{"title":"pKalculator: A pKa predictor for C–H bonds","authors":"Rasmus M Borup, Nicolai Ree, Jan H Jensen","doi":"10.3762/bjoc.20.144","DOIUrl":"https://doi.org/10.3762/bjoc.20.144","url":null,"abstract":"Determining the pKa values of various C–H sites in organic molecules offers valuable insights for synthetic chemists in predicting reaction sites. As molecular complexity increases, this task becomes more challenging. This paper introduces pKalculator, a quantum chemistry (QM)-based workflow for automatic computations of C–H pKa values, which is used to generate a training dataset for a machine learning (ML) model. The QM workflow is benchmarked against 695 experimentally determined C–H pKa values in DMSO. The ML model is trained on a diverse dataset of 775 molecules with 3910 C–H sites. Our ML model predicts C–H pKa values with a mean absolute error (MAE) and a root mean squared error (RMSE) of 1.24 and 2.15 pKa units, respectively. Furthermore, we employ our model on 1043 pKa-dependent reactions (aldol, Claisen, and Michael) and successfully indicate the reaction sites with a Matthew’s correlation coefficient (MCC) of 0.82.","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kevin A. Juarez-Ornelas, Manuel Solís-Hernández, P. Navarro‐Santos, J. Jiménez-Halla, C. Solorio-Alvarado
{"title":"Divergent role of PIDA and PIFA in the AlX3 (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study","authors":"Kevin A. Juarez-Ornelas, Manuel Solís-Hernández, P. Navarro‐Santos, J. Jiménez-Halla, C. Solorio-Alvarado","doi":"10.3762/bjoc.20.141","DOIUrl":"https://doi.org/10.3762/bjoc.20.141","url":null,"abstract":"The reaction mechanism for the chlorination and bromination of 2-naphthol with PIDA or PIFA and AlX3 (X = Cl, Br), previously reported by our group, was elucidated via quantum chemical calculations using density functional theory. The chlorination mechanism using PIFA and AlCl3 demonstrated a better experimental and theoretical yield compared to using PIDA. Additionally, the lowest-energy chlorinating species was characterized by an equilibrium of Cl–I(Ph)–OTFA–AlCl3 and [Cl–I(Ph)][OTFA–AlCl3], rather than PhICl2 being the active species. On the other hand, bromination using PIDA and AlBr3 was more efficient, wherein the intermediate Br–I(Ph)–OAc–AlBr3 was formed as active brominating species. Similarly, PhIBr2 was higher in energy than our proposed species. The reaction mechanisms are described in detail in this work and were found to be in excellent agreement with the experimental yield. These initial results confirmed that our proposed mechanism was energetically favored and therefore more plausible compared to halogenation via PhIX2.","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141648523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds","authors":"Ka-Lung Hung, Leong-Hung Cheung, Yikun Ren, Ming-Hin Chau, Yan-Yi Lam, Takashi Kajitani, Franco King‐Chi Leung","doi":"10.3762/bjoc.20.142","DOIUrl":"https://doi.org/10.3762/bjoc.20.142","url":null,"abstract":"In the design of photoharvesting and photoresponsive supramolecular systems in aqueous medium, the fabrication of amphiphilic photoswitches enables a noninvasive functional response through photoirradiation. Although most aqueous supramolecular assemblies are driven by high-energy and biodamaging UV light, we have previously reported a design of amphiphilic donor–acceptor Stenhouse adducts (DASAs) controlled by white light. Herein, we present a series of DASA amphiphiles (DAs) with minor structural modifications on the alkyl linker chain length connecting the DASA motif with the hydrophilic moiety. The excellent photoswitchability in organic medium and the photoresponsiveness in aqueous medium, driven by visible light, were investigated by UV–vis absorption spectroscopy. The assembled supramolecular nanostructures were confirmed by electron microscopy, while the supramolecular packing was revealed by X-ray diffraction analysis. Upon visible-light irradiation, significant transformations of the DA geometry enabled transformations of the supramolecular assemblies on a microscopic scale, subsequently disassembling macroscopic soft scaffolds of DAs. The current work shows promising use for the fabrication of visible-light-controlled macroscopic scaffolds, offering the next generation of biomedical materials with visible-light-controlled microenvironments and future soft-robotic systems.","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141648094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ana Flávia Candida Silva, Francisco A. Martins, Matheus P. Freitas
{"title":"Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines","authors":"Ana Flávia Candida Silva, Francisco A. Martins, Matheus P. Freitas","doi":"10.3762/bjoc.20.140","DOIUrl":"https://doi.org/10.3762/bjoc.20.140","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>Selective fluorination of the pyrrolidine ring in proline motifs has been found to induce significant conformational changes that impact the structure and biological roles of modified peptides and proteins. Vicinal difluorination of fluoroproline, for example, in (3<i>S</i>,4<i>R</i>)-3,4-difluoroproline, serves to mitigate the inherent conformational bias of the pyrrolidine ring by inducing stereoelectronic effects that attenuate this conformational bias. In this investigation, we present a quantumchemical analysis of the conformational equilibrium and effects that are induced in difluorinated pyrrolidines, with a particular focus on exploring the impact of <i>gauche</i> and anomeric effects on the conformer stabilities of different stereo- and regioisomers. Initially, we conducted a benchmark assessment comparing the optimal density functional theory method with coupled cluster with single and double excitations (CCSD) calculations and crystallographic data using the 3-fluoropyrrolidinium cation and 3-fluoropyrrolidine. Subsequently, we explored the relative energy of all favored conformations of all different stereoisomers of 2,3-, 2,4-, and 3,4-difluoropyrrolidines at the B3LYP-D3BJ/6-311++G** level. A generalized anomeric effect, arising from n<sub>N</sub>→σ*<sub>CF</sub> electron delocalization, is particularly important in modulating the energetics of the α-fluoro isomers and imparts a strong conformational bias. In contrast, the fluorine <i>gauche</i> effect assumes a secondary role, as it is overshadowed by steric and electrostatic interactions, referred to as Lewis interactions from a natural bond orbital perspective.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-140-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1572–1579. doi:10.3762/bjoc.20.140</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141609204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Electrocatalytic hydrogenation of cyanoarenes, nitroarenes, quinolines, and pyridines under mild conditions with a proton-exchange membrane reactor","authors":"Koichi Mitsudo, Atsushi Osaki, Haruka Inoue, Eisuke Sato, Naoki Shida, Mahito Atobe, Seiji Suga","doi":"10.3762/bjoc.20.139","DOIUrl":"https://doi.org/10.3762/bjoc.20.139","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>An electrocatalytic hydrogenation of cyanoarenes, nitroarenes, quinolines, and pyridines using a proton-exchange membrane (PEM) reactor was developed. Cyanoarenes were then reduced to the corresponding benzylamines at room temperature in the presence of ethyl phosphate. The reduction of nitroarenes proceeded at room temperature, and a variety of anilines were obtained. The quinoline reduction was efficiently promoted by adding a catalytic amount of <i>p</i>-toluenesulfonic acid (PTSA) or pyridinium <i>p</i>-toluenesulfonate (PPTS). Pyridine was also reduced to piperidine in the presence of PTSA.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-139-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1560–1571. doi:10.3762/bjoc.20.139</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Draco Kriger, Michael A. Pasquale, Brigitte G. Ampolini, Jonathan R. Chekan
{"title":"Mining raw plant transcriptomic data for new cyclopeptide alkaloids","authors":"Draco Kriger, Michael A. Pasquale, Brigitte G. Ampolini, Jonathan R. Chekan","doi":"10.3762/bjoc.20.138","DOIUrl":"https://doi.org/10.3762/bjoc.20.138","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>In recent years, genome and transcriptome mining have dramatically expanded the rate of discovering diverse natural products from bacteria and fungi. In plants, this approach is often more limited due to the lack of available annotated genomes and transcriptomes combined with a less consistent clustering of biosynthetic genes. The recently identified burpitide class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products offer a valuable opportunity for bioinformatics-guided discovery in plants due to their short biosynthetic pathways and gene encoded substrates. Using a high-throughput approach to assemble and analyze 700 publicly available raw transcriptomic data sets, we uncover the potential distribution of split burpitide precursor peptides in Streptophyta. Metabolomic analysis of target plants confirms our bioinformatic predictions of new cyclopeptide alkaloids from both known and new sources.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-138-graphical-abstract.jpg?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1548–1559. doi:10.3762/bjoc.20.138</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander P. Atkins, Alice C. Dean, Alastair J. J. Lennox
{"title":"Benzylic C(sp3)–H fluorination","authors":"Alexander P. Atkins, Alice C. Dean, Alastair J. J. Lennox","doi":"10.3762/bjoc.20.137","DOIUrl":"https://doi.org/10.3762/bjoc.20.137","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>The selective fluorination of C(sp<sup>3</sup>)–H bonds is an attractive target, particularly for pharmaceutical and agrochemical applications. Consequently, over recent years much attention has been focused on C(sp<sup>3</sup>)–H fluorination, and several methods that are selective for benzylic C–H bonds have been reported. These protocols operate via several distinct mechanistic pathways and involve a variety of fluorine sources with distinct reactivity profiles. This review aims to give context to these transformations and strategies, highlighting the different tactics to achieve fluorination of benzylic C–H bonds.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-137-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1527–1547. doi:10.3762/bjoc.20.137</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pooja Goyal, Akhil K. Dubey, Raghunath Chowdhury, Amey Wadawale
{"title":"Primary amine-catalyzed enantioselective 1,4-Michael addition reaction of pyrazolin-5-ones to α,β-unsaturated ketones","authors":"Pooja Goyal, Akhil K. Dubey, Raghunath Chowdhury, Amey Wadawale","doi":"10.3762/bjoc.20.136","DOIUrl":"https://doi.org/10.3762/bjoc.20.136","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>The enantioselective 1,4-addition reaction of pyrazolin-5-ones to α,β-unsaturated ketones catalyzed by a cinchona alkaloid-derived primary amine–Brønsted acid composite is reported. Both enantiomers of the anticipated pyrazole derivatives were obtained in good to excellent yields (up to 97%) and high enantioselectivities (up to 98.5% ee) under mild reaction conditions. In addition, this protocol was further expanded to synthesize highly enantioenriched hybrid molecules bearing biologically relevant heterocycles.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-136-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1518–1526. doi:10.3762/bjoc.20.136</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141566895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Tetrabutylammonium iodide-catalyzed oxidative α-azidation of β-ketocarbonyl compounds using sodium azide","authors":"Christopher Mairhofer, David Naderer, Mario Waser","doi":"10.3762/bjoc.20.135","DOIUrl":"https://doi.org/10.3762/bjoc.20.135","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>We herein report the oxidative α-azidation of carbonyl compounds by using NaN<sub>3</sub> in the presence of dibenzoyl peroxide catalyzed by tetrabutylammonium iodide (TBAI). By utilizing these readily available bulk chemicals a variety of cyclic β-ketocarbonyl derivatives can be efficiently α-azidated under operationally simple conditions. Control experiments support a mechanistic scenario involving in situ formation of an ammonium hypoiodite species which first facilitates the α-iodination of the pronucleophile, followed by a phase-transfer-catalyzed nucleophilic substitution by the azide. Furthermore, we also show that an analogous α-nitration by using NaNO<sub>2</sub> under otherwise identical conditions is possible as well.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-135-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1510–1517. doi:10.3762/bjoc.20.135</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141549168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Behzad Nasiri, Ghaffar Pasdar, Paul Zebrowski, Katharina Röser, David Naderer, Mario Waser
{"title":"Towards an asymmetric β-selective addition of azlactones to allenoates","authors":"Behzad Nasiri, Ghaffar Pasdar, Paul Zebrowski, Katharina Röser, David Naderer, Mario Waser","doi":"10.3762/bjoc.20.134","DOIUrl":"https://doi.org/10.3762/bjoc.20.134","url":null,"abstract":"<p><font size='+1'><b>Abstract</b></font></p>\u0000<p>We herein report the asymmetric organocatalytic addition of azlactones to allenoates. Upon using chiral quaternary ammonium salt catalysts, i.e., Maruoka’s binaphthyl-based spirocyclic ammonium salts, the addition of various azlactones to allenoates proceeds in a β-selective manner with moderate levels of enantioselectivities (up to 83:17 er). Furthermore, the obtained products can be successfully engaged in nucleophilic ring opening reactions, thus giving highly functionalized α-amino acid derivatives.</p>\u0000<p align='center'><img src='https://www.beilstein-journals.org/bjoc/content/figures/1860-5397-20-134-graphical-abstract.png?max-width=550' border='0'/></p>\u0000<p><i>Beilstein J. Org. Chem.</i> <b>2024,</b> <i>20,</i> 1504–1509. doi:10.3762/bjoc.20.134</p>","PeriodicalId":8756,"journal":{"name":"Beilstein Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141549169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}