1
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Nakajima H, Murata C, Noto N, Saito S. Database Construction for the Virtual Screening of the Ruthenium-Catalyzed Hydrogenation of Ketones. J Org Chem 2025; 90:1054-1060. [PMID: 39762115 DOI: 10.1021/acs.joc.4c02347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
Abstract
During the recent development of machine-learning (ML) methods for organic synthesis, the value of "failed experiments" has increasingly been acknowledged. Accordingly, we have developed an exhaustive database comprising 300 entries of experimental data obtained by performing ruthenium-catalyzed hydrogenation reactions using 10 ketones as substrates and 30 phosphine ligands. After evaluating the predictive performance of ML models using the constructed database, we conducted a virtual screening of commercially available phosphine ligands. For the virtual screening, we utilized several models, such as histogram-based gradient boosting and Ridge regression, combined with the Mordred descriptors and MACCSKeys, respectively. The disclosed approach resulted in the identification of high-performance phosphine ligands, and the rationale behind the predictions in the virtual screening was analyzed using SHAP.
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Affiliation(s)
- Haruno Nakajima
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Chihaya Murata
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Naoki Noto
- Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University, Nagoya 464-8602, Japan
| | - Susumu Saito
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University, Nagoya 464-8602, Japan
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2
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Yu G, Wang X, Luo Y, Li G, Ding R, Shi R, Huo X, Yang Y. Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor. J Chem Inf Model 2025; 65:312-325. [PMID: 39744764 DOI: 10.1021/acs.jcim.4c02120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2025]
Abstract
Despite remarkable advancements in the organic synthesis field facilitated by the use of machine learning (ML) techniques, the prediction of reaction outcomes, including yield estimation, catalyst optimization, and mechanism identification, continues to pose a significant challenge. This challenge arises primarily from the lack of appropriate descriptors capable of retaining crucial molecular information for accurate prediction while also ensuring computational efficiency. This study presents a successful application of ML for predicting the performance of Ir-catalyzed allylic substitution reactions. We introduce SubA, an innovative substrate-aware descriptor that is inspired by the fact that specific atoms or motifs in reactants drive the reaction outcomes. By employing graph matching algorithms for molecular backbone identification and incorporating atomic and molecular properties derived from density functional theory calculations, SubA extracts essential information at both the atomic level and the molecular level. Compared to four mainstream descriptors, SubA achieves reduced dimensionality and enhanced prediction accuracy with over 2% mean absolute error reduction in both random and scaffold splitting evaluations. It also demonstrates better generalization when confronted with previously unreported substrate combinations in extended experiments. Furthermore, an interpretable analysis of SubA shows that the predictor focuses on key molecular and atomic features, offering insights into reaction mechanisms.
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Affiliation(s)
- Gufeng Yu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Department of Computer Science and Engineering, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xi Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yichong Luo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guanlin Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rui Ding
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Runhan Shi
- Department of Computer Science and Engineering, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaohong Huo
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science and Engineering, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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3
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Niu X, Liu Y, Zhao R, Yuan M, Zhao H, Li H, Yang X, Wang K. Mechanisms for translating chiral enantiomers separation research into macroscopic visualization. Adv Colloid Interface Sci 2025; 335:103342. [PMID: 39561657 DOI: 10.1016/j.cis.2024.103342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 10/19/2024] [Accepted: 11/10/2024] [Indexed: 11/21/2024]
Abstract
Chirality is a common phenomenon in nature, including the dominance preference of small biomolecules, the special spatial conformation of biomolecules, and the biological and physiological processes triggered by chirality. The selective chiral recognition of molecules in nature from up-bottom or bottom-up is of great significance for living organisms. Such as the transcription of DNA, the recognition of membrane proteins, and the catalysis of enzymes all involve chiral recognition processes. The selective recognition between these macromolecules is mainly achieved through non covalent interactions such as hydrophobic interactions, ammonia bonding, electrostatic interactions, metal coordination, van der Waals forces, and π-π stacking. Researchers have been committed to studying how to convert this weak non covalent interaction into macroscopic visualization, which has further understood of the interactions between chiral molecules and is of great significance for simulating the interactions between molecules in living organisms. This article reviews several models of chiral recognition mechanisms, the interaction forces involved in the chiral recognition process, and the research progress of chiral recognition mechanisms. The outlook in this review points out that studying chiral recognition interactions provides an important bridge between chiral materials and the life sciences, providing an ideal platform for studying chiral phenomena in biological systems.
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Affiliation(s)
- Xiaohui Niu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China.
| | - Yongqi Liu
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Rui Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Mei Yuan
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Hongfang Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Hongxia Li
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China
| | - Xing Yang
- School of Materials Science and Engineering, Lanzhou Jiaotong University, Lanzhou 730070, PR China.
| | - Kunjie Wang
- College of Petrochemical Technology, Lanzhou University of Technology, 730050 Lanzhou, PR China.
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4
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Kulichenko M, Nebgen B, Lubbers N, Smith JS, Barros K, Allen AEA, Habib A, Shinkle E, Fedik N, Li YW, Messerly RA, Tretiak S. Data Generation for Machine Learning Interatomic Potentials and Beyond. Chem Rev 2024; 124:13681-13714. [PMID: 39572011 DOI: 10.1021/acs.chemrev.4c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
Abstract
The field of data-driven chemistry is undergoing an evolution, driven by innovations in machine learning models for predicting molecular properties and behavior. Recent strides in ML-based interatomic potentials have paved the way for accurate modeling of diverse chemical and structural properties at the atomic level. The key determinant defining MLIP reliability remains the quality of the training data. A paramount challenge lies in constructing training sets that capture specific domains in the vast chemical and structural space. This Review navigates the intricate landscape of essential components and integrity of training data that ensure the extensibility and transferability of the resulting models. We delve into the details of active learning, discussing its various facets and implementations. We outline different types of uncertainty quantification applied to atomistic data acquisition and the correlations between estimated uncertainty and true error. The role of atomistic data samplers in generating diverse and informative structures is highlighted. Furthermore, we discuss data acquisition via modified and surrogate potential energy surfaces as an innovative approach to diversify training data. The Review also provides a list of publicly available data sets that cover essential domains of chemical space.
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Affiliation(s)
- Maksim Kulichenko
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Benjamin Nebgen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicholas Lubbers
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Justin S Smith
- NVIDIA Corporation, Santa Clara, California 95051, United States
| | - Kipton Barros
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Alice E A Allen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Adela Habib
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Emily Shinkle
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nikita Fedik
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ying Wai Li
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Richard A Messerly
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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5
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Mandal S, Abild-Pedersen F. Metal-Independent Correlations for Site-Specific Binding Energies of Relevant Catalytic Intermediates. JACS AU 2024; 4:4790-4798. [PMID: 39735927 PMCID: PMC11672124 DOI: 10.1021/jacsau.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/08/2024] [Accepted: 10/28/2024] [Indexed: 12/31/2024]
Abstract
Establishing energy correlations among different metals can accelerate the discovery of efficient and cost-effective catalysts for complex reactions. Using a recently introduced coordination-based model, we can predict site-specific metal binding energies (ΔE M) that can be used as a descriptor for chemical reactions. In this study, we have examined a range of metals including Ag, Au, Co, Cu, Ir, Ni, Os, Pd, Pt, Rh, and Ru and found linear correlations between predicted ΔE M and adsorption energies of CH and O (ΔE CH and ΔE O) at various coordination environments for all the considered metals. Interestingly, all the metals correlate with one another under specific surface site coordination, indicating that different metals are interrelated in a particular coordination environment. Furthermore, we have tested and verified for PtPd- and PtIr-based alloys that they follow a similar behavior. Moreover, we have expanded the metal space by taking some early transition metals along with a few s-block metals and shown a cyclic behavior of the adsorbate binding energy (ΔE A) versus ΔE M. Therefore, ΔE CH and ΔE O can be efficiently interpolated between metals, alloys, and intermetallics based on information related to one metal only. This simplifies the process of screening new metal catalyst formulations and their reaction energies.
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Affiliation(s)
- Shyama
Charan Mandal
- SUNCAT
Center for Interface Science and Catalysis, Department of Chemical
Engineering, Stanford University, 443 Via Ortega, Stanford, California 94305, United States
- SUNCAT
Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
| | - Frank Abild-Pedersen
- SUNCAT
Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo
Park, California 94025, United States
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6
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Wei Y, Santana-Bonilla A, Kantorovich L. Global Optimization of Molybdenum Subnanoclusters on Graphene: A Consistent Approach toward Catalytic Applications. ACS APPLIED MATERIALS & INTERFACES 2024; 16:64177-64189. [PMID: 39504252 PMCID: PMC11583127 DOI: 10.1021/acsami.4c13102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 10/21/2024] [Accepted: 10/31/2024] [Indexed: 11/08/2024]
Abstract
The development of novel subnanometer clusters (SNCs) catalysts with superior catalytic performance depends on the precise control of clusters' atomistic sizes, shapes, and accurate deposition onto surfaces. The intrinsic complexity of the adsorption process complicates the ability to achieve an atomistic understanding of the most relevant structure-reactivity relationships hampering the rational design of novel catalytic materials. In most cases, existing computational approaches rely on just a few structures to draw conclusions on clusters' reactivity thereby neglecting the complexity of the existing energy landscapes thus leading to insufficient sampling and, most likely, unreliable predictions. Moreover, modeling of the actual experimental procedure that is responsible for the deposition of SNCs on surfaces is often not done even though in some cases this procedure may enhance the significance of certain (e.g., metastable) adsorption geometries. This study proposes a novel systematic approach that utilizes global search techniques, specifically, the particle swarm optimization (PSO) method, in conjunction with ab initio calculations, to simulate all stages in the beam experiments, from predicting the most relevant SNCs structures in the beam and on a surface, to their reactivity. To illustrate the main steps of our approach, we consider the deposition of Molybdenum SNC of 6 Mo atoms on a free-standing graphene surface, as well as their catalytic properties with respect to the CO molecule dissociation reaction. Even though our calculations are not exhaustive and serve only to produce an illustration of the method, they are still able to provide insight into the complicated energy landscape of Mo SNCs on graphene demonstrating the catalytic activity of Mo SNCs and the importance of performing statistical sampling of available configurations. This study establishes a reliable procedure for performing theoretical rational design predictions.
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Affiliation(s)
- Yao Wei
- Theory and Simulation of Condensed
Matter (TSCM), King’s College London, Strand, London WC2R 2LS, U.K.
| | - Alejandro Santana-Bonilla
- Theory and Simulation of Condensed
Matter (TSCM), King’s College London, Strand, London WC2R 2LS, U.K.
| | - Lev Kantorovich
- Theory and Simulation of Condensed
Matter (TSCM), King’s College London, Strand, London WC2R 2LS, U.K.
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7
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Kuddusi Y, Dobbelaere MR, Van Geem KM, Züttel A. Accelerated design of nickel-cobalt based catalysts for CO 2 hydrogenation with human-in-the-loop active machine learning. Catal Sci Technol 2024; 14:6307-6320. [PMID: 39282506 PMCID: PMC11391929 DOI: 10.1039/d4cy00873a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/08/2024] [Indexed: 09/19/2024]
Abstract
Thermo-catalytic conversion of CO2 into more valuable compounds, such as methane, is an attractive strategy for energy storage in chemical bonds and creating a carbon-based circular economy. However, designing heterogeneous catalysts remains a challenging, time- and resource-consuming task. Herein, we present an interpretable, human-in-the-loop active machine learning framework to efficiently plan catalytic experiments, execute them in an automated set-up, and estimate the effect of experimental variables on the catalytic activity. A dataset with 48 catalytic activity tests was compiled from a design space of Ni-Co/Al2O3 catalysts with over 50 million potential combinations in only eight iterations. This small dataset was found sufficient to predict CO2 conversion, methane selectivity, and methane space-time yield with remarkable accuracy (R 2 > 0.9) for untested catalysts and reaction conditions. New experiments and catalysts were selected with this methodology, leading to experimental conditions that improved the methane space-time yield by nearly 50% in comparison to the previously obtained maximum in the dataset. Interpretation of the model predictions unveiled the effect of each catalyst descriptor and reaction condition on the outcome. Particularly, the strong predicted inverse trend between the calcination temperature and the catalytic activity was validated experimentally, and characterization implied an underlying structure-performance relationship. Finally, it is demonstrated that the deployed active learning model is excellently suited to predict and fit kinetic trends with a minimal amount of data. This data-driven framework is a first step to faster, model-based, and interpretable design of catalysts and holds promise for broader applications across catalytic processes.
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Affiliation(s)
- Yasemen Kuddusi
- Laboratory of Materials for Renewable Energy (LMER), Institute of Chemical Sciences and Engineering (ISIC), Basic Science Faculty (SB), École Polytechnique Fédérale de Lausanne (EPFL) Valais/Wallis, Energypolis Rue de l'Industrie 17 1951 Sion Switzerland
- Empa Materials Science & Technology 8600 Dübendorf Switzerland
| | - Maarten R Dobbelaere
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University Technologiepark 125 9052 Gent Belgium
| | - Kevin M Van Geem
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University Technologiepark 125 9052 Gent Belgium
| | - Andreas Züttel
- Laboratory of Materials for Renewable Energy (LMER), Institute of Chemical Sciences and Engineering (ISIC), Basic Science Faculty (SB), École Polytechnique Fédérale de Lausanne (EPFL) Valais/Wallis, Energypolis Rue de l'Industrie 17 1951 Sion Switzerland
- Empa Materials Science & Technology 8600 Dübendorf Switzerland
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8
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Yang B, Schaefer AJ, Small BL, Leseberg JA, Bischof SM, Webster-Gardiner MS, Ess DH. Experimentally-based Fe-catalyzed ethene oligomerization machine learning model provides highly accurate prediction of propagation/termination selectivity. Chem Sci 2024:d4sc03433c. [PMID: 39449687 PMCID: PMC11495513 DOI: 10.1039/d4sc03433c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024] Open
Abstract
Linear α-olefins (1-alkenes) are critical comonomers for ethene copolymerization. A major impediment in the development of new homogeneous Fe catalysts for ethene oligomerization to produce comonomers and other important commercial products is the prediction of propagation versus termination rates that control the α-olefin distribution (e.g., 1-butene through 1-decene), which is often referred to as a K-value. Because the transition states for propagation versus termination are generally separated by less than a one kcal mol-1 difference in energy, this selectivity cannot be accurately predicted by either DFT or wavefunction methods (even DLPNO-CCSD(T)). Therefore, we developed a sub-kcal mol-1 accuracy machine learning model based on several hundred experimental selectivity values and straightforward 2D chemical and physical features that enables the prediction of α-olefin distribution K-values. As part of our model, we developed a new ad hoc feature that boosted the model performance. This machine learning model captures the effects of a broad range of ligand architectures and chemically nonintuitive trends in oligomerization selectivity. Our machine learning model was experimentally validated by prediction of a K-value for a new Fe phosphaneyl-pyridinyl-quinoline catalyst followed by experimental measurement that showed precise agreement. In addition to quantitative predictions, we demonstrate how this machine learning model can provide qualitative catalyst design using proximity of pairs type analysis.
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Affiliation(s)
- Bo Yang
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Anthony J Schaefer
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
| | - Brooke L Small
- Research & Technology, Chevron Phillips Chemical 1862 Kingwood Drive Kingwood Texas 77339 USA
| | - Julie A Leseberg
- Research & Technology, Chevron Phillips Chemical 1862 Kingwood Drive Kingwood Texas 77339 USA
| | - Steven M Bischof
- Research & Technology, Chevron Phillips Chemical 1862 Kingwood Drive Kingwood Texas 77339 USA
| | | | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University Provo Utah 84602 USA
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9
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Bellini G, Koch G, Girgsdies F, Dong J, Carey SJ, Timpe O, Auffermann G, Scheffler M, Schlögl R, Foppa L, Trunschke A. CO Oxidation Catalyzed by Perovskites: The Role of Crystallographic Distortions Highlighted by Systematic Experiments and Artificial Intelligence. Angew Chem Int Ed Engl 2024:e202417812. [PMID: 39433485 DOI: 10.1002/anie.202417812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 10/16/2024] [Accepted: 10/21/2024] [Indexed: 10/23/2024]
Abstract
The identification of key materials' parameters correlated with the performance can accelerate the development of heterogeneous catalysts and unveil the relevant underlying physical processes. However, the analysis of correlations is often hindered by inconsistent data. Besides, nontrivial, yet unknown relationships may be important, and the intricacy of the various processes may be significant. Here, we tackle these challenges for the CO oxidation catalyzed by perovskites using a combination of rigorous experiments and artificial intelligence. A series of 13 ABO3 (A=La, Pr, Nd, Sm; B=Cr, Mn, Fe, Co) perovskites was synthesized, characterized, and tested in catalysis. To the resulting dataset, we applied the symbolic-regression SISSO approach. We identified an analytical expression correlated with the activity that contains the normalized unit-cell volume, the Pauling electronegativity of the elements A and B, and the ionization energy of the element B. Therefore, the activity is described by crystallographic distortions and by the chemical nature of A and B elements. The generalizability of the identified descriptor is confirmed by the good quality of the predictions for 3 additional ABO3 and 16 chemically more complex AMn(1-x)B'xO3 (A=La, Pr, Nd; B'=Fe, Co, Ni, Cu, Zn) perovskites.
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Affiliation(s)
- Giulia Bellini
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gregor Koch
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Frank Girgsdies
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Jinhu Dong
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Spencer J Carey
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Olaf Timpe
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Gudrun Auffermann
- Max-Planck-Institut für Chemische Physik Fester Stoffe, Nöthnitzer Straße 40, 01187, Dresden, Germany
| | - Matthias Scheffler
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Robert Schlögl
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Lucas Foppa
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Annette Trunschke
- Inorganic Chemistry Department, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
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10
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Schmid SP, Schlosser L, Glorius F, Jorner K. Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis. Beilstein J Org Chem 2024; 20:2280-2304. [PMID: 39290209 PMCID: PMC11406055 DOI: 10.3762/bjoc.20.196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024] Open
Abstract
Organocatalysis has established itself as a third pillar of homogeneous catalysis, besides transition metal catalysis and biocatalysis, as its use for enantioselective reactions has gathered significant interest over the last decades. Concurrent to this development, machine learning (ML) has been increasingly applied in the chemical domain to efficiently uncover hidden patterns in data and accelerate scientific discovery. While the uptake of ML in organocatalysis has been comparably slow, the last two decades have showed an increased interest from the community. This review gives an overview of the work in the field of ML in organocatalysis. The review starts by giving a short primer on ML for experimental chemists, before discussing its application for predicting the selectivity of organocatalytic transformations. Subsequently, we review ML employed for privileged catalysts, before focusing on its application for catalyst and reaction design. Concluding, we give our view on current challenges and future directions for this field, drawing inspiration from the application of ML to other scientific domains.
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Affiliation(s)
- Stefan P Schmid
- Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
| | - Leon Schlosser
- Organisch-Chemisches Institut, Universität Münster, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, Universität Münster, 48149 Münster, Germany
| | - Kjell Jorner
- Institute of Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
- National Centre of Competence in Research (NCCR) Catalysis, ETH Zurich, Zurich CH-8093, Switzerland
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11
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Mashhadimoslem H, Abdol MA, Karimi P, Zanganeh K, Shafeen A, Elkamel A, Kamkar M. Computational and Machine Learning Methods for CO 2 Capture Using Metal-Organic Frameworks. ACS NANO 2024; 18:23842-23875. [PMID: 39173133 DOI: 10.1021/acsnano.3c13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Machine learning (ML) using data sets of atomic and molecular force fields (FFs) has made significant progress and provided benefits in the fields of chemistry and material science. This work examines the interactions between chemistry and materials computational science at the atomic and molecular scales for metal-organic framework (MOF) adsorbent development toward carbon dioxide (CO2) capture. Herein, a connection will be drawn between atomic forces predicted by ML algorithms and the structures of MOFs for CO2 adsorption. Our study also takes into account the successes of atomic computational screening in the field of materials science, especially quantum ML, and its relationship to ML algorithms that clarify advancements in the area of CO2 adsorption by MOFs. Additionally, we reviewed the processes for supplying data to ML algorithms for algorithm training, including text mining from scientific articles, and MOF's formula processing linked to the chemical properties of MOFs. To create ML algorithms for future research, we recommend that the digitization of scientific records can help efficiently synthesize advanced MOFs. Finally, a future vision for developing pioneer MOF synthesis routes for CO2 capture is presented in this review article.
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Affiliation(s)
- Hossein Mashhadimoslem
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Mohammad Ali Abdol
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Peyman Karimi
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Kourosh Zanganeh
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ahmed Shafeen
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ali Elkamel
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Chemical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Milad Kamkar
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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12
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Tom G, Schmid SP, Baird SG, Cao Y, Darvish K, Hao H, Lo S, Pablo-García S, Rajaonson EM, Skreta M, Yoshikawa N, Corapi S, Akkoc GD, Strieth-Kalthoff F, Seifrid M, Aspuru-Guzik A. Self-Driving Laboratories for Chemistry and Materials Science. Chem Rev 2024; 124:9633-9732. [PMID: 39137296 PMCID: PMC11363023 DOI: 10.1021/acs.chemrev.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Self-driving laboratories (SDLs) promise an accelerated application of the scientific method. Through the automation of experimental workflows, along with autonomous experimental planning, SDLs hold the potential to greatly accelerate research in chemistry and materials discovery. This review provides an in-depth analysis of the state-of-the-art in SDL technology, its applications across various scientific disciplines, and the potential implications for research and industry. This review additionally provides an overview of the enabling technologies for SDLs, including their hardware, software, and integration with laboratory infrastructure. Most importantly, this review explores the diverse range of scientific domains where SDLs have made significant contributions, from drug discovery and materials science to genomics and chemistry. We provide a comprehensive review of existing real-world examples of SDLs, their different levels of automation, and the challenges and limitations associated with each domain.
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Affiliation(s)
- Gary Tom
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Stefan P. Schmid
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 1, CH-8093 Zurich, Switzerland
| | - Sterling G. Baird
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Yang Cao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Kourosh Darvish
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Han Hao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Stanley Lo
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Sergio Pablo-García
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
| | - Ella M. Rajaonson
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Marta Skreta
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Naruki Yoshikawa
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Samantha Corapi
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Gun Deniz Akkoc
- Forschungszentrum
Jülich GmbH, Helmholtz Institute
for Renewable Energy Erlangen-Nürnberg, Cauerstr. 1, 91058 Erlangen, Germany
- Department
of Chemical and Biological Engineering, Friedrich-Alexander Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany
| | - Felix Strieth-Kalthoff
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- School of
Mathematics and Natural Sciences, University
of Wuppertal, Gaußstraße
20, 42119 Wuppertal, Germany
| | - Martin Seifrid
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States of America
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
- Department
of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department
of Materials Science & Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
- Lebovic
Fellow, Canadian Institute for Advanced
Research (CIFAR), 661
University Ave, Toronto, Ontario M5G 1M1, Canada
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13
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Wu X, Du J, Gao Y, Wang H, Zhang C, Zhang R, He H, Lu GM, Wu Z. Progress and challenges in nitrous oxide decomposition and valorization. Chem Soc Rev 2024; 53:8379-8423. [PMID: 39007174 DOI: 10.1039/d3cs00919j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Nitrous oxide (N2O) decomposition is increasingly acknowledged as a viable strategy for mitigating greenhouse gas emissions and addressing ozone depletion, aligning significantly with the UN's sustainable development goals (SDGs) and carbon neutrality objectives. To enhance efficiency in treatment and explore potential valorization, recent developments have introduced novel N2O reduction catalysts and pathways. Despite these advancements, a comprehensive and comparative review is absent. In this review, we undertake a thorough evaluation of N2O treatment technologies from a holistic perspective. First, we summarize and update the recent progress in thermal decomposition, direct catalytic decomposition (deN2O), and selective catalytic reduction of N2O. The scope extends to the catalytic activity of emerging catalysts, including nanostructured materials and single-atom catalysts. Furthermore, we present a detailed account of the mechanisms and applications of room-temperature techniques characterized by low energy consumption and sustainable merits, including photocatalytic and electrocatalytic N2O reduction. This article also underscores the extensive and effective utilization of N2O resources in chemical synthesis scenarios, providing potential avenues for future resource reuse. This review provides an accessible theoretical foundation and a panoramic vision for practical N2O emission controls.
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Affiliation(s)
- Xuanhao Wu
- Department of Environmental Engineering, Zhejiang University, China Zhejiang Provincial Engineering Research Center of Industrial Boiler & Furnace Flue Gas Pollution Control, Hangzhou, 310058, China.
| | - Jiaxin Du
- Department of Environmental Engineering, Zhejiang University, China Zhejiang Provincial Engineering Research Center of Industrial Boiler & Furnace Flue Gas Pollution Control, Hangzhou, 310058, China.
| | - Yanxia Gao
- Department of Environmental Engineering, Zhejiang University, China Zhejiang Provincial Engineering Research Center of Industrial Boiler & Furnace Flue Gas Pollution Control, Hangzhou, 310058, China.
| | - Haiqiang Wang
- Department of Environmental Engineering, Zhejiang University, China Zhejiang Provincial Engineering Research Center of Industrial Boiler & Furnace Flue Gas Pollution Control, Hangzhou, 310058, China.
| | - Changbin Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Runduo Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Hong He
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | | | - Zhongbiao Wu
- Department of Environmental Engineering, Zhejiang University, China Zhejiang Provincial Engineering Research Center of Industrial Boiler & Furnace Flue Gas Pollution Control, Hangzhou, 310058, China.
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14
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Shermukhamedov S, Mamurjonova D, Maihom T, Probst M. Structure to Property: Chemical Element Embeddings for Predicting Electronic Properties of Crystals. J Chem Inf Model 2024; 64:5762-5770. [PMID: 39007646 PMCID: PMC11323004 DOI: 10.1021/acs.jcim.3c01990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
We present a new general-purpose machine learning model that is able to predict a variety of crystal properties, including Fermi level energy and band gap, as well as spectral ones such as electronic densities of states. The model is based on atomic representations that enable it to effectively capture complex information about each atom and its surrounding environment in a crystal. The accuracy achieved for band gaps exceeds results previously published. By design, our model is not restricted to the electronic properties discussed here but can be extended to fit diverse chemical descriptors. Its advantages are (a) its low computational requirements, making it an efficient tool for high-throughput screening of materials; and (b) the simplicity and flexibility of its architecture, facilitating implementation and interpretation, especially for researchers in the field of computational chemistry.
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Affiliation(s)
| | - Dilorom Mamurjonova
- Department
of Inorganic Chemistry, Tashkent Chemical
Technological Institute, 100011 Tashkent, Uzbekistan
| | - Thana Maihom
- School
of Molecular Science and Engineering, Vidyasirimedhi
Institute of Science and Technology, 21201 Rayong, Thailand
- Division
of Chemistry, Department of Physical and Material Sciences, Faculty
of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, 73140 Nakhon Pathom, Thailand
| | - Michael Probst
- Institute
of Ion Physics and Applied Physics, University
of Innsbruck, 6020 Innsbruck, Austria
- School
of Molecular Science and Engineering, Vidyasirimedhi
Institute of Science and Technology, 21201 Rayong, Thailand
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15
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Su Y, Wang X, Ye Y, Xie Y, Xu Y, Jiang Y, Wang C. Automation and machine learning augmented by large language models in a catalysis study. Chem Sci 2024; 15:12200-12233. [PMID: 39118602 PMCID: PMC11304797 DOI: 10.1039/d3sc07012c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/21/2024] [Indexed: 08/10/2024] Open
Abstract
Recent advancements in artificial intelligence and automation are transforming catalyst discovery and design from traditional trial-and-error manual mode into intelligent, high-throughput digital methodologies. This transformation is driven by four key components, including high-throughput information extraction, automated robotic experimentation, real-time feedback for iterative optimization, and interpretable machine learning for generating new knowledge. These innovations have given rise to the development of self-driving labs and significantly accelerated materials research. Over the past two years, the emergence of large language models (LLMs) has added a new dimension to this field, providing unprecedented flexibility in information integration, decision-making, and interacting with human researchers. This review explores how LLMs are reshaping catalyst design, heralding a revolutionary change in the fields.
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Affiliation(s)
- Yuming Su
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
| | - Xue Wang
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
| | - Yuanxiang Ye
- Institute of Artificial Intelligence, Xiamen University Xiamen 361005 P. R. China
| | - Yibo Xie
- Institute of Artificial Intelligence, Xiamen University Xiamen 361005 P. R. China
| | - Yujing Xu
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
| | - Yibin Jiang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
| | - Cheng Wang
- iChem, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 P. R. China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM) Xiamen 361005 P. R. China
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16
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Song C, Shi Y, Li M, He Y, Xiong X, Deng H, Xia D. Prediction of g-C 3N 4-based photocatalysts in tetracycline degradation based on machine learning. CHEMOSPHERE 2024; 362:142632. [PMID: 38897319 DOI: 10.1016/j.chemosphere.2024.142632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
Investigating the effects of g-C3N4-based photocatalysts on experimental parameters during tetracycline (TC) degradation can be helpful in discovering the optimal parameter combinations to improve the degradation efficiencies in general. Machine learning methods can avoid the problems of high cost, time-consuming and possible instrumental errors in experimental methods, which have been proven to be an effective alternative for evaluating the entire experimental process. Eight typical machine learning models were explored for their effectiveness in predicting the TC degradation efficiencies of g-C3N4 based photocatalysts. XGBoost (XGB) was the most reliable model with R2, RMSE and MAE values of 0.985, 4.167 and 2.900, respectively. In addition, XGB's feature importance and SHAP method were used to rank the importance of features to provide interpretability to the results. This study provided a new idea for developing g-C3N4-based photocatalysts for TC degradation and intelligent algorithms for predicting the photocatalytic activity of g-C3N4-based photocatalysts.
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Affiliation(s)
- Chenyu Song
- Engineering Research Center Clean Production of Textile Dyeing and Printing, Ministry of Education, Wuhan, 430073, PR China.
| | - Yintao Shi
- Engineering Research Center Clean Production of Textile Dyeing and Printing, Ministry of Education, Wuhan, 430073, PR China; School of Environmental Engineering, Wuhan Textile University, Wuhan, 430073, PR China
| | - Meng Li
- Engineering Research Center Clean Production of Textile Dyeing and Printing, Ministry of Education, Wuhan, 430073, PR China; Textile Pollution Controlling Engineering Centre of Ministry of Ecology and Environment, College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, PR China
| | - Yuanyuan He
- Engineering Research Center Clean Production of Textile Dyeing and Printing, Ministry of Education, Wuhan, 430073, PR China
| | - Xiaorong Xiong
- School of Computing, Huanggang Normal University, Huanggang, 438000, PR China
| | - Huiyuan Deng
- Hubei Provincial Spatial Planning Research Institute, Wuhan, 430064, PR China
| | - Dongsheng Xia
- Engineering Research Center Clean Production of Textile Dyeing and Printing, Ministry of Education, Wuhan, 430073, PR China.
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17
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Suvarna M, Zou T, Chong SH, Ge Y, Martín AJ, Pérez-Ramírez J. Active learning streamlines development of high performance catalysts for higher alcohol synthesis. Nat Commun 2024; 15:5844. [PMID: 38992019 PMCID: PMC11239856 DOI: 10.1038/s41467-024-50215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Developing efficient catalysts for syngas-based higher alcohol synthesis (HAS) remains a formidable research challenge. The chain growth and CO insertion requirements demand multicomponent materials, whose complex reaction dynamics and extensive chemical space defy catalyst design norms. We present an alternative strategy by integrating active learning into experimental workflows, exemplified via the FeCoCuZr catalyst family. Our data-aided framework streamlines navigation of the extensive composition and reaction condition space in 86 experiments, offering >90% reduction in environmental footprint and costs over traditional programs. It identifies the Fe65Co19Cu5Zr11 catalyst with optimized reaction conditions to attain higher alcohol productivities of 1.1 gHA h-1 gcat-1 under stable operation for 150 h on stream, a 5-fold improvement over typically reported yields. Characterization reveals catalytic properties linked to superior activities despite moderate higher alcohol selectivities. To better reflect catalyst demands, we devise multi-objective optimization to maximize higher alcohol productivity while minimizing undesired CO2 and CH4 selectivities. An intrinsic trade-off between these metrics is uncovered, identifying Pareto-optimal catalysts not readily discernible by human experts. Finally, based on feature-importance analysis, we formulate data-informed guidelines to develop performance-specific FeCoCuZr systems. This approach goes beyond existing HAS catalyst design strategies, is adaptable to broader catalytic transformations, and fosters laboratory sustainability.
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Affiliation(s)
- Manu Suvarna
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Tangsheng Zou
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Sok Ho Chong
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Yuzhen Ge
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Antonio J Martín
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Javier Pérez-Ramírez
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland.
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18
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Lifar MS, Tereshchenko AA, Bulgakov AN, Guda SA, Guda AA, Soldatov AV. Optimal Dynamic Regimes for CO Oxidation Discovered by Reinforcement Learning. ACS OMEGA 2024; 9:27987-27997. [PMID: 38973853 PMCID: PMC11223201 DOI: 10.1021/acsomega.3c10422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/09/2024]
Abstract
Metal nanoparticles are widely used as heterogeneous catalysts to activate adsorbed molecules and reduce the energy barrier of the reaction. Reaction product yield depends on the interplay between elementary processes: adsorption, activation, desorption, and reaction. These processes, in turn, depend on the inlet gas composition, temperature, and pressure. At a steady state, the active surface sites may be inaccessible due to adsorbed reagents. Periodic regime may thus improve the yield, but the appropriate period and waveform are not known in advance. Dynamic control should account for surface and atmospheric modifications and adjust reaction parameters according to the current state of the system and its history. In this work, we applied a reinforcement learning algorithm to control CO oxidation on a palladium catalyst. The policy gradient algorithm was trained in the theoretical environment, parametrized from experimental data. The algorithm learned to maximize the CO2 formation rate based on CO and O2 partial pressures for several successive time steps. Within a unified approach, we found optimal stationary, periodic, and nonperiodic regimes for different problem formulations and gained insight into why the dynamic regime can be preferential. In general, this work contributes to the task of popularizing the reinforcement learning approach in the field of catalytic science.
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Affiliation(s)
- Mikhail S. Lifar
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
| | - Andrei A. Tereshchenko
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
| | - Aleksei N. Bulgakov
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
| | - Sergey A. Guda
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
- Institute
for Mathematics, Mechanics and Computer Science in the name of I.I.
Vorovich, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Alexander A. Guda
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
| | - Alexander V. Soldatov
- The
Smart Materials Research Institute, Southern
Federal University, 344090 Rostov-on-Don, Russia
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19
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Li S, Miyazaki T, Nakata A. Theoretical search for characteristic atoms in supported gold nanoparticles: a large-scale DFT study. Phys Chem Chem Phys 2024. [PMID: 38922670 DOI: 10.1039/d4cp01094a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
The size and site dependences of atomic and electronic structures in isolated and supported gold nanoparticles have been investigated using large-scale density functional theory (DFT) calculations using multi-site support functions. The effects of the substrate on nanoparticles with diameters of 2 nm and several different shapes have been examined. First, isolated gold nanoparticles with diameters of 0.6 nm (13 atoms) to 4.5 nm (2057 atoms), which have comparable sizes to nanoparticles used in experiments, were considered. To analyse huge amounts of data obtained from large-scale DFT calculations, we performed principal component analysis (PCA), which helps systematically and efficiently clarify the electronic structures of large nanoparticles. The PCA results reveal the site dependence of the electronic structures. Notably, the atoms in the surface and subsurface have different electronic structures to those located in the inner layers, especially at the vertexes of the particles. The convergence of local electronic structures with respect to the particle size has also been demonstrated. For supported nanoparticles, PCA helps indicate which atoms are affected, and how much, by the substrate. The correlation between the PCA results and site dependence of reaction activity is also discussed herein.
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Affiliation(s)
- Shengzhou Li
- Department of Computer Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan.
| | - Tsuyoshi Miyazaki
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan.
| | - Ayako Nakata
- Department of Computer Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
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20
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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024; 18:14791-14840. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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21
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Wang R, He Z, Chen H, Guo S, Zhang S, Wang K, Wang M, Ho SH. Enhancing biomass conversion to bioenergy with machine learning: Gains and problems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172310. [PMID: 38599406 DOI: 10.1016/j.scitotenv.2024.172310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/20/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
The growing concerns about environmental sustainability and energy security, such as exhaustion of traditional fossil fuels and global carbon footprint growth have led to an increasing interest in alternative energy sources, especially bioenergy. Recently, numerous scenarios have been proposed regarding the use of bioenergy from different sources in the future energy systems. In this regard, one of the biggest challenges for scientists is managing, modeling, decision-making, and future forecasting of bioenergy systems. The development of machine learning (ML) techniques can provide new opportunities for modeling, optimizing and managing the production, consumption and environmental effects of bioenergy. However, researchers in bioenergy fields have not widely utilized the ML concepts and practices. Therefore, a comparative review of the current ML techniques used for bioenergy productions is presented in this paper. This review summarizes the common issues and difficulties existing in integrating ML with bioenergy studies, and discusses and proposes the possible solutions. Additionally, a detailed discussion of the appropriate ML application scenarios is also conducted in every sector of the entire bioenergy chain. This indicates the modernized conversion processes supported by ML techniques are imperative to accurately capture process-level subtleties, and thus improving techno-economic resilience and socio-ecological integrity of bioenergy production. All the efforts are believed to help in sustainable bioenergy production with ML technologies for the future.
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Affiliation(s)
- Rupeng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Zixiang He
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Honglin Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Silin Guo
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150040, PR China
| | - Shiyu Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Ke Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Meng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150040, PR China.
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22
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Cao X, Huang J, Du K, Tian Y, Hu Z, Luo Z, Wang J, Guo Y. Machine-Learning-Assisted Descriptors Identification for Indoor Formaldehyde Oxidation Catalysts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8372-8379. [PMID: 38691628 DOI: 10.1021/acs.est.4c01691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The development of highly efficient catalysts for formaldehyde (HCHO) oxidation is of significant interest for the improvement of indoor air quality. Up to 400 works relating to the catalytic oxidation of HCHO have been published to date; however, their analysis for collective inference through conventional literature search is still a challenging task. A machine learning (ML) framework was presented to predict catalyst performance from experimental descriptors based on an HCHO oxidation catalysts database. MnOx, CeO2, Co3O4, TiO2, FeOx, ZrO2, Al2O3, SiO2, and carbon-based catalysts with different promoters were compiled from the literature. Notably, 20 descriptors including reaction catalyst composition, reaction conditions, and catalyst physical properties were collected for data mining (2263 data points). Furthermore, the eXtreme Gradient Boosting algorithm was employed, which successfully predicted the conversion efficiency of HCHO with an R-square value of 0.81. Shapley additive analysis suggested Pt/MnO2 and Ag/Ce-Co3O4 exhibited excellent catalytic performance of HCHO oxidation based on the analysis of the entire database. Validated by experimental tests and theoretical simulations, the key descriptor identified by ML, i.e., the first promoter, was further described as metal-support interactions. This study highlights ML as a useful tool for database establishment and the catalyst rational design strategy based on the importance of analysis between experimental descriptors and the performance of complex catalytic systems.
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Affiliation(s)
- Xinyuan Cao
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Jisi Huang
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Kexin Du
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Yawen Tian
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Zhixin Hu
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Zhu Luo
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Jinlong Wang
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
- Wuhan Institute of Photochemistry and Technology, Wuhan, Hubei 430083, P. R. China
- Engineering Research Center of Photoenergy Utilization for Pollution Control and Carbon Reduction, Ministry of Education, Wuhan 430079, P. R. China
| | - Yanbing Guo
- College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
- Wuhan Institute of Photochemistry and Technology, Wuhan, Hubei 430083, P. R. China
- Engineering Research Center of Photoenergy Utilization for Pollution Control and Carbon Reduction, Ministry of Education, Wuhan 430079, P. R. China
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23
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Shimakawa H, Kumada A, Sato M. Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties. J Chem Inf Model 2024; 64:3621-3629. [PMID: 38642039 DOI: 10.1021/acs.jcim.3c01894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2024]
Abstract
Machine learning (ML) has facilitated property prediction for intricate materials by integrating materials and experimental features such as processing and measurement conditions. However, ML models designed for material properties have often disregarded a common issue of "leakage," resulting in an overestimation of model performance and a decrease in model transferability. This issue can arise from biases inherent in multiple data points obtained from the same experimental group. We provide a critical examination and prevention method of leakage in property prediction for polymer composites. Our proposed method utilizes data partitioning based on the experimental group to ensure that data from the same group are not mixed in both the training and test sets. Evaluation results highlight that the conventional random partitioning unintentionally inflates ML performance through the misuse of experimental features for leaking data bias within the same experimental group rather than explaining the physical causality. In contrast, the proposed method enables the leakage-free utilization of experimental features to improve prediction accuracy while ensuring model transferability. Specifically, when integrating experimental features with polymer and filler features, the conventional method overestimates the prediction performance of electrical conductivity in reducing RMSE by 26% depending on leakage, whereas the proposed method achieves a reduction in RMSE by 5% without leakage. These findings offer valuable guidance for the effective utilization of experimental features in data-driven materials science.
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Affiliation(s)
- Hajime Shimakawa
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akiko Kumada
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Sato
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
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24
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Hisata Y, Washio T, Takizawa S, Ogoshi S, Hoshimoto Y. In-silico-assisted derivatization of triarylboranes for the catalytic reductive functionalization of aniline-derived amino acids and peptides with H 2. Nat Commun 2024; 15:3708. [PMID: 38714662 PMCID: PMC11076482 DOI: 10.1038/s41467-024-47984-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
Cheminformatics-based machine learning (ML) has been employed to determine optimal reaction conditions, including catalyst structures, in the field of synthetic chemistry. However, such ML-focused strategies have remained largely unexplored in the context of catalytic molecular transformations using Lewis-acidic main-group elements, probably due to the absence of a candidate library and effective guidelines (parameters) for the prediction of the activity of main-group elements. Here, the construction of a triarylborane library and its application to an ML-assisted approach for the catalytic reductive alkylation of aniline-derived amino acids and C-terminal-protected peptides with aldehydes and H2 is reported. A combined theoretical and experimental approach identified the optimal borane, i.e., B(2,3,5,6-Cl4-C6H)(2,6-F2-3,5-(CF3)2-C6H)2, which exhibits remarkable functional-group compatibility toward aniline derivatives in the presence of 4-methyltetrahydropyran. The present catalytic system generates H2O as the sole byproduct.
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Affiliation(s)
- Yusei Hisata
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takashi Washio
- Department of Reasoning for Intelligence and Artificial Intelligence Research Center, SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Shinobu Takizawa
- Department of Synthetic Organic Chemistry and Artificial Intelligence Research Center, SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Sensuke Ogoshi
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yoichi Hoshimoto
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Division of Applied Chemistry, Center for Future Innovation (CFi), Faculty of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
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25
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Gao Y, Zhu Z, Chen Z, Guo M, Zhang Y, Wang L, Zhu Z. Machine learning in nanozymes: from design to application. Biomater Sci 2024; 12:2229-2243. [PMID: 38497247 DOI: 10.1039/d4bm00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Nanozymes, a distinctive class of nanomaterials endowed with enzyme-like activity and kinetics akin to enzyme-catalysed reactions, present several advantages over natural enzymes, including cost-effectiveness, heightened stability, and adjustable activity. However, the conventional trial-and-error methodology for developing novel nanozymes encounters growing challenges as research progresses. The advent of artificial intelligence (AI), particularly machine learning (ML), has ushered in innovative design approaches for researchers in this domain. This review delves into the burgeoning role of ML in nanozyme research, elucidating the advancements achieved through ML applications. The review explores successful instances of ML in nanozyme design and implementation, providing a comprehensive overview of the evolving landscape. A roadmap for ML-assisted nanozyme research is outlined, offering a universal guideline for research in this field. In the end, the review concludes with an analysis of challenges encountered and anticipates future directions for ML in nanozyme research. The synthesis of knowledge in this review aims to foster a cross-disciplinary study, propelling the revolutionary field forward.
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Affiliation(s)
- Yubo Gao
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhicheng Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhen Chen
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Meng Guo
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Yiqing Zhang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Lina Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
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26
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Peng X, Zhang M, Zhang T, Zhou Y, Ni J, Wang X, Jiang L. Single-atom and cluster catalysts for thermocatalytic ammonia synthesis at mild conditions. Chem Sci 2024; 15:5897-5915. [PMID: 38665515 PMCID: PMC11041362 DOI: 10.1039/d3sc06998b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Ammonia (NH3) is closely related to the fields of food and energy that humans depend on. The exploitation of advanced catalysts for NH3 synthesis has been a research hotspot for more than one hundred years. Previous studies have shown that the Ru B5 sites (step sites on the Ru (0001) surface uniquely arranged with five Ru atoms) and Fe C7 sites (iron atoms with seven nearest neighbors) over nanoparticle catalysts are highly reactive for N2-to-NH3 conversion. In recent years, single-atom and cluster catalysts, where the B5 sites and C7 sites are absent, have emerged as promising catalysts for efficient NH3 synthesis. In this review, we focus on the recent advances in single-atom and cluster catalysts, including single-atom catalysts (SACs), single-cluster catalysts (SCCs), and bimetallic-cluster catalysts (BCCs), for thermocatalytic NH3 synthesis at mild conditions. In addition, we discussed and summarized the unique structural properties and reaction performance as well as reaction mechanisms over single-atom and cluster catalysts in comparison with traditional nanoparticle catalysts. Finally, the challenges and prospects in the rational design of efficient single-atom and cluster catalysts for NH3 synthesis were provided.
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Affiliation(s)
- Xuanbei Peng
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
- Qingyuan Innovat Lab Quanzhou Fujian 362801 China
| | - Mingyuan Zhang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Tianhua Zhang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Yanliang Zhou
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
- Qingyuan Innovat Lab Quanzhou Fujian 362801 China
| | - Jun Ni
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
| | - Xiuyun Wang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
- Qingyuan Innovat Lab Quanzhou Fujian 362801 China
| | - Lilong Jiang
- National Engineering Research Center of Chemical Fertilizer Catalyst, Fuzhou University Fuzhou Fujian 350002 China
- Qingyuan Innovat Lab Quanzhou Fujian 362801 China
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27
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Garcia-Escobar F, Taniike T, Takahashi K. MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models. J Chem Inf Model 2024; 64:1512-1521. [PMID: 38385190 DOI: 10.1021/acs.jcim.3c01952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proposing relevant catalyst descriptors that can relate the information on a catalyst's composition to its actual performance is an ongoing area in catalyst informatics, as it is a necessary step to improve our understanding on the target reactions. Herein, a small descriptor-engineered data set containing 3289 descriptor variables and the performance of 200 catalysts for the oxidative coupling of methane (OCM) is analyzed, and a descriptor search algorithm based on the workflow of the Basin-hopping optimization methodology is proposed to select the descriptors that better fit a predictive model. The algorithm, which can be considered wrapper in nature, consists of the successive generation of random-based modifications to the descriptor subset used in a regression model and adopting them depending on their effect on the model's score. The results are presented after being tested on linear and Support Vector Regression models with average cross-validation r2 scores of 0.8268 and 0.6875, respectively.
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Affiliation(s)
| | - Toshiaki Taniike
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Keisuke Takahashi
- Department of Chemistry, Hokkaido University, North 10, West 8, Sapporo 060-8510, Japan
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28
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Zhuang J, Midgley AC, Wei Y, Liu Q, Kong D, Huang X. Machine-Learning-Assisted Nanozyme Design: Lessons from Materials and Engineered Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2210848. [PMID: 36701424 DOI: 10.1002/adma.202210848] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Indexed: 05/11/2023]
Abstract
Nanozymes are nanomaterials that exhibit enzyme-like biomimicry. In combination with intrinsic characteristics of nanomaterials, nanozymes have broad applicability in materials science, chemical engineering, bioengineering, biochemistry, and disease theranostics. Recently, the heterogeneity of published results has highlighted the complexity and diversity of nanozymes in terms of consistency of catalytic capacity. Machine learning (ML) shows promising potential for discovering new materials, yet it remains challenging for the design of new nanozymes based on ML approaches. Alternatively, ML is employed to promote optimization of intelligent design and application of catalytic materials and engineered enzymes. Incorporation of the successful ML algorithms used in the intelligent design of catalytic materials and engineered enzymes can concomitantly facilitate the guided development of next-generation nanozymes with desirable properties. Here, recent progress in ML, its utilization in the design of catalytic materials and enzymes, and how emergent ML applications serve as promising strategies to circumvent challenges associated with time-expensive and laborious testing in nanozyme research and development are summarized. The potential applications of successful examples of ML-aided catalytic materials and engineered enzymes in nanozyme design are also highlighted, with special focus on the unified aims in enhancing design and recapitulation of substrate selectivity and catalytic activity.
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Affiliation(s)
- Jie Zhuang
- School of Medicine, and State, Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Adam C Midgley
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Yonghua Wei
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Qiqi Liu
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Deling Kong
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Xinglu Huang
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
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29
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Miyazaki R, Belthle KS, Tüysüz H, Foppa L, Scheffler M. Materials Genes of CO 2 Hydrogenation on Supported Cobalt Catalysts: An Artificial Intelligence Approach Integrating Theoretical and Experimental Data. J Am Chem Soc 2024; 146:5433-5444. [PMID: 38374731 PMCID: PMC10910553 DOI: 10.1021/jacs.3c12984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Designing materials for catalysis is challenging because the performance is governed by an intricate interplay of various multiscale phenomena, such as the chemical reactions on surfaces and the materials' restructuring during the catalytic process. In the case of supported catalysts, the role of the support material can be also crucial. Here, we address this intricacy challenge by a symbolic-regression artificial intelligence (AI) approach. We identify the key physicochemical parameters correlated with the measured performance, out of many offered candidate parameters characterizing the materials, reaction environment, and possibly relevant underlying phenomena. Importantly, these parameters are obtained by both experiments and ab initio simulations. The identified key parameters might be called "materials genes", in analogy to genes in biology: they correlate with the property or function of interest, but the explicit physical relationship is not (necessarily) known. To demonstrate the approach, we investigate the CO2 hydrogenation catalyzed by cobalt nanoparticles supported on silica. Crucially, the silica support is modified with the additive metals magnesium, calcium, titanium, aluminum, or zirconium, which results in six materials with significantly different performances. These systems mimic hydrothermal vents, which might have produced the first organic molecules on Earth. The key parameters correlated with the CH3OH selectivity reflect the reducibility of cobalt species, the adsorption strength of reaction intermediates, and the chemical nature of the additive metal. By using an AI model trained on basic elemental properties of the additive metals (e.g., ionization potential) as physicochemical parameters, new additives are suggested. The predicted CH3OH selectivity of cobalt catalysts supported on silica modified with vanadium and zinc is confirmed by new experiments.
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Affiliation(s)
- Ray Miyazaki
- The
NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft
and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, Berlin 14195, Germany
| | - Kendra S Belthle
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an
der Ruhr 45470, Germany
| | - Harun Tüysüz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an
der Ruhr 45470, Germany
| | - Lucas Foppa
- The
NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft
and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, Berlin 14195, Germany
| | - Matthias Scheffler
- The
NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft
and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, Berlin 14195, Germany
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30
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Sun C, Goel R, Kulkarni AR. Developing Cheap but Useful Machine Learning-Based Models for Investigating High-Entropy Alloy Catalysts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38314715 PMCID: PMC10883032 DOI: 10.1021/acs.langmuir.3c03401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
This work aims to address the challenge of developing interpretable ML-based models when access to large-scale computational resources is limited. Using CoMoFeNiCu high-entropy alloy catalysts as an example, we present a cost-effective workflow that synergistically combines descriptor-based approaches, machine learning-based force fields, and low-cost density functional theory (DFT) calculations to predict high-quality adsorption energies for H, N, and NHx (x = 1, 2, and 3) adsorbates. This is achieved using three specific modifications to typical DFT workflows including: (1) using a sequential optimization protocol, (2) developing a new geometry-based descriptor, and (3) repurposing the already-available low-cost DFT optimization trajectories to develop a ML-FF. Taken together, this study illustrates how cost-effective DFT calculations and appropriately designed descriptors can be used to develop cheap but useful models for predicting high-quality adsorption energies at significantly lower computational costs. We anticipate that this resource-efficient philosophy may be broadly relevant to the larger surface catalysis community.
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Affiliation(s)
- Chenghan Sun
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Rajat Goel
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
| | - Ambarish R Kulkarni
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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Taniike T, Fujiwara A, Nakanowatari S, García-Escobar F, Takahashi K. Automatic feature engineering for catalyst design using small data without prior knowledge of target catalysis. Commun Chem 2024; 7:11. [PMID: 38216711 PMCID: PMC10786848 DOI: 10.1038/s42004-023-01086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The empirical aspect of descriptor design in catalyst informatics, particularly when confronted with limited data, necessitates adequate prior knowledge for delving into unknown territories, thus presenting a logical contradiction. This study introduces a technique for automatic feature engineering (AFE) that works on small catalyst datasets, without reliance on specific assumptions or pre-existing knowledge about the target catalysis when designing descriptors and building machine-learning models. This technique generates numerous features through mathematical operations on general physicochemical features of catalytic components and extracts relevant features for the desired catalysis, essentially screening numerous hypotheses on a machine. AFE yields reasonable regression results for three types of heterogeneous catalysis: oxidative coupling of methane (OCM), conversion of ethanol to butadiene, and three-way catalysis, where only the training set is swapped. Moreover, through the application of active learning that combines AFE and high-throughput experimentation for OCM, we successfully visualize the machine's process of acquiring precise recognition of the catalyst design. Thus, AFE is a versatile technique for data-driven catalysis research and a key step towards fully automated catalyst discoveries.
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Affiliation(s)
- Toshiaki Taniike
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan.
| | - Aya Fujiwara
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Sunao Nakanowatari
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | | | - Keisuke Takahashi
- Department of Chemistry, Hokkaido University, North 10, West 8, Sapporo, 060-0810, Japan
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32
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Moon J, Beker W, Siek M, Kim J, Lee HS, Hyeon T, Grzybowski BA. Active learning guides discovery of a champion four-metal perovskite oxide for oxygen evolution electrocatalysis. NATURE MATERIALS 2024; 23:108-115. [PMID: 37919351 DOI: 10.1038/s41563-023-01707-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 10/02/2023] [Indexed: 11/04/2023]
Abstract
Multi-metal oxides in general and perovskite oxides in particular have attracted considerable attention as oxygen evolution electrocatalysts. Although numerous theoretical studies have been undertaken, the most promising perovskite-based catalysts continue to emerge from human-driven experimental campaigns rather than data-driven machine learning protocols, which are often limited by the scarcity of experimental data on which to train the models. This work promises to break this impasse by demonstrating that active learning on even small datasets-but supplemented by informative structural-characterization data and coupled with closed-loop experimentation-can yield materials of outstanding performance. The model we develop not only reproduces several non-obvious and actively studied experimental trends but also identifies a composition of a perovskite oxide electrocatalyst exhibiting an intrinsic overpotential at 10 mA cm-2oxide of 391 mV, which is among the lowest known of four-metal perovskite oxides.
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Affiliation(s)
- Junseok Moon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University (SNU), Seoul, Republic of Korea
| | - Wiktor Beker
- Allchemy, Inc., Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Science, Warsaw, Poland
| | - Marta Siek
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Jiheon Kim
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University (SNU), Seoul, Republic of Korea
| | - Hyeon Seok Lee
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University (SNU), Seoul, Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University (SNU), Seoul, Republic of Korea.
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Science, Warsaw, Poland.
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, Republic of Korea.
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
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33
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Niu J, Miao B, Guo J, Ding Z, He Y, Chi Z, Wang F, Ma X. Leveraging Deep Neural Networks for Estimating Vickers Hardness from Nanoindentation Hardness. MATERIALS (BASEL, SWITZERLAND) 2023; 17:148. [PMID: 38204003 PMCID: PMC10780037 DOI: 10.3390/ma17010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024]
Abstract
This research presents a comprehensive analysis of deep neural network models (DNNs) for the precise prediction of Vickers hardness (HV) in nitrided and carburized M50NiL steel samples, with hardness values spanning from 400 to 1000 HV. By conducting rigorous experimentation and obtaining corresponding nanoindentation data, we evaluated the performance of four distinct neural network architectures: Multilayer Perceptron (MLP), Convolutional Neural Network (CNN), Long Short-Term Memory network (LSTM), and Transformer. Our findings reveal that MLP and LSTM models excel in predictive accuracy and efficiency, with MLP showing exceptional iteration efficiency and predictive precision. The study validates models for broad application in various steel types and confirms nanoindentation as an effective direct measure for HV hardness in thin films and gradient-variable regions. This work contributes a validated and versatile approach to the hardness assessment of thin-film materials and those with intricate microstructures, enhancing material characterization and potential application in advanced material engineering.
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Affiliation(s)
- Junbo Niu
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Bin Miao
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Jiaxu Guo
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Zhifeng Ding
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Yin He
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Zhiyu Chi
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Feilong Wang
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
| | - Xinxin Ma
- School of Material Science & Engineering, Harbin Institute of Technology, Harbin 150001, China; (B.M.); (J.G.); (Z.D.); (Y.H.); (Z.C.); (F.W.)
- State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, Harbin 150001, China
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34
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Chen SS, Meyer Z, Jensen B, Kraus A, Lambert A, Ess DH. ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design. J Chem Inf Model 2023; 63:7412-7422. [PMID: 37987743 DOI: 10.1021/acs.jcim.3c01310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here, we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library, ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.
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Affiliation(s)
- Shu-Sen Chen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Zack Meyer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Brendan Jensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Alex Kraus
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Allison Lambert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
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35
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Hu W, Zhang L. First-principles, machine learning and symbolic regression modelling for organic molecule adsorption on two-dimensional CaO surface. J Mol Graph Model 2023; 124:108530. [PMID: 37321063 DOI: 10.1016/j.jmgm.2023.108530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Data-driven methods are receiving significant attention in recent years for chemical and materials researches; however, more works should be done to leverage the new paradigm to model and analyze the adsorption of the organic molecules on low-dimensional surfaces beyond using the traditional simulation methods. In this manuscript, we employ machine learning and symbolic regression method coupled with DFT calculations to investigate the adsorption of atmospheric organic molecules on a low-dimensional metal oxide mineral system. The starting dataset consisting of the atomic structures of the organic/metal oxide interfaces are obtained via the density functional theory (DFT) calculation and different machine learning algorithms are compared, with the random forest algorithm achieving high accuracies for the target output. The feature ranking step identifies that the polarizability and bond type of the organic adsorbates are the key descriptors for the adsorption energy output. In addition, the symbolic regression coupled with genetic programming automatically identifies a series of hybrid new descriptors displaying improved relevance with the target output, suggesting the viability of symbolic regression to complement the traditional machine learning techniques for the descriptor design and fast modeling purposes. This manuscript provides a framework for effectively modeling and analyzing the adsorption of the organic molecules on low-dimensional surfaces via comprehensive data-driven approaches.
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Affiliation(s)
- Wenguang Hu
- Department of Materials Physics, School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, 210044, Nanjing, China
| | - Lei Zhang
- Department of Materials Physics, School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, 210044, Nanjing, China.
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36
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Ge F, Chen G, Qian M, Xu C, Liu J, Cao J, Li X, Hu D, Xu Y, Xin Y, Wang D, Zhou J, Shi H, Tan Z. Artificial Intelligence Aided Lipase Production and Engineering for Enzymatic Performance Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14911-14930. [PMID: 37800676 DOI: 10.1021/acs.jafc.3c05029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
With the development of artificial intelligence (AI), tailoring methods for enzyme engineering have been widely expanded. Additional protocols based on optimized network models have been used to predict and optimize lipase production as well as properties, namely, catalytic activity, stability, and substrate specificity. Here, different network models and algorithms for the prediction and reforming of lipase, focusing on its modification methods and cases based on AI, are reviewed in terms of both their advantages and disadvantages. Different neural networks coupled with various algorithms are usually applied to predict the maximum yield of lipase by optimizing the external cultivations for lipase production, while one part is used to predict the molecule variations affecting the properties of lipase. However, few studies have directly utilized AI to engineer lipase by affecting the structure of the enzyme, and a set of research gaps needs to be explored. Additionally, future perspectives of AI application in enzymes, including lipase engineering, are deduced to help the redesign of enzymes and the reform of new functional biocatalysts. This review provides a new horizon for developing effective and innovative AI tools for lipase production and engineering and facilitating lipase applications in the food industry and biomass conversion.
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Affiliation(s)
- Feiyin Ge
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Gang Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Minjing Qian
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Cheng Xu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiao Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jiaqi Cao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Xinchao Li
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Die Hu
- School of Pharmacy & School of Biological and Food Engineering, Changzhou University, Changzhou 213164, People's Republic of China
| | - Yangsen Xu
- Dongtai Hanfangyuan Biotechnology Co. Ltd., Yancheng 224241, People's Republic of China
| | - Ya Xin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Dianlong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Jia Zhou
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Hao Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
| | - Zhongbiao Tan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, People's Republic of China
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37
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Manzhos S, Ihara M. Neural Network with Optimal Neuron Activation Functions Based on Additive Gaussian Process Regression. J Phys Chem A 2023; 127:7823-7835. [PMID: 37698519 DOI: 10.1021/acs.jpca.3c02949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Feed-forward neural networks (NNs) are a staple machine learning method widely used in many areas of science and technology, including physical chemistry, computational chemistry, and materials informatics. While even a single-hidden-layer NN is a universal approximator, its expressive power is limited by the use of simple neuron activation functions (such as sigmoid functions) that are typically the same for all neurons. More flexible neuron activation functions would allow the use of fewer neurons and layers and thereby save computational cost and improve expressive power. We show that additive Gaussian process regression (GPR) can be used to construct optimal neuron activation functions that are individual to each neuron. An approach is also introduced that avoids nonlinear fitting of neural network parameters by defining them with rules. The resulting method combines the advantage of robustness of a linear regression with the higher expressive power of an NN. We demonstrate the approach by fitting the potential energy surfaces of the water molecule and formaldehyde. Without requiring any nonlinear optimization, the additive-GPR-based approach outperforms a conventional NN in the high-accuracy regime, where a conventional NN suffers more from overfitting.
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Affiliation(s)
- Sergei Manzhos
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8552, Japan
| | - Manabu Ihara
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8552, Japan
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38
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Wang G, Mine S, Chen D, Jing Y, Ting KW, Yamaguchi T, Takao M, Maeno Z, Takigawa I, Matsushita K, Shimizu KI, Toyao T. Accelerated discovery of multi-elemental reverse water-gas shift catalysts using extrapolative machine learning approach. Nat Commun 2023; 14:5861. [PMID: 37735169 PMCID: PMC10514199 DOI: 10.1038/s41467-023-41341-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
Designing novel catalysts is key to solving many energy and environmental challenges. Despite the promise that data science approaches, including machine learning (ML), can accelerate the development of catalysts, truly novel catalysts have rarely been discovered through ML approaches because of one of its most common limitations and criticisms-the assumed inability to extrapolate and identify extraordinary materials. Herein, we demonstrate an extrapolative ML approach to develop new multi-elemental reverse water-gas shift catalysts. Using 45 catalysts as the initial data points and performing 44 cycles of the closed loop discovery system (ML prediction + experiment), we experimentally tested a total of 300 catalysts and identified more than 100 catalysts with superior activity compared to those of the previously reported high-performance catalysts. The composition of the optimal catalyst discovered was Pt(3)/Rb(1)-Ba(1)-Mo(0.6)-Nb(0.2)/TiO2. Notably, niobium (Nb) was not included in the original dataset, and the catalyst composition identified was not predictable even by human experts.
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Affiliation(s)
- Gang Wang
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Shinya Mine
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Duotian Chen
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Yuan Jing
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Kah Wei Ting
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Taichi Yamaguchi
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Motoshi Takao
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan
| | - Zen Maeno
- School of Advanced Engineering, Kogakuin University, 2665-1, Nakano-cho, Hachioji, 192-0015, Japan
| | - Ichigaku Takigawa
- RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
- Institute for Liberal Arts and Sciences, Kyoto University, 69-302, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8315, Japan.
| | - Koichi Matsushita
- Central Technical Research Laboratory, ENEOS Corporation, 8, Chidori-cho, Naka-ku, Yokohama, 231-0815, Japan
| | - Ken-Ichi Shimizu
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
| | - Takashi Toyao
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
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39
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Lindeboom W, Deacy AC, Phanopoulos A, Buchard A, Williams CK. Correlating Metal Redox Potentials to Co(III)K(I) Catalyst Performances in Carbon Dioxide and Propene Oxide Ring Opening Copolymerization. Angew Chem Int Ed Engl 2023; 62:e202308378. [PMID: 37409487 PMCID: PMC10952574 DOI: 10.1002/anie.202308378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
Carbon dioxide copolymerization is a front-runner CO2 utilization strategy but its viability depends on improving the catalysis. So far, catalyst structure-performance correlations have not been straightforward, limiting the ability to predict how to improve both catalytic activity and selectivity. Here, a simple measure of a catalyst ground-state parameter, metal reduction potential, directly correlates with both polymerization activity and selectivity. It is applied to compare performances of 6 new heterodinuclear Co(III)K(I) catalysts for propene oxide (PO)/CO2 ring opening copolymerization (ROCOP) producing poly(propene carbonate) (PPC). The best catalyst shows an excellent turnover frequency of 389 h-1 and high PPC selectivity of >99 % (50 °C, 20 bar, 0.025 mol% catalyst). As demonstration of its utility, neither DFT calculations nor ligand Hammett parameter analyses are viable predictors. It is proposed that the cobalt redox potential informs upon the active site electron density with a more electron rich cobalt centre showing better performances. The method may be widely applicable and is recommended to guide future catalyst discovery for other (co)polymerizations and carbon dioxide utilizations.
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Affiliation(s)
- Wouter Lindeboom
- Department ChemistryUniversity of OxfordChemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Arron C. Deacy
- Department ChemistryUniversity of OxfordChemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Andreas Phanopoulos
- Department of ChemistryImperial College LondonMolecular Sciences Research HubLondonW12 OBZUK
| | - Antoine Buchard
- Department of ChemistryInstitute for SustainabilityUniversity of BathBathBA2 7AYUK
| | - Charlotte K. Williams
- Department ChemistryUniversity of OxfordChemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
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40
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Ohno M, Hayashi Y, Zhang Q, Kaneko Y, Yoshida R. SMiPoly: Generation of a Synthesizable Polymer Virtual Library Using Rule-Based Polymerization Reactions. J Chem Inf Model 2023; 63:5539-5548. [PMID: 37604495 PMCID: PMC10498440 DOI: 10.1021/acs.jcim.3c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 08/23/2023]
Abstract
Recent advances in machine learning have led to the rapid adoption of various computational methods for de novo molecular design in polymer research, including high-throughput virtual screening and inverse molecular design. In such workflows, molecular generators play an essential role in creation or sequential modification of candidate polymer structures. Machine learning-assisted molecular design has made great technical progress over the past few years. However, the difficulty of identifying synthetic routes to such designed polymers remains unresolved. To address this technical limitation, we present Small Molecules into Polymers (SMiPoly), a Python library for virtual polymer generation that implements 22 chemical rules for commonly applied polymerization reactions. For given small organic molecules to form a candidate monomer set, the SMiPoly generator conducts possible polymerization reactions to generate an exhaustive list of potentially synthesizable polymers. In this study, using 1083 readily available monomers, we generated 169,347 unique polymers forming seven different molecular types: polyolefin, polyester, polyether, polyamide, polyimide, polyurethane, and polyoxazolidone. By comparing the distribution of the virtually created polymers with approximately 16,000 real polymers synthesized so far, it was found that the coverage and novelty of the SMiPoly-generated polymers can reach 48 and 53%, respectively. Incorporating the SMiPoly library into a molecular design workflow will accelerate the process of de novo polymer synthesis by shortening the step to select synthesizable candidate polymers.
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Affiliation(s)
- Mitsuru Ohno
- Daicel
Corporation, Kita-ku, 530-0011 Osaka, Japan
| | - Yoshihiro Hayashi
- The
Institute of Statistical Mathematics, Research Organization of Information
and Systems, Tachikawa, Tokyo 190-8562, Japan
- The
Graduate University for Advanced Studies, SOKENDAI, Tachikawa, Tokyo 190-8562, Japan
| | - Qi Zhang
- The
Institute of Statistical Mathematics, Research Organization of Information
and Systems, Tachikawa, Tokyo 190-8562, Japan
| | - Yu Kaneko
- Daicel
Corporation, Kita-ku, 530-0011 Osaka, Japan
| | - Ryo Yoshida
- The
Institute of Statistical Mathematics, Research Organization of Information
and Systems, Tachikawa, Tokyo 190-8562, Japan
- The
Graduate University for Advanced Studies, SOKENDAI, Tachikawa, Tokyo 190-8562, Japan
- National
Institute for Materials Science, 305-0047 Ibaraki, Japan
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41
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Ojelade OA. CO 2 Hydrogenation to Gasoline and Aromatics: Mechanistic and Predictive Insights from DFT, DRIFTS and Machine Learning. Chempluschem 2023; 88:e202300301. [PMID: 37580947 DOI: 10.1002/cplu.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023]
Abstract
The emission of CO2 from fossil fuels is the largest driver of global climate change. To realize the target of a carbon-neutrality by 2050, CO2 capture and utilization is crucial. The efficient conversion of CO2 to C5+ gasoline and aromatics remains elusive mainly due to CO2 thermodynamic stability and the high energy barrier of the C-C coupling step. Herein, advances in mechanistic understanding via Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS), density functional theory (DFT), and microkinetic modeling are discussed. It further emphasizes the power of machine learning (ML) to accelerate the search for optimal catalysts. A significant effort has been invested into this field of research with volumes of experimental and characterization data, this study discusses how they can be used as input features for machine learning prediction in a bid to better understand catalytic properties capable of accelerating breakthroughs in the process.
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Affiliation(s)
- Opeyemi A Ojelade
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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42
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Tsuji Y, Yoshioka Y, Okazawa K, Yoshizawa K. Exploring Metal Nanocluster Catalysts for Ammonia Synthesis Using Informatics Methods: A Concerted Effort of Bayesian Optimization, Swarm Intelligence, and First-Principles Computation. ACS OMEGA 2023; 8:30335-30348. [PMID: 37636907 PMCID: PMC10448644 DOI: 10.1021/acsomega.3c03456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023]
Abstract
This paper details the use of computational and informatics methods to design metal nanocluster catalysts for efficient ammonia synthesis. Three main problems are tackled: defining a measure of catalytic activity, choosing the best candidate from a large number of possibilities, and identifying the thermodynamically stable cluster catalyst structure. First-principles calculations, Bayesian optimization, and particle swarm optimization are used to obtain a Ti8 nanocluster as a catalyst candidate. The N2 adsorption structure on Ti8 indicates substantial activation of the N2 molecule, while the NH3 adsorption structure suggests that NH3 is likely to undergo easy desorption. The study also reveals several cluster catalyst candidates that break the general trade-off that surfaces that strongly adsorb reactants also strongly adsorb products.
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Affiliation(s)
- Yuta Tsuji
- Faculty
of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Yuta Yoshioka
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazuki Okazawa
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering and IRCCS, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
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43
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Mou L, Han T, Smith PES, Sharman E, Jiang J. Machine Learning Descriptors for Data-Driven Catalysis Study. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301020. [PMID: 37191279 PMCID: PMC10401178 DOI: 10.1002/advs.202301020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/07/2023] [Indexed: 05/17/2023]
Abstract
Traditional trial-and-error experiments and theoretical simulations have difficulty optimizing catalytic processes and developing new, better-performing catalysts. Machine learning (ML) provides a promising approach for accelerating catalysis research due to its powerful learning and predictive abilities. The selection of appropriate input features (descriptors) plays a decisive role in improving the predictive accuracy of ML models and uncovering the key factors that influence catalytic activity and selectivity. This review introduces tactics for the utilization and extraction of catalytic descriptors in ML-assisted experimental and theoretical research. In addition to the effectiveness and advantages of various descriptors, their limitations are also discussed. Highlighted are both 1) newly developed spectral descriptors for catalytic performance prediction and 2) a novel research paradigm combining computational and experimental ML models through suitable intermediate descriptors. Current challenges and future perspectives on the application of descriptors and ML techniques to catalysis are also presented.
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Affiliation(s)
- Li‐Hui Mou
- Hefei National Research Center for Physical Sciences at the MicroscaleSchool of Chemistry and Materials ScienceUniversity of Science and Technology of ChinaHefeiAnhui230026China
| | - TianTian Han
- Hefei JiShu Quantum Technology Co. Ltd.Hefei230026China
| | | | - Edward Sharman
- Department of NeurologyUniversity of CaliforniaIrvineCA92697USA
| | - Jun Jiang
- Hefei National Research Center for Physical Sciences at the MicroscaleSchool of Chemistry and Materials ScienceUniversity of Science and Technology of ChinaHefeiAnhui230026China
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44
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Karl TM, Bouayad-Gervais S, Hueffel JA, Sperger T, Wellig S, Kaldas SJ, Dabranskaya U, Ward JS, Rissanen K, Tizzard GJ, Schoenebeck F. Machine Learning-Guided Development of Trialkylphosphine Ni (I) Dimers and Applications in Site-Selective Catalysis. J Am Chem Soc 2023. [PMID: 37411044 DOI: 10.1021/jacs.3c03403] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Owing to the unknown correlation of a metal's ligand and its resulting preferred speciation in terms of oxidation state, geometry, and nuclearity, a rational design of multinuclear catalysts remains challenging. With the goal to accelerate the identification of suitable ligands that form trialkylphosphine-derived dihalogen-bridged Ni(I) dimers, we herein employed an assumption-based machine learning approach. The workflow offers guidance in ligand space for a desired speciation without (or only minimal) prior experimental data points. We experimentally verified the predictions and synthesized numerous novel Ni(I) dimers as well as explored their potential in catalysis. We demonstrate C-I selective arylations of polyhalogenated arenes bearing competing C-Br and C-Cl sites in under 5 min at room temperature using 0.2 mol % of the newly developed dimer, [Ni(I)(μ-Br)PAd2(n-Bu)]2, which is so far unmet with alternative dinuclear or mononuclear Ni or Pd catalysts.
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Affiliation(s)
- Teresa M Karl
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Samir Bouayad-Gervais
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Julian A Hueffel
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Theresa Sperger
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Sebastian Wellig
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Sherif J Kaldas
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | | | - Jas S Ward
- Department of Chemistry, University of Jyvaskyla, FIN40014 Jyväskylä, Finland
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, FIN40014 Jyväskylä, Finland
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, SO17 1BJ Southhampton, U.K
| | - Franziska Schoenebeck
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
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45
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Yang KR, Kyro GW, Batista VS. The landscape of computational approaches for artificial photosynthesis. NATURE COMPUTATIONAL SCIENCE 2023; 3:504-513. [PMID: 38177419 DOI: 10.1038/s43588-023-00450-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/11/2023] [Indexed: 01/06/2024]
Abstract
Artificial photosynthesis is an attractive strategy for converting solar energy into fuels, largely because the Earth receives enough solar energy in one hour to meet humanity's energy needs for an entire year. However, developing devices for artificial photosynthesis remains difficult and requires computational approaches to guide and assist the interpretation of experiments. In this Perspective, we discuss current and future computational approaches, as well as the challenges of designing and characterizing molecular assemblies that absorb solar light, transfer electrons between interfaces, and catalyze water-splitting and fuel-forming reactions.
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Affiliation(s)
- Ke R Yang
- Department of Chemistry, Yale University, New Haven, CT, USA
- Energy Sciences Institute, Yale University, West Haven, CT, USA
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, USA.
- Energy Sciences Institute, Yale University, West Haven, CT, USA.
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46
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A graph neural network for predicting the adsorption energy of molecules on metal surfaces. NATURE COMPUTATIONAL SCIENCE 2023; 3:372-373. [PMID: 38177839 DOI: 10.1038/s43588-023-00449-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
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47
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Liu L, Corma A. Bimetallic Sites for Catalysis: From Binuclear Metal Sites to Bimetallic Nanoclusters and Nanoparticles. Chem Rev 2023; 123:4855-4933. [PMID: 36971499 PMCID: PMC10141355 DOI: 10.1021/acs.chemrev.2c00733] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 03/29/2023]
Abstract
Heterogeneous bimetallic catalysts have broad applications in industrial processes, but achieving a fundamental understanding on the nature of the active sites in bimetallic catalysts at the atomic and molecular level is very challenging due to the structural complexity of the bimetallic catalysts. Comparing the structural features and the catalytic performances of different bimetallic entities will favor the formation of a unified understanding of the structure-reactivity relationships in heterogeneous bimetallic catalysts and thereby facilitate the upgrading of the current bimetallic catalysts. In this review, we will discuss the geometric and electronic structures of three representative types of bimetallic catalysts (bimetallic binuclear sites, bimetallic nanoclusters, and nanoparticles) and then summarize the synthesis methodologies and characterization techniques for different bimetallic entities, with emphasis on the recent progress made in the past decade. The catalytic applications of supported bimetallic binuclear sites, bimetallic nanoclusters, and nanoparticles for a series of important reactions are discussed. Finally, we will discuss the future research directions of catalysis based on supported bimetallic catalysts and, more generally, the prospective developments of heterogeneous catalysis in both fundamental research and practical applications.
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Affiliation(s)
- Lichen Liu
- Department
of Chemistry, Tsinghua University, Beijing 100084, China
| | - Avelino Corma
- Instituto
de Tecnología Química, Universitat
Politècnica de València−Consejo Superior de Investigaciones
Científicas (UPV-CSIC), Avenida de los Naranjos s/n, Valencia 46022, Spain
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48
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Ge L, Ke Y, Li X. Machine learning integrated photocatalysis: progress and challenges. Chem Commun (Camb) 2023; 59:5795-5806. [PMID: 37093605 DOI: 10.1039/d3cc00989k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Discovering efficient photocatalysts has long been the goal of photocatalysis, which has traditionally been driven by serendipitous or try-and-error strategies. Recent developments in photocatalysis integrated with machine learning techniques promise to accelerate the discovery of photocatalysts, but are also facing significant challenges. In this review, advances in machine learning integrated photocatalysis are first presented from the perspective of three main photocatalytic processes: light harvesting, charge generation and separation, and surface redox reactions. Next, progress in using machine learning to understand complex photoactivity-structure relationships and identify the factors governing activity follows. A future photocatalysis paradigm is then provided with the integration of artificial intelligence, robots and automation. Lastly, we discuss the current challenges in machine learning integrated photocatalysis. This review aims to provide a systematic overview and guidelines to the broad scientific community interested in photocatalysis and artificial intelligence for solar fuel synthesis.
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Affiliation(s)
- Luyao Ge
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Zhejiang Normal University, Jinhua 321004, China.
| | - Yuanzhen Ke
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Zhejiang Normal University, Jinhua 321004, China.
| | - Xiaobo Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Zhejiang Normal University, Jinhua 321004, China.
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49
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Wei C, Shi D, Zhou F, Yang Z, Zhang Z, Xue Z, Mu T. Analysis of the oxygen evolution activity of layered double hydroxides (LDHs) using machine learning guidance. Phys Chem Chem Phys 2023; 25:7917-7926. [PMID: 36861755 DOI: 10.1039/d2cp06052c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Layered double hydroxides (LDHs) are excellent catalysts for the oxygen evolution reaction (OER) because of their tunable properties, including chemical composition and structural morphology. An interplay between these adjustable properties and other (including external) factors might not always benefit the OER catalytic activity of LDHs. Therefore, we applied machine learning algorithms to simulate the double-layer capacitance to understand how to design/tune LDHs with targeted catalytic properties. The key factors of solving this task were identified using the Shapley Additive explanation and cerium was identified as an effective element to modify the double-layer capacitance. We also compared different modelling methods to identify the most promising one and the results revealed that binary representation is better than directly applying atom numbers as inputs for chemical compositions. Overpotentials of LDH-based materials as predicted targets were also carefully examined and evaluated, and it turns out that overpotentials can be predicted when measurement conditions about overpotentials are added as features. Finally, to confirm our findings, we reviewed additional experimental literature data and used them to test our machine algorithms to predict LDH properties. This analysis confirmed the very credible and robust generalization ability of our final model capable of achieving accurate results even with a relatively small dataset.
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Affiliation(s)
- Chenyang Wei
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
| | - Dingyi Shi
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fengyi Zhou
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
| | - Zhaohui Yang
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
| | - Zhenchuan Zhang
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
| | - Zhimin Xue
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Tiancheng Mu
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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50
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Tsuji N, Sidorov P, Zhu C, Nagata Y, Gimadiev T, Varnek A, List B. Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors. Angew Chem Int Ed Engl 2023; 62:e202218659. [PMID: 36688354 DOI: 10.1002/anie.202218659] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Catalyst optimization processes typically rely on inductive and qualitative assumptions of chemists based on screening data. While machine learning models using molecular properties or calculated 3D structures enable quantitative data evaluation, costly quantum chemical calculations are often required. In contrast, readily available binary fingerprint descriptors are time- and cost-efficient, but their predictive performance remains insufficient. Here, we describe a machine learning model based on fragment descriptors, which are fine-tuned for asymmetric catalysis and represent cyclic or polyaromatic hydrocarbons, enabling robust and efficient virtual screening. Using training data with only moderate selectivities, we designed theoretically and validated experimentally new catalysts showing higher selectivities in a challenging asymmetric tetrahydropyran synthesis.
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Affiliation(s)
- Nobuya Tsuji
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Pavel Sidorov
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Chendan Zhu
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | - Yuuya Nagata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Timur Gimadiev
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,Laboratory of Chemoinformatics, UMR 7140, CNRS, University of Strasbourg, 67081, Strasbourg, France
| | - Benjamin List
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.,Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
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