Define What Is Not Defined: In Chemistry and Beyond

A special issue of Sci (ISSN 2413-4155). This special issue belongs to the section "Chemistry Science".

Deadline for manuscript submissions: closed (30 May 2022) | Viewed by 18926

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Guest Editor
Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Spain
Interests: hydrogen bond; lewis acid–Lewis base interactions; atoms in molecules theory; ab initio calculations
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Special Issue Information

Dear Colleagues,

Sci is an open access journal which covers all research fields; special attention is paid to the interdisciplinary topics which go far beyond any specific field of knowledge and that try to discuss key issues for science.

This is why this Special Issue that is titled “Define what is not defined: in chemistry and beyond” concerns general issue that are applied commonly in chemistry, but the meaning of which, and in particular the definitions, are the subject of discussion and polemics. I mean concepts, phenomena, terms and processes that are extremely helpful in describing many research results. Let me give you a few examples: aromaticity, electronegativity, hydrogen bond, stabilizing interaction, proton transfer, halogen bond, charge transfer, substituent effect and many, many others.

There is no doubt that a number of the terms that are listed above (and numerous others not mentioned) are very useful to describe research results and they are controversial if defined. For example, there are strict mathematical expressions for electronegativity but there are various expressions that are used in scientific literature. There are definitions of the hydrogen bond but they are still controversial. One can also mention the aromaticity that is determined by numerous indices or there are other terms which are commonly used but that are debatable; chemical bond, reactivity, relation between interaction and reaction, and so on.

The topics mentioned here are very interesting and exciting; therefore, I would like to invite all researchers who work on such topics to send their contributions for consideration for this Special Issue. The Sci journal is a proper place for such articles. I would like to invite various types of contributions; reviews, regular research papers, communications, or short notes. Studies which go far beyond restricted areas of science are welcome, also interdisciplinary studies which combine fields of chemistry and physics or mathematics. Such contributions would be very useful for others who enthusiastically work in science.

Prof. Dr. Sławomir Grabowski
Guest Editor

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Published Papers (6 papers)

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Research

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20 pages, 3301 KiB  
Article
Benzene, an Unexpected Binding Unit in Anion–π Recognition: The Critical Role of CH/π Interactions
by David Quiñonero and Antonio Frontera
Sci 2022, 4(3), 32; https://doi.org/10.3390/sci4030032 - 22 Aug 2022
Cited by 1 | Viewed by 4181
Abstract
We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% [...] Read more.
We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% of the total interaction energy, which is indicative of the strong influence of the CH/π on the Anion–π interaction and vice versa. Moreover, the symmetry-adapted perturbation theory (SAPT) partition scheme was used to study the different energy contributions to the interaction energies and to investigate the physical nature of the interplay between both interactions. Furthermore, the Atoms in Molecules (AIM) theory and the Non-Covalent Interaction (NCI) approach were used to analyze the two interactions further. Finally, a few examples from the Protein Data Bank (PDB) are shown. All results stress that the concurrent formation of both interactions may play an important role in biological systems due to the ubiquity of CH bonds, phenyl rings, and anions in biomolecules. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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14 pages, 2522 KiB  
Article
σ-Hole Bonds and the VSEPR Model—From the Tetrahedral Structure to the Trigonal Bipyramid
by Sławomir J. Grabowski
Sci 2022, 4(2), 17; https://doi.org/10.3390/sci4020017 - 19 Apr 2022
Cited by 3 | Viewed by 2280
Abstract
Complexes linked by various interactions are analysed in this study. They are characterized by the tetrahedral configuration of the Lewis acid centre. Interactions, being a subject of this study, are classified as σ-hole bonds, such as the halogen, chalcogen, pnicogen, and tetrel bonds. [...] Read more.
Complexes linked by various interactions are analysed in this study. They are characterized by the tetrahedral configuration of the Lewis acid centre. Interactions, being a subject of this study, are classified as σ-hole bonds, such as the halogen, chalcogen, pnicogen, and tetrel bonds. In the case of strong interactions, the tetrahedral configuration of the Lewis acid centre changes into the trigonal bipyramid configuration. This change is in line with the Valence-Shell Electron-Pair Repulsion model, VSEPR, and this is supported here by the results of high-level ab initio calculations. The theoretical results concerning the geometries are supported mainly by the Natural Bond Orbital, NBO, method. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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16 pages, 3808 KiB  
Article
Halogen-Bonded Driven Tetra-Substituted Benzene Dimers and Trimers: Potential Hosts for Metal Ions
by Rubén D. Parra
Sci 2022, 4(1), 9; https://doi.org/10.3390/sci4010009 - 25 Feb 2022
Cited by 3 | Viewed by 2454
Abstract
Cyclic dimers and trimers of tetra-substituted benzenes, ((HOOC)2-C6H2-(NHI)2), are selected as convenient model systems for investigating NI…O=C halogen bond strength and cooperativity. The four substituents in benzene are chosen so that two of them act [...] Read more.
Cyclic dimers and trimers of tetra-substituted benzenes, ((HOOC)2-C6H2-(NHI)2), are selected as convenient model systems for investigating NI…O=C halogen bond strength and cooperativity. The four substituents in benzene are chosen so that two of them act as halogen bond acceptors (COOH) and two act as halogen bond donors (NHI), as shown in the graphical abstract below. The potential for metal ion binding by each of the halogen-bonded aggregates is also investigated using the monoatomic sodium ion, Na+. Density functional theory calculations performed using the wB97XD functional and the DGDZVP basis set confirmed the ability of halogen bonding to drive the formation of the cyclic dimers and trimers of the model system chosen for this study. Evidence of halogen bond cooperativity is seen, for example, in a 9% shortening of each NI…O=C halogen bond distance with a corresponding 53% increase in the respective critical point density value, ρNI…O=C. Cooperativity also results in a 36% increase in the magnitude of the complexation energy per halogen-bond of the trimer relative to that of the dimer. The results of this study confirm the potential for binding a single Na+ ion by either the dimer or the trimer through their respective halogen-bond networks. Binding of two metal ions was shown to be possible by the dimer. Likewise, the trimer was also found to bind three metal ions. Lastly, the overall structure of the halogen-bonded dimer or trimer endured after complexation of the Na+ ions. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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16 pages, 4464 KiB  
Article
Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance
by M. Merced Montero-Campillo, Otilia Mó and Manuel Yáñez
Sci 2022, 4(1), 7; https://doi.org/10.3390/sci4010007 - 13 Feb 2022
Viewed by 2534
Abstract
The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, [...] Read more.
The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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11 pages, 857 KiB  
Article
Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations
by Maria Cristina Caputo and Patricio Federico Provasi
Sci 2021, 3(4), 41; https://doi.org/10.3390/sci3040041 - 9 Nov 2021
Cited by 2 | Viewed by 2249
Abstract
Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin [...] Read more.
Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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Review

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22 pages, 15128 KiB  
Review
Aromaticity Concepts Derived from Experiments
by Halina Szatylowicz, Paweł A. Wieczorkiewicz and Tadeusz M. Krygowski
Sci 2022, 4(2), 24; https://doi.org/10.3390/sci4020024 - 9 Jun 2022
Cited by 4 | Viewed by 4058
Abstract
Aromaticity, a very important term in organic chemistry, has never been defined unambiguously. Various ways to describe it come from different phenomena that have been experimentally observed. The most important examples related to some theoretical concepts are presented here. Full article
(This article belongs to the Special Issue Define What Is Not Defined: In Chemistry and Beyond)
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