1
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He D, Ji H, Liu T, Yang M, Clowes R, Little MA, Liu M, Cooper AI. Self-Assembly of Chiral Porous Metal-Organic Polyhedra from Trianglsalen Macrocycles. J Am Chem Soc 2024; 146:17438-17445. [PMID: 38860872 PMCID: PMC11212058 DOI: 10.1021/jacs.4c04928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Metal-organic polyhedra (MOPs) can exhibit tunable porosity and functionality, suggesting potential for applications such as molecular separations. MOPs are typically constructed by the bottom-up multicomponent self-assembly of organic ligands and metal ions, and the final functionality can be hard to program. Here, we used trianglsalen macrocycles as preorganized building blocks to assemble octahedral-shaped MOPs. The resultant MOPs inherit most of the preorganized properties of the macrocyclic ligands, including their well-defined cavities and chirality. As a result, the porosity in the MOPs could be tuned by modifying the structure of the macrocycle building blocks. Using this strategy, we could systematically enlarge the size of the MOPs from 26.3 to 32.1 Å by increasing the macrocycle size. The family of MOPs shows experimental surface areas of up to 820 m2/g, and they are stable in water. One of these MOPs can efficiently separate the rare gases Xe from Kr because the prefabricated macrocyclic windows of MOPs can be modified to sit at the Xe/Kr size cutoff range.
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Affiliation(s)
- Donglin He
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Heng Ji
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Tao Liu
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
- Leverhulme
Research Centre for Functional Materials Design, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Miao Yang
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Rob Clowes
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Marc A. Little
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Ming Liu
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Andrew I. Cooper
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
- Leverhulme
Research Centre for Functional Materials Design, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
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2
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Rihm SD, Tan YR, Ang W, Hofmeister M, Deng X, Laksana MT, Quek HY, Bai J, Pascazio L, Siong SC, Akroyd J, Mosbach S, Kraft M. The digital lab manager: Automating research support. SLAS Technol 2024; 29:100135. [PMID: 38703999 DOI: 10.1016/j.slast.2024.100135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The integration of resources and the sharing of knowledge across organisations enable scientific discoveries to be accelerated by increasing the productivity of laboratories, optimising funding efficiency, and addressing emerging global challenges. This paper presents a novel framework for digitalising and automating the administration of research laboratories through The World Avatar, an all-encompassing dynamic knowledge graph. This Digital Laboratory Framework serves as a flexible tool, enabling users to efficiently leverage data from diverse systems and formats without being confined to a specific software or protocol. Establishing dedicated ontologies and agents and combining them with technologies such as QR codes, RFID tags, and mobile apps, enabled us to develop modular applications that tackle some key challenges related to lab management. Here, we showcase an automated tracking and intervention system for explosive chemicals as well as an easy-to-use mobile application for asset management and information retrieval. Implementing these, we have achieved semantic linking of BIM and BMS data with laboratory inventory and chemical knowledge. Our approach can capture the crucial data points and reduce inventory processing time. All data provenance is recorded following the FAIR principles, ensuring its accessibility and interoperability.
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Affiliation(s)
- Simon D Rihm
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Yong Ren Tan
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Wilson Ang
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Markus Hofmeister
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Xinhong Deng
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Michael Teguh Laksana
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Hou Yee Quek
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Jiaru Bai
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom
| | - Laura Pascazio
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Sim Chun Siong
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore
| | - Jethro Akroyd
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom
| | - Sebastian Mosbach
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom
| | - Markus Kraft
- CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 CREATE Way, CREATE Tower, #05-05, 138602, Singapore; Department of Chemical Engineering and Biotechnology, University of Cambridge, Philipppa Fawcett Drive, Cambridge, CB3 0AS, United Kingdom; CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, United Kingdom; School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore; The Alan Turing Institute, 2QR, John Dodson House, 96 Euston Rd, London, NW1 2DB, United Kingdom.
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3
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Zakrzewski J, Liberka M, Wang J, Chorazy S, Ohkoshi SI. Optical Phenomena in Molecule-Based Magnetic Materials. Chem Rev 2024; 124:5930-6050. [PMID: 38687182 PMCID: PMC11082909 DOI: 10.1021/acs.chemrev.3c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Since the last century, we have witnessed the development of molecular magnetism which deals with magnetic materials based on molecular species, i.e., organic radicals and metal complexes. Among them, the broadest attention was devoted to molecule-based ferro-/ferrimagnets, spin transition materials, including those exploring electron transfer, molecular nanomagnets, such as single-molecule magnets (SMMs), molecular qubits, and stimuli-responsive magnetic materials. Their physical properties open the application horizons in sensors, data storage, spintronics, and quantum computation. It was found that various optical phenomena, such as thermochromism, photoswitching of magnetic and optical characteristics, luminescence, nonlinear optical and chiroptical effects, as well as optical responsivity to external stimuli, can be implemented into molecule-based magnetic materials. Moreover, the fruitful interactions of these optical effects with magnetism in molecule-based materials can provide new physical cross-effects and multifunctionality, enriching the applications in optical, electronic, and magnetic devices. This Review aims to show the scope of optical phenomena generated in molecule-based magnetic materials, including the recent advances in such areas as high-temperature photomagnetism, optical thermometry utilizing SMMs, optical addressability of molecular qubits, magneto-chiral dichroism, and opto-magneto-electric multifunctionality. These findings are discussed in the context of the types of optical phenomena accessible for various classes of molecule-based magnetic materials.
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Affiliation(s)
- Jakub
J. Zakrzewski
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Lojasiewicza
11, 30-348 Krakow, Poland
| | - Michal Liberka
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Doctoral
School of Exact and Natural Sciences, Jagiellonian
University, Lojasiewicza
11, 30-348 Krakow, Poland
| | - Junhao Wang
- Department
of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, 1-1-1 Tonnodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Szymon Chorazy
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Shin-ichi Ohkoshi
- Department
of Chemistry, School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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4
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Tran D, Pascazio L, Akroyd J, Mosbach S, Kraft M. Leveraging Text-to-Text Pretrained Language Models for Question Answering in Chemistry. ACS OMEGA 2024; 9:13883-13896. [PMID: 38559914 PMCID: PMC10976360 DOI: 10.1021/acsomega.3c08842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In this study, we present a question answering (QA) system for chemistry, named Marie, with the use of a text-to-text pretrained language model to attain accurate data retrieval. The underlying data store is "The World Avatar" (TWA), a general world model consisting of a knowledge graph that evolves over time. TWA includes information about chemical species such as their chemical and physical properties, applications, and chemical classifications. Building upon our previous work on KGQA for chemistry, this advanced version of Marie leverages a fine-tuned Flan-T5 model to seamlessly translate natural language questions into SPARQL queries with no separate components for entity and relation linking. The developed QA system demonstrates competence in providing accurate results for complex queries that involve many relation hops as well as showcasing the ability to balance correctness and speed for real-world usage. This new approach offers significant advantages over the prior implementation that relied on knowledge graph embedding. Specifically, the updated system boasts high accuracy and great flexibility in accommodating changes and evolution of the data stored in the knowledge graph without necessitating retraining. Our evaluation results underscore the efficacy of the improved system, highlighting its superior accuracy and the ability in answering complex questions compared to its predecessor.
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Affiliation(s)
- Dan Tran
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
| | - Laura Pascazio
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
| | - Jethro Akroyd
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Sebastian Mosbach
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Markus Kraft
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
- The
Alan Turing Institute, 96 Euston Rd., London NW1 2DB, U.K.
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5
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Bai J, Mosbach S, Taylor CJ, Karan D, Lee KF, Rihm SD, Akroyd J, Lapkin AA, Kraft M. A dynamic knowledge graph approach to distributed self-driving laboratories. Nat Commun 2024; 15:462. [PMID: 38263405 PMCID: PMC10805810 DOI: 10.1038/s41467-023-44599-9] [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: 07/14/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
The ability to integrate resources and share knowledge across organisations empowers scientists to expedite the scientific discovery process. This is especially crucial in addressing emerging global challenges that require global solutions. In this work, we develop an architecture for distributed self-driving laboratories within The World Avatar project, which seeks to create an all-encompassing digital twin based on a dynamic knowledge graph. We employ ontologies to capture data and material flows in design-make-test-analyse cycles, utilising autonomous agents as executable knowledge components to carry out the experimentation workflow. Data provenance is recorded to ensure its findability, accessibility, interoperability, and reusability. We demonstrate the practical application of our framework by linking two robots in Cambridge and Singapore for a collaborative closed-loop optimisation for a pharmaceutically-relevant aldol condensation reaction in real-time. The knowledge graph autonomously evolves toward the scientist's research goals, with the two robots effectively generating a Pareto front for cost-yield optimisation in three days.
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Affiliation(s)
- Jiaru Bai
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Sebastian Mosbach
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Connor J Taylor
- Astex Pharmaceuticals, 436 Cambridge Science Park Milton Road, Cambridge, CB4 0QA, UK
- Innovation Centre in Digital Molecular Technologies, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Dogancan Karan
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Kok Foong Lee
- CMCL Innovations, Sheraton House, Cambridge, CB3 0AX, UK
| | - Simon D Rihm
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Jethro Akroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
| | - Alexei A Lapkin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore
- Innovation Centre in Digital Molecular Technologies, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), 1 Create Way, CREATE Tower, #05-05, Singapore, 138602, Singapore.
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore, Singapore.
- The Alan Turing Institute, London, NW1 2DB, UK.
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6
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Tarzia A, Wolpert EH, Jelfs KE, Pavan GM. Systematic exploration of accessible topologies of cage molecules via minimalistic models. Chem Sci 2023; 14:12506-12517. [PMID: 38020374 PMCID: PMC10646940 DOI: 10.1039/d3sc03991a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Cages are macrocyclic structures with an intrinsic internal cavity that support applications in separations, sensing and catalysis. These materials can be synthesised via self-assembly of organic or metal-organic building blocks. Their bottom-up synthesis and the diversity in building block chemistry allows for fine-tuning of their shape and properties towards a target property. However, it is not straightforward to predict the outcome of self-assembly, and, thus, the structures that are practically accessible during synthesis. Indeed, such a prediction becomes more difficult as problems related to the flexibility of the building blocks or increased combinatorics lead to a higher level of complexity and increased computational costs. Molecular models, and their coarse-graining into simplified representations, may be very useful to this end. Here, we develop a minimalistic toy model of cage-like molecules to explore the stable space of different cage topologies based on a few fundamental geometric building block parameters. Our results capture, despite the simplifications of the model, known geometrical design rules in synthetic cage molecules and uncover the role of building block coordination number and flexibility on the stability of cage topologies. This leads to a large-scale and systematic exploration of design principles, generating data that we expect could be analysed through expandable approaches towards the rational design of self-assembled porous architectures.
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Affiliation(s)
- Andrew Tarzia
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - Emma H Wolpert
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus Wood Lane London W12 0BZ UK
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus Wood Lane London W12 0BZ UK
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano Campus Est, Via la Santa 1 6962 Lugano-Viganello Switzerland
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7
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Pascazio L, Rihm S, Naseri A, Mosbach S, Akroyd J, Kraft M. Chemical Species Ontology for Data Integration and Knowledge Discovery. J Chem Inf Model 2023; 63:6569-6586. [PMID: 37883649 PMCID: PMC10647085 DOI: 10.1021/acs.jcim.3c00820] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023]
Abstract
Web ontologies are important tools in modern scientific research because they provide a standardized way to represent and manage web-scale amounts of complex data. In chemistry, a semantic database for chemical species is indispensable for its ability to interrelate and infer relationships, enabling a more precise analysis and prediction of chemical behavior. This paper presents OntoSpecies, a web ontology designed to represent chemical species and their properties. The ontology serves as a core component of The World Avatar knowledge graph chemistry domain and includes a wide range of identifiers, chemical and physical properties, chemical classifications and applications, and spectral information associated with each species. The ontology includes provenance and attribution metadata, ensuring the reliability and traceability of data. Most of the information about chemical species are sourced from PubChem and ChEBI data on the respective compound Web pages using a software agent, making OntoSpecies a comprehensive semantic database of chemical species able to solve novel types of problems in the field. Access to this reliable source of chemical data is provided through a SPARQL end point. The paper presents example use cases to demonstrate the contribution of OntoSpecies in solving complex tasks that require integrated semantically searchable chemical data. The approach presented in this paper represents a significant advancement in the field of chemical data management, offering a powerful tool for representing, navigating, and analyzing chemical information to support scientific research.
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Affiliation(s)
- Laura Pascazio
- CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
| | - Simon Rihm
- CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Ali Naseri
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Sebastian Mosbach
- CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Jethro Akroyd
- CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Markus Kraft
- CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602, Singapore
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
- The
Alan Turing Institute, 96 Euston Rd., London NW1 2DB, U.K.
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8
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Kondinski A, Bai J, Mosbach S, Akroyd J, Kraft M. Knowledge Engineering in Chemistry: From Expert Systems to Agents of Creation. Acc Chem Res 2022; 56:128-139. [PMID: 36516456 PMCID: PMC9850921 DOI: 10.1021/acs.accounts.2c00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Passing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer represents a cornerstone in artificial intelligence (AI) and lays the foundation for knowledge engineering (KE). In order to pass knowledge to machines, humans need to structure, formalize, and make knowledge machine-readable. Subsequently, humans also need to develop software that emulates their decision-making process. In order to engineer chemical knowledge, chemists are often required to challenge their understanding of chemistry and thinking processes, which may help improve the structure of chemical knowledge.Knowledge engineering in chemistry dates from the development of expert systems that emulated the thinking process of analytical and organic chemists. Since then, many different expert systems employing rather limited knowledge bases have been developed, solving problems in retrosynthesis, analytical chemistry, chemical risk assessment, etc. However, toward the end of the 20th century, the AI winters slowed down the development of expert systems for chemistry. At the same time, the increasing complexity of chemical research, alongside the limitations of the available computing tools, made it difficult for many chemistry expert systems to keep pace.In the past two decades, the semantic web, the popularization of object-oriented programming, and the increase in computational power have revitalized knowledge engineering. Knowledge formalization through ontologies has become commonplace, triggering the subsequent development of knowledge graphs and cognitive software agents. These tools enable the possibility of interoperability, enabling the representation of more complex systems, inference capabilities, and the synthesis of new knowledge.This Account introduces the history, the core principles of KE, and its applications within the broad realm of chemical research and engineering. In this regard, we first discuss how chemical knowledge is formalized and how a chemist's cognition can be emulated with the help of reasoning algorithms. Following this, we discuss various applications of knowledge graph and agent technology used to solve problems in chemistry related to molecular engineering, chemical mechanisms, multiscale modeling, automation of calculations and experiments, and chemist-machine interactions. These developments are discussed in the context of a universal and dynamic knowledge ecosystem, referred to as The World Avatar (TWA).
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Affiliation(s)
- Aleksandar Kondinski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Jiaru Bai
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Sebastian Mosbach
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, 138602 Singapore
| | - Jethro Akroyd
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Markus Kraft
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, 138602 Singapore,School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore,E-mail:
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9
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Helicate versus Mesocate in Quadruple-Stranded Lanthanide Cages: A Computational Insight. Int J Mol Sci 2022; 23:ijms231810619. [PMID: 36142519 PMCID: PMC9504305 DOI: 10.3390/ijms231810619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
To drive the synthesis of metallo-supramolecular assemblies (MSAs) and to fully exploit their functional properties, robust computational tools are crucial. The capability to model and to rationalize different parameters that can influence the outcome is mandatory. Here, we report a computational insight on the factors that can determine the relative stability of the supramolecular isomers helicate and mesocate in lanthanide-based quadruple-stranded assemblies. The considered MSAs have the general formula [Ln2L4]2− and possess a cavity suitable to allocate guests. The analysis was focused on three different factors: the ligand rigidity and the steric hindrance, the presence of a guest inside the cavity, and the guest dimension. Three different quantum mechanical calculation set-ups (in vacuum, with the solvent, and with the solvent and the dispersion correction) were considered. Comparison between theoretical and experimental outcomes suggests that all calculations correctly estimated the most stable isomer, while the inclusion of the dispersion correction is mandatory to reproduce the geometrical parameters. General guidelines can be drawn: less rigid and less bulky is the ligand and less stable is the helicate, and the presence of a guest can strongly affect the isomerism leading to an inversion of the stability by increasing the guest size when the ligand is flexible.
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