 c0 {2,S} +4 *4 Xo u0 {1,S} +""", + kinetics = None, +) tree( """ @@ -114,19 +139,33 @@ L3: C-H L4: CH3 L3: O-H + L2: R-N + L2: N-R L1: VacantSite """ ) forbidden( - label = "Bidentate", + label = "surf1", group = """ -1 *1 R!H u0 px cx {2,S} {4,S} -2 *2 R!H u0 px cx {1,S} {3,S} -3 *3 R u0 {2,S} +1 *1 R!H u0 px c0 {2,S} {4,S} +2 *2 R!H u0 px c0 {1,S} {3,S} {5,[S,D,T]} +3 *3 R u0 c0 {2,S} +4 *4 Xo u0 {1,S} +5 Xo u0 p0 c0 {2,[S,D,T]} +""", +) + +forbidden( + label = "surf2", + 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 R u0 c0 {2,S} {5,[S,D,T]} 4 *4 Xo u0 {1,S} -5 Xo u0 +5 Xo u0 p0 c0 {3,[S,D,T]} """, ) diff --git a/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py index 10371ade46..3ca4379cc8 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py @@ -12,7 +12,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.58, + alpha = 0.58, E0 = (112.9, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -31,7 +31,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.58, + alpha = 0.58, E0 = (112.9, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -50,7 +50,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0., - alpha =0.26, + alpha = 0.26, E0 = (73.3, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -61,4 +61,70 @@ E0 and alpha are taken from Table 5 for all metals from Sutton and Vlachos, "Ethanol Activation on closed-packed surfaces", Industrial & Engineering Chemistry Research, 2015, 54, 4213-4225, DOI: 10.1021/ie5043374. 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) """ -) \ No newline at end of file +) + +entry( + index = 4, + label = "R-N;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (2.8e21, '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 = "N-R;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (2.8e21, '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. +""" +) diff --git a/input/kinetics/families/Surface_Dissociation_Double/groups.py b/input/kinetics/families/Surface_Dissociation_Double/groups.py index 530f873a46..321b274af2 100755 --- a/input/kinetics/families/Surface_Dissociation_Double/groups.py +++ b/input/kinetics/families/Surface_Dissociation_Double/groups.py @@ -91,12 +91,51 @@ kinetics = None, ) +entry( + index = 6, + label = "C=N", + group = +""" +1 *1 C u0 p0 c0 {2,D} {3,[S,D]} +2 *2 N u0 p1 c0 {1,D} +3 *3 Xo u0 p0 {1,[S,D]} +""", + kinetics = None, +) + +entry( + index = 7, + label = "N=R", + group = +""" +1 *1 N u0 p1 c0 {2,D} {3,S} +2 *2 R!H u0 px c0 {1,D} +3 *3 Xo u0 p0 {1,S} +""", + kinetics = None, +) + +entry( + index = 8, + label = "N=C", + group = +""" +1 *1 N u0 p1 c0 {2,D} {3,S} +2 *2 C u0 p0 c0 {1,D} +3 *3 Xo u0 p0 {1,S} +""", + kinetics = None, +) + tree( """ L1: Combined L2: C=R L3: C=O - L3: C=C + L3: C=C + L3: C=N + L2: N=R + L3: N=C L1: VacantSite """ ) @@ -113,12 +152,12 @@ ) forbidden( - label = "Bidentate", + label = "Surf", group = """ 1 *1 R!H u0 px c0 {2,D} {3,[S,D]} -2 *2 R!H u0 px c0 {1,D} +2 *2 R!H u0 px c0 {1,D} {4,[S,D,T]} 3 *3 Xo u0 {1,[S,D]} -4 Xo u0 +4 Xo u0 p0 c0 {2,[S,D,T]} """, ) diff --git a/input/kinetics/families/Surface_Dissociation_Double/rules.py b/input/kinetics/families/Surface_Dissociation_Double/rules.py index 079ceeb00a..12b041ceb3 100755 --- a/input/kinetics/families/Surface_Dissociation_Double/rules.py +++ b/input/kinetics/families/Surface_Dissociation_Double/rules.py @@ -11,7 +11,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.84, + alpha = 0.84, E0 = (185.1, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -32,7 +32,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.77, + alpha = 0.77, E0 = (142.8, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -51,7 +51,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.72, + alpha = 0.72, E0 = (126.4, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -63,3 +63,36 @@ 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 = "N=R;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (9.88e21, '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. +""" +) diff --git a/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py b/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py index 3d501378bf..9a19f5fe0c 100644 --- a/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py +++ b/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py @@ -10,21 +10,28 @@ index = 1, label = "Combined;VacantSite1;VacantSite2", kinetics = SurfaceArrheniusBEP( - A = (1.41E22, 'm^4/(mol^2*s)'), + A = (2.68E30, 'cm^4/(mol^2*s)'), n = 0.0, - alpha = 0.87, - E0 = (77.188, 'kJ/mol'), + alpha = 0.636, + E0 = (85.5, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", longDesc = u""" -A and n factors are from the average rates of training reactions 1-2 and reverse of 3-4, and alpha and E0 are BEP -parameters from training reactions 1-2 and reverse of 3-4. +This BEP is created from a mixture of data in literature taken from the following papers: -Details on the computational method to derive the rate constants for the BEP relation are provided in "Automatic mechanism generation involving -kinetics of surface reactions with bidentate adsorbates" by B. Kreitz, K. Blöndal, K. Badger, R. H. West and C. F. Goldsmith, Digital Discovery, 2024, 3, 173 -doi:10.1039/d3dd00184a +Gomez-Díaz and Lopez +https://pubs.acs.org/doi/10.1021/jp1093349 + +Deng et al. +https://pubs.rsc.org/en/content/articlelanding/2014/ra/c3ra46544f + +kreitz et. al +https://doi.org/10.1021/acscatal.2c03378 + +and the current manuscript in progress by Badger et al. looking at the effects +of NO on the light out curves for hydrocarbons. """ ) diff --git a/input/kinetics/families/Surface_Dissociation_vdW/groups.py b/input/kinetics/families/Surface_Dissociation_vdW/groups.py index 662af7710a..8c2d3033a0 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/groups.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/groups.py @@ -241,6 +241,20 @@ kinetics = None, ) +entry( + index = 16, + label = "N-R", + group = +""" +multiplicity [1] +1 *1 R!H u0 px c0 {2,[S]} +2 *2 N u0 p1 c0 {1,[S]} +3 *3 Xv u0 p0 c0 +""", + kinetics = None, +) + + tree( """ L1: Combined @@ -256,7 +270,8 @@ L3: N-H L2: C-R L3: C-C - L3: C-OH + L3: C-OH + L2: N-R L1: VacantSite """ ) @@ -305,3 +320,33 @@ C should not match to *2 with a less heavy atom """, ) + +forbidden( + label = "N-O", + group = +""" +1 *2 O u0 {2,S} +2 *1 N u0 {1,S} +3 *3 Xv u0 p0 c0 +""", + shortDesc = u"""""", + longDesc = +u""" + should not match to *2 with a less heavy atom +""", +) + +forbidden( + label = "H-N", + group = +""" +1 *2 N u0 {2,S} +2 *1 H u0 {1,S} +3 *3 Xv u0 p0 c0 +""", + shortDesc = u"""""", + longDesc = +u""" + should not match to *2 with a less heavy atom +""", +) diff --git a/input/kinetics/families/Surface_Dissociation_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_vdW/rules.py index b8ebf1e99d..f0bfa34970 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/rules.py @@ -12,7 +12,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.84, + alpha = 0.84, E0 = (185.1, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -71,7 +71,7 @@ kinetics = SurfaceArrheniusBEP( A = (4.18e17, 'm^2/(mol*s)'), n = 0, - alpha =0.57, + alpha = 0.57, E0 = (75.25, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -85,12 +85,12 @@ ) entry( - index = 8, + index = 5, label = "C-C;VacantSite", kinetics = SurfaceArrheniusBEP( A = (2.09e17, 'm^2/(mol*s)'), n = 0, - alpha =0.72, + alpha = 0.72, E0 = (126.39, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), @@ -104,4 +104,38 @@ BK: This group is symmetrical, and RMG matches this node from both directions. Thus, a reaction degeneracy of 2 is applied, and the pre-exponential coefficient A is doubled. We divided the pre-exponential coefficient by a factor of 2 so that RMG predicts the correct rate. """ -) \ No newline at end of file +) + + +entry( + index = 6, + label = "N-R;VacantSite", + kinetics = SurfaceArrheniusBEP( + A = (2.80e21, '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. +""" +)