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Special Issue "Noncovalent pi-Interactions"

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

Deadline for manuscript submissions: closed (30 April 2015)

Special Issue Editor

Guest Editor
Prof. Dr. Antonio Frontera

Universitat de les Illes Balears Department of Chemistry Crta de Valldemossa km, 7.5 07122 Palma de Mallorca (Baleares) Spain
E-Mail
Fax: +34971173426
Interests: Non covalent interactions, aromaticity, crystal engineering, ab intio calculations, physical organic chemistry

Special Issue Information

Dear Colleagues,

Supramolecular chemists rely on the comprehension of non-covalent forces, which are the basis of highly specific recognition, transport, and regulation mechanisms. The orchestration of many chemical and biological processes is often dominated by an intricate combination of non-covalent interactions, which are the foundation of the life process itself, the most significant expression of function. By means of modern synthetic methods, organic/inorganic chemists can prepare host compounds for virtually guest any target molecule, even in very competitive medium. The action and development of drugs is the realm of medicinal chemistry, for which the understanding of noncovalent interactions is crucial for the rational design of new drugs.

The correct description of interactions between molecules is needed for the understanding and progress of the supramolecular chemistry that usually relies on strong, directional interactions, such as hydrogen bonding and halogen bonding, and less on directional forces like ion pairing. In addition, non-covalent interactions involving aromatic rings are enormously significant in this field. They play a crucial role in chemistry and biology, in particular drug–receptor interactions, crystal engineering, catalysis, transport, enzyme inhibition and protein folding. The continuous research on well-known cation–π, C–H/π, and π–π stacking interactions, less-known anion–π and lone pair–π interactions and other basically unknown like salt-bridge–π interactions is a good indication of the increasing interest by the scientific community on this topic.

Research articles covering all areas noncovalent interactions involving π-systems, such as crystal engineering, host-guest chemistry, catalysis, transport, or structural, computational, or biochemical matters, etc. are welcomed for inclusion in this Special Issue of Molecules.

Prof. Dr. Antonio Frontera
Guest Editor

Manuscript Submission Information

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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. Molecules 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 1800 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

  • cation-pi interactions
  • anion-pi interactions
  • pi-acidic interactions
  • pi-basic interactions
  • donor-acceptor interactions
  • unconventional pi interactions
  • pi-hole interactions

Published Papers (6 papers)

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Research

Open AccessArticle Quantification of CH-π Interactions Using Calix[4]pyrrole Receptors as Model Systems
Molecules 2015, 20(9), 16672-16686; doi:10.3390/molecules200916672
Received: 7 August 2015 / Revised: 1 September 2015 / Accepted: 7 September 2015 / Published: 14 September 2015
Cited by 6 | PDF Full-text (1931 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We describe the use of two series of aryl-extended calix[4]pyrrole receptors bearing two and four electronically tunable phenyl groups, respectively, in their meso-positions as model systems for the quantification of CH-π interactions in solution. The “four-wall” and the “two-wall” receptors formed thermodynamically
[...] Read more.
We describe the use of two series of aryl-extended calix[4]pyrrole receptors bearing two and four electronically tunable phenyl groups, respectively, in their meso-positions as model systems for the quantification of CH-π interactions in solution. The “four-wall” and the “two-wall” receptors formed thermodynamically stable 1:1 complexes in acetonitrile solution with both trimethylamine N-oxide and trimethylphosphine P-oxide as guests. The complexes were mainly stabilized by the formation of four convergent hydrogen bonds between the oxygen atom of the guests and the pyrrole NHs of the host. In general, the N-oxide produced thermodynamically more stable hydrogen bonding interactions than the P-oxide. Upon guest binding, the receptors adopted the cone conformation and the methyl groups of the included guests engaged in CH-π interactions with the aromatic walls. We show that the modification of the electronic properties of the aromatic surfaces, in any of the receptor series, did not have a significant impact in the measured binding affinities for a given guest. However, the larger binding affinities determined for the “four-wall” receptors in comparison to the “two-wall” counterparts supported the importance of CH-π interactions on guest complexation. The strength of the CH-π interactions present in the inclusion complexes was quantified employing the octamethyl calix[4]pyrrole as reference. We determined an average magnitude of ~1 kcal·mol−1 for each CH-π interaction. The CH-π interactions featured a reduced electrostatic nature and thus dispersion forces were assigned as main contributors of their strength. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
Figures

Open AccessArticle Anion Recognition by Pyrylium Cations and Thio-, Seleno- and Telluro- Analogues: A Combined Theoretical and Cambridge Structural Database Study
Molecules 2015, 20(7), 11632-11659; doi:10.3390/molecules200711632
Received: 5 June 2015 / Revised: 17 June 2015 / Accepted: 18 June 2015 / Published: 24 June 2015
Cited by 5 | PDF Full-text (3461 KB) | HTML Full-text | XML Full-text
Abstract
Pyrylium salts are a very important class of organic molecules containing a trivalent oxygen atom in a six-membered aromatic ring. In this manuscript, we report a theoretical study of pyrylium salts and their thio-, seleno- and telluro- analogues by means of DFT calculations.
[...] Read more.
Pyrylium salts are a very important class of organic molecules containing a trivalent oxygen atom in a six-membered aromatic ring. In this manuscript, we report a theoretical study of pyrylium salts and their thio-, seleno- and telluro- analogues by means of DFT calculations. For this purpose, unsubstituted 2,4,6-trimethyl and 2,4,6-triphenyl cations and anions with different morphologies were chosen (Cl, NO3 and BF4). The complexes were characterized by means of natural bond orbital and “atoms-in-molecules” theories, and the physical nature of the interactions has been analyzed by means of symmetry-adapted perturbation theory calculations. Our results indicate the presence of anion-π interactions and chalcogen bonds based on both σ- and π-hole interactions and the existence of very favorable σ-complexes, especially for unsubstituted cations. The electrostatic component is dominant in the interactions, although the induction contributions are important, particularly for chloride complexes. The geometrical features of the complexes have been compared with experimental data retrieved from the Cambridge Structural Database. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
Figures

Open AccessArticle Triel Bonds, π-Hole-π-Electrons Interactions in Complexes of Boron and Aluminium Trihalides and Trihydrides with Acetylene and Ethylene
Molecules 2015, 20(6), 11297-11316; doi:10.3390/molecules200611297
Received: 30 April 2015 / Accepted: 15 June 2015 / Published: 19 June 2015
Cited by 23 | PDF Full-text (1224 KB) | HTML Full-text | XML Full-text
Abstract
MP2/aug-cc-pVTZ calculations were performed on complexes of aluminium and boron trihydrides and trihalides with acetylene and ethylene. These complexes are linked through triel bonds where the triel center (B or Al) is characterized by the Lewis acid properties through its π-hole region while
[...] Read more.
MP2/aug-cc-pVTZ calculations were performed on complexes of aluminium and boron trihydrides and trihalides with acetylene and ethylene. These complexes are linked through triel bonds where the triel center (B or Al) is characterized by the Lewis acid properties through its π-hole region while π-electrons of C2H2 or C2H4 molecule play the role of the Lewis base. Some of these interactions possess characteristics of covalent bonds, i.e., the Al-π-electrons links as well as the interaction in the BH3-C2H2 complex. The triel-π-electrons interactions are classified sometimes as the 3c-2e bonds. In the case of boron trihydrides, these interactions are often the preliminary stages of the hydroboration reaction. The Quantum Theory of “Atoms in Molecules” as well as the Natural Bond Orbitals approach are applied here to characterize the π-hole-π-electrons interactions. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
Figures

Open AccessArticle Interplay between Beryllium Bonds and Anion-π Interactions in BeR2:C6X6:Y Complexes (R = H, F and Cl, X = H and F, and Y = Cl and Br)
Molecules 2015, 20(6), 9961-9976; doi:10.3390/molecules20069961
Received: 22 April 2015 / Revised: 23 May 2015 / Accepted: 26 May 2015 / Published: 29 May 2015
Cited by 6 | PDF Full-text (1342 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A theoretical study of the beryllium bonds in BeR2:C6X6 (R = H, F, Cl and X = H and F) has been carried out by means of MP2/aug′-cc-pVDZ computational methods. In addition, the ternary complexes BeR2:C
[...] Read more.
A theoretical study of the beryllium bonds in BeR2:C6X6 (R = H, F, Cl and X = H and F) has been carried out by means of MP2/aug′-cc-pVDZ computational methods. In addition, the ternary complexes BeR2:C6X6:Y (Y = Cl and Br) have been analyzed. Geometric, energetic and electronic aspects of the complexes have been taken into account. All the parameters analyzed provide a clear indication of favorable cooperativity in both interactions observed, beryllium bond and aromatic ring:anion interaction. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
Figures

Open AccessArticle Aromatic Amino Acids-Guanidinium Complexes through Cation-π Interactions
Molecules 2015, 20(5), 9214-9228; doi:10.3390/molecules20059214
Received: 23 April 2015 / Revised: 11 May 2015 / Accepted: 12 May 2015 / Published: 20 May 2015
Cited by 1 | PDF Full-text (1715 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Continuing with our interest in the guanidinium group and the different interactions than can establish, we have carried out a theoretical study of the complexes formed by this cation and the aromatic amino acids (phenylalanine, histidine, tryptophan and tyrosine) using DFT methods and
[...] Read more.
Continuing with our interest in the guanidinium group and the different interactions than can establish, we have carried out a theoretical study of the complexes formed by this cation and the aromatic amino acids (phenylalanine, histidine, tryptophan and tyrosine) using DFT methods and PCM-water solvation. Both hydrogen bonds and cation-π interactions have been found upon complexation. These interactions have been characterized by means of the analysis of the molecular electron density using the Atoms-in-Molecules approach as well as the orbital interactions using the Natural Bond Orbital methodology. Finally, the effect that the cation-π and hydrogen bond interactions exert on the aromaticity of the corresponding amino acids has been evaluated by calculating the theoretical NICS values, finding that the aromatic character was not heavily modified upon complexation. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
Figures

Open AccessArticle Pi-pi Stacking Mediated Cooperative Mechanism for Human Cytochrome P450 3A4
Molecules 2015, 20(5), 7558-7573; doi:10.3390/molecules20057558
Received: 13 January 2015 / Revised: 18 March 2015 / Accepted: 19 March 2015 / Published: 24 April 2015
Cited by 2 | PDF Full-text (1960 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate
[...] Read more.
Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN). Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions. Full article
(This article belongs to the Special Issue Noncovalent pi-Interactions)
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