From 786039e8fdd1f2061500f4e700f4516c53ad5713 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 c0bd3c1263a3ad234d74d90dba77845d81b73901 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 346bbd6dbe129d4f243d3ef73647b69524df51c9 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 80abce38987cd04b2a0b2a873bbdc4855c510af9 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 4367fac190edcf9ed66db4299990f76fad622762 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 860db04b8ddb0980ecc92e81f6501c673a35a8d8 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 8dd1ef56684e24840b81b9e4951ec53002859d87 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