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. [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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Kaplanskiy MV, Kruglov ML, Vanin AA, Tupikina EY. Dynamics of non-covalent interactions during the P-O bond cleavage reaction by ribonuclease A. Phys Chem Chem Phys 2024. [PMID: 39054927 DOI: 10.1039/d4cp01888e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
In this work, an atomistic-scale investigation of the phosphodiester P-O bond cleavage reaction by the enzyme ribonuclease A was carried out using computer simulation techniques. It is shown that during the reaction the network of non-covalent interactions in the active center of the ribonuclease changes significantly, while the role of these non-covalent interactions is different: coordination of the corresponding groups, electron density transfer, and ligand holding in the active center. It is shown that the process of proton transfer from Asp121 to His119 is the first stage of this reaction; at the same time, the hydrogen bond between the phosphate ligand and the imino group of Arg39 is broken, which, although keeping the ligand in the active center, does not allow the ligand to orient itself more conveniently for subsequent proton transfers. Furthermore, the key step of this reaction occurs: proton transfer with the participation of imidazole rings His12 and His119, in which the guiding role is played by several hydrogen bonds with the participation of Phe120, and the role of an electron density carrier is played by the pnictogen bond between the oxygen of the phosphate ligand and the pyridine-like nitrogen of the imidazole ring His119, which was detected for the first time.
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Affiliation(s)
- Mark V Kaplanskiy
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Maxim L Kruglov
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Aleksandr A Vanin
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
| | - Elena Yu Tupikina
- Institute of Chemistry, St Petersburg State University, St Petersburg, Russia.
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3
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Matveychuk YV, Regel RL, Bartashevich EV. Noncovalent Interactions of Silatranes and Germatranes with the Surface of Stoichiometric and Hydroxylated 2D Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:13227-13235. [PMID: 38870102 DOI: 10.1021/acs.langmuir.4c01367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Analysis of noncovalent interactions formed by the surface of a 2D silica bilayer and atrane molecules, as precursors of functional layers immobilized on a surface of silicatene, was performed. For this purpose, the systems of substituted silatranes and germatranes adsorbed on silicatene surfaces with different amounts of hydroxyl groups (0, 2, 4, and 30 per cell) were simulated by using quantum chemical modeling with periodic boundary conditions and full-electron basis sets. The observation results for interaction energy changes in the systems "atrane molecule-silicatene surface" with increasing silanol number of the silicatene surface can be used to predict the optimal degree of silicatene hydroxylation in order to control the effective progress of atrane deprotection on activated 2D silica materials. In addition to the typical hydrogen bonds, the ability of atranes to form noncovalent O···O and O···Hal interactions was discovered. In these bonds, the oxygen or halogen atoms of atranes act as electron-donor centers in relation to the silicatene oxygen atoms. The observed weakening of the Ge-O covalent bonds in germatranes, on which further deprotection reaction depends, is more manifested than for the Si-O bonds in adsorbed silatranes.
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Affiliation(s)
- Yury V Matveychuk
- MMMFM Research Laboratory, South Ural State University, Chelyabinsk 454080, Russia
| | - Roman L Regel
- MMMFM Research Laboratory, South Ural State University, Chelyabinsk 454080, Russia
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4
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Bartashevich EV, Levina EO, Yushina ID, Sozykin SA, Tsirelson VG. Electron delocalization in defect-containing graphene and its influence on tetrel bond formation. Phys Chem Chem Phys 2023; 25:24342-24354. [PMID: 37672065 DOI: 10.1039/d3cp03127f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Using the advanced analyses of electron density and fermionic potential, we show how electron delocalization influences the ability of defect-containing graphene to form tetrel bonds. The Cg atoms of a vacancy defect can produce one nonpolar interaction, alongside a peculiar polar Cg⋯Cg bond. The latter stems from the presence of a localized electron pair on a vacancy defect Cg atom and the local depletion of electron localization on another Cg atom. This interaction is an example of intralayer tetrel bond. In the presence of an absorbed molecule of bisphenol A diglycidyl ether (DGEBA), graphene is able to form incipient tetrel Cg⋯O bonds with an ether group oxygen. In contrast to an epoxy group oxygen, the disposition of the ether oxygen often causes the orientation of electron-rich π-domains of graphene carbon on the weakly expressed electrophilic region of the oxygen. In the case of graphene with a point Si defect, the Si atom can form quite strong Si⋯C interactions with the DGEBA aryl carbons. In contrast to other noncovalent bonds, this interaction significantly alters the electron (de)localization on the Si atom and in the aryl ring. The reliability of the obtained results is enhanced by the use of multiple 2D periodic models with defects located at different positions along the DGEBA skeleton.
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Affiliation(s)
| | - Elena O Levina
- South Ural State University, 454080 Chelyabinsk, Russia.
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | | | - Vladimir G Tsirelson
- South Ural State University, 454080 Chelyabinsk, Russia.
- D.I. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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5
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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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6
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Andreo L, Gomila RM, Priola E, Giordana A, Pantaleone S, Diana E, Mahmoudi G, Frontera A. Anion···Anion [AuI 4] -···[AuI 2] - Complex Trapped in the Solid State by Tetramethylammonium Cations. CRYSTAL GROWTH & DESIGN 2022; 22:6539-6544. [PMID: 36345385 PMCID: PMC9635596 DOI: 10.1021/acs.cgd.2c00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/01/2022] [Indexed: 05/24/2023]
Abstract
A discrete π-hole···σ-hole dimer is synthesized and X-ray characterized. It presents a perfect thumbtack geometry where the σ-hole of the linear [AuI2]- anion points to the π-hole located above the central Au-atom of the [AuI4]- anion. Such discrete π-hole···σ-hole dimers are unprecedented in literature, since all mixed-valence gold(I/III) iodide compounds reported to date form infinite ···([AuI4]-···[AuI2]-) n ·· chains in the solid state. If an excess of iodine is used for the synthesis, triiodide [I3]- ions are partially incorporated into the [AuI2]- sites, forming infinite chains. The nature of the anion···anion interaction has been studied considering two possibilities: (i) a π-hole coinage bond or (ii) σ-hole halogen bond using high-level density functional theory calculations, the quantum theory of atoms in molecules, and the noncovalent interaction plot index.
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Affiliation(s)
- Luca Andreo
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Emanuele Priola
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Alessia Giordana
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Stefano Pantaleone
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Eliano Diana
- Department of Chemistry, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh 83111-55181, Iran
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
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7
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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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8
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Abstract
Osme bonds have been recently defined as the attractive interaction between an element of group 8 acting as an electrophile and any atom or group of atoms acting as a nucleophile. To date, the known examples of osme bonds in X-ray structures involve mostly the highly reactive OsO4 and amines and amine oxides. In this work, evidence supporting the existence of osme bonds in osmium(VI) derivatives is reported. In particular, nitrido-osmium(VI) complexes that present square-pyramidal geometries are well disposed to participate in osme bonds opposite to the Os≡N bond. By using a combination of experimental and theoretical results, the existence and importance of this new class of σ-hole interactions is demonstrated in the solid state of several nitrido-osmium(VI) derivatives.
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9
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Bartashevich EV, Mukhitdinova SE, Klyuev IV, Tsirelson VG. Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions. Molecules 2022; 27:molecules27175411. [PMID: 36080180 PMCID: PMC9458139 DOI: 10.3390/molecules27175411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.
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Affiliation(s)
- Ekaterina V Bartashevich
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Svetlana E Mukhitdinova
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Iliya V Klyuev
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
| | - Vladimir G Tsirelson
- Chemistry Department, South Ural State University (National Research University), 76, Lenin Av., 454080 Chelyabinsk, Russia
- Quantum Chemistry Department, D.I. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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10
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The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength. Molecules 2022; 27:molecules27154848. [PMID: 35956799 PMCID: PMC9369751 DOI: 10.3390/molecules27154848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [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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11
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Tupikina EY. Non-covalent interactions in the glutathione peroxidase active center and their influence on the enzyme activity. Org Biomol Chem 2022; 20:5551-5557. [PMID: 35791825 DOI: 10.1039/d2ob00890d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this computational work, the structure of the active center of the enzyme glutathione peroxidase (in three forms -SeH, -SeOH and -Se(O)OH) and the non-covalent interactions in it were investigated using modern quantum chemistry methods. The non-covalent interactions are described in detail. The presence of σ-hole interactions (chalcogen, tetrel and pnictogen bonds) formed mostly by a selenium atom as an electrophile in the glutathione peroxidase active center is confirmed for the first time. It is shown that a number of non-covalent interactions stabilize intermediates along the catalytic cycle and that modelling of the whole enzyme active center is necessary for accurate predictions of thermodynamic parameters, in particular, activation barriers.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg University, Universitetskaya emb. 7/9, St. Petersburg, Russia.
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12
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Shestimerova TA, Bykov AV, Kuznetsov AN, Grishko AY, Wei Z, Dikarev EV, Shevelkov AV. Pattern of covalent and non‐covalent interactions within the pentaiodide anion in the structure of (3‐HOC5H9NH2)I5. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202200039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tatiana A. Shestimerova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Andrey V. Bykov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Alexey N. Kuznetsov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia. N. S. Kurnakov Institute of General and Inorganic Chemistry RAS, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Alexey Y. Grishko
- Department of Materials Sciences, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Zheng Wei
- Department of Chemistry, University at Albany, SUNY, Albany New York 12222, United States RUSSIAN FEDERATION
| | - Evgeny V. Dikarev
- Department of Chemistry, University at Albany, SUNY, Albany New York 12222, United States RUSSIAN FEDERATION
| | - Andrei V. Shevelkov
- Lomonosov Moscow State University Chemistry Leninskie Gory 1/3 119991 Moscow RUSSIAN FEDERATION
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13
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Wen M, Erb W, Mongin F, Halauko YS, Ivashkevich OA, Matulis VE, Roisnel T. Synthesis of Polysubstituted Ferrocenesulfoxides. Molecules 2022; 27:molecules27061798. [PMID: 35335161 PMCID: PMC8955965 DOI: 10.3390/molecules27061798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 01/21/2023] Open
Abstract
The purpose of the study is to design synthetic methodologies, especially directed deprotometalation using polar organometallic reagents, to access polysubstituted ferrocenesulfoxides. From enantiopure 2-substituted (SiMe3, PPh2) S-tert-butylferrocenesulfoxides, a third substituent was first introduced at the 5 position (SiMe3, I, D, C(OH)Ph2, Me, PPh2, CH2NMe2, F) and removal of the trimethylsilyl group then afforded 2-substituted ferrocenesulfoxides unreachable otherwise. Attempts to apply the “halogen dance” reaction to the ferrocenesulfoxide series led to unexpected results although rationalized in light of calculated pKa values. Further functionalizations were also possible. Thus, new enantiopure, planar chiral di- and trisubstituted ferrocenes have been obtained, in addition to several original 2-substituted, 2,3- and 2,5-disubstituted, 2,3,5-trisubstituted and even 2,3,4,5-tetrasubstituted ferrocenesulfoxides, also enantiopure.
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Affiliation(s)
- Min Wen
- ISCR—Institut des Sciences Chimiques de Rennes-UMR CNRS 6226, Université de Rennes 1, F-35000 Rennes, France; (M.W.); (F.M.); (T.R.)
| | - William Erb
- ISCR—Institut des Sciences Chimiques de Rennes-UMR CNRS 6226, Université de Rennes 1, F-35000 Rennes, France; (M.W.); (F.M.); (T.R.)
- Correspondence: (W.E.); (Y.S.H.)
| | - Florence Mongin
- ISCR—Institut des Sciences Chimiques de Rennes-UMR CNRS 6226, Université de Rennes 1, F-35000 Rennes, France; (M.W.); (F.M.); (T.R.)
| | - Yury S. Halauko
- UNESCO Chair of Belarusian State University, 4 Nezavisimosti Av., 220030 Minsk, Belarus
- Correspondence: (W.E.); (Y.S.H.)
| | - Oleg A. Ivashkevich
- Laboratory for Chemistry of Condensed Systems, Research Institute for Physical Chemical Problems of Belarusian State University, 14 Leningradskaya St., 220030 Minsk, Belarus;
| | - Vadim E. Matulis
- Department of Inorganic Chemistry, Belarusian State University, 4 Nezavisimosti Av., 220030 Minsk, Belarus;
| | - Thierry Roisnel
- ISCR—Institut des Sciences Chimiques de Rennes-UMR CNRS 6226, Université de Rennes 1, F-35000 Rennes, France; (M.W.); (F.M.); (T.R.)
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14
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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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15
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Zelenkov LE, Eliseeva AA, Baykov S, Ivanov DM, Sumina AI, Gomila RM, Frontera A, Kukushkin VY, Bokach NA. Inorganic–Organic {dz2-MIIS4}···π-Hole Stacking in Reverse Sandwich Structures. The Case of Cocrystals of Group 10 Metal Dithiocarbamates with Electron-deficient Arenes. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00438k] [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
Cocrystallization of the dithiocarbamate complexes [M(S2CNEt2)2] (M = Ni 1, Pd 2, Pt 3) and X-substituted perfluoroarenes (X = I, Br; 1,2-dibromoperfluorobenzene FBrB and 1,2-diiodoperfluorobenzene FIB) gives isomorphous cocrystals of...
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16
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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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17
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Erb W, Carré V, Roisnel T. HFIP‐Promoted Substitution in the Ferrocene Series: Smooth Approach towards Original Catalysts**. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- William Erb
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226 35000 Rennes France
| | - Victor Carré
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226 35000 Rennes France
| | - Thierry Roisnel
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226 35000 Rennes France
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18
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Fei Y, Chen Z, Zhang J, Yu M, Kong J, Wu Z, Cao J, Zhang J. Thiazolium-based ionic liquids: Synthesis, characterization and physicochemical properties. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117553] [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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19
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Mathuri A, Pramanik M, Parida A, Mal P. Disulfide metathesis via sulfur⋯iodine interaction and photoswitchability. Org Biomol Chem 2021; 19:8539-8543. [PMID: 34546277 DOI: 10.1039/d1ob01581h] [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 idea of constitutional dynamic chemistry (CDC) and dynamic combinatorial chemistry (DCC) is widespread in the literature using the chemistry of disulfides. The synthesis of unsymmetrical diaryl disulfides is challenging due to the presence of a weak S-S bond. We report herein the synthesis of unsymmetrical diaryl disulfides from two symmetrical disulfides via a cross-metathesis reaction which was controlled by a weak sulfur⋯iodine (S⋯I) interaction. The unsymmetrical disulfides were stable in acetonitrile solution in the presence of N-iodosuccinimide (NIS), and found to be reversibly photoswitchable to the symmetrical disulfides under visible light irradiation.
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Affiliation(s)
- Ashis Mathuri
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Milan Pramanik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Amarchand Parida
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
| | - Prasenjit Mal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), HBNI, Bhubaneswar, PO Bhimpur-Padanpur, Via Jatni, District Khurda, Odisha 752050, India.
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20
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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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21
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Zierkiewicz W, Grabarz A, Michalczyk M, Scheiner S. Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey. Chemphyschem 2021; 22:924-934. [PMID: 33876515 DOI: 10.1002/cphc.202100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Indexed: 01/02/2023]
Abstract
Crystal structures document the ability of a TF3 group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN- anionic base can approach the T either along the extension of a T-C or T-F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Anna Grabarz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah, 84322-0300, USA
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22
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Levina EO, Khrenova MG, Tsirelson VG. The explicit role of electron exchange in the hydrogen bonded molecular complexes. J Comput Chem 2021; 42:870-882. [PMID: 33675552 DOI: 10.1002/jcc.26507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 01/22/2023]
Abstract
We applied a set of advanced bonding descriptors to establish the hidden electron density features and binding energy characteristics of intermolecular DH∙∙∙A hydrogen bonds (OH∙∙∙O, NH∙∙∙O and SH∙∙∙O) in 150 isolated and solvated molecular complexes. The exchange-correlation and Pauli potentials as well as corresponding local one-electron forces allowed us to explicitly ascertain how electron exchange defines the bonding picture in the proximity of the H-bond critical point. The electron density features of DH∙∙∙A interaction are governed by alterations in the electron localization in the H-bond region displaying itself in the exchange hole. At that, they do not depend on the variations in the exchange hole mobility. The electrostatic interaction mainly defines the energy of H-bonds of different types, whereas the strengthening/weakening of H-bonds in complexes with varying substituents depends on the barrier height of the exchange potential near the bond critical point. Energy variations between H-bonds in isolated and solvated systems are also caused the electron exchange peculiarities as follows from the corresponding potential and the interacting quantum atom analyses complemented by electron delocalization index calculations. Our approach is based on the bonding descriptors associated with the characteristics of the observable electron density and can be recommended for in-depth studies of non-covalent bonding.
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Affiliation(s)
- Elena O Levina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maria G Khrenova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Lomonosov Moscow State University, Moscow, Russia
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23
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, 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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24
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Eliseeva A, Ivanov DM, Rozhkov AV, Ananyev IV, Frontera A, Kukushkin VY. Bifurcated Halogen Bonding Involving Two Rhodium(I) Centers as an Integrated σ-Hole Acceptor. JACS AU 2021; 1:354-361. [PMID: 34467299 PMCID: PMC8395620 DOI: 10.1021/jacsau.1c00012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 06/13/2023]
Abstract
The complexes [RhX(COD)]2 (X = Cl, Br; COD = 1,5-cyclooctadiene) form cocrystals with σ-hole iodine donors. X-ray diffraction studies and extensive theoretical considerations indicate that the d z 2-orbitals of two positively charged rhodium(I) centers provide sufficient nucleophilicity to form a three-center halogen bond (XB) with the σ-hole donors. The two metal centers function as an integrated XB acceptor, providing assembly via a metal-involving XB.
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Affiliation(s)
- Anastasiya
A. Eliseeva
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Daniil M. Ivanov
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Anton V. Rozhkov
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Ivan V. Ananyev
- A.
N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russian Federation
| | - Antonio Frontera
- Department
of Chemistry, Universitat de les Illes Balears, Crts de Valldemossa km. 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Vadim Yu. Kukushkin
- Institute
of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
- Laboratory
of Crystal Engineering of Functional Materials, South Ural State University, Lenin Av. 76, 454080 Chelyabinsk, Russian Federation
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25
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Mezentsev-Cherkes IA, Shestimerova TA, Medved'ko AV, Kalinin MA, Kuznetsov AN, Wei Z, Dikarev EV, Vatsadze SZ, Shevelkov AV. Synthesis and supramolecular organization of the iodide and triiodides of a polycyclic adamantane-based diammonium cation: the effects of hydrogen bonds and weak I⋯I interactions. CrystEngComm 2021. [DOI: 10.1039/d0ce01730b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adamantane-like divalent building blocks and iodide or polyiodide anions combine into supramolecular architectures with the help of various noncovalent forces ranging from strong hydrogen bonds to secondary and weak I⋯I interactions.
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Affiliation(s)
| | | | | | - Mikhail A. Kalinin
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
| | - Alexey N. Kuznetsov
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
- N. S. Kurnakov Institute of General and Inorganic Chemistry RAS
| | - Zheng Wei
- Department of Chemistry
- University at Albany
- Albany
- USA
| | | | - Sergey Z. Vatsadze
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS
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26
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Van der Maelen JF, Ceroni M, Ruiz J. The X-ray constrained wavefunction of the [Mn(CO) 4{(C 6H 5) 2P-S-C(Br 2)-P(C 6H 5) 2}]Br complex: a theoretical and experimental study of dihalogen bonds and other noncovalent interactions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:802-814. [PMID: 33017314 DOI: 10.1107/s2052520620009889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
The synthesis and X-ray structure determination of the [Mn(CO)4{(C6H5)2P-S-C(Br2)-P(C6H5)2}]Br complex (1) are described. The C-Br...Br dihalogen bond present in 1 has been characterized by means of topological studies of the electron density. Both the quantum theory of atoms in molecules and the electron localization function approaches have been applied to several theoretically calculated wavefunctions as well as to an X-ray constrained wavefunction. In addition, a number of theoretical techniques, such as the source function, the reduced density gradient method and the interacting quantum atoms approach, among others, have been used to analyse the dihalogen bond as well as several intramolecular interactions of the type C-H...Br-C which have also been detected in 1. The results show clearly that while bonding in the latter interactions are dominated by electrostatic components, the former has a high degree of covalency.
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Affiliation(s)
- Juan F Van der Maelen
- Dept. Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
| | - Mario Ceroni
- Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Javier Ruiz
- Dept. Química Orgánica e Inorgánica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo, Asturias E-33006, Spain
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27
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Bol’shakov OI, Yushina ID, Stash AI, Aysin RR, Bartashevich EV, Rakitin OA. Structure and properties of 4-phenyl-5H-1,2,3-dithiazole-5-thione polyiodide with S−I+−S bridged complex. Struct Chem 2020. [DOI: 10.1007/s11224-020-01584-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Katlenok EA, Haukka M, Levin OV, Frontera A, Kukushkin VY. Supramolecular Assembly of Metal Complexes by (Aryl)I⋅⋅⋅d[PtII] Halogen Bonds. Chemistry 2020; 26:7692-7701. [DOI: 10.1002/chem.202001196] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Eugene A. Katlenok
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Matti Haukka
- Department of ChemistryUniversity of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
| | - Oleg V. Levin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Antonio Frontera
- Department de QuímicaUniversitat de les Illes Balears Crta. de Valldemossa km 7.5 07122 Palma, de Mallorca Baleares Spain
| | - Vadim Yu. Kukushkin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
- South Ural State University Lenin Av. 76 454080 Chelyabinsk Russian Federation
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29
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Kaźmierczak M, Katrusiak A. The shortest chalcogen...halogen contacts in molecular crystals. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:865-869. [PMID: 32830766 DOI: 10.1107/s2052520619011004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/07/2019] [Indexed: 06/11/2023]
Abstract
The survey of the shortest contacts in structures deposited in the Cambridge Structural Database shows that chalcogen...halogen, halogen...halogen and chalcogen...chalcogen interactions can compete as cohesion forces in molecular crystals. The smallest parameter δ (defined as the interatomic distance minus the sum of relevant van der Waals radii) for Ch...X contacts between chalcogens (Ch: S, Se) and halogens (X: F, Cl, Br, I) is present only in 0.86% out of 30 766 deposited structures containing these atoms. Thus, in less than 1% of these structures can the Ch...X forces be considered as the main type of cohesion forces responsible for the molecular arrangement. Among the 263 structures with the shortest Ch...X contact, there are four crystals where no contacts shorter than the sums of van der Waals radii are present (so-called loose crystals). The smallest δ criterion has been used for distinguishing between the bonding (covalent bond) and non-bonding contacts and for validating the structural models of crystals.
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Affiliation(s)
- Michał Kaźmierczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznan, 61-614, Poland
| | - Andrzej Katrusiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, Poznan, 61-614, Poland
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30
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Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides. CRYSTALS 2019. [DOI: 10.3390/cryst9100506] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.
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31
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Zierkiewicz W, Wysokiński R, Michalczyk M, Scheiner S. Chalcogen bonding of two ligands to hypervalent YF 4 (Y = S, Se, Te, Po). Phys Chem Chem Phys 2019; 21:20829-20839. [PMID: 31517347 DOI: 10.1039/c9cp04006d] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability of two NH3 ligands to engage in simultaneous chalcogen bonds to a hypervalent YF4 molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another in a pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y = S, while Te, and Po tend toward the trans structure; they are nearly equally stable for Se. In either case, the binding energy rises rapidly with the size of the Y atom, exceeding 30 kcal mol-1 for PoF4.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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Comparison of non-covalent interactions and spectral properties in 1-methyl-3-methylthio-5-phenyl-1,2,4-triazinium mono- and tetraiodide crystals. Struct Chem 2019. [DOI: 10.1007/s11224-019-01372-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bartashevich E, Matveychuk Y, Tsirelson V. Identification of the Tetrel Bonds between Halide Anions and Carbon Atom of Methyl Groups Using Electronic Criterion. Molecules 2019; 24:E1083. [PMID: 30893831 PMCID: PMC6471983 DOI: 10.3390/molecules24061083] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 11/17/2022] Open
Abstract
The consideration of the disposition of minima of electron density and electrostatic potential along the line between non-covalently bound atoms in systems with Hal-···CH₃⁻Y (Hal- = Cl, Br; Y = N, O) fragments allowed to prove that the carbon atom in methyl group serves as an electrophilic site provider. These interactions between halide anion and carbon in methyl group can be categorized as the typical tetrel bonds. Statistics of geometrical parameters for such tetrel bonds in CSD is analyzed. It is established that the binding energy in molecular complexes with tetrel bonds correlate with the potential acting on an electron in molecule (PAEM). The PAEM barriers for tetrel bonds show a similar behavior for both sets of complexes with Br- and Cl- electron donors.
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Affiliation(s)
- Ekaterina Bartashevich
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
| | - Yury Matveychuk
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
| | - Vladimir Tsirelson
- Research Laboratory of Multiscale Modelling of Multicomponent Functional Materials, REC Nanotechnology, South Ural State University, 454080 Chelyabinsk, Russia.
- Quantum Chemistry Department, D.I. Mendeleev University of Chemical Technology, 125047 Moscow, Russia.
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