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      Topological Characterization of Metal–Organic Frameworks: A Perspective

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          Abstract

          Metal–organic frameworks (MOFs) began to emerge over two decades ago, resulting in the deposition of 120 000 MOF-like structures (and counting) into the Cambridge Structural Database (CSD). Topological analysis is a critical step toward understanding periodic MOF materials, offering insight into the design and synthesis of these crystals via the simplification of connectivity imposed on the complete chemical structure. While some of the most prevalent topologies, such as face-centered cubic ( fcu), square lattice ( sql), and diamond ( dia), are simple and can be easily assigned to structures, MOFs that are built from complex building blocks, with multiple nodes of different symmetry, result in difficult to characterize topological configurations. In these complex structures, representations can easily diverge where the definition of nodes and linkers are blurred, especially for cases where they are not immediately obvious in chemical terms. Currently, researchers have the option to use software such as ToposPro, MOFid, and CrystalNets to aid in the assignment of topology descriptors to new and existing MOFs. These software packages are readily available and are frequently used to simplify original MOF structures into their basic connectivity representations before algorithmically matching these condensed representations to a database of underlying mathematical nets. These approaches often require the use of in-built bond assignment algorithms alongside the simplification and matching rules. In this Perspective, we discuss the importance of topology within the field of MOFs, the methods and techniques implemented by these software packages, and their availability and limitations and review their uptake within the MOF community.

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          Open Babel: An open chemical toolbox

          Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.
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            Design and synthesis of an exceptionally stable and highly porous metal-organic framework

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              Reticular synthesis and the design of new materials.

              The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.
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                Author and article information

                Journal
                Chem Mater
                Chem Mater
                cm
                cmatex
                Chemistry of Materials
                American Chemical Society
                0897-4756
                1520-5002
                22 July 2024
                08 October 2024
                : 36
                : 19
                : 9013-9030
                Affiliations
                []Department of Chemical and Biological Engineering, The University of Sheffield , Sheffield S1 3JD, United Kingdom
                []Cambridge Crystallographic Data Centre , Cambridge CB2 1EZ, United Kingdom
                [§ ]Department of Chemical Engineering, University College London , London WC1E 7JE, United Kingdom
                Author notes
                Author information
                https://orcid.org/0000-0002-0291-6317
                https://orcid.org/0000-0002-1592-0139
                Article
                10.1021/acs.chemmater.4c00762
                11467834
                39398380
                dae6da3b-1669-4f5c-a314-8ecad980fe30
                © 2024 The Authors. Published by American Chemical Society

                Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 14 March 2024
                : 05 July 2024
                : 04 July 2024
                Funding
                Funded by: Royal Academy of Engineering, doi 10.13039/501100000287;
                Award ID: IF2223-110
                Funded by: Cambridge Crystallographic Data Centre, doi 10.13039/501100022029;
                Award ID: NA
                Funded by: Innovate UK, doi 10.13039/501100006041;
                Award ID: 10098491
                Categories
                Perspective
                Custom metadata
                cm4c00762
                cm4c00762

                Materials science
                Materials science

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