Optional
There are a number of arguments which can be used to modify the functionality and behavior of the quantum dot builder. Herein an overview is provided.
Note: Inclusion of this section in the input file is not required, assuming one is content with the default settings.
Index
Option 
Description 

The name of the directory where the database will be stored. 

Attempt to read results from the database before starting calculations. 

Export results to the database. 

Allow previous results in the database to be overwritten. 

Ensure that the created workdir has a threadsafe name. 

The file format(s) for exporting moleculair structures. 

Options related to the MongoDB format. 

The name of the directory where all cores will be stored. 

Atomic number of symbol of the core anchor atoms. 

How the tobe attached ligands should be alligned with the core. 

Settings related to the partial replacement of core anchor atoms. 

The name of the directory where all ligands will be stored. 

Optimize the geometry of the tobe attached ligands. 

Manually specify SMILES strings representing functional groups. 

If the ligand should be attached in its entirety to the core or not. 


Perform a property calculation with COSMORS on the ligand. 
Perform a conceptual DFT calculation with ADF on the ligand. 

Compute the smallest enclosing cone angle within a ligand. 

Compute the size of branches and their distance w.r.t. to the anchor within a ligand. 

The name of the directory where all quantum dots will be stored. 

Whether or not the quantum dot should actually be constructed or not. 

Optimize the quantum dot (i.e. core + all ligands). 

A workflow for attaching multiple nonunique ligands to a single quantum dot. 

Calculate the \(V_{bulk}\), a ligand and coresepcific descriptor of a ligands’ bulkiness. 

Perform an activation strain analyses. 

Calculate the ligand dissociation energy. 
Default Settings
optional:
database:
dirname: database
read: True
write: True
overwrite: False
thread_safe: False
mol_format: (pdb, xyz)
mongodb: False
core:
dirname: core
anchor: Cl
allignment: surface
subset: null
ligand:
dirname: ligand
optimize: True
anchor: null
split: True
cosmors: False
cdft: False
cone_angle: False
qd:
dirname: qd
construct_qd: True
optimize: False
activation_strain: False
dissociate: False
bulkiness: False
Arguments
Database
 optional.database
All databaserelated settings.
Note
For
optional.database
settings to take effect the DataCAT package has to be installed.Example:
optional: database: dirname: database read: True write: True overwrite: False mol_format: (pdb, xyz) mongodb: False
 optional.database.dirname
 Parameter
Type 
str
Default Value 
"database"
The name of the directory where the database will be stored.
The database directory will be created (if it does not yet exist) at the path specified in path.
 optional.database.read
Attempt to read results from the database before starting calculations.
Before optimizing a structure, check if a geometry is available from previous calculations. If a match is found, use that structure and avoid any geometry (re)optimizations. If one wants more control then the boolean can be substituted for a list of strings (i.e.
"core"
,"ligand"
and/or"qd"
), meaning that structures will be read only for a specific subset.Example
Example #1:
optional: database: read: (core, ligand, qd) # This is equivalent to read: TrueExample #2:
optional: database: read: ligand
 optional.database.write
Export results to the database.
Previous results will not be overwritten unless
optional.database.overwrite
=True
. If one wants more control then the boolean can be substituted for a list of strings (i.e."core"
,"ligand"
and/or"qd"
), meaning that structures written for a specific subset.See
optional.database.read
for a similar relevant example.
 optional.database.overwrite
Allow previous results in the database to be overwritten.
Only applicable if
optional.database.write
=True
. If one wants more control then the boolean can be substituted for a list of strings (i.e."core"
,"ligand"
and/or"qd"
), meaning that structures written for a specific subset.See
optional.database.read
for a similar relevant example.
 optional.database.thread_safe
 Parameter
Type 
bool
Default value 
False
Ensure that the created workdir has a threadsafe name.
Note that this disables the restarting of partially completed jobs.
 optional.database.mol_format
The file format(s) for exporting moleculair structures.
By default all structures are stored in the .hdf5 format as (partially) deserialized .pdb files. Additional formats can be requested with this keyword. Accepted values:
"pdb"
,"xyz"
,"mol"
and/or"mol2"
.
 optional.database.mongodb
Options related to the MongoDB format.
See also
More extensive options for this argument are provided in The Database Class:.
Core
 optional.core
All settings related to the core.
Example:
optional: core: dirname: core anchor: Cl allignment: surface subset: null
 optional.core.dirname
 Parameter
Type 
str
Default value –
"core"
The name of the directory where all cores will be stored.
The core directory will be created (if it does not yet exist) at the path specified in path.
 optional.core.anchor
Atomic number of symbol of the core anchor atoms.
The atomic number or atomic symbol of the atoms in the core which are to be replaced with ligands. Alternatively, anchor atoms can be manually specified with the core_indices variable.
Further customization can be achieved by passing a dictionary:
Note
optional: core: anchor: group: "[H]Cl" # Remove HCl and attach at previous Cl position group_idx: 1 group_format: "SMILES" remove: [0, 1]
 optional.core.allignment
 Parameter
Type 
str
Default value –
"surface"
How the tobe attached ligands should be alligned with the core.
Has four allowed values:
"surface"
: Define the core vectors as those orthogonal to the cores surface. Not this option requires at least four core anchor atoms. The surface is herein defined by a convex hull constructed from the core.
"sphere"
: Define the core vectors as those drawn from the core anchor atoms to the cores center.
"anchor"
: Define the core vectors based on the optimal vector of its anchors. Only available in when the core contains molecular anchors, e.g. acetates.
"surface invert"
/"surface_invert"
: The same as"surface"
, except the core vectors are inverted.
"sphere invert"
/"sphere_invert"
: The same as"sphere"
, except the core vectors are inverted.
"anchor invert"
/"anchor_invert"
: The same as"anchor"
, except the core vectors are inverted.Note that for a spherical core both approaches are equivalent.
 optional.core.subset
 Parameter
Type 
dict
, optionalDefault value –
None
Settings related to the partial replacement of core anchor atoms with ligands.
If not
None
, has access to six further keywords, the first two being the most important:
 optional.core.subset.f
 Parameter
Type 
float
The fraction of core anchor atoms that will actually be exchanged for ligands.
The provided value should satisfy the following condition: \(0 < f \le 1\).
Note
This argument has no value be default and must thus be provided by the user.
 optional.core.subset.mode
 Parameter
Type 
str
Default value –
"uniform"
Defines how the anchor atom subset, whose size is defined by the fraction \(f\), will be generated.
Accepts one of the following values:
"uniform"
: A uniform distribution; the nearestneighbor distances between each successive anchor atom and all previous anchor atoms is maximized. can be combined withsubset.cluster_size
to create a uniform distribution of clusters of a userspecified size.
"cluster"
: A clustered distribution; the nearestneighbor distances between each successive anchor atom and all previous anchor atoms is minimized.
"random"
: A random distribution.It should be noted that all three methods converge towards the same set as \(f\) approaches \(1.0\).
If \(\boldsymbol{D} \in \mathbb{R}_{+}^{n,n}\) is the (symmetric) distance matrix constructed from the anchor atom superset and \(\boldsymbol{a} \in \mathbb{N}^{m}\) is the vector of indices which yields the anchor atom subset. The definition of element \(a_{i}\) is defined below for the
"uniform"
distribution. All elements of \(\boldsymbol{a}\) are furthermore constrained to be unique.(1)\[\begin{split}\DeclareMathOperator*{\argmin}{\arg\!\min} a_{i} = \begin{cases} \argmin\limits_{k \in \mathbb{N}} \sum_{\hat{\imath}=0}^{n} f \left( D_{k, \hat{\imath}} \right) & \text{if} & i=0 \\ \argmin\limits_{k \in \mathbb{N}} \sum_{\hat{\imath}=0}^{i1} f \left( D[k, a_{\hat{\imath}}]\ \right) & \text{if} & i > 0 \end{cases} \begin{matrix} & \text{with} & f(x) = e^{x} \end{matrix}\end{split}\]For the
"cluster"
distribution all \(\text{argmin}\) operations are exchanged for \(\text{argmax}\).The old default, the pnorm with \(p=2\), is equivalent to:
(2)\[\DeclareMathOperator*{\argmax}{\arg\!\max} \begin{matrix} \argmin\limits_{k \in \mathbb{N}} \sum_{\hat{\imath}=0}^{n} f \left( D_{k, \hat{\imath}} \right) = \argmax\limits_{k \in \mathbb{N}} \left( \sum_{\hat{\imath}=0}^{n}  D_{k, \hat{\imath}} ^p \right)^{1/p} & \text{if} & f(x) = x^{2} \end{matrix}\]Note that as the elements of \(\boldsymbol{D}\) were defined as positive or zerovalued real numbers; operating on \(\boldsymbol{D}\) is thus equivalent to operating on its absolute.
 optional.core.subset.follow_edge
 Parameter
Type 
bool
Default value –
False
Construct the anchor atom distance matrix by following the shortest path along the edges of a (triangularfaced) polyhedral approximation of the core rather than the shortest path through space.
Enabling this option will result in more accurate
"uniform"
and"cluster"
distributions at the cost of increased computational time.Given the matrix of Cartesian coordinates \(\boldsymbol{X} \in \mathbb{R}^{n, 3}\), the matching edgedistance matrix \(\boldsymbol{D}^{\text{edge}} \in \mathbb{R}_{+}^{n, n}\) and the vector \(\boldsymbol{p} \in \mathbb{N}^{m}\), representing a (tobe optimized) path as the indices of edgeconnected vertices, then element \(D_{i,j}^{\text{edge}}\) is defined as following:
(3)\[D_{i, j}^{\text{edge}} = \min_{\boldsymbol{p} \in \mathbb{N}^{m}; m \in \mathbb{N}} \sum_{k=0}^{m1}  X_{p_{k},:}  X_{p_{k+1},:}  \quad \text{with} \quad p_{0} = i \quad \text{and} \quad p_{m} = j\]The polyhedron edges are constructed, after projecting all vertices on the surface of a sphere, using Qhull’s
ConvexHull
algorithm (The Quickhull Algorithm for Convex Hulls). The quality of the constructed edges is proportional to the convexness of the core, more specifically: how well the vertices can be projected on a spherical surface without severely distorting the initial structure. For example, spherical, cylindrical or cuboid cores will yield reasonably edges, while the edges resulting from torus will be extremely poor.
 optional.core.subset.cluster_size
Allow for the creation of uniformly distributed clusters of size \(r\); should be used in conjunction with
subset.mode = "uniform"
.The value of \(r\) can be either a single cluster size (e.g.
cluster_size = 5
) or an iterable of various sizes (e.g.cluster_size = [2, 3, 4]
). In the latter case the iterable will be repeated as long as necessary.Compared to Eq (2) the vector of indices \(\boldsymbol{a} \in \mathbb{N}^{m}\) is, for the purpose of book keeping, reshaped into the matrix \(\boldsymbol{A} \in \mathbb{N}^{q, r} \; \text{with} \; q*r = m\). All elements of \(\boldsymbol{A}\) are, again, constrained to be unique.
(4)\[\begin{split}\DeclareMathOperator*{\argmin}{\arg\!\min} A_{i,j} = \begin{cases} \argmin\limits_{k \in \mathbb{N}} \sum_{\hat{\imath}=0}^{n} f \left( D[k, \, \hat{\imath}] \right) & \text{if} & i=0 & \text{and} & j=0 \\ \argmin\limits_{k \in \mathbb{N}} \sum_{\hat{\imath}=0}^{i1} \sum_{\hat{\jmath}=0}^{r} f \left( D[k, A_{\hat{\imath}, \, \hat{\jmath}}] \right) & \text{if} & i > 0 & \text{and} & j = 0 \\ \argmin\limits_{k \in \mathbb{N}} \dfrac { \sum_{\hat{\imath}=0}^{i1} \sum_{\hat{\jmath}=0}^{r} f \left( D[k, A_{\hat{\imath}, \, \hat{\jmath}}] \right) } { \sum_{\hat{\jmath}=0}^{j1} f \left( D[k, A_{i, \, \hat{\jmath}}] \right) } &&& \text{if} & j > 0 \end{cases}\end{split}\]
 optional.core.subset.weight
 Parameter
Type 
str
Default value –
"numpy.exp(x)"
The function \(f(x)\) for weighting the distance.; its default value corresponds to: \(f(x) = e^{x}\).
For the old default, the pnorm with \(p=2\), one can use
weight = "x**2"
: \(f(x) = x^2\).Custom functions can be specified as long as they satisfy the following constraints:
The function must act an variable by the name of
x
, a 2D array of positive and/or zerovalued floats (\(x \in \mathbb{R}_{+}^{n, n}\)).The function must take a single array as argument and return a new one.
The function must be able to handle values of
numpy.nan
andnumpy.inf
without raising exceptions.The shape and data type of the output array should not change with respect to the input.
Modules specified in the weight function will be imported when required, illustrated here with SciPy’s
expit
function:weight = "scipy.special.expit(x)"
akaweight = "1 / (1 + numpy.exp(x))"
Multiline statements are allowed:
weight = "a = x**2; b = 5 * a; numpy.exp(b)"
. The last part of the statement is assumed to be the tobe returned value (i.e.return numpy.exp(b)
).
 optional.core.subset.randomness
 Parameter
Type 
float
, optionalDefault value –
None
The probability that each new core anchor atom will be picked at random.
Can be used in combination with
"uniform"
and"cluster"
to introduce a certain degree of randomness (i.e. entropy).If not
None
, the provided value should satisfy the following condition: \(0 \le randomness \le 1\). A value of \(0\) is equivalent to a"uniform"
/"cluster"
distribution while \(1\) is equivalent to"random"
.
Ligand
 optional.ligand
All settings related to the ligands.
Example:
optional: ligand: dirname: ligand optimize: True anchor: null split: True cosmors: False cdft: False cone_angle: False branch_distance: False
 optional.ligand.dirname
 Parameter
Type 
str
Default value –
"ligand"
The name of the directory where all ligands will be stored.
The ligand directory will be created (if it does not yet exist) at the path specified in path.
 optional.ligand.optimize
Optimize the geometry of the tobe attached ligands.
The ligand is split into one or multiple (more or less) linear fragments, which are subsequently optimized (RDKit UFF [1, 2, 3]) and reassembled while checking for the optimal dihedral angle. The ligand fragments are biased towards more linear conformations to minimize interligand repulsion once the ligands are attached to the core.
After the conformation search a final (unconstrained) geometry optimization is performed, RDKit UFF again being the default level of theory. Custom job types and settings can, respectivelly, be specified with the
job2
ands2
keys.Note
optional: ligand: optimize: job2: ADFJob
 optional.ligand.anchor
 Parameter
Type 
str
,Sequence[str]
ordict[str, Any]
Default value –
None
Manually specify SMILES strings representing functional groups.
For example, with
optional.ligand.anchor
=("O[H]", "[N+].[Cl]")
all ligands will be searched for the presence of hydroxides and ammonium chlorides.The first atom in each SMILES string (i.e. the “anchor”) will be used for attaching the ligand to the core, while the last atom (assuming
optional.ligand.split
=True
) will be dissociated from the ligand and discarded.If not specified, the default functional groups of CAT are used.
This option can alternatively be provided as
optional.ligand.functional_groups
.Further customization can be achieved by passing dictionaries:
Note
optional: ligand: anchor:  group: "[H]OC(=O)C" # Remove H and attach at the (formal) oxyanion group_idx: 1 remove: 0  group: "[H]OC(=O)C" # Remove H and attach at the mean position of both oxygens group_idx: [1, 3] remove: 0 kind: meanNote
This argument has no value be default and will thus default to SMILES strings of the default functional groups supported by CAT.
Note
The yaml format uses
null
rather thanNone
as in Python.
 optional.ligand.anchor.group
 Parameter
Type 
str
A SMILES string representing the anchoring group.
Note
This argument has no value be default and must thus be provided by the user.
 optional.ligand.anchor.group_idx
 Parameter
Type 
int
orSequence[int]
The indices of the anchoring atom(s) in
anchor.group
.Indices should be 0based. These atoms will be attached to the core, the manner in which is determined by the
anchor.kind
option.Note
This argument has no value be default and must thus be provided by the user.
 optional.ligand.anchor.group_format
 Parameter
Type 
str
Default value –
"SMILES"
The format used for representing
anchor.group
.Defaults to the SMILES format. The supported formats (and matching RDKit parsers) are as following:
>>> import rdkit.Chem >>> FASTA = rdkit.Chem.MolFromFASTA >>> HELM = rdkit.Chem.MolFromHELM >>> INCHI = rdkit.Chem.MolFromInchi >>> MOL2 = rdkit.Chem.MolFromMol2Block >>> MOL2_FILE = rdkit.Chem.MolFromMol2File >>> MOL = rdkit.Chem.MolFromMolBlock >>> MOL_FILE = rdkit.Chem.MolFromMolFile >>> PDB = rdkit.Chem.MolFromPDBBlock >>> PDB_FILE = rdkit.Chem.MolFromPDBFile >>> PNG = rdkit.Chem.MolFromPNGString >>> PNG_FILE = rdkit.Chem.MolFromPNGFile >>> SVG = rdkit.Chem.MolFromRDKitSVG >>> SEQUENCE = rdkit.Chem.MolFromSequence >>> SMARTS = rdkit.Chem.MolFromSmarts >>> SMILES = rdkit.Chem.MolFromSmiles >>> TPL = rdkit.Chem.MolFromTPLBlock >>> TPL_FILE = rdkit.Chem.MolFromTPLFile
 optional.ligand.anchor.remove
 Parameter
Type 
None
,int
orSequence[int]
Default value –
None
The indices of the tobe removed atoms in
anchor.group
.No atoms are removed when set to
None
. Indices should be 0based. See also thesplit
option.
 optional.ligand.anchor.kind
 Parameter
Type 
str
Default value –
"first"
How atoms are tobe attached when multiple anchor atoms are specified in
anchor.group_idx
.Accepts one of the following options:
"first"
: Attach the first atom to the core.
"mean"
: Attach the mean position of all anchoring atoms to the core.
"mean_translate"
: Attach the mean position of all anchoring atoms to the core and then translate back to the first atom.
 optional.ligand.anchor.angle_offset
Manually offset the angle of the ligand vector by a given number.
The plane of rotation is defined by the first three indices in
anchor.group_idx
.By default the angle unit is assumed to be in degrees, but if so desired one can explicitly pass the unit:
angle_offset: "0.25 rad"
.
 optional.ligand.anchor.dihedral
Manually specify the ligands vector dihedral angle, rather than optimizing it w.r.t. the interligand distance.
The dihedral angle is defined by three vectors:
The first two in dices in
anchor.group_idx
.The core vector(s).
The Cartesian Xaxis as defined by the core.
By default the angle unit is assumed to be in degrees, but if so desired one can explicitly pass the unit:
dihedral: "0.5 rad"
.
 optional.ligand.anchor.multi_anchor_filter
 Parameter
Type 
str
Default value –
"ALL"
How ligands with multiple valid anchor sites are tobe treated.
Accepts one of the following options:
"all"
: Construct a new ligand for each valid anchor/ligand combination.
"first"
: Pick only the first valid functional group, all others are ignored.
"raise"
: Treat a ligand as invalid if it has multiple valid anchoring sites.
 optional.ligand.split
 Parameter
Type 
bool
Default value –
True
If
False
: The ligand is to be attached to the core in its entirety .
Before
After
\({NR_4}^+\)
\({NR_4}^+\)
\(O_2 CR\)
\(O_2 CR\)
\(HO_2 CR\)
\(HO_2 CR\)
\(H_3 CO_2 CR\)
\(H_3 CO_2 CR\)
True
: A proton, counterion or functional group is to be removed from the ligand before attachment to the core.
Before
After
\(Cl^ + {NR_4}^+\)
\({NR_4}^+\)
\(HO_2 CR\)
\({O_2 CR}^\)
\(Na^+ + {O_2 CR}^\)
\({O_2 CR}^\)
\(HO_2 CR\)
\({O_2 CR}^\)
\(H_3 CO_2 CR\)
\({O_2 CR}^\)
 optional.ligand.cosmors
Perform a property calculation with COSMORS [4, 5, 6, 7] on the ligand.
The COSMO surfaces are by default constructed using ADF MOPAC [8, 9, 10].
The solvation energy of the ligand and its activity coefficient are calculated in the following solvents: acetone, acetonitrile, dimethyl formamide (DMF), dimethyl sulfoxide (DMSO), ethyl acetate, ethanol, nhexane, toluene and water.
 optional.ligand.cdft
Perform a conceptual DFT (CDFT) calculation with ADF on the ligand.
All global descriptors are, if installed, stored in the database. This includes the following properties:
Electronic chemical potential (mu)
Electronic chemical potential (mu+)
Electronic chemical potential (mu)
Electronegativity (chi=mu)
Hardness (eta)
Softness (S)
Hyperhardness (gamma)
Electrophilicity index (w=omega)
Dissocation energy (nucleofuge)
Dissociation energy (electrofuge)
Electrodonating power (w)
Electroaccepting power(w+)
Net Electrophilicity
Global Dual Descriptor Deltaf+
Global Dual Descriptor Deltaf
This block can be furthermore customized with one or more of the following keys:
"keep_files"
: Whether or not to delete the ADF output afterwards.
"job1"
: The type of PLAMS Job used for running the calculation. The only value that should be supplied here (if any) is"ADFJob"
.
"s1"
: The job Settings used for running the CDFT calculation. Can be left blank to use the default template (nanoCAT.cdft.cdft
).Examples
optional: ligand: cdft: Trueoptional: ligand: cdft: job1: ADFJob s1: ... # Insert custom settings here
 optional.ligand.cone_angle
Compute the smallest enclosing cone angle within a ligand.
The smallest enclosing cone angle is herein defined as two times the largest angle (\(2 * \phi_{max}\)) w.r.t. a central ligand vector, the ligand vector in turn being defined as the vector that minimizes \(\phi_{max}\).
Examples
optional: ligand: cone_angle: Trueoptional: ligand: cone_angle: distance: [0, 0.5, 1, 1.5, 2]
 optional.ligand.cone_angle.distance
 Parameter
Type 
float
orlist[float]
Default value –
0.0
The distance in
cone_angle
of each ligands’ anchor atom w.r.t. the nanocrystal surface.Accepts one or more distances.
QD
 optional.qd
All settings related to the quantum dots.
Example:
optional: qd: dirname: qd construct_qd: True optimize: False bulkiness: False activation_strain: False dissociate: False
 optional.qd.dirname
 Parameter
Type 
str
Default value –
"qd"
The name of the directory where all quantum dots will be stored.
The quantum dot directory will be created (if it does not yet exist) at the path specified in path.
 optional.qd.construct_qd
 Parameter
Type 
bool
Default value –
True
Whether or not the quantum dot should actually be constructed or not.
Setting this to
False
will still construct ligands and carry out ligand workflows, but it will not construct the actual quantum dot itself.
 optional.qd.optimize
Optimize the quantum dot (i.e. core + all ligands) .
By default the calculation is performed with ADF UFF [3, 11]. The geometry of the core and ligand atoms directly attached to the core are frozen during this optimization.
 optional.qd.multi_ligand
 Parameter
Type 
None
ordict
Default value –
None
A workflow for attaching multiple nonunique ligands to a single quantum dot.
Note that this is considered a seperate workflow besides the normal ligand attachment. Consequently, these structures will not be passed to further workflows.
See Multiligand attachment for more details regarding the available options.
 optional.qd.bulkiness
Calculate the \(V_{bulk}\), a ligand and corespecific descriptor of a ligands’ bulkiness.
Supplying a dictionary grants access to the two additional
h_lim
andd
subkeys.(5)\[V(r_{i}, h_{i}; d, h_{lim}) = \sum_{i=1}^{n} e^{r_{i}} (\frac{2 r_{i}}{d}  1)^{+} (1  \frac{h_{i}}{h_{lim}})^{+}\]
 optional.qd.bulkiness.h_lim
Default value of the \(h_{lim}\) parameter in
bulkiness
.Set to
None
to disable the \(h_{lim}\)based cutoff.
 optional.qd.bulkiness.d
 Parameter
Type 
float
/list[float]
,None
or"auto"
Default value –
"auto"
Default value of the \(d\) parameter in
bulkiness
.Set to
"auto"
to automatically infer this parameters value based on the mean nearestneighbor distance among the core anchor atoms. Set toNone
to disable the \(d\)based cutoff. Supplying multiple floats will compute the bulkiness for all specified values.
 optional.qd.activation_strain
Perform an activation strain analysis [12, 13, 14].
The activation strain analysis (kcal mol^{1}) is performed on the ligands attached to the quantum dot surface with RDKit UFF [1, 2, 3].
The core is removed during this process; the analysis is thus exclusively focused on ligand deformation and interligand interaction. Yields three terms:
1. dE_{strain} : The energy required to deform the ligand from their equilibrium geometry to the geometry they adopt on the quantum dot surface. This term is, by definition, destabilizing. Also known as the preparation energy (dE_{prep}).
2. dE_{int} : The mutual interaction between all deformed ligands. This term is characterized by the noncovalent interaction between ligands (UFF LennardJones potential) and, depending on the interligand distances, can be either stabilizing or destabilizing.
3. dE : The sum of dE_{strain} and dE_{int}. Accounts for both the destabilizing ligand deformation and (de)stabilizing interaction between all ligands in the absence of the core.
See EnsembleAveraged Activation Strain Analysis for more details.
 optional.qd.dissociate
Calculate the ligand dissociation energy.
Calculate the ligand dissociation energy (BDE) of ligands attached to the surface of the core. See Bond Dissociation Energy for more details. The calculation consists of five distinct steps:
1. Dissociate all combinations of \({n}\) ligands (\(Y\)) and an atom from the core (\(X\)) within a radius r from aforementioned core atom. 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 thermochemical 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.
\(\Delta G_{tot} = \Delta E_{1} + \Delta \Delta G_{2} = \Delta E_{1} + (\Delta G_{2}  \Delta E_{2})\).
See also
More extensive options for this argument are provided in Bond Dissociation Energy:.