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Murray JS. The Formation of σ-Hole Bonds: A Physical Interpretation. Molecules 2024; 29:600. [PMID: 38338346 PMCID: PMC10856353 DOI: 10.3390/molecules29030600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
This paper discusses two quite different computational experiments relating to the formation of σ-hole bonds A···B. The first involves looking at the complex at equilibrium and finding the contour X of the electronic density which allows the iso-density envelopes of A and B to be nearly touching. This contour increases, becoming closer to the nuclei, as the strength of the interaction increases. The second experiment involves allowing A and B to approach each other, with the aim of finding the distance at which their 0.001 a.u. iso-density envelopes are nearly merging into one envelope. What is found in the second experiment may be somewhat surprising, in that the ratio of the distance between interacting atoms at this nearly merging point-divided by the sum of the van der Waals radii of these atoms-covers a narrow range, typically between 1.2 and 1.3. It is intriguing to note that for the dataset presented, approaching molecules attracted to each other appear to do so unknowing of the strength of their ultimate interaction. This second experiment also supports the notion that one should expect favorable interactions, in some instances, to have close contacts significantly greater than the sums of the van der Waals radii.
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Affiliation(s)
- Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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2
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Das A, Arunan E. Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding. Phys Chem Chem Phys 2023; 25:22583-22594. [PMID: 37435670 DOI: 10.1039/d3cp00370a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.
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Affiliation(s)
- Arijit Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Elangannan Arunan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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Gao M, Zhao Q, Yu H, Fu M, Li Q. Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study. Molecules 2022; 27:molecules27092885. [PMID: 35566234 PMCID: PMC9101229 DOI: 10.3390/molecules27092885] [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: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023] Open
Abstract
The spodium–π bonding between MX2 (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C2H2/C2H4 acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX2⋯C2F2 complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.
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Affiliation(s)
- Meng Gao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
- Correspondence: (M.G.); (Q.L.)
| | - Qibo Zhao
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Hao Yu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Min Fu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao 266590, China; (Q.Z.); (H.Y.); (M.F.)
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
- Correspondence: (M.G.); (Q.L.)
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Jemmis ED, Ghorai S. Orbital Engineering in Chemistry. Isr J Chem 2021. [DOI: 10.1002/ijch.202100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eluvathingal D. Jemmis
- Department of Inorganic and Physical Chemistry Indian Institute of Science Tala Marg, Mathikere Bengaluru Karnataka 560012 India
| | - Sagar Ghorai
- Department of Inorganic and Physical Chemistry Indian Institute of Science Tala Marg, Mathikere Bengaluru Karnataka 560012 India
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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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Gomila RM, Bauzá A, Mooibroek TJ, Frontera A. Spodium bonding in five coordinated Zn(ii): a new player in crystal engineering? CrystEngComm 2021. [DOI: 10.1039/d1ce00221j] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This highlight evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(ii) spodium atom.
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Affiliation(s)
- Rosa M. Gomila
- Universitat de les Illes Balears
- Serveis Científico-Tècnics
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- Netherlands
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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Basak T, Gomila RM, Frontera A, Chattopadhyay S. Differentiating intramolecular spodium bonds from coordination bonds in two polynuclear zinc( ii) Schiff base complexes. CrystEngComm 2021. [DOI: 10.1039/d1ce00214g] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two new zinc(ii) complexes have been synthesized and characterized. Theoretical study is devoted to distinguish between conventional coordination bonds and spodium bonds between the zinc and oxygen centers.
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Affiliation(s)
- Tanmoy Basak
- Department of Chemistry
- Inorganic Section
- Jadavpur University
- Kolkata-700032
- India
| | - Rosa M. Gomila
- Serveis Cientificotècnics
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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Kumar P, Frontera A, Pandey SK. Coordination versus spodium bonds in dinuclear Zn( ii) and Cd( ii) complexes with a dithiophosphate ligand. NEW J CHEM 2021. [DOI: 10.1039/d1nj03165a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two new d10-metal dithiophosphate complexes have been synthesized in purely aqueous media and characterized by elemental and spectral analyses. DFT calculations, QTAIM and NCI Plot index methods are preformed to differentiate the coordination and spodium bonds in the complexes.
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Affiliation(s)
- Pretam Kumar
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Sushil K. Pandey
- Post Graduate Department of Chemistry, University of Jammu, Baba Saheb Ambedkar Road, Jammu Tawi-180006, J&K, India
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Intramolecular Spodium Bonds in Zn(II) Complexes: Insights from Theory and Experiment. Int J Mol Sci 2020; 21:ijms21197091. [PMID: 32993027 PMCID: PMC7582961 DOI: 10.3390/ijms21197091] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/04/2023] Open
Abstract
Two new dinuclear zinc(II) complexes, [Zn2(µ1,3-OAc)(L1)2]I·MeOH (1) and [Zn2(µ1,3-OAc)(L2)(NCS)] (2), (where HL1 = 2-(((3-(dimethylamino)propyl)amino)methyl)-6-methoxy-phenol and H2L2 = 2,2′-[(1-Methyl-1,2-ethanediyl)bis(iminomethylene)]bis[6-ethoxyphenol]) have been synthesized and characterized by elemental and spectral analysis. Their X-ray solid state structures have been determined, revealing the existence of intramolecular Zn···O spodium bonds in both complexes due to the presence of methoxy (1) or ethoxy (2) substituents adjacent to the coordinated phenolic O-atom. These noncovalent interactions have been studied using density functional theory (DFT) calculations, the quantum theory of “atoms-in-molecules” and the noncovalent interaction plot. Moreover, a search in the Cambridge structure database (CSD) has been conducted in order to investigate the prevalence of intramolecular spodium bonds in Zn complexes. To our knowledge this is the first investigation dealing with intramolecular spodium bonds.
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Bauzá A, Alkorta I, Elguero J, Mooibroek TJ, Frontera A. Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007814] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Antonio Bauzá
- Departament de Química Universitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares Spain
| | - Ibon Alkorta
- Instituto de Química Médica Juan de la Cierva, 3 28006- Madrid Spain
| | - José Elguero
- Instituto de Química Médica Juan de la Cierva, 3 28006- Madrid Spain
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park A, 904, E1.26 1098 XH Amsterdam The Netherlands
| | - Antonio Frontera
- Departament de Química Universitat de les Illes Balears Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares Spain
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Bauzá A, Alkorta I, Elguero J, Mooibroek TJ, Frontera A. Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements. Angew Chem Int Ed Engl 2020; 59:17482-17487. [PMID: 32542948 DOI: 10.1002/anie.202007814] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Indexed: 02/06/2023]
Abstract
The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma, de Mallorca (Baleares, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Juan de la Cierva, 3, 28006-, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, Juan de la Cierva, 3, 28006-, Madrid, Spain
| | - Tiddo J Mooibroek
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park A, 904, E1.26, 1098 XH, Amsterdam, The Netherlands
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122, Palma, de Mallorca (Baleares, Spain
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