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Kammeraad JA, Goetz J, Walker EA, Tewari A, Zimmerman PM. What Does the Machine Learn? Knowledge Representations of Chemical Reactivity. J Chem Inf Model 2020; 60:1290-1301. [PMID: 32091880 DOI: 10.1021/acs.jcim.9b00721] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the field of chemistry. To examine the knowledgebase of machine-learning models-what does the machine learn-this article deconstructs black-box machine-learning models of a diverse chemical reaction data set. Through experimentation with chemical representations and modeling techniques, the analysis provides insights into the nature of how statistical accuracy can arise, even when the model lacks informative physical principles. By peeling back the layers of these complicated models we arrive at a minimal, chemically intuitive model (and no machine learning involved). This model is based on systematic reaction-type classification and Evans-Polanyi relationships within reaction types which are easily visualized and interpreted. Through exploring this simple model, we gain deeper understanding of the data set and uncover a means for expert interactions to improve the model's reliability.
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Affiliation(s)
- Joshua A Kammeraad
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Jack Goetz
- Department of Statistics, University of Michigan, 1085 South University Avenue, Ann Arbor, Michigan 48109, United States
| | - Eric A Walker
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Ambuj Tewari
- Department of Statistics, University of Michigan, 1085 South University Avenue, Ann Arbor, Michigan 48109, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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Curtis ER, Hannigan MD, Vitek AK, Zimmerman PM. Quantum Chemical Investigation of Dimerization in the Schlenk Equilibrium of Thiophene Grignard Reagents. J Phys Chem A 2020; 124:1480-1488. [DOI: 10.1021/acs.jpca.9b09985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ethan R. Curtis
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan 48109, United States
| | - Matthew D. Hannigan
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan 48109, United States
| | - Andrew K. Vitek
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan 48109, United States
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3
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Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018; 123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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4
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Li MW, Zimmerman PM. Stepwise basis set selection. J Comput Chem 2018; 39:2153-2162. [DOI: 10.1002/jcc.25363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/01/2018] [Indexed: 11/08/2022]
Affiliation(s)
- M. W. Li
- Department of ChemistryUniversity of Michigan930 N. University Ave, Ann Arbor MI48109
| | - P. M. Zimmerman
- Department of ChemistryUniversity of Michigan930 N. University Ave, Ann Arbor MI48109
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5
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Vitek AK, Leone AK, McNeil AJ, Zimmerman PM. Spin-Switching Transmetalation at Ni Diimine Catalysts. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03974] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andrew K. Vitek
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Amanda K. Leone
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Anne J. McNeil
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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6
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Alherz A, Lim CH, Hynes JT, Musgrave CB. Predicting Hydride Donor Strength via Quantum Chemical Calculations of Hydride Transfer Activation Free Energy. J Phys Chem B 2018; 122:1278-1288. [PMID: 29251933 DOI: 10.1021/acs.jpcb.7b12093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a method to approximate the kinetic properties of hydride donor species by relating the nucleophilicity (N) of a hydride to the activation free energy ΔG⧧ of its corresponding hydride transfer reaction. N is a kinetic parameter related to the hydride transfer rate constant that quantifies a nucleophilic hydridic species' tendency to donate. Our method estimates N using quantum chemical calculations to compute ΔG⧧ for hydride transfers from hydride donors to CO2 in solution. A linear correlation for each class of hydrides is then established between experimentally determined N values and the computationally predicted ΔG⧧; this relationship can then be used to predict nucleophilicity for different hydride donors within each class. This approach is employed to determine N for four different classes of hydride donors: two organic (carbon-based and benzimidazole-based) and two inorganic (boron and silicon) hydride classes. We argue that silicon and boron hydrides are driven by the formation of the more stable Si-O or B-O bond. In contrast, the carbon-based hydrides considered herein are driven by the stability acquired upon rearomatization, a feature making these species of particular interest, because they both exhibit catalytic behavior and can be recycled.
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Affiliation(s)
- Abdulaziz Alherz
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Chern-Hooi Lim
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States.,Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
| | - James T Hynes
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States.,Chemistry Department, Ecole Normale Supérieure-PSL Research University, Sorbonne Universités-UPMC University Paris 06 , CNRS UMR 8640 Pasteur, 24 rue Lhomond, 75005 Paris, France
| | - Charles B Musgrave
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States.,Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States.,Materials Science and Engineering Program, University of Colorado , Boulder, Colorado 80309, United States
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7
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Ilic S, Alherz A, Musgrave CB, Glusac KD. Thermodynamic and kinetic hydricities of metal-free hydrides. Chem Soc Rev 2018; 47:2809-2836. [DOI: 10.1039/c7cs00171a] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Thermodynamic and kinetic hydricities provide useful guidelines for the design of hydride donors with desirable properties for catalytic chemical reductions.
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Affiliation(s)
- Stefan Ilic
- Department of Chemistry
- University of Illinois at Chicago
- Chicago
- USA
- Chemical Sciences and Engineering Division
| | - Abdulaziz Alherz
- Department of Chemical and Biological Engineering
- University of Colorado
- Boulder
- USA
| | - Charles B. Musgrave
- Department of Chemical and Biological Engineering
- University of Colorado
- Boulder
- USA
- Department of Chemistry and Biochemistry
| | - Ksenija D. Glusac
- Department of Chemistry
- University of Illinois at Chicago
- Chicago
- USA
- Chemical Sciences and Engineering Division
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8
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Jafari M, Zimmerman PM. Uncovering reaction sequences on surfaces through graphical methods. Phys Chem Chem Phys 2018; 20:7721-7729. [DOI: 10.1039/c8cp00044a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ZStruct is a graph-based model that generates an ensemble of plausible reaction pathways starting from a given initial state, without requiring prior knowledge of reaction intermediates.
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Affiliation(s)
- Mina Jafari
- Department of Chemistry, University of Michigan
- Ann Arbor
- USA
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Dewyer AL, Argüelles AJ, Zimmerman PM. Methods for exploring reaction space in molecular systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1354] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Amanda L. Dewyer
- Department of Chemistry; University of Michigan; Ann Arbor MI USA
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Roy L, Ghosh B, Paul A. Lewis Acid Promoted Hydrogenation of CO2 and HCOO– by Amine Boranes: Mechanistic Insight from a Computational Approach. J Phys Chem A 2017. [DOI: 10.1021/acs.jpca.7b03843] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa Roy
- Raman Centre for Atomic Molecular
and Optical Sciences, Indian Association for the Cultivation of Science, 2A and 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Boyli Ghosh
- Raman Centre for Atomic Molecular
and Optical Sciences, Indian Association for the Cultivation of Science, 2A and 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ankan Paul
- Raman Centre for Atomic Molecular
and Optical Sciences, Indian Association for the Cultivation of Science, 2A and 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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Zhao Y, Nett AJ, McNeil AJ, Zimmerman PM. Computational Mechanism for Initiation and Growth of Poly(3-hexylthiophene) Using Palladium N-Heterocyclic Carbene Precatalysts. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yu Zhao
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alex J. Nett
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anne J. McNeil
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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