1
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Boström HLB, Emmerling S, Heck F, Koschnick C, Jones AJ, Cliffe MJ, Al Natour R, Bonneau M, Guillerm V, Shekhah O, Eddaoudi M, Lopez-Cabrelles J, Furukawa S, Romero-Angel M, Martí-Gastaldo C, Yan M, Morris AJ, Romero-Muñiz I, Xiong Y, Platero-Prats AE, Roth J, Queen WL, Mertin KS, Schier DE, Champness NR, Yeung HHM, Lotsch BV. How Reproducible is the Synthesis of Zr-Porphyrin Metal-Organic Frameworks? An Interlaboratory Study. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304832. [PMID: 37669645 DOI: 10.1002/adma.202304832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/17/2023] [Indexed: 09/07/2023]
Abstract
Metal-organic frameworks (MOFs) are a rapidly growing class of materials that offer great promise in various applications. However, the synthesis remains challenging: for example, a range of crystal structures can often be accessed from the same building blocks, which complicates the phase selectivity. Likewise, the high sensitivity to slight changes in synthesis conditions may cause reproducibility issues. This is crucial, as it hampers the research and commercialization of affected MOFs. Here, it presents the first-ever interlaboratory study of the synthetic reproducibility of two Zr-porphyrin MOFs, PCN-222 and PCN-224, to investigate the scope of this problem. For PCN-222, only one sample out of ten was phase pure and of the correct symmetry, while for PCN-224, three are phase pure, although none of these show the spatial linker order characteristic of PCN-224. Instead, these samples resemble dPCN-224 (disordered PCN-224), which has recently been reported. The variability in thermal behavior, defect content, and surface area of the synthesised samples are also studied. The results have important ramifications for field of metal-organic frameworks and their crystallization, by highlighting the synthetic challenges associated with a multi-variable synthesis space and flat energy landscapes characteristic of MOFs.
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Affiliation(s)
- Hanna L B Boström
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany
- Present address: Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Sebastian Emmerling
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - Fabian Heck
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - Charlotte Koschnick
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany
| | - Andrew J Jones
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Matthew J Cliffe
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Rawan Al Natour
- King Abdullah University of Science and Technology (KAUST), Division of Physical Sciences and Engineering, Advanced Membranes & Porous Materials Center (AMPM), Functional Materials Design, Discovery & Development Research Group (FMD3), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mickaële Bonneau
- King Abdullah University of Science and Technology (KAUST), Division of Physical Sciences and Engineering, Advanced Membranes & Porous Materials Center (AMPM), Functional Materials Design, Discovery & Development Research Group (FMD3), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Vincent Guillerm
- King Abdullah University of Science and Technology (KAUST), Division of Physical Sciences and Engineering, Advanced Membranes & Porous Materials Center (AMPM), Functional Materials Design, Discovery & Development Research Group (FMD3), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Osama Shekhah
- King Abdullah University of Science and Technology (KAUST), Division of Physical Sciences and Engineering, Advanced Membranes & Porous Materials Center (AMPM), Functional Materials Design, Discovery & Development Research Group (FMD3), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mohamed Eddaoudi
- King Abdullah University of Science and Technology (KAUST), Division of Physical Sciences and Engineering, Advanced Membranes & Porous Materials Center (AMPM), Functional Materials Design, Discovery & Development Research Group (FMD3), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Javier Lopez-Cabrelles
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, 606-8501, Japan
| | - Shuhei Furukawa
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, 606-8501, Japan
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - María Romero-Angel
- Instituto de Ciencia Molecular (ICMol), Universitat de València, Catedrático José Beltrán-2, Paterna, 46980, Spain
| | - Carlos Martí-Gastaldo
- Instituto de Ciencia Molecular (ICMol), Universitat de València, Catedrático José Beltrán-2, Paterna, 46980, Spain
| | - Minliang Yan
- Macromolecules innovation institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda J Morris
- Macromolecules innovation institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ignacio Romero-Muñiz
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Ying Xiong
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Ana E Platero-Prats
- Departamento de Química Inorgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jocelyn Roth
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Sion, CH-1950, Switzerland
| | - Wendy L Queen
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Sion, CH-1950, Switzerland
| | - Kalle S Mertin
- Institute of Inorganic Chemistry, Christian-Albrechts-University Kiel, 24118, Kiel, Germany
| | - Danielle E Schier
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Neil R Champness
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Hamish H-M Yeung
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Bettina V Lotsch
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569, Stuttgart, Germany
- Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, Haus D, 81377, Munich, Germany
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2
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Tang H, Duan L, Jiang J. Leveraging Machine Learning for Metal-Organic Frameworks: A Perspective. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15849-15863. [PMID: 37922472 DOI: 10.1021/acs.langmuir.3c01964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Metal-organic frameworks (MOFs) have attracted tremendous interest because of their tunable structures, functionalities, and physiochemical properties. The nearly infinite combinations of metal nodes and organic linkers have led to the synthesis of over 100,000 experimental MOFs and the construction of millions of hypothetical counterparts. It is intractable to identify the best candidates in the immense chemical space of MOFs for applications via conventional trial-to-error experiments or brute-force simulations. Over the past several years, machine learning (ML) has substantially transformed the way of MOF discovery, design, and synthesis. Driven by the abundant data from experiments or simulations, ML can not only efficiently and accurately predict MOF properties but also quantitatively derive structure-property relationships for rational design and screening. In this Perspective, we summarize recent achievements in leveraging ML for MOFs from the aspects of data acquisition, featurization, model training, and applications. Then, current challenges and new opportunities are discussed for the future exploration of ML to accelerate the development of new MOFs in this vibrant field.
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Affiliation(s)
- Hongjian Tang
- Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, School of Energy & Environment, Southeast University, Nanjing 210096, China
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117576 Singapore
| | - Lunbo Duan
- Key Laboratory of Energy Thermal Conversion and Control of Ministry of Education, School of Energy & Environment, Southeast University, Nanjing 210096, China
| | - Jianwen Jiang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117576 Singapore
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3
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Chandrasekhar V, Sharma N, Schaub J, Steinbeck C, Rajan K. Cheminformatics Microservice: unifying access to open cheminformatics toolkits. J Cheminform 2023; 15:98. [PMID: 37845745 PMCID: PMC10577930 DOI: 10.1186/s13321-023-00762-4] [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: 07/07/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net . The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice .
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Affiliation(s)
- Venkata Chandrasekhar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Nisha Sharma
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Jonas Schaub
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
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4
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Korolev V, Protsenko P. Accurate, interpretable predictions of materials properties within transformer language models. PATTERNS (NEW YORK, N.Y.) 2023; 4:100803. [PMID: 37876904 PMCID: PMC10591138 DOI: 10.1016/j.patter.2023.100803] [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: 03/28/2023] [Revised: 06/06/2023] [Accepted: 07/04/2023] [Indexed: 10/26/2023]
Abstract
Property prediction accuracy has long been a key parameter of machine learning in materials informatics. Accordingly, advanced models showing state-of-the-art performance turn into highly parameterized black boxes missing interpretability. Here, we present an elegant way to make their reasoning transparent. Human-readable text-based descriptions automatically generated within a suite of open-source tools are proposed as materials representation. Transformer language models pretrained on 2 million peer-reviewed articles take as input well-known terms such as chemical composition, crystal symmetry, and site geometry. Our approach outperforms crystal graph networks by classifying four out of five analyzed properties if one considers all available reference data. Moreover, fine-tuned text-based models show high accuracy in the ultra-small data limit. Explanations of their internal machinery are produced using local interpretability techniques and are faithful and consistent with domain expert rationales. This language-centric framework makes accurate property predictions accessible to people without artificial-intelligence expertise.
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Affiliation(s)
- Vadim Korolev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Pavel Protsenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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5
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Jablonka K, Rosen AS, Krishnapriyan AS, Smit B. An Ecosystem for Digital Reticular Chemistry. ACS CENTRAL SCIENCE 2023; 9:563-581. [PMID: 37122448 PMCID: PMC10141625 DOI: 10.1021/acscentsci.2c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The vastness of the materials design space makes it impractical to explore using traditional brute-force methods, particularly in reticular chemistry. However, machine learning has shown promise in expediting and guiding materials design. Despite numerous successful applications of machine learning to reticular materials, progress in the field has stagnated, possibly because digital chemistry is more an art than a science and its limited accessibility to inexperienced researchers. To address this issue, we present mofdscribe, a software ecosystem tailored to novice and seasoned digital chemists that streamlines the ideation, modeling, and publication process. Though optimized for reticular chemistry, our tools are versatile and can be used in nonreticular materials research. We believe that mofdscribe will enable a more reliable, efficient, and comparable field of digital chemistry.
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Affiliation(s)
- Kevin
Maik Jablonka
- Laboratory of molecular simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, CH-1951 Sion, Switzerland
| | - Andrew S. Rosen
- Department of Materials
Science and Engineering, University of California, Berkeley, California 94720, United States
- Miller Institute for Basic Research in Science, University of California, Berkeley, California 94720, United States
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aditi S. Krishnapriyan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Electrical Engineering and
Computer Science, University of California, Berkeley, California 94720, United States
- Computational
Research Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Berend Smit
- Laboratory of molecular simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, CH-1951 Sion, Switzerland
- E-mail:
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6
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Domingues NP, Moosavi SM, Talirz L, Jablonka KM, Ireland CP, Ebrahim FM, Smit B. Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF. Commun Chem 2022; 5:170. [PMID: 36697847 PMCID: PMC9814730 DOI: 10.1038/s42004-022-00785-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The synthesis of metal-organic frameworks (MOFs) is often complex and the desired structure is not always obtained. In this work, we report a methodology that uses a joint machine learning and experimental approach to optimize the synthesis conditions of Al-PMOF (Al2(OH)2TCPP) [H2TCPP = meso-tetra(4-carboxyphenyl)porphine], a promising material for carbon capture applications. Al-PMOF was previously synthesized using a hydrothermal reaction, which gave a low throughput yield due to its relatively long reaction time (16 hours). Here, we use a genetic algorithm to carry out a systematic search for the optimal synthesis conditions and a microwave-based high-throughput robotic platform for the syntheses. We show that, in just two generations, we could obtain excellent crystallinity and yield close to 80% in a much shorter reaction time (50 minutes). Moreover, by analyzing the failed and partially successful experiments, we could identify the most important experimental variables that determine the crystallinity and yield.
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Affiliation(s)
- Nency P. Domingues
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland
| | - Seyed Mohamad Moosavi
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland ,grid.14095.390000 0000 9116 4836Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Leopold Talirz
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland ,grid.5333.60000000121839049Theory and Simulation of Materials (THEOS), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud Switzerland
| | - Kevin Maik Jablonka
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland
| | - Christopher P. Ireland
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland
| | - Fatmah Mish Ebrahim
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland ,grid.5335.00000000121885934Cavendish Laboratory, School of Physical Sciences, University of Cambridge, Cambridge, UK
| | - Berend Smit
- grid.5333.60000000121839049Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Sion, Valais Switzerland
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7
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Smith II PL. Exploring electronic lab notebooks (ELNs) at a R1 institution in the Southeast USA. DIGITAL LIBRARY PERSPECTIVES 2022. [DOI: 10.1108/dlp-02-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
This study aims to build a better understanding of researcher needs regarding support for data that you create, store, and/or manage using an electronic lab notebook (ELN), also referred to as electronic research notebook (ERN). The study also articulates the need for risk assessment for ELN products used by researchers for both open data and sensitive data that require standards.
Design/methodology/approach
The author used a participatory action research mixed-methods approach. A working group was formed from an ELN initial meeting. The working group team investigated several institutional ERN solutions by setting up trials, speaking with representatives from other research universities with ERN solutions and conducting internal and external research. This culminated in a broader-scale survey exploration.
Findings
Findings reveal there is no single institutional ELN license solution to satisfy all scientific disciplines. There is a need to develop foundational tools needed by all, provide additional tools and uses cases with best practices that can be tailored to various labs and research processes and develop a how-to guide on how to assemble the parts to create a useful ELN solution.
Research limitations/implications
The research implications include providing support for researchers selecting an ERN solution through a combination of online guides, short tutorials and training. There is a need to develop foundational tools, uses cases with best practices that can be tailored to various labs and research processes and how-to guide on how to assemble the parts to create a useful hybrid-ELN solution.
Practical implications
Practical implications include aligning available ERN solutions with other institution provided technologies across the research life cycle to provide researchers a suite of tools to conduct and manage their research. Further investigating educational license discounts for courses using eLabJournal, RSpace, Protocols.io, Open Science Framework, LabArchives or other ERNs currently funded by student course fees via grant funded projects are key implications.
Social implications
Social implications include the research computing environments of researchers that use ELN solutions approved through institutional risk assessment for open data are in compliance with university regulatory frameworks for use of the software in research.
Originality/value
The originality of this study includes risk assessments of ELNs solutions to better guide researchers in the selection process. To the best of the author’s knowledge, this survey was the first exploration of ELN on campus resulting in a final report to senior stakeholders. This study also highlights a developing grant proposal to further develop support across labs and campus.
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8
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Nandy A, Duan C, Kulik HJ. Audacity of huge: overcoming challenges of data scarcity and data quality for machine learning in computational materials discovery. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2021.100778] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Nagoya A, Kikkawa N, Ohba N, Baba T, Kajita S, Yanai K, Takeno T. Autonomous Search for Polymers with High Thermal Conductivity Using a Rapid Green–Kubo Estimation. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akihiro Nagoya
- Quantum Computing Research Division, Toyota Central R&D Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Nobuaki Kikkawa
- Quantum Computing Research Division, Toyota Central R&D Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Nobuko Ohba
- Quantum Computing Research Division, Toyota Central R&D Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Takeshi Baba
- Quantum Computing Research Division, Toyota Central R&D Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Seiji Kajita
- Quantum Computing Research Division, Toyota Central R&D Laboratories, Inc., 41-1, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Kazuma Yanai
- Advanced Research and Innovation Center, DENSO Corporation, 500-1, Miyamiyama, Komenoki-cho, Nisshin, Aichi 470-0111, Japan
| | - Takanori Takeno
- Advanced Research and Innovation Center, DENSO Corporation, 500-1, Miyamiyama, Komenoki-cho, Nisshin, Aichi 470-0111, Japan
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10
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Jablonka KM, Patiny L, Smit B. Making the collective knowledge of chemistry open and machine actionable. Nat Chem 2022; 14:365-376. [PMID: 35379967 DOI: 10.1038/s41557-022-00910-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 02/10/2022] [Indexed: 11/09/2022]
Abstract
Large amounts of data are generated in chemistry labs-nearly all instruments record data in a digital form, yet a considerable proportion is also captured non-digitally and reported in ways non-accessible to both humans and their computational agents. Chemical research is still largely centred around paper-based lab notebooks, and the publication of data is often more an afterthought than an integral part of the process. Here we argue that a modular open-science platform for chemistry would be beneficial not only for data-mining studies but also, well beyond that, for the entire chemistry community. Much progress has been made over the past few years in developing technologies such as electronic lab notebooks that aim to address data-management concerns. This will help make chemical data reusable, however it is only one step. We highlight the importance of centring open-science initiatives around open, machine-actionable data and emphasize that most of the required technologies already exist-we only need to connect, polish and embrace them.
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Affiliation(s)
- Kevin Maik Jablonka
- Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Luc Patiny
- Institut des Sciences et Ingénierie Chimiques (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Berend Smit
- Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland.
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11
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Majumdar S, Moosavi SM, Jablonka KM, Ongari D, Smit B. Diversifying Databases of Metal Organic Frameworks for High-Throughput Computational Screening. ACS APPLIED MATERIALS & INTERFACES 2021; 13:61004-61014. [PMID: 34910455 PMCID: PMC8719320 DOI: 10.1021/acsami.1c16220] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/03/2021] [Indexed: 05/19/2023]
Abstract
By combining metal nodes and organic linkers, an infinite number of metal organic frameworks (MOFs) can be designed in silico. Therefore, when making new databases of such hypothetical MOFs, we need to ensure that they not only contribute toward the growth of the count of structures but also add different chemistries to the existing databases. In this study, we designed a database of ∼20,000 hypothetical MOFs, which are diverse in terms of their chemical design space─metal nodes, organic linkers, functional groups, and pore geometries. Using machine learning techniques, we visualized and quantified the diversity of these structures. We find that on adding the structures of our database, the overall diversity metrics of hypothetical databases improve, especially in terms of the chemistry of metal nodes. We then assessed the usefulness of diverse structures by evaluating their performance, using grand-canonical Monte Carlo simulations, in two important environmental applications─post-combustion carbon capture and hydrogen storage. We find that many of these structures perform better than widely used benchmark materials such as Zeolite-13X (for post-combustion carbon capture) and MOF-5 (for hydrogen storage). All the structures developed in this study, and their properties, are provided on the Materials Cloud to encourage further use of these materials for other applications.
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12
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Altintas C, Altundal OF, Keskin S, Yildirim R. Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation. J Chem Inf Model 2021; 61:2131-2146. [PMID: 33914526 PMCID: PMC8154255 DOI: 10.1021/acs.jcim.1c00191] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 02/06/2023]
Abstract
The acceleration in design of new metal organic frameworks (MOFs) has led scientists to focus on high-throughput computational screening (HTCS) methods to quickly assess the promises of these fascinating materials in various applications. HTCS studies provide a massive amount of structural property and performance data for MOFs, which need to be further analyzed. Recent implementation of machine learning (ML), which is another growing field in research, to HTCS of MOFs has been very fruitful not only for revealing the hidden structure-performance relationships of materials but also for understanding their performance trends in different applications, specifically for gas storage and separation. In this review, we highlight the current state of the art in ML-assisted computational screening of MOFs for gas storage and separation and address both the opportunities and challenges that are emerging in this new field by emphasizing how merging of ML and MOF simulations can be useful.
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Affiliation(s)
- Cigdem Altintas
- Department
of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey
| | - Omer Faruk Altundal
- Department
of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey
| | - Seda Keskin
- Department
of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey
| | - Ramazan Yildirim
- Department
of Chemical Engineering, Boğaziçi
University, Bebek, 34342 Istanbul, Turkey
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