1
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Ibrahim MAA, Saeed RRA, Shehata MNI, Moussa NAM, Tawfeek AM, Ahmed MN, Abd El-Rahman MK, Shoeib T. Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases. ACS OMEGA 2023; 8:32828-32837. [PMID: 37720791 PMCID: PMC10500585 DOI: 10.1021/acsomega.3c03981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
For the first time, sigma (σ)- and lone-pair (lp)-hole site-based interactions of SF4 and SeF4 molecules in seesaw geometry with NH3 and FH Lewis bases were herein comparatively investigated. The obtained findings from the electrostatic potential analysis outlined the emergence of sundry holes on the molecular entity of the SF4 and SeF4 molecules, dubbed the σ- and lp-holes. The energetic viewpoint announced splendid negative binding energy values for σ-hole site-based interactions succeeded by lp-hole analogues, which were found to be -9.21 and -0.50 kcal/mol, respectively, for SeF4···NH3 complex as a case study. Conspicuously, a proper concurrence between the strength of chalcogen σ-hole site-based interactions and the chalcogen's atomic size was obtained, whereas a reverse pattern was proclaimed for the lp-hole counterparts. Further, a higher preference for the YF4···NH3 complexes with elevated negative binding energy was promulgated over the YF4···FH ones, indicating the eminent role of Lewis basicity. The indications of the quantum theory of atoms in molecules generally asserted the closed-shell nature of all the considered interactions. The observation of symmetry-adapted perturbation theory revealed the substantial contributing role of the electrostatic forces beyond the occurrence of σ-hole site-based interactions. In comparison, the dispersion forces were specified to govern the lp-hole counterparts. Such emerging findings would be a gate for the fruitful forthcoming applications of chalcogen bonding interactions in crystal engineering and biological systems.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Rehab R. A. Saeed
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohammed N. I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M. Tawfeek
- Chemistry
Department, College of Science, King Saud
University, Riyadh 11451, Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed K. Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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2
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Michalczyk M, Wojtkowiak K, Panek JJ, Jezierska A, Zierkiewicz W. Static and Dynamical Quantum Studies of CX 3-AlX 2 and CSiX 3-BX 2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center. Int J Mol Sci 2023; 24:ijms24097881. [PMID: 37175586 PMCID: PMC10177972 DOI: 10.3390/ijms24097881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX3-AlX2) and least (SiX3-BX2) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jarosław J Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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3
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Ibrahim MAA, Mohamed YAM, Abd Elhafez HSM, Shehata MNI, Soliman MES, Ahmed MN, Abd El-Mageed HR, Moussa NAM. R •-hole interactions of group IV-VII radical-containing molecules: A comparative study. J Mol Graph Model 2021; 111:108097. [PMID: 34890896 DOI: 10.1016/j.jmgm.2021.108097] [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: 08/30/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 11/30/2022]
Abstract
For the first time, the potentiality of the sp2-hybridized group IV-VII radical (R•)-containing molecules to participate in R•-hole interactions was comparatively assessed using •SiF3,•POF2, •SO2F, and •ClO3 models in the trigonal pyramidal geometry. In that spirit, a plethora of quantum mechanical calculations was performed at the MP2/aug-cc-pVTZ level of theory. According to the results, all the investigated R•-containing molecules exhibited potent versatility to engage in R•-hole … Lewis base interactions with significant negative binding energies for the NCH-based complexes. The strength of R•-hole interactions was perceived to obey the •ClO3 … > •SO2F … > •POF2 … > •SiF3 … Lewis base order, outlining an inverse correlation between the binding energy and the atomic size of the R•-hole donor. Benchmarking of the binding energy at the CCSD/CBS(T) computational level was executed for all the explored interactions and addressed an obvious similarity between the MP2 and CCSD energetic findings. QTAIM analysis critically unveiled the closed-shell nature of the explored R•-hole interactions. SAPT-EDA proclaimed the reciprocal contributions of electrostatic and dispersion forces to the total binding energy. These observations demonstrate in better detail the nature of R•-hole interactions, leading to a convincing amelioration for versatile fields relevant to materials science and drug design.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt.
| | - Yasmeen A M Mohamed
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Heba S M Abd Elhafez
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mohammed N I Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Muhammad Naeem Ahmed
- Department of Chemistry, The University of Azad Jammu and Kashmir, Muzaffarabad, 13100, Pakistan
| | - H R Abd El-Mageed
- Micro-Analysis, Environmental Research nd Community Affairs Center (MAESC), Faculty of Science, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
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4
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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5
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Veluthaparambath RVP, Saha A, Saha BK. The Effects of Electronegativity of X and Hybridization of C on the X-C⋅⋅⋅O Interactions: A Statistical Analysis on Tetrel Bonding. Chempluschem 2021; 86:1123-1127. [PMID: 34402218 DOI: 10.1002/cplu.202100095] [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: 02/27/2021] [Revised: 04/13/2021] [Indexed: 11/08/2022]
Abstract
Cone and distance-cone corrected statistical analyses have been performed on X-C⋅⋅⋅O (X=H, B, C, N, O and F; the C atom is sp2 and sp3 hybridized) tetrel bonds. The sp3 -C and sp2 -C prefer to form the interactions through σ-hole (∠XCO≈180°) and π-hole (∠XCO≈90°), respectively. With the increase in electronegativity of X, the preference for the particular angles of the respective geometries increases and the C⋅⋅⋅O distance becomes shorter. The angular preference is found to be more prominent in the cases of π-hole interactions than that in the σ-hole interactions. A similar distance-cone corrected statistical analysis on O=C⋅⋅⋅O interaction also suggests that the preferred ∠OCO angle is ∼90° and the preferred C⋅⋅⋅O distance is around the sum of van der Waals radii (3.22 Å) of the C and O atoms. However, a cone-corrected statistical analysis on X-Si⋅⋅⋅O interactions suggests that the preference for linearity in this case is much higher than that for the X-C⋅⋅⋅O σ-hole interactions.
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Affiliation(s)
| | - Arijit Saha
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Binoy K Saha
- Department of Chemistry, Pondicherry University, Puducherry, 605014, India
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6
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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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7
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Michalczyk M, Malik M, Zierkiewicz W, Scheiner S. Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond. J Phys Chem A 2021; 125:657-668. [PMID: 33423496 DOI: 10.1021/acs.jpca.0c10814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl4, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Magdalena Malik
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, Utah 84322-0300, United States
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8
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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.
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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
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9
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Scheiner S. Competition between a Tetrel and Halogen Bond to a Common Lewis Acid. J Phys Chem A 2020; 125:308-316. [DOI: 10.1021/acs.jpca.0c10060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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10
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Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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11
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Voronova ED, Golub IE, Pavlov A, Belkova NV, Filippov OA, Epstein LM, Shubina ES. Dichotomous Si-H Bond Activation by Alkoxide and Alcohol in Base-Catalyzed Dehydrocoupling of Silanes. Inorg Chem 2020; 59:12240-12251. [PMID: 32805120 DOI: 10.1021/acs.inorgchem.0c01293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The activation of silanes in dehydrogenative coupling with alcohols under general base catalysis was studied experimentally (using multinuclear NMR, IR, and UV-visible spectroscopies) and computationally (at DFT M06/6-311++G(d,p) theory level) on the example of Ph4-nSiHn (n = 1-3) interaction with (CF3)2CHOH in the presence of Et3N. The effect of the phenyl groups' number and H- substitution by the electron-withdrawing (CF3)2CHO- group on Si-H bond hydricity (quantified as hydride-donating ability, HDA) and Lewis acidity of silicon atom (characterized by maxima of molecular electrostatic potential) was accessed. Our results show the coordination of Lewis base (Y = Me3N, ROH, OR-) leads to the increased hydricity of pentacoordinate hypervalent Ph4-nSi(Y)Hn complexes and a decrease of the reaction barrier for H2 release. The formation of tertiary complexes [Ph4-nSi(Y)Hn]···HOR is a critical prerequisite for the dehydrocoupling with alkoxides being ideal activators. The latter can be external or internal, generated by in situ HOR deprotonation. The mutual effect of tetrel interaction and dihydrogen bonding in tertiary complexes (RO-)Ph4-nSiHn···HOR leads to dichotomous activation of Si-H bond promoting the proton-hydride transfer and H2 release.
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Affiliation(s)
- Evgenia D Voronova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Igor E Golub
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Alexander Pavlov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Natalia V Belkova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Oleg A Filippov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., Moscow 117997, Russia
| | - Lina M Epstein
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
| | - Elena S Shubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 28 Vavilova St., 119991 Moscow, Russia
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12
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Bhattarai S, Sutradhar D, Chandra AK, Zeegers-Huyskens T. A theoretical investigation of the interaction between substituted pyridines and CS2. Versatility of the CS2 molecule. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Nature of the Interaction of Pyridines with OCS. A Theoretical Investigation. Molecules 2020; 25:molecules25020416. [PMID: 31963861 PMCID: PMC7024555 DOI: 10.3390/molecules25020416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 02/06/2023] Open
Abstract
Ab initio calculations were carried out to investigate the interaction between para-substituted pyridines (X-C5H4N, X=NH2, CH3, H, CN, NO2) and OCS. Three stable structures of pyridine.OCS complexes were detected at the MP2=full/aug-cc-pVDZ level. The A structure is characterized by N…S chalcogen bonds and has binding energies between −9.58 and −12.24 kJ/mol. The B structure is bonded by N…C tetrel bond and has binding energies between −10.78 and −11.81 kJ/mol. The C structure is characterized by π-interaction and has binding energies between −10.76 and −13.33 kJ/mol. The properties of the systems were analyzed by AIM, NBO, and SAPT calculations. The role of the electrostatic potential of the pyridines on the properties of the systems is outlined. The frequency shift of relevant vibrational modes is analyzed.
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14
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Michalczyk M, Zierkiewicz W, Wysokiński R, Scheiner S. Hexacoordinated Tetrel‐Bonded Complexes between TF4(T=Si, Ge, Sn, Pb) and NCH: Competition between σ‐ and π‐Holes. Chemphyschem 2019; 20:959-966. [DOI: 10.1002/cphc.201900072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 02/15/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Mariusz Michalczyk
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Wiktor Zierkiewicz
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Rafał Wysokiński
- Faculty of ChemistryWrocław University of Science and Technology Wybrzeże, Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan, Utah 84322-0300 United States
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15
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Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives. Molecules 2019; 24:molecules24020376. [PMID: 30669688 PMCID: PMC6359171 DOI: 10.3390/molecules24020376] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
When an N-base approaches the tetrel atom of TF4 (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.
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16
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Tetrel Bond between 6-OTX₃-Fulvene and NH₃: Substituents and Aromaticity. Molecules 2018; 24:molecules24010010. [PMID: 30577501 PMCID: PMC6337681 DOI: 10.3390/molecules24010010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 11/24/2022] Open
Abstract
Carbon bonding is a weak interaction, particularly when a neutral molecule acts as an electron donor. Thus, there is an interesting question of how to enhance carbon bonding. In this paper, we found that the –OCH3 group at the exocyclic carbon of fulvene can form a moderate carbon bond with NH3 with an interaction energy of about −10 kJ/mol. The –OSiH3 group engages in a stronger tetrel bond than does the –OGeH3 group, while a reverse result is found for both –OSiF3 and –OGeF3 groups. The abnormal order in the former is mainly due to the stronger orbital interaction in the –OSiH3 complex, which has a larger deformation energy. The cyano groups adjoined to the fulvene ring not only cause a change in the interaction type, from vdW interactions in the unsubstituted system of –OCF3 to carbon bonding, but also greatly strengthen tetrel bonding. The formation of tetrel bonding has an enhancing effect on the aromaticity of the fulvene ring.
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