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Baykov SV, Semenov AV, Presnukhina SI, Tarasenko MV, Shetnev AA, Frontera A, Boyarskiy VP, Kukushkin VY. Hybrid 2D Supramolecular Organic Frameworks (SOFs) Assembled by the Cooperative Action of Hydrogen and Halogen Bonding and π⋯π Stacking Interactions. Int J Mol Sci 2024; 25:2062. [PMID: 38396739 PMCID: PMC10889172 DOI: 10.3390/ijms25042062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The cis- and trans-isomers of 6-(3-(3,4-dichlorophenyl)-1,2,4-oxadiazol-5-yl)cyclohex-3-ene-1-carboxylic acid (cis-A and trans-A) were obtained by the reaction of 3,4-dichloro-N'-hydroxybenzimidamide and cis-1,2,3,6-tetrahydrophthalic anhydride. Cocrystals of cis-A with appropriate solvents (cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C6H14) were grown from 1,2-dichloroethane (1,2-DCE), 1,2-dibromoethane (1,2-DBE), and a n-hexane/CHCl3 mixture and then characterized by X-ray crystallography. In their structures, cis-A is self-assembled to give a hybrid 2D supramolecular organic framework (SOF) formed by the cooperative action of O-H⋯O hydrogen bonding, Cl⋯O halogen bonding, and π⋯π stacking. The self-assembled cis-A divides the space between the 2D SOF layers into infinite hollow tunnels incorporating solvent molecules. The energy contribution of each noncovalent interaction to the occurrence of the 2D SOF was verified by several theoretical approaches, including MEP and combined QTAIM and NCIplot analyses. The consideration of the theoretical data proved that hydrogen bonding (approx. -15.2 kcal/mol) is the most important interaction, followed by π⋯π stacking (approx. -11.1 kcal/mol); meanwhile, the contribution of halogen bonding (approx. -3.6 kcal/mol) is the smallest among these interactions. The structure of the isomeric compound trans-A does not exhibit a 2D SOF architecture. It is assembled by the combined action of hydrogen bonding and π⋯π stacking, without the involvement of halogen bonds. A comparison of the cis-A structures with that of trans-A indicated that halogen bonding, although it has the lowest energy in cis-A-based cocrystals, plays a significant role in the crystal design of the hybrid 2D SOF. The majority of the reported porous halogen-bonded organic frameworks were assembled via iodine and bromine-based contacts, while chlorine-based systems-which, in our case, are structure-directing-were unknown before this study.
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Affiliation(s)
- Sergey V. Baykov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia; (S.V.B.); (A.V.S.); (S.I.P.); (V.Y.K.)
| | - Artem V. Semenov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia; (S.V.B.); (A.V.S.); (S.I.P.); (V.Y.K.)
| | - Sofia I. Presnukhina
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia; (S.V.B.); (A.V.S.); (S.I.P.); (V.Y.K.)
| | - Marina V. Tarasenko
- Pharmaceutical Technology Transfer Center, Ushinsky Yaroslavl State Pedagogical University, 108 Respublikanskaya St., 150000 Yaroslavl, Russia; (M.V.T.); (A.A.S.)
| | - Anton A. Shetnev
- Pharmaceutical Technology Transfer Center, Ushinsky Yaroslavl State Pedagogical University, 108 Respublikanskaya St., 150000 Yaroslavl, Russia; (M.V.T.); (A.A.S.)
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca, Spain;
| | - Vadim P. Boyarskiy
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia; (S.V.B.); (A.V.S.); (S.I.P.); (V.Y.K.)
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia; (S.V.B.); (A.V.S.); (S.I.P.); (V.Y.K.)
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russia
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Presnukhina SI, Tarasenko MV, Geyl KK, Baykova SO, Baykov SV, Shetnev AA, Boyarskiy VP. Unusual Formation of 1,2,4-Oxadiazine Core in Reaction of Amidoximes with Maleic or Fumaric Esters. Molecules 2022; 27:molecules27217508. [PMID: 36364335 PMCID: PMC9655267 DOI: 10.3390/molecules27217508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
We have developed a simple and convenient method for the synthesis of 3-aryl- and 3-hetaryl-1,2,4-oxadiazin-5-ones bearing an easily functionalizable (methoxycarbonyl)methyl group at position 6 via the reaction of aryl or hetaryl amidoximes with maleates or fumarates. The conditions for this reaction were optimized. Different products can be synthesized selectively in good yields depending on the base used and the ratio of reactants: substituted (1,2,4-oxadiazin-6-yl)acetic acids, corresponding methyl esters, or hybrid 3-(aryl)-6-((3-(aryl)-1,2,4-oxadiazol-5-yl)methyl)-4H-1,2,4-oxadiazin-5(6H)-ones. The reaction is tolerant to substituents’ electronic and steric effects in amidoximes. As a result, a series of 2-(5-oxo-3-(p-tolyl)-5,6-dihydro-4H-1,2,4-oxadiazin-6-yl)acetic acids, their methyl esters, and 1,2,4-oxadiazoles based on them were prepared and characterized by HRMS, 1H, and 13C NMR spectroscopy. The structures of three of them were elucidated with X-ray diffraction.
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Affiliation(s)
- Sofia I. Presnukhina
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
| | - Marina V. Tarasenko
- Pharmaceutical Technology Transfer Centre, Yaroslavl State Pedagogical University Named after K.D. Ushinsky, 108 Respublikanskaya St., 150000 Yaroslavl, Russia
| | - Kirill K. Geyl
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
| | - Svetlana O. Baykova
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
| | - Sergey V. Baykov
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
| | - Anton A. Shetnev
- Pharmaceutical Technology Transfer Centre, Yaroslavl State Pedagogical University Named after K.D. Ushinsky, 108 Respublikanskaya St., 150000 Yaroslavl, Russia
| | - Vadim P. Boyarskiy
- Institute of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya Nab., 199034 Saint Petersburg, Russia
- Correspondence:
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Baykov S, Tarasenko M, Kotlyarova V, Shetnev A, Zelenkov LE, Boyarskaya IA, Boyarskiy VP. 2‐(1,2,4‐Oxadiazol‐5‐yl)aniline as a New Scaffold for Blue Luminescent Materials. ChemistrySelect 2022. [DOI: 10.1002/slct.202201201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sergey Baykov
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- Research School of Chemistry and Applied Biomedical Sciences Tomsk Polytechnic University 634034 Tomsk Russian Federation
| | - Marina Tarasenko
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Valentina Kotlyarova
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Anton Shetnev
- Pharmaceutical Technology Transfer Center Yaroslavl State Pedagogical University named after K.D. Ushinsky 108 Respublikanskaya St. 150000 Yaroslavl Russian Federation
| | - Lev E. Zelenkov
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- ITMO University 191002 Saint Petersburg Russian Federation
| | - Irina A. Boyarskaya
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Vadim P. Boyarskiy
- Institute of Chemistry Saint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
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Baykov SV, Tarasenko MV, Semenov AV, Katlenok EA, Shetnev AA, Boyarskiy VP. Dualism of 1,2,4-oxadiazole ring in noncovalent interactions with carboxylic group. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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External oxidant-free and transition metal-free synthesis of 5-amino-1,2,4-thiadiazoles as promising antibacterials against ESKAPE pathogen strains. Mol Divers 2022; 27:651-666. [PMID: 35639224 DOI: 10.1007/s11030-022-10445-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022]
Abstract
A new route to 5-amino-1,2,4-thiadiazole derivatives via reaction of N-chloroamidines with isothiocyanates has been proposed. The advantages of this method are high product yields (up to 93%), the column chromatography-free workup procedure, scalability and the absence of additive oxidizing agents or transition metal catalysts. The 28 examples of 5-amino-1,2,4-thiadiazole derivatives obtaining via the proposing protocol were evaluated in vitro against ESKAPE pathogens strains (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae). It was found that compounds 5ba, 5bd, 6a, 6d and 6c have potent antibacterial activity (MIC values 0.09-1.5 μg mL-1), which is superior to the activity of commercial antibiotics such as pefloxacin (MIC 4-8 μg mL-1) and streptomycin (MIC 2-32 μg mL-1). The additional cytotoxic assay of hit compounds on PANC-1 cell line demonstrated the low or non-cytotoxicity activity at the same level of concentrations. Thus, these 5 compounds are promising starting point for further antimicrobial drug development.
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Tarasenko MV, Kotlyarova VD, Baykov SV, Shetnev AA. 2-(1,2,4-Oxadiazol-5-yl)anilines Based on Amidoximes and Isatoic Anhydrides: Synthesis and Structure Features. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221050030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Anjali Jha, Sen A, Malla RR. Chemistry of Oxadiazole Analogues: Current Status and Applications. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tarasenko MV, Presnukhina SI, Baikov SV, Shetnev AA. Synthesis and Evaluation of Antibacterial Activity of 1,2,4-Oxadiazole-Containing Biphenylcarboxylic Acids. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220090042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Presnukhina S, Tarasenko M, Baykov S, Smirnov SN, Boyarskiy VP, Shetnev A, Korsakov MK. Entry into (E)-3-(1,2,4-oxadiazol-5-yl)acrylic acids via a one-pot ring-opening/ring-closing/retro-Diels-Alder reaction sequence. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2019.151543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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