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Puttreddy R, Kumar P, Rissanen K. Pyridine Iodine(I) Cations: Kinetic Trapping as a Sulfonate Complexes. Chemistry 2024; 30:e202304178. [PMID: 38193788 DOI: 10.1002/chem.202304178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/10/2024]
Abstract
Seven pyridine iodine(I) sulfonate complexes were prepared and isolated at low temperatures and characterized by X-ray diffraction analysis. The inherently instable pyridine iodine(I) cations are stabilized by an oxygen of sulfonate anions via the I⋅⋅⋅O halogen bond. In these complexes, the iodine atom of the pyridine iodine(I) cation acts as an electron acceptor and the sulfonate oxygen as the electron donor. These complexes are stable enough in the crystalline state, yet decompose rapidly under ambient conditions, also being unstable in solution. The (pyridine)N-I bond lengths [2.140(3)-2.197(2) Å] and the I⋅⋅⋅O halogen bonds [2.345(6)-2.227(3) Å] are analogous to (imide)N-I⋅⋅⋅O-N-pyridine uncharged halogen-bonded complexes formed from N-haloimides and pyridine N-oxides, thus confirming the existence of elusive pyridine iodine(I) cation.
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Affiliation(s)
- Rakesh Puttreddy
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
| | - Parveen Kumar
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
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2
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Medvedev AG, Medved'ko AV, Vener MV, Churakov AV, Prikhodchenko PV, Vatsadze SZ. Dioxygen-halogen bonding exemplified by crystalline peroxosolvates of N, N'-bis(haloacetyl) bispidines. Phys Chem Chem Phys 2024; 26:5195-5206. [PMID: 38261463 DOI: 10.1039/d3cp05834d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The halogen bonding in molecular crystals and supramolecular assemblies has been widely investigated. Special attention is given to the molecular structures capable of simultaneously exhibiting different types of non-covalent interactions, including conventional hydrogen bonds and halogen bonds. This paper systematically analyzes crystalline peroxosolvates of bispidine-based bis-amide derivatives, containing haloacetic acid residues, namely previously reported 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodooethanone) peroxosolvate C13H20I2N2O2·H2O2 (1) and four new crystalline compounds, 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O2·H2O2 (2), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodoethanone) peroxosolvate C13H20I2N2O5·0.5H2O2 (3), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O5·H2O2 (4), and 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-chloroethanone) peroxosolvate C13H20Cl2N2O5·H2O2 (5). Compounds 2-5 were synthesized for the first time and their crystal structures were determined by single-crystal X-ray diffractometry (SCXRD). To the best of our knowledge, 3-5 are unprecedented crystalline hydrogen peroxide adducts of organic hydroperoxides (R-OOH). Short intermolecular contacts between halogen and hydroperoxo oxygen atoms were found in 1-3. The halogen bonding of C-I(Br) fragments with dioxygen species in compounds 1-3 as well as in the previously reported cocrystal of diacetone diperoxide with triodotrinitrobenzene (6) was identified through reduced density gradient analysis, Hirshfeld surface analysis, and Bader analysis of crystalline electron density. The interactions were quantified using the electron density topological properties acquired from the periodic DFT calculations and evaluated to lie in the range of 9-19 kJ mol-1. A distinctive spectral feature was revealed for this type of interaction, involving a red shift of the characteristic O-O stretching vibration by about 6 cm-1, which appeared in IR spectra as a narrow low-intensity band in the region 837-872 cm-1.
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Affiliation(s)
- Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Aleksei V Medved'ko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Mikhail V Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Sergey Z Vatsadze
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
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3
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Wieske LE, Erdelyi M. Halogen Bonds of Halogen(I) Ions─Where Are We and Where to Go? J Am Chem Soc 2024; 146:3-18. [PMID: 38117016 PMCID: PMC10785816 DOI: 10.1021/jacs.3c11449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Halenium ions, X+, are particularly strong halogen-bond donors that interact with two Lewis bases simultaneously to form linear [D···X···D]+-type halonium complexes. Their three-center, four-electron halogen bond is both fundamentally interesting and technologically valuable as it tames the reactivity of halogen(I) ions, opening up new horizons in a variety of fields including synthetic organic and supramolecular chemistry. Understanding this bonding situation enables the development of improved halogen(I) transfer reactions and of advanced functional materials. Following a decade of investigations of basic principles, the range of applications is now rapidly widening. In this Perspective, we assess the status of the field and identify its key advances and the main bottlenecks. Clearing common misunderstandings that may hinder future progress, we aim to inspire and direct future research efforts.
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Affiliation(s)
- Lianne
H. E. Wieske
- Department of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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4
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Piña MDLN, Bauzá A. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Int J Mol Sci 2023; 24:13035. [PMID: 37685843 PMCID: PMC10488009 DOI: 10.3390/ijms241713035] [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: 07/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.
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Affiliation(s)
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Baleares, Spain;
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5
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Puttreddy R, Rautiainen JM, Yu S, Rissanen K. N-X⋅⋅⋅O-N Halogen Bonds in Complexes of N-Haloimides and Pyridine-N-oxides: A Large Data Set Study. Angew Chem Int Ed Engl 2023; 62:e202307372. [PMID: 37314001 DOI: 10.1002/anie.202307372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/15/2023]
Abstract
N-X⋅⋅⋅- O-N+ halogen-bonded systems formed by 27 pyridine N-oxides (PyNOs) as halogen-bond (XB) acceptors and two N-halosuccinimides, two N-halophthalimides, and two N-halosaccharins as XB donors are studied in silico, in solution, and in the solid state. This large set of data (132 DFT optimized structures, 75 crystal structures, and 168 1 H NMR titrations) provides a unique view to structural and bonding properties. In the computational part, a simple electrostatic model (SiElMo) for predicting XB energies using only the properties of halogen donors and oxygen acceptors is developed. The SiElMo energies are in perfect accord with energies calculated from XB complexes optimized with two high-level DFT approaches. Data from in silico bond energies and single-crystal X-ray structures correlate; however, data from solution do not. The polydentate bonding characteristic of the PyNOs' oxygen atom in solution, as revealed by solid-state structures, is attributed to the lack of correlation between DFT/solid-state and solution data. XB strength is only slightly affected by the PyNO oxygen properties [(atomic charge (Q), ionization energy (Is,min ) and local negative minima (Vs,min )], as the σ-hole (Vs,max ) of the donor halogen is the key determinant leading to the sequence N-halosaccharin>N-halosuccinimide>N-halophthalimide on the XB strength.
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Affiliation(s)
- Rakesh Puttreddy
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, 40014, Jyväskylä, Finland
| | - J Mikko Rautiainen
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, 40014, Jyväskylä, Finland
| | - Shilin Yu
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, 40014, Jyväskylä, Finland
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, 40014, Jyväskylä, Finland
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6
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Rostami N, Faridghiasi F, Ghebleh A, Noei H, Samadzadeh M, Gomari MM, Tajiki A, Abdouss M, Aminoroaya A, Kumari M, Heidari R, Uversky VN, Smith BR. Design, Synthesis, and Comparison of PLA-PEG-PLA and PEG-PLA-PEG Copolymers for Curcumin Delivery to Cancer Cells. Polymers (Basel) 2023; 15:3133. [PMID: 37514522 PMCID: PMC10385204 DOI: 10.3390/polym15143133] [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: 06/19/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Curcumin (CUR) has potent anticancer activities, and its bioformulations, including biodegradable polymers, are increasingly able to improve CUR's solubility, stability, and delivery to cancer cells. In this study, copolymers comprising poly (L-lactide)-poly (ethylene glycol)-poly (L-lactide) (PLA-PEG-PLA) and poly (ethylene glycol)-poly (L-lactide)-poly (ethylene glycol) (PEG-PLA-PEG) were designed and synthesized to assess and compare their CUR-delivery capacity and inhibitory potency on MCF-7 breast cancer cells. Molecular dynamics simulations and free energy analysis indicated that PLA-PEG-PLA has a higher propensity to interact with the cell membrane and more negative free energy, suggesting it is the better carrier for cell membrane penetration. To characterize the copolymer synthesis, Fourier transform-infrared (FT-IR) and proton nuclear magnetic resonance (1H-NMR) were employed, copolymer size was measured using dynamic light scattering (DLS), and their surface charge was determined by zeta potential analysis. Characterization indicated that the ring-opening polymerization (ROP) reaction was optimal for synthesizing high-quality polymers. Microspheres comprising the copolymers were then synthesized successfully. Of the two formulations, PLA-PEG-PLA experimentally exhibited better results, with an initial burst release of 17.5%, followed by a slow, constant release of the encapsulated drug up to 80%. PLA-PEG-PLA-CUR showed a significant increase in cell death in MCF-7 cancer cells (IC50 = 23.01 ± 0.85 µM) based on the MTT assay. These data were consistent with gene expression studies of Bax, Bcl2, and hTERT, which showed that PLA-PEG-PLA-CUR induced apoptosis more efficiently in these cells. Through the integration of nano-informatics and in vitro approaches, our study determined that PLA-PEG-PLA-CUR is an optimal system for delivering curcumin to inhibit cancer cells.
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Affiliation(s)
- Neda Rostami
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Farzaneh Faridghiasi
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Aida Ghebleh
- School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Hadi Noei
- Department of Medical Biology and Genetics, Faculty of Medicine, Istinye University, Istanbul 34010, Turkey
| | - Meisam Samadzadeh
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34010, Turkey
| | - Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Alireza Tajiki
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Majid Abdouss
- Department of Chemistry, Amirkabir University of Technology, Tehran 1591634311, Iran
| | - Alireza Aminoroaya
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Manisha Kumari
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Bryan R Smith
- Department of Biomedical Engineering and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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7
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A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies. Int J Mol Sci 2023; 24:ijms24065530. [PMID: 36982603 PMCID: PMC10056977 DOI: 10.3390/ijms24065530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
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8
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Wang H, Wu WX, Jin WJ. Cocrystals assembled from iodoperfluorobenzene and flexible NTPO via halogen and π-hole bonds. Acta Crystallogr C 2023; 79:36-42. [PMID: 36739608 DOI: 10.1107/s2053229622011822] [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: 09/04/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023] Open
Abstract
Two binary cocrystals of 1,4-diiodotetrafluorobenzene (1,4-DITFB, C6F4I2) and 1,3,5-trifluoro-2,4,6-triiodobenzene (1,3,5-TITFB, C6F3I3) with the flexible 2-{[(naphthalen-2-yl)methyl]sulfanyl}pyridine 1-oxide (NTPO, C16H13NOS) molecule were successfully prepared and characterized by X-ray diffraction and quantum chemistry calculation methods. X-ray diffraction analysis reveals that the conformation of the flexible NTPO molecule has been changed significantly after introducing the 1,4-DITFB or 1,3,5-TITFB molecule into the NTPO lattice. Also the formation of the binary cocrystals is driven mainly by robust C-I...-O-N+ halogen bonds and π-hole...π-bond interactions, and they possess `sandwich' structural frameworks. Moreover, interaction energy analysis and AIM analysis were used to explore the contribution of different fragments to the structural stability and the corresponding electronic properties, which reveals that the robust halogen bonds with shorter bonding lengths [2.768 (4) and 2.789 (3) Å] are suggested to be covalent to a certain degree.
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Affiliation(s)
- Hui Wang
- College of Chemistry and Material Science, Shanxi Normal University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Wen Xin Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Wei Jun Jin
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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9
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Ward JS, Martõnova J, Wilson LME, Kramer E, Aav R, Rissanen K. Carbonyl hypoiodites from pivalic and trimesic acid and their silver(I) intermediates. Dalton Trans 2022; 51:14646-14653. [PMID: 36093683 DOI: 10.1039/d2dt01988d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first tris(O-I-N) carbonyl hypoiodites have been synthesised based on trimesic acid and pyridine or 4-methylpyridine, with their structures definitively confirmed by single crystal X-ray diffraction (SCXRD). The more soluble carbonyl hypoiodites based on pivalic acid have also been studied via NMR, SCXRD, and computational analyses, enabling the study of the direct silver(I) precursor and intermediates of the resulting carbonyl hypoiodites generated using a range of substituted pyridines.
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Affiliation(s)
- Jas S Ward
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Jevgenija Martõnova
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Laura M E Wilson
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Eric Kramer
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Riina Aav
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
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10
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Sušanj R, Nemec V, Bedeković N, Cinčić D. Halogen Bond Motifs in Cocrystals of N, N, O and N, O, O Acceptors Derived from Diketones and Containing a Morpholine or Piperazine Moiety. CRYSTAL GROWTH & DESIGN 2022; 22:5135-5142. [PMID: 36097548 PMCID: PMC9461725 DOI: 10.1021/acs.cgd.2c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/26/2022] [Indexed: 06/15/2023]
Abstract
In this study, we investigate the halogen bond acceptor potential of oxygen and nitrogen atoms of morpholine and piperazine fragments when they are peripherally located on N,O,O or N,N,O acceptor molecules. We synthesized four acceptor molecules derived from either acetylacetone or benzoylacetone and cocrystallized them with 1,4-diiodotetrafluorobenzene and 1,3,5-triiodotrifluorobenzene. This resulted in eight cocrystals featuring different topicities and geometric dispositions of donor atoms. In all cocrystals, halogen bonds are formed with either the morpholinyl oxygen atom or the terminal piperazine nitrogen atom. The I···Omorpholine halogen bonds feature lower relative shortening values than I···Nterminal, I···Ocarbonyl, and I···Nproximal halogen bonds. The N and O halogen bond acceptor sites were evaluated through calculations of molecular electrostatic potential values.
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11
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Shi R, Yu D, Zhou F, Yu J, Mu T. An emerging deep eutectic solvent based on halogen-bond. Chem Commun (Camb) 2022; 58:4607-4610. [DOI: 10.1039/d2cc00528j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new deep eutectic solvents (DES) driven by halogen-bond was exploited. A family of eutectic mixtures in liquid state were obtained by combination of quaternary ammonium salts and dihalogens. The...
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12
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Abstract
A detailed investigation of ligand exchange between iodine(I) ions in [N···I···N]+ halogen-bonded complexes is presented. Ligand exchange reactions were conducted to successfully confirm whether iodine(I) complex formation, via the classical...
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13
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Altunayar-Unsalan C, Unsalan O. Structural and anharmonic vibrational spectroscopic analysis of artificial sweetener alitame: A DFT study for molecular basis of sweet taste. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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14
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Fotović L, Bedeković N, Stilinović V. Evaluation of Halogenopyridinium Cations as Halogen Bond Donors. CRYSTAL GROWTH & DESIGN 2021; 21:6889-6901. [PMID: 34880714 PMCID: PMC8641392 DOI: 10.1021/acs.cgd.1c00805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Indexed: 06/13/2023]
Abstract
We have performed a database survey and a structural and computational study of the potential and the limitations of halogenopyridinium cations as halogen bond donors. The database survey demonstrated that adding a positive charge on a halogenopyridine ring increases the probability that the halogen atom will participate in a halogen bond, although for chloropyridines it remains below 60%. Crystal structures of both protonated and N-methylated monohalogenated pyridinium cations revealed that the iodo- and bromopyridinium cations always form halogen-bonding contacts with the iodide anions shorter than the sum of the vdW radii, while chloropyridinium cations mostly participate in longer contacts or fail to form halogen bonds. Although a DFT study of the electrostatic potential has shown that both protonation and N-methylation of halogenopyridines leads to a considerable increase in the ESP of the halogen σ-hole, it is generally not the most positive site on the cation, allowing for alternate binding sites.
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Affiliation(s)
- Luka Fotović
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Nikola Bedeković
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vladimir Stilinović
- Department of Chemistry,
Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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15
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Wu WX, Liu HC, Jin WJ. Halogen Bonding Adsorbent Pyridine N-oxides for Iodine Capture in Water. Chemistry 2021; 28:e202103336. [PMID: 34791726 DOI: 10.1002/chem.202103336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Rapid capture of 129 I with high volatility and toxicity in the environment has attracted much attention. Herein we reported a firstly synthesized nonporous material: pyridine N-oxides (NTPO and ATPO) as iodine adsorbent. Both of NTPO and ATPO exhibit remarkable performance on the adsorption of iodine in aqueous solution, vapor state and organic solvents. Upon the capture of iodine, pyridine N-oxides were transformed to binary cocrystals combined with the pyridine N-oxides and iodine which is driven by halogen bond between iodine and oxygen atoms. Moreover, pyridine N-oxides shows high chemical, thermal and moisture stability.
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Affiliation(s)
- Wen Xin Wu
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Hu Cheng Liu
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Wei Jun Jin
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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16
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Kramer E, Yu S, Ward JS, Rissanen K. Dihypoiodites stabilised by 4-ethylpyridine through O-I-N halogen bonds. Dalton Trans 2021; 50:14990-14993. [PMID: 34671792 DOI: 10.1039/d1dt03324g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Four bis(O-I-N) compounds have been synthesised from various dihypoiodites and 4-ethylpyridine. The compounds were characterised in both the solution and solid states by NMR spectroscopy (1H, 15N), X-ray diffraction, and computational calculations.
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Affiliation(s)
- Eric Kramer
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Shilin Yu
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Jas S Ward
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
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17
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Abstract
We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.
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18
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Yu S, Ward JS, Truong K, Rissanen K. Carbonyl Hypoiodites as Extremely Strong Halogen Bond Donors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shilin Yu
- Department of Chemistry University of Jyvaskyla Survontie 9 B 40014 Jyväskylä Finland
| | - Jas S. Ward
- Department of Chemistry University of Jyvaskyla Survontie 9 B 40014 Jyväskylä Finland
| | - Khai‐Nghi Truong
- Department of Chemistry University of Jyvaskyla Survontie 9 B 40014 Jyväskylä Finland
| | - Kari Rissanen
- Department of Chemistry University of Jyvaskyla Survontie 9 B 40014 Jyväskylä Finland
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19
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Yu S, Ward JS, Truong K, Rissanen K. Carbonyl Hypoiodites as Extremely Strong Halogen Bond Donors. Angew Chem Int Ed Engl 2021; 60:20739-20743. [PMID: 34268851 PMCID: PMC8518949 DOI: 10.1002/anie.202108126] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 12/19/2022]
Abstract
Neutral halogen-bonded O-I-N complexes were prepared from in situ formed carbonyl hypoiodites and aromatic organic bases. The carbonyl hypoiodites have a strongly polarized iodine atom with larger σ-holes than any known uncharged halogen bond donor. Modulating the Lewis basicity of the selected pyridine derivatives and carboxylates leads to halogen-bonded complexes where the classical O-I⋅⋅⋅N halogen bond transforms more into a halogen-bonded COO- ⋅⋅⋅I-N+ ion-pair (salt) with an asymmetric O-I-N moiety. X-ray analyses, NMR studies, and calculations reveal the halogen bonding geometries of the carbonyl hypoiodite-based O-I-N complexes, confirming that in the solid-state the iodine atom is much closer to the N-atom of the pyridine derivatives than its original position at the carboxylate O-atom.
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Affiliation(s)
- Shilin Yu
- Department of ChemistryUniversity of JyvaskylaSurvontie 9 B40014JyväskyläFinland
| | - Jas S. Ward
- Department of ChemistryUniversity of JyvaskylaSurvontie 9 B40014JyväskyläFinland
| | - Khai‐Nghi Truong
- Department of ChemistryUniversity of JyvaskylaSurvontie 9 B40014JyväskyläFinland
| | - Kari Rissanen
- Department of ChemistryUniversity of JyvaskylaSurvontie 9 B40014JyväskyläFinland
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20
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Anyfanti G, Bauzá A, Gentiluomo L, Rodrigues J, Portalone G, Frontera A, Rissanen K, Puttreddy R. Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor. Front Chem 2021. [DOI: https://doi.org/10.3389/fchem.2021.623595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X–X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X–X···N with the chloride of N-chlorosuccinimide lead to Cl–X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (−11.2 to −12.5 kcal/mol) are smaller than the values for (imide)I···N (−8.4 to −29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N–I covalent bond and I···N non-covalent bond of a (saccharin)N–I···N motif signify the covalent character for I···N halogen bonding.
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21
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Hou C, Sun S, Liu Z, Zhang H, Liu Y, An Q, Zhao J, Ma J, Sun Z, Chu W. Visible‐Light‐Induced Decarboxylative Acylation of Pyridine
N
‐Oxides with α‐Oxocarboxylic Acids Using Fluorescein Dimethylammonium as a Photocatalyst. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chuanfu Hou
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Shouneng Sun
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Ziqi Liu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Hui Zhang
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Yue Liu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Qi An
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Jian Zhao
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Junjie Ma
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Zhizhong Sun
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
| | - Wenyi Chu
- School of Chemistry and Materials Science Heilongjiang University Harbin 150080 People's Republic of China
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22
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Frosch J, Koneczny M, Bannenberg T, Tamm M. Halogen Complexes of Anionic N-Heterocyclic Carbenes. Chemistry 2021; 27:4349-4363. [PMID: 33094865 PMCID: PMC7986712 DOI: 10.1002/chem.202004418] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/12/2022]
Abstract
The lithium complexes [(WCA-NHC)Li(toluene)] of anionic N-heterocyclic carbenes with a weakly coordinating anionic borate moiety (WCA-NHC) reacted with iodine, bromine, or CCl4 to afford the zwitterionic 2-halogenoimidazolium borates (WCA-NHC)X (X=I, Br, Cl; WCA=B(C6 F5 )3 , B{3,5-C6 H3 (CF3 )2 }3 ; NHC=IDipp=1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene, or NHC=IMes=1,3-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene). The iodine derivative (WCA-IDipp)I (WCA=B(C6 F5 )3 ) formed several complexes of the type (WCA-IDipp)I⋅L (L=C6 H5 Cl, C6 H5 Me, CH3 CN, THF, ONMe3 ), revealing its ability to act as an efficient halogen bond donor, which was also exploited for the preparation of hypervalent bis(carbene)iodine(I) complexes of the type [(WCA-IDipp)I(NHC)] and [PPh4 ][(WCA-IDipp)I(WCA-NHC)] (NHC=IDipp, IMes). The corresponding bromine complex [PPh4 ][(WCA-IDipp)2 Br] was isolated as a rare example of a hypervalent (10-Br-2) system. DFT calculations reveal that London dispersion contributes significantly to the stability of the bis(carbene)halogen(I) complexes, and the bonding was further analyzed by quantum theory of atoms in molecules (QTAIM) analysis.
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Affiliation(s)
- Jenni Frosch
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Marvin Koneczny
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Thomas Bannenberg
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Matthias Tamm
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
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23
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Liang WJ, Wang H, Chen X, Zhang TT, Bai YF, Feng F, Jin WJ. Ternary Cocrystals with Large Soft Cavities: A 1,4-diiodotetrafluorobenzene (DITFB)⋅4-Biphenylpyridine N-oxide (BPNO) Host Assembled by Inclusion of Planar Aromatic Guests. Chempluschem 2021; 86:252-258. [PMID: 33555637 DOI: 10.1002/cplu.202000779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/27/2021] [Indexed: 11/10/2022]
Abstract
A large soft-cavity host composed of 1,4-diiodotetrafluorobenzene (DITFB) and 4-biphenylpyridine N-oxide (BPNO) is assembled under the mediation of a planar aromatic guest molecule (pyrene or perylene) through C-I⋅⋅⋅- O-N+ halogen bonds and π-hole⋅⋅⋅π bonds. Single-crystal X-ray diffraction reveals that guest molecules can be completely encapsulated in the four-layer host cavity to assemble ternary host-guest cocrystals; namely, Pyr@DITFB ⋅ BPNO and Per@DITFB ⋅ BPNO. The luminescence of these ternary cocrystals originates from their discrete guest molecules, which exhibit pure-blue and yellow emissions, respectively, that are localized at 425 nm and in the range of 485 to 578 nm, respectively. In addition, the contribution of different fragments to the stabilization of the crystal structure is estimated by computational chemistry. These cocrystals have significant potential for use in optical applications or materials, such as photonics or organic light-emitting diodes, respectively, that require to avoid the aggregation between luminophores.
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Affiliation(s)
- Wen Juan Liang
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, 037009, P. R. China
| | - Hui Wang
- College of Chemistry and Material Science, Shanxi Normal University, Linfen, Shanxi, 041004, P. R. China
| | - Xue Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ting Ting Zhang
- College of Chemistry and Material Science, Shanxi Normal University, Linfen, Shanxi, 041004, P. R. China
| | - Yun Feng Bai
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, 037009, P. R. China
| | - Feng Feng
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, 037009, P. R. China
| | - Wei Jun Jin
- School of Chemistry and Chemical Engineering, Shanxi Datong University, Datong, Shanxi, 037009, P. R. China.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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24
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Zarechnaya OM, Anisimov AA, Belov EY, Burakov NI, Kanibolotsky AL, Mikhailov VA. Polycentric binding in complexes of trimethylamine- N-oxide with dihalogens. RSC Adv 2021; 11:6131-6145. [PMID: 35423161 PMCID: PMC8694807 DOI: 10.1039/d0ra08165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/13/2021] [Indexed: 02/01/2023] Open
Abstract
Dihalogens readily interact with trimethylamine-N-oxide under ambient conditions. Accordingly, herein, stable 1 : 1 adducts were obtained in the case of iodine chloride and iodine bromide. The crystal and molecular structure of the trimethylamine-N-oxide-iodine chloride adduct was solved. Furthermore, the geometry and electronic structure of the trimethylamine-N-oxide-dihalogen complexes were studied computationally. Only molecular ensembles were found in the global minimum for the 1 : 1 stoichiometry. The O⋯X-Y halogen bond is the main factor for the thermodynamic stability of these complexes. Arguments for electrostatic interactions as the driving force for this noncovalent interaction were discussed. Also, the equilibrium structures are additionally stabilised by weak C-H⋯X hydrogen bonds. Consequently, formally monodentate ligands are bound in a polycentric manner.
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Affiliation(s)
- Olga M Zarechnaya
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | - Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences 28 Vavilov St. 119991 Moscow Russia
- D.I. Mendeleev Russian Chemical Technological University 9 Miusskaya Sq. 125047 Moscow Russia
| | - Eugenii Yu Belov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | - Nikolai I Burakov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | | | - Vasilii A Mikhailov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
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25
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Moriyama K, Kuramochi M, Tsuzuki S, Fujii K, Morita T. Nitroxyl Catalysts for Six-Membered Ring Bromolactonization and Intermolecular Bromoesterification of Alkenes with Carboxylic Acids. Org Lett 2021; 23:268-273. [PMID: 33300800 DOI: 10.1021/acs.orglett.0c03546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a nitroxyl-catalyzed bromoesterification of alkenes with bromo reagents, which includes a six-membered ring bromolactonization of alkenyl carboxylic acids catalyzed by AZADO as the nitroxyl radical catalyst, and an intermolecular bromoesterification of alkenes with carboxylic acids using NMO as the N-oxide catalyst. We also accomplished a remote diastereoselective bromohydroxylation via an AZADO-catalyzed six-membered ring bromolactonization and a subsequent ring cleavage reaction with alkylamines to furnish ε-bromo-δ-hydroxy amides with high diastereoselectivity.
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Affiliation(s)
- Katsuhiko Moriyama
- Department of Chemistry, Graduate School of Science and Soft Molecular Activation Research Center, Chiba University 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masako Kuramochi
- Department of Chemistry, Graduate School of Science and Soft Molecular Activation Research Center, Chiba University 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Seiji Tsuzuki
- Research Initiative of Computational Sciences (RICS), Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kozo Fujii
- Department of Chemistry, Graduate School of Science and Soft Molecular Activation Research Center, Chiba University 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Takeshi Morita
- Department of Chemistry, Graduate School of Science and Soft Molecular Activation Research Center, Chiba University 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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26
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Anyfanti G, Bauzá A, Gentiluomo L, Rodrigues J, Portalone G, Frontera A, Rissanen K, Puttreddy R. Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor. Front Chem 2021; 9:623595. [PMID: 33996740 PMCID: PMC8116742 DOI: 10.3389/fchem.2021.623595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/01/2021] [Indexed: 02/05/2023] Open
Abstract
Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.
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Affiliation(s)
- Goulielmina Anyfanti
- Department of Chemistry, University of Jyvaskyla, Jyvaskyla, Finland
- Centro de Química da Madeira, MMRG, Universidade da Madeira, Funchal, Portugal
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Palma de Mallorca (Balearus), Spain
| | - Lorenzo Gentiluomo
- Department of Chemistry, University of Jyvaskyla, Jyvaskyla, Finland
- Department of Chemistry, “La Sapienza” University of Rome, Rome, Italy
| | - João Rodrigues
- Centro de Química da Madeira, MMRG, Universidade da Madeira, Funchal, Portugal
| | - Gustavo Portalone
- Department of Chemistry, “La Sapienza” University of Rome, Rome, Italy
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Palma de Mallorca (Balearus), Spain
- *Correspondence: Antonio Frontera
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, Jyvaskyla, Finland
- Kari Rissanen
| | - Rakesh Puttreddy
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
- Rakesh Puttreddy
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27
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Nemec V, Lisac K, Bedeković N, Fotović L, Stilinović V, Cinčić D. Crystal engineering strategies towards halogen-bonded metal–organic multi-component solids: salts, cocrystals and salt cocrystals. CrystEngComm 2021. [DOI: 10.1039/d1ce00158b] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This highlight presents an overview of the current advances in the preparation of halogen bonded metal–organic multi-component solids, including salts and cocrystals comprising neutral and ionic constituents.
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Affiliation(s)
- Vinko Nemec
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Katarina Lisac
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Nikola Bedeković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Luka Fotović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Vladimir Stilinović
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Dominik Cinčić
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
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28
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Twum K, Rissanen K, Beyeh NK. Recent Advances in Halogen Bonded Assemblies with Resorcin[4]arenes. CHEM REC 2020; 21:386-395. [PMID: 33369108 DOI: 10.1002/tcr.202000140] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/12/2022]
Abstract
Resorcinarenes are cavity-containing compounds when in the crown conformation, from the calixarene family of concave compounds. These easy to synthesize macrocycles can be decorated at the upper rim through the eight hydroxyl groups and/or the 2-position of the aromatic ring. They are good synthons in supramolecular chemistry leading to appealing assemblies such as open-inclusion complexes, capsules and tubes through multiple weak interactions with various guests. Halogen bonding (XB) is a highly directional non-covalent interaction by an electron-deficient halogen atom as a donor that interacts with a Lewis base, the XB acceptor. This tutorial review provides an overview of recent advances in halogen-bonded assemblies based on resorcinarenes and their derivatives, specifically focusing on discrete and capsular assemblies.
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Affiliation(s)
- Kwaku Twum
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, 48309, Michigan, USA
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, P. O. Box 35, 40014, Jyvaskyla, Finland
| | - Ngong Kodiah Beyeh
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, 48309, Michigan, USA
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29
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Sethio D, Raggi G, Lindh R, Erdélyi M. Halogen Bond of Halonium Ions: Benchmarking DFT Methods for the Description of NMR Chemical Shifts. J Chem Theory Comput 2020; 16:7690-7701. [PMID: 33136388 PMCID: PMC7726912 DOI: 10.1021/acs.jctc.0c00860] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Because of their anisotropic electron distribution and electron deficiency, halonium ions are unusually strong halogen-bond donors that form strong and directional three-center, four-electron halogen bonds. These halogen bonds have received considerable attention owing to their applicability in supramolecular and synthetic chemistry and have been intensely studied using spectroscopic and crystallographic techniques over the past decade. Their computational treatment faces different challenges to those of conventional weak and neutral halogen bonds. Literature studies have used a variety of wave functions and DFT functionals for prediction of their geometries and NMR chemical shifts, however, without any systematic evaluation of the accuracy of these methods being available. In order to provide guidance for future studies, we present the assessment of the accuracy of 12 common DFT functionals along with the Hartree-Fock (HF) and the second-order Møller-Plesset perturbation theory (MP2) methods, selected from an initial set of 36 prescreened functionals, for the prediction of 1H, 13C, and 15N NMR chemical shifts of [N-X-N]+ halogen-bond complexes, where X = F, Cl, Br, and I. Using a benchmark set of 14 complexes, providing 170 high-quality experimental chemical shifts, we show that the choice of the DFT functional is more important than that of the basis set. The M06 functional in combination with the aug-cc-pVTZ basis set is demonstrated to provide the overall most accurate NMR chemical shifts, whereas LC-ωPBE, ωB97X-D, LC-TPSS, CAM-B3LYP, and B3LYP to show acceptable performance. Our results are expected to provide a guideline to facilitate future developments and applications of the [N-X-N]+ halogen bond.
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Affiliation(s)
- Daniel Sethio
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Gerardo Raggi
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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30
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Lindblad S, Németh FB, Földes T, Vanderkooy A, Pápai I, Erdélyi M. O-I-O halogen bond of halonium ions. Chem Commun (Camb) 2020; 56:9671-9674. [PMID: 32696769 DOI: 10.1039/d0cc03513k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The reactivity of halonium ions is conveniently modulated by three-center, four-electron halogen bonds. Such stabilized halonium complexes are valuable reagents for oxidations and halofunctionalization reactions. We report the first example of the stabilization of a halenium ion in a three-center, four-electron halogen bond with two oxygen ligands. The influence of electron density and solvent on the stability of the complexes is assessed. O-I-O halogen bond complexes are applicable as synthetic reagents and as supramolecular synthons.
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Affiliation(s)
- Sofia Lindblad
- Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden.
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31
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Maxson T, Jalilov AS, Zeller M, Rosokha SV. Halogen Bonding Between Anions: Association of Anion Radicals of Tetraiodo‐
p
‐benzoquinone with Iodide Anions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tristan Maxson
- Department of Chemistry Ball State University Muncie IN 47306 USA
| | - Almaz S. Jalilov
- Department of Chemistry King Fahd University of Petroleum and Minerals Dhahran 31261 Saudi Arabia
| | - Matthias Zeller
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
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Maxson T, Jalilov AS, Zeller M, Rosokha SV. Halogen Bonding Between Anions: Association of Anion Radicals of Tetraiodo-p-benzoquinone with Iodide Anions. Angew Chem Int Ed Engl 2020; 59:17197-17201. [PMID: 32497382 DOI: 10.1002/anie.202004384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/26/2020] [Indexed: 12/14/2022]
Abstract
Halogen bonding between two negatively charged species, tetraiodo-p-benzoquinone anion radicals (I4 Q-. ) and iodide anions, was observed and characterized for the first time. X-ray structural and EPR/UV-Vis spectral studies revealed that the anion-anion bonding led to the formation of crystals comprising 2D layers of I4 Q-. anion radicals linked by iodides and separated by Et4 N+ counter-ions. Computational analysis suggested that the seemingly antielectrostatic halogen bonds in these systems were formed via a combination of several factors. First, an attenuation of the interionic repulsion by the solvent facilitated close approach of the anions leading to their mutual polarization. This resulted in the appearance of positively charged areas (σ-holes) on the surface of the iodine substituents in I4 Q-. responsible for the attractive interaction. Finally, the solid-state associations were also stabilized by multicenter (4:4) halogen bonding between I4 Q-. and iodide.
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Affiliation(s)
- Tristan Maxson
- Department of Chemistry, Ball State University, Muncie, IN, 47306, USA
| | - Almaz S Jalilov
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Sergiy V Rosokha
- Department of Chemistry, Ball State University, Muncie, IN, 47306, USA
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Piña MDLN, Frontera A, Bauzá A. Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study. ACS Chem Biol 2020; 15:1942-1948. [PMID: 32469201 DOI: 10.1021/acschembio.0c00292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
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Abstract
Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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Mikherdov AS, Novikov AS, Boyarskiy VP, Kukushkin VY. The halogen bond with isocyano carbon reduces isocyanide odor. Nat Commun 2020; 11:2921. [PMID: 32523100 PMCID: PMC7286913 DOI: 10.1038/s41467-020-16748-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/21/2020] [Indexed: 12/24/2022] Open
Abstract
Predominantly, carbon atoms of various species function as acceptors of noncovalent interactions when they are part of a π-system. Here, we report on the discovery of a halogen bond involving the isocyano carbon lone pair. The co-crystallization or mechanochemical liquid-assisted grinding of model mesityl isocyanide with four iodoperfluorobenezenes leads to a series of halogen-bonded adducts with isocyanides. The obtained adducts were characterized by single-crystal and powder X-ray diffraction, solid-state IR and 13C NMR spectroscopies, and also by thermogravimetric analysis. The formation of the halogen bond with the isocyano group leads to a strong reduction of the isocyanide odor (3- to 46-fold gas phase concentration decrease). This manipulation makes isocyanides more suitable for laboratory storage and usage while preserving their reactivity, which is found to be similar between the adducts and the parent isocyanide in some common transformations, such as ligation to metal centers and the multi-component Ugi reaction. Carbon atoms of various species typically function as acceptors of noncovalent interactions when they are part of a π-system. Here, the authors report their discovery of a noncovalent halogen bond involving the isocyano carbon lone pair, which results in adducts with strongly reduced isocyanide odor.
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Affiliation(s)
- Alexander S Mikherdov
- Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation.
| | - Alexander S Novikov
- Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation
| | - Vadim P Boyarskiy
- Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation
| | - Vadim Yu Kukushkin
- Saint Petersburg State University, Universitetskaya Nab., 7/9, Saint Petersburg, Russian Federation.
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Piña MDLN, Bauzá A, Frontera A. Halogen⋯halogen interactions in decahalo-closo-carboranes: CSD analysis and theoretical study. Phys Chem Chem Phys 2020; 22:6122-6130. [DOI: 10.1039/d0cp00114g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We theoretically (PBE0-D3/def2TZVP) and experimentally (CSD analysis) demonstrate the importance of “like–like” halogen interactions for the stability of several decahalo-closo-carborane dimers.
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Affiliation(s)
- Maria de las Nieves Piña
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Bauzá
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
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Schumacher C, Fergen H, Puttreddy R, Truong KN, Rinesch T, Rissanen K, Bolm C. N-(2,3,5,6-Tetrafluoropyridyl)sulfoximines: synthesis, X-ray crystallography, and halogen bonding. Org Chem Front 2020. [DOI: 10.1039/d0qo01139h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
N-(Tetrafluoropyridyl)sulfoximines are obtained from NH-sulfoximines and pentafluoropyridine under solution-based or mechanochemical conditions, and the solid-state structures of 26 products have been determined by X-ray diffraction analysis.
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Affiliation(s)
| | - Hannah Fergen
- Institute of Organic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Rakesh Puttreddy
- Institute of Organic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
- University of Jyvaskyla
| | - Khai-Nghi Truong
- University of Jyvaskyla
- Department of Chemistry
- FI-40014 Jyväskylä
- Finland
| | - Torsten Rinesch
- Institute of Organic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Kari Rissanen
- University of Jyvaskyla
- Department of Chemistry
- FI-40014 Jyväskylä
- Finland
| | - Carsten Bolm
- Institute of Organic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
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