Adsorption Energy

This is especially important for surface intermediates (OH*, COOH*, CHO*) that are only in the local DB, not in CatHub as gas→surface reactions.

Definition

Adsorption energy is the energy change when a gas-phase molecule binds to a surface:

E_ads = E(slab+adsorbate) - E(slab) - E(gas)

• E(slab+adsorbate) -- total DFT energy of the adsorbate bound to the surface
• E(slab) -- total DFT energy of the clean surface slab
• E(gas) -- total DFT energy of the isolated gas-phase molecule

All energies in eV. Negative = favorable (exothermic), positive = unfavorable (endothermic).

Data Source 1: CatHub GraphQL API

Use the cathub skill for all GraphQL query mechanics. This section only covers which queries yield adsorption energies.

Method A: Reaction Energy as Adsorption Energy

When a CatHub reaction has the form Xgas + star -> Xstar, the reactionEnergy field IS the adsorption energy. Use these filters:

• reactants: "~{adsorbate}gas" -- gas-phase molecule (partial match)
• products: "~{adsorbate}star" -- adsorbed species
• chemicalComposition and facet to select the surface

Note: Including +star in the reactants filter (e.g., "COgas+star") is accepted by the API but unnecessary -- the API matches adsorption reactions without it.

Verified CatHub E_ads values

Warnings

Partial match and short species names:

• For short species (H, O, OH), use exact match (no ~ prefix). ~Hgas matches HCOOHgas, SiHgas, CHgas — giving false positives.
• Use ~ only for longer, unambiguous names like COgas, H2Ogas.
• ~COOHgas is unsafe — it matches HCOOHgas (HCOOH decomposition, not COOH adsorption).

OH*, COOH*, and other surface intermediates are NOT gas-phase species: Method A only works for species that exist as gas-phase molecules in CatHub (CO, H, H2O, O2, etc.). Intermediates like OH* and COOH* are formed on surfaces through reactions, not adsorbed from gas phase. CatHub has no OHgas → OHstar or COOHgas → COOHstar entries. To get their formation energies, use the local database (Data Source 2) or query the surface reactions that produce them (e.g., H2Ogas → OHstar + Hstar).

Method B: From Individual System Energies

For reactions that are not simple molecular adsorption (e.g., dissociative adsorption), request the reactionSystems field with the nested systems { energy } to get individual DFT total energies. Then compute:

{ reactions(first: 1, chemicalComposition: "Cu", facet: "111", reactants: "~COgas", products: "~COstar") {
    edges { node { reactionSystems { name energyCorrection systems { energy Formula } } } }
}}

E_ads = E(COstar) - E(star) - E(COgas)
      = -250.06 - (-234.52) - (-14.69) = -0.85 eV

Note: The energy field is on the nested systems object (type System), NOT on reactionSystems directly (type ReactionSystem). Many CatHub entries return null for system-level energies -- in that case, fall back to Method A where reactionEnergy is already the computed E_ads.

Data Source 2: Local Database (co2r-suncat.db)

The local SQLite database (data/co2r-suncat.db) contains curated DFT data for CO2 reduction on transition metals. It is the preferred source for CO2R intermediates (COOH*, CHO*, COH*, OH*, etc.) that are not available as gas-phase species in CatHub.

Database Coverage

Adsorbate species (42 total): C, CCH, CCH2, CCH3, CCHO, CCO, CCO2chem, CCO2phys, CCOH, CH, CH2, CH2CH3, CH2CHOH, CH2CO, CH2COH, CH3, CH3CO, CH3COH, CHCH, CHCH2, CHCH3, CHCHOH, CHCO, CHCOH, CHO, CHOH, CO, CO2phys, COH, COOH, H, H2O, HCOO, OCCO, OCCOH, OCH2CH, OCH2CH2, OCH2CH3, OCHCH, OCHCH2, OCHCH3, OCHO, OH

Querying the Database

The FormationEnergy table uses foreign key IDs (status_id, species_id, surface_id, facet_id, reference_id). Always use the FormationEnergyView which joins all lookup tables and provides human-readable columns:

SELECT species_name, formation_energy, active_site, surface_name, facet, reference
FROM FormationEnergyView
WHERE status='ads' AND species_name='CO' AND surface_name='Cu' AND facet='100' AND efield=0.0;

Available columns in FormationEnergyView: formation_energy_id, formation_energy, active_site, cell_size, coverage, efield, reference, surface_name, facet, species_name, status.

Do NOT query FormationEnergy directly with status='ads' — the raw table has status_id (integer), not status (text), and the query will error.

Multiple Values Per System

The database often has multiple entries for the same species + surface + facet because:

• Multiple binding sites (active_site): atop, bridge, fcc, 4foldhollow, bidentate, etc. Different sites give different E_ads.
• Multiple references: Different DFT studies may give slightly different values (~0.06 eV spread for CO on Cu(100) atop across references).

Always check which active_site and reference you need. The most stable (most negative) E_ads is typically the preferred binding site.

Reference System

Three gas-phase reference molecules are set to formation_energy = 0.0 eV:

The clean slab is also set to 0.0 eV as the surface reference.

All other species have formation energies computed relative to this reference set.

Verified gas-phase formation energies

Formation Energy = Adsorption Energy (for adsorbates only)

For adsorbates (status='ads'): The formation_energy column IS the adsorption energy. Since both the gas-phase reference and the slab are 0.0 eV, the stored value is directly:

-- CO* on Cu(100), atop site, from Ara reference:
formation_energy(CO*) = E_DFT(CO + Cu_slab) - E_DFT(Cu_slab) - E_DFT(CO_gas) = -0.659 eV = E_ads(CO)

This holds for ALL adsorbates. No further subtraction needed.

For gas-phase species (status='gas'): Formation energy is NOT an adsorption energy. It is the energy relative to the reference set {CO=0, H2=0, H2O=0}, computed by decomposing into reference molecules:

CO2 = CO + H2O - H2    (atom balance: C+2O = C+O + 2H+O - 2H ✓)
E_form(CO2) = E_DFT(CO2) - E_DFT(CO) - E_DFT(H2O) + E_DFT(H2) = -0.284 eV

This is the reverse water-gas shift reaction energy (CO + H2O → CO2 + H2).

For transition states (status='ts'): Formation energy = sum of initial-state formation energies + activation energy (Ea):

CO2-H-ele: IS = CO2_gas + H_gas + 2*slab + ele_gas
E_form(TS) = (-0.284) + 0.0 + 0.0 + 0.0 + 0.06 (Ea) = -0.224 eV

Verified Adsorption Energies

CO binding across metals — (111) facet, fcc site, PengRole2020

Follows the expected d-band center trend.

CO binding on Cu across facets — fcc site, PengRole2020

Under-coordinated step/kink sites bind CO strongest; close-packed terraces bind weakest.

CO2R intermediates on Cu(100) — most stable site, Ara reference

Key intermediates on coinage metals — (211) facet

Cu binds all intermediates strongest among coinage metals. H is endothermic on Ag and Au (HER suppressed). COOH/OH data only available for Cu.

Electric Field Data

The database contains E-field dependent adsorption energies from PasumarthiFacetDependence2023:

SELECT species_name, efield, formation_energy, active_site, facet
FROM FormationEnergyView
WHERE status='ads' AND species_name='CO' AND surface_name='Cu' AND facet='211'
ORDER BY efield;

Example — CO on Cu(211) ontop-step site:

Positive field slightly strengthens CO binding (Stark effect).

Why CatHub "Reaction Energy" = DB "Formation Energy" for Adsorbates

Both compute the same formula, just named differently:

Values may differ between CatHub and the local DB if they come from different DFT calculations.

Gotchas

1. Formation energy = adsorption energy ONLY for adsorbates. The database stores energies already referenced to gas-phase species (CO=0, H2=0, H2O=0) and clean slabs (slab=0). For adsorbates, this directly equals the adsorption energy. Do not subtract slab or gas energy again. For gas-phase species, formation energy is NOT an adsorption energy -- it is the energy relative to the reference molecule set.
2. Gas-phase reference system: Three molecules are set to 0.0 eV: CO, H2, H2O. Other gas species (CO2=-0.284 eV, CH4=-2.805 eV) have formation energies computed by decomposing into these references. E.g., CO2 = CO + H2O - H2 gives E_form(CO2) = -0.284 eV (the water-gas shift reaction energy).
3. Use FormationEnergyView, not FormationEnergy. The raw table uses integer foreign keys (status_id, species_id, etc.). Querying WHERE status='ads' on the raw table will error. The view provides human-readable columns.
4. Multiple entries per system. The same species/surface/facet combination often has multiple rows due to different binding sites (active_site) and DFT references (~0.06 eV spread for CO on Cu(100) atop across references). Always filter or aggregate appropriately.
5. CatHub Method A only works for true gas-phase species. CO, H, H2O, O2 can be queried as Xgas → Xstar. Surface intermediates (OH*, COOH*, CHO*, COH*) do not exist as gas-phase species in CatHub — use the local database instead.
6. CatHub partial match (~) is unsafe for short names. ~Hgas matches HCOOHgas, SiHgas, CHgas. ~COOHgas matches HCOOHgas. Use exact match for short species.
7. CatHub reactionEnergy is not always E_ads -- it depends on the reaction. A dissociative adsorption (e.g., O2(g) -> 2O*) gives a different quantity than simple molecular adsorption. Check the reactants/products to understand what the energy represents.
8. CatHub API specifics -- see the cathub skill for API limits, partial matching, species naming conventions, and pagination constraints.

Current Limitations

• Local database focused on CO2 reduction species -- may not have data for all adsorbates
• COOH, OH, CHO data in local DB only available for Cu (not Ag, Au, Pt, etc.)
• No automatic comparison across different DFT functionals
• Electric field data only from PasumarthiFacetDependence2023, limited facets (211, 310, 511)
• Coverage-dependent adsorption energies not systematically available
• CatHub Method B (reactionSystems { systems { energy } }) often returns null