adding resonance for adsorbates

rmgpy/molecule/molecule.pxd

@@ -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

rmgpy/molecule/molecule.py

@@ -2731,6 +2731,16 @@ 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.

rmgpy/molecule/pathfinder.pxd

@@ -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)

rmgpy/molecule/pathfinder.py

@@ -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

rmgpy/molecule/resonance.pxd

@@ -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)

rmgpy/molecule/resonance.py

@@ -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
@@ -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
@@ -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
 
 
@@ -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']:
@@ -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