Predicting face-to-face arene–arene binding energies

Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu

Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.

Interplay of π-stacking and inter-stacking interactions in two-component crystals of neutral closed-shell aromatic compounds: periodic DFT study

This paper bridges the gap between high-level ab initio computations of gas-phase models of 1 : 1 arene–arene complexes and calculations of the two-component (binary) organic crystals using atom–atom potentials. The studied crystals consist of electron-rich and electron-deficient compounds, which form infinite stacks (columns) of heterodimers. The sublimation enthalpy of crystals has been evaluated by DFT periodic calculations, while intermolecular interactions have been characterized by Bader analysis of the periodic electronic density. The consideration of aromatic compounds without a dipole moment makes it possible to reveal the contribution of quadrupole–quadrupole interactions to the π-stacking energy. These interactions are significant for heterodimers formed by arenes with more than 2 rings, with absolute values of the traceless quadrupole moment (Q_zz) larger than 10 D Å. The further aggregation of neighboring stacks is due to the C–H⋯F interactions in arene/perfluoroarene crystals. In crystals consisting of arene and an electron-deficient compound such as pyromellitic dianhydride, aggregation occurs due to the C–H⋯O interactions. The C–H⋯F and C–H⋯O inter-stacking interactions make the main contribution to the sublimation enthalpy, which exceeds 150 kJ mol⁻¹ for the two-component crystals formed by arenes with more than 2 rings.

The interplay of π-stacking and inter-stacking interactions in two-component organic crystals without conventional hydrogen bonds.

Understanding substituent effects in noncovalent interactions involving aromatic rings

Noncovalent interactions involving aromatic rings such as π-stacking, cation/π, and anion/π interactions are central to many areas of modern chemistry. Decades of experimental studies have provided key insights into the impact of substituents on these interactions, leading to the development of simple intuitive models. However, gas-phase computational studies have raised some doubts about the physical underpinnings of these widespread models. In this Account we review our recent efforts to unravel the origin of substituent effects in π-stacking and ion/π interactions through computational studies of model noncovalent dimers. First, however, we dispel the notion that so-called aromatic interactions depend on the aromaticity of the interacting rings by studying model π-stacked dimers in which the aromaticity of one of the monomers can be "switched off". Somewhat surprisingly, the results show that not only is aromaticity unnecessary for π-stacking interactions, but it actually hinders these interactions to some extent. Consequently, when thinking about π-stacking interactions, researchers should consider broader classes of planar molecules, not just aromatic systems. Conventional models maintain that substituent effects in π-stacking interactions result from changes in the aryl π-system. This view suggests that π-stacking interactions are maximized when one ring is substituted with electron-withdrawing groups and the other with electron donors. In contrast to these prevailing models, we have shown that substituent effects in π-stacking interactions can be described in terms of direct, local interactions between the substituents and the nearby vertex of the other arene. As a result, in polysubstituted π-stacked dimers the substituents operate independently unless they are in each other's local environment. This means that in π-stacked dimers in which one arene is substituted with electron donors and the other with electron acceptors the interactions will be enhanced only to the extent provided by each substituent on its own, unless the substituents on opposing rings are in close proximity. Overall, this local, direct interaction model predicts that substituent effects in π-stacking interactions will be additive and transferable and will also depend on the relative position of substituents on opposing rings. For cation/π and anion/π interactions, similar π-resonance-based models pervade the literature. Again, computational results indicate that substituent effects in model ion/π complexes can be described primarily in terms of direct interactions between the ion and the substituent. Changes in the aryl π-system do not significantly affect these interactions. We also present a simple electrostatic model that further demonstrates this effect and suggests that the dominant interaction for simple substituents is the interaction of the charged ion with the local dipole associated with the substituents. Finally, we discuss substituent effects in electrostatic potentials (ESPs), which are widely used in discussions of noncovalent interactions. In the past, widespread misconceptions have confused the relationship between changes in ESPs and local changes in the electron density. We have shown that computed ESP plots of diverse substituted arenes can be reproduced without altering the aryl π-density. This is because substituent-induced changes in the ESP above the center of aryl rings result primarily from through-space effects of substituents rather than through changes in the distribution of the π-electron density.

The use of hammett constants to understand the non-covalent binding of aromatics

Non-covalent interactions of aromatics are important in a wide range of chemical and biological applications. The past two decades have seen numerous reports of arene-arene binding being understood in terms Hammett substituent constants, and similar analyses have recently been extended to cation-arene and anion-arene binding. It is not immediately clear why electrostatic Hammett parameters should work so well in predicting the binding for all three interactions, given that different intermolecular forces dominate each interaction. This review explores such anomalies, and summarizes how Hammett substituent constants have been employed to understand the non-covalent binding in arene-arene, cation-arene and anion-arene interactions.

Reassessment of Hammett σ as an effective parameter representing intermolecular interaction energy-links between traditional and modern QSAR approaches

The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.

Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry

Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Origin of Substituent Effects in Edge-to-Face Aryl-Aryl Interactions

Substituent effects in the edge-to-face configuration of the benzene dimer have been studied using modern density functional theory. An accurate interaction potential energy curve has been computed for the unsubstituted dimer using ab initio methods with large basis sets. The recommended binding energy for the edge-to-face benzene dimer is 2.31 kcal mol(-1), estimated at the counterpoise-corrected CCSD(T)/aug-cc-pVTZ level of theory. For both edge-ring and face-ring-substituted dimers, interaction energies correlate with sigma(m) for the substituents, indicating that substituent effects can be understood qualitatively in terms of simple electrostatic effects, although in the latter case dispersion results in some scatter in the data. In contrast to prevailing models of substituent effects in benzene dimers, polarization of the pi-system of the substituted ring does not induce substituent effects. For edge-ring-substituted dimers, substituent effects arise from differential electrostatic interactions between the hydrogens on the substituted ring and the pi-cloud of the face ring and direct interactions of the substituents with the unsubstituted ring. For face-ring-substituted dimers, substituent effects arise from direct electrostatic and dispersion interactions of the substituents with the edge ring. Substituents with sigma(m) > 0.12 favor edge ring substitution while for sigma(m) < 0.12 substitution on the face ring is preferred.

Probing substituent effects in aryl-aryl interactions using stereoselective Diels-Alder cycloadditions

Stereoselective Diels-Alder cycloadditions that probe substituent effects in aryl-aryl sandwich complexes were studied experimentally and theoretically. Computations on model systems demonstrate that the stereoselectivity in these reactions is mediated by differential pi-stacking interactions in competing transition states. This allows relative stacking free energies of substituted and unsubstituted sandwich complexes to be derived from measured product distributions. In contrast to gas-phase computations, dispersion effects do not appear to play a significant role in the substituent effects, in accord with previous experiments. The experimental pi-stacking free energies are shown to correlate well with Hammett sigma(m) constants (r = 0.96). These substituent constants primarily provide a measure of the inductive electron-donating and -withdrawing character of the substituents, not donation into or out of the benzene pi-system. The present experimental results are most readily explained using a recently proposed model of substituent effects in the benzene sandwich dimer in which the pi-system of the substituted benzene is relatively unimportant and substituent effects arise from direct through-space interactions. Specifically, these results are the first experiments to clearly show that OMe enhances these pi-stacking interactions, despite being a pi-electron donor. This is in conflict with popular models in which substituent effects in aryl-aryl interactions are modulated by polarization of the aryl pi-system.

Substituent effects in sandwich configurations of multiply substituted benzene dimers are not solely governed by electrostatic control

Noncovalent interactions between pi systems are central to understanding protein folding and the stability of DNA. Considerable controversy exists about whether substituent effects in pi-pi interactions can be understood purely on the basis of electrostatic interactions or whether other effects must be included to understand observed trends. In this work, we show that in general, pi-pi interactions are not governed solely by electrostatic control. We do not observe a linear correlation between the relative interaction energies and the sums of Hammett parameters in the case of multiply substituted face-to-face benzene dimers. Instead, differential dispersion effects can be so large that even molecules with wildly different electrostatic potentials can exhibit similar attractions to benzene.

Novel chiral molecular tweezer from (+)-usnic acid

A new chiral molecular tweezer was synthesized with (1R,2R)-1,2-diaminocyclohexane as spacer and two molecules of (+)-usnic acid as pincers. The ability of this molecular tweezer to bind 2,4,7-trinitrofluorenone was studied. A charge-transfer complex was formed in which TNF was sandwiched between the two usnic acid units with pi-pi-stacked aromatic interactions.