Roles of electrostatic interaction and dispersion in CH···CH,CH···π, and π···π ethylene dimers

The structural, mechanical, electronic, and optical properties of orthorhombic Bi₂S₃ and Bi₂Se₃ compounds have been investigated by means of first principles calculations. The calculated lattice parameters and internal coordinates are in very good agreement with the experimental findings. The elastic constants are obtained, then the secondary results such as bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, anisotropy factor, and Debye temperature of polycrystalline aggregates are derived, and the relevant mechanical properties are also discussed. Furthermore, the band structures and optical properties such as real and imaginary parts of dielectric functions, energy-loss function, the effective number of valance electrons, and the effective optical dielectric constant have been computed. We also calculated some nonlinearities for Bi₂S₃ and Bi₂Se₃ (tensors of elasto-optical coefficients) under pressure.

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...     

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.     

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.     

The cooperativity between hydrogen and halogen bond in the XY···HNC···XY (X,Y = F,Cl, Br) complexes

The cooperativity between hydrogen and halogen bonds in XY···HNC···XY (X, Y = F, Cl, Br) complexes was studied at the MP2/aug-cc-pVTZ level. Two hydrogen-bonded dimers, five hydrogen-bonded dimers, and ten trimers were obtained. The hydrogen- and halogen-bonded interaction energies in the trimers were larger than those in the dimers, indicating that both the hydrogen bonding interaction and the halogen bonding interaction are enhanced. The binary halogen bonding interaction plays the most important role in the ternary system. The hydrogen donor molecule influences the magnitude of the halogen bonding interaction much more than the hydrogen bonding interaction in the trimers with respect to the dimers. Our calculations are consistent with the conclusion that the stronger noncovalent interaction has a bigger effect on the weaker one. The variation in the vibrational frequency in the HNC molecule was considered. The NH antisymmetry vibration frequency has a blue shift, whereas the symmetry vibration frequency has a red shift. A dipole moment enhancement is observed upon formation of the trimers. The variation in topological properties at bond critical points was obtained using the atoms in molecules method, and was consistent with the results of the interaction energy analysis.     

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.     

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.     

Interplay between halogen bonds and hydrogen bonds in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes

The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller?Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V _S,min) and the most positive electrostatic potentials (V _S,max) on the electron density contours of the individual species. The greater the V _S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V _S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species.

Biosynthesis,isolation, purification and separation of nivalenol,fusarenone — X and zearalenone

Fusarium, graminearum KF 370 isolate is able to simultaneous biosynthesis of three toxic metabolites, namely: fusarenone-X (FUS), nivalenol (NIV) and zearalenone (F-2). After metabolites extraction with methanol — water (3:1) and defatting with n-heptane toxins were partitioned into chloroform layer. Purification of the? compounds was performed on Celite 545 — charcoal — Aluminiumoxid 90 column then metabolites were separated on Kieselgel 60 (200–300 mesh) column with developing solvent chloroform — methanol. This way FUS, NIV and F-2 were obtained as crystalline or high purity standards.     

Non-canonical H-bonds in β-lactamases: importance of C–H···π interactions

β-Lactamase production is the common mechanism of resistance of β-lactam antibiotics. Knowledge of inter-residue interactions in protein structures increases our understanding of protein structure and stability. We have systematically analysed the contribution of C–H···π interactions to the stability of β-lactamases. Most of the interactions are long range and most of the interacting residues are evolutionarily conserved. The occurrence of C–H···π interactions in active sites and metal binding sites is very low in β-lactamases. Hence, C–H···π interactions are important determinants of stability in β-lactamases and they may not play a significant role in specificity. The results from this study provide valuable insights for understanding the stability patterns of β-lactamases and their relation to various other environmental preferences.     

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.     

Cation-π interactions in lipocalins: structural and functional implications

The cation-π interaction impacts protein folding, structural stability, specificity, and molecular recognition. Cation-π interactions have been overlooked in the lipocalin family. To fill this gap, these interactions were analyzed in the 113 crystal and solution structures from the lipocalin family. The cation-π interactions link previously identified structurally conserved regions and reveal new motifs, which are beyond the reach of a sequence alignment algorithm. Functional and structural significance of the interactions were tested experimentally in human tear lipocalin (TL). TL, a prominent and promiscuous lipocalin, has a key role in lipid binding at the ocular surface. Ligand binding modulation through the loop AB at the "open" end of the barrel has been erroneously attributed solely to electrostatic interactions. Data revealed that the interloop cation-π interaction in the pair Phe28-Lys108 contributes significantly to stabilize the holo-conformation of the loop AB. Numerous energetically significant and conserved cation-π interactions were uncovered in TL and throughout the lipocalin family. Cation-π interactions, such as the highly conserved Trp17-Arg118 pair in TL, were educed in low temperature experiments of mutants with Trp to Tyr substitutions.     

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.     

Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH₂ complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?C_carbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E _coop are all negative with much larger E _coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis.

Structures and aromaticity of X2Y 2 − (X = C, Si, Ge and Y = N, P, As) anions

The equilibrium geometries, total energies, and vibrational frequencies of anions X₂Y₂ ⁻ (X = C, Si, Ge and Y = N, P, As) are theoretically investigated with density functional theory (DFT) method. Our calculation shows that for C₂N₂ ⁻ species, the D _2h isomer is the most stable four-membered structure, and for other species the C _2v isomer in which two X atoms are contrapuntal is the most stable structure at the B3LYP/6-311 +G_* level. Wiberg bond index (WBI) and negative nucleus-independent chemical shift (NICS) value indicate the existence of delocalization in stable X₂Y₂ ⁻ structures. A detailed molecular orbital (MO) analysis further reveals that stable isomers of these species have strongly aromatic character, which strengthens the structural stability and makes them closely connected with the concept of aromaticity.     

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.

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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.

     

π Delocalization in iridathiabenzenes

Fenske-Hall calculations were carried out for (PEt₃)₃Ir(C₇H₉) (1), [(PEt₃)₃Ir(C₆H₈S)]⁺ (2), [(S-t-but)(PEt₃)₂]Ir(C₆H₈S) (3), and [(S-t-but)(PMet₃)₃]Ir(C₆H₈S) (4) in order to compare the degree of π delocalization in the metallathiacycle rings of (2) and (3). In comparison to (1), a true iridabenzene and (4), an iridathiacyclobutadiene, the π ring systems in (2) and (3) are considerably more localized than the π system in (1) but are not totally localized. Strong metal-sulfur bonding in (2) disrupts the π ring system and results in some localization of the ring π bonds. The introduction of the donor thiolate ligand in (3) disrupts the ring of π system even more by destabilizing the metal orbitals used for metal-sulfur interactions. This weakens the metal-sulfur interaction seen in (2) and leads to even more localization of the ring π system in (3).     

Coordination geometry isomerism induced by N-H?Cl, C-H?Cl, C-H?N, C-H?π and π?π supramolecular interactions in mercury(II) complexes with tripyridylimidazole chelating ligands

Reaction of HgCl₂ with trans-(±)2-(2,5-di(pyridin-2-yl)-4,5-dihydro-1H-imidazol-4-yl)pyridine (L1) and cis-(±)-(phenyl(2,4,5-tri(pyridin-2-yl)-4,5-dihydroimidazol-1- yl)methanone (L2) gives mononuclear complexes, 1 and 2. In these complexes L1 and L2 behave as tridentate and bidentate chelating ligands, giving distorted trigonal bipyramidal and tetrahedral coordination geometries, respectively. X-ray diffraction studies revealed a series of N-H?Cl, C-H?Cl, C-H?N and C-H?π interactions in 1 giving a 3D network, and N-H?Cl, C-H?Cl, C-H?π and π?π interactions in 2 giving a 2D network in the crystal lattice. Since both ligands should have a similar binding capacity to the mercury ions, the variations observed for coordination number and geometry should be a consequence of supramolecular stabilizing effects.     

A theoretical study on unusual intermolecular T-shaped X–H...π interactions between the singlet state HB=BH and HF, HCl, HCN or H2C2

The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid hydrogen of HF, HCl, HCN and H₂C₂ using MP2 and B3LYP methods at 6-311++G(2df,2p) and aug-cc-pVTZ levels. The binding energies follow the order of HB=BH...HF>HB=BH...HCl>HB=BH...HCN>HB=BH...H₂C₂. The hydrogen-bonded interactions in HB=BH...HX are found to be stronger than those in H₂C=CH₂...HX and OCB≡BCO...HX. The analyses of natural bond orbital (NBO) and the electron density shifts reveal that the nature of the T-shaped X–H...π hydrogen-bonded interaction is that much of the lost density from the π-orbital of B=B bond is shifted toward the hydrogen atom of the proton donor, leading to the electron density accumulation and the formation of the hydrogen bond. The atoms in molecules (AIM) theory have also been applied to characterize bond critical points and confirm that the B=B double bond can be a potential proton acceptor. The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid hydrogen of HF, HCl, HCN and H₂C₂     

Theoretical study of X- · 1 · YF (1 = triazine,X = Cl,Br and I,Y = H,Cl, Br,I, PH2 and AsH2): noncovalently electron-withdrawing effects on anion-arene interactions

The ternary complexes X^- · 1 · YF (1 = triazine, X = Cl, Br and I, Y = H, Cl, Br, I, PH₂ and AsH₂) have been investigated by MP2 calculations to understand the noncovalently electron-withdrawing effects on anion-arene interactions. The results indicate that in binary complexes (1 · X^-), both weak σ-type and anion-π complexes can be formed for Cl^- and Br^-, but only anion-π complex can be formed for I^-. Moreover, the hydrogen-bonding complex is the global minimum for all three halides in binary complexes. However, in ternary complexes, anion-π complex become unstable and only σ complex can retain in many cases for Cl^- and Br^-. Anion-π complex keeps stable only when YF = HF. In contrast with binary complexes, σ complex become the global minimum for Cl^- and Br^- in ternary complexes. These changes in binding mode and strength are consistent with the results of covalently electron-withdrawing effects. However, in contrast with the covalently electron-withdrawing substituents, Cl^- and Br^- can attack the aromatic carbon atom to form a strong σ complex when the noncovalently electron-withdrawing effect is induced by halogen bonding. The binding behavior for I^- is different from that for Cl^- and Br^- in two aspects. First, the anion-π complex for I^- can also keep stable when the noncovalent interaction is halogen bonding. Second, the anion-π complex for I^- is the global minimum when it can retain as a stable structure.