Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions
Bio-orthogonal click chemistry based on [3 + 2] dipolar cycloadditions has had a profound impact on the field of biochemistry and significant effort has been devoted to identify promising new candidate reactions for this purpose. To gauge whether a prospective reaction could be a suitable bio-orthog...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2025
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| Online Access: | https://hdl.handle.net/1721.1/158194 |
| _version_ | 1824458435971776512 |
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| author | Stuyver, Thijs Jorner, Kjell Coley, Connor W |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Stuyver, Thijs Jorner, Kjell Coley, Connor W |
| author_sort | Stuyver, Thijs |
| collection | MIT |
| description | Bio-orthogonal click chemistry based on [3 + 2] dipolar cycloadditions has had a profound impact on the field of biochemistry and significant effort has been devoted to identify promising new candidate reactions for this purpose. To gauge whether a prospective reaction could be a suitable bio-orthogonal click reaction, information about both on- and off-target activation and reaction energies is highly valuable. Here, we use an automated workflow, based on the autodE program, to compute over 5000 reaction profiles for [3 + 2] cycloadditions involving both synthetic dipolarophiles and a set of biologically-inspired structural motifs. Based on a succinct benchmarking study, the B3LYP-D3(BJ)/def2-TZVP//B3LYP-D3(BJ)/def2-SVP level of theory was selected for the DFT calculations, and standard conditions and an (aqueous) SMD model were imposed to mimic physiological conditions. We believe that this data, as well as the presented workflow for high-throughput reaction profile computation, will be useful to screen for new bio-orthogonal reactions, as well as for the development of novel machine learning models for the prediction of chemical reactivity more broadly. |
| first_indexed | 2025-02-19T04:25:51Z |
| format | Article |
| id | mit-1721.1/158194 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-02-19T04:25:51Z |
| publishDate | 2025 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1581942025-02-11T20:54:19Z Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions Stuyver, Thijs Jorner, Kjell Coley, Connor W Massachusetts Institute of Technology. Department of Chemical Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Bio-orthogonal click chemistry based on [3 + 2] dipolar cycloadditions has had a profound impact on the field of biochemistry and significant effort has been devoted to identify promising new candidate reactions for this purpose. To gauge whether a prospective reaction could be a suitable bio-orthogonal click reaction, information about both on- and off-target activation and reaction energies is highly valuable. Here, we use an automated workflow, based on the autodE program, to compute over 5000 reaction profiles for [3 + 2] cycloadditions involving both synthetic dipolarophiles and a set of biologically-inspired structural motifs. Based on a succinct benchmarking study, the B3LYP-D3(BJ)/def2-TZVP//B3LYP-D3(BJ)/def2-SVP level of theory was selected for the DFT calculations, and standard conditions and an (aqueous) SMD model were imposed to mimic physiological conditions. We believe that this data, as well as the presented workflow for high-throughput reaction profile computation, will be useful to screen for new bio-orthogonal reactions, as well as for the development of novel machine learning models for the prediction of chemical reactivity more broadly. 2025-02-11T20:54:18Z 2025-02-11T20:54:18Z 2023 2025-02-11T20:48:46Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/158194 Stuyver, T., Jorner, K. & Coley, C.W. Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions. Sci Data 10, 66 (2023). en 10.1038/s41597-023-01977-8 Scientific Data Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Springer Science and Business Media LLC |
| spellingShingle | Stuyver, Thijs Jorner, Kjell Coley, Connor W Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title | Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title_full | Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title_fullStr | Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title_full_unstemmed | Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title_short | Reaction profiles for quantum chemistry-computed [3 + 2] cycloaddition reactions |
| title_sort | reaction profiles for quantum chemistry computed 3 2 cycloaddition reactions |
| url | https://hdl.handle.net/1721.1/158194 |
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