Additivity of Cation−π Interactions: An ab Initio Computational Study on π−Cation−π Sandwich Complexes

Metal Ion-Directed Functional Metal-Phenolic Materials

Metal ions are ubiquitous in nature and play significant roles in assembling functional materials in fields spanning chemistry, biology, and materials science. Metal-phenolic materials are assembled from phenolic components in the presence of metal ions through the formation of metal-organic complexes. Alkali, alkali-earth, transition, and noble metal ions as well as metalloids interacting with phenolic building blocks have been widely exploited to generate diverse hybrid materials. Despite extensive studies on the synthesis of metal-phenolic materials, a comprehensive summary of how metal ions guide the assembly of phenolic compounds is lacking. A fundamental understanding of the roles of metal ions in metal-phenolic materials engineering will facilitate the assembly of materials with specific and functional properties. In this review, we focus on the diversity and function of metal ions in metal-phenolic material engineering and emerging applications. Specifically, we discuss the range of underlying interactions, including (i) cation-π, (ii) coordination, (iii) redox, and (iv) dynamic covalent interactions, and highlight the wide range of material properties resulting from these interactions. Applications (e.g., biological, catalytic, and environmental) and perspectives of metal-phenolic materials are also highlighted.

σ-Hole Bond vs π-Hole Bond: A Comparison Based on Halogen Bond

The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.

Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine

Aromatic groups are now acknowledged to play an important role in many systems of interest. However, existing molecular mechanics methods provide a poor representation of these groups. In a previous paper, we have shown that the molecular mechanics treatment of benzene can be improved by the incorporation of an explicit representation of the aromatic π electrons. Here, we develop this concept further, developing charge-separation models for toluene, phenol, and pyridine. Monte Carlo simulations are used to parametrize the models, via the reproduction of experimental thermodynamic data, and our models are shown to outperform an existing atom-centered model. The models are then used to make predictions about the structures of the liquids at the molecular level and are tested further through their application to the modeling of gas-phase dimers and cation-π interactions.

A theoretical study of ternary indole-cation-anion complexes

The simultaneous interactions of an anion and a cation with a π system were investigated by MP2 and M06-2X theoretical calculations. Indole was chosen as a model π system for its relevance in biological environments. Two different orientations of the anion, interacting with the N-H and with the C-H groups of indole, were considered. The four cations (Na(+), NH4(+), C(NH2)3(+) and N(CH3)4(+)) and the four anions (Cl(-), NO3(-), HCOO(-) and BF4(-)) included in the study are of biological interest. The total interaction energy of the ternary complexes was calculated and separated into its two- and three-body components and all of them are further divided into their electrostatic, exchange, repulsion, polarization and dispersion contributions using the local molecular orbital-energy decomposition analysis (LMO-EDA) methodology. The binding energy of the indole-cation-anion complexes depends on both ions, with the cation having the strongest effect. The intense cation-anion attraction determines the geometric and energetic features in all ternary complexes. These structures, with both ions on the same side of the π system, show an anti-cooperative interaction. However, the interaction is not only determined by electrostatics, but also the polarization contribution is important. Specific interactions like the one established between the anion and the N-H group of indole or the proton transfer between an acidic cation and a basic anion play a significant role in the energetics and the structure of particular complexes. The presence of the polar solvent as modelled with the polarizable continuum model (PCM) does not seem to have a significant effect on the geometry of the ternary complexes, but drastically weakens the interaction energy. Also, the strength of the interaction is reduced at a faster rate when the anion is pushed away, compared to the results obtained in the gas phase. The combination of PCM with the addition of one water molecule indicates that the PCM method properly reproduces the main energetic and geometrical changes, even at the quantitative level, but the explicit hydration allows refining the solvent effect and detecting cases that do not follow the general trend.

Acute toxicity of 8 antidepressants: what are their modes of action?

Currently, the hazard posed by pharmaceutical residues is a major concern of ecotoxicology. Most of the antidepressants belong to a family named the Cationic Amphipathic Drugs known to have specific interactions with cell membranes. The present study assessed the impact of eight antidepressants belonging to selective serotonin reuptake inhibitors or serotonin norepinephrine reuptake inhibitors by the combination of multi-approaches (in vivo, in vitro, in silico) and gives some insights on the mode of action for these molecules. Antidepressants were from the most to the least toxic compound for Daphnia magna: Sertraline (EC50=1.15 mg L(-1))>Clomipramine (2.74 mg L(-1))>Amitriptyline (4.82 mg L(-1))>Fluoxetine (5.91 mg L(-1))>Paroxetine (6.24 mg L(-1))>Mianserine (7.81 mg L(-1))>Citalopram (30.14 mg L(-1)) and Venlafaxine (141.28 mg L(-1)). These acute toxicities were found correlated to Log Kow coefficients (R=0.93, p<0.001) and to cytotoxicity assessed on abalone hemocytes through the neutral red uptake assay (R=0.96, p<0.001). If narcosis as mode of action is typically expected during acute ecotoxicity bioassays, we showed by molecular modeling that particular interactions can exist between antidepressants and phosphatidylcholine, a major component of cell membranes, leading to a more specific mode of action corresponding to a potential acidic hydrolysis of ester functions.

Effects of the aromatic substitution pattern in cation-π sandwich complexes

A computational study investigating the effects of the aromatic substitution pattern on the structure and binding energies of cation-π sandwich complexes is reported. The correlation between the binding energies (Ebind) and Hammett substituent constants is approximately the same as what is observed for cation-π half-sandwich complexes. For cation-π sandwich complexes where both aromatics contain substituents the issue of relative conformation is a possible factor in the strength of the binding; however, the work presented here shows the Ebind values are approximately the same regardless of the relative conformation of the two substituted aromatics. Finally, recent computational work has shown conflicting results on whether cation-π sandwich Ebind values (Ebind,S) are approximately equal to twice the respective half-sandwich Ebind values (Ebind,HS), or if cation-π sandwich Ebind,S values are less than double the respective half-sandwich Ebind,HS values. The work presented here shows that for cation-π sandwich complexes involving substituted aromatics the Ebind,S values are less than twice the respective half-sandwich Ebind,HS values, and this is termed nonadditive. The extent to which the cation-π sandwich complexes investigated here are nonadditive is greater for B3LYP calculated values than for MP2 calculated values and for sandwich complexes with electron-donating substituents than those with electron-withdrawing groups.

Quantitative assessment of substituent effects on cation-π interactions using molecular electrostatic potential topography

A molecular electrostatic potential (MESP) topography based approach has been proposed to quantify the substituent effects on cation-π interactions in complexes of mono-, di-, tri-, and hexasubstituted benzenes with Li(+), Na(+), K(+), and NH(4)(+). The MESP minimum (V(min)) on the π-region of C(6)H(5)X showed strong linear dependency to the cation-π interaction energy, E(M(+)). Further, cation-π distance correlated well with V(min)-π distance. The difference between V(min) of C(6)H(5)X and C(6)H(6) (ΔV(min)) is proposed as a good parameter to quantify the substituent effect on cation-π interaction. Compared to benzene, electron-donating groups stabilize the di-, tri-, and hexasubstituted cation-π complexes while electron-withdrawing groups destabilize them. In multiple substituted complexes, E(M(+)) is almost equal (∼95%) to the sum of the individual substituent contributions (E(M(+)) ≈ Σ(ΔE(M(+)))), suggesting that substituent effect on cation-π interactions is largely additive. The ΔV(min) of C(6)H(5)X systems and additivity feature have been used to make predictions on the interaction energies of 80 multiple substituted cation-π complexes with above 97% accuracy. The average mean absolute deviation of the V(min)-predicted interaction energy, E(M(+))(V) from the calculated E(M(+)) is -0.18 kcal/mol for Li(+), -0.09 kcal/mol for Na(+), -0.43 kcal/mol for K(+), and -0.67 kcal/mol for NH(4)(+), which emphasize the predictive power of V(min) as well as the additive feature of the substituent effect.

The Accuracy of Density Functional Theory in the Description of Cation-π and π-Hydrogen Bond Interactions

Cation-π and π-hydrogen bond interactions are ubiquitous in protein folding, molecular recognition, and ligand-receptor associations. As such systems are routinely studied at the DFT level, it becomes essential to understand the underlying accuracy of the plethora of density functionals currently available for the description of these interactions. For that purpose, we carried out theoretical calculations on two small model systems (benzene-Na(+) and benzene-H2O) that represent a paradigm for those intermolecular interactions and systematically tested 46 density functionals against the results of high-level post-HF methods, ranging from MP2 to extrapolated CCSD(T)/CBS. A total of 13 basis sets were also tested to examine the convergence of the interaction energy with basis set size. The convergence was surprisingly fast, with deviations below 0.2 kcal/mol for double-ζ polarized basis sets with diffuse functions. Concerning functional benchmarking, the Truhlar group functionals were particularly well suited for the description of the π-hydrogen bond interactions. In the case of cation-π interactions, there was not a clear correlation between accuracy and functional sophistication. Despite the large number of functionals predicting interaction energies within chemical accuracy (five for π-hydrogen bond and 20 for cation-π interactions), not a single functional has shown chemical accuracy in both cases. Moreover, if we calculate the average error for these two interactions, only two density functionals resulted in an average error below 1.0 kcal/mol (M06 and HCTH, with average errors of 0.6 and 0.8 kcal/mol). The obtained results serve as a guide for future computer simulations on this kind of system.

Study of the interaction between water and hydrogen sulfide with polycyclic aromatic hydrocarbons

A computational study has been carried out for determining the characteristics of the interaction between one water and hydrogen sulfide molecule with a series of polycyclic aromatic hydrocarbons of increasing size, namely, benzene, anthracene, triphenylene, coronene, circumcoronene, and dicircumcoronene. Potential energy curves were calculated for structures where H(2)X (X=O,S) molecule is located over the central six-membered ring with its hydrogen atoms pointing toward to (mode A) or away from (mode B) the hydrocarbon. The accuracy of different methods has been tested against the results of coupled cluster calculations extrapolated to basis set limit for the smaller hydrocarbons. The spin component scaled MP2 (SCS-MP2) method and a density functional theory method empirically corrected for dispersion (DFT-D) reproduce fairly well the results of high level calculations and therefore were employed for studying the larger systems, though DFT-D seems to underestimate the interaction in hydrogen sulfide clusters. Water complexes in mode A have interaction energies that hardly change with the size of the hydrocarbon due to compensation between the increase in the correlation contribution to the interaction energy and the increase in the repulsive character of the Hartree-Fock energy. For all the other clusters studied, there is a continuous increase in the intensity of the interaction as the size of the hydrocarbon increases, suggesting already converged values for circumcoronene. The interaction energy for water clusters extrapolated to an infinite number of carbon atoms amounts to -13.0 and -15.8 kJ/mol with SCS-MP2 and DFT-D, respectively. Hydrogen sulfide interacts more strongly than water with the hydrocarbons studied, leading to a limiting value of -21.7 kJ/mol with the SCS-MP2 method. Also, complexes in mode B are less stable than the corresponding A structures, with interaction energies amounting to -8.2 and -18.2 kJ/mol for water and hydrogen sulfide, respectively. The DFT-D calculations give values of -16.2 and -9.3 kJ/mol for hydrogen sulfide complexes in modes A and B, less negative than those predicted by the SCS-MP2 method, probably indicating problems with sulfur dispersion parameters.

Chiral recognition mass spectrometry: remarkable effects observed from the relative ion abundances of ternary diastereomeric complexes using electrospray ionization

The relative abundances of ternary diastereomeric complexes (composed each from a cinchonane-type chiral selector, a model chiral acid, and an alkali cation) are shown to change remarkably and fortuitously with variation in concentration and type of alkali metal using electrospray ionization-mass spectrometry and competitive binding analysis.

Actions between neonicotinoids and key residues of insect nAChR based on an ab initio quantum chemistry study: Hydrogen bonding and cooperative π–π interaction

Neonicotinoid insecticides show selective actions on insect nicotinic acetylcholine receptor (nAChR). Two key residues (Trp and Arg/Lys) have been identified as contributing to the neonicotinois binding. To investigate the selective mechanism, a computational model was set up to simulate the interaction between residues (Trp and Arg) of insect nAChR and neonicotinoids by quantum chemistry method. Three analogues of neonicotinoid derivatives without the chloropyridinyl moiety and 3-methyl-indole (3MI), guanidinium (Gua) were used to mimic the neonicotinoids and the side chain of key residues Trp and Arg accordingly. Interaction features of 3MI-analogues, analogues-Gua and 3MI-analogues -Gua complexes were analyzed comparatively. Hydrogen bonding between the nitro group of analogues and Gua was found to be the most important for binding. Moreover, the cooperative pi-pi interaction between analogues and the indole ring, which is strengthened by the existence of Gua, also contributes to the binding. The alternative binding model of neonicotinoids proposed here, although slightly different from others, might be close to the actual.

A Computational Study on the Interaction of the Nitric Oxide Ions NO+ and NO- with the Side Groups of the Aromatic Amino Acids

The interaction of the nitric oxide ions NO+ and NO- with benzene (C6H6) and the aromatic R-groups of the amino acids phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp) have been examined using the DFT method B3LYP and the conventional electron correlation method MP2. In particular, the structures and complexation energies of the resulting half-sandwich Ar...NO+/- and sandwich [Ar...NO...Ar]+/- complexes have been considered. For the Ar...NO+ complexes, the presence of an electron rich heteroatom within or attached to the ring is found to not preclude the cation...pi bound complex from being the most stable. Furthermore, unlike the anionic complexes, the pi...cation...pi ([Ar...NO...Ar]+) complexes do not correspond to a "doubling" of the parent half-sandwich.

How Does Ammonium Dynamically Interact with Benzene in Aqueous Media? A First Principle Study Using the Car−Parrinello Molecular Dynamics Method

The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between ammonium and benzene is stable even in aqueous solution. Thus, this CPMD study suggested that the cation-pi interaction between an ammonium (group) and an aromatic structure could take place even on surfaces of protein or nucleic acids in solution.

Approximate Additivity of Anion−π Interactions: An Ab Initio Study on Anion−π, Anion−π2 and Anion−π3 Complexes

We have studied the additivity of the anion-pi interaction using high level ab initio calculations. We have optimized chloride and bromide complexes with one, two and three aromatic units (such as trifluoro-s-triazine and s-triazine). We have analyzed the interaction using the atoms in molecules theory and studied the charge transfer using several methods for deriving atomic charges. The results revealed additivities of both the geometries and the binding energies. We have also proposed a neutral receptor for chloride based on multiple anion-pi interactions. Finally, we have simulated solvent effects within the self-consistent reaction field model.