From 9f31d16950af92174b65f7033e50656cb5e086e0 Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:11:48 -0400 Subject: [PATCH 1/7] Abstraction and Beta Abs --- .../families/Surface_Abstraction/rules.py | 129 +----------------- .../Surface_Abstraction_Beta/rules.py | 43 +----- .../rules.py | 42 +----- 3 files changed, 3 insertions(+), 211 deletions(-) diff --git a/input/kinetics/families/Surface_Abstraction/rules.py b/input/kinetics/families/Surface_Abstraction/rules.py index 680b613b9d..e14329048d 100644 --- a/input/kinetics/families/Surface_Abstraction/rules.py +++ b/input/kinetics/families/Surface_Abstraction/rules.py @@ -103,131 +103,4 @@ 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 = "O;*=CH-H", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, '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""" -These numbers for the BEP are from the abstraction reaction of C-H to O. -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) -Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms) - """ -) - -entry( - index = 7, - label = "O;*-CH-H", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, '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""" -These numbers for the BEP are from the abstraction reaction of C-H to O. -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) -Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms) - """ -) - -entry( - index = 8, - label = "C;*-CH-H", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.37, - E0 = (99.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -These numbers for the general BEP are from the abstraction reaction of C-H to C. -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) -Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms) -""" -) - -entry( - index = 9, - label = "C;*=CH-H", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.37, - E0 = (99.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -These numbers for the general BEP are from the abstraction reaction of C-H to C. -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) -Divided by 2 because of reaction path degeneracy for CH2 (2 equivalent H atoms) - """ -) - - -entry( - index = 10, - label = "C;*-CH2-H", - kinetics = SurfaceArrheniusBEP( - A = (1.393e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.37, - E0 = (99.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -These numbers for the general BEP are from the abstraction reaction of C-H to C. -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) -Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) - """ -) - -entry( - index = 11, - label = "O;*-CH2-H", - 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""" -These numbers for the BEP are from the abstraction reaction of C-H to O. -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) -Divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) - """ -) +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction_Beta/rules.py b/input/kinetics/families/Surface_Abstraction_Beta/rules.py index afe7db0743..c2cfcf8b4f 100644 --- a/input/kinetics/families/Surface_Abstraction_Beta/rules.py +++ b/input/kinetics/families/Surface_Abstraction_Beta/rules.py @@ -62,45 +62,4 @@ 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 = "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, 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) -A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) -""" -) - -entry( - index = 5, - 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'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -These numbers for the general BEP are from the abstraction reaction of C-H to O. -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) -A divided by 3 because of reaction path degeneracy for CH3 (3 equivalent H atoms) -""" -) +) \ No newline at end of file diff --git a/input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py index 913ee3c470..93acdec533 100644 --- a/input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py +++ b/input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py @@ -61,44 +61,4 @@ 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 =0.68, - E0 = (106.1, '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 = 5, - label = "OH;R-CH3", - kinetics = SurfaceArrheniusBEP( - A = (1.393e17, 'm^2/(mol*s)'), - n = 0., - alpha =0.68, - E0 = (106.1, '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) -""" -) +) \ No newline at end of file From daf1a78222a766f7d6fce4a5792946871e19122e Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:12:22 -0400 Subject: [PATCH 2/7] Abstraction Beta vdW --- .../Surface_Abstraction_Beta_vdW/rules.py | 42 +------------------ 1 file changed, 1 insertion(+), 41 deletions(-) diff --git a/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py b/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py index a531f157ef..09444ba85d 100755 --- a/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py +++ b/input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py @@ -61,44 +61,4 @@ 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'), - ), - 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 = 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) -""" -) +) \ No newline at end of file From 93d07c25bf82bac9fab6a24d1e7a1b687e7a63f6 Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:12:58 -0400 Subject: [PATCH 3/7] Dissociation --- .../families/Surface_Dissociation/rules.py | 82 +------------------ 1 file changed, 1 insertion(+), 81 deletions(-) diff --git a/input/kinetics/families/Surface_Dissociation/rules.py b/input/kinetics/families/Surface_Dissociation/rules.py index de4b4af389..b84ec00e45 100644 --- a/input/kinetics/families/Surface_Dissociation/rules.py +++ b/input/kinetics/families/Surface_Dissociation/rules.py @@ -139,84 +139,4 @@ 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) """ -) - -entry( - index = 8, - label = "CH2;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 2 because of reaction path degeneracy for CH2 -""" -) - -entry( - index = 9, - label = "CH3;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.39e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 3 because of reaction path degeneracy for CH3 -""" -) - -entry( - index = 10, - label = "CH2R;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom) -""" -) - -entry( - index = 11, - label = "CHR;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (4.18e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.3, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 2 because of reaction path degeneracy for X-CH2-R (Abstraction of the alpha H atom) -""" -) +) \ No newline at end of file From f565ce68c07303dd71c1faa00e299ca6fb9e2dd9 Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:13:29 -0400 Subject: [PATCH 4/7] Dissociation Beta --- .../Surface_Dissociation_Beta/rules.py | 22 +------------------ 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/input/kinetics/families/Surface_Dissociation_Beta/rules.py b/input/kinetics/families/Surface_Dissociation_Beta/rules.py index 3b27eb255a..21fa41d8de 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta/rules.py +++ b/input/kinetics/families/Surface_Dissociation_Beta/rules.py @@ -63,24 +63,4 @@ 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) """ -) - -entry( - index = 4, - label = "CH3;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.393e17, 'm^2/(mol*s)'), - n = 0., - alpha =0.58, - E0 = (112.9, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -E0 and alpha are taken from Table 6 for oxygenates for 3x3 cell size from "A Theoretical and Computational Analysis of Linear Free Energy Relations for the Estimation of Activation Energies" Jonathan E. Sutton, Dionisios G. Vlachos, ACS Catal., 2012, 2, 1624-1634, DOI:10.1021/cs3003269. -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) -A divided by 3 because of reaction path degeneracy for =R-CH3 dissociation (3 equivalent H atoms) -""" -) +) \ No newline at end of file From 1675e76ccf6cdf8d9f1ea6261c79b55337530401 Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:14:03 -0400 Subject: [PATCH 5/7] Dissociation Beta vdW --- .../Surface_Dissociation_Beta_vdW/rules.py | 22 +------------------ 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py index 5743c338ca..10371ade46 100755 --- a/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_Beta_vdW/rules.py @@ -61,24 +61,4 @@ 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) """ -) - -entry( - index = 4, - label = "CH3;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.393e17, 'm^2/(mol*s)'), - n = 0., - alpha =0.58, - E0 = (112.9, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -E0 and alpha are taken from Table 6 for oxygenates for 3x3 cell size from "A Theoretical and Computational Analysis of Linear Free Energy Relations for the Estimation of Activation Energies" Jonathan E. Sutton, Dionisios G. Vlachos, ACS Catal., 2012, 2, 1624-1634, DOI:10.1021/cs3003269. -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) -A divided by 3 because of reaction path degeneracy for -R-CH3 dissociation (3 equivalent H atoms) -""" -) +) \ No newline at end of file From 1af418f27d4d2b79cb18041235438fc1f340b05a Mon Sep 17 00:00:00 2001 From: Chris B <56306881+ChrisBNEU@users.noreply.github.com> Date: Wed, 10 Jul 2024 18:14:34 -0400 Subject: [PATCH 6/7] Dissociation vdW --- .../Surface_Dissociation_vdW/rules.py | 111 +----------------- 1 file changed, 4 insertions(+), 107 deletions(-) diff --git a/input/kinetics/families/Surface_Dissociation_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_vdW/rules.py index ba7b8b7b16..66025e3b3b 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/rules.py @@ -29,9 +29,9 @@ entry( index = 2, - label = "H2O;VacantSite", + label = "O-H;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), + A = (4.18e17, 'm^2/(mol*s)'), n = 0, alpha =0.51, E0 = (97.5, 'kJ/mol'), @@ -43,7 +43,6 @@ longDesc = u""" BEP relation for all metals and facets from Wang et al. "Universal transition state scaling relations for (de)hydrogenation over transition metals", Physical chemistry chemical physics, 2011, 13, 20760-20765, DOI:10.1039/c1cp20547a. Technically this is a relation for dissociative adsorption. -A divided by 2 because of reaction path degeneracy for H2O """ ) @@ -85,71 +84,11 @@ """ ) -entry( - index = 5, - label = "CH4;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.045e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.25, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 4 because of reaction path degeneracy for CH4 -""" -) - -entry( - index = 6, - label = "CH3R;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.39e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.25, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 3 because of reaction path degeneracy for 3 equivalent H atoms for bond fission (example CH3OH) -""" -) - -entry( - index = 7, - label = "CH2R;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.25, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 2 because of reaction path degeneracy for 2 equivalent H atoms for bond fission (example CH2O) -""" -) - entry( index = 8, label = "C-C;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (2.09e17, 'm^2/(mol*s)'), + A = (4.18e17, 'm^2/(mol*s)'), n = 0, alpha =0.72, E0 = (126.39, 'kJ/mol'), @@ -161,47 +100,5 @@ longDesc = u""" 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) -A divided by 2 because of reaction path degeneracy for 2 equivalent C atoms for bond fission (example CH3CH3) """ -) - - -entry( - index = 9, - label = "C2H6;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (0.69e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.25, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 6 because of reaction path degeneracy for 6 equivalent H atoms for bond fission (example CH3CH3) -""" -) - -entry( - index = 10, - label = "C2H4;VacantSite", - kinetics = SurfaceArrheniusBEP( - A = (1.045e17, 'm^2/(mol*s)'), - n = 0, - alpha =0.57, - E0 = (75.25, 'kJ/mol'), - Tmin = (200, 'K'), - Tmax = (3000, 'K'), - ), - rank = 0, - shortDesc = u"""Default""", - longDesc = u""" -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) -A divided by 4 because of reaction path degeneracy for 4 equivalent H atoms for bond fission (example C2H4) -""" -) +) \ No newline at end of file From be199c85cc6422a8b26b7e2f67e5a97ef545af94 Mon Sep 17 00:00:00 2001 From: Bjarne Kreitz Date: Mon, 22 Jul 2024 13:37:38 -0400 Subject: [PATCH 7/7] Dissociation vdW C-C degeneracy --- input/kinetics/families/Surface_Dissociation_vdW/rules.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/input/kinetics/families/Surface_Dissociation_vdW/rules.py b/input/kinetics/families/Surface_Dissociation_vdW/rules.py index 66025e3b3b..b8ebf1e99d 100644 --- a/input/kinetics/families/Surface_Dissociation_vdW/rules.py +++ b/input/kinetics/families/Surface_Dissociation_vdW/rules.py @@ -88,9 +88,9 @@ index = 8, label = "C-C;VacantSite", kinetics = SurfaceArrheniusBEP( - A = (4.18e17, 'm^2/(mol*s)'), + 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'), @@ -100,5 +100,8 @@ longDesc = u""" 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) + +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