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Merge pull request #677 from ssun30/CO2RR
Add thermo and kinetics data for electrocatalytic CO2 reduction
2 parents d1ed9ca + 8910565 commit 2c90c69

13 files changed

Lines changed: 1736 additions & 12 deletions

‎families/images/Surface_Proton_Electron_Reduction_Alpha.png‎

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‎families/images/Surface_Proton_Electron_Reduction_Alpha_vdW.png‎

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‎families/images/Surface_Proton_Electron_Reduction_Beta.png‎

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‎families/images/Surface_Proton_Electron_Reduction_Beta_Dissociation.png‎

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‎families/images/Surface_Proton_Electron_Reduction_Beta_vdW.png‎

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‎input/kinetics/families/recommended.py‎

Lines changed: 23 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -116,7 +116,7 @@
116116
'Surface_Adsorption_Bidentate',
117117
'Surface_Bidentate_Dissociation',
118118
'Surface_Monodentate_to_Bidentate',
119-
'Surface_Dissociation_to_Bidentate',
119+
'Surface_Dissociation_to_Bidentate',
120120
'Surface_vdW_to_Bidentate',
121121
'Surface_Adsorption_Dissociative_Double',
122122
'Surface_Abstraction_Beta',
@@ -152,7 +152,7 @@
152152
'Surface_Migration',
153153
}
154154

155-
# Electrochemical families!
155+
# Electrochemical families.
156156
electrochem = {
157157
'Surface_Proton_Electron_Reduction_Alpha',
158158
'Surface_Proton_Electron_Reduction_Alpha_vdW',
@@ -170,3 +170,24 @@
170170
'Li_Abstraction',
171171
'R_Addition_MultipleBond_Disprop',
172172
}
173+
174+
# Electrocatalytic CO2 Reduction families.
175+
surface_CO2 = {
176+
'Surface_Abstraction',
177+
'Surface_Abstraction_vdW',
178+
'Surface_Abstraction_Single_vdW',
179+
'Surface_Abstraction_Beta_double_vdW',
180+
'Surface_Adsorption_Dissociative',
181+
'Surface_Adsorption_Dissociative_Double',
182+
'Surface_Adsorption_vdW',
183+
'Surface_Dissociation',
184+
'Surface_Dissociation_Double_vdW',
185+
'Surface_Dissociation_vdW',
186+
'Surface_EleyRideal_Addition_Multiple_Bond',
187+
'Surface_Migration',
188+
'Surface_Proton_Electron_Reduction_Alpha',
189+
'Surface_Proton_Electron_Reduction_Alpha_vdW',
190+
'Surface_Proton_Electron_Reduction_Beta',
191+
'Surface_Proton_Electron_Reduction_Beta_vdW',
192+
'Surface_Proton_Electron_Reduction_Beta_Dissociation',
193+
}

‎input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt‎

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@@ -0,0 +1,81 @@
1+
2+
X
3+
1 X u0 p0 c0
4+
5+
proton
6+
1 H u0 p0 c+1
7+
8+
e
9+
1 e u0 p0 c-1
10+
11+
H2O
12+
1 O u0 p2 c0 {2,S} {3,S}
13+
2 H u0 p0 c0 {1,S}
14+
3 H u0 p0 c0 {1,S}
15+
16+
CO2X
17+
1 O u0 p2 c0 {2,D}
18+
2 C u0 p0 c0 {1,D} {3,D}
19+
3 O u0 p2 c0 {2,D}
20+
4 X u0 p0 c0
21+
22+
CO2HX
23+
1 O u0 p2 c0 {3,S} {4,S}
24+
2 O u0 p2 c0 {3,D}
25+
3 C u0 p0 c0 {1,S} {2,D} {5,S}
26+
4 H u0 p0 c0 {1,S}
27+
5 X u0 p0 c0 {3,S}
28+
29+
CHO2X
30+
1 O u0 p2 c0 {3,S} {5,S}
31+
2 O u0 p2 c0 {3,D}
32+
3 C u0 p0 c0 {1,S} {2,D} {4,S}
33+
4 H u0 p0 c0 {3,S}
34+
5 X u0 p0 c0 {1,S}
35+
36+
OCX
37+
1 O u0 p2 c0 {2,D}
38+
2 C u0 p0 c0 {1,D} {3,D}
39+
3 X u0 p0 c0 {2,D}
40+
41+
HCOOHX
42+
1 O u0 p2 c0 {3,S} {5,S}
43+
2 O u0 p2 c0 {3,D}
44+
3 C u0 p0 c0 {1,S} {2,D} {4,S}
45+
4 H u0 p0 c0 {3,S}
46+
5 H u0 p0 c0 {1,S}
47+
6 X u0 p0 c0
48+
49+
CHOX
50+
1 O u0 p2 c0 {2,D}
51+
2 C u0 p0 c0 {1,D} {3,S} {4,S}
52+
3 H u0 p0 c0 {2,S}
53+
4 X u0 p0 c0 {2,S}
54+
55+
XCHOH
56+
1 O u0 p2 c0 {2,S} {4,S}
57+
2 C u0 p0 c0 {1,S} {3,S} {5,D}
58+
3 H u0 p0 c0 {2,S}
59+
4 H u0 p0 c0 {1,S}
60+
5 X u0 p0 c0 {2,D}
61+
62+
CH2OX
63+
1 O u0 p2 c0 {2,D}
64+
2 C u0 p0 c0 {1,D} {3,S} {4,S}
65+
3 H u0 p0 c0 {2,S}
66+
4 H u0 p0 c0 {2,S}
67+
5 X u0 p0 c0
68+
69+
XCH2OH
70+
1 O u0 p2 c0 {2,S} {3,S}
71+
2 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S}
72+
3 H u0 p0 c0 {1,S}
73+
4 H u0 p0 c0 {2,S}
74+
5 H u0 p0 c0 {2,S}
75+
6 X u0 p0 c0 {2,S}
76+
77+
XCH2
78+
1 H u0 p0 c0 {2,S}
79+
2 C u0 p0 c0 {1,S} {3,S} {4,D}
80+
3 H u0 p0 c0 {2,S}
81+
4 X u0 p0 c0 {2,D}

‎input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py‎

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1+
#!/usr/bin/env python
2+
# encoding: utf-8
3+
4+
name = "CO2RR_DFT_Ag111"
5+
shortDesc = u"Calculated by Manish Kumar Kothakonda at Northeastern University"
6+
longDesc = u"""
7+
Place holder for long description
8+
"""
9+
10+
11+
entry(
12+
index = 1,
13+
label = "CO2X + proton <=> CO2HX",
14+
degeneracy = 1,
15+
kinetics = SurfaceChargeTransfer(
16+
alpha = 0.62, # charge transfer coeff
17+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
18+
n = 0, # temperature coeff
19+
V0 = (-0.0, 'V'), # reference potential
20+
Ea = (0.75, 'eV/molecule'), # activation energy
21+
Tmin = (298, 'K'),
22+
Tmax = (3000, 'K'),
23+
electrons = 1, # electron stochiometric coeff
24+
),
25+
shortDesc = u"""CO2RR_Ag111""",
26+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
27+
metal = "Ag",
28+
facet = "111",
29+
)
30+
31+
entry(
32+
index = 2,
33+
label = "CO2X + proton <=> CHO2X",
34+
kinetics = SurfaceChargeTransfer(
35+
alpha = 0.46, # charge transfer coeff
36+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
37+
n = 0, # temperature coeff
38+
V0 = (-0.0, 'V'), # reference potential
39+
Ea = (1.25, 'eV/molecule'), # activation energy
40+
Tmin = (298, 'K'),
41+
Tmax = (3000, 'K'),
42+
electrons = 1, # electron stochiometric coeff
43+
),
44+
shortDesc = u"""CO2RR_Ag111""",
45+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
46+
metal = "Ag",
47+
facet = "111",
48+
)
49+
50+
entry(
51+
index = 3,
52+
label = "CO2HX + proton <=> OCX + H2O",
53+
kinetics = SurfaceChargeTransfer(
54+
alpha = 0.36, # charge transfer coeff
55+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
56+
n = 0, # temperature coeff
57+
V0 = (-0.0, 'V'), # reference potential
58+
Ea = (0.25, 'eV/molecule'), # activation energy
59+
Tmin = (298, 'K'),
60+
Tmax = (3000, 'K'),
61+
electrons = 1, # electron stochiometric coeff
62+
),
63+
shortDesc = u"""CO2RR_Ag111""",
64+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
65+
metal = "Ag",
66+
facet = "111",
67+
)
68+
69+
entry(
70+
index = 4,
71+
label = "CO2HX + proton <=> HCOOHX",
72+
kinetics = SurfaceChargeTransfer(
73+
alpha = 0.62, # charge transfer coeff
74+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
75+
n = 0, # temperature coeff
76+
V0 = (-0.0, 'V'), # reference potential
77+
Ea = (2.40, 'eV/molecule'), # activation energy
78+
Tmin = (298, 'K'),
79+
Tmax = (3000, 'K'),
80+
electrons = 1, # electron stochiometric coeff
81+
),
82+
shortDesc = u"""CO2RR_Ag111""",
83+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
84+
metal = "Ag",
85+
facet = "111",
86+
)
87+
88+
entry(
89+
index = 5,
90+
label = "CHO2X + proton <=> HCOOHX",
91+
kinetics = SurfaceChargeTransfer(
92+
alpha = 0.12, # charge transfer coeff
93+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
94+
n = 0, # temperature coeff
95+
V0 = (-0.0, 'V'), # reference potential
96+
Ea = (2.64, 'eV/molecule'), # activation energy
97+
Tmin = (298, 'K'),
98+
Tmax = (3000, 'K'),
99+
electrons = 1, # electron stochiometric coeff
100+
),
101+
shortDesc = u"""CO2RR_Ag111""",
102+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
103+
metal = "Ag",
104+
facet = "111",
105+
)
106+
107+
entry(
108+
index = 6,
109+
label = "OCX + proton <=> CHOX",
110+
kinetics = SurfaceChargeTransfer(
111+
alpha = 0.49, # charge transfer coeff
112+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
113+
n = 0, # temperature coeff
114+
V0 = (-0.0, 'V'), # reference potential
115+
Ea = (0.45, 'eV/molecule'), # activation energy
116+
Tmin = (298, 'K'),
117+
Tmax = (3000, 'K'),
118+
electrons = 1, # electron stochiometric coeff
119+
),
120+
shortDesc = u"""CO2RR_Ag111""",
121+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
122+
metal = "Ag",
123+
facet = "111",
124+
)
125+
126+
entry(
127+
index = 7,
128+
label = "CHOX + proton <=> XCHOH",
129+
kinetics = SurfaceChargeTransfer(
130+
alpha = 0.71, # charge transfer coeff
131+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
132+
n = 0, # temperature coeff
133+
V0 = (-0.0, 'V'), # reference potential
134+
Ea = (2.14, 'eV/molecule'), # activation energy
135+
Tmin = (298, 'K'),
136+
Tmax = (3000, 'K'),
137+
electrons = 1, # electron stochiometric coeff
138+
),
139+
shortDesc = u"""CO2RR_Ag111""",
140+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
141+
metal = "Ag",
142+
facet = "111",
143+
)
144+
145+
entry(
146+
index = 8,
147+
label = "CHOX + proton <=> CH2OX",
148+
kinetics = SurfaceChargeTransfer(
149+
alpha = 0.36, # charge transfer coeff
150+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
151+
n = 0, # temperature coeff
152+
V0 = (-0.0, 'V'), # reference potential
153+
Ea = (2.60, 'eV/molecule'), # activation energy
154+
Tmin = (298, 'K'),
155+
Tmax = (3000, 'K'),
156+
electrons = 1, # electron stochiometric coeff
157+
),
158+
shortDesc = u"""CO2RR_Ag111""",
159+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
160+
metal = "Ag",
161+
facet = "111",
162+
)
163+
164+
entry(
165+
index = 9,
166+
label = "XCH2OH + proton <=> XCH2 + H2O",
167+
kinetics = SurfaceChargeTransfer(
168+
alpha = 0.19, # charge transfer coeff
169+
A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+
170+
n = 0, # temperature coeff
171+
V0 = (-0.0, 'V'), # reference potential
172+
Ea = (0.79, 'eV/molecule'), # activation energy
173+
Tmin = (298, 'K'),
174+
Tmax = (3000, 'K'),
175+
electrons = 1, # electron stochiometric coeff
176+
),
177+
shortDesc = u"""CO2RR_Ag111""",
178+
longDesc = u"""Calculated by Manish Kumar Kothakonda""",
179+
metal = "Ag",
180+
facet = "111",
181+
)

‎input/recommended_libraries.yml‎

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Original file line numberDiff line numberDiff line change
@@ -225,18 +225,18 @@ halogens:
225225
thermo:
226226
- Chlorinated_Hydrocarbons #Chlorinated hydrocarbons used to fit/validate Cl GAV's and non-NNI's
227227
- Chlorination #chlorinated species from many sources (CBS-QB3, Burcat, etc.), recommended as a secondary library for Chlorine models
228-
- CHOBr_G4 #non-cyclic and cyclic closed & radical small molecules with at least 1 Br & C, H, O. G4 method.
229-
- CHOClBr_G4 # non-cyclic, closed/radical, at least 1 Cl and 1 Br & C, H, O. G4 method.
230-
- CHOCl_G4 # non-cyclic/cyclic, closed/radical, at least 1 Cl & C, H, O. G4 method.
231-
- CHOFBr_G4 # non-cyclic, closed/radical, at least 1 F and 1 Br & C, H, O. G4 method.
232-
- CHOFClBr_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl, 1 Br & C, H, O. G4 method.
233-
- CHOFCl_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl & C, H, O. G4 method.
234-
- CHOF_G4 # non-cyclic/cyclic closed/radical, at least 1 F & C, H, O. G4 method.
228+
- CHOBr_G4 #non-cyclic and cyclic closed & radical small molecules with at least 1 Br & C, H, O. G4 method.
229+
- CHOClBr_G4 # non-cyclic, closed/radical, at least 1 Cl and 1 Br & C, H, O. G4 method.
230+
- CHOCl_G4 # non-cyclic/cyclic, closed/radical, at least 1 Cl & C, H, O. G4 method.
231+
- CHOFBr_G4 # non-cyclic, closed/radical, at least 1 F and 1 Br & C, H, O. G4 method.
232+
- CHOFClBr_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl, 1 Br & C, H, O. G4 method.
233+
- CHOFCl_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl & C, H, O. G4 method.
234+
- CHOF_G4 # non-cyclic/cyclic closed/radical, at least 1 F & C, H, O. G4 method.
235235
- Fluorine #thermo to pair with "NIST_Fluorine" kinetic library
236236
- halogens #to be used for F/Cl/Br-containing systems, various sources (i.e. G4/RRHO, ATcT)
237-
- iodinated_Hydrocarbons
238-
- 2-BTP_G4 #to pair with the 2-BTP thermo library. F- and Br-containing species, G4 level of theory, RRHO approx.
239-
- 2-BTP #to use with "2-BTP" kinetic library. Computed with G3MP2B3 & G3B3 composite ab initio methods; Geometries, vib. freq.,and ZPE calculated at B3LYP/6–31G(d) level of theory.
237+
- iodinated_Hydrocarbons
238+
- 2-BTP_G4 #to pair with the 2-BTP thermo library. F- and Br-containing species, G4 level of theory, RRHO approx.
239+
- 2-BTP #to use with "2-BTP" kinetic library. Computed with G3MP2B3 & G3B3 composite ab initio methods; Geometries, vib. freq.,and ZPE calculated at B3LYP/6–31G(d) level of theory.
240240
kinetics:
241241
- 2-BTP #flame suppression chemistry for 2-bromo-3,3,3-trifluoropropene
242242
- CH3Cl #chloromethane pyrolysis/oxidation and relevant H-abstraction reactions, combined with CRECK C1-C3 mechanism
@@ -265,4 +265,9 @@ electrochem:
265265
- LithiumAnalogyKinetics
266266
- LithiumSurface
267267
- LithiumSurfaceAnalogy
268+
- Surface_Proton_Electron_Reduction_Alpha
269+
- Surface_Proton_Electron_Reduction_Alpha_vdW
270+
- Surface_Proton_Electron_Reduction_Beta
271+
- Surface_Proton_Electron_Reduction_Beta_vdW
272+
- Surface_Proton_Electron_Reduction_Beta_Dissociation
268273
transport: []

‎input/surface/libraries/metal.py‎

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@@ -429,3 +429,22 @@
429429
Lattice constant using PW91 is a=2.85 Angstrom.
430430
""",
431431
)
432+
433+
entry(
434+
index = 22,
435+
label = "Cu3Sn0001",
436+
bindingEnergies = {
437+
'H': (-2.3766, 'eV/molecule'),
438+
'C': (-4.2480, 'eV/molecule'),
439+
'N': (-3.3060, 'eV/molecule'),
440+
'O': (-4.1415, 'eV/molecule'),
441+
},
442+
surfaceSiteDensity = (1.4319e-09, 'mol/cm^2'),
443+
facet = "0001",
444+
metal = "Cu3Sn",
445+
shortDesc = """Cu3Sn(0001)""",
446+
longDesc =
447+
"""
448+
Calculated by Colin Gallagher and Su Sun at Northeastern University. Only Cu sites considered as active adsorption sites from thermodynamics analysis.
449+
""",
450+
)

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