1
|
Dana AG, Johnson MS, Allen JW, Sharma S, Raman S, Liu M, Gao CW, Grambow CA, Goldman MJ, Ranasinghe DS, Gillis RJ, Payne AM, Li Y, Dong X, Spiekermann KA, Wu H, Dames EE, Buras ZJ, Vandewiele NM, Yee NW, Merchant SS, Buesser B, Class CA, Goldsmith F, West RH, Green WH. Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software. INT J CHEM KINET 2023. [DOI: 10.1002/kin.21637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Alon Grinberg Dana
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
- The Wolfson Department of Chemical Engineering and Grand Technion Energy Program (GTEP) Technion – Israel Institute of Technology Haifa Israel
| | - Matthew S. Johnson
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Joshua W. Allen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Sandeep Sharma
- Department of Chemistry University of Colorado Boulder CO USA
| | - Sumathy Raman
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Mengjie Liu
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Connie W. Gao
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Colin A. Grambow
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Mark J. Goldman
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Duminda S. Ranasinghe
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Ryan J. Gillis
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - A. Mark Payne
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Yi‐Pei Li
- Department of Chemical Engineering National Taiwan University Taipei Taiwan
| | - Xiaorui Dong
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Kevin A. Spiekermann
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Haoyang Wu
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Enoch E. Dames
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Zachary J. Buras
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Nick M. Vandewiele
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Nathan W. Yee
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Shamel S. Merchant
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Beat Buesser
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Caleb A. Class
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | | | - Richard H. West
- Department of Chemical Engineering Northeastern University Boston Massachusetts USA
| | - William H. Green
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| |
Collapse
|
2
|
Johnson MS, Dong X, Grinberg Dana A, Chung Y, Farina D, Gillis RJ, Liu M, Yee NW, Blondal K, Mazeau E, Grambow CA, Payne AM, Spiekermann KA, Pang HW, Goldsmith CF, West RH, Green WH. RMG Database for Chemical Property Prediction. J Chem Inf Model 2022; 62:4906-4915. [PMID: 36222558 DOI: 10.1021/acs.jcim.2c00965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Reaction Mechanism Generator (RMG) database for chemical property prediction is presented. The RMG database consists of curated datasets and estimators for accurately predicting the parameters necessary for constructing a wide variety of chemical kinetic mechanisms. These datasets and estimators are mostly published and enable prediction of thermodynamics, kinetics, solvation effects, and transport properties. For thermochemistry prediction, the RMG database contains 45 libraries of thermochemical parameters with a combination of 4564 entries and a group additivity scheme with 9 types of corrections including radical, polycyclic, and surface absorption corrections with 1580 total curated groups and parameters for a graph convolutional neural network trained using transfer learning from a set of >130 000 DFT calculations to 10 000 high-quality values. Correction schemes for solvent-solute effects, important for thermochemistry in the liquid phase, are available. They include tabulated values for 195 pure solvents and 152 common solutes and a group additivity scheme for predicting the properties of arbitrary solutes. For kinetics estimation, the database contains 92 libraries of kinetic parameters containing a combined 21 000 reactions and contains rate rule schemes for 87 reaction classes trained on 8655 curated training reactions. Additional libraries and estimators are available for transport properties. All of this information is easily accessible through the graphical user interface at https://rmg.mit.edu. Bulk or on-the-fly use can be facilitated by interfacing directly with the RMG Python package which can be installed from Anaconda. The RMG database provides kineticists with easy access to estimates of the many parameters they need to model and analyze kinetic systems. This helps to speed up and facilitate kinetic analysis by enabling easy hypothesis testing on pathways, by providing parameters for model construction, and by providing checks on kinetic parameters from other sources.
Collapse
Affiliation(s)
- Matthew S Johnson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Xiaorui Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alon Grinberg Dana
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States.,The Wolfson Department of Chemical Engineering, Grand Technion Energy Program (GTEP), Technion─Israel Institute of Technology, Haifa3200003, Israel
| | - Yunsie Chung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - David Farina
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts02115, United States
| | - Ryan J Gillis
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Mengjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Nathan W Yee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Katrin Blondal
- School of Engineering, Brown University, Providence, Rhode Island02912, United States
| | - Emily Mazeau
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts02115, United States
| | - Colin A Grambow
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - A Mark Payne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Kevin A Spiekermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Wei Pang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - C Franklin Goldsmith
- School of Engineering, Brown University, Providence, Rhode Island02912, United States
| | - Richard H West
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts02115, United States
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| |
Collapse
|
3
|
Spiekermann K, Pattanaik L, Green WH. High accuracy barrier heights, enthalpies, and rate coefficients for chemical reactions. Sci Data 2022; 9:417. [PMID: 35851390 PMCID: PMC9293986 DOI: 10.1038/s41597-022-01529-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
Quantitative chemical reaction data, including activation energies and reaction rates, are crucial for developing detailed kinetic mechanisms and accurately predicting reaction outcomes. However, such data are often difficult to find, and high-quality datasets are especially rare. Here, we use CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states. We report the results from these quantum chemistry calculations and extract the barrier heights and reaction enthalpies to create a kinetics dataset of nearly 12,000 gas-phase reactions. These reactions involve H, C, N, and O, contain up to seven heavy atoms, and have cleaned atom-mapped SMILES. Our higher-accuracy coupled-cluster barrier heights differ significantly (RMSE of ∼5 kcal mol−1) relative to those calculated at ωB97X-D3/def2-TZVP. We also report accurate transition state theory rate coefficients \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${k}_{\infty }(T)$$\end{document}k∞(T) between 300 K and 2000 K and the corresponding Arrhenius parameters for a subset of rigid reactions. We believe this data will accelerate development of automated and reliable methods for quantitative reaction prediction. Measurement(s) | Barrier Heights • Enthalpies • Rate Coefficients | Technology Type(s) | ab initio quantum chemistry computational method |
Collapse
Affiliation(s)
- Kevin Spiekermann
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Lagnajit Pattanaik
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
| |
Collapse
|
4
|
Farina DS, Sirumalla SK, Mazeau EJ, West RH. Extensive High-Accuracy Thermochemistry and Group Additivity Values for Halocarbon Combustion Modeling. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c03076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Farina
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sai Krishna Sirumalla
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Emily J. Mazeau
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Richard H. West
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
5
|
Johnson MS, Nimlos MR, Ninnemann E, Laich A, Fioroni GM, Kang D, Bu L, Ranasinghe D, Khanniche S, Goldsborough SS, Vasu SS, Green WH. Oxidation and pyrolysis of methyl propyl ether. INT J CHEM KINET 2021. [DOI: 10.1002/kin.21489] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Matthew S. Johnson
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Mark R. Nimlos
- National Bioenergy Center National Renewable Energy Laboratory Golden Colorado USA
| | - Erik Ninnemann
- Center for Advanced Turbomachinery and Energy Research (CATER), Mechanical and Aerospace Engineering University of Central Florida Orlando Florida USA
| | - Andrew Laich
- Center for Advanced Turbomachinery and Energy Research (CATER), Mechanical and Aerospace Engineering University of Central Florida Orlando Florida USA
| | - Gina M. Fioroni
- National Bioenergy Center National Renewable Energy Laboratory Golden Colorado USA
| | - Dongil Kang
- Center for Transportation Research, Energy Systems Division Argonne National Laboratory Argonne Illinois USA
| | - Lintao Bu
- National Bioenergy Center National Renewable Energy Laboratory Golden Colorado USA
| | - Duminda Ranasinghe
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Sarah Khanniche
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - S. Scott Goldsborough
- Center for Transportation Research, Energy Systems Division Argonne National Laboratory Argonne Illinois USA
| | - Subith S. Vasu
- Center for Advanced Turbomachinery and Energy Research (CATER), Mechanical and Aerospace Engineering University of Central Florida Orlando Florida USA
| | - William H. Green
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| |
Collapse
|
6
|
Wei N, Xu D, Hao B, Guo S, Guo Y, Wang S. Chemical reactions of organic compounds in supercritical water gasification and oxidation. WATER RESEARCH 2021; 190:116634. [PMID: 33290907 DOI: 10.1016/j.watres.2020.116634] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
Supercritical water is a benign reaction medium to convert organic matters through supercritical water gasification and supercritical water oxidation into flammable gaseous and harmless substances, respectively. This work systematically summarizes main chemical reactions of some typical organic compounds in supercritical water with or without oxidant for the first time. These compounds include hydrocarbons, proteins, cellulose, lignins, phenols, alcohols, aldehydes, ketones, organic acids, and some N-, Cl-, Br-, F-, S- and P-containing organic matters. Their main conversion pathways, reaction processes, intermediate products, final products and influence factors are analyzed deeply. This information helps to understand and predict corresponding reaction mechanisms and to better achieve objective products in supercritical water gasification and supercritical water oxidation.
Collapse
Affiliation(s)
- Ning Wei
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China
| | - Donghai Xu
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China.
| | - Botian Hao
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China
| | - Shuwei Guo
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China
| | - Yang Guo
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China
| | - Shuzhong Wang
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710049, China
| |
Collapse
|
7
|
|
8
|
Kang J, Sim S, Jung H, Han B, Lee YW. Desulfurization of hexyl sulfide and hexanethiol using supercritical water. J Supercrit Fluids 2020. [DOI: 10.1016/j.supflu.2019.104734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|