1
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Cheranyova AM, Zelenkov LE, Baykov SV, Izotova YA, Ivanov DM, Bokach NA, Kukushkin VY. Intermolecular Metal-Involving Pnictogen Bonding: The Case of σ-(Sb III)-Hole···d z2[Pt II] Interaction. Inorg Chem 2024; 63:14943-14957. [PMID: 39066736 DOI: 10.1021/acs.inorgchem.4c01570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Cocrystallizations of trans-[PtX'2(NCNR2)2] (R2 = Me2, X' = Cl 1a, Br 1b, I 1c; R2 = (CH2)5, X' = I 2c) with SbX3 (X = Cl, Br, I) gave 1:2 cocrystals 1a·2SbCl3, 1b·2SbBr3, 1c·2SbCl3, 1c·2SbBr3, 1c·2SbI3, and 2c·2SbI3. In all six X-ray structures, the association of the molecular coformers is achieved mainly by SbIII···dz2[PtII] metal-involving intermolecular pnictogen bonding. Density functional theory (DFT) calculations (based on experimentally determined geometries) using both gas-phase and solid-state approximations revealed that a σ-(Sb)-hole interacts with an area of negative potential associated with the dz2-orbital of the positively charged platinum(II) sites, thus forming a pnictogen bond whose energy falls in the range between -7.3 and -16.9 kcal/mol.
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Affiliation(s)
- Anna M Cheranyova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Lev E Zelenkov
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao 266000, Shandong, China
| | - Sergey V Baykov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Yulia A Izotova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Daniil M Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Nadezhda A Bokach
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, Barnaul 656049, Russian Federation
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2
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Pizzi A, Dhaka A, Beccaria R, Resnati G. Anion⋯anion self-assembly under the control of σ- and π-hole bonds. Chem Soc Rev 2024; 53:6654-6674. [PMID: 38867604 DOI: 10.1039/d3cs00479a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The electrostatic attraction between charges of opposite signs and the repulsion between charges of the same sign are ubiquitous and influential phenomena in recognition and self-assembly processes. However, it has been recently revealed that specific attractive forces between ions with the same sign are relatively common. These forces can be strong enough to overcome the Coulomb repulsion between ions with the same sign, leading to the formation of stable anion⋯anion and cation⋯cation adducts. Hydroden bonds (HBs) are probably the best-known interaction that can effectively direct these counterintuitive assembly processes. In this review we discuss how σ-hole and π-hole bonds can break the paradigm of electrostatic repulsion between like-charges and effectively drive the self-assembly of anions into discrete as well as one-, two-, or three-dimensional adducts. σ-Hole and π-hole bonds are the attractive forces between regions of excess electron density in molecular entities (e.g., lone pairs or π bond orbitals) and regions of depleted electron density that are localized at the outer surface of bonded atoms opposite to the σ covalent bonds formed by atoms (σ-holes) and above and below the planar portions of molecular entities (π-holes). σ- and π-holes can be present on many different elements of the p and d block of the periodic table and the self-assembly processes driven by their presence can thus involve a wide diversity of mono- and di-anions. The formed homomeric and heteromeric adducts are typically stable in the solid phase and in polar solvents but metastable or unstable in the gas phase. The pivotal role of σ- and π-hole bonds in controlling anion⋯anion self-assembly is described in key biopharmacological systems and in molecular materials endowed with useful functional properties.
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Affiliation(s)
- Andrea Pizzi
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Arun Dhaka
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Roberta Beccaria
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Giuseppe Resnati
- NFMLab, Department of Chemistry, Materials, Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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3
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Saifina AF, Kartashov SV, Saifina LF, Fayzullin RR. Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis(2-hydroxyethyl)-6-methyluracil. IUCRJ 2023; 10:584-602. [PMID: 37668216 PMCID: PMC10478519 DOI: 10.1107/s2052252523007108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
We considered it timely to test the applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. The procedure was carried out on the crystal of 1,3-bis(2-hydroxyethyl)-6-methyluracil, and some derived properties of the scalar potential and vector force fields were compared with those obtained from the experimental multipole model and from the aspherical pseudo-atom model with parameters fitted to the calculated structure factors. The procedure was shown to accurately replicate the general vector-field behavior, the peculiarities of the quantum potentials and the characteristics of the force-field pseudoatoms, such as charge, shape and volume, as well as to reproduce the relative arrangement of atomic and pseudoatomic zero-flux surfaces along internuclear regions. It was found that, in addition to the quantum-topological atoms, the force-field pseudoatoms are spatially reproduced within a single structural fragment and similar environment. In addition, the classical and nonclassical hydrogen bonds in the uracil derivative crystal, as well as the H...O, N...O and N...C interactions in the free π-stacked dimer of the uracil derivative molecules, were studied using the potential and force fields within the concepts of interatomic charge transfer and electron lone pair donation-acceptance. Remarkably, the nitrogen atoms in the N...O and N...C interactions behave rather like a Lewis base and an electron contributor. At the same time, the hydrogen atom in the H...O interaction, being a Lewis acid, also participates in the interatomic electron transfer by acting as a contributor. Thus, it has been argued that, when describing polar interatomic interactions within orbital-free considerations, it makes more physical sense to identify electronegative (electron occupier) and electropositive (electron contributor) atoms or subatomic fragments rather than nucleophilic and electrophilic sites.
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Affiliation(s)
- Alina F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Sergey V. Kartashov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Liliya F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
| | - Robert R. Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan 420088, Russian Federation
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4
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Zakharov AY, Kovalenko IV, Meshcheriakova EA, Nykhrikova EV, Zharova AO, Kiseleva MA, Kalle P, Tekshina EV, Kozyukhin SA, Emets VV, Bezzubov SI. The Effect of the Ancillary Ligand on Optical and Redox Properties of Cyclometalated Iridium(III) 2,5-Diphenyloxazole Complexes. RUSS J COORD CHEM+ 2022. [DOI: 10.1134/s1070328422700051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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5
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Aliyarova IS, Tupikina EY, Soldatova NS, Ivanov DM, Postnikov PS, Yusubov M, Kukushkin VY. Halogen Bonding Involving Gold Nucleophiles in Different Oxidation States. Inorg Chem 2022; 61:15398-15407. [PMID: 36137295 DOI: 10.1021/acs.inorgchem.2c01858] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A single-crystal X-ray diffraction (XRD) study of diaryliodonium tetrachloroaurates (or, in the recent terminology, tetrachloridoaurates), [(p-XC6H4)2I][AuCl4] (X = Cl, 1; Br, 2), was performed for 1 (the structure is denoted as 1a to show similarity with the isomorphic structure 2a) and two polymorphs─2a (obtained from MeOH) and 2b (from 1,2-C2H4Cl2). Examination of the XRD data for these three structures revealed 2-center C-X···AuIII (X = Cl and Br) and 3-center bifurcated C-Br···(Cl-Au) halogen bonding (abbreviated as XB) between the p-Cl or p-Br atoms of the diaryliodonium cations and the gold(III) atom of [AuCl4]-. The noncovalent nature of AuIII-involving interactions, the nucleophilicity of the gold(III) atoms, and the electrophilic role of p-X atoms of the diaryliodonium cations in the XBs were studied by a set of complementary computational methods. Combined experimental and theoretical studies allowed the recognition of the d-nucleophilicity of the [d8AuIII] atom which, regardless of its rather substantial formal 3+ charge, can function as a d-nucleophilic partner of XB. This conclusion was also supported by theoretical calculations performed for the structures' refcodes BINXOM and ICSD 62511; the obtained data verified the nucleophilicity of AuIII toward a K+ ions or a σ-(Cl)-hole, respectively. All our results, together with consideration of relevant literature, indicate that gold atoms in the three oxidation states (0, I, and even III) exhibit nucleophilicity in XBs.
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Affiliation(s)
- Irina S Aliyarova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation.,Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk 634034, Russian Federation
| | - Elena Yu Tupikina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Natalia S Soldatova
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk 634034, Russian Federation
| | - Daniil M Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation.,Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk 634034, Russian Federation
| | - Pavel S Postnikov
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk 634034, Russian Federation.,Department of Solid State Engineering, Institute of Chemical Technology, Prague 16628, Czech Republic
| | - Mekhman Yusubov
- Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk 634034, Russian Federation
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation.,Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russian Federation
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6
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Matsumoto S, Sumida R, Akazome M. Relationship between halogen-halogen interaction and electric conductivity in thiazolo[2,3-a]isoquinolin-7-ium triiodides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Chakalov ER, Tupikina EY, Ivanov DM, Bartashevich EV, Tolstoy PM. The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength. Molecules 2022; 27:4848. [PMID: 35956799 PMCID: PMC9369751 DOI: 10.3390/molecules27154848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me3PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.
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Affiliation(s)
- Edem R. Chakalov
- Institute of Chemistry, St. Petersburg State University, 198504 St. Petersburg, Russia; (E.R.C.); (E.Y.T.)
| | - Elena Yu. Tupikina
- Institute of Chemistry, St. Petersburg State University, 198504 St. Petersburg, Russia; (E.R.C.); (E.Y.T.)
| | - Daniil M. Ivanov
- Institute of Chemistry, St. Petersburg State University, 198504 St. Petersburg, Russia; (E.R.C.); (E.Y.T.)
| | | | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, 198504 St. Petersburg, Russia; (E.R.C.); (E.Y.T.)
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8
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Aliyarova IS, Tupikina EY, Ivanov DM, Kukushkin VY. Metal-Involving Halogen Bonding Including Gold(I) as a Nucleophilic Partner. The Case of Isomorphic Dichloroaurate(I)·Halomethane Cocrystals. Inorg Chem 2022; 61:2558-2567. [DOI: 10.1021/acs.inorgchem.1c03482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Irina S. Aliyarova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Elena Yu. Tupikina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Daniil M. Ivanov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, Barnaul 656049, Russian Federation
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9
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Weimer GH, Copetti JPP, Orlando T, Zanatta N, Bonacorso HG, Salbego PRS, Martins MAP. The role of attractive and repulsive interactions in the stabilization of ammonium salts structures. CrystEngComm 2022. [DOI: 10.1039/d2ce00891b] [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 series of ammonium salts was used to propose a step-by-step approach to obtain the stabilization energy and contact area data of supramolecular clusters in charged molecules. A new parameter was presented to assess the cluster energy efficiency.
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Affiliation(s)
- Gustavo H. Weimer
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - João P. P. Copetti
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Tainára Orlando
- Department of Chemistry, Federal University of Maranhão (UFMA), São Luís, MA, Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Helio G. Bonacorso
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Paulo R. S. Salbego
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Engineering and Environmental Technology (DETA), Federal University of Santa Maria (UFSM), Frederico Westphalen Campus, RS, Brazil
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos (NUQUIMHE), Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
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10
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Kinzhalov MA, Ivanov DM, Melekhova AA, Bokach NA, Gomila RM, Frontera A, Kukushkin VY. Chameleonic Metal-bound Isocyanides: π-Donating CuI-center Imparts a Nucleophilicity to the Isocyanide Carbon toward Halogen Bonding. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00034b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the structures of the isostructural cocrystals [CuI3(CNXyl)3]·CHX3 (X = Br, I), two adjacent CuI-bound isocyanide groups, whose carbon lone pairs are blocked by the ligation, exhibit nucleophilic properties induced...
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11
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Tu D, Li J, Sun F, Yan H, Poater J, Solà M. Cage -···Cage - Interaction: Boron Cluster-Based Noncovalent Bond and Its Applications in Solid-State Materials. JACS AU 2021; 1:2047-2057. [PMID: 34841417 PMCID: PMC8611790 DOI: 10.1021/jacsau.1c00348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Carboranes are boron-carbon clusters with important applications in the fields of materials, catalysis, pharmaceuticals, etc. However, the noncovalent interactions that could determine the solid-state structures and properties of such boron clusters have rarely been investigated. Herein, inspired by the coordinate bond in metallacarborane or ferrocene, the boron cluster-based noncovalent interaction (denoted as cage-···cage- interaction) between two nido-carborane clusters was successfully realized by using a pyridinium-based molecular barrier. The X-ray diffraction studies uncover that the cage-···cage- interaction has a contacting distance of 5.4-7.0 Å from centroid to centroid in the systems reported here. Theoretical calculations validate the formation of the noncovalent interaction and disclose its repulsive bonding nature that is overcome thanks to the positively charged pyridinium-based framework. Interestingly, such bulk crystalline materials containing the cage-···cage- interaction show relevant properties such as full-color absorption in the visible light range and important photothermal effect, which are absent for the control compound without carboranes. This study may offer fundamental insights into the boron cluster-based noncovalent interactions and open a new research avenue to rationally design boron cluster-based materials.
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Affiliation(s)
- Deshuang Tu
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jiaxin Li
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Fangxiang Sun
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hong Yan
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jordi Poater
- Departament
de Química Inorgànica i Orgànica & Institut
de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Miquel Solà
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, C/Maria Aurèlia Capmany,
69, Girona 17003, Catalonia Spain
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12
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Kalle P, Bezzubov SI. Synthesis and Crystal Structures of Cobalt(II/III) Tris-Phenanthrolines with Various Polyiodide Anions. RUSS J INORG CHEM+ 2021. [DOI: 10.1134/s0036023621110103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Bulatova M, Ivanov DM, Rautiainen JM, Kinzhalov MA, Truong KN, Lahtinen M, Haukka M. Studies of Nature of Uncommon Bifurcated I-I···( I- M) Metal-Involving Noncovalent Interaction in Palladium(II) and Platinum(II) Isocyanide Cocrystals. Inorg Chem 2021; 60:13200-13211. [PMID: 34357775 PMCID: PMC8424624 DOI: 10.1021/acs.inorgchem.1c01591] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 12/03/2022]
Abstract
Two isostructural trans-[MI2(CNXyl)2]·I2 (M = Pd or Pt; CNXyl = 2,6-dimethylphenyl isocyanide) metallopolymeric cocrystals containing uncommon bifurcated iodine···(metal-iodide) contact were obtained. In addition to classical halogen bonding, single-crystal X-ray diffraction analysis revealed a rare type of metal-involved stabilizing contact in both cocrystals. The nature of the noncovalent contact was studied computationally (via DFT, electrostatic surface potential, electron localization function, quantum theory of atoms in molecules, and noncovalent interactions plot methods). Studies confirmed that the I···I halogen bond is the strongest noncovalent interaction in the systems, followed by weaker I···M interaction. The electrophilic and nucleophilic nature of atoms participating in I···M interaction was studied with ED/ESP minima analysis. In trans-[PtI2(CNXyl)2]·I2 cocrystal, Pt atoms act as weak nucleophiles in I···Pt interaction. In the case of trans-[PdI2(CNXyl)2]·I2 cocrystal, electrophilic/nucleophilic roles of Pd and I are not clear, and thus the quasimetallophilic nature of the I···Pd interaction was suggested.
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Affiliation(s)
- Margarita Bulatova
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Daniil M. Ivanov
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - J. Mikko Rautiainen
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Mikhail A. Kinzhalov
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg 199034, Russian Federation
| | - Khai-Nghi Truong
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Manu Lahtinen
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Matti Haukka
- Department
of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
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14
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The Isocyanide Complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd, Pt; X = Cl, Br) as Tectons in Crystal Engineering Involving Halogen Bonds. CRYSTALS 2021. [DOI: 10.3390/cryst11070799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The isocyanide complexes cis-[MCl2(CNC6H4-4-X)2] (M = Pd; X = Cl, Br; M = Pt; X = Br) form isomorphous crystal structures exhibiting the Cl/Br and Pd/Pt exchanges featuring 1D chains upon crystallisation. Crystal packing is supported by the C–X···X–C halogen bonds (HaBs), C–H···X–C hydrogen bonds (HB), X···M semicoordination, and C···C contacts between the C atoms of aryl isocyanide ligands. The results of DFT calculations and topological analysis indicate that all the above contact types belong to attractive noncovalent interactions. A projection of the electron localization function (ELF) and an inspection of the electron density (ED) and the electrostatic potential (ESP) reveal the amphiphilic nature of X atoms playing the role of HaB donors, HaB and HB acceptors, and a nucleophilic partner in X···M semicoordination.
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15
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Poręba T, Świątkowski M, Kruszyński R. Molecular self-assembly of 1D infinite polyiodide helices in a phenanthrolinium salt. Dalton Trans 2021; 50:2800-2806. [PMID: 33533384 DOI: 10.1039/d0dt04042h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new linear polymeric polyiodide, catena-poly[tris(1,10-phenanthrolin-1-ium)tris(1,10-phenanthroline)heptaiodide], was prepared by one-step synthesis. Its formation is driven by hydrogen-bond assisted supramolecular assembly in the presence of chromium(iii) acetate. Its structure has been characterized by the means of single-crystal X-ray diffraction. To date, this is only one of the few examples of organized linear infinite polyiodides with a known structure. The interplay between the interactions within the hypervalent iodine chain and its supramolecular environment is elucidated. The electrical, thermal, and spectroscopic properties of the studied compound were investigated and associated with the structural features. The infinite character of the polyiodide chain and its similarity to the blue starch-iodine complex has been additionally confirmed by Raman spectroscopy. Despite the apparent structural and spectroscopic similarities with the previously reported 1D polymeric polyiodide, its physical properties, i.e. electrical conductivity and thermal stability, differ significantly. This can be rationalized by the differences in the orbital overlap within the iodine chain, as well as the distinct interactions with the cation.
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Affiliation(s)
- Tomasz Poręba
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - Marcin Świątkowski
- Institute of General and Ecological Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Rafał Kruszyński
- Institute of General and Ecological Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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16
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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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17
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Savinkina EV, Golubev DV, Grigoriev MS, Kornilov AV. Synthesis and crystal structure of rare-earth biuret complexes with linear pentaiodide ions: Infinite polyiodide chains in a cationic framework. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Savastano M. Words in supramolecular chemistry: the ineffable advances of polyiodide chemistry. Dalton Trans 2021; 50:1142-1165. [PMID: 33496303 DOI: 10.1039/d0dt04091f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Polyiodide chemistry has a rich history deeply intertwined with the development of supramolecular chemistry. Technological and theoretical interest in polyiodides has not diminished in the last decade, quite the contrary; yet the advances this perspective intends to cover are muddled by the involution of supramolecular vocabulary, preventing their unbiased discussion. Herein we discuss the pressing necessity of ordering the current babel of novel - and less so - supramolecular terms. Shared decisions at the community level might be required to shape the field into a harmonious body of knowledge, dominated by concepts rather than words. Secondary, σ-hole and halogen bonding schools of thought are all addressed here, together with their respective impact on the field. Then, on the basis of a shared vocabulary, a discussion of polyiodide chemistry is presented, starting with a revisited view of triiodide. The contemporary fields of supramolecular caging and polyiodide networks are then discussed, with emphasis on how the terms we choose to use deeply affect scientific progress.
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Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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19
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Quiñonero D, Alkorta I, Elguero J. Metastable Dianions and Dications. Chemphyschem 2020; 21:1597-1607. [PMID: 32314864 DOI: 10.1002/cphc.202000172] [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: 05/03/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX3 2- and LX4 2- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3 X2+ (M=Li and Na, X=F and Cl), YH3 2+ and ZH4 2+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.
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Affiliation(s)
- David Quiñonero
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3. 28006, Madrid, Spain
| | - Jose Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3. 28006, Madrid, Spain
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20
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Azofra LM, Elguero J, Alkorta I. A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds. J Phys Chem A 2020; 124:2207-2214. [DOI: 10.1021/acs.jpca.9b10681] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas, CSIC, avalada por el Instituto de Ciencia de Materiales de Sevilla, Universidad de Sevilla), Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
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21
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Fourmigué M, Dhaka A. Chalcogen bonding in crystalline diselenides and selenocyanates: From molecules of pharmaceutical interest to conducting materials. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213084] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Edis Z, Haj Bloukh S, Abu Sara H, Bhakhoa H, Rhyman L, Ramasami P. "Smart" Triiodide Compounds: Does Halogen Bonding Influence Antimicrobial Activities? Pathogens 2019; 8:E182. [PMID: 31658760 PMCID: PMC6963602 DOI: 10.3390/pathogens8040182] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial agents containing symmetrical triiodides complexes with halogen bonding may release free iodine molecules in a controlled manner. This happens due to interactions with the plasma membrane of microorganisms which lead to changes in the structure of the triiodide anion. To verify this hypothesis, the triiodide complex [Na(12-crown-4)2]I3 was prepared by an optimized one-pot synthesis and tested against 18 clinical isolates, 10 reference strains of pathogens and five antibiotics. The antimicrobial activities of this symmetrical triiodide complex were determined by zone of inhibition plate studies through disc- and agar-well-diffusion methods. The triiodide complex proved to be a broad spectrum microbicidal agent. The biological activities were related to the calculated partition coefficient (octanol/water). The microstructural analysis of SEM and EDS undermined the purity of the triiodide complex. The anionic structure consists of isolated, symmetrical triiodide anions [I-I-I]- with halogen bonding. Computational methods were used to calculate the energy required to release iodine from [I-I-I]- and [I-I···I]-. The halogen bonding in the triiodide ion reduces the antibacterial activities in comparison to the inhibitory actions of pure iodine but increases the long term stability of [Na(12-crown-4)2]I3.
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Affiliation(s)
- Zehra Edis
- College of Pharmacy and Health Science, Ajman University, Ajman P.O. Box 346, UAE.
| | - Samir Haj Bloukh
- College of Pharmacy and Health Science, Ajman University, Ajman P.O. Box 346, UAE.
| | - Hamed Abu Sara
- College of Pharmacy and Health Science, Ajman University, Ajman P.O. Box 346, UAE.
| | - Hanusha Bhakhoa
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius.
| | - Lydia Rhyman
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius.
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa.
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius.
- Department of Chemical Sciences, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa.
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23
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Poręba T, Ernst M, Zimmer D, Macchi P, Casati N. Pressure‐Induced Polymerization and Electrical Conductivity of a Polyiodide. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tomasz Poręba
- Laboratory for Synchrotron Radiation—Condensed MatterPaul Scherrer Institute 5232 Villigen–PSI Switzerland
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Michelle Ernst
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Dominik Zimmer
- Institute of GeosciencesGoethe-University Frankfurt, Crystallography/Mineralogy Altenhoeferallee 1 60438 Frankfurt am Main Germany
| | - Piero Macchi
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
- Department of ChemistryMaterials and Chemical Engineering Polytechnic of Milan Via Mancinelli 7 20131 Milano Italy
| | - Nicola Casati
- Laboratory for Synchrotron Radiation—Condensed MatterPaul Scherrer Institute 5232 Villigen–PSI Switzerland
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24
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Poręba T, Ernst M, Zimmer D, Macchi P, Casati N. Pressure-Induced Polymerization and Electrical Conductivity of a Polyiodide. Angew Chem Int Ed Engl 2019; 58:6625-6629. [PMID: 30844119 DOI: 10.1002/anie.201901178] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Indexed: 11/11/2022]
Abstract
We report the high-pressure structural characterization of an organic polyiodide salt in which a progressive addition of iodine to triiodide groups occurs. Compression leads to the initial formation of discrete heptaiodide units, followed by polymerization to a 3D anionic network. Although the structural changes appear to be continuous, the insulating salt becomes a semiconducting polymer above 10 GPa. The features of the pre-reactive state and the polymerized state are revealed by analysis of the computed electron and energy densities. The unusually high electrical conductivity can be explained with the formation of new bonds.
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Affiliation(s)
- Tomasz Poręba
- Laboratory for Synchrotron Radiation-Condensed Matter, Paul Scherrer Institute, 5232, Villigen-PSI, Switzerland.,Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Michelle Ernst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Dominik Zimmer
- Institute of Geosciences, Goethe-University Frankfurt, Crystallography/Mineralogy, Altenhoeferallee 1, 60438, Frankfurt am Main, Germany
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.,Department of Chemistry, Materials and Chemical Engineering Polytechnic of Milan, Via Mancinelli 7, 20131, Milano, Italy
| | - Nicola Casati
- Laboratory for Synchrotron Radiation-Condensed Matter, Paul Scherrer Institute, 5232, Villigen-PSI, Switzerland
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25
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Wzgarda-Raj K, Rybarczyk-Pirek AJ, Wojtulewski S, Pindelska E, Palusiak M. Oxidation of 2-mercaptopyridine N-oxide upon iodine agent: structural and FT-IR studies on charge-assisted hydrogen bonds CAHB(+) and I…I halogen interactions in 2,2′-dithiobis(pyridine N-oxide) ionic cocrystal. Struct Chem 2019. [DOI: 10.1007/s11224-019-1290-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Dash SG, Thakur TS. Cation⋯cation hydrogen bonds in synephrine salts: a typical interaction in an unusual environment. Phys Chem Chem Phys 2019; 21:20647-20660. [DOI: 10.1039/c9cp03164b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Computational studies of hydrogen-bonded cationic species observed in the synephrine salts point towards the stabilizing nature of hydrogen bonds and highlights their contribution in reducing destabilization caused by coulombic repulsion.
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Affiliation(s)
- Sibananda G. Dash
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
| | - Tejender S. Thakur
- Academy of Scientific and Innovative Research (AcSIR)
- CSIR-Central Drug Research Institute (CSIR-CDRI) campus
- Lucknow 226 031
- India
- Molecular and Structural Biology Division
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27
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Genoni A, Bučinský L, Claiser N, Contreras-García J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa L, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. Quantum Crystallography: Current Developments and Future Perspectives. Chemistry 2018; 24:10881-10905. [PMID: 29488652 DOI: 10.1002/chem.201705952] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Indexed: 11/09/2022]
Abstract
Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.
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Affiliation(s)
- Alessandro Genoni
- Université de Lorraine, CNRS, Laboratoire LPCT, 1 Boulevard Arago, F-57078, Metz, France
| | - Lukas Bučinský
- Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology, FCHPT SUT, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Nicolas Claiser
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Chimie Théorique (LCT), 4 Place Jussieu, F-75252, Paris Cedex 05, France
| | - Birger Dittrich
- Anorganische und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Enrique Espinosa
- Université de Lorraine, CNRS, Laboratoire CRM2, Boulevard des Aiguillettes, BP 70239, F-54506, Vandoeuvre-lès-Nancy, France
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, Milano, I-20133, Italy.,Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milano, Italy
| | - Paolo Giannozzi
- Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 208, I-33100, Udine, Italy
| | - Jean-Michel Gillet
- Structure, Properties and Modeling of Solids Laboratory, CentraleSupelec, Paris-Saclay University, 3 rue Joliot-Curie, 91191, Gif-sur-Yvette, France
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Anders Ø Madsen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Lou Massa
- Hunter College & the Ph.D. Program of the Graduate Center, City University of New York, New York, USA
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, B3M 2J6, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3, Canada.,Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada.,Département de Chimie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan, 48824, USA.,Institute for Cyber Enabled Research, Michigan State University, 567 Wilson Road, Room 1440, East Lansing, Michigan, 48824, USA
| | - Philip N H Nakashima
- Department of Materials Science and Engineering, Monash University, Victoria, 3800, Australia
| | - Holger Ott
- Bruker AXS GmbH, Östliche Rheinbrückenstraße 49, 76187, Karlsruhe, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-22100, Lund, Sweden
| | - Karlheinz Schwarz
- Technische Universität Wien, Institut für Materialwissenschaften, Getreidemarkt 9, A-1060, Vienna, Austria
| | - Marek Sierka
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany
| | - Simon Grabowsky
- Fachbereich 2-Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Universität Bremen, Leobener Str. 3, 28359, Bremen, Germany
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28
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Savastano M, Bazzicalupi C, García C, Gellini C, López de la Torre MD, Mariani P, Pichierri F, Bianchi A, Melguizo M. Iodide and triiodide anion complexes involving anion-π interactions with a tetrazine-based receptor. Dalton Trans 2018; 46:4518-4529. [PMID: 28262880 DOI: 10.1039/c7dt00134g] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protonated forms of the tetrazine ligand L2 (3,6-bis(morpholin-4-ylethyl)-1,2,4,5-tetrazine) interact with iodide in aqueous solution forming relatively stable complexes (ΔG° = -11.6(4) kJ mol-1 for HL2+ + I- = (HL2)I and ΔG° = -13.4(2) kJ mol-1 for H2L22+ + I- = [(H2L2)I]+). When solutions of [(H2L2)I]+ are left in contact with air, crystals of the oxidation product (H2L2)2(I3)3I·4H2O are formed. Unfortunately, the low solubility of I3- complexes prevents the determination of their stability constants. The crystal structures of H2L2I2·H2O (1), H2L2(I3)2·2H2O (2) and (H2L2)2(I3)3I·4H2O (3) were determined by means of X-ray diffraction analyses. In all crystal structures, it was found that the interaction between I- and I3- with H2L22+ is dominated by anion interactions with the π electron density of the receptor. Only in the case of 1, the iodide anions involved in close anion-π interactions with the ligand tetrazine ring form an additional H-bond with the protonated morpholine nitrogen of an adjacent ligand molecule. Conversely, in crystals of 2 and 3 there are alternate segregated planes which contain only protonated ligands hydrogen-bonded to cocrystallized water molecules or I3- and I- forming infinite two-dimensional networks established through short interhalogen contacts, making these crystalline products good candidates to behave as solid conductors. In the solid complexes, the triiodide anion displays both end-on and side-on interaction modes with the tetrazine ring, in agreement with density functional theory calculations indicating a preference for the alignment of the I3- molecular axis with the molecular axis of the ligand. Further information about geometries and structures of triiodide anions in 2 and 3 was acquired by the analysis of their Raman spectra.
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Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Celeste García
- Department of Inorganic and Organic Chemistry, University of Jaén 23071, Jaén, Spain.
| | - Cristina Gellini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | | | - Palma Mariani
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Fabio Pichierri
- Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan.
| | - Antonio Bianchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Manuel Melguizo
- Department of Inorganic and Organic Chemistry, University of Jaén 23071, Jaén, Spain.
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29
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Aubert E, Espinosa E, Nicolas I, Jeannin O, Fourmigué M. Toward a reverse hierarchy of halogen bonding between bromine and iodine. Faraday Discuss 2017; 203:389-406. [DOI: 10.1039/c7fd00067g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compare here the halogen bond characteristics of bimolecular adducts involving either N-bromo- or N-iodosaccharin as strong halogen bond donors, with 4-picoline as a common XB acceptor. In the NBSac·Pic system, the bromine atom of NBSac is displaced toward the picoline, almost at a median position between the two nitrogen atoms, NSac and N′Pic, with NSac⋯Br and Br⋯N′Pic distances at 2.073(6) and 2.098(6) Å respectively. This extreme situation contrasts with the analogous iodine derivative, NISac·Pic, where the NSac–I and I⋯N′Pic distances amount to 2.223(4) and 2.301(4) Å respectively. Periodic DFT calculations, and molecular calculations of adducts (PBEPBE-D2 aug-cc-pVTZ) either at the experimental frozen geometry or with optimization of the halogen position, indicate a more important degree of covalency (i.e. shared-shell character) in the adduct formed with the bromine atom. A stronger charge transfer to the picoline is also found for the bromine (+0.27 |e|) than for the iodine (+0.18 |e|) system. This inversion of halogen bond strength between I and Br finds its origin in the strong covalent character of the interaction in these adducts, in line with the strength of covalent N–Br and N–I bonds. Detailed characterization of the critical points (CPs) of the L(r) = −∇2ρ(r) function along bonding directions has permitted the adducts to be distinguished and they can be respectively described as “neutral” NISac/Pic and “intermediate” NSac/Br/Pic, the latter with Br being close to formal equivalent NSac⋯Br and Br⋯N′Pic interactions but still more associated to the XB donor than to the picoline, as indicated by the topological and energetic properties of the ρ(r) function at the bond critical points (BCPs).
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Affiliation(s)
- Emmanuel Aubert
- Laboratoire CRM2
- UMR CNRS 7036
- Institut Jean Barriol
- Université de Lorraine
- 54506 Vandoeuvre-les-Nancy
| | - Enrique Espinosa
- Laboratoire CRM2
- UMR CNRS 7036
- Institut Jean Barriol
- Université de Lorraine
- 54506 Vandoeuvre-les-Nancy
| | - Irène Nicolas
- Institut des Sciences Chimiques de Rennes (ISCR)
- UMR CNRS 6226
- Université de Rennes 1
- Campus de Beaulieu
- 35042 Rennes
| | - Olivier Jeannin
- Institut des Sciences Chimiques de Rennes (ISCR)
- UMR CNRS 6226
- Université de Rennes 1
- Campus de Beaulieu
- 35042 Rennes
| | - Marc Fourmigué
- Institut des Sciences Chimiques de Rennes (ISCR)
- UMR CNRS 6226
- Université de Rennes 1
- Campus de Beaulieu
- 35042 Rennes
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