On the Nature of σ–σ, σ–π, and π–π Stacking in Extended Systems

Stacking interactions have been evaluated, employing computational methods, in dimers formed by analogous aliphatic and aromatic species of increasing size. Changes in stability as the systems become larger are mostly controlled by the balance of increasing repulsion and dispersion contributions, while electrostatics plays a secondary but relevant role. The interaction energy increases as the size of the system grows, but it does much faster in π–π dimers than in σ–π complexes and more remarkably than in σ–σ dimers. The main factor behind the larger stability of aromatic dimers compared to complexes containing aliphatic molecules is related to changes in the properties of the aromatic systems due to electron delocalization leading to larger dispersion contributions. Besides, an extra stabilization in π–π complexes is due to the softening of the repulsive wall in aromatic species that allows the molecules to come closerThe authors thank the financial support from the Consellerı́a de Cultura, Educación e Ordenación Universitaria e da Consellerı́a de Economı́a, Emprego e Industria (Axuda para Consolidación e Estruturación de unidades de investigación competitivas do Sistema Universitario de Galicia, Xunta de Galicia ED431C 2017/17)S

Computational Study on the effect of microhydration on amonium···phenol and methylammonium···phenol complexes

Interactions between cations and aromatic molecules can be often find on a large number of biomolecular systems, such as proteins and receptor-ligand complexes. In addition, its important role in biological processes such as molecular recognition, drug action, and protein folding has been revealed by extensive experimental and theoretical investigations. Most previous theoretical investigations of cation···p interactions, have been focused on their characteristics in the gas phase, with less attention to their behavior in aqueous environment. In this latter case, most of the work has been focused on the whole effect of water solution as a medium on the cation···p interactions. Hence, it is important studying the influence of individual water molecules on the interaction as the cation···p complex is sequentially hydrated. The ammonium···phenol and methylammonium···phenol cation···p complex was selected as a model system to explore how water molecules affect the cation···p interaction. To mimic the process of water molecules binding to a cation···p complex, water molecules were introduced into the complex one by one. The purpose of this study is studying the geometrical characteristic of cation···p complexes with different numbers of water molecules and to investigate how the binding of water molecules to an existing cation···p complex affects the cation···p interactio

A computational study of the role of water molecules on cation···p interactions

The 15th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryAmong the different forces observed in biological complexes, the cation···p interaction is a strong, non-covalent binding force which participates in a wide variety of processes such as molecular recognition in biological receptors, enzymatic catalysis, etc. The nature and characteristics of this kind of interaction has been mainly theoretically studied in the gas phase, despite being known that the presence of water molecules modulates the strength of the interaction between metal ions and aromatic species. Besides, most studies have employed benzene as a prototype of aromatic unit. On the other hand, an also simple aromatic system as phenol presents two coordination sites for cations: the aromatic ring and the hydroxyl oxygen, thus allowing a greater variety of structures to be formed than in benzene. The hydroxyl group can also be hydrated and participate in the formation of the hydrogen bond network. In the present work, a study of the interaction between cations and phenol has been carried out to shed light on the effect of successive hydration on the interaction. So, ab initio and DFT methods were employed for studying the stepwise microhydration of phenol···cation complexes, locating the most stable structures and obtaining the corresponding complexation energies. The results suggest that the participation of the hydroxyl group is already relevant in clusters containing a small number of water molecule

A computational study of phenylalanine interaction with guanidinium cation

Despite being intense in the gas phase, the strength of the interaction between a cation and an aromatic cloud decreases significantly when solvated. This effect has an important impact on a variety of systems where the cation•••pi interaction is known to play a key role. In the case of cation•••pi contacts involving aromatic amino acid residues, the degree of exposure to the solvent can be widely variable, so the interaction can be modulated by the environment in an almost continuous way. Most theoretical studies regarding cation•••amino acid interactions have been performed by considering simple alkaline cations in the gas phase. However, interactions can also be established with more complex cations from other amino acids, such as it is the case with arginine cationic side chain and the aromatic units in phenylalanine, tyrosine and tryptophan. In the present work ab initio and DFT methods were employed to study complexes formed by phenylalanine and a guanidinium cation representing the cationic chain of arginine. The results help understanding the impact of the interaction on the structure of phenylalanine, and constitute a first step towards the study of the effects caused by water molecules in the characteristics of these system

Computational Study of the interaction between Sumanene and Cations as a function of the cation–π separation

With the aim of enhancing the comprehension of the cation-π interaction, a computational study of the interaction established between sumanene molecule and various cations was performed. Sumanene is a polycyclic aromatic hydrocarbon with a bowl-shaped structure. The curvature of the molecule causes an asymmetry in the distribution of its molecular electrostatic potential that is more negative in its outer (convex) side. This feature allows testing the role of the electrostatic contribution to cation-π interaction using the same molecule. Five cations with different sizes and shapes were selected for the study: sodium, potassium, ammonium, tetramethylammonium, guanidinium and imidazolium. These are monoatomic cations and models of cationic amino acids side-chains, all of which are known to participate in the formation of cation-π complexes in biological systems. The polyatomic cations were placed in different orientations with respect to the sumanene molecule including the “T-shaped” and “stacked” configurations of the flat cations. The study was accomplished at the RI‑MP2/aug-cc-pVTZ level of calculation, to ensure the correct retrieving of the correlation energy and also that the wavefunction size is appropriate for the modeling of effects more complicated than the electrostatic contribution. The interaction energy (Eint) was computed at different sumanene-cation distances following the C3v symmetry axe of sumanene and exploring it’s both sides: concave and convex. The rigid scans of the potential energy surface indicate that at sumanene-cation distances around the Eint minima, the complexes are more stable with the cation placed by the inner (concave) side of sumanene, with the only exception of the complexes with Na+, the smallest of the cations studied. This result is the opposite of that expected from the pure electrostatic interpretation of the cation-π interaction. As the cation moves away from the sumanene molecule the situation is reversed, and at long distances the outer complexes are more stable than its inner partners. These findings suggest that at long cation-molecule separations the electrostatic contribution dominates because its influence propagates to long distances but at short distances the cation-π interaction is controlled by other stabilizing contributions (induction and dispersion) defining the minimum of the Eint profile. The results obtained contribute to a better understanding the cation-π interaction and emphasize the importance of using the correct level of calculations in its theoretical modelin

Theoretical Study of the Solvent Effect on the properties of Indole‑Cation‑Anion Complexes

The 18th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryThe properties of ternary indole-cation-anion (IMX) complexes are theoretically studied as simplified models of real systems in which some of the fragments used are parts of bigger and complicated structures, like proteins. The electro-neutrality of real systems and the presence of ions of both charges interacting simultaneously with aromatic residues in the proteins modeled justify the move from cation-π or anion-π (non-bonding interactions analyzed by our group in previous studies) to cation-π-anion complexes. With the intention of approaching more the model to reality, the solvent was also included in the study: aqueous solvent was represented by a combination of PCM + explicit addition of one water molecule to some IMX complexes. As model systems for this study the complexes with indole and the following cations and anions were selected: M = Na+, NH4+; X = HCOO–, NO3– or Cl–. The effect of the solvent was studied not only on the energy but as well on some structural parameters like the proton transfer from the ammonium cation to the basic anion and the cation-anion separation. The results indicate that the PCM method alone properly reproduces the main energetic and geometrical changes, even at quantitative level, but the explicit hydration allows refining the solvent effect and detecting cases that do not follow the general tren

Cation–π complexes between alkaline cations and molecular bowls related with fullerene: a DFT study

The 14th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryThe formation of complexes between alkaline cations and molecular bowls (MBs), curved conjugated systems related with fullerene (C 60 ), is studied using DFT calculations. The series of MBs is constructed starting with benzene and additional hexagonal or pentagonal rings are added symmetrically to complete the C 60 structure. All the MBs studied form stable cation–π complexes by both of its sides: concave and convex. In all cases complexes with the cation in the convex side are more stable than their corresponding partner inside the bowl. The stability of the complexes is determined by the polarizing power of the cation and by the molecular electrostatic potential and the polarizability of the bowl. Additionally, size effects are observed when bulky cations are placed in the concave side of the largest bowl

Influence of the substitution on the inversion barrier of corannulene: a theoretical study.

The 15th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryThe lower molecular weight hydrocarbons that can be mapped on the buckminsterfullerene (C60) structure are commonly known as "buckybowls" or "geodesic polyarenes" and have the distinctive characteristics of preserving the curvature and aromaticity of fullerene. These bowl-shaped structures are expected to be quite rigid. Nevertheless, the smaller members of the family, in spite of its substantial curvature are surprisingly flexible undergoing rapid bowl-to-bowl inversion in solution as evidenced by the dynamic NMR behavior of C20H10 (corannulene) and several of its derivatives. With the aim of gaining understanding in the bowl-to-bowl inversion, the present theoretical study has explored the effect that substitution of some of the hydrogen atoms of corannulene has on this process. The model systems studied have the formula C20H10-nRn with R = -Cl, -Br, -C≡CH, -CH3 and n = 0, 2, 4, 5, 6, 8, and 10. It is observed that the bowl depth is reduced only by high substitution levels or by a substitution pattern that conduces to important peri interactions. Full substitution with bulky groups causes a pronounced repulsion and the deformation of the transition structure for bowl inversion that otherwise is planar. The activation barrier for the inversion – bowl depth data fit an empirical quartic/quadratic function used previously in similar systems but the coefficients of the fitting don\'t follow the predicted substituent independenc

Identificación polínica de Ericaceae en mieles gallegas

Se ha identificado el polen de Ericaceae contenido en 14 mieles procedentes de distintas poblaciones de las provincias de Orense y Lugo. En cinco de ellas, el taxon dominante es Ericaceae (principalmente los tipos polínicos Erica cinerea y Erina australis), en las demás domina Castanea sativa Miller, excepto en dos ellas que son milflorales.The Ericaceae pollen of 14 honeys from different localities in the provinces of Orense and Lugo (Spain), have been analysed. In five of them, the dominant taxon is Ericaceae (mainly Erica cinerea and Erica australis pollen types) while Castanea sativa Miller predominates in all the others except two multifloral samples

Ab Initio and Dft Study of Interaction Between Corannulene and Alkali Cations

The 15th International Electronic Conference on Synthetic Organic Chemistry session Computational ChemistryCorannulene is an unsaturated hydrocarbon composed of fused rings, one central five-membered ring and five peripheral six-membered rings. Its structure can be considered as a portion of C60. Corannulene is a curved pi surface, but unlike C60, it has two completely different faces: one concave (inside) and one convex (outside). In this work, computational modeling of the binding between alkali metals cations and corannulene has been performed at the DFT and MP2 levels. Different isomers of the corannulene/M+ binding have been studied and the transition states interconnecting local minima were located. The alkali cations can be bound to five or six membered ring in both faces. In DFT calculations, the binding to the convex face (outside) is favored relative to the concave face for the three alkali cations as it already has been published [R.C. Dunbar, J. Phys. Chem. A 2002, 106, 9809]. For Li+ and Na+, MP2 calculations are very similar and show the same trend, but for K+ the calculations are quite different and the trend is reversed. According to our results, migration of cations can take place over the convex or the concave pi-face. There are two ways to transform a concave complex in a convex complex: migration across the edge of corannulene and bowl-to-bowl inversio