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Exploring Inter- and Intramolecular Interactions as Building Blocks of Larger Systems

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A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Chemistry: Symmetry/Asymmetry".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 29730

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Special Issue Editor

Dr. Aneta Jezierska

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Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland
Interests: chemistry; computational chemistry; toxicology and pharmaceutics; chemical physics; biochemistry; materials science; molecular dynamics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I would like to draw your attention to a new Special Issue devoted to exploration and understanding of inter- and intramolecular interactions. An elusive concept of “chemical intuition”, natural attraction to elegance and beauty—these and many other factors motivate us to look for symmetry and order in molecules and their assemblies. Many known factors affect the presence of symmetry in molecular systems, e.g., protonation, aromaticity, neighboring molecules, and a more distant environment. Here are some examples of not-so-obvious manifestations of the role of internal molecular reorganization and intermolecular interactions responsible for self-organization of molecules to large systems. Let us look for a moment at “proton sponge” types of compounds. In their protonated forms, they could be of high symmetry in the case of a single-well bridge proton potential function. What happens when such symmetry is broken? What if the energy barrier is low enough so that the proton jumps very fast between the minima and the effective potential can be symmetric at the experimental time scale? Another case: What is the role of the solvation shell on the symmetry of the solvated molecule? Vice versa, how strong can the solvation shell ordering effect of a strongly polar molecule in solution be? Additionally, what happens to a molecule of high symmetry in a lower-symmetry crystal environment? A lot of the effort of physical and computational chemistry is devoted to such questions concerning very diverse classes of compounds. Therefore, this Special Issue will cover recent examples of the interplay between intramolecular bonds, intermolecular interactions, symmetry, and order of small and extended molecular systems.

Dr. Aneta Jezierska
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Symmetry is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

intra- and intermolecular interaction
IR
NMR
X-ray diffraction
computational chemistry/physics
bonding and non-bonding interactions
nanomaterials
drug design

Published Papers (12 papers)

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Research

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19 pages, 7515 KiB

Open AccessArticle

Interactions between Artificial Channel Protein, Water Molecules, and Ions Based on Theoretical Approaches

by Kamil Wojtkowiak, Aneta Jezierska and Jarosław J. Panek

Symmetry 2022, 14(4), 691; https://doi.org/10.3390/sym14040691 - 27 Mar 2022

Cited by 3 | Viewed by 1817

Abstract

Contemporary techniques of molecular modeling allow for rational design of several specific classes of artificial proteins. Transmembrane channels are among these classes. A recent successful synthesis of self-assembling, highly symmetrical 12- or 16-helix channels by David Baker’s group prompted us to study interactions between one of these proteins, TMHC6, and low-molecular-weight components of the environment: water molecules and ions. To examine protein stability in a polar environment, molecular dynamics (MD) with classical force fields of the AMBER family was employed. Further characteristics of the chosen interactions were obtained using interaction energy calculations with usage of partially polarizable GFN-FF force field of Spicher and Grimme, symmetry-adapted perturbation theory (SAPT) and atoms in molecules (AIM) approaches for models of residues from the channel entry, crucial for interactions with water molecules and ions. The comparison of the interaction energy values between the gas phase and solvent reaction field gives the quantitative estimation of the strength of the interactions. The energy decomposition via the SAPT method showed that the electrostatics forces play a dominant role in the substructure stabilization. An application of the AIM theory enabled a description of the intermolecular hydrogen bonds and other noncovalent interactions. Full article

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

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19 pages, 6924 KiB

Open AccessEditor’s ChoiceArticle

Energetic and Geometric Characteristics of Substituents, Part 3: The Case of NO₂ and NH₂ Groups in Their Mono-Substituted Derivatives of Six-Membered Heterocycles

by Paweł A. Wieczorkiewicz, Halina Szatylowicz and Tadeusz M. Krygowski

Symmetry 2022, 14(1), 145; https://doi.org/10.3390/sym14010145 - 12 Jan 2022

Cited by 2 | Viewed by 1906

Abstract

Substituted heterocyclic arenes play important roles in biochemistry, catalysis, and in the design of functional materials. Exemplary six-membered heteroaromatic molecules, that differ from benzene by inclusion of one heteroatom, are pyridine, phosphorine, arsabenzene, and borabenzene. This theoretical study concerns the influence of the heteroatom present in these molecules on the properties of substituents of two types: electron-donating (ED) NH₂ group and electron-accepting (EA) NO₂ group, attached at the 2-, 3-, or 4-position. The effect is evaluated by the energy of interaction (E_rel) between the substituent and the substituted system and electronic properties of the substituents described by the charge of the substituent active region (cSAR) index. In addition, several geometric descriptors of the substituent and heteroaromatic ring, as well as changes in the aromaticity, are considered. The latter are assessed using the Electron Density of Delocalized Bonds (EDDBs) property of delocalized π electrons. The obtained results show that the electronegativity (EN) of the heteroatom has a profound effect on the EA/ED properties of the substituents. This effect is also reflected in the geometry of studied molecules. The E_rel parameter indicates that the relative stability of the molecules is highly related to the electronic interactions between the substituent and the heteroarene. This especially applies to the enhancement or weakening of π-resonance due to the EN of the heteroatom. Additionally, in the 2-heteroarene derivatives, specific through-space ortho interactions contribute to the heteroatom effects. Full article

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

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16 pages, 3609 KiB

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 12 | Viewed by 1762

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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13 pages, 2288 KiB

Open AccessArticle

Vibrational Properties of Benzoxaboroles and Their Interactions with Candida albicans’ LeuRS

by Ewa Kaczorowska, Agnieszka Adamczyk-Woźniak, Grażyna Zofia Żukowska, Paulina Kostecka and Andrzej Sporzyński

Symmetry 2021, 13(10), 1845; https://doi.org/10.3390/sym13101845 - 2 Oct 2021

Cited by 2 | Viewed by 1508

Abstract

Benzoxaboroles have emerged over the past decade mainly due to their growing medicinal importance. Regarding the wide application of IR spectroscopy in the pharmaceutical industry, the vibrational properties of over a dozen of benzoxaboroles were described, based on results of DFT calculations as well as IR and Raman spectra measurements. Investigated series of compounds included the currently available antifungal drug (Tavaborole, AN2690) as well as its derivatives. An intense and well-isolated band corresponding to the B-OH group stretching vibrations was present in all experimental IR spectra in the range of 1446–1414 cm⁻¹ and can be considered as characteristic for benzoxaboroles. The vibrational properties of benzoxaboroles are shown to be affected by the formation of intramolecular as well as intermolecular hydrogen bonds, which should also influence the interactions of benzoxaboroles with biomolecules and impact on their biological functions. Docking studies of the benzoxaboroles’ adenosine monophosphate (AMP) spiroboronates into the Candida albicans leucyl-RS synthetase binding pocket showed that the introduction of an amine substituent has a strong influence on their binding. The determined values of inhibition constants manifest high potential of some of the investigated molecules as possible inhibitors of that enzyme. Full article

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

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11 pages, 2263 KiB

Open AccessArticle

Novel Coordination Mode in the Potassium Mefenamate Trihydrate Polymeric Structure

by Marta S. Krawczyk and Irena Majerz

Symmetry 2021, 13(10), 1761; https://doi.org/10.3390/sym13101761 - 22 Sep 2021

Viewed by 1128

Abstract

As a result of the synthesis of mefenamic acid with potassium hydroxide, a salt with a polymeric structure is formed. The one-dimensional polymeric structure was studied by single crystal X-ray diffraction. The potassium cation is coordinated to one oxygen atom of the carboxylate group and six water oxygen atoms. Potassium ions are bridged by oxygen atoms of water molecules. The crystal structure was used as an input to QTAIM and NCI approaches to investigate the K-O interactions linking the cation with the water oxygen and carboxylate groups. The weak K-O interactions of the potassium cation and water oxygen atoms were strong enough to form a polymeric structure. The flexibility of the weak interactions is responsible for a novel coordination mode in the potassium mefenamate trihydrate. Full article

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

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15 pages, 1290 KiB

Open AccessArticle

NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor

by Ilya G. Shenderovich and Gleb S. Denisov

Symmetry 2021, 13(7), 1298; https://doi.org/10.3390/sym13071298 - 19 Jul 2021

Cited by 2 | Viewed by 3194

Abstract

The isotopically enriched cyanide anion, (¹³C≡¹⁵N)⁻, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of ¹⁵N≡¹³CH···X and ¹³C≡¹⁵NH···X hydrogen bonding complexes in solution, where X = ¹⁹F, ¹⁵N, and O=³¹P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic ¹³C and ¹⁵N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. ¹J(¹⁵N¹³C) strongly correlates with the length of the N≡C bond. Full article

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

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21 pages, 16283 KiB

Open AccessArticle

Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers

by Anna Jezuita, Paweł A. Wieczorkiewicz, Halina Szatylowicz and Tadeusz M. Krygowski

Symmetry 2021, 13(7), 1223; https://doi.org/10.3390/sym13071223 - 7 Jul 2021

Cited by 4 | Viewed by 1809

Abstract

The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO₂ group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers. Full article

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

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15 pages, 3042 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY₃ (X = Cl, Br; Y = H, F)

by Barbara Bankiewicz and Marcin Palusiak

Symmetry 2021, 13(5), 766; https://doi.org/10.3390/sym13050766 - 28 Apr 2021

Cited by 6 | Viewed by 2366

Abstract

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY₃ molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems. Full article

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

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13 pages, 3034 KiB

Open AccessFeature PaperArticle

Magnetic Properties of Nickel-Titanium Alloy during Martensitic Transformations under Plastic and Elastic Deformation

by Ludmila I. Kveglis, Fedor M. Noskov, Mikhail N. Volochaev, Alexander V. Nyavro and Aleksander Filarowski

Symmetry 2021, 13(4), 665; https://doi.org/10.3390/sym13040665 - 13 Apr 2021

Cited by 4 | Viewed by 1904

Abstract

This paper focuses on the processes of the occurrence of magnetization during structure formation in samples of Ni₅₁Ti₄₉ alloy under deformation conditions. The possibility of the existence of a phase with an FCC (face-centered cubic) lattice in titanium nickelide has been demonstrated by electron microscopy and electron diffraction. It has been discovered that the interplanar distances of BCC₁₁₀ (body-centered cubic), FCC₁₁₁, and HCP₀₀₂ (hexagonal close packed) in the alloy under study have similar values, which indicates the possibility of their mutual polymorphic transformation. Based on the modular self-organization, a scheme of martensitic transformations in titanium nickelide from the B2 structure (BCC lattice) to the B19’ structure (HCP lattice) through an intermediate phase with an FCC lattice is proposed. It is shown that lenticular crystals appear in the Ni₅₁Ti₄₉ alloy under tensile deformation until rupture, which is accompanied by the onset of ferromagnetism. The effect of magnetization in Ni₅₁Ti₄₉ samples when immersed in liquid nitrogen has been also discovered. In this case, the reason for the appearance and disappearance of magnetization can be associated with microdeformation processes caused by direct and reverse martensitic transitions that occur during cooling and heating of the samples. Full article

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

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18 pages, 5063 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Structure-Property Relationship in Selected Naphtho- and Anthra-Quinone Derivatives on the Basis of Density Functional Theory and Car–Parrinello Molecular Dynamics

by Beata Kizior, Jarosław J. Panek, Bartłomiej M. Szyja and Aneta Jezierska

Symmetry 2021, 13(4), 564; https://doi.org/10.3390/sym13040564 - 29 Mar 2021

Cited by 5 | Viewed by 2476

Abstract

Intra- and inter-molecular interactions were studied in 2,3-dichloro-5,8-dihydroxy-1,4-naphthoquinone and 1,4-dihydroxy-anthraquinone to shed more light on the molecular assembly phenomena. The electronic ground and excited states features of the compounds were investigated to find structure-property dependencies. The theoretical study was carried out on the basis of Density Functional Theory (DFT), its Time-Dependent (TD-DFT) extension, and using Car–Parrinello Molecular Dynamics (CPMD). In order to show how the environmental effects modulate the physico-chemical properties, the simulations were performed in vacuo, with the solvent reaction field (Polarizable Continuum Model (PCM) and water as a solvent) and crystalline phase. The intramolecular hydrogen bonds and the bridged proton dynamics were analyzed in detail. The aromatic rings and electronic structure changes were estimated using the Harmonic Oscillator Model of Aromaticity (HOMA) and Atoms in Molecules (AIM) theory. The Symmetry-Adapted Perturbation Theory (SAPT) was employed for interaction energy decomposition in the studied dimers and trimers. It was found that the presence of a polar solvent decreased the energy barrier for the bridged proton transfer. However, it did not significantly affect the aromaticity and electronic structure. The SAPT results showed that the mutual polarization of the monomers in the dimer was weak and that the dispersion was responsible for most of the intermolecular attraction. The intermolecular hydrogen bonds seem to be much weaker than the intramolecular bridges. The TD-DFT results confirmed that the electronic excitations do not play any significant role in the intramolecular proton transfer. The CPMD results indicated that the protons are very labile in the hydrogen bridges. Short proton transfer and proton-sharing events were observed, and a correlation between them in the twin bridges was noticed, especially for the first investigated compound. Full article

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

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12 pages, 1704 KiB

Open AccessEditor’s ChoiceArticle

Self-Assembly of Hydrogen-Bonded Cage Tetramers of Phosphonic Acid

by Ivan S. Giba and Peter M. Tolstoy

Symmetry 2021, 13(2), 258; https://doi.org/10.3390/sym13020258 - 4 Feb 2021

Cited by 9 | Viewed by 2975

Abstract

The self-association of phosphonic acids with general formula RP(O)(OH)₂ in solution state remains largely unexplored. The general understanding is that such molecules form multiple intermolecular hydrogen bonds, but the stoichiometry of self-associates and the bonding motifs are unclear. In this work, we report the results of the study of self-association of tert-butylphosphonic acid using low temperature liquid-state ¹H and ³¹P NMR spectroscopy (100 K; CDF₃/CDF₂Cl) and density functional theory (DFT) calculations. For the first time, we demonstrate conclusively that polar aprotic medium tert-butylphosphonic acid forms highly symmetric cage-like tetramers held by eight OHO hydrogen bonds, which makes the complex quite stable. In these associates. each phosphonic acid molecule is bonded to three other molecules by forming two hydrogen bonds as proton donor and two hydrogen bonds as proton acceptor. Though the structure of such cage-like tetramers is close to tetrahedral, the formal symmetry of the self-associate is C₂. Full article

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

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Review

Jump to: Research

23 pages, 3155 KiB

Open AccessReview

Actual Symmetry of Symmetric Molecular Adducts in the Gas Phase, Solution and in the Solid State

by Ilya G. Shenderovich

Symmetry 2021, 13(5), 756; https://doi.org/10.3390/sym13050756 - 27 Apr 2021

Cited by 8 | Viewed by 5356

Abstract

This review discusses molecular adducts, whose composition allows a symmetric structure. Such adducts are popular model systems, as they are useful for analyzing the effect of structure on the property selected for study since they allow one to reduce the number of parameters. The main objectives of this discussion are to evaluate the influence of the surroundings on the symmetry of these adducts, steric hindrances within the adducts, competition between different noncovalent interactions responsible for stabilizing the adducts, and experimental methods that can be used to study the symmetry at different time scales. This review considers the following central binding units: hydrogen (proton), halogen (anion), metal (cation), water (hydrogen peroxide). Full article

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

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