Haydar Mohammad-Salim, Jesus Vicente de Julián-Ortiz, Kholood A. Dahlous, Mohammad Shahidul Islam, Tahani Mazyad Almutairi, Sofiane Benmetir
{"title":"阐明 [3 + 2] 环加成的机理和选择性:对 6-丁氧基-5,6-二氢-4H-1,2-恶嗪 2-氧化物与马来酸二甲酯反应的 DFT 和分子对接研究","authors":"Haydar Mohammad-Salim, Jesus Vicente de Julián-Ortiz, Kholood A. Dahlous, Mohammad Shahidul Islam, Tahani Mazyad Almutairi, Sofiane Benmetir","doi":"10.1007/s11224-024-02373-7","DOIUrl":null,"url":null,"abstract":"<p>The [3 + 2] cycloaddition (32CA) reactions involving 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide and dimethyl maleate are examined in this study. Molecular electron density theory (MEDT) is applied at the M06-2X/6-311G(d,p) level, coupled with the D3 dispersion correction. The nitronate <b>1</b> species are identified as zwitterionic entities through an analysis of the electron localization function (ELF). This 32CA reaction follows an asynchronous one-step mechanism. Conceptual DFT indices are utilized to classify dimethyl maleate as the electrophilic component and the nitronate as the nucleophilic counterpart. The [3 + 2] cycloaddition processes are predominantly governed by kinetic control, as indicated by activation free energies of − 23.6 and − 11.4 kcal.mol<sup>−1</sup> for the <i>exo</i> and <i>endo</i> pathways, respectively, aligning with experimental findings. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather polar 32CA reactions. The formation of a pseudoradical center initiates at carbon atoms C3 and C4. A subsequent docking analysis is conducted on cycloadducts <b>3</b> and <b>4</b> in relation to the main protease of SARS-CoV-2 (6LU7), alongside the co-crystal ligand. The results of this analysis reveal that cycloadducts <b>3</b> exhibit higher binding energy, while cycloadducts <b>4</b> display lower binding energy compared to the co-crystal ligand. The results confirm that the presence of isoxazolidine ring increases the affinity of the product <b>3</b>.</p>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Elucidating the mechanism and selectivity of [3 + 2] cycloaddition: a DFT and molecular docking investigation of the reaction of 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide with dimethyl maleate\",\"authors\":\"Haydar Mohammad-Salim, Jesus Vicente de Julián-Ortiz, Kholood A. Dahlous, Mohammad Shahidul Islam, Tahani Mazyad Almutairi, Sofiane Benmetir\",\"doi\":\"10.1007/s11224-024-02373-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>The [3 + 2] cycloaddition (32CA) reactions involving 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide and dimethyl maleate are examined in this study. Molecular electron density theory (MEDT) is applied at the M06-2X/6-311G(d,p) level, coupled with the D3 dispersion correction. The nitronate <b>1</b> species are identified as zwitterionic entities through an analysis of the electron localization function (ELF). This 32CA reaction follows an asynchronous one-step mechanism. Conceptual DFT indices are utilized to classify dimethyl maleate as the electrophilic component and the nitronate as the nucleophilic counterpart. The [3 + 2] cycloaddition processes are predominantly governed by kinetic control, as indicated by activation free energies of − 23.6 and − 11.4 kcal.mol<sup>−1</sup> for the <i>exo</i> and <i>endo</i> pathways, respectively, aligning with experimental findings. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather polar 32CA reactions. The formation of a pseudoradical center initiates at carbon atoms C3 and C4. A subsequent docking analysis is conducted on cycloadducts <b>3</b> and <b>4</b> in relation to the main protease of SARS-CoV-2 (6LU7), alongside the co-crystal ligand. The results of this analysis reveal that cycloadducts <b>3</b> exhibit higher binding energy, while cycloadducts <b>4</b> display lower binding energy compared to the co-crystal ligand. The results confirm that the presence of isoxazolidine ring increases the affinity of the product <b>3</b>.</p>\",\"PeriodicalId\":780,\"journal\":{\"name\":\"Structural Chemistry\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2024-09-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Structural Chemistry\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1007/s11224-024-02373-7\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Structural Chemistry","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1007/s11224-024-02373-7","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Elucidating the mechanism and selectivity of [3 + 2] cycloaddition: a DFT and molecular docking investigation of the reaction of 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide with dimethyl maleate
The [3 + 2] cycloaddition (32CA) reactions involving 6-butoxy-5,6-dihydro-4H-1,2-oxazine 2-oxide and dimethyl maleate are examined in this study. Molecular electron density theory (MEDT) is applied at the M06-2X/6-311G(d,p) level, coupled with the D3 dispersion correction. The nitronate 1 species are identified as zwitterionic entities through an analysis of the electron localization function (ELF). This 32CA reaction follows an asynchronous one-step mechanism. Conceptual DFT indices are utilized to classify dimethyl maleate as the electrophilic component and the nitronate as the nucleophilic counterpart. The [3 + 2] cycloaddition processes are predominantly governed by kinetic control, as indicated by activation free energies of − 23.6 and − 11.4 kcal.mol−1 for the exo and endo pathways, respectively, aligning with experimental findings. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather polar 32CA reactions. The formation of a pseudoradical center initiates at carbon atoms C3 and C4. A subsequent docking analysis is conducted on cycloadducts 3 and 4 in relation to the main protease of SARS-CoV-2 (6LU7), alongside the co-crystal ligand. The results of this analysis reveal that cycloadducts 3 exhibit higher binding energy, while cycloadducts 4 display lower binding energy compared to the co-crystal ligand. The results confirm that the presence of isoxazolidine ring increases the affinity of the product 3.
期刊介绍:
Structural Chemistry is an international forum for the publication of peer-reviewed original research papers that cover the condensed and gaseous states of matter and involve numerous techniques for the determination of structure and energetics, their results, and the conclusions derived from these studies. The journal overcomes the unnatural separation in the current literature among the areas of structure determination, energetics, and applications, as well as builds a bridge to other chemical disciplines. Ist comprehensive coverage encompasses broad discussion of results, observation of relationships among various properties, and the description and application of structure and energy information in all domains of chemistry.
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