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Halogen bonding and Other σ-Hole Interactions: Insights from Theory and...
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Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 14983

Special Issue Editor

Dr. Tanja van Mourik

E-Mail Website
Guest Editor
School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
Interests: computational chemistry; electronic structure; intermolecular interactions; halogen bonding; density functional theory; ab initio

Special Issue Information

Dear Colleagues,

The last two decades have seen a huge upsurge in studies on halogen bonding, both experimentally and computationally. Halogen bonding plays important roles in many aspects of chemistry and biology, including materials science, molecular crystals, biological molecules, and molecular recognition. Halogen bonding arises from the interaction of a nucleophile with a positive region (dubbed the σ-hole) located at the elongation of the R–X bond (where R is the atom or group the halogen X is covalently bonded to). Additionally, chalcogens, pnicogens, tetrels, and even aerogens (noble gases) may contain σ-holes at the elongation of a covalent bond, leading to chalcogen, pnicogen, tetrel, and aerogen bonding. Although these have been much less studied compared to halogen bonding, they may have similar beneficial applications to halogen bonds. This Special issue will cover experimental and computational studies on the whole range of σ-hole interactions.

Dr. Tanja van Mourik
Guest Editor

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Published Papers (6 papers)

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Research

13 pages, 2854 KiB  
Article
External Electric Field Effect on the Strength of σ-Hole Interactions: A Theoretical Perspective in Like⋯Like Carbon-Containing Complexes
by Mahmoud A. A. Ibrahim, Nayra A. M. Moussa, Afnan A. K. Kamel, Mohammed N. I. Shehata, Muhammad Naeem Ahmed, Fouad Taha, Mohammed A. S. Abourehab, Ahmed M. Shawky, Eslam B. Elkaeed and Mahmoud E. S. Soliman
Molecules 2022, 27(9), 2963; https://doi.org/10.3390/molecules27092963 - 5 May 2022
Cited by 5 | Viewed by 2241
Abstract
For the first time, σ-hole interactions within like⋯like carbon-containing complexes were investigated, in both the absence and presence of the external electric field (EEF). The effects of the directionality and strength of the utilized EEF were thoroughly unveiled in the (F-C-F3) [...] Read more.
For the first time, σ-hole interactions within like⋯like carbon-containing complexes were investigated, in both the absence and presence of the external electric field (EEF). The effects of the directionality and strength of the utilized EEF were thoroughly unveiled in the (F-C-F3)2, (F-C-H3)2, and (H-C-F3)2 complexes. In the absence of the EEF, favorable interaction energies, with negative values, are denoted for the (F-C-F3)2 and (H-C-F3)2 complexes, whereas the (F-C-H3)2 complex exhibits unfavorable interactions. Remarkably, the strength of the applied EEF exhibits a prominent role in turning the repulsive forces within the latter complex into attractive ones. The symmetrical nature of the considered like⋯like carbon-containing complexes eradicated the effect of directionality of the EEF. The quantum theory of atoms in molecules (QTAIM), and the noncovalent interaction (NCI) index, ensured the occurrence of the attractive forces, and also outlined the substantial contributions of the three coplanar atoms to the total strength of the studied complexes. Symmetry-adapted perturbation theory (SAPT) results show the dispersion-driven nature of the interactions. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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13 pages, 3342 KiB  
Article
The Bifurcated σ-Hole···σ-Hole Stacking Interactions
by Yu Zhang and Weizhou Wang
Molecules 2022, 27(4), 1252; https://doi.org/10.3390/molecules27041252 - 13 Feb 2022
Cited by 3 | Viewed by 1700
Abstract
The bifurcated σ-hole···σ-hole stacking interactions between organosulfur molecules, which are key components of organic optical and electronic materials, were investigated by using a combined method of the Cambridge Structural Database search and quantum chemical calculation. Due to the geometric constraints, the binding energy [...] Read more.
The bifurcated σ-hole···σ-hole stacking interactions between organosulfur molecules, which are key components of organic optical and electronic materials, were investigated by using a combined method of the Cambridge Structural Database search and quantum chemical calculation. Due to the geometric constraints, the binding energy of one bifurcated σ-hole···σ-hole stacking interaction is in general smaller than the sum of the binding energies of two free monofurcated σ-hole···σ-hole stacking interactions. The bifurcated σ-hole···σ-hole stacking interactions are still of the dispersion-dominated noncovalent interactions. However, in contrast to the linear monofurcated σ-hole···σ-hole stacking interaction, the contribution of the electrostatic energy to the total attractive interaction energy increases significantly and the dispersion component of the total attractive interaction energy decreases significantly for the bifurcated σ-hole···σ-hole stacking interaction. Another important finding of this study is that the low-cost spin-component scaled zeroth-order symmetry-adapted perturbation theory performs perfectly in the study of the bifurcated σ-hole···σ-hole stacking interactions. This work will provide valuable information for the design and synthesis of novel organic optical and electronic materials. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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16 pages, 6706 KiB  
Article
Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics
by Frank Weinhold
Molecules 2022, 27(2), 377; https://doi.org/10.3390/molecules27020377 - 7 Jan 2022
Cited by 9 | Viewed by 2582
Abstract
Intermolecular bonding attraction at π-bonded centers is often described as “electrostatically driven” and given quasi-classical rationalization in terms of a “pi hole” depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like [...] Read more.
Intermolecular bonding attraction at π-bonded centers is often described as “electrostatically driven” and given quasi-classical rationalization in terms of a “pi hole” depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO−, CN−) with simple atomic anions (H−, F−) or with one another. Such “anti-electrostatic” anion–anion attractions are shown to lead to robust metastable binding wells (ranging up to 20–30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi–Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that “deletion” of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi–Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency (“charge transfer”) rather than envisioned Coulombic properties of unperturbed monomers. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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17 pages, 868 KiB  
Article
Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments
by Rafał Wysokiński, Wiktor Zierkiewicz, Mariusz Michalczyk and Steve Scheiner
Molecules 2021, 26(21), 6394; https://doi.org/10.3390/molecules26216394 - 22 Oct 2021
Cited by 10 | Viewed by 2065
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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21 pages, 3296 KiB  
Article
A–X⋯σ Interactions—Halogen Bonds with σ-Electrons as the Lewis Base Centre
by Sławomir J. Grabowski
Molecules 2021, 26(17), 5175; https://doi.org/10.3390/molecules26175175 - 26 Aug 2021
Cited by 3 | Viewed by 2339
Abstract
CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F [...] Read more.
CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F2, Cl2, Br2 and I2 molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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15 pages, 1107 KiB  
Article
Astatine Facing Janus: Halogen Bonding vs. Charge-Shift Bonding
by Serigne Sarr, Julien Pilmé, Gilles Montavon, Jean-Yves Le Questel and Nicolas Galland
Molecules 2021, 26(15), 4568; https://doi.org/10.3390/molecules26154568 - 28 Jul 2021
Cited by 3 | Viewed by 2738
Abstract
The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor [...] Read more.
The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin–orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C–At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts. Full article
(This article belongs to the Special Issue Halogen bonding and Other σ-Hole Interactions: Insights from Theory and Experiment)
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