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      Three-Dimensional Fully π-Conjugated Macrocycles: When 3D-Aromatic and When 2D-Aromatic-in-3D?

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          Abstract

          Several fully π-conjugated macrocycles with puckered or cage-type structures were recently found to exhibit aromatic character according to both experiments and computations. We examine their electronic structures and put them in relation to 3D-aromatic molecules ( e.g., closo-boranes) and to 2D-aromatic polycyclic aromatic hydrocarbons. Using qualitative theory combined with quantum chemical calculations, we find that the macrocycles explored hitherto should be described as 2D-aromatic with three-dimensional molecular structures (abbr. 2D-aromatic-in-3D) and not as truly 3D-aromatic. 3D-aromatic molecules have highly symmetric structures (or nearly so), leading to (at least) triply degenerate molecular orbitals, and for tetrahedral or octahedral molecules, an aromatic closed-shell electronic structure with 6 n + 2 electrons. Conversely, 2D-aromatic-in-3D structures exhibit aromaticity that results from the fulfillment of Hückel’s 4 n + 2 rule for each macrocyclic path, yet their π-electron counts are coincidentally 6 n + 2 numbers for macrocycles with three tethers of equal lengths. It is notable that 2D-aromatic-in-3D macrocyclic cages can be aromatic with tethers of different lengths, i.e., with π-electron counts different from 6 n + 2, and they are related to naphthalene. Finally, we identify tetrahedral and cubic π-conjugated molecules that fulfill the 6 n + 2 rule and exhibit significant electron delocalization. Yet, their properties resemble those of analogous compounds with electron counts that differ from 6 n + 2. Thus, despite the fact that these molecules show substantial π-electron delocalization, they cannot be classified as true 3D-aromatics.

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          Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

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            Density-functional thermochemistry. III. The role of exact exchange

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              Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

              Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.
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                Author and article information

                Journal
                J Am Chem Soc
                J Am Chem Soc
                ja
                jacsat
                Journal of the American Chemical Society
                American Chemical Society
                0002-7863
                1520-5126
                06 May 2022
                18 May 2022
                : 144
                : 19
                : 8560-8575
                Affiliations
                []Department of Chemistry - Ångström Laboratory, Uppsala University , Box 523, Uppsala 751 20, Sweden
                []Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , C/ Maria Aurèlia Capmany 6, Girona, Catalonia 17003, Spain
                [§ ]K. Guminski Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, Kraków 30-387, Poland
                []Department of Chemistry, Ghent University , Krijgslaan 281 S3, Gent 9000, Belgium
                Author notes
                Author information
                https://orcid.org/0000-0002-4019-3754
                https://orcid.org/0000-0002-2013-0617
                https://orcid.org/0000-0002-4191-6790
                https://orcid.org/0000-0003-2128-6733
                https://orcid.org/0000-0003-2766-2672
                https://orcid.org/0000-0002-1917-7450
                https://orcid.org/0000-0001-8076-1165
                Article
                10.1021/jacs.1c13478
                9121391
                35523019
                fc49c27b-5ebf-4e12-b691-6ee1e5d7e41f
                © 2022 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
                : 28 December 2021
                Funding
                Funded by: H2020 Marie Sklodowska-Curie Actions, doi 10.13039/100010665;
                Award ID: 797335 MulArEffect
                Funded by: Ministerio de Ciencia e Innovación, doi 10.13039/501100004837;
                Award ID: PID2020-113711GB-I00
                Funded by: Vetenskapsrådet, doi 10.13039/501100004359;
                Award ID: 2019-05618
                Funded by: Vetenskapsrådet, doi 10.13039/501100004359;
                Award ID: 2015-04538
                Funded by: Narodowe Centrum Nauki, doi 10.13039/501100004281;
                Award ID: 2021/42/E/ST4/00332
                Funded by: Departament d''Innovació, Universitats i Empresa, Generalitat de Catalunya, doi 10.13039/501100002943;
                Award ID: 2017SGR39
                Funded by: Wenner-Gren Stiftelserna, doi 10.13039/100014437;
                Award ID: UPD 2018-0305
                Categories
                Article
                Custom metadata
                ja1c13478
                ja1c13478

                Chemistry
                Chemistry

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