r"""Reaction intermediates for |CO2RR|, NRR/UOR, OER/ORR, and HER.
|CO2RR| Intermediates from Nitopi et al. [1]_
NRR/UOR Intermediates Wan et al. [2]_ and Li et al. [3]_
Bond lengths, angles and positions from NIST_.
Example:
>>> from ccu.adsorption.adsorbates import get_adsorbate
>>> get_adsorbate("CO2")
Atoms(symbols='CO2', pbc=False)
.. [1] |ref1|_
.. |ref1| replace:: Chem. Rev. **2019**, 119, 12, 7610-7672.
.. _ref1: https://pubs.acs.org/doi/10.1021/acs.chemrev.8b00705
.. [2] |ref2|_
.. |ref2| replace:: ACS Catal. **2023**, 13, 3, 1926-1933.
.. _ref2: https://pubs.acs.org/doi/abs/10.1021/acscatal.2c05315
.. [3] |ref3|_
.. |ref3| replace:: Angew. Chem. Int. Ed. **2021**, 60, 51, 26656.
.. _ref3: https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202107886
.. _NIST: https://cccbdb.nist.gov
"""
import ase
from ase import Atoms
from ase.build import molecule
from ase.data.pubchem import pubchem_atoms_search
def _co2rr_adsorbates() -> dict[str, ase.Atoms]:
co2 = molecule("CO2")
# C-O: HCOOH; C=0: HCOOH, O-H: HCOOH
cooh_cis = ase.Atoms(
"CO2H",
positions=[[0, 0, 0], [1.202, 0, 0], [0, 1.343, 0], [0.972, 1.343, 0]],
)
# <OCO: HCOOH
cooh_cis.set_angle(2, 0, 1, angle=124.9)
# <COH: HCOOH
cooh_cis.set_angle(0, 2, 3, angle=106.3)
cooh_cis.info["special centres"] = (0,)
cooh_trans = ase.Atoms(
"CO2H",
positions=[
[0, 0, 0],
[1.202, 0, 0],
[0, 1.343, 0],
[-0.972, 1.343, 0],
],
)
# <OCO: HCOOH
cooh_trans.set_angle(2, 0, 1, angle=124.9)
# <COH: HCOOH (flipped)
cooh_trans.set_angle(0, 2, 3, angle=106.3)
cooh_trans.info["special centres"] = (0,)
# C-O: HCOOH; C-H: HCOOH
ocho = ase.Atoms(
"CO2H",
positions=[[0, 0, 0], [1.343, 0, 0], [0, 1.343, 0], [-1.097, 0, 0]],
)
# <OCO: symmetry
ocho.set_angle(2, 0, 1, angle=120)
# <COH: HCOOH
ocho.set_angle(1, 0, 3, angle=120)
ocho.info["special centres"] = (0,)
hcooh = molecule("HCOOH")
hcooh.info["special centres"] = (1,)
co = ase.Atoms("CO", positions=[[0, 0, 0], [1.128, 0, 0]])
# C-O: CH3OH; O-H: CH3OH
coh = ase.Atoms("COH", positions=[[0, 0, 0], [1.427, 0, 0], [0, 0.956, 0]])
# <COH: CH3OH
coh.set_angle(1, 0, 2, angle=108.87)
coh.info["special centres"] = (0,)
# C-H: CHO; C-O: CHO
cho = ase.Atoms("CHO", positions=[[0, 0, 0], [1.080, 0, 0], [0, 1.198, 0]])
# <HCO: CHO
cho.set_angle(1, 0, 2, angle=119.5)
cho.info["special centres"] = (0,)
c = ase.Atoms("C", positions=[[0, 0, 0]])
# C-H: HCOOH; C-O: HCOOH; O-H: HCOOH
choh = ase.Atoms(
"CHOH",
positions=[
[0, 0, 0],
[0, -1.097, 0],
[1.343, 0, 0],
[1.343, 0.972, 0],
],
)
# <OCO: HCOOH
choh.set_angle(1, 0, 2, angle=128.8)
# <COH: HCOOH
choh.set_angle(0, 2, 3, angle=106.3)
choh.info["special centres"] = (0,)
# C-H: H2CO; C-O: H2CO
ch2o = ase.Atoms(
"CH2O",
positions=[[0, 0, 0], [0, -1.111, 0], [1.111, 0, 0], [0, 1.205, 0]],
)
# <HCH: H2CO
ch2o.set_angle(2, 0, 1, angle=116.133)
# <HCO: H2CO
ch2o.set_angle(1, 0, 3, angle=121.9)
ch2o.info["special centres"] = (0,)
# C-H: CH3OH; C-O: CH3OH; O-H: CH3OH
ch2oh = ase.Atoms(
"CH2OH",
positions=[
[0, 0, 0],
[-1.096, 0, 0],
[0, -1.096, 0],
[1.427, 0, 0],
[1.427, 0.956, 0],
],
)
# <HCH: H2CO
ch2oh.set_angle(2, 0, 1, angle=116.133)
# <HCO: symmetry
ch2oh.set_angle(1, 0, 3, angle=121.9)
# <HOC: CH3OH
ch2oh.set_angle(0, 3, 4, angle=108.87)
ch2oh.info["special centres"] = (0,)
# Positions from CH3O
och3 = ase.Atoms(
"OCH3",
positions=[
[0, 0, 0.8151],
[0, 0, -0.5899],
[0, 1.0360, -0.9938],
[0.8972, -0.5180, -0.9938],
[-0.8972, -0.5180, -0.9938],
],
)
och3.info["special centres"] = (0,)
# C-H: H2CO
ch2 = ase.Atoms(
"CH2", positions=[[0, 0, 0], [0, -1.111, 0], [1.111, 0, 0]]
)
# <HCH: H2CO
ch2.set_angle(1, 0, 2, angle=116.133)
ch2.info["special centres"] = (0,)
# Positions from CH3O
ch3 = ase.Atoms(
"CH3",
positions=[
[0, 0, -0.5899],
[0, 1.0360, -0.9938],
[0.8972, -0.5180, -0.9938],
[-0.8972, -0.5180, -0.9938],
],
)
ch3.info["special centres"] = (0,)
return {
"CO2": co2,
"COOH_CIS": cooh_cis,
"COOH_TRANS": cooh_trans,
"OCHO": ocho,
"HCOOH": hcooh,
"CO": co,
"COH": coh,
"CHO": cho,
"C": c,
"CHOH": choh,
"CH2O": ch2o,
"HC2OH": ch2oh,
"OCH3": och3,
"CH2": ch2,
"CH3": ch3,
}
def _nrr_adsorbates() -> dict[str, ase.Atoms]:
# N-O: NO3
no3 = ase.Atoms(
"NO3",
positions=[[0, 0, 0], [0, 1.238, 0], [-1.238, 0, 0], [1.238, 0, 0]],
)
# <ONO: NO3
no3.set_angle(2, 0, 1, angle=120)
no3.set_angle(1, 0, 3, angle=120)
# N-O: HNO3; O-H: HNO3
no3h = ase.Atoms(
"NO3H",
positions=[
[0, 0, 0],
[-1.199, 0, 0],
[0, 1.211, 0],
[1.406, 0, 0],
[1.406, 0.964, 0],
],
)
# <ONO: HNO3; <HON: HNO3
no3h = pubchem_atoms_search(cid=944)
no3h.info["special centres"] = (3,)
# N-O: HNO2
no2 = ase.Atoms("NO2", positions=[[0, 0, 0], [0, 1.442, 0], [1.442, 0, 0]])
# <ONO: HNO2
no2.set_angle(1, 0, 2, angle=110.6)
# N-O: HNO2; N=0: HNO2
no2h = ase.Atoms(
"NO2H",
positions=[
[0, 0, 0],
[-1.442, 0, 0],
[0, 1.169, 0],
[-1.442, -0.959, 0],
],
)
# <ONO: HNO2
no2h.set_angle(1, 0, 2, angle=110.6)
# <HON: HNO2
no2h.set_angle(0, 1, 3, angle=102.1)
no2h.info["special centres"] = (0,)
# N=O: NO
no = ase.Atoms("NO", positions=[[0, 0, 0], [1.154, 0, 0]])
# N-O: HNO2 & NH2OH (average); O-H: HNO2 & NH2OH (average)
noh = ase.Atoms(
"NOH",
positions=[
[0, 0, 0],
[0.5 * (1.442 + 1.453), 0, 0],
[0.5 * (1.442 + 1.453), 0.5 * (0.959 + 0.962), 0],
],
)
# <NOH: HNO2 & NH2OH (average)
noh.set_angle(0, 1, 2, angle=0.5 * (102.1 + 101.37))
noh.info["special centres"] = (0,)
# N-H: NH2OH & HNO (average); N-O: NH2OH & HNO (average)
nho = ase.Atoms(
"HNO",
positions=[
[0, 0, 0],
[0.5 * (1.016 + 1.090), 0, 0],
[0.5 * (1.016 + 1.090), 0.5 * (1.453 + 1.209), 0],
],
)
# <HNO: NH2OH & HNO (average)
nho.set_angle(0, 1, 2, angle=0.5 * (107.01 + 108.047))
nho.info["special centres"] = (2,)
# N-H: NH2OH; N-O: NH2OH; O-H: NH2OH
nhoh = ase.Atoms(
"HNOH",
positions=[
[0, 0, 0],
[1.016, 0, 0],
[1.016, 1.453, 0],
[1.016 + 0.962, 1.453, 0],
],
)
# <HNO: NH2OH
nhoh.set_angle(0, 1, 2, angle=107.1)
# <HON: NH2OH
nhoh.set_angle(1, 2, 3, angle=101.37)
nhoh.info["special centres"] = (1,)
n = ase.Atoms("N")
# N-H: NH
nh = ase.Atoms("NH", positions=[[0, 0, 0], [1.036, 0, 0]])
# N-H: NH2
nh2 = ase.ase.Atoms(
"HNH",
positions=[
[0, 0, 0],
[1.024, 0, 0],
[0, 1.024, 0],
],
)
# <HNH: NH2
nh2.set_angle(0, 1, 2, angle=103.4)
# N-H: NH2; N-O: NH2OH
nh2o = ase.ase.Atoms(
"NH2O",
positions=[
[0, 0, 0],
[1.024, 0, 0],
[0, 1.024, 0],
[-0.8523, -0.8523, 0],
],
)
nh2o.info["special centres"] = (
0,
3,
)
# N-H: NH2OH
nh2oh = ase.ase.Atoms(
"NH2OH",
positions=[
[-0.0094, 0.704, 0],
[0.5469, 1.0012, 0.7965],
[0.5469, 1.0012, -0.7965],
[-0.0094, -0.7490, 0],
[-0.9525, -0.9386, 0],
],
)
nh2oh.info["special centres"] = (
0,
3,
)
# Positions from NH3
nh3 = ase.Atoms(
"NH3",
positions=[
[0, 0, 0],
[0, -0.9377, -0.3816],
[0.812, 0.4689, -0.3816],
[-0.812, 0.4689, -0.3816],
],
)
n2 = molecule("N2")
n2o = molecule("N2O")
return {
"NO3": no3,
"NO3H": no3h,
"NO2": no2,
"NO2H": no2h,
"NO": no,
"NOH": noh,
"NHO": nho,
"NHOH": nhoh,
"N": n,
"NH": nh,
"NH2": nh2,
"NH2O": nh2o,
"NH2OH": nh2oh,
"NH3": nh3,
"N2": n2,
"N2O": n2o,
}
def _orr_adsorbates() -> dict[str, ase.Atoms]:
return {
"O": ase.Atoms("O"),
# O-H: OH-
"OH": ase.Atoms("OH", positions=[[0, 0, 0], [0.964, 0, 0]]),
"H2O": molecule("H2O"),
}
CO2RR_ADSORBATES = _co2rr_adsorbates()
NRR_ADSORBATES = _nrr_adsorbates()
ORR_ADSORBATES = _orr_adsorbates()
HER_ADSORBATES = {
"H": ase.Atoms("H"),
"OH": ORR_ADSORBATES["OH"],
"H2O": ORR_ADSORBATES["H2O"],
}
ALL: dict[str, Atoms] = {}
ALL.update(CO2RR_ADSORBATES)
ALL.update(NRR_ADSORBATES)
ALL.update(ORR_ADSORBATES)
ALL.update(HER_ADSORBATES)
for name, adsorbate in ALL.items():
adsorbate.info["name"] = name
[docs]
def get_adsorbate(adsorbate: str) -> ase.Atoms:
"""Return the requested adsorbate as an ase.Atoms object.
Args:
adsorbate: The name of the adsorbate to retrieve as a string
(case-insensitive).
Raises:
NotImplementedError: The requested adsorbate is neither a molecule
supported by ASE nor a defined adsorbate in
:mod:`ccu.adsorption.adsorbates`.
Returns:
An :class:`.atoms.Atoms` instance representing the requested adsorbate.
"""
name = adsorbate.upper()
try:
atoms = molecule(name)
atoms.info["name"] = name
return atoms
except KeyError:
pass
try:
return ALL[name]
except KeyError as error:
msg = f"The {adsorbate} adsorbate is not supported yet."
raise NotImplementedError(msg) from error