Add thermo and kinetics data for electrocatalytic CO2 reduction

input/kinetics/families/recommended.py

@@ -116,7 +116,7 @@
     'Surface_Adsorption_Bidentate',
     'Surface_Bidentate_Dissociation',
     'Surface_Monodentate_to_Bidentate',
-    'Surface_Dissociation_to_Bidentate', 
+    'Surface_Dissociation_to_Bidentate',
     'Surface_vdW_to_Bidentate',
     'Surface_Adsorption_Dissociative_Double',
     'Surface_Abstraction_Beta',
@@ -152,7 +152,7 @@
     'Surface_Migration',
 }
 
-# Electrochemical families!
+# Electrochemical families.
 electrochem = {
     'Surface_Proton_Electron_Reduction_Alpha',
     'Surface_Proton_Electron_Reduction_Alpha_vdW',
@@ -170,3 +170,24 @@
     'Li_Abstraction',
     'R_Addition_MultipleBond_Disprop',
 }
+
+# Electrocatalytic CO2 Reduction families.
+surface_CO2 = {
+    'Surface_Abstraction',
+    'Surface_Abstraction_vdW',
+    'Surface_Abstraction_Single_vdW',
+    'Surface_Abstraction_Beta_double_vdW',
+    'Surface_Adsorption_Dissociative',
+    'Surface_Adsorption_Dissociative_Double',
+    'Surface_Adsorption_vdW',
+    'Surface_Dissociation',
+    'Surface_Dissociation_Double_vdW',
+    'Surface_Dissociation_vdW',
+    'Surface_EleyRideal_Addition_Multiple_Bond',
+    'Surface_Migration',
+    'Surface_Proton_Electron_Reduction_Alpha',
+    'Surface_Proton_Electron_Reduction_Alpha_vdW',
+    'Surface_Proton_Electron_Reduction_Beta',
+    'Surface_Proton_Electron_Reduction_Beta_vdW',
+    'Surface_Proton_Electron_Reduction_Beta_Dissociation',
+}

input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt

@@ -0,0 +1,81 @@
+
+X
+1 X u0 p0 c0
+
+proton
+1 H u0 p0 c+1
+
+e
+1 e u0 p0 c-1
+
+H2O
+1 O u0 p2 c0 {2,S} {3,S}
+2 H u0 p0 c0 {1,S}
+3 H u0 p0 c0 {1,S}
+
+CO2X
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 O u0 p2 c0 {2,D}
+4 X u0 p0 c0
+
+CO2HX
+1 O u0 p2 c0 {3,S} {4,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {5,S}
+4 H u0 p0 c0 {1,S}
+5 X u0 p0 c0 {3,S}
+
+CHO2X
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+
+OCX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 X u0 p0 c0 {2,D}
+
+HCOOHX
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 H u0 p0 c0 {1,S}
+6 X u0 p0 c0
+
+CHOX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 X u0 p0 c0 {2,S}
+
+XCHOH
+1 O u0 p2 c0 {2,S} {4,S}
+2 C u0 p0 c0 {1,S} {3,S} {5,D}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {1,S}
+5 X u0 p0 c0 {2,D}
+
+CH2OX
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {2,S}
+5 X u0 p0 c0
+
+XCH2OH
+1 O u0 p2 c0 {2,S} {3,S}
+2 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S}
+3 H u0 p0 c0 {1,S}
+4 H u0 p0 c0 {2,S}
+5 H u0 p0 c0 {2,S}
+6 X u0 p0 c0 {2,S}
+
+XCH2
+1 H u0 p0 c0 {2,S}
+2 C u0 p0 c0 {1,S} {3,S} {4,D}
+3 H u0 p0 c0 {2,S}
+4 X u0 p0 c0 {2,D}

input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py

@@ -0,0 +1,181 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+name = "CO2RR_DFT_Ag111"
+shortDesc = u"Calculated by Manish Kumar Kothakonda at Northeastern University"
+longDesc = u"""
+Place holder for long description
+"""
+
+
+entry(
+    index = 1,
+    label = "CO2X + proton <=> CO2HX",
+    degeneracy = 1,
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.62, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.75, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 2,
+    label = "CO2X + proton <=> CHO2X",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.46, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (1.25, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 3,
+    label = "CO2HX + proton <=> OCX + H2O",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.36, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.25, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 4,
+    label = "CO2HX + proton <=> HCOOHX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.62, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.40, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 5,
+    label = "CHO2X + proton <=> HCOOHX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.12, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.64, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 6,
+    label = "OCX + proton <=> CHOX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.49, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.45, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 7,
+    label = "CHOX + proton <=> XCHOH",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.71, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.14, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 8,
+    label = "CHOX + proton <=> CH2OX",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.36, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (2.60, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)
+
+entry(
+    index = 9,
+    label = "XCH2OH + proton <=> XCH2 + H2O",
+    kinetics = SurfaceChargeTransfer(
+        alpha = 0.19, # charge transfer coeff
+        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+
+        n = 0, # temperature coeff
+        V0 = (-0.0, 'V'), # reference potential
+        Ea = (0.79, 'eV/molecule'), # activation energy
+        Tmin = (298, 'K'),
+        Tmax = (3000, 'K'),
+        electrons = 1, # electron stochiometric coeff
+    ),
+    shortDesc = u"""CO2RR_Ag111""",
+    longDesc = u"""Calculated by Manish Kumar Kothakonda""",
+    metal = "Ag",
+    facet = "111",
+)

input/recommended_libraries.yml

@@ -225,18 +225,18 @@ halogens:
   thermo:
     - Chlorinated_Hydrocarbons #Chlorinated hydrocarbons used to fit/validate Cl GAV's and non-NNI's
     - Chlorination #chlorinated species from many sources (CBS-QB3, Burcat, etc.), recommended as a secondary library for Chlorine models
-    - CHOBr_G4 #non-cyclic and cyclic closed & radical small molecules with at least 1 Br & C, H, O. G4 method. 
-    - CHOClBr_G4 # non-cyclic, closed/radical, at least 1 Cl and 1 Br & C, H, O. G4 method. 
-    - CHOCl_G4 # non-cyclic/cyclic, closed/radical, at least 1 Cl & C, H, O. G4 method. 
-    - CHOFBr_G4 # non-cyclic, closed/radical, at least 1 F and 1 Br & C, H, O. G4 method. 
-    - CHOFClBr_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl, 1 Br & C, H, O. G4 method. 
-    - CHOFCl_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl & C, H, O. G4 method. 
-    - CHOF_G4 # non-cyclic/cyclic closed/radical, at least 1 F & C, H, O. G4 method. 
+    - CHOBr_G4 #non-cyclic and cyclic closed & radical small molecules with at least 1 Br & C, H, O. G4 method.
+    - CHOClBr_G4 # non-cyclic, closed/radical, at least 1 Cl and 1 Br & C, H, O. G4 method.
+    - CHOCl_G4 # non-cyclic/cyclic, closed/radical, at least 1 Cl & C, H, O. G4 method.
+    - CHOFBr_G4 # non-cyclic, closed/radical, at least 1 F and 1 Br & C, H, O. G4 method.
+    - CHOFClBr_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl, 1 Br & C, H, O. G4 method.
+    - CHOFCl_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl & C, H, O. G4 method.
+    - CHOF_G4 # non-cyclic/cyclic closed/radical, at least 1 F & C, H, O. G4 method.
     - Fluorine #thermo to pair with "NIST_Fluorine" kinetic library
     - halogens #to be used for F/Cl/Br-containing systems, various sources (i.e. G4/RRHO, ATcT)
-    - iodinated_Hydrocarbons 
-    - 2-BTP_G4 #to pair with the 2-BTP thermo library. F- and Br-containing species, G4 level of theory, RRHO approx. 
-    - 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. 
+    - iodinated_Hydrocarbons
+    - 2-BTP_G4 #to pair with the 2-BTP thermo library. F- and Br-containing species, G4 level of theory, RRHO approx.
+    - 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.
   kinetics:
     - 2-BTP #flame suppression chemistry for 2-bromo-3,3,3-trifluoropropene
     - CH3Cl #chloromethane pyrolysis/oxidation and relevant H-abstraction reactions, combined with CRECK C1-C3 mechanism
@@ -265,4 +265,9 @@ electrochem:
     - LithiumAnalogyKinetics
     - LithiumSurface
     - LithiumSurfaceAnalogy
+    - Surface_Proton_Electron_Reduction_Alpha
+    - Surface_Proton_Electron_Reduction_Alpha_vdW
+    - Surface_Proton_Electron_Reduction_Beta
+    - Surface_Proton_Electron_Reduction_Beta_vdW
+    - Surface_Proton_Electron_Reduction_Beta_Dissociation
   transport: []

input/surface/libraries/metal.py

@@ -429,3 +429,22 @@
 Lattice constant using PW91 is a=2.85 Angstrom.
 """,
 )
+
+entry(
+    index = 22,
+    label = "Cu3Sn0001",
+    bindingEnergies = {
+        'H': (-2.3766, 'eV/molecule'),
+        'C': (-4.2480, 'eV/molecule'),
+        'N': (-3.3060, 'eV/molecule'),
+        'O': (-4.1415, 'eV/molecule'),
+    },
+    surfaceSiteDensity = (1.4319e-09, 'mol/cm^2'),
+    facet = "0001",
+    metal = "Cu3Sn",
+    shortDesc = """Cu3Sn(0001)""",
+    longDesc =
+"""
+Calculated by Colin Gallagher and Su Sun at Northeastern University. Only Cu sites considered as active adsorption sites from thermodynamics analysis.
+""",
+)