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σ and π Holes: A New Class of Non-Covalent Interactions

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

Deadline for manuscript submissions: closed (30 April 2019) | Viewed by 18389

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Dr. Antonio Caballero

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Departamento de Química Orgánica, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain
Interests: halogen bond; chalcogen bond; anion recognition; supramolecular polymers; interlocked structures
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Special Issue Information

Dear Colleagues,

For many years, the research field of the non-covalent interactions has been largely dominated by electrostatic interactions and especially hydrogen bonding interactions. Recently, the study of new non-covalent interactions, based on the existence of the denominated sigma or pi hole, has grown enormously from a theoretical and experimental point of view. Without any doubt, halogen bonding interactions have become in the most promising interactions and numerous examples have been reported. Motivated by the relevance of the results obtained for halogen atoms, many researchers have focused their research on the study of other groups: aerogen, chalcogen, pnicogen, tetrel and icosagen atoms.

This Special Issue aims to highlight the role of this brand new form of noncovalent interaction that has recently appeared in several research fields, including catalysis, crystal engineering, molecular recognition, materials science, as well as theoretical aspects.

Dr. Antonio Caballero
Guest Editor

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Keywords

Halogen bonding
Aerogen bonding
Chalcogen bonding
Pnicogen bonding
Tetrel bonding
Icosagen bonding
Hydrogen bonding

Published Papers (5 papers)

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Research

9 pages, 5396 KiB

Open AccessArticle

Chalcogen Bonding due to the Exo-Substitution of Icosahedral Dicarbaborane

by Jindřich Fanfrlík, Drahomír Hnyk and Pavel Hobza

Molecules 2019, 24(14), 2657; https://doi.org/10.3390/molecules24142657 - 23 Jul 2019

Cited by 6 | Viewed by 2732

Abstract

Chalcogen atoms are a class of substituents capable of generating inner and outer derivatives of boron clusters. It is well known that chalcogenated boron clusters can form strong σ-hole interactions when a chalcogen atom is a part of an icosahedron. This paper studies σ-hole interactions of dicarbaboranes with two exopolyhedral chalcogen atoms bonded to carbon vertices. Specifically, a computational investigation has been carried out on the co-crystal of (1,2-C₂B₁₀H₁₀)₂Se₄•toluene and a single crystal of (1,2-C₂B₁₀H₁₀)₂Te₄. Full article

(This article belongs to the Special Issue σ and π Holes: A New Class of Non-Covalent Interactions)

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21 pages, 11791 KiB

Open AccessArticle

What Is the Nature of Supramolecular Bonding? Comprehensive NBO/NRT Picture of Halogen and Pnicogen Bonding in RPH₂···IF/FI Complexes (R = CH₃, OH, CF₃, CN, NO₂)

by Yinchun Jiao and Frank Weinhold

Molecules 2019, 24(11), 2090; https://doi.org/10.3390/molecules24112090 - 31 May 2019

Cited by 20 | Viewed by 3656

Abstract

We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH₂···IF/FI binary complexes (R = CH₃, OH, CF₃, CN, and NO₂) and the tuning effects of R-substituents. Though such interactions are commonly attributed to “sigma-hole”-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type “electrostatics” are known to play only a secondary modulating role. The general 3c/4e resonance perspective corresponds to a continuous range of interatomic A···B bond orders (b_AB), spanning both the stronger “covalent” interactions of the molecular domain (say, b_AB ≥ ½) and the weaker interactions (b_AB ˂ ½, often misleadingly termed “noncovalent”) that underlie supramolecular complexation phenomena. We show how a unified NBO/NRT-based description of hydrogen, halogen, pnicogen, and related bonding yields an improved predictive utility and intuitive understanding of empirical trends in binding energies, structural geometry, and other measurable properties that are expected to be manifested in all such supramolecular interaction phenomena. Full article

(This article belongs to the Special Issue σ and π Holes: A New Class of Non-Covalent Interactions)

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19 pages, 1559 KiB

Open AccessArticle

Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives

by Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński and Steve Scheiner

Molecules 2019, 24(2), 376; https://doi.org/10.3390/molecules24020376 - 21 Jan 2019

Cited by 28 | Viewed by 4439

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. Full article

(This article belongs to the Special Issue σ and π Holes: A New Class of Non-Covalent Interactions)

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17 pages, 3526 KiB

Open AccessEditor’s ChoiceArticle

Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions

by Steve Scheiner

Molecules 2019, 24(2), 227; https://doi.org/10.3390/molecules24020227 - 09 Jan 2019

Cited by 20 | Viewed by 3385

Abstract

Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl⁻ was thus compared to that of HCOO⁻, HSO₄⁻, and H₂PO₄⁻ with a wide variety of bidentate receptors. A pair of SnFH₂ groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)_n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO₂⁻ > Cl⁻ > H₂PO₄⁻ > HSO₄⁻ general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor. Full article

(This article belongs to the Special Issue σ and π Holes: A New Class of Non-Covalent Interactions)

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13 pages, 1714 KiB

Open AccessArticle

Tetrel Bond between 6-OTX₃-Fulvene and NH₃: Substituents and Aromaticity

by Ming-Chang Hou, Shu-Bin Yang, Qing-Zhong Li, Jian-Bo Cheng, Hai-Bei Li and Shu-Feng Liu

Molecules 2019, 24(1), 10; https://doi.org/10.3390/molecules24010010 - 20 Dec 2018

Cited by 15 | Viewed by 3417

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. Full article

(This article belongs to the Special Issue σ and π Holes: A New Class of Non-Covalent Interactions)

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