1
|
Velasquez JD, Keshtkar N, Polo V, Munárriz J, Echeverría J. Unveiling the Potential of Haloalkenes as Electron Density Acceptors. CRYSTAL GROWTH & DESIGN 2024; 24:5775-5780. [PMID: 38983119 PMCID: PMC11232035 DOI: 10.1021/acs.cgd.4c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
We report herein, by means of structural and computational analyses, a comprehensive study of the capability of differently substituted haloalkenes to behave as electron density acceptors in noncovalent interactions. The nature of these interactions between haloalkenes and Lewis bases highly depends on the number and nature of the halogen atoms bound to the carbon-carbon double bond. When hydrogen bonds, which generally dominate for mono- and dihaloalkenes, cannot be formed, we observe the establishment of attractive interactions in which an sp2 carbon atom, belonging to an acyclic C=C double bond, plays the role of the Lewis acid via its π* antibonding orbital.
Collapse
Affiliation(s)
- Juan D Velasquez
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Noushin Keshtkar
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Víctor Polo
- Departmento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Julen Munárriz
- Departmento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jorge Echeverría
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| |
Collapse
|
2
|
Scheiner S, Amonov A. Types of noncovalent bonds within complexes of thiazole with CF 4 and SiF 4. Phys Chem Chem Phys 2024; 26:6127-6137. [PMID: 38299682 DOI: 10.1039/d4cp00057a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan, Utah 84322-0300, USA.
| | - Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University 140104, University blv. 15, Samarkand, Uzbekistan
| |
Collapse
|
3
|
Intermolecular (Isocyano group)···PtII interactions involving coordinated isocyanides in cyclometalated PtII complexes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
4
|
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...
Collapse
|
5
|
Scheiner S. Dissection of the Origin of π-Holes and the Noncovalent Bonds in Which They Engage. J Phys Chem A 2021; 125:6514-6528. [PMID: 34310147 DOI: 10.1021/acs.jpca.1c05431] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accompanying the rapidly growing list of σ-hole bonds has come the acknowledgment of parallel sorts of noncovalent bonds which owe their stability in large part to a deficiency of electron density in the area above the molecular plane, known as a π-hole. The origins of these π-holes are probed for a wide series of molecules, comprising halogen, chalcogen, pnicogen, tetrel, aerogen, and spodium bonds. Much like in the case of their σ-hole counterparts, formation of the internal covalent π-bond in the Lewis acid molecule pulls density toward the bond midpoint and away from its extremities. This depletion of density above the central atom is amplified by an electron-withdrawing substituent. At the same time, the amplitude of the π*-orbital is enhanced in the region of the density-depleted π-hole, facilitating a better overlap with the nucleophile's lone pair orbital and a stabilizing n → π* charge transfer. The presence of lone pairs on the central atom acts to attenuate the π-hole and shift its position somewhat, resulting in an overall weakening of the π-hole bond. There is a tendency for π-hole bonds to include a higher fraction of induction energy than σ-bonds with proportionately smaller electrostatic and dispersion components, but this distinction is less a product of the σ- or π-character and more a function of the overall bond strength.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| |
Collapse
|
6
|
Mooibroek TJ. DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering. Chemphyschem 2021; 22:141-153. [PMID: 33241585 PMCID: PMC7898519 DOI: 10.1002/cphc.202000927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/25/2020] [Indexed: 11/25/2022]
Abstract
The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.
Collapse
Affiliation(s)
- Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van Amsterdam, Science Park 9041098 XHAmsterdamThe Netherlands
| |
Collapse
|
7
|
Ayhan MM, Özcan E, Dedeoglu B, Chumakov Y, Zorlu Y, Coşut B. Carbon (sp 3) tetrel bonding mediated BODIPY supramolecular assembly via unprecedented synergy of C sp3⋯N and C sp3⋯F pair interactions. CrystEngComm 2021. [DOI: 10.1039/d0ce01640c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Here, we present the first example of sp3 hybridized carbon centered (Csp3) tetrel bonding mediated 3D BODIPY assembly via the exceptional synergy of Csp3⋯N and Csp3⋯F pair interactions.
Collapse
Affiliation(s)
| | - Emrah Özcan
- Department of Chemistry
- Gebze Technical University
- Gebze
- Turkey
- Institute of Physics
| | - Burcu Dedeoglu
- Department of Chemistry
- Gebze Technical University
- Gebze
- Turkey
| | - Yurii Chumakov
- Department of Physics
- Gebze Technical University
- Gebze
- Turkey
- Institute of Applied Physics
| | - Yunus Zorlu
- Department of Chemistry
- Gebze Technical University
- Gebze
- Turkey
| | - Bünyemin Coşut
- Department of Chemistry
- Gebze Technical University
- Gebze
- Turkey
| |
Collapse
|
8
|
Scheiner S. Versatility of the Cyano Group in Intermolecular Interactions. Molecules 2020; 25:E4495. [PMID: 33007991 PMCID: PMC7582283 DOI: 10.3390/molecules25194495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/17/2022] Open
Abstract
Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA
| |
Collapse
|
9
|
Coordination environment variations in multinuclear trigonal bipyramid Co(II) complexes bearing tetradentate sulfonamide N-donors and phenoxazinone synthase activities. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
10
|
Roeleveld JJ, Lekanne Deprez SJ, Verhoofstad A, Frontera A, van der Vlugt JI, Mooibroek TJ. Engineering Crystals Using sp 3 -C Centred Tetrel Bonding Interactions. Chemistry 2020; 26:10126-10132. [PMID: 32557861 PMCID: PMC7496358 DOI: 10.1002/chem.202002613] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/16/2020] [Indexed: 11/06/2022]
Abstract
1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.
Collapse
Affiliation(s)
- Julius J. Roeleveld
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Siebe J. Lekanne Deprez
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Abraham Verhoofstad
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta de Valldemossa km 7.507122Palmade Mallorca (BalearesSpain
| | - Jarl Ivar van der Vlugt
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
- Institute of ChemistryCarl von Ossietzky University OldenburgCarl-von-Ossietzky-Straße 9–1126219OldenburgGermany
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| |
Collapse
|
11
|
Kia R, Kalaghchi A. Intra- and intermolecular interactions in a series of chlorido-tricarbonyl-diazabutadienerhenium(I) complexes: structural and theoretical studies. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:417-426. [PMID: 32831260 DOI: 10.1107/s2052520620004333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
A series of new chlorido-tricarbonylrhenium(I) complexes bearing alkyl-substituted diazabutadiene (DAB) ligands, namely N,N'-bis(2,4-dimethylbenzene)-1,4-diazabutadiene (L1), N,N'-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L2), N,N'-bis(2,4,6-trimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L3) and N,N'-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene (L4), were synthesized and investigated. The crystal structures have been fully characterized by X-ray diffraction and spectroscopic methods. Density functional theory, natural bond orbital and non-covalent interaction index methods have been used to study the optimized geometry in the gas phase and intra- and intermolecular interactions in the complexes, respectively. The most important studied interactions in these metal carbonyl complexes are n→π*, n→σ* and π→π*. Among complexes 1-4, only 2 shows interesting intermolecular n→π* interactions due to lp(C[triple-bond]O)...π* and lp(Cl)...π* (lp = lone pair) contacts.
Collapse
Affiliation(s)
- Reza Kia
- Department of Chemistry, Sharif University of Technology, Tehran, 11155-3516, Iran
| | - Azadeh Kalaghchi
- Department of Chemistry, Sharif University of Technology, Tehran, 11155-3516, Iran
| |
Collapse
|
12
|
Heywood VL, Alford TPJ, Roeleveld JJ, Lekanne Deprez SJ, Verhoofstad A, van der Vlugt JI, Domingos SR, Schnell M, Davis AP, Mooibroek TJ. Observations of tetrel bonding between sp 3-carbon and THF. Chem Sci 2020; 11:5289-5293. [PMID: 34122986 PMCID: PMC8159407 DOI: 10.1039/d0sc01559h] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
We report the direct observation of tetrel bonding interactions between sp3-carbons of the supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas and crystalline phase. The intermolecular contact is established via σ-holes and is driven mainly by electrostatic forces. The complex manifests distinct binding geometries when captured in the crystalline phase and in the gas phase. We elucidate these binding trends using complementary gas phase quantum chemical calculations and find a total binding energy of -11.2 kcal mol-1 for the adduct. Our observations pave the way for novel strategies to engineer sp3-C centred non-covalent bonding schemes for supramolecular chemistry.
Collapse
Affiliation(s)
- Victoria L Heywood
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Thomas P J Alford
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Julius J Roeleveld
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Siebe J Lekanne Deprez
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Abraham Verhoofstad
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Jarl Ivar van der Vlugt
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
- Institute of Chemistry, Carl von Ossietzky University Oldenburg Carl-von-Ossietzky-Straße 9-11 D-12629 Oldenburg Germany
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Anthony P Davis
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tiddo J Mooibroek
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| |
Collapse
|
13
|
Structural, Non-Covalent Interaction, and Natural Bond Orbital Studies on Bromido-Tricarbonyl Rhenium(I) Complexes Bearing Alkyl-Substituted 1,4-Diazabutadiene (DAB) Ligands. CRYSTALS 2020. [DOI: 10.3390/cryst10040267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The synthesis, characterization, structural and computational studies of Re(I) tricarbonyl bromo complexes bearing alkyl-substituted 1,4-diazabutadiene ligands, [Re(CO)3(1,4-DAB)Br], where 1,4-DAB = N,N-bis(2,4-dimethylbenzene)-1,4-diazabutadiene, 2,4-Me2DAB (1); N,N-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene, 2,4-Me2DABMe (2); N,N-bis(2,4,6-trimethylbenzene)-1,4-diazabutadiene, 2,4,6-Me3DAB (3); and N,N-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene, 2,6-ipr2DAB (4) are reported. The complexes were characterized by different spectroscopic methods such as FT-IR, 1H-NMR, 13C-NMR, and elemental analyses and their solid-state structures were confirmed by X-ray diffraction. In each complex, the Re(I) centre shows a distorted octahedral shape with a facial geometry of carbonyl groups. The gas phase geometry of the complexes was identified by density functional theory. Interesting intermolecular n…π* interactions of complexes 1 and 3 were investigated by non-covalent interaction index (NCI), and natural bond orbital (NBO) analyses. The intramolecular n…σ*, σ…π*, π…σ* interactions were also studied in complexes 3 and 4.
Collapse
|
14
|
Kia R, Taghavi T, Raithby PR. Supramolecular assembly through intermolecular n → π* interactions through a coordinated perrhenate formed via superoxidation of Re( i) to Re( vii) in the formation of substituted Re(CO) 3 complexes bearing Diimine ligands. CrystEngComm 2020. [DOI: 10.1039/d0ce01073a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Two Re(i) tricarbonyl complexes bearing Ph4TAP and dafone ligands and having a coordinated perrhenate group obtained via in situ superoxidation of Re(i) to Re(vii) have been characterized.
Collapse
Affiliation(s)
- Reza Kia
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
| | - Tahereh Taghavi
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
| | | |
Collapse
|
15
|
Mikherdov AS, Katkova SA, Novikov AS, Efremova MM, Reutskaya EY, Kinzhalov MA. (Isocyano group)⋯lone pair interactions involving coordinated isocyanides: experimental, theoretical and CSD studies. CrystEngComm 2020. [DOI: 10.1039/c9ce01741k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both carbon and nitrogen centers in the coordinated isocyano group are capable of acting as a π-hole donor toward lone pairs.
Collapse
Affiliation(s)
| | | | | | - Mariia M. Efremova
- Saint Petersburg State University
- 199034 Saint Petersburg
- Russian Federation
| | | | | |
Collapse
|
16
|
Kia R. Non-covalent sulfoxide⋯(nitrosyl group) interactions involving coordinated nitrosyl in a Ru( ii) nitrosyl complex with an α-diimine ligand: structural and computational studies. CrystEngComm 2020. [DOI: 10.1039/d0ce01063d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inspection of the X-ray structure of the newly prepared Ru–nitrosyl complex bearing an α-diimine ligand revealed for the first time the π-hole interaction involving the coordinated nitrosyl group with DMSO.
Collapse
Affiliation(s)
- Reza Kia
- Chemistry Department
- Sharif University of Technology
- Tehran
- Iran
| |
Collapse
|
17
|
Bauzá A, Frontera A, Mooibroek TJ. π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. Chemistry 2019; 25:13436-13443. [PMID: 31453653 PMCID: PMC6856858 DOI: 10.1002/chem.201903404] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/03/2023]
Abstract
Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.
Collapse
Affiliation(s)
- Antonio Bauzá
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| |
Collapse
|
18
|
Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study. Molecules 2019; 24:molecules24183370. [PMID: 31527496 PMCID: PMC6767229 DOI: 10.3390/molecules24183370] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X-CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ -1.5 kcal·mol-1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤-5 kcal·mol-1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol-1 in cationic species like [Me3O+-CH3···OH2]+ (8a).
Collapse
|
19
|
A. Katkova S, S. Mikherdov A, A. Kinzhalov M, S. Novikov A, A. Zolotarev A, Boyarskiy VP, Kukushkin VY. (Isocyano Group π‐Hole)⋅⋅⋅[d‐M
II
] Interactions of (Isocyanide)[M
II
] Complexes, in which Positively Charged Metal Centers (d
8
‐M=Pt, Pd) Act as Nucleophiles. Chemistry 2019; 25:8590-8598. [DOI: 10.1002/chem.201901187] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Svetlana A. Katkova
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Alexander S. Mikherdov
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Mikhail A. Kinzhalov
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Alexander S. Novikov
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Andrey A. Zolotarev
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Vadim P. Boyarskiy
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| | - Vadim Yu. Kukushkin
- Saint Petersburg State University Universitetskaya Nab., 7/9 Saint Petersburg Russian Federation
| |
Collapse
|
20
|
Rozhkov AV, Krykova MA, Ivanov DM, Novikov AS, Sinelshchikova AA, Volostnykh MV, Konovalov MA, Grigoriev MS, Gorbunova YG, Kukushkin VY. Reverse Arene Sandwich Structures Based upon π‐Hole⋅⋅⋅[M
II
] (d
8
M=Pt, Pd) Interactions, where Positively Charged Metal Centers Play the Role of a Nucleophile. Angew Chem Int Ed Engl 2019; 58:4164-4168. [DOI: 10.1002/anie.201814062] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Anton V. Rozhkov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Mariya A. Krykova
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Daniil M. Ivanov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Alexander S. Novikov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Anna A. Sinelshchikova
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Marina V. Volostnykh
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Mikhail A. Konovalov
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Mikhail S. Grigoriev
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Yulia G. Gorbunova
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Vadim Yu. Kukushkin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| |
Collapse
|
21
|
Rozhkov AV, Krykova MA, Ivanov DM, Novikov AS, Sinelshchikova AA, Volostnykh MV, Konovalov MA, Grigoriev MS, Gorbunova YG, Kukushkin VY. Reverse Arene Sandwich Structures Based upon π‐Hole⋅⋅⋅[M
II
] (d
8
M=Pt, Pd) Interactions, where Positively Charged Metal Centers Play the Role of a Nucleophile. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anton V. Rozhkov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Mariya A. Krykova
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Daniil M. Ivanov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Alexander S. Novikov
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| | - Anna A. Sinelshchikova
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Marina V. Volostnykh
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Mikhail A. Konovalov
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Mikhail S. Grigoriev
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Yulia G. Gorbunova
- Frumkin Institute of Physical Chemistry and ElectrochemistryRussian Academy of Sciences Leninsky Pr. 31-4 119071 Moscow Russian Federation
| | - Vadim Yu. Kukushkin
- Institute of ChemistrySaint Petersburg State University Universitetskaya Nab. 7/9 199034 Saint Petersburg Russian Federation
| |
Collapse
|
22
|
Doppert MT, van Overeem H, Mooibroek TJ. Intermolecular π-hole/n→π* interactions with carbon monoxide ligands in crystal structures. Chem Commun (Camb) 2018; 54:12049-12052. [PMID: 30294741 DOI: 10.1039/c8cc07557c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A thorough analysis of the Cambridge Structure Database reveals that intermolecular π-hole/n→π* interactions with carbon monoxide ligands are abundant in the solid state and somewhat directional, particularly with fac-like M(CO)3 fragments (P < 4.0). High level DFT calculations suggest interacting energies up to about -10 kcal mol-1 for adducts of charge neutral complexes.
Collapse
Affiliation(s)
- Michael Timothy Doppert
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | | | | |
Collapse
|