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14 pages, 8297 KB

Open AccessArticle

Characteristics of Intermolecular Interactions between Encapsulated Molecules and the Lantern-Like Carcerand Superphanes

by Mirosław Jabłoński

Molecules 2024, 29(3), 601; https://doi.org/10.3390/molecules29030601 - 26 Jan 2024

Cited by 4 | Viewed by 1895

Abstract

The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the

H_{2}

{NH}_{3}

, HF, HCN, and MeOH molecules trapped inside them. Despite the large cavity, the freedom of [...] Read more.

The main topic of the article is to provide the characteristics of individual intermolecular interactions present between three lantern-like superphanes and the

H_{2}

{NH}_{3}

, HF, HCN, and MeOH molecules trapped inside them. Despite the large cavity, the freedom of the trapped molecules is significantly limited by the presence of numerous interaction sites on the side chains of the superphane molecule. It is shown that the molecule trapped inside the superphane is stabilized mainly by only one or, less often, two strong hydrogen bonds involving the imino nitrogen atom, but QTAIM calculations also suggest the presence of many other intermolecular interactions, mainly hydrogen bonds involving imino or central hydrogen atoms from the side chains of the superphane molecule. Moreover, it is also shown that the structural simplification of the side chains does not significantly affect both the size of the superphane molecule and the obtained encapsulation energies, which is important in modeling this type of carceplexes. Noticeably, the parent superphane considered here was previously synthesized by the group of Qing He, so the results obtained will help in understanding this type and similar systems. Full article

(This article belongs to the Special Issue Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions (Volume II))

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22 pages, 9468 KB

Open AccessArticle

Bader’s Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction—Proof Studies Based on the Ng@[3_n]cyclophane Endohedral Complexes

by Mirosław Jabłoński

Molecules 2023, 28(17), 6353; https://doi.org/10.3390/molecules28176353 - 30 Aug 2023

Cited by 12 | Viewed by 2532

Abstract

According to Bader’s quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly ‘troublesome’ are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host’s cage system usually ‘produces’ many counterintuitive bond paths. In the author’s opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host’s cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3

_{n}

]cyclophane (3

\leq n \leq

6) endohedral complexes is used. As a result, arguments are presented showing that Bader’s topological bond path does not necessarily indicate a stabilizing interaction. Full article

(This article belongs to the Special Issue Fundamental Aspects of Chemical Bonding)

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18 pages, 2089 KB

Open AccessViewpoint

Determining Repulsion in Cyclophane Cages

by Mirosław Jabłoński

Molecules 2022, 27(13), 3969; https://doi.org/10.3390/molecules27133969 - 21 Jun 2022

Cited by 9 | Viewed by 2596

Abstract

Superphane, i.e., [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane, is a very convenient molecule in studying the nature of guest⋯host interactions in endohedral complexes. Nevertheless, the presence of as many as six ethylene bridges in the superphane molecule makes it practically impossible for the trapped entity to escape out of the superphane cage. Thus, in this article, I have implemented the idea of using the superphane derivatives with a reduced number of ethylene linkers, which leads to the [2

_{n}

] cyclophanes where

n < 6

. Seven such cyclophanes are then allowed to form endohedral complexes with noble gas (Ng) atoms (He, Ne, Ar, Kr). It is shown that in the vast majority of cases, the initially trapped Ng atom spontaneously escapes from the cyclophane cage, creating an exohedral complex. This is the best proof that the Ng⋯cyclophane interaction in endohedral complexes is indeed highly repulsive, i.e., destabilizing. Apart from the ‘sealed’ superphane molecule, endohedral complexes are only formed in the case of the smallest He atom. However, it has been shown that in these cases, the Ng⋯cyclophane interaction inside the cyclophane cage is nonbonding, i.e., repulsive. This highly energetically unfavorable effect causes the cyclophane molecule to ‘swell’. Full article

(This article belongs to the Special Issue Endohedral Chemistry)

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16 pages, 3609 KB

Open AccessArticle

Does the Presence of a Bond Path Really Mean Interatomic Stabilization? The Case of the Ng@Superphane (Ng = He, Ne, Ar, and Kr) Endohedral Complexes

by Mirosław Jabłoński

Symmetry 2021, 13(12), 2241; https://doi.org/10.3390/sym13122241 - 24 Nov 2021

Cited by 16 | Viewed by 3121

Abstract

Using a fairly structurally flexible and, therefore, very suitable for this type of research, superphane molecule, we demonstrate that the inclusion of a noble gas atom (Ng = He, Ne, Ar, and Kr) inside it and, thus, the formation of the Ng@superphane endohedral complex, leads to its ‘swelling’. Positive values of both the binding and strain energies prove that encapsulation and in turn ‘swelling’ of the superphane molecule is energetically unfavorable and that the Ng⋯C interactions in the interior of the cage are destabilizing, i.e., repulsive. Additionally, negative Mayer Bond Orders indicate the antibonding nature of Ng⋯C contacts. This result in combination with the observed Ng⋯C bond paths shows that the presence of a bond path in the molecular graph does not necessarily prove interatomic stabilization. It is shown that the obtained conclusions do not depend on the computational methodology, i.e., the method and the basis set used. However, on the contrary, the number of bond paths may depend on the methodology. This is yet another disadvantageous finding that does not favor the treatment of bond paths on molecular graphs as indicators of chemical bonds. The Kr@superphane endohedral complex features one of the longest C–C bonds ever reported (1.753 Å). Full article

(This article belongs to the Special Issue Exploring Inter- and Intramolecular Interactions as Building Blocks of Larger Systems)

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