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adding resonance for adsorbates
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bjkreitz committed Jul 31, 2023
1 parent 65dfeca commit a97d2d3
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2 changes: 2 additions & 0 deletions rmgpy/molecule/molecule.pxd
Original file line number Diff line number Diff line change
Expand Up @@ -289,6 +289,8 @@ cdef class Molecule(Graph):

cpdef list get_adatoms(self)

cpdef bint is_bidentate(self)

cpdef list get_desorbed_molecules(self)

cdef atom_id_counter
10 changes: 10 additions & 0 deletions rmgpy/molecule/molecule.py
Original file line number Diff line number Diff line change
Expand Up @@ -2759,6 +2759,16 @@ def get_surface_sites(self):
cython.declare(atom=Atom)
return [atom for atom in self.atoms if atom.is_surface_site()]

def is_bidentate(self):
"""
Return ``True`` if the adsorbate contains at least two binding sites,
or ``False`` otherwise.
"""
cython.declare(atom=Atom)
if len([atom for atom in self.atoms if atom.is_surface_site()])>=2:
return True
return False

def get_adatoms(self):
"""
Get a list of adatoms in the molecule.
Expand Down
4 changes: 4 additions & 0 deletions rmgpy/molecule/pathfinder.pxd
Original file line number Diff line number Diff line change
Expand Up @@ -58,3 +58,7 @@ cpdef list find_N5dc_radical_delocalization_paths(Vertex atom1)
cpdef bint is_atom_able_to_gain_lone_pair(Vertex atom)

cpdef bint is_atom_able_to_lose_lone_pair(Vertex atom)

cpdef list find_adsorbate_delocalization_paths(Vertex atom1)

cpdef list find_adsorbate_conjugate_delocalization_paths(Vertex atom1)
48 changes: 48 additions & 0 deletions rmgpy/molecule/pathfinder.py
Original file line number Diff line number Diff line change
Expand Up @@ -480,3 +480,51 @@ def is_atom_able_to_lose_lone_pair(atom):
return (((atom.is_nitrogen() or atom.is_sulfur()) and atom.lone_pairs in [1, 2, 3])
or (atom.is_oxygen() and atom.lone_pairs in [2, 3])
or atom.is_carbon() and atom.lone_pairs == 1)

def find_adsorbate_delocalization_paths(atom1):
"""
Find all bidentate adsorbates which have a bonding configuration X-C-C-X.
Examples:
- XCXC, XCHXCH, XCXCH, where X is the surface site
In this transition atom1 and atom4 are surface sites while atom2 and atom3 are carbon atoms.
"""
cython.declare(paths=list, atom2=Vertex, atom3=Vertex, atom4=Vertex, bond12=Edge, bond23=Edge, bond34=Edge)

path=[]
if atom1.is_surface_site():
for atom2, bond12 in atom1.edges.items():
if atom2.is_carbon():
for atom3, bond23 in atom2.edges.items():
if atom1 is not atom3 and atom3.is_carbon():
for atom4, bond34 in atom3.edges.items():
if atom2 is not atom4 and atom4.is_surface_site():
path.append([atom1, atom2, atom3, atom4, bond12, bond23, bond34])
return path
return path

def find_adsorbate_conjugate_delocalization_paths(atom1):
"""
Find all bidentate adsorbates which have a bonding configuration X-C-C-C-X.
Examples:
- XCHCHXCH/XCHCHXC, where X is the surface site
In this transition atom1 and atom5 are surface sites while atom2, atom3, and atom4 are carbon atoms.
"""

cython.declare(paths=list, atom2=Vertex, atom3=Vertex, atom4=Vertex, atom5=Vertex, bond12=Edge, bond23=Edge, bond34=Edge, bond45=Edge)

path=[]
if atom1.is_surface_site():
for atom2, bond12 in atom1.edges.items():
for atom3, bond23 in atom2.edges.items():
if atom1 is not atom3 and atom3.is_carbon():
for atom4, bond34 in atom3.edges.items():
if atom2 is not atom4 and atom4.is_carbon():
for atom5, bond45 in atom4.edges.items():
if atom3 is not atom5 and atom5.is_surface_site():
path.append([atom1, atom2, atom3, atom4, atom5, bond12, bond23, bond34, bond45])
return path
return path
10 changes: 10 additions & 0 deletions rmgpy/molecule/resonance.pxd
Original file line number Diff line number Diff line change
Expand Up @@ -63,3 +63,13 @@ cpdef list generate_clar_structures(Graph mol, bint save_order=?)
cpdef list _clar_optimization(Graph mol, list constraints=?, max_num=?, save_order=?)

cpdef list _clar_transformation(Graph mol, list aromatic_ring)

cpdef list generate_adsorbate_shift_down_resonance_structures(Graph mol)

cpdef list generate_adsorbate_shift_up_resonance_structures(Graph mol)

cpdef list generate_adsorbate_double_shift_up_resonance_structures(Graph mol)

cpdef list generate_adsorbate_double_shift_down_resonance_structures(Graph mol)

cpdef list generate_adsorbate_conjugate_resonance_structures(Graph mol)
199 changes: 198 additions & 1 deletion rmgpy/molecule/resonance.py
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,12 @@
- ``generate_kekule_structure``: generate a single Kekule structure for an aromatic compound (single/double bond form)
- ``generate_opposite_kekule_structure``: for monocyclic aromatic species, rotate the double bond assignment
- ``generate_clar_structures``: generate all structures with the maximum number of pi-sextet assignments
- Multidentate adsorbates only
- ``generate_adsorbate_shift_down_resonance_structures``: shift 2 electrons from a C=/#C bond to the X-C bond
- ``generate_adsorbate_shift_up_resonance_structures``: shift 2 electrons from a X=/#C bond to a C-C bond
- ``generate_adsorbate_double_shift_down_resonance_structures``: shift 4 elecrons from a C#C bond to a X-C bond
- ``generate_adsorbate_double_shift_up_resonance_structures``: shift 4 electrons from a X#C bond to a C-C bond
- ``generate_adsorbate_conjugate_resonance_structures``: shift 2 electrons in a conjugate pi system for bridged X-C-C-C-X adsorbates
"""

import logging
Expand Down Expand Up @@ -86,6 +92,11 @@ def populate_resonance_algorithms(features=None):
generate_aryne_resonance_structures,
generate_kekule_structure,
generate_clar_structures,
generate_adsorbate_shift_down_resonance_structures,
generate_adsorbate_shift_up_resonance_structures,
generate_adsorbate_double_shift_down_resonance_structures,
generate_adsorbate_double_shift_up_resonance_structures,
generate_adsorbate_conjugate_resonance_structures
]
else:
# If the molecule is aromatic, then radical resonance has already been considered
Expand All @@ -109,7 +120,12 @@ def populate_resonance_algorithms(features=None):
# solution. A more holistic approach would be to identify these cases in generate_resonance_structures,
# and pass a list of forbidden atom ID's to find_lone_pair_multiple_bond_paths.
method_list.append(generate_lone_pair_multiple_bond_resonance_structures)

if features['is_bidentate']:
method_list.append(generate_adsorbate_shift_down_resonance_structures)
method_list.append(generate_adsorbate_shift_up_resonance_structures)
method_list.append(generate_adsorbate_double_shift_down_resonance_structures)
method_list.append(generate_adsorbate_double_shift_up_resonance_structures)
method_list.append(generate_adsorbate_conjugate_resonance_structures)
return method_list


Expand All @@ -129,6 +145,7 @@ def analyze_molecule(mol, save_order=False):
'is_aryl_radical': False,
'hasNitrogenVal5': False,
'hasLonePairs': False,
'is_bidentate':mol.is_bidentate(),
}

if features['is_cyclic']:
Expand Down Expand Up @@ -1116,3 +1133,183 @@ def _clar_transformation(mol, aromatic_ring):

for bond in bond_list:
bond.order = 1.5


def generate_adsorbate_shift_down_resonance_structures(mol):
"""
Generate all of the resonance structures formed by the shift a pi bond between two C-C atoms to both X-C bonds.
Example XCXCH: [X]C=C=[X] <=> [X]=CC#[X]
(where '=' denotes a double bond, '#' denotes a triple bond)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Graph)
cython.declare(atom=Vertex, atom1=Vertex, atom2=Vertex, atom3=Vertex, atom4=Vertex, bond12=Edge, bond23=Edge, bond34=Edge)
cython.declare(v1=Vertex, v2=Vertex)

structures = []
if mol.is_bidentate():
for atom in mol.vertices:
# print(atom)
paths = pathfinder.find_adsorbate_delocalization_paths(atom)
for atom1, atom2, atom3, atom4, bond12, bond23, bond34 in paths:
if bond23.is_single():
pass
else:
bond12.increment_order()
bond23.decrement_order()
bond34.increment_order()
structure = mol.copy(deep=True)
bond12.decrement_order()
bond23.increment_order()
bond34.decrement_order()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass
else:
structures.append(structure)
return structures

def generate_adsorbate_shift_up_resonance_structures(mol):
"""
Generate all of the resonance structures formed by the shift of two electrons from X-C bonds to increase the bond
order between two C-C atoms by 1.
Example XCXCH: [X]=CC#[X] <=> [X]C=C=[X]
(where '=' denotes a double bond, '#' denotes a triple bond)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Graph)
cython.declare(atom=Vertex, atom1=Vertex, atom2=Vertex, atom3=Vertex, atom4=Vertex, bond12=Edge, bond23=Edge, bond34=Edge)
cython.declare(v1=Vertex, v2=Vertex)

structures = []
if mol.is_bidentate():
for atom in mol.vertices:
paths = pathfinder.find_adsorbate_delocalization_paths(atom)
for atom1, atom2, atom3, atom4, bond12, bond23, bond34 in paths:
if (bond12.is_double() and bond23.is_single() and bond34.is_double()) or (bond23.is_double() and bond12.is_double() and bond34.is_double()) or (bond12.is_triple() and bond23.is_single() and bond34.is_triple()) or (bond12.is_triple() and bond23.is_single() and bond34.is_double()):
bond12.decrement_order()
bond23.increment_order()
bond34.decrement_order()
structure = mol.copy(deep=True)
bond12.increment_order()
bond23.decrement_order()
bond34.increment_order()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass
else:
structures.append(structure)
return structures

def generate_adsorbate_double_shift_up_resonance_structures(mol):
"""
Generate all of the resonance structures formed by the shift of four electrons from X-C bonds to increase the bond
order between two C-C atoms by 2.
Example XCXC: [X]#CC#[X] <=> [X]C#C[X]
(where '#' denotes a triple bond)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Graph)
cython.declare(atom=Vertex, atom1=Vertex, atom2=Vertex, atom3=Vertex, atom4=Vertex, bond12=Edge, bond23=Edge, bond34=Edge)
cython.declare(v1=Vertex, v2=Vertex)

structures = []
if mol.is_bidentate():
for atom in mol.vertices:
paths = pathfinder.find_adsorbate_delocalization_paths(atom)
for atom1, atom2, atom3, atom4, bond12, bond23, bond34 in paths:
if bond23.is_single() and bond12.is_triple() and bond34.is_triple():
bond12.decrement_order()
bond12.decrement_order()
bond23.increment_order()
bond23.increment_order()
bond34.decrement_order()
bond34.decrement_order()
structure = mol.copy(deep=True)
bond12.increment_order()
bond12.increment_order()
bond23.decrement_order()
bond23.decrement_order()
bond34.increment_order()
bond34.increment_order()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass
else:
structures.append(structure)
return structures

def generate_adsorbate_double_shift_down_resonance_structures(mol):
"""
Generate all of the resonance structures formed by the shift of four electrons from a C#C bond to increase the bond
order between two X-C atoms by 2.
Example XCXC: [X]C#C[X] <=> [X]#CC#[X]
(where '#' denotes a triple bond)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Graph)
cython.declare(atom=Vertex, atom1=Vertex, atom2=Vertex, atom3=Vertex, atom4=Vertex, bond12=Edge, bond23=Edge, bond34=Edge)
cython.declare(v1=Vertex, v2=Vertex)

structures = []
if mol.is_bidentate():
for atom in mol.vertices:
paths = pathfinder.find_adsorbate_delocalization_paths(atom)
for atom1, atom2, atom3, atom4, bond12, bond23, bond34 in paths:
if bond23.is_triple() and bond12.is_single() and bond34.is_single():
bond12.increment_order()
bond12.increment_order()
bond23.decrement_order()
bond23.decrement_order()
bond34.increment_order()
bond34.increment_order()
structure = mol.copy(deep=True)
bond12.decrement_order()
bond12.decrement_order()
bond23.increment_order()
bond23.increment_order()
bond34.decrement_order()
bond34.decrement_order()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass
else:
structures.append(structure)
return structures

def generate_adsorbate_conjugate_resonance_structures(mol):
"""
Generate all of the resonance structures formed by the shift of two electrons in a conjugated pi bond system of
a bidentate adsorbate with a bridging C atom in between.
Example XCHCHXC: [X]#CC=C[X] <=> [X]=C=CC=[X]
(where '#' denotes a triple bond, '=' denotes a double bond)
"""
cython.declare(structures=list, paths=list, index=cython.int, structure=Graph)
cython.declare(atom=Vertex, atom1=Vertex, atom2=Vertex, atom3=Vertex, atom4=Vertex, atom5=Vertex, bond12=Edge, bond23=Edge, bond34=Edge, bond45=Edge)
cython.declare(v1=Vertex, v2=Vertex)

structures = []
if mol.is_bidentate():
for atom in mol.vertices:
paths = pathfinder.find_adsorbate_conjugate_delocalization_paths(atom)
for atom1, atom2, atom3, atom4, atom45, bond12, bond23, bond34, bond45 in paths:
if bond23.is_single():
if (bond12.is_double() or bond12.is_triple()):
if (bond34.is_double() or bond34.is_triple()):
if (bond45.is_single() or bond45.is_double()):
bond12.decrement_order()
bond23.increment_order()
bond34.decrement_order()
bond45.increment_order()
structure = mol.copy(deep=True)
bond12.increment_order()
bond23.decrement_order()
bond34.increment_order()
bond45.decrement_order()
try:
structure.update_atomtypes(log_species=False)
except AtomTypeError:
pass
else:
structures.append(structure)
return structures

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