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Chemical Bonding in Organic Compounds

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

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 8798

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Guest Editor
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,

The concept of a chemical bond in organic compounds has a history spanning more than 160 years. Kekulé, Lewis, Langmuir, Polling, Woodward, Hoffmann, Dewar, and many others created the concepts that organic chemists still use to qualitatively describe the bonds in organic compounds. In the field of the quantitative description of the structure of organic compounds, another revolution occurred in the 1990s with the widespread use of density-functional theory (DFT) methods in organic chemistry.

The quantum theory of atoms in molecules (QTAIM) advanced the development of the concept of chemical bonding in organic compounds. Although this theory has certain drawbacks and limitations, it is currently a generally accepted and indispensable tool for the theoretical study of an important area of ​​modern organic chemistry: non-covalent interactions. In recent decades, the main experimental efforts of scientists working in the field of chemical bonding in organic and organometallic compounds have been focused on the study of non-covalent interactions (hydrogen, halogen, chalcogen, pnictogen, tetrel bonding, π–π stacking interaction, π-hole interaction, etc.). This is no coincidence. Many of these interactions determine the properties and behavior of organic molecules at both the molecular and supramolecular levels. The formed non-covalent bonds have found applications in organic synthesis, catalysis, supramolecular chemistry, material design, medicinal chemistry, etc.

Due to this development in the field of chemical bonding research in organic compounds, the main goal of this Special iIsue is to collect theoretical and experimental studies devoted to the features of non-covalent interactions with the participation of organic compounds.

Prof. Dr. Vadim P. Boyarskiy
Guest Editor

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Keywords

  • non-covalent interactions
  • π-hole interaction
  • tetrel bond
  • QTAIM

Published Papers (3 papers)

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Research

18 pages, 3029 KiB  
Article
Hydrogen and Lithium Bonds—Lewis Acid Units Possessing Multi-Center Covalent Bonds
by Mohammad Aarabi, Samira Gholami and Sławomir J. Grabowski
Molecules 2021, 26(22), 6939; https://doi.org/10.3390/molecules26226939 - 17 Nov 2021
Cited by 8 | Viewed by 2418
Abstract
MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular [...] Read more.
MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions—the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method. Full article
(This article belongs to the Special Issue Chemical Bonding in Organic Compounds)
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15 pages, 5546 KiB  
Article
π–π Noncovalent Interaction Involving 1,2,4- and 1,3,4-Oxadiazole Systems: The Combined Experimental, Theoretical, and Database Study
by Sergey V. Baykov, Alexander S. Mikherdov, Alexander S. Novikov, Kirill K. Geyl, Marina V. Tarasenko, Maxim A. Gureev and Vadim P. Boyarskiy
Molecules 2021, 26(18), 5672; https://doi.org/10.3390/molecules26185672 - 18 Sep 2021
Cited by 38 | Viewed by 3039
Abstract
A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, 1H and 13C NMR spectroscopy, as well as X-ray [...] Read more.
A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, 1H and 13C NMR spectroscopy, as well as X-ray diffraction. The inspection of the crystal structures of (13)a,b and the Hirshfeld surface analysis made possible the recognition of the (oxadiazole)···(pyridine) and (oxadiazole)···(oxadiazole) interactions. The presence of these interactions was confirmed theoretically by DFT calculations, including NCI analysis for experimentally determined crystal structures as well as QTAIM analysis for optimized equilibrium structures. The preformed database survey allowed the verification of additional examples of relevant (oxadiazole)···π interactions both in Cambridge Structural Database and in Protein Data Bank, including the cocrystal of commercial anti-HIV drug Raltegravir. Full article
(This article belongs to the Special Issue Chemical Bonding in Organic Compounds)
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15 pages, 2671 KiB  
Article
Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction
by Sergey V. Baykov, Artem V. Semenov, Eugene A. Katlenok, Anton A. Shetnev and Nadezhda A. Bokach
Molecules 2021, 26(11), 3119; https://doi.org/10.3390/molecules26113119 - 23 May 2021
Cited by 1 | Viewed by 2282
Abstract
Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of [...] Read more.
Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs. Full article
(This article belongs to the Special Issue Chemical Bonding in Organic Compounds)
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