Is polarization important in cation-pi interactions?

Anion-π Interactions in Cyanuric Acids: A Combined Crystallographic and Computational Study

Several structures of pi complexes of isocyanuric acid and of several thio derivatives with anions have been computed by using high level ab initio calculations. The nature of the complexes has been studied by means of the method of molecular interaction potential with polarization (MIPp) and Bader's theory of atoms-in-molecules. These molecules form favorable complexes with anions and can be used as binding units for building receptors for the molecular recognition of anions. In several cases, the anion-pi interaction has been demonstrated experimentally by means of X-ray crystallography.

Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

The intrinsic stability of Watson-Crick d(AT) and r(AU) hydrogen bonds was analyzed by employing a variety of quantum-mechanical techniques, such as energy calculations, determination of reactivity indexes, and analysis of electron density topology. The analyses were performed not only for equilibrium gas-phase geometries, but also on hundreds of conformations derived from molecular dynamics (MD) and database analysis. None of our results support the idea that r(AU) hydrogen bonds are intrinsically more stable than those of d(AT). Instead, our data are in accordance with the traditional view that the greater stability of RNA relative to DNA is attributable to a variety of effects (e.g., stacking, sugar puckering, solvation) rather than to a significant difference in the hydrogen bonding of DNA and RNA base pairs.

Structure and Binding Energy of Anion−π and Cation−π Complexes: A Comparison of MP2, RI-MP2, DFT, and DF-DFT Methods

Several complexes of benzene with cations, hexafluorobenzene with anions, 1,3,5-trifluorobenzene with cations and anions, and s-triazine with cations and anions have been evaluated and compared at the MP2 and resolution of the identity MP2 (RI-MP2) levels. The RI-MP2 method is considerably faster than the MP2 and the interaction energies and equilibrium distances are almost identical for both methods. A similar result is found when comparing DFT and density fitting DFT (DF-DFT) levels. Therefore RI-MP2 and DF-DFT methods are well suited for the study of ion-pi interactions.

A Molecular Dynamics Investigation of Rare-Gas Solvated Cation−Benzene Clusters Using a New Model Potential

The main static and dynamic properties of some ionic heteroclusters, involving K+, C6H6, and Ar, have been investigated. A new representation of the intermolecular potential energy, which takes into account both electrostatic and non-electrostatic contributions to the overall noncovalent interaction, was used. Dynamical calculations were performed for a microcanonical ensemble. Particular attention was paid to the opening of the isomerization and dissociation processes for K+-C6H6-Ar(n) and to the formation of some of its fragments at increasing temperatures of the cluster considered.

Development of Molecular Probes for the Identification of Extra Interaction Sites in the Mid-Gorge and Peripheral Sites of Butyrylcholinesterase (BuChE). Rational Design of Novel, Selective, and Highly Potent BuChE Inhibitors†

Tacrine heterobivalent ligands were designed as novel and reversible inhibitors of cholinesterases. On the basis of the investigation of the active site gorge topology of butyrylcholinesterase (BuChE) and acetylcholinesterase (AChE) and by using flexible docking procedures, molecular modeling studies formulated the hypothesis of extra interaction sites in the active gorge of hBuChE, namely, a mid-gorge interaction site and a peripheral interaction site. The design strategy led to novel BuChE inhibitors, balancing potency and selectivity. Among the compounds identified, the heterobivalent ligand 4m, containing an amide nitrogen and a sulfur atom at the 8-membered tether level, is one of the most potent and selective BuChE inhibitors described to date. The novel inhibitors, bearing postulated key features, validated the hypothesis of the presence of extra interaction sites within the hBuChE active site gorge.

The geometry and efficacy of cation-pi interactions in a diagonal position of a designed beta-hairpin

Cation-pi interactions are common in proteins, but their contribution to the stability and specificity of protein structure has not been well established. In this study, we examined the impact of cation-pi interactions in a diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe or Trp with Lys or Arg. The diagonal interactions ranged from -0.20 to -0.48 kcal/mole. Our experimental values for the diagonal cation-pi interactions are similar to those found in alpha-helical studies. Upfield shifting of the Lys and Arg side chains indicates that the geometries of cation-pi interactions adopted in the 12-residue beta-hairpin are comparable to those found in protein structures. The Lys was found to interact through the polarized Cepsilon, and the Arg is stacked against the aromatic ring of Phe or Trp. Folding of these peptides was found to be enthalpically favorable (DeltaH degrees equals approximately -3 kcal/mole) and entropically unfavorable (DeltaS degrees equals approximately -8 cal mole(-1) K(-1)).

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.

Dual binding mode of s-triazine to anions and cations

Ab initio calculations were performed on complexes between cations and s-triazine, which has a small and positive quadrupole moment. Minimum energy pi-complexes were found between s-triazine and cations. Minimum pi-complexes with anions were previously reported. This ability of s-triazine to form stable complexes with either anions or cations is studied using several theoretical methods. A likely explanation of this duality is the stabilization obtained from the ion-induced polarization. [structure: see text]

Weak C-H/pi interaction participates in the diastereoselectivity of a host-guest complex in the presence of six strong hydrogen bonds

[structure: see text] We report a study of the interaction between methylmethanetriacetic acid (MMTA) and a tripodal amidopyridine receptor 1, where the geometry of the binding is in part governed by a weak C-H/pi interaction in the presence of six strong N(O)-H.O(N) hydrogen bonds. There are two possible binding geometries for the 1:1 complex 1.MMTA; combining computational and experimental evidence we demonstrate that the endo binding mode is more favorable as the result of a C-H/pi interaction.

Impact of multiple cation-pi interactions upon calix[4]arene substrate binding and specificity

The cation-pi interaction influence on the conformation and binding of calix[4]arenes to alkali-metal cations has been studied using a dehydroxylated model. The model allows for the separation of cooperative cation-pi and electrostatic forces commonly found in the binding motifs found in calixarene complexes. Starting from the four well-known calix[4]arene conformations, six conformers for this dehydroxylated model (cone, partial cone, flattened cone, chair, 1,2-alternate, and 1,3-alternate) have been characterized by geometry optimization and frequency analysis using the Becke three-parameter exchange functional with the nonlocal correlation functional of Lee, Yang, and Parr and the 6-31G(d) basis set. Without the stabilization provided by the hydroxyl hydrogen bonds in calix[4]arene, neither the cone nor the 1,2-alternate conformation is computed to be a ground-state structure. The partial cone, flattened cone, chair, and 1,3-alternate conformers have been identified as ground-state structures in a vacuum, with the partial cone and the 1,3-alternate as the lowest energy minima in the aromatic model. The C(4)(v)() cone conformation is found to be a transition structure separating the flattened cone (C(2)(v)()) conformers. The energetic and structural preferences of the calix[4]arene model change dramatically when it is bound to Li(+), Na(+), and K(+). The number of pi-faces, the positioning of these pi-faces with respect to the cations, and the nature of the cation were studied as factors in the binding strength. A detailed study of the distances and angles between the aromatic ring centroids and the cations reveals the energetic advantages of multiple weak cation-pi interactions. The geometries are often far from the optimal cation-pi interaction in which the cation approaches in a perpendicular path the aromatic ring center, where the quadrupole moment is strongest. The results reveal that multiple weaker nonoptimal cation-pi interactions contribute significantly to the overall binding strength. This theoretical analysis underscores the importance of neighboring aromatic faces and provides new insight into the significance of cation-pi binding, not only for calix[4]arenes, but also for other supramolecular and biological systems.

Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water

Cation-pi interactions have been proposed to be important contributors to protein structure and function. In particular, these interactions have been suggested to provide significant stability at the solvent-exposed surface of a protein. We have investigated the magnitude of cation-pi interactions between phenylalanine (Phe) and lysine (Lys), ornithine (Orn), and diaminobutanoic acid (Dab) in the context of an alpha-helix and have found that only the Phe...Orn interaction provides significant stability to the helix, stabilizing it by -0.4 kcal/mol. This interaction energy is in the same range as a salt bridge in an alpha-helix, and equivalent to the recently reported Trp...Arg interaction in an alpha-helix, despite the fact that Trp...guanidinium interactions have been proposed to be stronger than Phe...ammonium interactions. These results indicate that even the simplest cation-pi interaction can provide significant stability to protein structure and demonstrate the subtle factors that can influence the observed interaction energies in designed systems.

Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces

The binding of different anions to calix[4]pyrrole has been studied by means of molecular dynamics coupled to thermodynamic integration calculations. The effect of different apolar solvents, octafluoro substitution, and the change in binding free energy derived from the presence of cosolute and water traces (the hydrated salt used to introduce the anion in the solution) were examined. Calculations allow us to rationalize the differential binding of ions to calix[4]pyrrole and octafluorocalix[4]pyrrole as well as to predict the behavior in new solvents for which experimental data are not available yet. It is found that both calix[4]pyrrole and octafluorocalix[4]pyrrole have a dramatic preference for F- in the gas phase and pure aprotic solvents, but the situation can change dramatically in protic solvents or in the presence of the hydrated cation which is used as cosolute of the anion. Overall, our results provide interesting clues for a better understanding of the process detected experimentally as "binding".

Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment

Quantum mechanical and quantum mechanical/molecular mechanical calculations in conjunction with continuum solvation models have been used to analyze CH-pi interactions in model systems of aryl- and alkyl-aromatic interactions, as well as in a model folding system designed to study those interactions. High level calculations reproduced accurately the interaction of CH-pi interactions in both alkyl- and aryl-based model systems. Dispersion effects dominate the interaction, but the electrostatics term is also relevant for aryl CH-pi interactions. Theoretical calculations were also used to examine the influence of CH-pi interactions in determining the conformational flexibility of folding models. Finally, a critical comparison of the results obtained from high level calculations on model systems and the experimental data derived for folding models in apolar solvents was carried out, which allowed us to reconcile the apparent discrepancy found between both data.

Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study

The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. Attention is paid to i) the reliability of semiempirical versus ab initio treatments of the quantum mechanical molecule, ii) the role of solvation, and iii) the effect of including the polarization energy component in the calculation of the GMIPp functional. The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds.

Interaction of anions with perfluoro aromatic compounds

The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the pi-cloud of the aromatic compounds. The interaction energies obtained range between -8 and -19 kcal mol(-1). The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.

New structural insights from Raman spectroscopy of proteins and their assemblies

Protein structure and stability are sensitive to and dependent on the local interactions of amino acid side chains. A diverse and important type of side-chain interaction is the hydrogen bond. Although numerous hydrogen bonds are resolved in protein 3-dimensional structures, those of the cysteine sulfhydryl group (S-H) are elusive to high-resolution X-ray and NMR methods. However, the nature and strength of sulfhydryl hydrogen bonds (S-H* * *X) are amenable to investigation by Raman spectroscopy. The power of the Raman method for characterizing S-H* * *X interactions is illustrated by resolving the Raman S-H stretching band for each of the eight cysteines per 666-residue subunit in the trimeric tailspike of icosahedral bacteriophage P22. The Raman sulfhydryl signatures of the wild-type tailspike and eight single-site cysteine to serine mutants reveal a heretofore unrecognized diversity of S-H hydrogen bonds in a native protein. The use of Raman spectroscopy to identify the non-hydrogen-bonded state of the tyrosine phenoxyl group is also described. This unusual and unexpected state occurs for all tyrosines in the assembled capsids of filamentous viruses Ff and Pf1. The Raman spectral signature of the non-hydrogen-bonded tyrosine phenoxyl, which is characterized by an extraordinary Raman Fermi doublet intensity ratio (I850/I830 = 6.7), extends and refines the existing correlation for hydrogen-bonded tyrosines. Finally, a novel Raman signature for tryptophan in the Pf3 filamentous virus is identified, which is proposed as diagnostic of "cation-pi interaction" involving the guanidinium group of Arg 37 as a cation donor and the indolyl ring of Trp 38 as a pi-electron acceptor. These studies demonstrate the power of Raman spectroscopy for investigating the interactions of key side chains in native protein assemblies.

Cation-pi interactions: an energy decomposition analysis and its implication in delta-opioid receptor-ligand binding

The nature and strength of the cation-pi interaction in protein-ligand binding are modeled by considering a series of nonbonded complexes involving N-substituted piperidines and substituted monocylic aromatics that mimic the delta-opioid receptor-ligand binding. High-level ab initio quantum mechanical calculations confirm the importance of such cation-pi interactions, whose intermolecular interaction energy ranges from -6 to -12 kcal/mol. A better understanding of the electrostatics, polarization, and other intermolecular interactions is obtained by appropriately decomposing the total interaction energy into their individual components. The energy decomposition analysis is also useful for parametrizing existing molecular mechanics force fields that could then account for energetic contributions arising out of cation-pi interactions in biomolecules. The present results further provide a framework for interpreting experimental results from point mutation reported for the delta-opioid receptor.

Investigation of synthetic hosts that model cation-pi sites found at protein binding domains

Small cyclophanes containing aromatic groups and dialkyl ammonium ions were created as model systems of the cation-pi complexes found at some protein binding domains. The hosts had different shapes in order to investigate the effect the arrangement of ammonium ions to aromatic surfaces has on their reactivity. pK(a) values of the hosts were substantially different in DMSO or (95/5) DMSO/D(2)O solutions, which showed that the ions existed in different environments of the hosts. Electrostatic charges, as determined by density functional calculations, revealed that the magnitude of a cationic charge depends on its position relative to an aromatic ring. Association constants of the hosts bound to the sodium salt of N-acetyl phenylalanine in d(6)-DMSO and in (95/5) d(6)-DMSO/D(2)O solutions were inversely proportional to the magnitude of the hosts' acidity constants. These results suggest that the magnitude of the positive charge for cationic groups of cation-pi complexes is reduced by being associated with electron-rich faces of aromatic rings. The aromatic rings, however, lessen the desolvation penalty that must be overcome for ligand binding, giving an overall more favorable association.

Cation-pi interaction in model alpha-helical peptides

Cation-pi interactions are increasingly recognized as important in chemistry and biology. Here we investigate the cation-pi interaction by determining its effect on the helicity of model peptides using a combination of CD and NMR spectroscopy. The data show that a single Trp/Arg interaction on the surface of a peptide can make a significant net favorable free energy contribution to helix stability if the two residues are positioned with appropriate spacing and orientation. The solvent-exposed Trp-->Arg (i, i + 4) interaction in helices can contribute -0.4 kcal/mol to the helix stability, while no free energy gain is detected if the two residues have the reversed orientation, Arg-->Trp (i, i + 4). The derived free energy is consistent with other experimental results studied in proteins or model peptides on cation-pi interactions. However in the same system the postulated Phe/Arg (i, i + 4) cation-pi interaction provides no net free energy to helix stability. Thus the Trp-->Arg interaction is stronger than Phe-->Arg. The cation-pi interactions are not sensitive to the screening effect by adding neutral salt as indicated by salt titration. Our results are in qualitative agreement with theoretical calculations emphasizing that cation-pi interactions can contribute significantly to protein stability with the order Trp > Phe. However, our and other experimental values are significantly smaller than estimates from theoretical calculations.

Understanding the congener-specific toxicity in polychlorinated dibenzo-p-dioxins: chlorination pattern and molecular quadrupole moment

It is well known that the biological activities and toxicities of planar polychlorinated aromatic compounds are extremely sensitive to chlorination pattern. Although their toxic responses have been correlated with the relative affinity for the receptor, the origin of this congener specificity is not well understood. We present a general interpretation of the congener-specific activity in polychlorinated dibenzo-p-dioxins, which concludes that molecular electrostatics is the principal factor determining the structure-activity relationship in this highly controversial environmental pollutant even though this electrostatic interaction represents only a part of the total interaction energy. Through calculations of the molecular charge distribution in the complete set of 76 dioxin congeners, we show that all active congeners share a unique charge distribution pattern, which is quantitatively described in terms of the molecular quadrupole moment (QM). The QM of dioxins changes sensitively and systematically with chlorination pattern. The three-dimensional electrostatic interactions at the receptor-binding site, which are optimized at a specific QM pattern represented by that of 2,3,7,8-tetrachlorodibenzo-p-dioxin, could explain the congener specificity in the binding affinity and toxicity. Although the polarizability also changes systematically with chlorination, it can only account for the effect of the degree of chlorination, not the congener specificity.

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains

Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.