'''Chemical Engineering Design Library (ChEDL). Utilities for process modeling.
Copyright (C) 2022 Caleb Bell <Caleb.Andrew.Bell@gmail.com>
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SOFTWARE.
This module contains an implementation of the Wilson-Jasperson
group-contribution method.
This functionality requires the RDKit library to work.
.. contents:: :local:
.. autofunction:: thermo.group_contribution.Wilson_Jasperson
'''
__all__ = ['Wilson_Jasperson', 'Wilson_Jasperson_Tc_increments',
'Wilson_Jasperson_Pc_increments',
'Wilson_Jasperson_Tc_groups', 'Wilson_Jasperson_Pc_groups']
from math import exp
from chemicals.elements import simple_formula_parser
from thermo.functional_groups import (
alcohol_smarts,
aldehyde_smarts,
all_amine_smarts,
carboxylic_acid_smarts,
disulfide_smarts,
ester_smarts,
ether_smarts,
is_haloalkane,
ketone_smarts,
mercaptan_smarts,
nitrile_smarts,
nitro_smarts,
siloxane_smarts,
smarts_mol_cache,
sulfide_smarts,
)
Wilson_Jasperson_Tc_increments = {
'H': 0.002793,
'D': 0.002793,
'T': 0.002793,
'He': 0.32,
'B': 0.019,
'C': 0.008532,
'N': 0.019181,
'O': 0.020341,
'F': 0.00881,
'Ne': 0.0364,
'Al': 0.088,
'Si': 0.02,
'P': 0.012,
'S': 0.007271,
'Cl': 0.011151,
'Ar': 0.0168,
'Ti': 0.014,
'V': 0.0186,
'Ga': 0.059,
'Ge': 0.031,
'As': 0.007,
'Se': 0.0103,
'Br': 0.012447,
'Kr': 0.0133,
'Rb': -0.027,
'Zr': 0.175,
'Nb': 0.0176,
'Mo': 0.007,
'Sn': 0.02,
'Sb': 0.01,
'Te': 0,
'I': 0.0059,
'Xe': 0.017,
'Cs': -0.0275,
'Hf': 0.219,
'Ta': 0.013,
'W': 0.011,
'Re': 0.014,
'Os': -0.05,
'Hg': 0,
'Bi': 0,
'Rn': 0.007,
'U': 0.015,
}
Wilson_Jasperson_Pc_increments = {
'H': 0.1266,
'D': 0.1266,
'T': 0.1266,
'He': 0.434,
'B': 0.91,
'C': 0.72983,
'N': 0.44805,
'O': 0.4336,
'F': 0.32868,
'Ne': 0.126,
'Al': 6.05,
'Si': 1.34,
'P': 1.22,
'S': 1.04713,
'Cl': 0.97711,
'Ar': 0.796,
'Ti': 1.19,
'V': None ,
'Ga': None ,
'Ge': 1.42,
'As': 2.68,
'Se': 1.2,
'Br': 0.97151,
'Kr': 1.11,
'Rb': None ,
'Zr': 1.11,
'Nb': 2.71,
'Mo': 1.69,
'Sn': 1.95,
'Sb': None ,
'Te': 0.43,
'I': 1.31593,
'Xe': 1.66,
'Cs': 6.33,
'Hf': 1.07,
'Ta': None ,
'W': 1.08,
'Re': None ,
'Os': None ,
'Hg': -0.08,
'Bi': 0.69,
'Rn': 2.05,
'U': 2.04,
}
Wilson_Jasperson_Tc_groups = {'OH_large': 0.01, 'OH_small': 0.0350, '-O-': -0.0075, 'amine': -0.004,
'-CHO': 0, '>CO': -0.0550, '-COOH': 0.017, '-COO-': -0.015,
'-CN': 0.017, '-NO2': -0.02, 'halide': 0.002, 'sulfur_groups': 0.0,
'siloxane': -0.025}
Wilson_Jasperson_Pc_groups = {'OH_large': 0, 'OH_small': 0, '-O-': 0, 'amine': 0,
'-CHO': 0.5, '>CO': 0, '-COOH': 0.5, '-COO-': 0,
'-CN': 1.5, '-NO2': 1.0, 'halide': 0, 'sulfur_groups': 0.0,
'siloxane': -0.5}
[docs]def Wilson_Jasperson(mol, Tb, second_order=True):
r'''Estimate the critical temperature and pressure of a molecule using
the molecule itself, and a known or estimated boiling point
using the Wilson-Jasperson method.
Parameters
----------
mol : str or rdkit.Chem.rdchem.Mol, optional
Smiles string representing a chemical or a rdkit molecule, [-]
Tb : float
Known or estimated boiling point, [K]
second_order : bool
Whether to use the first order method (False), or the second order
method, [-]
Returns
-------
Tc : float
Estimated critical temperature, [K]
Pc : float
Estimated critical pressure, [Pa]
missing_Tc_increments : bool
Whether or not there were missing atoms for the `Tc` calculation, [-]
missing_Pc_increments : bool
Whether or not there were missing atoms for the `Pc` calculation, [-]
Notes
-----
Raises an exception if rdkit is not installed, or `smi` or `rdkitmol` is
not defined.
Calculated values were published in [3]_ for 448 compounds, as calculated
by NIST TDE. There appear to be further modifications to the method in
NIST TDE, as ~25% of values have differences larger than 5 K.
Examples
--------
Example for 2-ethylphenol in [2]_:
>>> Tc, Pc, _, _ = Wilson_Jasperson('CCC1=CC=CC=C1O', Tb=477.67) # doctest:+SKIP
>>> (Tc, Pc) # doctest:+SKIP
(693.567, 3743819.6667)
>>> Tc, Pc, _, _ = Wilson_Jasperson('CCC1=CC=CC=C1O', Tb=477.67, second_order=False) # doctest:+SKIP
>>> (Tc, Pc) # doctest:+SKIP
(702.883, 3794106.49)
References
----------
.. [1] Wilson, G. M., and L. V. Jasperson. "Critical Constants Tc, Pc,
Estimation Based on Zero, First and Second Order Methods." In
Proceedings of the AIChE Spring Meeting, 21, 1996.
.. [2] Poling, Bruce E. The Properties of Gases and Liquids. 5th edition.
New York: McGraw-Hill Professional, 2000.
.. [3] Yan, Xinjian, Qian Dong, and Xiangrong Hong. "Reliability Analysis
of Group-Contribution Methods in Predicting Critical Temperatures of
Organic Compounds." Journal of Chemical & Engineering Data 48, no. 2
(March 1, 2003): 374-80. https://doi.org/10.1021/je025596f.
'''
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
if type(mol) is Chem.rdchem.Mol:
rdkitmol = Chem.Mol(mol)
no_H_mol = mol
else:
rdkitmol = Chem.MolFromSmiles(mol)
no_H_mol = Chem.Mol(rdkitmol)
ri = no_H_mol.GetRingInfo()
atom_rings = ri.AtomRings()
Nr = len(atom_rings)
atoms = simple_formula_parser(rdMolDescriptors.CalcMolFormula(rdkitmol))
group_contributions = {}
OH_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(alcohol_smarts))
if 'C' in atoms:
if atoms['C'] >= 5:
group_contributions['OH_large'] = len(OH_matches)
else:
group_contributions['OH_small'] = len(OH_matches)
ether_O_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(ether_smarts))
group_contributions['-O-'] = len(ether_O_matches)
group_contributions['-CN'] = 0
amine_groups = set()
if 'N' in atoms:
nitro_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(nitro_smarts))
group_contributions['-NO2'] = len(nitro_matches)
nitrile_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(nitrile_smarts))
group_contributions['-CN'] = len(nitrile_matches)
for s in all_amine_smarts:
amine_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(s))
for h in amine_matches:
# Get the N atom and store its index
for at in h:
atom = rdkitmol.GetAtomWithIdx(at)
if atom.GetSymbol() == 'N':
amine_groups.add(at)
# print(amine_groups)
group_contributions['amine'] = len(amine_groups)
if 'O' in atoms and 'C' in atoms:
aldehyde_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(aldehyde_smarts))
group_contributions['-CHO'] = len(aldehyde_matches)
ketone_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(ketone_smarts))
group_contributions['>CO'] = len(ketone_matches)
carboxylic_acid_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(carboxylic_acid_smarts))
group_contributions['-COOH'] = len(carboxylic_acid_matches)
ester_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(ester_smarts))
group_contributions['-COO-'] = len(ester_matches)
group_contributions['halide'] = 1 if is_haloalkane(rdkitmol) else 0
group_contributions['sulfur_groups'] = 0
if 'S' in atoms:
for s in (mercaptan_smarts, sulfide_smarts, disulfide_smarts):
group_contributions['sulfur_groups'] += len(rdkitmol.GetSubstructMatches(smarts_mol_cache(s)))
group_contributions['siloxane'] = 0
if 'Si' in atoms:
siloxane_matches = rdkitmol.GetSubstructMatches(smarts_mol_cache(siloxane_smarts))
group_contributions['siloxane'] = len(siloxane_matches)
# group_contributions = {'OH_large': 0, '-O-': 0, 'amine': 0, '-CHO': 0,
# '>CO': 0, '-COOH': 0, '-COO-': 0, '-CN': 0,
# '-NO2': 0, 'halide': 0, 'sulfur_groups': 0, 'siloxane': 0}
missing_Tc_increments = False
Tc_inc = 0.0
for k, v in atoms.items():
try:
Tc_inc += Wilson_Jasperson_Tc_increments[k]*v
except KeyError:
missing_Tc_increments = True
missing_Pc_increments = False
Pc_inc = 0.0
for k, v in atoms.items():
try:
Pc_inc += Wilson_Jasperson_Pc_increments[k]*v
except (KeyError, TypeError):
missing_Pc_increments = True
second_order_Pc = 0.0
second_order_Tc = 0.0
if second_order:
for k, v in group_contributions.items():
second_order_Tc += Wilson_Jasperson_Tc_groups[k]*v
for k, v in group_contributions.items():
second_order_Pc += Wilson_Jasperson_Pc_groups[k]*v
# print(atoms)
# print(group_contributions)
# print('rings', Nr)
# print(Tc_inc, second_order_Tc)
den = 0.048271 - 0.019846*Nr + Tc_inc + second_order_Tc
if den >= 0:
Tc = Tb/(den)**0.2
else:
# Can't make a prediction
missing_Tc_increments = True
Tc = Tb*2.5
Y = -0.00922295 - 0.0290403*Nr + 0.041*(second_order_Pc + Pc_inc)
Pc = 0.0186233*Tc/(-0.96601 + exp(Y))
return Tc, Pc*1e5, missing_Tc_increments, missing_Pc_increments