Substituent effects in cation/pi interactions and electrostatic potentials above the centers of substituted benzenes are due primarily to through-space effects of the substituents

Are anion/pi interactions actually a case of simple charge-dipole interactions?

Substituent effects in Cl(-)...C(6)H(6-n)X(n) complexes, models for anion/pi interactions, have been examined using density functional theory and robust ab initio methods paired with large basis sets. Predicted interaction energies for 83 model Cl(-)...C(6)H(6-n)X(n) complexes span almost 40 kcal mol(-1) and show an excellent correlation (r = 0.99) with computed electrostatic potentials. In contrast to prevailing models of anion/pi interactions, which rely on substituent-induced changes in the aryl pi-system, it is shown that substituent effects in these systems are due mostly to direct interactions between the anion and the substituents. Specifically, interaction energies for Cl(-)...C(6)H(6-n)X(n) complexes are recovered using a model system in which the substituents are isolated from the aromatic ring and pi-resonance effects are impossible. Additionally, accurate potential energy curves for Cl(-) interacting with prototypical anion-binding arenes can be qualitatively reproduced by adding a classical charge-dipole interaction to the Cl(-)...C(6)H(6) interaction potential. In substituted benzenes, binding of anions arises primarily from interactions of the anion with the local dipoles induced by the substituents, not changes in the interaction with the aromatic ring itself. When designing anion-binding motifs, phenyl rings should be viewed as a scaffold upon which appropriate substituents can be placed, because there are no attractive interactions between anions and the aryl pi-system of substituted benzenes.

Appraisal of through-bond and through-space substituent effects via molecular electrostatic potential topography

Through-bond (TB) and through-space (TS) substituent effects in substituted alkyl, alkenyl, and alkynyl arenes are quantified separately using molecular electrostatic potential (MESP) topographical analysis. The deepest MESP point over the aromatic ring (V(min)) is considered as a probe for monitoring these effects for a variety of substituents. In the case of substituted alkyl chains, the TS effect (79.6%) clearly dominates the TB effect, whereas in the unsaturated analogues the TB effect (∼55%) overrides the TS effect.

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.

Relative substituent position on the strength of pi-pi stacking interactions

It was observed that the relative position of the arene substituents have a profound influence on the strength of pi-pi stacking in the 9-benzyl substituted triptycene system. A new series of model compounds (3a-i) capable of revealing quantitatively pi-pi stacking interactions was studied. This series of compounds (3a-i) has an ortho substituted methyl group in one of the two interacting arenes and the syn/anti ratios were determined and compared to a series previously studied compounds (4a-i) that have a para methyl group on the corresponding arene. A greater than 50% increase in the strength of pi-pi stacking interactions was observed with the methyl group in the ortho position comparing to that in the para position. No difference in pi-pi stacking interactions was observed when the other aromatic ring was a pentafluorobenzoate group.

Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes

Model systems have been studied using density functional theory to assess the contributions of π-resonance and through-space effects on electrostatic potentials of substituted arenes. The results contradict the widespread assumption that changes in molecular ESPs reflect only local changes in the electron density. Substituent effects on the ESP above the molecular plane are commonly attributed to changes in the aryl π-system. We show that ESP changes for a collection of substituted benzenes and more complex aromatic systems can be accounted for mostly by through-space effects, with no change in the aryl π-electron density. Only when π-resonance effects are substantial do they influence changes in the ESP above the aromatic ring to any extent. Examples of substituted arenes studied here are taken from the fields of drug design, host-guest chemistry, and crystal engineering. These findings emphasize the potential pitfalls of assuming ESP changes reflect changes in the local electron density. Since ESP changes are frequently used to rationalize and predict intermolecular interactions, these findings have profound implications for our understanding of substituent effects in countless areas of chemistry and molecular biology. Specifically, in many non-covalent interactions there are significant, often neglected, through-space interactions with the substituents. Finally, the present results explain the perhaps unexpectedly good performance of many molecular mechanics force-fields applied to supramolecular assembly phenomena and π-π interactions in biological systems despite the neglect of the polarization of the aryl π-system by substituents.