Is polarization important in cation-pi interactions?

Evaluation of stabilization energies in π-π and cation-π interactions involved in biological macromolecules by ab initio calculations

Non-covalent interactions involving aromatic rings contribute significantly to the stability of three-dimensional structures of biological macromolecules. Therefore, accurate descriptions of such interactions are crucial in understanding the functional mechanisms of biological molecules. However, it is also well known that, for some cases where van der Waals interactions make a dominant contribution, conventional ab initio electronic structure calculations, such as density functional theory, do not produce accurate interaction energies. In this study, we evaluated molecular mechanics (MM) calculations for two types of interactions involving aromatic rings, π-π interactions and cation-π interactions, by comparing our results with those obtained by advanced ab initio calculations at the coupled-cluster with singles, doubles and perturbative triples level. In structures with stacked aromatic rings, interaction energies obtained by MM calculations are overestimated. On the other hand, for cation-π interactions, the energies in MM calculations are significantly underestimated. In both cases, addition of an induction energy based on polarization effects also fails to improve the estimate given by MM calculations. The results indicate that current effective pairwise potentials are inappropriate to represent π-π and cation-π interactions.

Targeting the purinome

Purines are critical cofactors in the enzymatic reactions that create and maintain living organisms. In humans, there are approximately 3,266 proteins that utilize purine cofactors and these proteins constitute the so-called purinome. The human purinome encompasses a wide-ranging functional repertoire and many of these proteins are attractive drug targets. For example, it is estimated that 30% of modern drug discovery projects target protein kinases and that modulators of small G-proteins comprise more than 50% of currently marketed drugs. Given the importance of purine-binding proteins to drug discovery, the following review will discuss the forces that mediate protein:purine recognition, the factors that determine druggability of a protein target, and the process of structure-based drug design. A review of purine recognition in representatives of the various purine-binding protein families, as well as the challenges faced in targeting members of the purinome in drug discovery campaigns will also be given.

High concentration formulations of recombinant human interleukin-1 receptor antagonist: I. Physical characterization

At relatively high protein concentrations (i.e., up to 100 mg/mL), recombinant human interleukin-1 receptor antagonist (rhIL-1ra) was found to exist in a monomer-dimer equilibrium controlled by solution ionic strength. Sedimentation equilibrium at 25 degrees C was used to measure the increase in the dimer dissociation constant (K(d)) as a function of ionic strength. K(d) increased from 2.0 to 12.6 mM as the solution ionic strength was increased from 0.011 to 0.184 molal. These K(d) values were used with both static light scattering and membrane osmometry data collected over a protein concentration range of 1-100 mg/mL to determine second osmotic virial coefficients. Expanding the second osmotic virial coefficient model to account for separate monomer-monomer (B(22)), monomer-dimer (B(23)), and dimer-dimer (B(33)) interactions reveals net monomer-dimer interactions are attractive, whereas the others are repulsive. Lastly, isothermal titration calorimetry dilution experiments showed that rhIL-1ra dimerization is enthalpically driven (DeltaH(dimerization) << 0), which is consistent with intermolecular cation-pi interactions previously proposed as the monomer-monomer contact sites in dimers.

Exploring the size dependence of cyclic and acyclic pi-systems on cation-pi binding

MP2(FULL)/6-311++G** calculations are performed on the cation-pi complexes of Li+ and Mg2+ with the pi-face of linear (ethylene, butadiene, hexatriene, and octatetraene) and cyclic (benzene, naphthalene, anthracene, phenanthrene and naphthacene) unsaturated hydrocarbons. The interaction energy is found to increase systematically as the size of the pi-system increases. The higher interaction energy is in good correlation with the extent of charge transfer. The increase in the interaction energy is more dramatic in the case of acyclic systems. The computations reveal that larger pi-systems tend to have higher complexation energy with the metal ions, which will have important implications in our understanding of the structural and functional aspects of metal binding.

Calcium block of single sodium channels: role of a pore-lining aromatic residue

Extracellular Ca(2+) ions cause a rapid block of voltage-gated sodium channels, manifest as an apparent reduction of the amplitude of single-channel currents. We examined the influence of residue Tyr-401 in the isoform rNa(V)1.4 on both single-channel conductance and Ca(2+) block. An aromatic residue at this position in the outer mouth of the pore plays a critical role in high-affinity block by the guanidinium toxin tetrodotoxin, primarily due to an electrostatic attraction between the cationic blocker and the system of pi electrons on the aromatic face. We tested whether a similar attraction between small metal cations (Na(+) and Ca(2+)) and this residue would enhance single-channel conductance or pore block, using a series of fluorinated derivatives of phenylalanine at this position. Our results show a monotonic decrease in Ca(2+) block as the aromatic ring is increasingly fluorinated, a result in accord with a cation-pi interaction between Ca(2+) and the aromatic ring. This occurred without a change of single-channel conductance, consistent with a greater electrostatic effect of the pi system on divalent than on monovalent cations. High-level quantum mechanical calculations show that Ca(2+) ions likely do not bind directly to the aromatic ring because of the substantial energetic penalty of dehydrating a Ca(2+) ion. However, the complex of a Ca(2+) ion with its inner hydration shell, Ca(2+)(H(2)O)(6), interacts electrostatically with the aromatic ring in a way that affects the local concentration of Ca(2+) ions in the extracellular vestibule.

Refined models for the preferential interactions of tryptophan with phosphocholines

A series of molecular models of the adducts formed between N-acetyl-l-tryptophan ethylamide and diacetyl-sn-glycero-3-phosphocholine have been generated. Using rOesy data that enabled us to place restrictions on the proximity of a number of key protons in the amino acid/phosphocholine pairs, a series of structures were generated following molecular dynamics and mechanics experiments using the CHARMM27 force field. These structures were then subjected to a series of clustering algorithms in order to classify the tight binding interactions between a single tryptophan and a phosphocholine. From these analyses, it is evident that: (i) binding is characterised by hydrogen bonding between the indole NH as donor and phosphate oxygen as acceptor, cation-carbonyl interactions between the choline ammonium and amide carbonyl groups and cation-pi interactions; (ii) cation-pi interactions are not always observed, particularly when their formation is at the expense of cation-carbonyl and hydrogen bonding interactions; (iii) on the basis of amino acid torsional parameters, it is possible to predict whether the phosphocholine headgroup will bind in a compact or elongated conformation. Extension of the procedures to characterise 2 : 1 Trp-PC binding revealed that the same intermolecular interactions are predominant; however, combinations of all three intermolecular interactions within the same adduct occur much more frequently due to the availability of donor/acceptor groups from both tryptophans in the 2 : 1 system.

Block-Localized Wavefunction (BLW) Method at the Density Functional Theory (DFT) Level

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

Complexation of AlIII by Aromatic Amino Acids in the Gas Phase

The coordination properties of three natural aromatic amino acids (AAAs)-phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp)-to AlIII are studied in this work, devoting special attention to the role of the aromatic side chain. A comparison with aluminum(III)-alanine complexes is also presented. The polarizability arising from the ring has been seen to be a key factor in the stability of the complexes, with the order being Trp-AlIII > Tyr-AlIII > Phe-AlIII, starting from the most stable one. Cation-pi interactions between the metal and the aromatic ring are present in the lowest energy conformers, especially for Trp, which seems to be very well suited for these kinds of interactions, occurring with both the six- and five-membered rings of the indole side chain. The most stable coordination mode for the three AAAs is found to be tricoordinated with the N and O of the backbone chain and the aromatic ring, as was found theoretically and experimentally for other metals.

Cation-pi interaction in potassium-polyene complexes and the fate of potassium ion: a theoretical study

Ab initio studies have been done at B3LYP/6-31G* level of theory to determine the structural changes on the substitution of potassium to odd-numbered all-trans conjugated polyenes ranging from C(5) to C(13). The results show that potassium is always positioned in the form of K(+) above an odd carbon other than the terminal carbons and that the stablest structural isomer is the one with K(+) lying above the central odd carbon. If a central odd carbon does not exist (as in C(11)-system), then K(+) will be positioned above the odd carbon nearest to the central carbon to achieve maximum stability. The difference in the binding energies of the isomers is generally small and it becomes insignificantly small as the carbon chain length increases so that under suitable conditions K(+) ion may be made to move between the ends of the polyene. The metal-polyene complexes are seen to have a considerably reduced HOMO-LUMO gap. Further, the interaction of potassium with the polyene not only caused a total rearrangement of the bond lengths, bond angles and dihedral angles, but also induced a bend (warping) to the polyenic fragment that pockets K(+). The structural changes and stability of the metal-polyene complexes are explained in terms of electrostatic interaction and cation-pi cloud interaction.

Origin of Attraction, Magnitude, and Directionality of Interactions in Benzene Complexes with Pyridinium Cations

Geometries and interaction energies of benzene complexes with pyridine, pyridinium, N-methylpyridinium were studied by ab initio molecular orbital calculations. Estimated CCSD(T) interaction energies of the complexes at the basis set limit were -3.04, -14.77, and -9.36 kcal/mol, respectively. The interactions in the pyridinium and N-methylpyridinium complexes should be categorized into a cation/pi interaction, because the electrostatic and induction interactions greatly contribute to the attraction. On the other hand, the interaction in the pyridine complex is a pi/pi interaction. The dispersion interaction is mainly responsible for the attraction in the benzene-pyridine complex. Short-range interactions including charge-transfer interactions are not important for the attraction in the three complexes. The most stable pyridinium complex has a T-shaped structure, in which the N-H bond points toward the benzene, while the N-methylpyridinium complex prefers a slipped-parallel structure. The benzene-pyridine complex has two nearly isoenergetic (Slipped-parallel and T-shaped) structures.

Dissecting the General Physicochemical Properties of Noncovalent Interactions Involving Tyrosine Side Chain as a Second-Shell Ligand in Biomolecular Metal-Binding Site Mimetics: An Experimental Study Combining Fluorescence,13C NMR Spectroscopy and ESI Mass Spectrometry

Detailed physicochemical features inherent in the dynamic cation-pi interactions of aromatic amino acid side chains in the secondary coordination spheres around metal ions were extracted and mapped by intrinsic tyrosine fluorescence titration experiments with two homologous, artificially engineered metal-binding scaffolds which mimic metal-binding sites in metalloproteins. A newly formulated method for the treatment of fluorescence titration data allows straightforward assessment of both the magnitudes and properties of metal-chelation-assisted cation-aromatic interactions (K2) underlying a proposed two-step metallosupramolecular association process. The unprecedented linear platform-motif correlations between the two contrasting scaffolds in their changes in tyrosine fluorescence on binding of 3d metal cations help to elucidate the properties of general cation-arene recognition corresponding to the metal-responsive characteristics of the second-shell Tyr residue surrounding the metal-binding sites in the supramolecular context, and thereby define a new noncovalent design principle for metal-ion recognition in aqueous solution. As supported by NMR spectroscopic and ESI-MS analyses and molecular mechanics force field calculations, the systematic study exemplifies the concept of using steady-state tyrosine fluorescence as a powerful tool for comprehensive descriptions of cation-pi interactions in the extended environment of a metal-binding site. We established that the physicochemical properties pertaining to indirect metal-arene interactions are highly dependent on the electronic properties of the metal ions. This work suggests that second-shell cation-pi interactions may play more diverse roles, including modulation of structure, reactivity, and function of metal-binding sites, than the previously well-established direct cation-pi interactions involving hard cations (e.g., alkali metal ions). Moreover, such a study will continue to complement theoretical predications and/or the early experimental investigations in organic solvents.

Dual Cation and Anion Acceptor Molecules. The Case of the (η6-C6H6)(η6C6F6)Cr(0) Complex

In this manuscript we report high-level ab initio (RI-MP2(full)/6-31++G**) and DFT (B3LYP/ 6-31++G** and MPWB1K/6-31++G**) calculations on complexes between the bis(arene)chromium complex (eta6-C6H6)(eta6C6F6)Cr(0) (1) and cations/anions. This interesting molecule 1, which is synthetically available, exhibits a dual binding mode to anions and cations, with interaction energies similar to those previously reported for benzene with cations and hexafluorobenzene with anions. In addition, the simultaneous interaction with cations and anions is also studied.

Rigid-rod anion–π slides for multiion hopping across lipid bilayers

Shape-persistent oligo-p-phenylene-N,N-naphthalenediimide (O-NDI) rods are introduced as anion-pi slides for chloride-selective multiion hopping across lipid bilayers. Results from end-group engineering and covalent capture as O-NDI hairpins suggested that self-assembly into transmembrane O-NDI bundles is essential for activity. A halide topology VI (Cl > F > Br approximately I, Cl/Br approximately Cl/I > 7) implied strong anion binding along the anion-pi slides with relatively weak contributions from size exclusion (F >or= OAc). Anomalous mole fraction effects (AMFE) supported the occurrence of multiion hopping along the pi-acidic O-NDI rods. The existence of anion-pi interactions was corroborated by high-level ab initio and DFT calculations. The latter revealed positive NDI quadrupole moments far beyond the hexafluorobenzene standard. Computational studies further suggested that anion binding occurs at the confined, pi-acidic edges of the sticky NDI surface and is influenced by the nature of the phenyl spacer between two NDIs. With regard to methods development, a detailed analysis of the detection of ion selectivity with the HPTS assay including AMFE in vesicles is provided.

Arene−Cation Interactions of Positive Quadrupole Moment Aromatics and Arene−Anion Interactions of Negative Quadrupole Moment Aromatics

Intermolecular interactions involving aromatic pi-electron density are widely believed to be governed by the aromatic molecular quadrupole moment, Theta(zz). Arene-cation binding is believed to occur primarily with negative Theta(zz) aromatics, and arene-anion binding is believed to occur largely with positive Theta(zz) aromatics. We have performed quantum mechanical computations that show the cation binding of positive Theta(zz) aromatics and the anion binding of negative Theta(zz) aromatics is quite common in the gas phase. The pi-electron density of hexafluorobenzene, the prototypical positive Theta(zz ) aromatic (experimental Theta(zz) = 9.5 +/- 0.5 DA), has a Li+ binding enthalpy of -4.37 kcal/mol at the MP2(full)/6-311G**level of theory. The RHF/6-311G** calculated Theta(zz) value of 1,4-dicyanobenzene is +11.81 DA, yet it has an MP2(full)/6-311G** Li+ binding enthalpy of -12.65 kcal/mol and a Na+ binding enthalpy of -3.72 kcal/mol. The pi-electron density of benzene, the prototypical negative Theta(zz) aromatic (experimental Theta(zz) = -8.7 +/- 0.5 DA), has a F- binding enthalpy of -5.51 kcal/mol. The RHF/6-311G** calculated Theta(zz) of C6H2I4 is -10.45 DA, yet it has an MP2(full)/6-311++G** calculated F- binding enthalpy of -20.13 kcal/mol. Our results show that as the aromatic Theta(zz) value increases the cation binding enthalpy decreases; a plot of cation binding enthalpies versus aromatic Theta(zz) gives a line of best of fit with R2 = 0.778. No such correlation exists between the aromatic Theta(zz) value and the anion binding enthalpy; the line of best fit has R2 = 0.297. These results are discussed in terms of electrostatic and polarizability contributions to the overall binding enthalpies.

Indole localization in lipid membranes revealed by molecular simulation

It is commonly known that the amino acid residue tryptophan and its side-chain analogs, e.g., indole, are strongly attracted to the interfacial region of lipid bilayers. Phenylalanine and its side-chain analogs, e.g., benzene, do not localize in the interface but are distributed throughout the lipid bilayer. We use molecular dynamics to investigate the details of indole and benzene localization and orientation within a POPC bilayer and the factors that lead to their different properties. We identify three sites in the bilayer at which indole is localized: 1), a site in the interface near the glycerol moiety; 2), a weakly bound site in the interface near the choline moiety; and 3), a weakly bound site in the center of the bilayer's hydrocarbon core. Benzene is localized in the same three positions, but the most stable position is the hydrocarbon core followed by the site near the glycerol moiety. Transfer of indole from water to the hydrocarbon core shows a classic hydrophobic effect. In contrast, interfacial binding is strongly enthalpy driven. We use several different sets of partial charges to investigate the factors that contribute to indole's and benzene's orientational and spatial distribution. Our simulations show that a number of electrostatic interactions appear to contribute to localization, including hydrogen bonding to the lipid carbonyl groups, cation-pi interactions, interactions between the indole dipole and the lipid bilayer's strong interfacial electric field, and nonspecific electrostatic stabilization due to a mismatch in the variation of the nonpolar forces and local dielectric with position in the bilayer.

Atom−Bond Pairwise Additive Representation for Cation−Benzene Potential Energy Surfaces: An ab Initio Validation Study

The achievement of extensive and meaningful molecular dynamics simulations requires both the detailed knowledge of the basic features of the intermolecular interaction and the representation of the involved potential energy surface in a simple, natural and analytical form. This double request stimulated us to extend to ion-molecule systems a semiempirical method previously introduced for the description of weakly interacting atom-molecule aggregates and formulated in terms of atomic species-molecular bond interaction additivity. The method is here applied to the investigation of the prototypical M(+)-C6H6 systems (M = Li, Na, K, Rb and Cs) and some of its predictions are tested against accurate ab initio calculations. Such calculations have been performed by employing the MP2 method and large basis sets, privileging the description of the metal atoms. The agreement between potential energy scans semiempirically obtained and ab initio results is good for all the investigated geometries, thus showing that the adopted representation is in general able to reproduce all the main features of the potential energy surface for these systems. The role of the various noncovalent interaction components, as a function of the geometry and of the intermolecular distance in the M(+)-C6H6 complexes, is also investigated for a more detailed assessment of the results of the semiempirical method.

Interactions of Neutral and Cationic Transition Metals with the Redox System of Hydroquinone and Quinone: Theoretical Characterization of the Binding Topologies, and Implications for the Formation of Nanomaterials

To understand the self-assembly process of the transition metal (TM) nanoclusters and nanowires self-synthesized by hydroquinone (HQ) and calix[4]hydroquinone (CHQ) by electrochemical redox processes, we have investigated the binding sites of HQ for the transition-metal cations TM(n+)=Ag(+), Au(+), Pd(2+), Pt(2+), and Hg(2+) and those of quinone (Q) for the reduced neutral metals TM(0), using ab initio calculations. For comparison, TM(0)-HQ and TM(n+)-Q interactions, as well as the cases for Na(+) and Cu(+) (which do not take part in self-synthesis by CHQ) are also included. In general, TM-ligand coordination is controlled by symmetry constraints imposed on the respective orbital interactions. Calculations predict that, due to synergetic interactions, silver and gold are very efficient metals for one-dimensional (1D) nanowire formation in the self-assembly process, platinum and mercury favor both nanowire/nanorod and thin film formation, while palladium favors two-dimensional (2D) thin film formation.

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

Electrostatics calculations: latest methodological advances

Electrostatics plays a major role in the stabilization and function of biomolecules; as such, it remains a major focus of theoretical and computational studies of macromolecules. Electrostatic interactions are long range, and strongly dependent on the solvent and ions surrounding the biomolecule under study. During the past year, progress has been reported in the treatment of electrostatics in explicit and implicit solvent models. Interesting new developments of explicit solvent models include more efficient Ewald summation methods, as well as alternative approaches based on reaction field theory, periodic images and Euler summations. Implicit solvent models remain divided into those that solve the Poisson-Boltzmann equation numerically and those based on the generalized Born formalism. Both approaches are now included in molecular dynamics simulations and their accuracies may be assessed by direct comparison against experimental data. It is worth mentioning the recent development of web interfaces that facilitate access to and usage of existing tools for computing electrostatic interactions.

Ab Initio Study of [n.n]Paracyclophane (n = 2, 3) Complexes with Cations: Unprecedented Through-Space Substituent Effects

Several cation-pi complexes between substituted [n.n]paracyclophanes (n = 2, 3) and cations have been studied using high level ab initio calculations. The chemical substitution at the aromatic ring that is not interacting with the cation has a strong influence upon the binding energy. This strong through-space substituent effect has been studied using the "atoms-in-molecules" theory, which has been found useful to explain the energetic results.

Specific targeting highly conserved residues in the HIV-1 reverse transcriptase primer grip region. Design, synthesis, and biological evaluation of novel, potent, and broad spectrum NNRTIs with antiviral activity

Pyrrolobenzoxazepinones (PBOs) represent a new class of human immunodeficiency virus type 1 (HIV-1) nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) whose prototype is 5. Molecular modeling studies based on the X-ray structures of HIV-1 RT prompted the synthesis of novel analogues which were tested as anti-HIV agents. The PBO derivatives specifically designed to target the highly conserved amino acid residues within the beta12-beta13 hairpin, namely primer grip, proved to be very potent against the most common mutant enzymes, including the highly resistant K103N mutant strain. Structure-activity relationships (SARs) are discussed in terms of a possible interaction with the RT binding site, depending on the nature of the substituents at C-6. Among the pyrrolobenzoxazepines investigated, 15c appeared to be the most promising NNRTI of the series characterized by potent antiviral activity, broad spectrum, and low cytotoxicity. 15c showed synergistic antiviral activity with AZT.

Interfacial tryptophan residues: a role for the cation-pi effect?

Integral membrane proteins are characterized by having a preference for aromatic residues, e.g., tryptophan (W), at the interface between the lipid bilayer core and the aqueous phase. The reason for this is not clear, but it seems that the preference is related to a complex interplay between steric and electrostatic forces. The flat rigid paddle-like structure of tryptophan, associated with a quadrupolar moment (aromaticity) arising from the pi-electron cloud of the indole, interacts primarily with moieties in the lipid headgroup region hardly penetrating into the bilayer core. We have studied the interaction between the nitrogen moiety of lipid molecule headgroups and the pi-electron distribution of gramicidin (gA) tryptophan residues (W9, W11, W13, and W15) using molecular dynamics (MD) simulations of gA embedded in two hydrated lipid bilayers composed of 1-palmitoyl-2-oleoylphosphatidylethanolamine (POPE) and 1-palmitoyl-2-oleoylphosphatidyl-choline (POPC), respectively. We use a force field model for tryptophan in which polarizability is only implicit, but we believe that classical molecular dynamics force fields are sufficient to capture the most prominent features of the cation-pi interaction. Our criteria for cation-pi interactions are based on distance and angular requirements, and the results from our model suggest that cation-pi interactions are relevant for W(PE)1), W(PE)13, W(PE)15, and, to some extent, W(PC)11 and W(PC)13. In our model, W9 does not seem to engage in cation-pi interactions with lipids, neither in POPE nor POPC. The criteria for the cation-pi effect are satisfied more often in POPE than in POPC, whereas the H-bonding ability between the indole donor and the carbonyl acceptor is similar in POPE and POPC. This suggests an increased affinity for lipids with ethanolamine headgroups to transmembrane proteins enriched in interfacial tryptophans.

Cation−π Interactions with a Model for the Side Chain of Tryptophan: Structures and Absolute Binding Energies of Alkali Metal Cation−Indole Complexes†

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.

MD Simulation of the Na+−Phenylalanine Complex in Water: Competition between Cation−π Interaction and Aqueous Solvation

The competition between cation-pi interaction and aqueous solvation for the Na+ ion has been investigated by molecular dynamics simulations, using the phenylalanine amino acid as the test pi system. Starting from one of the best standard force fields, we have developed new parameters that significantly improve the agreement with experimental and high quality quantum mechanical results for the complexes of Na+ with phenylalanine, benzene, and water. The modified force field performs very well in forecasting energy and geometry of cation coordination for the complexes. Next, analysis of MD trajectories and steered MD simulations indicate that the Na+-phenylalanine complex survives for a significant time in aqueous solution and that the free energy barrier opposing dissociation of the complex is sizable. Finally, we analyze the role of different intermolecular interactions in determining the preference for cation-pi bonding with respect to aqueous solvation. We thus confirm that the Na+-phenylalanine stabilization energy may overcome the interactions with water.