1
|
Wu Y, Su T, Du B, Hu S, Xiong J, Pan D. Kolmogorov-Arnold Network Made Learning Physics Laws Simple. J Phys Chem Lett 2024; 15:12393-12400. [PMID: 39656192 DOI: 10.1021/acs.jpclett.4c02589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
Abstract
In recent years, contrastive learning has gained widespread adoption in machine learning applications to physical systems primarily due to its distinctive cross-modal capabilities and scalability. Building on the foundation of Kolmogorov-Arnold Networks (KANs) [Liu, Z. et al. Kan: Kolmogorov-arnold networks. arXiv 2024, 2404.19756], we introduce a novel contrastive learning framework, Kolmogorov-Arnold Contrastive Crystal Property Pretraining (KCCP), which integrates the principles of CLIP and KAN to establish robust correlations between crystal structures and their physical properties. During the training process, we conducted a comparative analysis between Multilayer Perceptron (MLP) and KAN, revealing that KAN significantly outperforms MLP in both accuracy and convergence speed for this task. By extending the capabilities of contrastive learning to the realm of physical systems, KCCP offers a promising approach for constructing cross-data structural and cross-modal physical models, representing an area of considerable potential.
Collapse
Affiliation(s)
- Yue Wu
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Tianhao Su
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Bingsheng Du
- Yunnan Province Crystalline Silicon Material Technology Innovation Center, Yunnan Tongwei High Purity Crystalline Silicon Co., Ltd., Baoshan, Yunnan 678000, China
| | - Shunbo Hu
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
- Institute for the Conservation of Cultural Heritage, School of Cultural Heritage and Information Management, Shanghai University, 200444 Shanghai, China
- Ministry of Education Key Laboratory of Silicate Cultural Relics Conservation, Shanghai University, 200444 Shanghai, China
| | - Jie Xiong
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
| | - Deng Pan
- Materials Genome Institute, Shanghai University, 200444 Shanghai, China
- Ministry of Education Key Laboratory of Silicate Cultural Relics Conservation, Shanghai University, 200444 Shanghai, China
| |
Collapse
|
2
|
Uceda RG, Gijón A, Míguez‐Lago S, Cruz CM, Blanco V, Fernández‐Álvarez F, Álvarez de Cienfuegos L, Molina‐Solana M, Gómez‐Romero J, Miguel D, Mota AJ, Cuerva JM. Can Deep Learning Search for Exceptional Chiroptical Properties? The Halogenated [6]Helicene Case. Angew Chem Int Ed Engl 2024; 63:e202409998. [PMID: 39329214 PMCID: PMC11586703 DOI: 10.1002/anie.202409998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 09/11/2024] [Accepted: 09/24/2024] [Indexed: 09/28/2024]
Abstract
The relationship between chemical structure and chiroptical properties is not always clearly understood. Nowadays, efforts to develop new systems with enhanced optical properties follow the trial-error method. A large number of data would allow us to obtain more robust conclusions and guide research toward molecules with practical applications. In this sense, in this work we predict the chiroptical properties of millions of halogenated [6]helicenes in terms of the rotatory strength (R). We have used DFT calculations to randomly create derivatives including from 1 to 16 halogen atoms, that were then used as a data set to train different deep neural network models. These models allow us to i) predict the Rmax for any halogenated [6]helicene with a very low computational cost, and ii) to understand the physical reasons that favour some substitutions over others. Finally, we synthesized derivatives with higher predicted Rmax obtaining excellent correlation among the values obtained experimentally and the predicted ones.
Collapse
Affiliation(s)
- Rafael G. Uceda
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Alfonso Gijón
- Departamento de Ciencias de la Computación e Inteligencia Artificial, UGRE.T.S. de Ingenierías Informática y de TelecomunicaciónC/ Periodista Daniel Saucedo Aranda S/N18071GranadaSpain
| | - Sandra Míguez‐Lago
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Carlos M. Cruz
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Víctor Blanco
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Fátima Fernández‐Álvarez
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
- Instituto de Investigación BiosanitariaAvda. Madrid, 1518016GranadaSpain
| | - Miguel Molina‐Solana
- Departamento de Ciencias de la Computación e Inteligencia Artificial, UGRE.T.S. de Ingenierías Informática y de TelecomunicaciónC/ Periodista Daniel Saucedo Aranda S/N18071GranadaSpain
| | - Juan Gómez‐Romero
- Departamento de Ciencias de la Computación e Inteligencia Artificial, UGRE.T.S. de Ingenierías Informática y de TelecomunicaciónC/ Periodista Daniel Saucedo Aranda S/N18071GranadaSpain
| | - Delia Miguel
- Departamento de Fisicoquímica, UEQ, UGRFacultad de FarmaciaAvda. Profesor Clavera s/nC. U. Cartuja18071GranadaSpain
| | - Antonio J. Mota
- Departamento de Química Inorgánica, UEQ, UGRFacultad de CienciasC. U. Fuentenueva18071GranadaSpain
| | - Juan M. Cuerva
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a la Biomedicina y Medioambiente (UEQ)Universidad de Granada (UGR), Facultad de CienciasC. U. Fuentenueva18071GranadaSpain
| |
Collapse
|
3
|
Deng L, Ran J, Wang B, Boziki A, Tkatchenko A, Jiang J, Prezhdo OV. Strong Dependence of Point Defect Properties in Metal Halide Perovskites on Description of van der Waals Interaction. J Phys Chem Lett 2024; 15:10465-10472. [PMID: 39392450 PMCID: PMC11514007 DOI: 10.1021/acs.jpclett.4c02390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 10/01/2024] [Accepted: 10/07/2024] [Indexed: 10/12/2024]
Abstract
Weaker than ionic and covalent bonding, van der Waals (vdW) interactions can have a significant impact on structure and function of molecules and materials, including stabilities of conformers and phases, chemical reaction pathways, electro-optical response, electron-vibrational dynamics, etc. Metal halide perovskites (MHPs) are widely investigated for their excellent optoelectronic properties, stemming largely from high defect tolerance. Although MHPs are primarily ionic compounds, we demonstrate that vdW interactions contribute ∼5% to the total energy, and that static, dynamics, electronic and optical properties of point defects in MHPs depend significantly on the vdW interaction model used. Focusing on widely studied CsPbBr3 with the common Br vacancy and interstitial defects, we compare the PBE, PBE+D3, PBE+TS, PBE+TS/HI and PBE+MBD-NL models and show that vdW interactions strongly alter the global and local geometric structure, and change the fundamental bandgap, midgap state energies and electron-vibrational coupling. The vdW interaction sensitivity stems from involvement of heavy and highly polarizable chemical elements and the soft MHP structure.
Collapse
Affiliation(s)
- Linjie Deng
- School of
Chemistry and Materials Science, University
of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jingyi Ran
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Bipeng Wang
- Department
of Chemical Engineering, University of Southern
California, Los Angeles, California 90089, United States
| | - Ariadni Boziki
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Jun Jiang
- Key
Laboratory of Precision and Intelligent Chemistry, Hefei National
Research Center for Physical Sciences at the Microscale, School of
Chemistry and Materials Science, University
of Science and Technology of China, Hefei, Anhui 230026, China
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department
of Physics and Astronomy, University of
Southern California, Los Angeles, California 90089, United States
| |
Collapse
|
4
|
Yan C, Fang C, Gan J, Wang J, Zhao X, Wang X, Li J, Zhang Y, Liu H, Li X, Bai J, Liu J, Hong W. From Molecular Electronics to Molecular Intelligence. ACS NANO 2024; 18:28531-28556. [PMID: 39395180 DOI: 10.1021/acsnano.4c10389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2024]
Abstract
Molecular electronics is a field that explores the ultimate limits of electronic device dimensions by using individual molecules as operable electronic devices. Over the past five decades since the proposal of a molecular rectifier by Aviram and Ratner in 1974 ( Chem. Phys. Lett.1974,29, 277-283), researchers have developed various fabrication and characterization techniques to explore the electrical properties of molecules. With the push of electrical characterizations and data analysis methodologies, the reproducibility issues of the single-molecule conductance measurement have been chiefly resolved, and the origins of conductance variation among different devices have been investigated. Numerous prototypical molecular electronic devices with external physical and chemical stimuli have been demonstrated based on the advances of instrumental and methodological developments. These devices enable functions such as switching, logic computing, and synaptic-like computing. However, as the goal of molecular electronics, how can molecular-based intelligence be achieved through single-molecule electronic devices? At the fiftieth anniversary of molecular electronics, we try to answer this question by summarizing recent progress and providing an outlook on single-molecule electronics. First, we review the fabrication methodologies for molecular junctions, which provide the foundation of molecular electronics. Second, the preliminary efforts of molecular logic devices toward integration circuits are discussed for future potential intelligent applications. Third, some molecular devices with sensing applications through physical and chemical stimuli are introduced, demonstrating phenomena at a single-molecule scale beyond conventional macroscopic devices. From this perspective, we summarize the current challenges and outlook prospects by describing the concepts of "AI for single-molecule electronics" and "single-molecule electronics for AI".
Collapse
Affiliation(s)
- Chenshuai Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Chao Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jinyu Gan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jia Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xin Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xiaojing Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Yanxi Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Haojie Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| |
Collapse
|
5
|
Zhang T, Wang D, Liu J. Periodic Single-Metal Site Catalysts: Creating Homogeneous and Ordered Atomic-Precision Structures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2408259. [PMID: 39149786 DOI: 10.1002/adma.202408259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Heterogeneous single-metal-site catalysts (SMSCs), often referred to as single-atom catalysts (SACs), demonstrate promising catalytic activity, selectivity, and stability across a wide spectrum of reactions due to their rationally designed microenvironments encompassing coordination geometry, binding ligands, and electronic configurations. However, the inherent disorderliness of SMSCs at both atomic scale and nanoscale poses challenges in deciphering working principles and establishing the correlations between microenvironments and the catalytic performances of SMSCs. The rearrangement of randomly dispersed single metals into homogeneous and atomic-precisely structured periodic single-metal site catalysts (PSMSCs) not only simplifies the chaos in SMSCs systems but also unveils new opportunities for manipulating catalytic performance and gaining profound insights into reaction mechanisms. Moreover, the synergistic effects of adjacent single metals and the integration effects of periodic single-metal arrangement further broaden the industrial application scope of SMSCs. This perspective offers a comprehensive overview of recent advancements and outlines prospective avenues for research in the design and characterizations of PSMSCs, while also acknowledging the formidable challenges encountered and the promising prospects that lie ahead.
Collapse
Affiliation(s)
- Tianyu Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dingsheng Wang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junfeng Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| |
Collapse
|
6
|
Cho IH, Chapagain A. Self-evolving artificial intelligence framework to better decipher short-term large earthquakes. Sci Rep 2024; 14:21934. [PMID: 39304711 DOI: 10.1038/s41598-024-72667-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024] Open
Abstract
Large earthquakes (EQs) occur at surprising loci and timing, and their descriptions remain a long-standing enigma. Finding answers by traditional approaches or recently emerging machine learning (ML)-driven approaches is formidably difficult due to data scarcity, interwoven multiple physics, and absent first principles. This paper develops a novel artificial intelligence (AI) framework that can transform raw observational EQ data into ML-friendly new features via basic physics and mathematics and that can self-evolve in a direction to better reproduce short-term large EQs. An advanced reinforcement learning (RL) architecture is placed at the highest level to achieve self-evolution. It incorporates transparent ML models to reproduce magnitude and spatial location of large EQs ([Formula: see text] 6.5) weeks before of the failure. Verifications with 40-year EQs in the western U.S. and comparisons against a popular EQ forecasting method are promising. This work will add a new dimension of AI technologies to large EQ research. The developed AI framework will help establish a new database of all EQs in terms of ML-friendly new features and continue to self-evolve in a direction of better reproducing large EQs.
Collapse
Affiliation(s)
- In Ho Cho
- CCEE Department, Iowa State University, Ames, IA, 50011, USA.
| | | |
Collapse
|
7
|
Xu L, Jiang J. Synergistic Integration of Physical Embedding and Machine Learning Enabling Precise and Reliable Force Field. J Chem Theory Comput 2024. [PMID: 39264358 DOI: 10.1021/acs.jctc.4c00618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Machine-learning force fields have achieved significant strides in accurately reproducing the potential energy surface with quantum chemical accuracy. However, this approach still faces several challenges, e.g., extrapolating to uncharted chemical spaces, interpreting long-range electrostatics, and mapping complex macroscopic properties. To address these issues, we advocate for a synergistic integration of physical principles and machine learning techniques within the framework of a physically informed neural network (PINN). This approach involves incorporating physical knowledge into the parameters of the neural network, coupled with an efficient global optimizer, the Tabu-Adam algorithm, proposed in this work to augment optimization under strict physical constraint. We choose the AMOEBA+ force field as the physics-based model for embedding and then train and test it using the diethylene glycol dimethyl ether (DEGDME) data set as a case study. The results reveal a breakthrough in constructing a precise and noise-robust machine learning force field. Utilizing two training sets with hundreds of samples, our model exhibits remarkable generalization and density functional theory (DFT) accuracy in describing molecular interactions and enables a precise prediction of the macroscopic properties such as the diffusion coefficient with minimal cost. This work provides valuable insight into establishing a fundamental framework of the PINN force field.
Collapse
Affiliation(s)
- Lifeng Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Jiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| |
Collapse
|
8
|
Schwalbe S, Schulze WT, Trepte K, Lehtola S. Ensemble Generalization of the Perdew-Zunger Self-Interaction Correction: A Way Out of Multiple Minima and Symmetry Breaking. J Chem Theory Comput 2024; 20:7144-7154. [PMID: 39140402 PMCID: PMC11360130 DOI: 10.1021/acs.jctc.4c00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024]
Abstract
The Perdew-Zunger (PZ) self-interaction correction (SIC) is an established tool to correct unphysical behavior in density functional approximations. Yet, the PZ-SIC is well-known to sometimes break molecular symmetries. An example of this is the benzene molecule, for which the PZ-SIC predicts a symmetry-broken electron density and molecular geometry, since the method does not describe the two possible Kekulé structures on an even footing, leading to local minima [Lehtola et al. J. Chem. Theory Comput. 2016, 12, 3195]. The PZ-SIC is often implemented with Fermi-Löwdin orbitals (FLOs), yielding the FLO-SIC method, which likewise has issues with symmetry breaking and local minima [Trepte et al. J. Chem. Phys. 2021, 155, 224109]. In this work, we propose a generalization of the PZ-SIC─the ensemble PZ-SIC (E-PZ-SIC) method─which shares the asymptotic computational scaling of the PZ-SIC (albeit with an additional prefactor). The E-PZ-SIC is straightforwardly applicable to various molecules, merely requiring one to average the self-interaction correction over all possible Kekulé structures, in line with chemical intuition. We showcase the implementation of the E-PZ-SIC with FLOs, as the resulting E-FLO-SIC method is easy to realize on top of an existing implementation of the FLO-SIC. We show that the E-FLO-SIC indeed eliminates symmetry breaking, reproducing a symmetric electron density and molecular geometry for benzene. The ensemble approach suggested herein could also be employed within approximate or locally scaled variants of the PZ-SIC and its FLO-SIC versions.
Collapse
Affiliation(s)
- Sebastian Schwalbe
- Center
for Advanced Systems Understanding (CASUS), D-02826 Görlitz, Germany
- Helmholtz-Zentrum
Dresden-Rossendorf (HZDR), D-01328 Dresden, Germany
| | - Wanja Timm Schulze
- Institute
for Physical Chemistry, Friedrich Schiller
University, D-07743 Jena, Germany
| | - Kai Trepte
- Taiwan
Semiconductor Manufacturing Company North America, San Jose, California 95134, United States
| | - Susi Lehtola
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| |
Collapse
|
9
|
Kim EH, Gu JH, Lee JH, Kim SH, Kim J, Shin HG, Kim SH, Lee D. Boosting-Crystal Graph Convolutional Neural Network for Predicting Highly Imbalanced Data: A Case Study for Metal-Insulator Transition Materials. ACS APPLIED MATERIALS & INTERFACES 2024; 16:43734-43741. [PMID: 39121441 DOI: 10.1021/acsami.4c07851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
Applying machine-learning techniques for imbalanced data sets presents a significant challenge in materials science since the underrepresented characteristics of minority classes are often buried by the abundance of unrelated characteristics in majority of classes. Existing approaches to address this focus on balancing the counts of each class using oversampling or synthetic data generation techniques. However, these methods can lead to loss of valuable information or overfitting. Here, we introduce a deep learning framework to predict minority-class materials, specifically within the realm of metal-insulator transition (MIT) materials. The proposed approach, termed boosting-CGCNN, combines the crystal graph convolutional neural network (CGCNN) model with a gradient-boosting algorithm. The model effectively handled extreme class imbalances in MIT material data by sequentially building a deeper neural network. The comparative evaluations demonstrated the superior performance of the proposed model compared to other approaches. Our approach is a promising solution for handling imbalanced data sets in materials science.
Collapse
Affiliation(s)
- Eun Ho Kim
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Jun Hyeong Gu
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - June Ho Lee
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Seong Hun Kim
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Jaeseon Kim
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Hyo Gyeong Shin
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Shin Hyun Kim
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Donghwa Lee
- Department of Materials Science and Engineering (MSE), and Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
- Institute for Convergence Research and Education in Advanced Technology (I_CREATE), Yonsei University, Incheon 21983, South Korea
| |
Collapse
|
10
|
Li S, Xie BB, Yin BW, Liu L, Shen L, Fang WH. Construction of Highly Accurate Machine Learning Potential Energy Surfaces for Excited-State Dynamics Simulations Based on Low-Level Data Sets. J Phys Chem A 2024; 128:5516-5524. [PMID: 38954640 DOI: 10.1021/acs.jpca.4c02028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Machine learning is capable of effectively predicting the potential energies of molecules in the presence of high-quality data sets. Its application in the construction of ground- and excited-state potential energy surfaces is attractive to accelerate nonadiabatic molecular dynamics simulations of photochemical reactions. Because of the huge computational cost of excited-state electronic structure calculations, the construction of a high-quality data set becomes a bottleneck. In the present work, we first built two data sets. One was obtained from surface hopping dynamics simulations at the semiempirical OM2/MRCI level. Another was extracted from the dynamics trajectories at the CASSCF level, which was reported previously. The ground- and excited-state potential energy surfaces of ethylene-bridged azobenzene at the CASSCF computational level were constructed based on the former low-level data set. Although non-neural network machine learning methods can achieve good or modest performance during the training process, only neural network models provide reliable predictions on the latter external test data set. The BPNN and SchNet combined with the Δ-ML scheme and the force term in the loss functions are recommended for dynamics simulations. Then, we performed excited-state dynamics simulations of the photoisomerization of ethylene-bridged azobenzene on machine learning potential energy surfaces. Compared with the lifetimes of the first excited state (S1) estimated at different computational levels, our results on the E isomer are in good agreement with the high-level estimation. However, the overestimation of the Z isomer is unimproved. It suggests that smaller errors during the training process do not necessarily translate to more accurate predictions on high-level potential energies or better performance on nonadiabatic dynamics simulations, at least in the present case.
Collapse
Affiliation(s)
- Shuai Li
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou 311231, Zhejiang, P. R. China
| | - Bo-Wen Yin
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, Hangzhou 311231, Zhejiang, P. R. China
| | - Lihong Liu
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Yantai-Jingshi Institute of Material Genome Engineering, Yantai 265505, Shandong, P. R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing, Yantai 264006, Shandong, P. R. China
| |
Collapse
|
11
|
Gould T, Chan B, Dale SG, Vuckovic S. Identifying and embedding transferability in data-driven representations of chemical space. Chem Sci 2024; 15:11122-11133. [PMID: 39027290 PMCID: PMC11253166 DOI: 10.1039/d4sc02358g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/02/2024] [Indexed: 07/20/2024] Open
Abstract
Transferability, especially in the context of model generalization, is a paradigm of all scientific disciplines. However, the rapid advancement of machine learned model development threatens this paradigm, as it can be difficult to understand how transferability is embedded (or missed) in complex models developed using large training data sets. Two related open problems are how to identify, without relying on human intuition, what makes training data transferable; and how to embed transferability into training data. To solve both problems for ab initio chemical modelling, an indispensable tool in everyday chemistry research, we introduce a transferability assessment tool (TAT) and demonstrate it on a controllable data-driven model for developing density functional approximations (DFAs). We reveal that human intuition in the curation of training data introduces chemical biases that can hamper the transferability of data-driven DFAs. We use our TAT to motivate three transferability principles; one of which introduces the key concept of transferable diversity. Finally, we propose data curation strategies for general-purpose machine learning models in chemistry that identify and embed the transferability principles.
Collapse
Affiliation(s)
- Tim Gould
- Queensland Micro- and Nanotechnology Centre, Griffith University Nathan Qld 4111 Australia
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University Bunkyo 1-14 Nagasaki 852-8521 Japan
| | - Stephen G Dale
- Queensland Micro- and Nanotechnology Centre, Griffith University Nathan Qld 4111 Australia
- Institute of Functional Intelligent Materials, National University of Singapore 4 Science Drive 2 Singapore 117544
| | - Stefan Vuckovic
- Department of Chemistry, University of Fribourg Fribourg Switzerland
| |
Collapse
|
12
|
Qin H, Zhang H, Wu K, Wang X, Fan W. A systematic theoretical study of CO 2 hydrogenation towards methanol on Cu-based bimetallic catalysts: role of the CHO&CH 3OH descriptor in thermodynamic analysis. Phys Chem Chem Phys 2024; 26:19088-19104. [PMID: 38842113 DOI: 10.1039/d4cp01009d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The application of density functional theory (DFT) has enriched our understanding of methanol synthesis through CO2 hydrogenation on Cu-based catalysts. However, variations in catalytic performance under different metal doping conditions have hindered the development of universal catalytic principles. To address these challenges, we systematically investigated the scaling relationships of adsorption energy among different reaction intermediates on pure Cu, Au-Cu, Ni-Cu, Pt-Cu, Pd-Cu and Zn-Cu models. Additionally, by summing the respective adsorption energies of two separate species, we have developed a dual intermediate descriptor of CHO&CH3OH, capable of achieving computational accuracy on par with DFT results using the multiple linear regression method, all the while enabling the rapid prediction of thermodynamic properties at various stages of methanol synthesis. This method facilitates a better understanding of the coupling mechanisms between energy and linear expressions on copper-based substrates, and the universal linear criterion can be applied to other catalytic systems, with the aim of pursuing potential catalysts having both high efficiency and low cost.
Collapse
Affiliation(s)
- Huang Qin
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Hai Zhang
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Kunmin Wu
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xingzi Wang
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Weidong Fan
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
13
|
Medrano Sandonas L, Van Rompaey D, Fallani A, Hilfiker M, Hahn D, Perez-Benito L, Verhoeven J, Tresadern G, Kurt Wegner J, Ceulemans H, Tkatchenko A. Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules. Sci Data 2024; 11:742. [PMID: 38972891 PMCID: PMC11228031 DOI: 10.1038/s41597-024-03521-8] [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: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.
Collapse
Affiliation(s)
- Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany.
| | - Dries Van Rompaey
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Alessio Fallani
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Mathias Hilfiker
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - David Hahn
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jonas Verhoeven
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Joerg Kurt Wegner
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
- Drug Discovery Data Sciences (D3S), Johnson & Johnson Innovative Medicine, 301 Binney Street, MA 02142, Cambridge, USA
| | - Hugo Ceulemans
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
| |
Collapse
|
14
|
Kalikadien AV, Mirza A, Hossaini AN, Sreenithya A, Pidko EA. Paving the road towards automated homogeneous catalyst design. Chempluschem 2024; 89:e202300702. [PMID: 38279609 DOI: 10.1002/cplu.202300702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Indexed: 01/28/2024]
Abstract
In the past decade, computational tools have become integral to catalyst design. They continue to offer significant support to experimental organic synthesis and catalysis researchers aiming for optimal reaction outcomes. More recently, data-driven approaches utilizing machine learning have garnered considerable attention for their expansive capabilities. This Perspective provides an overview of diverse initiatives in the realm of computational catalyst design and introduces our automated tools tailored for high-throughput in silico exploration of the chemical space. While valuable insights are gained through methods for high-throughput in silico exploration and analysis of chemical space, their degree of automation and modularity are key. We argue that the integration of data-driven, automated and modular workflows is key to enhancing homogeneous catalyst design on an unprecedented scale, contributing to the advancement of catalysis research.
Collapse
Affiliation(s)
- Adarsh V Kalikadien
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Adrian Mirza
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Aydin Najl Hossaini
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Avadakkam Sreenithya
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| |
Collapse
|
15
|
Fan L, Shen Y, Lou D, Gu N. Progress in the Computer-Aided Analysis in Multiple Aspects of Nanocatalysis Research. Adv Healthc Mater 2024:e2401576. [PMID: 38936401 DOI: 10.1002/adhm.202401576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/08/2024] [Indexed: 06/29/2024]
Abstract
Making the utmost of the differences and advantages of multiple disciplines, interdisciplinary integration breaks the science boundaries and accelerates the progress in mutual quests. As an organic connection of material science, enzymology, and biomedicine, nanozyme-related research is further supported by computer technology, which injects in new vitality, and contributes to in-depth understanding, unprecedented insights, and broadened application possibilities. Utilizing computer-aided first-principles method, high-speed and high-throughput mathematic, physic, and chemic models are introduced to perform atomic-level kinetic analysis for nanocatalytic reaction process, and theoretically illustrate the underlying nanozymetic mechanism and structure-function relationship. On this basis, nanozymes with desirable properties can be designed and demand-oriented synthesized without repeated trial-and-error experiments. Besides that, computational analysis and device also play an indispensable role in nanozyme-based detecting methods to realize automatic readouts with improved accuracy and reproducibility. Here, this work focuses on the crossing of nanocatalysis research and computational technology, to inspire the research in computer-aided analysis in nanozyme field to a greater extent.
Collapse
Affiliation(s)
- Lin Fan
- Medical School of Nanjing University, Nanjing, 210093, P. R. China
- School of Integrated Circuit Science and Engineering (Industry-Education Integration School), Nanjing University of Posts and Telecommunications, Nanjing, 210023, P. R. China
| | - Yilei Shen
- School of Integrated Circuit Science and Engineering (Industry-Education Integration School), Nanjing University of Posts and Telecommunications, Nanjing, 210023, P. R. China
| | - Doudou Lou
- Nanjing Institute for Food and Drug Control, Nanjing, 211198, P. R. China
| | - Ning Gu
- Medical School of Nanjing University, Nanjing, 210093, P. R. China
| |
Collapse
|
16
|
Yan G, Zhang X. Interlayer Interactions and Macroscopic Property Calculations of Squaric-Acid-Linked Zwitterionic Covalent Organic Frameworks: Structures, Photocatalytic Carrier Transport, and a DFT Study. Molecules 2024; 29:2739. [PMID: 38930807 PMCID: PMC11207002 DOI: 10.3390/molecules29122739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Squaric-acid-linked zwitterionic covalent organic frameworks (Z-COFs), assembled through interlayer interactions, are emerging as potential materials in the field of photocatalysis. However, the study of their interlayer interactions has been largely overlooked. To address this, this work systematically calculated interlayer interactions via density functional theory (DFT) and analyzed the differences in interlayer interactions of different structures of Z-COFs through interlayer slippage, planarity, and an independent gradient model based on the Hirshfeld partition (IGMH). Furthermore, it revealed the relationship between the interactions and the macroscopic photocatalytic carrier transport performance of the material. The results indicated that both preventing interlayer slippage and enhancing planarity can enhance the interlayer interactions of Z-COFs, thereby improving their macroscopic carrier transport performance in photocatalysis.
Collapse
Affiliation(s)
| | - Xiaojie Zhang
- Hebei Key Laboratory of Functional Polymers, Department of Polymer Materials and Engineering, Hebei University of Technology, Tianjin 300401, China;
| |
Collapse
|
17
|
Chen N, Yu J, Zhe L, Wang F, Li X, Wong KC. TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation. Brief Bioinform 2024; 25:bbae308. [PMID: 38920345 PMCID: PMC11200197 DOI: 10.1093/bib/bbae308] [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: 04/08/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Bioactive peptide therapeutics has been a long-standing research topic. Notably, the antimicrobial peptides (AMPs) have been extensively studied for its therapeutic potential. Meanwhile, the demand for annotating other therapeutic peptides, such as antiviral peptides (AVPs) and anticancer peptides (ACPs), also witnessed an increase in recent years. However, we conceive that the structure of peptide chains and the intrinsic information between the amino acids is not fully investigated among the existing protocols. Therefore, we develop a new graph deep learning model, namely TP-LMMSG, which offers lightweight and easy-to-deploy advantages while improving the annotation performance in a generalizable manner. The results indicate that our model can accurately predict the properties of different peptides. The model surpasses the other state-of-the-art models on AMP, AVP and ACP prediction across multiple experimental validated datasets. Moreover, TP-LMMSG also addresses the challenges of time-consuming pre-processing in graph neural network frameworks. With its flexibility in integrating heterogeneous peptide features, our model can provide substantial impacts on the screening and discovery of therapeutic peptides. The source code is available at https://github.com/NanjunChen37/TP_LMMSG.
Collapse
Affiliation(s)
- Nanjun Chen
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Jixiang Yu
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Liu Zhe
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Chang Chun, Ji Lin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guang Dong, China
| |
Collapse
|
18
|
Erlebach A, Šípka M, Saha I, Nachtigall P, Heard CJ, Grajciar L. A reactive neural network framework for water-loaded acidic zeolites. Nat Commun 2024; 15:4215. [PMID: 38760371 PMCID: PMC11101627 DOI: 10.1038/s41467-024-48609-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
Under operating conditions, the dynamics of water and ions confined within protonic aluminosilicate zeolite micropores are responsible for many of their properties, including hydrothermal stability, acidity and catalytic activity. However, due to high computational cost, operando studies of acidic zeolites are currently rare and limited to specific cases and simplified models. In this work, we have developed a reactive neural network potential (NNP) attempting to cover the entire class of acidic zeolites, including the full range of experimentally relevant water concentrations and Si/Al ratios. This NNP has the potential to dramatically improve sampling, retaining the (meta)GGA DFT level accuracy, with the capacity for discovery of new chemistry, such as collective defect formation mechanisms at the zeolite surface. Furthermore, we exemplify how the NNP can be used as a basis for further extensions/improvements which include data-efficient adoption of higher-level (hybrid) references via Δ-learning and the acceleration of rare event sampling via automatic construction of collective variables. These developments represent a significant step towards accurate simulations of realistic catalysts under operando conditions.
Collapse
Affiliation(s)
- Andreas Erlebach
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic.
| | - Martin Šípka
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
- Mathematical Institute, Faculty of Mathematics and Physics, Charles University, Sokolovská 83, 186 75, Prague, Czech Republic
| | - Indranil Saha
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Petr Nachtigall
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Christopher J Heard
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Lukáš Grajciar
- Department of Physical and Macromolecular Chemistry, Faculty of Sciences, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic.
| |
Collapse
|
19
|
Strieth-Kalthoff F, Hao H, Rathore V, Derasp J, Gaudin T, Angello NH, Seifrid M, Trushina E, Guy M, Liu J, Tang X, Mamada M, Wang W, Tsagaantsooj T, Lavigne C, Pollice R, Wu TC, Hotta K, Bodo L, Li S, Haddadnia M, Wołos A, Roszak R, Ser CT, Bozal-Ginesta C, Hickman RJ, Vestfrid J, Aguilar-Granda A, Klimareva EL, Sigerson RC, Hou W, Gahler D, Lach S, Warzybok A, Borodin O, Rohrbach S, Sanchez-Lengeling B, Adachi C, Grzybowski BA, Cronin L, Hein JE, Burke MD, Aspuru-Guzik A. Delocalized, asynchronous, closed-loop discovery of organic laser emitters. Science 2024; 384:eadk9227. [PMID: 38753786 DOI: 10.1126/science.adk9227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Contemporary materials discovery requires intricate sequences of synthesis, formulation, and characterization that often span multiple locations with specialized expertise or instrumentation. To accelerate these workflows, we present a cloud-based strategy that enabled delocalized and asynchronous design-make-test-analyze cycles. We showcased this approach through the exploration of molecular gain materials for organic solid-state lasers as a frontier application in molecular optoelectronics. Distributed robotic synthesis and in-line property characterization, orchestrated by a cloud-based artificial intelligence experiment planner, resulted in the discovery of 21 new state-of-the-art materials. Gram-scale synthesis ultimately allowed for the verification of best-in-class stimulated emission in a thin-film device. Demonstrating the asynchronous integration of five laboratories across the globe, this workflow provides a blueprint for delocalizing-and democratizing-scientific discovery.
Collapse
Affiliation(s)
- Felix Strieth-Kalthoff
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Han Hao
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
| | - Vandana Rathore
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joshua Derasp
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Théophile Gaudin
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Nicholas H Angello
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Martin Seifrid
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | | | - Mason Guy
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Junliang Liu
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Xun Tang
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Masashi Mamada
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Wesley Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tuul Tsagaantsooj
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Cyrille Lavigne
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Robert Pollice
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Tony C Wu
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Kazuhiro Hotta
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Mitsubishi Chemical Corporation Science & Innovation Center, Kanagawa, Japan
| | - Leticia Bodo
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Shangyu Li
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mohammad Haddadnia
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Agnieszka Wołos
- Allchemy Inc., Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Rafał Roszak
- Allchemy Inc., Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Cher Tian Ser
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Carlota Bozal-Ginesta
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Catalonia Institute for Energy Research, Barcelona, Spain
| | - Riley J Hickman
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jenya Vestfrid
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Andrés Aguilar-Granda
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | | | - Wenduan Hou
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Daniel Gahler
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Slawomir Lach
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Adrian Warzybok
- School of Chemistry, University of Glasgow, Glasgow, UK
- Department of Chemical Physics, Jagiellonian University, Krakow, Poland
| | - Oleg Borodin
- School of Chemistry, University of Glasgow, Glasgow, UK
| | | | | | - Chihaya Adachi
- Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, Fukuoka, Japan
| | - Bartosz A Grzybowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Center for Algorithmic and Robotized Synthesis, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Chemistry, Ulsan Institute of Science and Technology, Ulsan, Republic of Korea
| | - Leroy Cronin
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- School of Chemistry, University of Glasgow, Glasgow, UK
| | - Jason E Hein
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of Bergen, Bergen, Norway
| | - Martin D Burke
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab Institute, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Acceleration Consortium, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Materials Science and Engineering, University of Toronto, Toronto, ON, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| |
Collapse
|
20
|
Gibbas B, Kaledin M, Kaledin AL. Quantum Monte Carlo Simulations of the Vibrational Wavefunction of the Aromatic Cyclo[10]carbon Using a Full Dimensional Permutationally Invariant Potential Energy Surface. J Phys Chem Lett 2024; 15:5070-5075. [PMID: 38701515 PMCID: PMC11103689 DOI: 10.1021/acs.jpclett.4c00893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/05/2024]
Abstract
New experimental measurements [Sun et al., Nature 2023, 623, 972] of the cyclic C10 reveal a cumulenic pentagon-like D5h structure at ∼5 K. However, the long-standing presumption that a large zero-point vibrational energy combined with an extremely flat D5h ↔ D10h ↔ D5h isomerization pathway washes out the pentagonal D5h structure and yields a symmetric D10h decagon remains at odds with the experiment. We resolve this issue with our fitting approach based on a bond-order charge-density matrix expressed in permutationally invariant polynomials. We train the model on τHCTH/cc-pVQZ data morphed to reproduce a relativistic all-electron CCSDT(Q)/CBS D5h-D10h potential energy barrier (benchmarked previously by others). Large scale diffusion Monte Carlo simulations in full dimensionality show that the vibrational ground state of C10 has compositional character of more than 96% D5h, fully reflecting the experimental imaging data. Quantum mechanical variational calculations in 1-D further suggest persistence of the D5h symmetry structure at higher temperatures.
Collapse
Affiliation(s)
- Benjamin
D. Gibbas
- Department
of Chemistry & Biochemistry, Kennesaw
State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Martina Kaledin
- Department
of Chemistry & Biochemistry, Kennesaw
State University, 370 Paulding Ave NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Alexey L. Kaledin
- Cherry
L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| |
Collapse
|
21
|
Beck A, Newton MA, van de Water LGA, van Bokhoven JA. The Enigma of Methanol Synthesis by Cu/ZnO/Al 2O 3-Based Catalysts. Chem Rev 2024; 124:4543-4678. [PMID: 38564235 DOI: 10.1021/acs.chemrev.3c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The activity and durability of the Cu/ZnO/Al2O3 (CZA) catalyst formulation for methanol synthesis from CO/CO2/H2 feeds far exceed the sum of its individual components. As such, this ternary catalytic system is a prime example of synergy in catalysis, one that has been employed for the large scale commercial production of methanol since its inception in the mid 1960s with precious little alteration to its original formulation. Methanol is a key building block of the chemical industry. It is also an attractive energy storage molecule, which can also be produced from CO2 and H2 alone, making efficient use of sequestered CO2. As such, this somewhat unusual catalyst formulation has an enormous role to play in the modern chemical industry and the world of global economics, to which the correspondingly voluminous and ongoing research, which began in the 1920s, attests. Yet, despite this commercial success, and while research aimed at understanding how this formulation functions has continued throughout the decades, a comprehensive and universally agreed upon understanding of how this material achieves what it does has yet to be realized. After nigh on a century of research into CZA catalysts, the purpose of this Review is to appraise what has been achieved to date, and to show how, and how far, the field has evolved. To do so, this Review evaluates the research regarding this catalyst formulation in a chronological order and critically assesses the validity and novelty of various hypotheses and claims that have been made over the years. Ultimately, the Review attempts to derive a holistic summary of what the current body of literature tells us about the fundamental sources of the synergies at work within the CZA catalyst and, from this, suggest ways in which the field may yet be further advanced.
Collapse
Affiliation(s)
- Arik Beck
- Institute for Chemistry and Bioengineering, ETH Zurich, 8093 Zürich, Switzerland
- Institute for Chemical Technology and Polymer Chemistry (ITCP), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Mark A Newton
- Institute for Chemistry and Bioengineering, ETH Zurich, 8093 Zürich, Switzerland
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, 182 23 Prague 8, Czech Republic
| | | | - Jeroen A van Bokhoven
- Institute for Chemistry and Bioengineering, ETH Zurich, 8093 Zürich, Switzerland
- Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| |
Collapse
|
22
|
Zhao H, Gould T, Vuckovic S. Deep Mind 21 functional does not extrapolate to transition metal chemistry. Phys Chem Chem Phys 2024; 26:12289-12298. [PMID: 38597718 DOI: 10.1039/d4cp00878b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The development of density functional approximations stands at a crossroads: while machine-learned functionals show potential to surpass their human-designed counterparts, their extrapolation to unseen chemistry lags behind. Here we assess how well the recent Deep Mind 21 (DM21) machine-learned functional [Science, 2021, 374, 1385-1389], trained on main-group chemistry, extrapolates to transition metal chemistry (TMC). We show that DM21 demonstrates comparable or occasionally superior accuracy to B3LYP for TMC, but consistently struggles with achieving self-consistent field convergence for TMC molecules. We also compare main-group and TMC machine-learning DM21 features to shed light on DM21's challenges in TMC. We finally propose strategies to overcome limitations in the extrapolative capabilities of machine-learned functionals in TMC.
Collapse
Affiliation(s)
- Heng Zhao
- Department of Chemistry, University of Fribourg, Fribourg, Switzerland.
| | - Tim Gould
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111, Australia
| | - Stefan Vuckovic
- Department of Chemistry, University of Fribourg, Fribourg, Switzerland.
| |
Collapse
|
23
|
Zhao D, Zhao Y, Xu E, Liu W, Ayers PW, Liu S, Chen D. Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates. J Chem Theory Comput 2024; 20:2655-2665. [PMID: 38441881 DOI: 10.1021/acs.jctc.3c01415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Simultaneous prediction of the molecular response properties, such as polarizability and the NMR shielding constant, at a low computational cost is an unresolved issue. We propose to combine a linear-scaling generalized energy-based fragmentation (GEBF) method and deep learning (DL) with both molecular and atomic information-theoretic approach (ITA) quantities as effective descriptors. In GEBF, the total molecular polarizability can be assembled as a linear combination of the corresponding quantities calculated from a set of small embedded subsystems in GEBF. In the new GEBF-DL(ITA) protocol, one can predict subsystem polarizabilities based on the corresponding molecular wave function (thus electron density and ITA quantities) and DL model rather than calculate them from the computationally intensive coupled-perturbed Hartree-Fock or Kohn-Sham equations and finally obtain the total molecular polarizability via a linear combination equation. As a proof-of-concept application, we predict the molecular polarizabilities of large proteins and protein aggregates. GEBF-DL(ITA) is shown to be as accurate enough as GEBF, with mean absolute percentage error <1%. For the largest protein aggregate (>4000 atoms), GEBF-DL(ITA) gains a speedup ratio of 3 compared with GEBF. It is anticipated that when more advanced electronic structure methods are used, this advantage will be more appealing. Moreover, one can also predict the NMR chemical shieldings of proteins with reasonably good accuracy. Overall, the cost-efficient GEBF-DL(ITA) protocol should be a robust theoretical tool for simultaneously predicting polarizabilities and NMR shieldings of large systems.
Collapse
Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Yilin Zhao
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Enhua Xu
- Graduate School of System Informatics, Kobe University, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Wenqi Liu
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, P. R. China
| |
Collapse
|
24
|
Sammüller F, Hermann S, Schmidt M. Why neural functionals suit statistical mechanics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:243002. [PMID: 38467072 DOI: 10.1088/1361-648x/ad326f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
We describe recent progress in the statistical mechanical description of many-body systems via machine learning combined with concepts from density functional theory and many-body simulations. We argue that the neural functional theory by Sammülleret al(2023Proc. Natl Acad. Sci.120e2312484120) gives a functional representation of direct correlations and of thermodynamics that allows for thorough quality control and consistency checking of the involved methods of artificial intelligence. Addressing a prototypical system we here present a pedagogical application to hard core particle in one spatial dimension, where Percus' exact solution for the free energy functional provides an unambiguous reference. A corresponding standalone numerical tutorial that demonstrates the neural functional concepts together with the underlying fundamentals of Monte Carlo simulations, classical density functional theory, machine learning, and differential programming is available online athttps://github.com/sfalmo/NeuralDFT-Tutorial.
Collapse
Affiliation(s)
- Florian Sammüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Sophie Hermann
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| |
Collapse
|
25
|
Widdifield CM, Zakeri F. Can simple 'molecular' corrections outperform projector augmented-wave density functional theory in the prediction of 35 Cl electric field gradient tensor parameters for chlorine-containing crystalline systems? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:156-168. [PMID: 37950622 DOI: 10.1002/mrc.5408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/13/2023]
Abstract
Many-body expansion (MBE) fragment approaches have been applied to accurately compute nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent examples demonstrate that electric field gradient (EFG) tensor parameters can be accurately calculated for 14 N and 17 O. A key additional development is the simple molecular correction (SMC) approach, which uses two one-body fragment (i.e., isolated molecule) calculations to adjust NMR parameter values established using 'benchmark' projector augmented-wave (PAW) density functional theory (DFT) values. Here, we apply a SMC using the hybrid PBE0 exchange-correlation (XC) functional to see if this can improve the accuracy of calculated 35 Cl EFG tensor parameters. We selected eight organic and two inorganic crystal structures and considered 15 chlorine sites. We find that this SMC improves the accuracy of computed values for both the 35 Cl quadrupolar coupling constant (CQ ) and the asymmetry parameter ( η Q ) by approximately 30% compared with benchmark PAW DFT values. We also assessed a SMC that offers local improvements not only in terms of the quality of the XC functional but simultaneously in the quality of the description of relativistic effects via the inclusion of spin-orbit effects. As the inorganic systems considered contain heavy atoms bonded to the chlorine atoms, we find further improvements in the accuracy of calculated 35 Cl EFG tensor parameters when both a hybrid functional and spin-orbit effects are included in the SMC. On the contrary, for chlorine-containing organics, the inclusion of spin-orbit relativistic effects using a SMC does not improve the accuracy of computed 35 Cl EFG tensor parameters.
Collapse
Affiliation(s)
- Cory M Widdifield
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Fatemeh Zakeri
- Department of Chemistry and Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| |
Collapse
|
26
|
Ha GS, Rashid MAM, Oh DH, Ha JM, Yoo CJ, Jeon BH, Koo B, Jeong K, Kim KH. Integrating experimental and computational approaches for deep eutectic solvent-catalyzed glycolysis of post-consumer polyethylene terephthalate. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 174:411-419. [PMID: 38103351 DOI: 10.1016/j.wasman.2023.12.028] [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: 06/02/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
To achieve a sustainable and circular economy, developing effective plastic recycling methods is essential. Despite advances in the chemical recycling of plastic waste, modern industries require highly efficient and sustainable solutions to address environmental problems. In this study, we propose an efficient glycolysis strategy for post-consumer polyethylene terephthalate (PET) using deep eutectic solvents (DESs) to produce bis(2-hydroxyethyl) terephthalate (BHET) with high selectivity. Choline chloride (ChCl)- and urea-based DESs were synthesized using various metal salts and were tested for the glycolysis of PET waste; ChCl-Zn(OAc)2 exhibited the best performance. The DES-containing solvent system afforded a complete PET conversion, producing BHET at a high yield (91.6%) under optimal reaction conditions. The degradation mechanism of PET and its interaction with DESs were systematically investigated using density functional theory-based calculations. Furthermore, an intuitive machine learning model was developed to predict the PET conversion and BHET selectivity for different DES compositions. Our findings demonstrate that the DES-catalyzed glycolysis of post-consumer PET could enable the development of a sustainable chemical recycling process, providing insights to identify the new design of DESs for plastic decomposition.
Collapse
Affiliation(s)
- Geon-Soo Ha
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Md Al Mamunur Rashid
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Da Hae Oh
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jeong-Myeong Ha
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Chun-Jae Yoo
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Bonwook Koo
- School of Forestry Sciences and Landscape Architecture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Keunhong Jeong
- Department of Chemistry, Korea Military Academy, Seoul 01805, Republic of Korea.
| | - Kwang Ho Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea; KIST-SKKU Carbon-Neutral Research Center, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| |
Collapse
|
27
|
Dawson JA. Going against the Grain: Atomistic Modeling of Grain Boundaries in Solid Electrolytes for Solid-State Batteries. ACS MATERIALS AU 2024; 4:1-13. [PMID: 38221922 PMCID: PMC10786132 DOI: 10.1021/acsmaterialsau.3c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 01/16/2024]
Abstract
Atomistic modeling techniques, including density functional theory and molecular dynamics, play a critical role in the understanding, design, discovery, and optimization of bulk solid electrolyte materials for solid-state batteries. In contrast, despite the fact that the atomistic simulation of microstructural inhomogeneities, such as grain boundaries, can reveal essential information regarding the performance of solid electrolytes, such simulations have so far only been limited to a relatively small selection of materials. In this Perspective, the fundamental properties of grain boundaries in solid electrolytes that can be determined and manipulated through state-of-the-art atomistic modeling are illustrated through recent studies in the literature. The insights and examples presented here will inspire future computational studies of grain boundaries with the aim of overcoming their often detrimental impact on ion transport and dendrite growth inhibition in solid electrolytes.
Collapse
Affiliation(s)
- James A. Dawson
- Chemistry
− School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- Centre
for Energy, Newcastle University, Newcastle upon Tyne NE1
7RU, United Kingdom
- The
Faraday Institution, Didcot OX11 0RA, United
Kingdom
| |
Collapse
|
28
|
Karandashev K, Weinreich J, Heinen S, Arismendi Arrieta DJ, von Rudorff GF, Hermansson K, von Lilienfeld OA. Evolutionary Monte Carlo of QM Properties in Chemical Space: Electrolyte Design. J Chem Theory Comput 2023; 19:8861-8870. [PMID: 38009856 PMCID: PMC10720348 DOI: 10.1021/acs.jctc.3c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Optimizing a target function over the space of organic molecules is an important problem appearing in many fields of applied science but also a very difficult one due to the vast number of possible molecular systems. We propose an evolutionary Monte Carlo algorithm for solving such problems which is capable of straightforwardly tuning both exploration and exploitation characteristics of an optimization procedure while retaining favorable properties of genetic algorithms. The method, dubbed MOSAiCS (Metropolis Optimization by Sampling Adaptively in Chemical Space), is tested on problems related to optimizing components of battery electrolytes, namely, minimizing solvation energy in water or maximizing dipole moment while enforcing a lower bound on the HOMO-LUMO gap; optimization was carried out over sets of molecular graphs inspired by QM9 and Electrolyte Genome Project (EGP) data sets. MOSAiCS reliably generated molecular candidates with good target quantity values, which were in most cases better than the ones found in QM9 or EGP. While the optimization results presented in this work sometimes required up to 106 QM calculations and were thus feasible only thanks to computationally efficient ab initio approximations of properties of interest, we discuss possible strategies for accelerating MOSAiCS using machine learning approaches.
Collapse
Affiliation(s)
| | - Jan Weinreich
- Faculty
of Physics, University of Vienna, Kolingasse 14-16, AT-1090 Wien, Austria
| | - Stefan Heinen
- Vector
Institute for Artificial Intelligence, Toronto, M5S 1M1 Ontario, Canada
| | | | - Guido Falk von Rudorff
- Department
of Chemistry, University Kassel, Heinrich-Plett-Str.40, 34132 Kassel, Germany
- Center
for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Kersti Hermansson
- Department
of Chemistry-Ångström Laboratory, Uppsala University, Box 538, SE-75121 Uppsala, Sweden
| | - O. Anatole von Lilienfeld
- Vector
Institute for Artificial Intelligence, Toronto, M5S 1M1 Ontario, Canada
- Departments
of Chemistry, Materials Science and Engineering, and Physics, University of Toronto, St. George
Campus, Toronto, M5S 1A1 Ontario, Canada
- Machine
Learning Group, Technische Universität
Berlin and Institute for the Foundations of Learning and Data, 10587 Berlin, Germany
| |
Collapse
|
29
|
Hostaš J, Pérez-Becerra KO, Calaminici P, Barrios-Herrera L, Lourenço MP, Tchagang A, Salahub DR, Köster AM. How important is the amount of exact exchange for spin-state energy ordering in DFT? Case study of molybdenum carbide cluster, Mo4C2. J Chem Phys 2023; 159:184301. [PMID: 37947508 DOI: 10.1063/5.0169409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree-Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated.
Collapse
Affiliation(s)
- Jiří Hostaš
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Kevin O Pérez-Becerra
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Patrizia Calaminici
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Lizandra Barrios-Herrera
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física - Centro de Ciências Exatas, Naturais e da Saúde - CCENS - Universidade Federal do Espírito Santo, 29500-000 Alegre, Espírito Santo, Brazil
| | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, 1200 Montréal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Andreas M Köster
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| |
Collapse
|