pgradd 2.9.14

Citing this work

G.R. Wittreich, D.G. Vlachos, Python Group Additivity (pGrAdd) software for estimating species thermochemical properties Comput. Phys. Commun. 273 (2022) 108277 https://doi.org/10.1016/j.cpc.2021.108277

Developers

• Gerhard R Wittreich, Ph.D., P.E.

• Geun Ho Gu, Ph.D.

• Michael Salciccioli, Ph.D.

• Stephen M. Edie

Required Packages

• Python2/Python3

• pmutt >= 1.3.2

• rdkit >= 2018.03.4.0

• ipython >= 7.3.1

• numpy >= 1.21.5

• pyyaml >= 6.0

• scipy >= 1.9.3

Getting Started

1. Install using pip:

   pip install --user pgradd

2. Run the unit tests. Navigate to the tests directory, input the command shown below, and look for an OK response. (Note: The number of tests/time may change with subsequent versions):

   python -m unittest
   
   ........................................
   ----------------------------------------------------------------------
   Ran 40 tests in 7.849s
   
   OK

3. Look at examples below

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contributing

If you have a suggestion or find a bug, please post to our Issues page with the or tag respectively.

Finally, if you would like to add to the body of code, please:

• fork the development branch

• make the desired changes

• write the appropriate unit tests

• submit a pull request.

Questions

If you are having issues, please post to our Issues page with the help wanted or question tag. We will do our best to assist.

Special Thanks

• Dr. Jeffrey Frey (pip and conda compatibility)

Citations

• Rangarajan et al. “Language-oriented rule-based reaction network generation and analysis: Algorithms of RING”, Comput. Chem. Eng. 2014, 64, 124. https://doi.org/10.1016/j.compchemeng.2014.02.007

• Rangarajan et al. “Language-oriented rule-based reaction network generation and analysis: Descrpition of RING”, Comput. Chem. Eng. 2012, 45, 114. https://doi.org/10.1016/j.compchemeng.2012.06.008

• Benson et al. “Additivity rules for the estimation of thermochemical properties.” Chem. Rev., 1969, 69 (3), 279-324

• Salciccioli et al. “Density Functional Theory-Derived Group Additivity and Linear Scaling Methods for Prediction of Oxygenate Stability on Metal Catalysts: Adsorption of Open-Ring Alcohol and Polyol Dehydrogenation Intermediates on Pt-Based Metals.” J. Phys. Chem. C, 2010, 114 (47) 20155-20166. https://doi.org/10.1021/jp107836a

• Kua J, Goddard WA (1998) Chemisorption of Organics on Platinum. 2. Chemisorption of C 2 H x and CH x on Pt(111). J Phys Chem B 102:9492–9500. https://doi.org/10.1021/jp982527s

• Kua J, Faglioni F, Goddard WA (2000) Thermochemistry for hydrocarbon intermediates chemisorbed on metal surfaces: CH(n-m)(CH3)(m) with n = 1, 2, 3 and m ≤ n on Pt, Ir, Os, Pd, Rh, and Ru. J Am Chem Soc 122:2309–2321. https://doi.org/10.1021/ja993336l

• Salciccioli et al. “Adsorption of Acid, Ester, and Ether Functional Groups on Pt: Fast Prediction of Thermochemical Properties of Adsorbed Oxygenates via DFT-Based Group Additivity Methods.” J. Phys. Chem. C, 2012, 116(2), 1873-1886. https://doi.org/10.1021/jp2091413

• Vorotnikov et al. “Group Additivity for Estimating Thermochemical Properties of Furanic Compounds on Pd(111).” Ind. Eng. Chem. Res., 2014, 53 (30), 11929-11938. https://doi.org/10.1021/ie502049a

• Vorotnikov et al. “Group Additivity and Modified Linear Scaling Relations for Estimating Surface Thermochemistry on Transition Metal Surfaces: Application to Furanics.” J. Phys. Chem. C, 2015, 119 (19), 10417-10426. https://doi.org/10.1021/acs.jpcc.5b01696

• Gu et al. “Group Additivity for Thermochemical Property Estimation of Lignin Monomers on Pt(111).” J. Phys. Chem. C, 2016, 120 (34), 19234-19241. https://doi.org/10.1021/acs.jpcc.6b06430

• Gu GH, Schweitzer B, Michel C, et al (2017) Group additivity for aqueous phase thermochemical properties of alcohols on Pt(111). J Phys Chem C 121:21510–21519. https://doi.org/10.1021/acs.jpcc.7b07340

• Xie, T.; Wittreich, G. R.; Vlachos, D. G. Multiscale Modeling of Hydrogenolysis of Ethane and Propane on Ru(0001): Implications for Plastics Recycling. Appl. Catal. B Environ. 2022, 316 (June), 121597. https://doi.org/10.1016/j.apcatb.2022.121597

• Eccles, S; Pellizzeri, S. Expanded Group Additivity Framework for Thermochemical Prediction of Fluorocarbons and PFAS from Large-Scale DFT Data. J. Phys. Chem. A (2026) 130 (34): 6825–6834. https://doi.org/10.1021/acs.jpca.6c03256

Examples

Benson’s Gas Group Additivity Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('BensonGA')
descriptors = lib.GetDescriptors('C1CO1')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(298.15))

Out:
defaultdict(int, {'C(C)(H)2(O)': 2, 'O(C)2': 1, 'Oxirane': 1})
-21.09467743150278

Salciccioli et al. J. Phys. Chem. C, 2012, 116 (2), pp 1873-1886 Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('SalciccioliGA2012')
descriptors = lib.GetDescriptors('C([Pt])C[Pt]')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_H(298.15, units='kcal/mol'))

Out:
defaultdict(<class 'int'>, {'C(C)(H)2(Pt)': 2, 'surface-ring strain': 0.217})
-11.307743997749277

Gu et al. J. Phys. Chem. C, 2017, 121 pp 21510–21519 Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('GuSolventGA2017Aq')
descriptors = lib.GetDescriptors('C(=O)([Pt])O')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(500))

Out:
defaultdict(<class 'int'>, {'CO(O)(Pt)+O(CO)(H)': 1.0})
-109.86212002776878

Wittreich Surface Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('GRWSurface2018')
descriptors = lib.GetDescriptors('[Pt]C([Pt])C([Pt])([Pt])C=O')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(750), '[Dimensionless]')
print(thermochem.get_H(750, 'kcal/mol'), '[kcal/mol]')

Out:
defaultdict(<class 'int'>, {'C(C)(H)(Pt)2': 1, 'C(C)(CO)(Pt)2': 1, 'CO(C)(H)': 1,
                            'CPt2CPt2': 1, 'CCPt2': 1, 'surface-ring strain': 0.392})
-13.423119203382337 [Dimensionless]
-20.005853103142883 [kcal/mol]

Wittreich Solvated Surface Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('GRWAqueous2018')
descriptors = lib.GetDescriptors('C(=O)([Pt])O')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(500), '[Dimensionless]')
print(thermochem.get_H(500, 'kJ/mol'), '[kJ/mol]')

Out:
defaultdict(<class 'int'>, {'CO(O)(Pt)+O(CO)(H)': 1.0})
-107.57909464133714 [Dimensionless]
-447.23102885789655 [kJ/mol]

Xie Ru(0001) Surface Example 1:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('XieGA2022')
descriptors = lib.GetDescriptors('[Ru]C([Ru])C([Ru])([Ru])C')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(500), '[Dimensionless]')
print(thermochem.get_H(500, 'kJ/mol'), '[kJ/mol]')

Out:
defaultdict(<class 'int'>, {'C(C)(H)(Ru)2': 1, 'C(C)2(Ru)2': 1, 'C(C)(H)3': 1, 'CRu2CRu2': 1})
 -35.040312149773726 [Dimensionless]
-145.6706333743726   [kJ/mol]

Xie Ru(0001) Surface Example 2:

 In:
 from pgradd.GroupAdd.Library import GroupLibrary
 import pgradd.ThermoChem
 lib = GroupLibrary.Load('XieGA2022')
 descriptors = lib.GetDescriptors('CCC')
 print(descriptors)
 thermochem = lib.Estimate(descriptors,'thermochem')
 print(thermochem.get_HoRT(500), '[Dimensionless]')
 print(thermochem.get_H(500, 'kJ/mol'), '[kJ/mol]')

 Out:
 defaultdict(<class 'int'>, {'C(C)(H)3': 2, 'C(C)2(H)2': 1})
 -41.49969417868688 [Dimensionless]
-172.52376948049303 [kJ/mol]

Eccles and Pellizzeri J. Phys. Chem. A 27 August 2026; 130 (34): 6825–6834. Example:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('PellizzeriGAF2026')
descriptors = lib.GetDescriptors('C(F)(F)(F)C(F)(F)C(=O)O')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_HoRT(298.15))
print(thermochem.get_H(500, 'kJ/mol'), '[kJ/mol]')

Out:
defaultdict(<class 'int'>, {'C(C[d])(F)2(O)': 1, 'F(C)': 2, 'O(C)(H)': 2, 'C[d](C)(O)(O[d])': 1, 'O[d](C[d])': 1})
-407.6827446197806 [Dimensionless]
-985.3759086950399 [kJ/mol]

Free Energy of Formation by including Entropy of the Elements:

In:
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
lib = GroupLibrary.Load('BensonGA')
descriptors = lib.GetDescriptors('CCCCCC')
print(descriptors)
thermochem = lib.Estimate(descriptors,'thermochem')
print(thermochem.get_GoRT(T=298.15, S_elements=True), '[Dimensionless]')
print(thermochem.get_G(T=298.15, units='kJ/mol', S_elements=True), '[kJ/mol]')

Out:
defaultdict(<class 'int'>, {'C(C)(H)3': 2, 'C(C)2(H)2': 4})
-3.1192349163716244 [Dimensionless]
-7.732446702038452  [kJ/mol]