"""
M4L6 Tetrahedron with Spacer
============================
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class M4L6TetrahedronSpacer(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
iron_atom = stk.BuildingBlock(
smiles='[Fe+2]',
functional_groups=(
stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(6)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC(C=NBr)=CC=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=iron_atom,
ligands=bb2,
optimizer=stk.MCHammer(),
),
)
# Assign Bromo functional groups to the metal complex.
iron_oct_delta = stk.BuildingBlock.init_from_molecule(
molecule=complex,
functional_groups=[stk.BromoFactory()],
)
# Define building blocks.
bb3 = stk.BuildingBlock(
smiles=(
'C1=CC(=CC=C1C2=CC=C(C=C2)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L6TetrahedronSpacer(
building_blocks={
iron_oct_delta: (0, 1, 2, 3),
bb3: (4, 5, 6, 7, 8, 9),
},
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cage.get_atoms(),
cage.get_position_matrix(),
)
),
bonds=(
molecule.Bond(
atom1_id=bond.get_atom1().get_id(),
atom2_id=bond.get_atom2().get_id(),
order=(
1
if bond.get_order() == 9
else bond.get_order()
),
) for bond in cage.get_bonds()
),
)
:class:`.MCHammer` optimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
iron_atom = stk.BuildingBlock(
smiles='[Fe+2]',
functional_groups=(
stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(6)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC(C=NBr)=CC=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=iron_atom,
ligands=bb2,
optimizer=stk.MCHammer(),
),
)
# Assign Bromo functional groups to the metal complex.
iron_oct_delta = stk.BuildingBlock.init_from_molecule(
molecule=complex,
functional_groups=[stk.BromoFactory()],
)
# Define building blocks.
bb3 = stk.BuildingBlock(
smiles=(
'C1=CC(=CC=C1C2=CC=C(C=C2)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L6TetrahedronSpacer(
building_blocks={
iron_oct_delta: (0, 1, 2, 3),
bb3: (4, 5, 6, 7, 8, 9),
},
optimizer=stk.MCHammer(),
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cage.get_atoms(),
cage.get_position_matrix(),
)
),
bonds=(
molecule.Bond(
atom1_id=bond.get_atom1().get_id(),
atom2_id=bond.get_atom2().get_id(),
order=(
1
if bond.get_order() == 9
else bond.get_order()
),
) for bond in cage.get_bonds()
),
)
This topology places a ditopic spacer between the vertices of the
tetrahedron.
When using a :class:`dict` for the `building_blocks` parameter,
as in :ref:`cage-topology-graph-examples`:
*Multi-Building Block Cage Construction*, a
:class:`.BuildingBlock`, with the following number of functional
groups, needs to be assigned to each of the following vertex ids:
| 3-functional groups: 0 to 3
| 2-functional groups: 4 to 9
Examples
--------
*Building Metal-Organic Tetrahedron*
Many metal-organic cages are built using a process called
subcomponent self-assembly, which is a complex chemical process
that occurs in solution. In :class:`.Cage`, an example is
provided of an alchemical approach using
:class:`.M4L6TetrahedronSpacer` to
build these types of cages. It is alchemical because the bonds
formed during construction are not the same as the experimental
reaction. Instead of forming bonds at the metal centre, we create
bonds between disconnected ligands.
The :class:`.M4L6TetrahedronSpacer` topology is provided for cases
where the linkers cannot be disconnected symmetrically. However,
in the case that the linker can be disconnected
in a symmetrical fashion, the
:class:`.M4L6Tetrahedron` topology can be used.
"""
_non_linears = (
NonLinearVertex(0, np.array([0, 0, np.sqrt(6) / 2])),
NonLinearVertex(1, np.array([-1, -np.sqrt(3) / 3, -np.sqrt(6) / 6])),
NonLinearVertex(2, np.array([1, -np.sqrt(3) / 3, -np.sqrt(6) / 6])),
NonLinearVertex(3, np.array([0, 2 * np.sqrt(3) / 3, -np.sqrt(6) / 6])),
)
_vertex_prototypes = (
*_non_linears,
LinearVertex.init_at_center(
id=4,
vertices=(_non_linears[0], _non_linears[1]),
),
LinearVertex.init_at_center(
id=5,
vertices=(_non_linears[0], _non_linears[2]),
),
LinearVertex.init_at_center(
id=6,
vertices=(_non_linears[0], _non_linears[3]),
),
LinearVertex.init_at_center(
id=7,
vertices=(_non_linears[1], _non_linears[2]),
),
LinearVertex.init_at_center(
id=8,
vertices=(_non_linears[1], _non_linears[3]),
),
LinearVertex.init_at_center(
id=9,
vertices=(_non_linears[2], _non_linears[3]),
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[0], _vertex_prototypes[4]),
Edge(1, _vertex_prototypes[0], _vertex_prototypes[5]),
Edge(2, _vertex_prototypes[0], _vertex_prototypes[6]),
Edge(3, _vertex_prototypes[1], _vertex_prototypes[4]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[7]),
Edge(5, _vertex_prototypes[1], _vertex_prototypes[8]),
Edge(6, _vertex_prototypes[2], _vertex_prototypes[5]),
Edge(7, _vertex_prototypes[2], _vertex_prototypes[7]),
Edge(8, _vertex_prototypes[2], _vertex_prototypes[9]),
Edge(9, _vertex_prototypes[3], _vertex_prototypes[6]),
Edge(10, _vertex_prototypes[3], _vertex_prototypes[8]),
Edge(11, _vertex_prototypes[3], _vertex_prototypes[9]),
)
_num_windows = 4
_num_window_types = 1