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Bonding in Supramolecular Organic Assemblies

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (20 August 2024) | Viewed by 5704

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Prof. Dr. Vadim P. Boyarskiy

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Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii prospect, Petergof, 198504 Saint Petersburg, Russia
Interests: organometallic chemistry of Pd and Pt; homogeneous catalysis; non-covalent interactions; azaheterocycles
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Special Issue Information

Dear Colleagues,

For more than a century and a half, since the appearance of Kekule's reports, the scientific community has focused on various aspects of bonding in organic compounds. By the end of the 20^th century—thanks to discoveries by Lewis, Pauling, Woodward, Hoffmann, Dewar, and other researchers—a complete understanding of covalent bonding seemed to have been attained. However, in the new millennium, this was proven to not be the case, since chemistry in general, and organic chemistry in particular, moved to a higher level of studying the properties of individual compounds and materials.

Technologies using nanometer-sized objects are coming to the fore. The use of these processes leads to a significant reduction in the energy consumption of devices and an increase in the efficiency of production processes. Moreover, new physical and physicochemical phenomena have been discovered at the nanometer scale. It is obvious that the regulated production of nanometer objects is one of the cutting-edge directions of modern science and technology. To design and fabricate nanostructures, either top-down or bottom-up approaches can be applied. The latter method is based on molecular self-assembly that occurs in supramolecular processes. It is not, therefore, unusual that supramolecular chemistry has assumed a leading role in basic science and in nanotechnology.

The self-assembly of nanosized structures requires structural control over individual molecules and molecular ensembles. It is provided by molecular attributes such as morphology, positioning, and geometry of functional groups, which requires thoughtful design. Therefore, in recent decades, the main experimental efforts of scientists studying chemical bonding in organic and organometallic compounds have been focused on structure-directing non-covalent interactions, including hydrogen, halogen, chalcogen, pnictogen, tetrel bonding, π-π stacking interactions, π-hole interaction, etc., which determine the properties and behavior of organic molecules, both at the molecular and supramolecular levels.

In this regard, the main goal of this Special Issue is to collect theoretical and experimental works related to non-covalent bonding involving organic compounds.

Prof. Dr. Vadim P. Boyarskiy
Guest Editor

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Keywords

structure-directing non-covalent interactions
supramolecular organic chemistry
molecular ensembles
molecular self-assembly

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Published Papers (4 papers)

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Research

13 pages, 5340 KiB

Open AccessCommunication

Hybrid 2D Supramolecular Organic Frameworks (SOFs) Assembled by the Cooperative Action of Hydrogen and Halogen Bonding and π⋯π Stacking Interactions

by Sergey V. Baykov, Artem V. Semenov, Sofia I. Presnukhina, Marina V. Tarasenko, Anton A. Shetnev, Antonio Frontera, Vadim P. Boyarskiy and Vadim Yu. Kukushkin

Int. J. Mol. Sci. 2024, 25(4), 2062; https://doi.org/10.3390/ijms25042062 - 8 Feb 2024

Cited by 1 | Viewed by 1307

Abstract

The cis- and trans-isomers of 6-(3-(3,4-dichlorophenyl)-1,2,4-oxadiazol-5-yl)cyclohex-3-ene-1-carboxylic acid (cis-A and trans-A) were obtained by the reaction of 3,4-dichloro-N′-hydroxybenzimidamide and cis-1,2,3,6-tetrahydrophthalic anhydride. Cocrystals of cis-A with appropriate solvents (cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C₆H₁₄) were grown from 1,2-dichloroethane (1,2-DCE), 1,2-dibromoethane (1,2-DBE), and a n-hexane/CHCl₃ mixture and then characterized by X-ray crystallography. In their structures, cis-A is self-assembled to give a hybrid 2D supramolecular organic framework (SOF) formed by the cooperative action of O–H⋯O hydrogen bonding, Cl⋯O halogen bonding, and π⋯π stacking. The self-assembled cis-A divides the space between the 2D SOF layers into infinite hollow tunnels incorporating solvent molecules. The energy contribution of each noncovalent interaction to the occurrence of the 2D SOF was verified by several theoretical approaches, including MEP and combined QTAIM and NCIplot analyses. The consideration of the theoretical data proved that hydrogen bonding (approx. −15.2 kcal/mol) is the most important interaction, followed by π⋯π stacking (approx. −11.1 kcal/mol); meanwhile, the contribution of halogen bonding (approx. −3.6 kcal/mol) is the smallest among these interactions. The structure of the isomeric compound trans-A does not exhibit a 2D SOF architecture. It is assembled by the combined action of hydrogen bonding and π⋯π stacking, without the involvement of halogen bonds. A comparison of the cis-A structures with that of trans-A indicated that halogen bonding, although it has the lowest energy in cis-A-based cocrystals, plays a significant role in the crystal design of the hybrid 2D SOF. The majority of the reported porous halogen-bonded organic frameworks were assembled via iodine and bromine-based contacts, while chlorine-based systems—which, in our case, are structure-directing—were unknown before this study. Full article

(This article belongs to the Special Issue Bonding in Supramolecular Organic Assemblies)

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17 pages, 6311 KiB

Open AccessArticle

Supramolecular Nature of Multicomponent Crystals Formed from 2,2′-Thiodiacetic Acid with 2,6-Diaminopurine or N9-(2-Hydroxyethyl)adenine

by Jeannette Carolina Belmont-Sánchez, Duane Choquesillo-Lazarte, María Eugenia García-Rubiño, Antonio Matilla-Hernández, Juan Niclós-Gutiérrez, Alfonso Castiñeiras and Antonio Frontera

Int. J. Mol. Sci. 2023, 24(24), 17381; https://doi.org/10.3390/ijms242417381 - 12 Dec 2023

Cited by 2 | Viewed by 1290

Abstract

The synthesis and characterization of the multicomponent crystals formed by 2,2′-thiodiacetic acid (H₂tda) and 2,6-diaminopurine (Hdap) or N9-(2-hydroxyethyl)adenine (9heade) are detailed in this report. These crystals exist in a salt rather than a co-crystal form, as confirmed by single crystal X-ray diffractometry, which reflects their ionic nature. This analysis confirmed proton transfer from the 2,2′-thiodiacetic acid to the basic groups of the coformers. The new multicomponent crystals have molecular formulas [(H9heade⁺)(Htda⁻)] 1 and [(H₂dap⁺)₂(tda²⁻)]·2H₂O 2. These were also characterized using FTIR, ¹H and ¹³C NMR and mass spectroscopies, elemental analysis, and thermogravimetric/differential scanning calorimetry (TG/DSC) analyses. In the crystal packing the ions interact with each other via O–H⋯N, O–H⋯O, N–H⋯O, and N–H⋯N hydrogen bonds, generating cyclic hydrogen-bonded motifs with graph-set notation of

R_{2}^{2}

(16),

R_{2}^{2}

(10),

R_{3}^{2}

(10),

R_{3}^{3}

(10),

R_{2}^{2}

(9),

R_{3}^{2}

(8), and

R_{4}^{2}

(8), to form different supramolecular homo- and hetero-synthons. In addition, in the crystal packing of 2, pairs of diaminopurinium ions display a strong anti-parallel π,π-stacking interaction, characterized by short inter-centroids and interplanar distances (3.39 and 3.24 Å, respectively) and a fairly tight angle (17.5°). These assemblies were further analyzed energetically using DFT calculations, MEP surface analysis, and QTAIM characterization. Full article

(This article belongs to the Special Issue Bonding in Supramolecular Organic Assemblies)

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13 pages, 4261 KiB

Open AccessArticle

Porous and Close Packed Supramolecular Assemblies from 2,4-Difluoronitrobenzene with Three Different Linkers and an n-Butylamine Cap

by M. John Plater, Abbie J. Esslemont and William T. A. Harrison

Int. J. Mol. Sci. 2023, 24(19), 14683; https://doi.org/10.3390/ijms241914683 - 28 Sep 2023

Cited by 1 | Viewed by 962

Abstract

A porous structure formed from sheets with cavities and two close packed structures were crystallised from building blocks prepared from 2,4-difluoronitrobenzene, a diamine linker and n-butylamine. The porous structure crystallised from a flexible building block prepared using 1,4-diaminobutane as linker. The close [...] Read more.

(This article belongs to the Special Issue Bonding in Supramolecular Organic Assemblies)

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17 pages, 4111 KiB

Open AccessArticle

Halogen Bonding Involving Isomeric Isocyanide/Nitrile Groups

by Andrey S. Smirnov, Eugene A. Katlenok, Alexander S. Mikherdov, Mariya A. Kryukova, Nadezhda A. Bokach and Vadim Yu. Kukushkin

Int. J. Mol. Sci. 2023, 24(17), 13324; https://doi.org/10.3390/ijms241713324 - 28 Aug 2023

Cited by 4 | Viewed by 1519

Abstract

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···C_isocyanide or I···N_nitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor. Full article

(This article belongs to the Special Issue Bonding in Supramolecular Organic Assemblies)

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