Strength of CH···π interactions in the C-terminal subdomain of villin headpiece

The relative free energies of the folded structures of the seven model peptides with PLX (X = W, Y, F, H, and A) and ALX (X = W and A) sequences to the corresponding extended structures are calculated using the density functional methods in water to evaluate the relative strengths of CH···π interactions, especially proline···aromatic interactions for the PLX motif of the C-terminal subdomain of villin headpiece. It has been found that the Pro···π contacts for the folded structures of the PLW, PLY, PLF, and PLH peptides have in common a geometric pattern having the edge of the Pro ring interacting with the face of the aromatic ring, as found for functionally important Pro residues in proteins. At the M06-2X/cc-pVTZ//SMD M06-2X/6-31+G(d) level of theory, the relative stabilities of the folded structures to the extended structures are obtained in the order PLW > ALW > PLA > PLH > PLY > ALA > PLF by the conformational Gibbs free energies in water, which is reasonably consistent with the observed results from the CD thermal analysis for wild-type and mutants of the C-terminal subdomains of villin headpieces. Although the interaction energies excluding the solvation free energies play a role in determining the relative stabilities of the PLX and ALX peptides, the solvation and entropic terms are found to be of consequence, too. In particular, it has been known that ～40% of the total interaction energy of the PLW peptide is ascribed to the CH···π interactions of the contacting side chains for Pro and Trp residues, in which the dispersion terms play a role.     

CH/π interactions of π-system of acetylacetonato chelate ring: Comparison of CH/π interactions of Ni(II)-acetylacetonato chelate and benzene rings

The calculations have been done for CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring. The results show that there is an attractive electrostatic interaction, while dispersion component is a major source of attractive interacting energies. The interaction was compared with CH/π interaction between two benzene rings. The comparison shows that two interactions are quite similar, enabling to estimate the energy of CH/π interaction with π-system of Ni(II)-acetylacetonato chelate ring to be about 10.5 kJ/mol. The results indicate that CH/π interactions of chelate ring in various molecular systems can be as important as CH/π interactions of phenyl ring.     

Cation-π Interactions and their Functional Roles in Membrane Proteins

Cation-π interactions arise as a result of strong attractive forces between positively charged entities and the π-electron cloud of aromatic groups. The physicochemical characteristics of cation-π interactions are particularly well-suited to the dual hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins bring molecular features into increasingly sharper view, cation-π interactions are gaining traction as essential contributors to membrane protein chemistry, function, and pharmacology. Here we review the physicochemical properties of cation-π interactions and present several prominent examples which demonstrate significant roles for this specialized biological chemistry.     

Effect of stepwise microhydration on the guanidinium···π interaction

Polychlorinated biphenyls (PCBs) are potentially hazardous to the environment because of their chemical stability and biological toxicity. In this study, we identified the binding mode of a representative PCB180 to human serum albumin (HSA) using fluorescence and molecular dynamics (MD) simulation methods. PCB180 bound exactly at subdomain IIIA of HSA based on the fluorescence study along with site marker displacement experiments. PCB180 also induced conformational changes that were governed mainly by hydrophobic forces. MD studies and free energy calculations also made important contributions to the understanding of the effects of an HSA-PCB180 system on conformational changes. The simulations on binding behavior proved that PCB180 was located only in subdomain IIIA. Hydrophobic interactions dominated the mode of binding behavior. The results obtained using the two methods correlated well with each other. Our findings provide a framework for elucidating the mechanisms of PCB180-HSA binding, and may also help in further research on the transportation, distribution, and toxicity effects of PCBs when introduced into human blood serum.     

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins

Aromatic-aromatic hydrogen bonds are important in many areas of chemistry, biology and materials science. In this study we haveanalyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-πinteracting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal thatthese interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, thearomatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-πinteractions and π-π networks play important roles in the structural stability of ILs and TNF proteins.     

Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool,HBPredicT

A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously–the structural water–is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.     

Observation of carbonyl oxygen-π interaction in a metal complex

X-ray crystallography shows that [Ag₂L₂(H₂O)₂](BF₄)₂ where L is a 1:1 condensate of 1,2-diphenylethane-1,2-dione and 2-(2-aminoethyl pyridine), contains an Ag(I)-Ag(I) bond of length 2.979(2) Å and an angular, intraligand interaction of the keto O with the π cloud of the pyridine moiety (O-pyridine centroid = 3.12 Å). Model MP2/6-311++G(d,p) calculations indicate that the observed lone pair-π type interaction is stabilising and not merely a tolerated short contact.     

Crystal packing driven by metal-ligand interactions, hydrogen bonds, π-π stacking and anion-π stacking

Two polymeric copper(II) compounds have been synthesized with the ligand bis(pyrimidin-2yl)amine (dipm), by means of coordination bonds, Watson-Crick type hydrogen bond interactions and π-π stacking. Both supramolecules hold the same cationic building block, namely [Cu(dipm)₂(H₂O)₂]²⁺. However, their crystal structure significantly differs and this variation apparently arises from the nature of the anion which induces dissimilar crystal packings. The crystal growth is driven by several synergistic intermolecular interactions, i.e., coordination and hydrogen bonds, π-π and anion-π stacks.     

Cation-π and π-π stacking interactions allow selective inhibition of butyrylcholinesterase by modified quinine and cinchonidine alkaloids

Scaffold varied quaternized quinine and cinchonidine alkaloid derivatives were evaluated for their selective butyrylcholinesterase (BChE) inhibitory potential. K_i values were between 0.4–260.5 μM (non-competitive inhibition) while corresponding K_ivalues to acetylcholinesterase (AChE) ranged from 7.0–400 μM exhibiting a 250-fold selectivity for BChE.Docking arrangements (GOLD, PLANT) revealed that the extended aromatic moieties and the quaternized nitrogen of the inhibitors were responsible for specific π–π stacking and π–cation interactions with the choline binding site and the peripheral anionic site of BChE’s active site.     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

Rhodium paddlewheel dimers containing the π···π stacking, 1,8-naphthalimide supramolecular synthon

The bifunctional ligand 3-(1,8-naphthalimido)propanoate (L_C2⁻), which contains a carboxylate group linked to the robust π···π stacking 1,8-naphthalimide supramolecular synthon, has been used to prepare two new rhodium carboxylate dimer complexes, [Rh₂(L_C2)₄(DMF)₂] (1) and [Rh₂(L_C2)₄(py)₂]·3DMF (2). Both complexes have been structurally characterized and contain the Rh₂(O₂CR)₄ paddlewheel core, but have different axial ligands. The four naphthalimide side arms in the carboxylate ligands are arranged in the square shape imposed by the SBU in complex 1, but are bent in 2. In both cases, the supramolecular structure is organized into one-dimensional chains by strong π···π stacking interactions between only two of the 1,8-naphthalimide moieties on each dimeric unit. In 1, the other naphthalimide units do not interact strongly and in 2 they intramolecularly π···π stack with the adjacent axial pyridine molecules.     

Silver(I) complexes of dibenzo-18-crown-6-ether having cation-π and π-π interactions

Three silver(I) complexes of dibenzo-18-crown-6-ether (DB[18]C6), [Ag(DB[18]C6)(ClO₄)](THF) (1), [Ag(DB[18]6)(CF₃SO₃)]₂(acetone)₂ (2) and [Ag(DB[18]C6)(CF₃COO)]₂(AgCF₃COO)₂ (3) have been synthesized in different solvents and characterized structurally. In each complex, silver ions prefer an octahedral coordination geometry and form close dinuclear complex with DB[18]C6 based on cation-π interaction in η²-fashion. In particular, the coordination unit involving σ bonding at an oxygen group and π-π bonding between two benzene rings is quite unique.     

The origin of the generalized anomeric effect: possibility of CH/n and CH/π hydrogen bonds

Ab initio MO calculations were carried out at the MP4/6-311++G(3df,3pd)//MP2/6-311++G(3df,3pd) level to investigate the conformational Gibbs energy of a series of methyl ethers CH₃O-CH₂-X (X = OH, OCH₃, F, Cl, Br, CN, CCH, C₆H₅, CHO). It was found that the Gibbs energy of the gauche conformers is lower in every case than that of the corresponding anti conformers. In the more stable gauche conformers, the interatomic distance between X and the hydrogen atom was shorter than the sum of the van der Waals radii. The natural bonding orbital (NBO) charges of group X were more negative in the gauche conformers than in the anti conformers. We suggest that the CH/n and CH/π hydrogen bonds play an important role in stabilizing the gauche conformation of these compounds.     

A sterically congested aryltrimethylstannane - Synthesis, reactivity, transmetalation and CH-π interaction

The synthesis of a novel sterically congested tetraorganotin compound, (4-tert-butyl-2,6-dimesitylphenyl)trimethylstannane (1), is reported and its reactivity with special focus on transmetalation studied. The reaction of compound 1 with reagents such as HgCl₂, BiCl₃ and HOTf gave (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin chloride (2) and (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin triflate (3), respectively, as a result of selective tin-methyl bond cleavage. Less bulky aryltrimethyltin derivatives react with BiCl₃ to give both tin-methyl and tin-aryl bond cleavage. Hydrolysis of compound 3 proceeds slowly to give bis-(4-tert-butyl-2,6-dimesitylphenyl)dimethyl stannoxane (5) via the intermediate (4-tert-butyl-2,6-dimesitylphenyl)dimethyltin hydroxide (4). All terphenyldimethyltin derivatives that were characterized by single crystal X-ray diffraction analysis show C-H?π interactions. Based on these results, the optimum C-H?π distance (C?centroid_aryl distance) is suggested to be in the range 3.4 and 3.5 Å.     

Rational redesign of a cation···π···π stacking at cardiovascular Fbw7–Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction

The Fbw7–Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation ···π···π stacking system at the complex interface, which is formed by the Trp1159 residue of qGlu-peptide with the Lys2299 and His2359 residues of Fbw7 F-box domain. Both hybrid quantum mechanics/molecular mechanics (QM/MM) analysis of the real domain–peptide complex and electron-correlation ab initio calculation of the stacking system model suggested that the cation···π···π plays an important role in stabilizing the complex; substitution of peptide Trp1159 residue with aromatic Phe and Tyr would not cause a considerable effect on the configuration and energetics of cation···π···π stacking system, whereas His substitution seems to largely destabilize the system. Subsequently, the qGlu-peptide was stripped from the full-length Skp1 protein to define a so-called self-inhibitory peptide, which may rebind to the domain–peptide complex interface and thus disrupt the complex interaction. Fluorescence polarization (FP) assays revealed that the Trp1159Phe and Trp1159Tyr variants have a comparable or higher affinity (K _d = 41 and 62 μM) than the wild-type qGlu-peptide (K _d = 56 μM), while the Trp1159His mutation would largely impair the binding potency of qGlu-peptide to Fbw7 F-box domain (K _d = 280 μM), confirming that the cation···π···π confers both affinity and specificity to the domain–peptide recognition, which can be reshaped by rational molecular design of the nonbonded interaction system.

Open image in new window

Graphical abstract Stereoview of the complex structure of Fbw7 with Skp1 (PDB: 2ovp), where the Trp1159 residue of Skp1 qGlu-peptide can form a cation···π···π stacking system with the Lys2299 and His2359 residues of Fbw7 F-box domain.

     

CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides

The crystal structure of class I major histocompatibility complex antigens (MHC) bound to their specific ligand peptides were analyzed, in the context of the CH/π interaction, with use of a computer program CHPI. A number of short CH/C_sp² distances have been shown at the boundary of the heavy chain and β2 microglobulin. These interactions are conserved between species, human versus murine. A number of contacts shorter than the conventional van der Waals distance have been disclosed between CH hydrogens and aromatic side-chain groups in the MHC/peptide complexes. The CH/π interaction has been suggested to contribute to the specificity in the complex formation of class I MHC.     

A comprehensive analysis of P···π pnicogen bonds: substitution effects and comparison with Br···π halogen bonds

Journal of Molecular Modeling - Ab initio calculations were carried out in a systematic investigation of P···π pnicogen-bonded complexes XH2P···C2H2/C2H4 and...     

Assessing the dispersive and electrostatic components of the selenium–aromatic interaction energy by DFT

Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form their selenium analogues, selenocysteine (Sec) and selenomethionine (SeM). The nature of amino acid pockets in proteins is dependent on their composition and thus different non-covalent forces determine the interactions between selenium of Sec or SeM and other functional groups, resulting in specific biophysical behavior. The discrimination of selenium toward sulfur has been reported. In order to elucidate the difference between the nature of S-π and Se-π interactions, we performed extensive DFT calculations of dispersive and electrostatic contributions of Se-π interactions in substituted benzenes/hydrogen selenide (H₂Se) complexes. The results are compared with our earlier reported S-π calculations, as well as with available experimental data. Our results show a larger contribution of dispersive interactions in Se-π systems than in S-π ones, which mainly originate from the attraction between Se and substituent groups. We found that selenium exhibits a strong interaction with aromatic systems and may thus play a significant role in stabilizing protein folds and protein–inhibitor complexes. Our findings can also provide molecular insights for understanding enzymatic specificity discrimination between single selenium versus a sulfur atom, notwithstanding their very similar chemical properties.