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Remove reaction path degeneracy adjustments in surface families #655

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Dec 5, 2024
Merged

Remove reaction path degeneracy adjustments in surface families #655

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786039e
Abstraction and Beta Abs
ChrisBNEU Jul 10, 2024
c0bd3c1
Abstraction Beta vdW
ChrisBNEU Jul 10, 2024
346bbd6
Dissociation
ChrisBNEU Jul 10, 2024
80abce3
Dissociation Beta
ChrisBNEU Jul 10, 2024
4367fac
Dissociation Beta vdW
ChrisBNEU Jul 10, 2024
860db04
Dissociation vdW
ChrisBNEU Jul 10, 2024
8dd1ef5
Dissociation vdW C-C degeneracy
bjkreitz Jul 22, 2024
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129 changes: 1 addition & 128 deletions input/kinetics/families/Surface_Abstraction/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
43 changes: 1 addition & 42 deletions input/kinetics/families/Surface_Abstraction_Beta/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
42 changes: 1 addition & 41 deletions input/kinetics/families/Surface_Abstraction_Beta_double_vdW/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
42 changes: 1 addition & 41 deletions input/kinetics/families/Surface_Abstraction_Beta_vdW/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
82 changes: 1 addition & 81 deletions input/kinetics/families/Surface_Dissociation/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
22 changes: 1 addition & 21 deletions input/kinetics/families/Surface_Dissociation_Beta/rules.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
"""
)
)
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