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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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Wysokiński R, Zierkiewicz W, Michalczyk M, Scheiner S. Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments. Molecules 2021; 26:molecules26216394. [PMID: 34770803 PMCID: PMC8586936 DOI: 10.3390/molecules26216394] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Molecules of the type XYT = Ch (T = C, Si, Ge; Ch = S, Se; X,Y = H, CH3, Cl, Br, I) contain a σ-hole along the T = Ch bond extension. This hole can engage with the N lone pair of NCH and NCCH3 so as to form a chalcogen bond. In the case of T = C, these bonds are rather weak, less than 3 kcal/mol, and are slightly weakened in acetone or water. They owe their stability to attractive electrostatic energy, supplemented by dispersion, and a much smaller polarization term. Immersion in solvent reverses the electrostatic interaction to repulsive, while amplifying the polarization energy. The σ-holes are smaller for T = Si and Ge, even negative in many cases. These Lewis acids can nonetheless engage in a weak chalcogen bond. This bond owes its stability to dispersion in the gas phase, but it is polarization that dominates in solution.
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Affiliation(s)
- Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
- Correspondence: (R.W.); (W.Z.); (S.S.)
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
- Correspondence: (R.W.); (W.Z.); (S.S.)
| | - 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, UT 84322-0300, USA
- Correspondence: (R.W.); (W.Z.); (S.S.)
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Anion-Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment. Molecules 2021; 26:molecules26082116. [PMID: 33917030 PMCID: PMC8067769 DOI: 10.3390/molecules26082116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022] Open
Abstract
Ab initio calculations are applied to the question as to whether a AeX5- anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F-, Cl-, or CN-. The latter approaches the central Ae atom from above the molecular plane, along its C5 axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.
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Cheng W, Zheng Y, Herbers S, Zheng H, Gou Q. Conformational Equilibria of 2-Methoxypyridine⋅⋅⋅CO 2 : Cooperative and Competitive Tetrel and Weak Hydrogen Bonds. Chemphyschem 2021; 22:154-159. [PMID: 33315294 DOI: 10.1002/cphc.202000910] [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: 11/02/2020] [Revised: 11/16/2020] [Indexed: 11/11/2022]
Abstract
The rotational spectrum of 2-methoxypyridine⋅⋅⋅CO2 was recorded and analysed employing a cavity-based Fourier transform microwave spectrometer, complemented with quantum chemical calculations which predicted three possible isomers within energies less than 1000 cm-1 . The two most stable isomers were observed in the pulsed jet, which are stabilized by a network of C⋅⋅⋅N/O tetrel and C-H⋅⋅⋅O weak hydrogen bonds. The relative population ratio of the two detected isomers was estimated to be NI /NII ≈2.5. The competition and cooperation of the present non-covalent interactions in both isomers are discussed within the framework of Bader's quantum theory of atoms in molecules and Johnson's non-covalent interaction analyses. The study shows, that when looking for CO2 adsorbents, one might prefer candidates with multiple interactions in one site over candidates with few but strong interactions.
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Affiliation(s)
- Wanying Cheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Sven Herbers
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
| | - Huaili Zheng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, State Ministry of Education, Chongqing University, No.83 Shabei Str., Shapingba, 400045, Chongqing, China
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, 401331, Chongqing, China
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Li W, Usabiaga I, Calabrese C, Evangelisti L, Maris A, Favero LB, Melandri S. Characterizing the lone pair⋯π–hole interaction in complexes of ammonia with perfluorinated arenes. Phys Chem Chem Phys 2021; 23:9121-9129. [DOI: 10.1039/d1cp00451d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stronger and more flexible lone pair⋯π–hole interaction of ammonia with respect to water in complexes with perfluorinated arenes.
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Affiliation(s)
- Weixing Li
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- Bologna
- Italy
| | - Imanol Usabiaga
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- Bologna
- Italy
| | - Camilla Calabrese
- Department of Physical Chemistry, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N
- Leioa
- Spain
- Biofisika Institute, (CSIC, UPV/EHU)
- Barrio Sarriena, S/N
| | - Luca Evangelisti
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- Bologna
- Italy
| | - Assimo Maris
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- Bologna
- Italy
| | - Laura B. Favero
- Istituto per lo studio dei materiali nanostrutturati CNR – ISMN
- Bologna
- Italy
| | - Sonia Melandri
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- Bologna
- Italy
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Abstract
The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.
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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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Structures and energetics of clusters surrounding diatomic anions stabilized by hydrogen, halogen, and other noncovalent bonds. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lu J, Scheiner S. Comparison of halogen with proton transfer. Symmetric and asymmetric systems. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Scheiner S, Michalczyk M, Zierkiewicz W. Structures of clusters surrounding ions stabilized by hydrogen, halogen, chalcogen, and pnicogen bonds. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Li X, Jin Y, Gou Q, Xia Z, Feng G. Microwave spectrum and non-covalent interactions of the 1, 2, 3, 4-tetrafluorobenzene-water complex. J Chem Phys 2018; 149:164306. [PMID: 30384754 DOI: 10.1063/1.5048101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 1, 2, 3, 4-tetrafluorobenzene-water complex was investigated by pulsed-jet Fourier transform microwave spectroscopy. One isomer was detected in the jet expansion. Ab initio calculations and non-covalent interaction (NCI) analysis were performed to characterize the intermolecular NCIs. In the observed isomer, the water molecule lies almost in the plane of the benzene ring acting as a proton donor to one of the fluorine atoms and as an acceptor to one of the hydrogen atoms forming a six-membered ring structure. The CH⋯O and H⋯FC bonding distances are determined to be 2.385(1) Å and 2.429(1) Å, respectively. The interaction energy is calculated to be -18.0 kJ mol-1 at the SAPT2+(3)/aug-cc-pVDZ level of theory. The observed transitions exhibit splitting in the order of tens to hundreds of kHz due to the internal rotation of water moiety. The possible tunneling paths of water were investigated by ab initio calculations resulting in a barrier for an internal rotation of about 201 cm-1.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Yan Jin
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Qian Gou
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Zhining Xia
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331 Chongqing, China
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Scheiner S. Ability of IR and NMR Spectral Data to Distinguish between a Tetrel Bond and a Hydrogen Bond. J Phys Chem A 2018; 122:7852-7862. [DOI: 10.1021/acs.jpca.8b07631] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S, Lu J. Halogen, Chalcogen, and Pnicogen Bonding Involving Hypervalent Atoms. Chemistry 2018; 24:8167-8177. [DOI: 10.1002/chem.201800511] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
| | - Jia Lu
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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Van der Waals interaction between perhalogenated ethylene and rare gas: A rotational study of chlorotrifluorethylene-argon. J Chem Phys 2018; 148:154302. [DOI: 10.1063/1.5024984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Halogen Bonds Formed between Substituted Imidazoliums and N Bases of Varying N-Hybridization. Molecules 2017; 22:molecules22101634. [PMID: 28961202 PMCID: PMC6151534 DOI: 10.3390/molecules22101634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/16/2022] Open
Abstract
Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.
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Scheiner S. Systematic Elucidation of Factors That Influence the Strength of Tetrel Bonds. J Phys Chem A 2017; 121:5561-5568. [DOI: 10.1021/acs.jpca.7b05300] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Scheiner S. Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds. Chemistry 2016; 22:18850-18858. [PMID: 27740702 DOI: 10.1002/chem.201603891] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/09/2022]
Abstract
The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA
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