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 (\(X\), see optional.qd.dissociate.core_atom) within a radius \(r\) from aforementioned core atom (see optional.qd.dissociate.lig_core_dist and optional.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
            lig_count: 2
            keep_files: True
            core_core_dist: 5.0  # Ångström
            lig_core_dist: 5.0  # Ångström
            core_index: False
            topology: {}

            job1: AMSJob
            s1: True
            job2: AMSJob
            s2: True

Arguments¶

optional.qd.dissociate

optional:
    qd:
        dissociate:
            core_atom: Cd
            lig_count: 2
            keep_files: True
            core_core_dist: 5.0  # Ångström
            lig_core_dist: 5.0  # Ångström
            core_index: False
            topology:
                7: vertice
                8: edge
                10: face

optional.qd.dissociate.core_atom¶

Parameter:

Type - str or int

Default value – None

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 optional.qd.dissociate.lig_count). Yields a compound with the general formula \(XY_{n}\).

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 poly-atomic 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.

Note

The yaml format uses null rather than None as in Python.

optional.qd.dissociate.lig_count¶

Parameter:

Type - int

Default value – None

The number of ligands, \(n\), which is to be dissociated in combination with a single core atom (\(X\), see optional.qd.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.

Note

The yaml format uses null rather than None as in Python.

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.core_core_dist¶

Parameter:

Type - float or int

Default value – 0.0

The maximum to be considered distance (Ångström) between atoms in optional.qd.dissociate.core_atom. Used for determining the topology of the core atom (see optional.qd.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:

Type - float or int

Default value – 5.0

Dissociate all possible combinations of \(n\) ligands and a single core atom (see optional.qd.dissociate.core_atom) within a given radius (Ångström) from aforementioned core atom. The number of ligands dissociated in combination with a single core atom is controlled by optional.qd.dissociate.lig_count.

optional.qd.dissociate.core_index¶

Parameter:

Type - int or tuple [int]

Default value – None

Alternative to optional.qd.dissociate.lig_core_dist and optional.qd.dissociate.core_atom. Manually specify the indices of all to-be dissociated atoms in the core. Core atoms will be dissociated in combination with the \(n\) closest ligands.

Note

Atom numbering follows the PLAMS [1, 2] convention of starting from 1 rather than 0.

Note

The yaml format uses null rather than None as in Python.
optional.qd.dissociate.topology¶
Parameter:

Type - dict

Default value – {}

A dictionary which translates the number neighbouring core atoms (see optional.qd.dissociate.core_atom and optional.qd.dissociate.core_core_dist) into a topology. Keys represent the number of neighbours, values represent the matching topology.
Example

Given a optional.qd.dissociate.core_core_dist of 5.0 Ångström, the following options can be interpreted as following:
optional:
    qd:
        dissociate:
            7: vertice
            8: edge
            10: face
Core atoms with 7 other neighbouring core atoms (within a radius of 5.0 Ångström) are marked as "vertice", the ones with 8 neighbours are marked as "edge" and the ones with 10 neighbours as "face".

Arguments - Job Customization¶

optional.qd.dissociate

optional:
    qd:
        dissociate:
            job1: AMSJob
            s1: True
            job2: AMSJob
            s2: True

optional.qd.dissociate.job1¶

Parameter:

Type - type, str or bool

Default value – plams.AMSJob

A type object of a plams.Job 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 to plams.AMSJob, while False is equivalent to optional.qd.dissociate = False.
optional.qd.dissociate.s1¶
Parameter:

Type - dict, str or bool

Default value – See below
s1:
    input:
        mopac:
            model: PM7
        ams:
            system:
                charge: 0
The 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, while False is equivalent to optional.qd.dissociate = False.
optional.qd.dissociate.job2¶

Parameter:

Type - type, str or bool

Default value – plams.AMSJob

A type object of a plams.Job 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 to plams.AMSJob, while False will skip the thermochemical analysis completely.
optional.qd.dissociate.s1
Parameter:

Type - dict, str or bool

Default value – See below
s2:
    input:
        uff:
            library: uff
        ams:
            system:
                charge: 0
                bondorders:
                    _1: null
The 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, while False will skip the thermochemical analysis completely.