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Zheng P, Yang W, Wu W, Isayev O, Dral PO. Toward Chemical Accuracy in Predicting Enthalpies of Formation with General-Purpose Data-Driven Methods. J Phys Chem Lett 2022; 13:3479-3491. [PMID: 35416675 DOI: 10.1021/acs.jpclett.2c00734] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enthalpies of formation and reaction are important thermodynamic properties that have a crucial impact on the outcome of chemical transformations. Here we implement the calculation of enthalpies of formation with a general-purpose ANI-1ccx neural network atomistic potential. We demonstrate on a wide range of benchmark sets that both ANI-1ccx and our other general-purpose data-driven method AIQM1 approach the coveted chemical accuracy of 1 kcal/mol with the speed of semiempirical quantum mechanical methods (AIQM1) or faster (ANI-1ccx). It is remarkably achieved without specifically training the machine learning parts of ANI-1ccx or AIQM1 on formation enthalpies. Importantly, we show that these data-driven methods provide statistical means for uncertainty quantification of their predictions, which we use to detect and eliminate outliers and revise reference experimental data. Uncertainty quantification may also help in the systematic improvement of such data-driven methods.
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Affiliation(s)
- Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wudi Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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2
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Dobbelaere MR, Plehiers PP, Van de Vijver R, Stevens CV, Van Geem KM. Learning Molecular Representations for Thermochemistry Prediction of Cyclic Hydrocarbons and Oxygenates. J Phys Chem A 2021; 125:5166-5179. [PMID: 34081474 DOI: 10.1021/acs.jpca.1c01956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate thermochemistry estimation of polycyclic molecules is crucial for kinetic modeling of chemical processes that use renewable and alternative feedstocks. In kinetic model generators, molecular properties are estimated rapidly with group additivity, but this method is known to have limitations for polycyclic structures. This issue has been resolved in our work by combining a geometry-based molecular representation with a deep neural network trained on ab initio data. Each molecule is transformed into a probabilistic vector from its interatomic distances, bond angles, and dihedral angles. The model is tested on a small experimental dataset (200 molecules) from the literature, a new medium-sized set (4000 molecules) with both open-shell and closed-shell species, calculated at the CBS-QB3 level with empirical corrections, and a large G4MP2-level QM9-based dataset (40 000 molecules). Heat capacities between 298.15 and 2500 K are calculated in the medium set with an average deviation of about 1.5 J mol-1 K-1 and the standard entropy at 298.15 K is predicted with an average error below 4 J mol-1 K-1. The standard enthalpy of formation at 298.15 K has an average out-of-sample error below 4 kJ mol-1 on a QM9 training set size of around 15 000 molecules. By fitting NASA polynomials, the enthalpy of formation at higher temperatures can be calculated with the same accuracy as the standard enthalpy of formation. Uncertainty quantification by means of the ensemble standard deviation is included to indicate when molecules that are on the edge or outside of the application range of the model are evaluated.
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Affiliation(s)
- Maarten R Dobbelaere
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Pieter P Plehiers
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Ruben Van de Vijver
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Christian V Stevens
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Kevin M Van Geem
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
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3
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Zhang IY, Wu J, Xu X. Accurate heats of formation of polycyclic saturated hydrocarbons predicted by using the XYG3 type of doubly hybrid functionals. J Comput Chem 2018; 40:1113-1122. [PMID: 30379331 DOI: 10.1002/jcc.25726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 11/06/2022]
Abstract
Polycyclic saturated hydrocarbons (PSHs) are attractive candidates as hydrocarbon propellants. To assess their potential values, one of the key factors is to determine their energy contents, such as to calculate their heats of formation (HOF). In this work, we have calculated HOFs for a set of 36 PSHs including exo-Tricyclo[5.2.1.0(2,6) ] decane, the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. The results from B3LYP, B3LYP-D3BJ, M06-2X, B2PLYP, B2PLYP-D3BJ, and the XYG3 type of doubly hybrid (xDH) functionals are presented. It is demonstrated here that the xDH functionals yield accurate HOFs in good agreement with those from experiments or the G4 theory. In particular, XYGJ-OS, a low scaling xDH functional, is shown to hold the promise for accurate prediction of HOFs for PSHs of larger sizes. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jianming Wu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
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Liu Q, Wang J, Du P, Hu L, Zheng X, Chen G. Improving the Performance of Long-Range-Corrected Exchange-Correlation Functional with an Embedded Neural Network. J Phys Chem A 2017; 121:7273-7281. [DOI: 10.1021/acs.jpca.7b07045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Qin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - JingChun Wang
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - PengLi Du
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - LiHong Hu
- School
of Computer Science and Information Technology, Northeast Normal University, Changchun, Jilin 130000, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale & Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - GuanHua Chen
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Su NQ, Xu X. Beyond energies: geometry predictions with the XYG3 type of doubly hybrid density functionals. Chem Commun (Camb) 2016; 52:13840-13860. [DOI: 10.1039/c6cc04886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scaled mean absolute deviations (s-MADs) of the optimized geometric parameters for covalent bondings (the CCse set), nonbonded interactions (the S22G30 set) and the transition state structures (the TSG36 set), with Tot referring to the averaged s-MAD for general performances.
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Affiliation(s)
- Neil Qiang Su
- Collaborative Innovation Center of Chemistry for Energy Materials
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- MOE Laboratory for Computational Physical Science
- Department of Chemistry
- Fudan University
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- MOE Laboratory for Computational Physical Science
- Department of Chemistry
- Fudan University
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Li H, Zhong Z, Li L, Gao R, Cui J, Gao T, Hu LH, Lu Y, Su ZM, Li H. A cascaded QSAR model for efficient prediction of overall power conversion efficiency of all-organic dye-sensitized solar cells. J Comput Chem 2015; 36:1036-46. [DOI: 10.1002/jcc.23886] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/25/2014] [Accepted: 02/08/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Hongzhi Li
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
| | - Ziyan Zhong
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
| | - Lin Li
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
| | - Rui Gao
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University; Changchun 130024 China
| | - Jingxia Cui
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University; Changchun 130024 China
| | - Ting Gao
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
| | - Li Hong Hu
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
| | - Yinghua Lu
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University; Changchun 130024 China
| | - Zhong-Min Su
- Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University; Changchun 130024 China
| | - Hui Li
- School of Computer Science and Information Technology; Northeast Normal University; Changchun 130117 China
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Su NQ, Xu X. Construction of a parameter-free doubly hybrid density functional from adiabatic connection. J Chem Phys 2014; 140:18A512. [DOI: 10.1063/1.4866457] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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9
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Zhang IY, Su NQ, Brémond ÉAG, Adamo C, Xu X. Doubly hybrid density functional xDH-PBE0 from a parameter-free global hybrid model PBE0. J Chem Phys 2012; 136:174103. [DOI: 10.1063/1.3703893] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Zhang IY, Xu X. Gas-Phase Thermodynamics as a Validation of Computational Catalysis on Surfaces: A Case Study of Fischer-Tropsch Synthesis. Chemphyschem 2012; 13:1486-94. [DOI: 10.1002/cphc.201100909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Indexed: 11/10/2022]
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11
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Zhang IY, Wu J, Luo Y, Xu X. Accurate bond dissociation enthalpies by using doubly hybrid XYG3 functional. J Comput Chem 2011; 32:1824-38. [DOI: 10.1002/jcc.21764] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 01/04/2010] [Accepted: 01/11/2010] [Indexed: 01/06/2023]
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12
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Zhang IY, Xu X. Doubly hybrid density functional for accurate description of thermochemistry, thermochemical kinetics and nonbonded interactions. INT REV PHYS CHEM 2011. [DOI: 10.1080/0144235x.2010.542618] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Weng C, Kouvetakis J, Chizmeshya AVG. A novel predictive model for formation enthalpies of Si and Ge hydrides with propane- and butane-like structures. J Comput Chem 2010; 32:835-53. [DOI: 10.1002/jcc.21662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 08/07/2010] [Indexed: 11/09/2022]
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Zhang IY, Luo Y, Xu X. Basis set dependence of the doubly hybrid XYG3 functional. J Chem Phys 2010; 133:104105. [DOI: 10.1063/1.3488649] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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15
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Wu J, Ying Zhang I, Xu X. The X1s Method for Accurate Bond Dissociation Energies. Chemphyschem 2010; 11:2561-7. [DOI: 10.1002/cphc.201000273] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Mathieu D, Pipeau Y. Formation Enthalpies of Ions: Routine Prediction Using Atom Equivalents. J Chem Theory Comput 2010; 6:2126-39. [DOI: 10.1021/ct100024r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Zhang IY, Luo Y, Xu X. XYG3s: Speedup of the XYG3 fifth-rung density functional with scaling-all-correlation method. J Chem Phys 2010; 132:194105. [DOI: 10.1063/1.3424845] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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18
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Zhang IY, Wu J, Luo Y, Xu X. Trends in R−X Bond Dissociation Energies (R• = Me, Et, i-Pr, t-Bu, X• = H, Me, Cl, OH). J Chem Theory Comput 2010; 6:1462-9. [DOI: 10.1021/ct100010d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Igor Ying Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College for Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, KTH, Sweden
| | - Jianming Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College for Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, KTH, Sweden
| | - Yi Luo
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College for Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, KTH, Sweden
| | - Xin Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College for Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China, and Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, KTH, Sweden
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19
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Zhang IY, Wu J, Xu X. Extending the reliability and applicability of B3LYP. Chem Commun (Camb) 2010; 46:3057-70. [DOI: 10.1039/c000677g] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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20
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Gao T, Sun SL, Shi LL, Li H, Li HZ, Su ZM, Lu YH. An accurate density functional theory calculation for electronic excitation energies: The least-squares support vector machine. J Chem Phys 2009; 130:184104. [DOI: 10.1063/1.3126773] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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