Python Group Additivity (pGrAdd) software for estimating species thermochemical properties

Wittreich, Gerhard R.; Vlachos, Dionisios G.

doi:10.1016/j.cpc.2021.108277

Title: Python Group Additivity (pGrAdd) software for estimating species thermochemical properties

Journal Article · 04 January 2022 · Computer Physics Communications

DOI: https://doi.org/10.1016/j.cpc.2021.108277 · OSTI ID:1977048

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University of Delaware, Newark, DE (United States); OSTI
University of Delaware, Newark, DE (United States)

ncreasingly complex chemistry models require thermochemical data for many species often estimated from costly first-principles DFT computations. Here we introduce the Python Group Additivity software (pGrAdd) that implements comprehensive group additivity in a simple, modular, lightweight Python package that is extensible and easy to implement. It includes 6 group additivity databases for gas species and Pt(111) adsorbates allowing users to immediately compute thermochemical properties for a wide range of molecules and build new databases.

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Research Organization:: American Institute of Chemical Engineers (AIChE), New York, NY (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: EE0007888

OSTI ID:: 1977048

Journal Information:: Computer Physics Communications, Journal Name: Computer Physics Communications Journal Issue: C Vol. 273; ISSN 0010-4655

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (28)

Universality in Heterogeneous Catalysis Nørskov, J. K.; Bligaard, T.; Logadottir, A. Journal of Catalysis, Vol. 209, Issue 2 https://doi.org/10.1006/jcat.2002.3615	journal	July 2002
Universal Brønsted-Evans-Polanyi Relations for C–C, C–O, C–N, N–O, N–N, and O–O Dissociation Reactions Wang, Shengguang; Temel, Burcin; Shen, Juan Catalysis Letters, Vol. 141, Issue 3 https://doi.org/10.1007/s10562-010-0477-y	journal	November 2010
High throughput multiscale modeling for design of experiments, catalysts, and reactors: Application to hydrogen production from ammonia Prasad, V.; Karim, A. M.; Ulissi, Z. Chemical Engineering Science, Vol. 65, Issue 1 https://doi.org/10.1016/j.ces.2009.05.054	journal	January 2010
Language-oriented rule-based reaction network generation and analysis: Description of RING Rangarajan, Srinivas; Bhan, Aditya; Daoutidis, Prodromos Computers & Chemical Engineering, Vol. 45 https://doi.org/10.1016/j.compchemeng.2012.06.008	journal	October 2012
A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation Lym, Jonathan; Wittreich, Gerhard R.; Vlachos, Dionisios G. Computer Physics Communications, Vol. 247 https://doi.org/10.1016/j.cpc.2019.106864	journal	February 2020
The Brønsted–Evans–Polanyi relation and the volcano curve in heterogeneous catalysis Bligaard, T.; Nørskov, J. K.; Dahl, S. Journal of Catalysis, Vol. 224, Issue 1 https://doi.org/10.1016/j.jcat.2004.02.034	journal	May 2004
Silver: An extensible attribute grammar system Van Wyk, Eric; Bodin, Derek; Gao, Jimin Science of Computer Programming, Vol. 75, Issue 1-2 https://doi.org/10.1016/j.scico.2009.07.004	journal	January 2010
A generalized inverse for matrices Penrose, R. Mathematical Proceedings of the Cambridge Philosophical Society, Vol. 51, Issue 3 https://doi.org/10.1017/S0305004100030401	journal	July 1955
Microkinetic Modeling: A Tool for Rational Catalyst Design Motagamwala, Ali Hussain; Dumesic, James A. Chemical Reviews, Vol. 121, Issue 2 https://doi.org/10.1021/acs.chemrev.0c00394	journal	November 2020
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation Liu, Mengjie; Grinberg Dana, Alon; Johnson, Matthew S. Journal of Chemical Information and Modeling, Vol. 61, Issue 6 https://doi.org/10.1021/acs.jcim.0c01480	journal	May 2021
Group Additivity for Thermochemical Property Estimation of Lignin Monomers on Pt(111) Gu, Geun Ho; Vlachos, Dionisios G. The Journal of Physical Chemistry C, Vol. 120, Issue 34 https://doi.org/10.1021/acs.jpcc.6b06430	journal	August 2016
Group Additivity for Aqueous Phase Thermochemical Properties of Alcohols on Pt(111) Gu, Geun Ho; Schweitzer, Benjamin; Michel, Carine The Journal of Physical Chemistry C, Vol. 121, Issue 39 https://doi.org/10.1021/acs.jpcc.7b07340	journal	September 2017
Open Catalyst 2020 (OC20) Dataset and Community Challenges Chanussot, Lowik; Das, Abhishek; Goyal, Siddharth ACS Catalysis, Vol. 11, Issue 10 https://doi.org/10.1021/acscatal.0c04525	journal	May 2021
Accurate Thermochemistry of Complex Lignin Structures via Density Functional Theory, Group Additivity, and Machine Learning Li, Qiang; Wittreich, Gerhard; Wang, Yifan ACS Sustainable Chemistry & Engineering, Vol. 9, Issue 8 https://doi.org/10.1021/acssuschemeng.0c08856	journal	February 2021
Additivity rules for the estimation of thermochemical properties Benson, Sidney W.; Cruickshank, F. R.; Golden, D. M. Chemical Reviews, Vol. 69, Issue 3 https://doi.org/10.1021/cr60259a002	journal	June 1969
Group Additivity for Estimating Thermochemical Properties of Furanic Compounds on Pd(111) Vorotnikov, Vassili; Wang, Shengguang; Vlachos, Dionisios G. Industrial & Engineering Chemistry Research, Vol. 53, Issue 30 https://doi.org/10.1021/ie502049a	journal	July 2014
Multiscale Model and Informatics-Based Optimal Design of Experiments: Application to the Catalytic Decomposition of Ammonia on Ruthenium Prasad, Vinay; Vlachos, Dionisios G. Industrial & Engineering Chemistry Research, Vol. 47, Issue 17 https://doi.org/10.1021/ie800343s	journal	July 2008
Identification of General Linear Relationships between Activation Energies and Enthalpy Changes for Dissociation Reactions at Surfaces Michaelides, Angelos; Liu, Z. -P.; Zhang, C. J. Journal of the American Chemical Society, Vol. 125, Issue 13 https://doi.org/10.1021/ja027366r	journal	April 2003
Thermochemistry for Hydrocarbon Intermediates Chemisorbed on Metal Surfaces: CH _n _- _m (CH ₃ ) _m with n = 1, 2, 3 and m ≤ n on Pt, Ir, Os, Pd, Rh, and Ru Kua, Jeremy; Faglioni, Francesco; Goddard, William A. Journal of the American Chemical Society, Vol. 122, Issue 10 https://doi.org/10.1021/ja993336l	journal	March 2000
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 Salciccioli, M.; Chen, Y.; Vlachos, D. G. The Journal of Physical Chemistry C, Vol. 114, Issue 47 https://doi.org/10.1021/jp107836a	journal	November 2010
Principal component analysis Lever, Jake; Krzywinski, Martin; Altman, Naomi Nature Methods, Vol. 14, Issue 7 https://doi.org/10.1038/nmeth.4346	journal	July 2017
Array programming with NumPy Harris, Charles R.; Millman, K. Jarrod; van der Walt, Stéfan J. Nature, Vol. 585, Issue 7825 https://doi.org/10.1038/s41586-020-2649-2	journal	September 2020
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Thermochemistry of gas-phase and surface species via LASSO-assisted subgraph selection Gu, Geun Ho; Plechac, Petr; Vlachos, Dionisios G. Reaction Chemistry & Engineering, Vol. 3, Issue 4 https://doi.org/10.1039/C7RE00210F	journal	January 2018
LIII. On lines and planes of closest fit to systems of points in space Pearson, Karl The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, Vol. 2, Issue 11 https://doi.org/10.1080/14786440109462720	journal	November 1901
The fourteenth western meeting of the American Mathematical Society Dresden, Arnold Bulletin of the American Mathematical Society, Vol. 26, Issue 9 https://doi.org/10.1090/S0002-9904-1920-03322-7	journal	January 1920
IPython: A System for Interactive Scientific Computing Perez, Fernando; Granger, Brian E. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.53	journal	January 2007
The lasso problem and uniqueness Tibshirani, Ryan J. Electronic Journal of Statistics, Vol. 7, Issue 0 https://doi.org/10.1214/13-EJS815	journal	January 2013

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References (28)

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