CosmoRSSpeciesDatabase

class CosmoRSSpeciesDatabase
categories()
Returns:

A list of the chemical categories used in the database.

Return type:

list of str

deleteSpecies(name)

Delete the the given named entry from the database. This can only be done for user-added entries.

Parameters:

name (str) – The name of the species to delete.

exportSpecies(name)

Return the CosmoRealSpecies for the given named entry.

Parameters:

name (str) – The name of the species to return.

findSpecies(category=None, formula=None, smiles=None)

Return the list of the names of the available species. Different selection criteria can be used to return subsets of species names.

Parameters:

  • category (str) – Return only species that are in the given category.

  • formula (str) – Return only species that have the given chemical formula.

  • smiles (str) – Return only species whose bond graph matches the bond graph given by the SMILES string. Note that this does not distinguish between cis/trans isomers or stereoisomers.

Returns:

A list names of species that match the given selection criteria.

Return type:

list of str

importSpecies(name, cosmo_data, category=None, description=None, melting_point=None, enthalpy_of_fusion=None, specific_heat_capacity_change=None, antoine_a=None, antoine_b=None, antoine_c=None, boiling_point=None, flash_point=None, density=None)

Add a new configuration to the COSMO-RS database.

Parameters:

  • name (str) – The name of the data entry.

  • cosmo_data (CosmoRS | CosmoRealSpecies) – The COSMO data including solvent and gas phase DFT calculations.

  • category (str) – The classification category of the configuration.

  • description (str) – A text description of the database entry.

  • melting_point (PhysicalQuantity of type temperature) – The melting point of the pure substance.

  • enthalpy_of_fusion (PhysicalQuantity of type energy) – The enthalpy or heat of fusion of the pure substance.

  • specific_heat_capacity_change (PhysicalQuantity of type energy per temperature) – The difference in the molar isobaric specific heat capacity between the liquid and solid phase.

  • antoine_a (PhysicalQuantity of type pressure) – The A parameter of the Antoine equation. The units indicate the pressure units in the equation.

  • antoine_b (PhysicalQuantity of type temperature) – The B parameter of the Antoine equation.

  • antoine_c (PhysicalQuantity of type temperature) – The C parameter of the Antoine equation.

  • boiling_point (PhysicalQuantity of type temperature) – The boiling point of the pure substance.

  • flash_point (PhysicalQuantity of type temperature) – Minimum temperature required for the vaporized pure substance to be combustible in air.

  • density (PhysicalQuantity of type density) – The liquid density of the pure substance.

Usage Examples

Find names of molecules in the COSMO-RS database by category, chemical formula and bond graph.

# Load the COSMO database
database = CosmoRSSpeciesDatabase()

# Find all species with the chemical formula C4H8O
species_names = database.findSpecies(formula='C4H8O')
nlprint(species_names)

# Find specifically the molecule tetrahydrofuran
species_names = database.findSpecies(formula='C4H8O', smiles='O1CCCC1')
nlprint(species_names)

find_species_example.py

Load water and SO2 molecules from the database and calculate the solubility of SO2 in water.

# Load the COSMO species
database = CosmoRSSpeciesDatabase()
water = database.exportSpecies('water')
sulfur_dioxide = database.exportSpecies('sulfur dioxide')

# Determine the gas solubility.
gas_solubility = GasSolubility(
    sulfur_dioxide,
    water,
    solvent_density=1*kiloGram/liter,
    temperature=298*Kelvin,
    parameters=CosmoRSParameters(),
)

# Retrieve the Henry constant.
h_cp = gas_solubility.henryConstantCP()[0].convertTo(molar/bar)
nlprint(f'The Henry constant of SO2 in water is {h_cp}')

# Retrieve the Henry volatility.
h_px = gas_solubility.henryVolatilityPX()[0].convertTo(bar)
nlprint(f'The Henry volatility of SO2 in water is {h_px}')

water_so2_example.py

Add and then remove an azide (ammonia) molecule.

# Create the COSMO-RS object
solvation_energy = SolvationEnergy(
    configuration=azane
)
azane_cosmo_rs = CosmoRS(
    configuration=azane,
    solvation_energy=solvation_energy
)

# Load the database
database = CosmoRSSpeciesDatabase()

# Add the molecule to the database
database.importSpecies(
    'azane',
    azane_cosmo_rs,
    category='Inorganic bases',
    description='Added as example of COSMO-RS molecular database',
    boiling_point=239.81*Kelvin,
    melting_point=195.42*Kelvin,
    density=0.682*kiloGram/liter,
    antoine_a=4.86886*bar,
    antoine_b=1113.928*Kelvin,
    antoine_c=-10.409*Kelvin,
)

# Remove the species from the database
database.deleteSpecies('azane')

add_remove_example.py

Notes

The CosmoRSSpeciesDatabase object provides a script interface to the molecule database in the Cosmo-RS Analyzer. Through this class CosmoRealSpecies objects can be exported from the database using the exportSpecies method. These CosmoRealSpecies objects can then be used directly in a COSMO-RS calculation. CosmoRealSpecies or CosmoRS objects can also be saved into the database using the importSpecies method. As well as the data object, the importSpecies method can optionally take a category label, a description or a range of experimental data that may be used in COSMO-RS calculations. These data can also be set when running the COSMO-RS calculation. Configurations that have been added to the database can also be removed by the deleteSpecies method. Configuration entries that are shipped with QuantumATK cannot be deleted.

In the database species have a name as a primary key. This is often the common name for the molecule, rather than the systematic IUPAC name. Specific molecules can be searched for using a combination of classification class, chemical formula and SMILES string in the findSpecies method. Classification class and chemical formula match all records with the same data. SMILES strings use graph matching to match all records that have the same bond graph. Note that this does not distinguish between cis and trans isomers. The findSpecies method returns the name of all records that match the given criteria.