Bond Dissociation Energy¶
Calculate the bond dissociation energy (BDE) of ligands attached to the surface of the core. The calculation consists of five distinct steps:
1. Dissociate all combinations of \({n}\) ligands (\(Y\), see
optional.qd.dissociate.lig_count
) a nd an atom from the core (\(X\), seeoptional.qd.dissociate.core_atom
) within a radius \(r\) from aforementioned core atom (seeoptional.qd.dissociate.lig_core_dist
andoptional.qd.dissociate.core_core_dist
). The dissociated compound has the general structure of \(XY_{n}\).2. Optimize the geometry of \(XY_{n}\) at the first level of theory (\(1\)). Default: ADF MOPAC [1, 2, 3].
3. Calculate the “electronic” contribution to the BDE (\(\Delta E\)) at the first level of theory (\(1\)): ADF MOPAC [1, 2, 3]. This step consists of single point calculations of the complete quantum dot, \(XY_{n}\) and all \(XY_{n}\)dissociated quantum dots.
4. Calculate the thermalchemical contribution to the BDE (\(\Delta \Delta G\)) at the second level of theory (\(2\)). Default: ADF UFF [4, 5]. This step consists of geometry optimizations and frequency analyses of the same compounds used for step 3.
 \(\Delta G_{tot} = \Delta E_{1} + \Delta \Delta G_{2} = \Delta E_{1} + (\Delta G_{2}  \Delta E_{2})\).
Default Settings¶
optional:
qd:
dissociate:
core_atom: Cd
core_index: null
lig_count: 2
core_core_dist: 5.0 # Ångström
lig_core_dist: 5.0 # Ångström
lig_core_pairs: 1
topology: {}
keep_files: True
job1: AMSJob
s1: True
job2: AMSJob
s2: True
Arguments¶

optional.qd.
dissociate
optional: qd: dissociate: core_atom: Cd core_index: null lig_count: 2 lig_pairs: 1 core_core_dist: null # Ångström lig_core_dist: 5.0 # Ångström topology: 7: vertice 8: edge 10: face
optional.qd.dissociate.
core_atom
¶
Parameter: The atomic number or atomic symbol of the core atoms (\(X\)) which are to be dissociated. The core atoms are dissociated in combination with \(n\) ligands (\(Y\), see
dissociate.lig_count
). Yields a compound with the general formula \(XY_{n}\).Atomic indices can also be manually specified with
dissociate.core_index
If one is interested in dissociating ligands in combination with a molecular species (e.g. \(X = {NR_4}^+\)) the atomic number (or symbol) can be substituted for a SMILES string represting a polyatomic ion (e.g. tetramethyl ammonium: C[N+](C)(C)C).
If a SMILES string is provided it must satisfy the following 2 requirements:
 The SMILES string must contain a single charged atom; unpredictable behaviour can occur otherwise.
 The provided structure (including its bonds) must be present in the core.
Warning
This argument has no value be default and thus must be provided by the user.
optional.qd.dissociate.
lig_count
¶
Parameter:
 Type 
int
The number of ligands, \(n\), which is to be dissociated in combination with a single core atom (\(X\), see
dissociate.core_atom
).Yields a compound with the general formula \(XY_{n}\).
Warning
This argument has no value be default and thus must be provided by the user.
optional.qd.dissociate.
core_index
¶
Parameter: Alternative to
dissociate.lig_core_dist
anddissociate.core_atom
. Manually specify the indices of all tobe dissociated atoms in the core. Core atoms will be dissociated in combination with the \(n\) closest ligands.Note
The yaml format uses
null
rather thanNone
as in Python.
optional.qd.dissociate.
core_core_dist
¶
Parameter: The maximum to be considered distance (Ångström) between atoms in
dissociate.core_atom
. Used for determining the topology of the core atom(see
dissociate.topology
) and whether it is exposed to the surface of the core or not. It is recommended to use a radius which encapsulates a single (complete) shell of neighbours.If not specified (or equal to
0.0
) CAT will attempt to guess a suitable value based on the cores’ radial distribution function.
optional.qd.dissociate.
lig_core_dist
¶
Parameter: Dissociate all combinations of a single core atom (see
dissociate.core_atom
) and the \(n\) closests ligands within a userspecified radius.Serves as an alternative to
dissociate.lig_core_dist
, which removes a set number of combinations rather than everything withing a certain radius.The number of ligands dissociated in combination with a single core atom is controlled by
dissociate.lig_count
.
optional.qd.dissociate.
lig_pairs
¶
Parameter:
 Type 
int
, optional Default value –
None
Dissociate a userspecified number of combinations of a single core atom (see
dissociate.core_atom
) and the \(n\) closests ligands.Serves as an alternative to
dissociate.lig_core_dist
, removing a preset number of (closest) pairs rather than all combinations within a certain radius.The number of ligands dissociated in combination with a single core atom is controlled by
dissociate.lig_count
.
optional.qd.dissociate.
topology
¶
Parameter:
 Type 
dict
 Default value –
{}
A dictionary which translates the number neighbouring core atoms (see
dissociate.core_atom
anddissociate.core_core_dist
) into a topology. Keys represent the number of neighbours, values represent the matching topology.Example
Given a
dissociate.core_core_dist
of5.0
Ångström, the following options can be interpreted as following:optional: qd: dissociate: 7: vertice 8: edge 10: faceCore atoms with
7
other neighbouring core atoms (within a radius of5.0
Ångström) are marked as"vertice"
, the ones with8
neighbours are marked as"edge"
and the ones with10
neighbours as"face"
.
Arguments  Job Customization¶

optional.qd.
dissociate
optional: qd: dissociate: keep_files: True job1: AMSJob s1: True job2: AMSJob s2: True
optional.qd.dissociate.
keep_files
¶
Parameter:
 Type 
bool
 Default value –
True
Whether to keep or delete all BDE files after all calculations are finished.
optional.qd.dissociate.
job1
¶
Parameter: A
type
object of aJob
subclass, used for calculating the “electronic” component (\(\Delta E_{1}\)) of the bond dissociation energy. Involves single point calculations.Alternatively, an alias can be provided for a specific job type (see Type Aliases).
Setting it to
True
will default toAMSJob
, whileFalse
is equivalent tooptional.qd.dissociate
=False
.
optional.qd.dissociate.
s1
¶
Parameter: s1: input: mopac: model: PM7 ams: system: charge: 0The job settings used for calculating the “electronic” component (\(\Delta E_{1}\)) of the bond dissociation energy.
Alternatively, a path can be provided to .json or .yaml file containing the job settings.
Setting it to
True
will default to the["MOPAC"]
block in CAT/data/templates/qd.yaml, whileFalse
is equivalent tooptional.qd.dissociate
=False
.
optional.qd.dissociate.
job2
¶
Parameter: A
type
object of aJob
subclass, used for calculating the thermal component (\(\Delta \Delta G_{2}\)) of the bond dissociation energy. Involves a geometry reoptimizations and frequency analyses.Alternatively, an alias can be provided for a specific job type (see Type Aliases).
Setting it to
True
will default toAMSJob
, whileFalse
will skip the thermochemical analysis completely.
optional.qd.dissociate.
s2
¶
Parameter: s2: input: uff: library: uff ams: system: charge: 0 bondorders: _1: nullThe job settings used for calculating the thermal component (\(\Delta \Delta G_{2}\)) of the bond dissociation energy.
Alternatively, a path can be provided to .json or .yaml file containing the job settings.
Setting it to
True
will default to the the MOPAC block in CAT/data/templates/qd.yaml, whileFalse
will skip the thermochemical analysis completely.
Index¶
dissociate_ligand (mol, lig_count[, …]) 
Remove \(XY_{n}\) from mol with the help of the MolDissociater class. 
MolDissociater (mol, core_idx, ligand_count) 
The MolDissociater class; serves as an API for dissociate_ligand() . 
MolDissociater.remove_bulk ([max_vec_len]) 
Remove out atoms specified in MolDissociater.core_idx which are present in the bulk. 
MolDissociater.assign_topology () 
Assign a topology to all core atoms in MolDissociater.core_idx . 
MolDissociater.get_pairs_closest (lig_idx[, …]) 
Create and return the indices of each core atom and the \(n\) closest ligands. 
MolDissociater.get_pairs_distance (lig_idx[, …]) 
Create and return the indices of each core atom and all ligand pairs with max_dist. 
MolDissociater.combinations (cor_lig_pairs[, …]) 
Create a list with all tobe removed atom combinations. 
MolDissociater.__call__ (combinations) 
Start the dissociation process. 
API¶

nanoCAT.bde.dissociate_xyn.
dissociate_ligand
(mol, lig_count, lig_core_pairs=1, lig_core_dist=None, core_atom=None, core_index=None, core_smiles=None, core_core_dist=None, topology=None, **kwargs)[source]¶ Remove \(XY_{n}\) from mol with the help of the
MolDissociater
class.The dissociation process consists of 5 general steps:
 Constructing a
MolDissociater
instance for managing the dissociation workflow.  Assigning a topologydescriptor to each atom with
MolDissociater.assign_topology()
.  Identifying all valid core/ligand pairs using either
MolDissociater.get_pairs_closest()
orMolDissociater.get_pairs_distance()
.  Creating all tobe dissociated core/ligand combinations with
MolDissociater.get_combinations()
.  Start the dissociation process by calling the earlier
created
MolDissociater
instance.
Examples
>>> from typing import Iterator >>> import numpy as np >>> from scm.plams import Molecule # Define parameters >>> mol = Molecule(...) >>> core_idx = [1, 2, 3, 4, 5] >>> lig_idx = [10, 20, 30, 40] >>> lig_count = 2 # Start the workflow >>> dissociate = MolDissociater(mol, core_idx, lig_count) >>> dissociate.assign_topology() >>> pairs: np.ndarray = dissociate.get_pairs_closest(lig_idx) >>> combinations: Iterator[tuple] = dissociate.get_combinations(pairs) # Create the final iterator >>> mol_iterator: Iterator[Molecule] = dissociate(cor_lig_combinations)
Parameters:  mol (
plams.Molecule
) – A molecule.  lig_count (
int
) – The number of tobe dissociated ligands per core atom/molecule.  lig_core_pairs (
int
, optional) – The number of tobe dissociated core/ligand pairs per core atom. Core/ligand pairs are picked based on whichever ligands are closest to each core atom. This option is irrelevant if a distance based criterium is used (see lig_dist).  lig_core_dist (
float
, optional) – Instead of dissociating a given number of core/ligand pairs (see lig_pairs) dissociate all pairs within a given distance from a core atom.  core_index (
int
orIterable
[int
]) – An index or set of indices with all tobe dissociated core atoms. See core_atom to define core_idx based on a common atomic symbol/number.  core_atom (
int
orstr
, optional) – An atomic number or symbol used for automatically defining core_idx. Core atoms within the bulk (rather than on the surface) are ignored.  core_smiles (
str
, optional) – A SMILES string representing molecule containing core_idx. Provide a value here if one wants to disociate an entire molecules from the core and not just atoms.  core_core_dist (
float
, optional) – A value representing the mean distance between the core atoms in core_idx. IfNone
, guess this value based on the radial distribution function of mol (this is generally recomended).  topology (
Mapping
[int
,str
], optional) – A mapping neighbouring of atom counts to a user specified topology descriptor (e.g."edge"
,"vertice"
or"face"
).  **kwargs (
Any
) – For catching excess keyword arguments.
Returns: A generator yielding new molecules with \(XY_{n}\) removed.
Return type: Raises: TypeError – Raised if core_atom and core_idx are both
None
or lig_core_pairs and lig_core_dist are bothNone
. Constructing a

class
nanoCAT.bde.dissociate_xyn.
MolDissociater
(mol, core_idx, ligand_count, max_dist=None, topology=None)[source]¶ The
MolDissociater
class; serves as an API fordissociate_ligand()
.Parameters:  mol (
plams.Molecule
) – A PLAMS molecule consisting of cores and ligands. SeeMolDissociater.mol
.  core_idx (
int
orIterable
[int
]) – An iterable with (1based) atomic indices of all core atoms valid for dissociation. SeeMolDissociater.core_idx
.  ligand_count (
int
) – The number of ligands tobe dissociation with a single atom fromMolDissociater.core_idx
. SeeMolDissociater.ligand_count
.  max_dist (
float
, optional) – The maximum distance between core atoms for them tobe considered neighbours. IfNone
, this value will be guessed based on the radial distribution function of mol. SeeMolDissociater.ligand_count
.  topology (
dict
[int
,str
], optional) – A mapping of neighbouring atom counts to a userspecified topology descriptor. SeeMolDissociater.topology
.

mol
¶ A PLAMS molecule consisting of cores and ligands.
Type: plams.Molecule

core_idx
¶ An iterable with (1based) atomic indices of all core atoms valid for dissociation.
Type: int
orIterable
[int
]

ligand_count
¶ The number of ligands tobe dissociation with a single atom from
MolDissociater.core_idx
.Type: int

max_dist
¶ The maximum distance between core atoms for them tobe considered neighbours. If
None
, this value will be guessed based on the radial distribution function ofMolDissociater.mol
.Type: float
, optional
 mol (

MolDissociater.
remove_bulk
(max_vec_len=0.5)[source]¶ Remove out atoms specified in
MolDissociater.core_idx
which are present in the bulk.The function searches for all neighbouring core atoms within a radius
MolDissociater.max_dist
. Vectors are then constructed from the core atom to the mean positioon of its neighbours. Vector lengths close to 0 thus indicate that the core atom is surrounded in a (nearly) spherical pattern, i.e. it’s located in the bulk of the material and not on the surface.Performs in inplace update of
MolDissociater.core_idx
.Parameters: max_vec_len ( float
) – The maximum length of an atom vector tobe considered part of the bulk. Atoms producing smaller values are removed fromMolDissociater.core_idx
. Units are in Angstroem.

MolDissociater.
assign_topology
()[source]¶ Assign a topology to all core atoms in
MolDissociater.core_idx
.The topology descriptor is based on:
 The number of neighbours within a radius defined by
MolDissociater.max_dist
.  The mapping defined in
MolDissociater.topology
, which maps the number of neighbours to a userdefined topology description.
If no topology description is available for a particular neighbouring atom count, then a generic
f"{i}_neighbours"
descriptor is used (where i is the neighbouring atom count).Performs an inplace update of all
Atom.properties.topology
values. The number of neighbours within a radius defined by

MolDissociater.
get_pairs_closest
(lig_idx, n_pairs=1)[source]¶ Create and return the indices of each core atom and the \(n\) closest ligands.
Parameters: Returns: A 2D array with the indices of all valid ligand/core pairs.
Return type: 2D
numpy.ndarray
[int
]

MolDissociater.
get_pairs_distance
(lig_idx, max_dist=5.0)[source]¶ Create and return the indices of each core atom and all ligand pairs with max_dist.
Parameters: Returns: A 2D array with the indices of all valid ligand/core pairs.
Return type: 2D
numpy.ndarray
[int
]

MolDissociater.
combinations
(cor_lig_pairs, lig_mapping=None, core_mapping=None)[source]¶ Create a list with all tobe removed atom combinations.
Parameters:  cor_lig_pairs (
numpy.ndarray
) – An array with the indices of all core/ligand pairs.  lig_mapping (
Mapping
, optional) – A mapping for translating (1based) atomic indices incor_lig_pairs[:, 0]
to lists of (1based) atomic indices. Used for mapping ligand anchor atoms to the rest of the tobe dissociated ligands.  core_mapping (
Mapping
, optional) – A mapping for translating (1based) atomic indices incor_lig_pairs[:, 1:]
to lists of (1based) atomic indices. Used for mapping core atoms to the tobe dissociated sub structures.
Returns: A set of 2tuples. The first element of each tuple is a
frozenset
with the (1based) indices of all tobe removed core atoms. The second element contains afrozenset
with the (1based) indices of all tobe removed ligand atoms.Return type:  cor_lig_pairs (