diff --git a/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py b/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py index 5b05d3f531..e646edb87d 100644 --- a/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py +++ b/input/kinetics/families/Surface_Bidentate_Dissociation/rules.py @@ -12,14 +12,18 @@ A = (1.187E12, '1/s'), n = 0.0, alpha = 0.842, - E0 = (34.82, 'kcal/mol'), + E0 = (145.69, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", longDesc = u""" -A and n factors are averages of training reactions 1-3 and the reverse direction of training reactions 4-7, -and alpha and E0 are BEP parameters from training reactions 1-3 and the reverse of training reactions 4-7. +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. + +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 """ ) diff --git a/input/kinetics/families/Surface_Bidentate_Dissociation/training/reactions.py b/input/kinetics/families/Surface_Bidentate_Dissociation/training/reactions.py index 5222ebcdaf..390bb5b9fc 100644 --- a/input/kinetics/families/Surface_Bidentate_Dissociation/training/reactions.py +++ b/input/kinetics/families/Surface_Bidentate_Dissociation/training/reactions.py @@ -8,31 +8,24 @@ training set for generating rate rules to populate this kinetics family. """ -#!/usr/bin/env python -# encoding: utf-8 - -name = "Surface_Bidentate_Dissociation/training" -shortDesc = u"Reaction kinetics used to generate rate rules" -longDesc = u""" -Put kinetic parameters for specific reactions in this file to use as a -training set for generating rate rules to populate this kinetics family. -""" - entry( index = 1, label = "CC_2X <=> CX_3 + CX_4 ", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(2.202E12, '1/s'), - n = 0.09, - Ea=(103497.2, 'J/mol'), + A=(4.22E12, '1/s'), + n = 0.0, + Ea=(104, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) @@ -42,16 +35,19 @@ label = "CCH_2X <=> CX_3 + CHX_4", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(5.272E11, '1/s'), + A=(1.3E12, '1/s'), n = 0.126, - Ea=(76699.8, 'J/mol'), + Ea=(77, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) @@ -61,35 +57,41 @@ label = "HCCH_2X <=> CHX_3 + CHX_4", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(7.062E11, '1/s'), - n = 0.320, - Ea=(88220.0, 'J/mol'), + A=(7.93E12, '1/s'), + n = 0.0, + Ea=(90, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), - rank=10, + rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) entry( index = 4, - label = "CHX_3 + CH2X_4 <=> HCCH2_2X", + label = "HCCH2_2X <=> CHX_3 + CH2X_4", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(4.256E17, 'm^2/(mol*s)'), - n = 0.106, - Ea=(138024.4, 'J/mol'), + A=(2.74E13, '1/s'), + n = 0.0, + Ea=(140, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) @@ -99,16 +101,19 @@ label = "CH2X_3 + CH2X_4 <=> H2CCH2_2X", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(1.161E19, 'm^2/(mol*s)'), - n = 0.281, - Ea=(152439.3, 'J/mol'), + A=(9.89E23, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(154, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) @@ -118,16 +123,19 @@ label = "CHX_3 + OX_4 <=> HCO_2X", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(6.922E17, 'm^2/(mol*s)'), - n = 0.049, - Ea=(142325.0, 'J/mol'), + A=(6.54E21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(142, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) @@ -137,16 +145,19 @@ label = "CH2X_3 + OX_4 <=> H2CO_2X", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(1.174E18, 'm^2/(mol*s)'), - n = 0.082, - Ea=(114251.7, 'J/mol'), + A=(2.2E22, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(115, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", -) +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation/rules.py b/input/kinetics/families/Surface_Dissociation/rules.py index 0cfe67ed73..de4b4af389 100644 --- a/input/kinetics/families/Surface_Dissociation/rules.py +++ b/input/kinetics/families/Surface_Dissociation/rules.py @@ -30,10 +30,10 @@ index = 2, label = "C-H_Bidentate;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (7.250e16, 'm^2/(mol*s)'), + A = (1.36e18, 'm^2/(mol*s)'), n = 0.0, - alpha = 0.961, - E0 = (22.37, 'kcal/mol'), + alpha = 0.85, + E0 = (65.61, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), diff --git a/input/kinetics/families/Surface_Dissociation/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation/training/dictionary.txt index f6dc17fedd..48810eff9c 100644 --- a/input/kinetics/families/Surface_Dissociation/training/dictionary.txt +++ b/input/kinetics/families/Surface_Dissociation/training/dictionary.txt @@ -185,3 +185,51 @@ HCO_2X 3 O u0 p2 {1,S} {5,S} 4 *3 X u0 p0 {1,D} 5 X u0 p0 {3,S} + + +XCXCH2_1 +1 C u0 p0 {2,S} {5,T} +2 *1 C u0 p0 {1,S} {3,S} {4,S} {6,S} +3 *2 H u0 p0 {2,S} +4 H u0 p0 {2,S} +5 X u0 p0 {1,T} +6 *3 X u0 p0 {2,S} + +XCXCH_3 +1 C u0 p0 {2,S} {4,T} +2 *1 C u0 p0 {1,S} {3,S} {5,D} +3 H u0 p0 {2,S} +4 X u0 p0 {1,T} +5 *3 X u0 p0 {2,D} + +XCHXCH2_1 +1 *1 C u0 p0 {2,S} {3,S} {6,D} +2 C u0 p0 {1,S} {4,S} {5,S} {7,S} +3 *2 H u0 p0 {1,S} +4 H u0 p0 {2,S} +5 H u0 p0 {2,S} +6 *3 X u0 p0 {1,D} +7 X u0 p0 {2,S} + +XCXCH2_3 +1 *1 C u0 p0 {2,S} {5,T} +2 C u0 p0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 {2,S} +4 H u0 p0 {2,S} +5 *3 X u0 p0 {1,T} +6 X u0 p0 {2,S} + +XCHXCH_1 +1 *1 C u0 p0 {2,S} {3,S} {5,D} +2 C u0 p0 {1,S} {4,S} {6,D} +3 *2 H u0 p0 {1,S} +4 H u0 p0 {2,S} +5 *3 X u0 p0 {1,D} +6 X u0 p0 {2,D} + +XCXCH_4 +1 *1 C u0 p0 {2,S} {4,T} +2 C u0 p0 {1,S} {3,S} {5,D} +3 H u0 p0 {2,S} +4 *3 X u0 p0 {1,T} +5 X u0 p0 {2,D} diff --git a/input/kinetics/families/Surface_Dissociation/training/reactions.py b/input/kinetics/families/Surface_Dissociation/training/reactions.py index f8b5754454..1d43215879 100644 --- a/input/kinetics/families/Surface_Dissociation/training/reactions.py +++ b/input/kinetics/families/Surface_Dissociation/training/reactions.py @@ -373,16 +373,21 @@ label = "HCCH2_2X + Ni_4 <=> HCCH_2X + HX_5", degeneracy = 2, kinetics = SurfaceArrhenius( - A=(1.9460e16, 'm^2/(mol*s)'), - n = 0.512, - Ea=(69707.5, 'J/mol'), + A=(4.75e21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(72, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 2 because of the degeneracy. + """, metal = "Pt", ) @@ -392,16 +397,20 @@ label = "H2CCH2_2X + Ni_4 <=> H2CCH_2X + HX_5", degeneracy = 2, kinetics = SurfaceArrhenius( - A=(3.034e15, 'm^2/(mol*s)'), - n = 0.661, - Ea=(55411.0, 'J/mol'), + A=(2.225e21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(59, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 2 because of the degeneracy. """, metal = "Pt", ) @@ -411,16 +420,88 @@ label = "H2CO_2X + Ni_4 <=> HCO_2X + HX_5", degeneracy = 2, kinetics = SurfaceArrhenius( - A=(1.438e17, 'm^2/(mol*s)'), - n = 0.043, - Ea=(1417.1, 'J/mol'), + A=(0.875e21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(2, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank=8, shortDesc = u"""Default""", longDesc = u""" -Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 2 because of the degeneracy. """, metal = "Pt", ) + +entry( + index = 63, + label = "XCXCH_3 + HX_5 <=> XCXCH2_1 + Ni_4", + degeneracy = 2, + kinetics = SurfaceArrhenius( + A=(2.595e19, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(34, 'kJ/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=8, + shortDesc = u"""Default""", + longDesc = u""" +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 2 because of the degeneracy. +""", + metal = "Pt", +) + +entry( + index = 64, + label = "XCXCH_4 + HX_5 <=> XCHXCH_1 + Ni_4", + degeneracy = 2, + kinetics = SurfaceArrhenius( + A=(1.66e21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(62, 'kJ/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=8, + shortDesc = u"""Default""", + longDesc = u""" +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 2 because of the degeneracy. +""", + metal = "Pt", +) + +entry( + index = 65, + label = "XCHXCH2_1 + Ni_4 <=> XCXCH2_3 + HX_5", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(9.69e21, 'cm^2/(mol*s)'), + n = 0.0, + Ea=(48, 'kJ/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank=8, + shortDesc = u"""Default""", + longDesc = u""" +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +""", + metal = "Pt", +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py b/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py index f056b64ece..3d501378bf 100644 --- a/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py +++ b/input/kinetics/families/Surface_Dissociation_to_Bidentate/rules.py @@ -8,21 +8,23 @@ entry( index = 1, - label = "Combined;VacantSite1;VacantSite2", + label = "Combined;VacantSite1;VacantSite2", kinetics = SurfaceArrheniusBEP( - A = (5.726E21, 'm^4/(mol^2*s)'), - n = 0.0, - alpha = 0.0824, - E0 = (12.11, 'kcal/mol'), + A = (1.41E22, 'm^4/(mol^2*s)'), + n = 0.0, + alpha = 0.87, + E0 = (77.188, '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 1-3, and alpha and E0 are BEP -parameters from training reactions 1-3 (in the Surface_Dissociation_to_Bidentate -forward direction). -The A factor has been divided by 2.33 here to account for the average degeneracy of the training reactions. +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. + +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 """ ) diff --git a/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/dictionary.txt b/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/dictionary.txt index 2d464c9684..89ea569960 100644 --- a/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/dictionary.txt +++ b/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/dictionary.txt @@ -62,3 +62,19 @@ H2CO_2X 4 *2 O u0 p2 {1,S} {6,S} 5 *4 X u0 p0 {1,S} 6 *5 X u0 p0 {4,S} + +XCXCH2 +1 *1 C u0 p0 {2,S} {5,T} +2 *2 C u0 p0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 {2,S} +4 H u0 p0 {2,S} +5 *4 X u0 p0 {1,T} +6 *5 X u0 p0 {2,S} + +XCCH3 +1 *1 C u0 p0 {2,S} {6,T} +2 *2 C u0 p0 {1,S} {3,S} {4,S} {5,S} +3 *3 H u0 p0 {2,S} +4 H u0 p0 {2,S} +5 H u0 p0 {2,S} +6 *4 X u0 p0 {1,T} diff --git a/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/reactions.py b/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/reactions.py index ebb1593251..54bf68e6e2 100644 --- a/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/reactions.py +++ b/input/kinetics/families/Surface_Dissociation_to_Bidentate/training/reactions.py @@ -13,16 +13,20 @@ label = "H2CCH3_X + Pt_5 + Pt_6 <=> H2CCH2_2X + H_X", degeneracy = 3, kinetics = SurfaceArrhenius( - A=(1.163E20, 'm^4/(mol^2*s)'), - n = 0.644, - Ea=(42144.629, 'J/mol'), + A=(0.557E22, 'm^4/(mol^2*s)'), + n = 0.0, + Ea=(46, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank = 8, shortDesc = u"""Deutschmann Ni""", longDesc = u""" -Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 3 due to the degeneracy. """, metal = "Pt", ) @@ -32,16 +36,20 @@ label = "HCCH3_X + Pt_5 + Pt_6 <=> HCCH2_2X + H_X", degeneracy = 3, kinetics = SurfaceArrhenius( - A=(2.057E20, 'm^4/(mol^2*s)'), - n = 0.598, - Ea=(45301.1, 'J/mol'), + A=(0.65E22, 'm^4/(mol^2*s)'), + n = 0.0, + Ea=(49, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank = 8, shortDesc = u"""Default""", longDesc = u""" -Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +A divided by 3 due to the degeneracy. """, metal = "Pt", ) @@ -51,16 +59,41 @@ label = "H2CO_2X + H_X <=> H2COH_X + Pt_5 + Pt_6", degeneracy = 1, kinetics = SurfaceArrhenius( - A=(4.857E16, 'm^2/(mol*s)'), - n = 0.063, - Ea=(28353.5, 'J/mol'), + A=(8.22E16, 'm^2/(mol*s)'), + n = 0.0, + Ea=(29, 'kJ/mol'), Tmin = (298, 'K'), Tmax = (2000, 'K'), ), rank = 8, shortDesc = u"""Default""", longDesc = u""" -Calculated by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 """, metal = "Pt", ) + +entry( + index = 4, + label = "XCXCH2 + H_X <=> XCCH3 + Pt_5 + Pt_6", + degeneracy = 1, + kinetics = SurfaceArrhenius( + A=(1.07E18, 'm^2/(mol*s)'), + n = 0.0, + Ea=(72, 'kJ/mol'), + Tmin = (298, 'K'), + Tmax = (2000, 'K'), + ), + rank = 8, + shortDesc = u"""Default""", + longDesc = u""" +Calculated with DFT by Katrín Blöndal and Bjarne Kreitz at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. +Details on the computational method to derive the rate constants 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 +""", + metal = "Pt", +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_vdW_to_Bidentate/rules.py b/input/kinetics/families/Surface_vdW_to_Bidentate/rules.py index c41a59b831..07471ef41c 100644 --- a/input/kinetics/families/Surface_vdW_to_Bidentate/rules.py +++ b/input/kinetics/families/Surface_vdW_to_Bidentate/rules.py @@ -9,14 +9,20 @@ index = 1, label = "Combined;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (1.0e17, 'm^2/(mol*s)'), + A = (1.78e21, 'cm^2/(mol*s)'), n = 0, alpha = 0.0, - E0 = (7, 'kcal/mol'), + E0 = (12, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 0, shortDesc = u"""Default""", - longDesc = u"""These values are made up.""" + longDesc = u""" +These values are based on training reaction 2. +The other training reactions are barrierless. +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 +""" ) diff --git a/input/kinetics/families/Surface_vdW_to_Bidentate/training/reactions.py b/input/kinetics/families/Surface_vdW_to_Bidentate/training/reactions.py index 13ec26a5b4..96a317934a 100644 --- a/input/kinetics/families/Surface_vdW_to_Bidentate/training/reactions.py +++ b/input/kinetics/families/Surface_vdW_to_Bidentate/training/reactions.py @@ -13,7 +13,7 @@ index = 1, label = "HCCHX_vdW + X <=> HCCH_2X", kinetics = SurfaceArrhenius( - A = (5.0E17, 'm^2/(mol*s)'), + A = (1.0E21, 'cm^2/(mol*s)'), n = 0, Ea = (0, 'J/mol'), Tmin = (200, 'K'), @@ -22,7 +22,11 @@ rank = 8, shortDesc = u"""Default""", longDesc = u""" - Barrierless according to DFT calculations by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.""", + Barrierless according to DFT calculations by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. + Details on the computational method to derive the rate constants 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 + """, metal = "Pt", ) @@ -31,16 +35,20 @@ index = 2, label = "H2CCH2X_vdW + X <=> H2CCH2_2X", kinetics = SurfaceArrhenius( - A = (9.122E16, 'm^2/(mol*s)'), - n = 0.088, - Ea = (11732.0, 'J/mol'), + A = (1.78E21, 'cm^2/(mol*s)'), + n = 0.0, + Ea = (12, 'kJ/mol'), Tmin = (200, 'K'), Tmax = (3000, 'K'), ), rank = 8, shortDesc = u"""Default""", longDesc = u""" - Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.""", + Calculated with DFT by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. + Details on the computational method to derive the rate constants 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 + """, metal = "Pt", ) @@ -48,7 +56,7 @@ index = 3, label = "H2COX_vdW + X <=> H2CO_2X", kinetics = SurfaceArrhenius( - A = (5.0E17, 'm^2/(mol*s)'), + A = (1.0E21, 'cm^2/(mol*s)'), n = 0, Ea = (0, 'J/mol'), Tmin = (200, 'K'), @@ -57,6 +65,10 @@ rank = 8, shortDesc = u"""Default""", longDesc = u""" - Barrierless according to DFT calculations by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO.""", + Barrierless according to DFT calculations by Katrín Blöndal at Brown University, using the vdW-DF-cx functional in Quantum ESPRESSO. + Details on the computational method to derive the rate constants 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 + """, metal = "Pt", )