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

Intramolecular Cation-π Interactions Organize Bowl-Shaped, Luminescent Molecular Containers

Molecules with nonplanar architectures are highly desirable due to their unique topological structures and functions. We report here the synthesis of two molecular containers (1 ⋅ 3Br- and 1 ⋅ 3Cl-), which utilize intramolecular cation-π interactions to enforce macrocylic arrangements and exhibit high binding affinity and luminescent properties. Remarkably, the geometry of the cation-π interaction can be flexibly tailored to achieve a precise ring arrangement, irrespective of the angle of the noncovalent bonds. Additionally, the C-H⋅⋅⋅Br- hydrogen bonds within the container are also conducive to stabilizing the bowl-shaped conformation. These bowl-shaped conformations were confirmed both in solution through NMR spectroscopy and in the solid state by X-ray studies. 1 ⋅ 3Br- shows high binding affinity and selectivity: F->Cl-, through C-H⋅⋅⋅X- (X=F, Cl) hydrogen bonds. Additionally, these containers exhibited blue fluorescence in solution and yellow room-temperature phosphorescence (RTP) in the solid state. Our findings illustrate the utility of cation-π interactions in designing functional molecules.

Self-Adaptive Aromatic Cation-π Driven Dimensional Polymorphism in Supramolecular Polymers for the Photocatalytic Oxidation and Separation of Aromatic/Cyclic Aliphatic Compounds

The phenomenon of polymorphism is ubiquitous in nature, the controlled manipulation of which not only increases our ontological understanding of nature but also facilitates the conceptualization and realization of novel functional materials. However, achieving targeted polymorphism in supramolecular assemblies (SAs) remains a formidable challenge, largely because of the constraints inherent in controlling the specific binding motifs of noncovalent interactions. Herein, we propose self-adaptive aromatic cation-π binding motifs to construct polymorphic SAs in both the solid and solution states. Using distinct discrete cation-π-cation and long-range cation-π binding motifs enables control of the self-assembly directionality of a C2h-symmetric bifunctional monomer, resulting in the successful formation of both two-dimensional and three-dimensional crystalline SAs (2D-CSA and 3D-CSA). The differences in the molecular packing of 3D-CSA compared with that of 2D-CSA significantly improve the charge separation and carrier mobility, leading to enhanced photocatalytic activity for the aerobic oxidation of thioanisole to methyl phenyl sulfoxide (yield of 99 % vs 57 %). 2D-CSA, which has a vertical extended structure with favorable stronger interaction with toluene though face-to-face cation-π interactions than methylcyclohexane, shows higher toluene/methylcyclohexane separation efficiency than 3D-CSA (96.9 % for 2D-CSA vs 56.3 % for 3D-CSA).

Boron-Nitrogen-Embedded Polycyclic Aromatic Hydrocarbon-Based Controllable Hierarchical Self-Assemblies through Synergistic Cation-π and C-H···π Interactions for Bifunctional Photo- and Electro-Catalysis

Boron-Nitrogen-embedded polycyclic aromatic hydrocarbons (BN-PAHs) as novel π-conjugated systems have attracted immense attention owing to their superior optoelectronic properties. However, constructing long-range ordered supramolecular assemblies based on BN-PAHs remains conspicuously scarce, primarily attributed to the constraints arising from coordinating multiple noncovalent interactions and the intrinsic characteristics of BN-PAHs, which hinder precise control over delicate self-assembly processes. Herein, we achieve the successful formation of BN-PAH-based controllable hierarchical assemblies through synergistically leveraged cation-π and C-H···π interactions. By carefully adjusting the solvent conditions in two progressive assembly hierarchies, the one-dimensional (1D) supramolecular assemblies with "rigid yet flexible" assembled units are first formed by cation-π interactions, and then they can be gradually fused into two-dimensional (2D) structures under specific C-H···π interactions, thus realizing the precise control of the transformation process from BN-PAH-based 1D primary structures to 2D higher-order assemblies. The resulting 2D-BNSA, characterized by enhanced electrical conductivity and ordered 2D layered structure, provides anchoring and dispersion sites for loading two appropriate nanocatalysts, thus facilitating the efficient photocatalytic CO2 reduction (with a remarkable CH4 evolution rate of 938.7 μmol g-1 h-1) and electrocatalytic acetylene semihydrogenation (reaching a Faradaic efficiency for ethylene up to 98.5%).

Revealing the Role of N Heteroatoms in Noncovalent Aromatic Interactions by Ultrafast Intermolecular Coulombic Decay

Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural patterns, especially the impact of heteroaromaticity, is still incomplete. Here, we investigate the relaxation processes that follow inner-valence ionization in a range of molecular dimers involving various combinations of benzene, pyridine, and pyrimidine, which initiate an ultrafast intermolecular Coulombic decay process. Multiparticle coincidence momentum spectroscopy, combined with ab initio calculations, enables us to explore the principal orientations of these fundamental dimers and, thus, to elucidate the influence of N heteroatoms on the relative preference of the aromatic π-stacking, H-bonding, and CH-π interactions and their dependence on the number of nitrogen atoms in the rings. Our studies reveal a sensitive tool for the structural imaging of molecular complexes and provide a more complete understanding of the effects of N heteroatoms on the noncovalent aromatic interactions at the molecular level.

G-quadruplex DNA selective targeting for anticancer therapy: a computational study of a novel PtII monofunctional complex activated by adaptive binding

Targeting of G-quadruplex (G-Q) nucleic acids, which are helical four-stranded structures formed from guanine-rich nucleic acid sequences, has emerged in recent years as an appealing opportunity for drug intervention in anticancer therapy. Small-molecule drugs can stabilize quadruplex structures, promoting selective downregulation of gene expression and telomerase inhibition and also activating DNA damage responses. Thus, rational design of small molecular ligands able to selectively interact with and stabilize G-Q structures is a promising strategy for developing potent anti-cancer drugs with selective toxicity towards cancer cells over normal ones. Here, the outcomes of a thorough computational investigation of a recently synthesized monofunctional PtII complex (Pt1), whose selectivity for G-Q is activated by what is called adaptive binding, are reported. Quantum mechanics and molecular dynamics calculations have been employed for studying the classical key steps of the mechanism of action of PtII complexes, the conversion of the non-charged and non-planar Pt1 complex into a planar and charged PtII (Pt2) complex able to play the role of a G-Q binder and, finally, the interaction of Pt2 with G-Q. The information obtained from such an investigation allows us to rationalize the behavior of the novel PtII complex proposed to be activated by adaptive binding toward selective interaction with G-Q or similar molecules and can be exploited for designing ligands with more effective recognition ability toward G-quadruplex DNA.

Single-Molecule Force Spectroscopy Reveals Cation-π Interactions in Aqueous Media Are Highly Affected by Cation Dehydration

Cation-π interactions underlie many important processes in biology and materials science. However, experimental investigations of cation-π interactions in aqueous media remain challenging. Here, we studied the cation-π binding strength and mechanism by pulling two hydrophobic polymers with distinct cation binding properties, i.e., poly-pentafluorostyrene and polystyrene, in aqueous media using single-molecule force spectroscopy and nuclear magnetic resonance measurement. We found that the interaction strengths linearly depend on the cation concentrations, following the order of Li^{+}<NH_{4}^{+}<Na^{+}<K^{+}. The binding energies are 0.03-0.23  kJ mol^{-1} M^{-1}. This order is distinct from the strength of cation-π interactions in gas phase and may be caused by the different dehydration ability of the cations. Taken together, our method provides a unique perspective to investigate cation-π interactions under physiologically relevant conditions.

Effect of noncovalent interactions in ion pairs on hypervalent iodines: inversion of regioselectivity in sulfonyloxylactonization

The noncovalent interactions between the sulfonyloxy group and the cationic nitrogen-containing heterocyclic moiety substituted in hypervalent iodines caused specific regioselectivity in the sulfonyloxylactonization of 2-vinyl benzoic acids.

Molecular Simulation of αvβ6 Integrin Inhibitors

The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dynamics (MD) simulations of αvβ6 in complex with its natural ligand, pro-TGF-β1, show the persistence over time of a bidentate Arg-Asp ligand-receptor interaction and a metal chelate interaction between an aspartate on the ligand and an Mg²⁺ ion in the active site. This is typical of RGD binding ligands. Additional binding site interactions, which are not observed in the static crystal structure, are also identified. We investigate an RGD mimetic, which serves as a framework for a series of potential αvβ6 antagonists. The scaffold includes a derivative of the widely utilized 1,8-naphthyridine moiety, for which we present force field parameters, to enable MD and relative free energy perturbation (FEP) simulations. The MD simulations highlight the importance of hydrogen bonding and cation-π interactions. The FEP calculations predict relative binding affinities, within 1.5 kcal mol^-1, on average, of experiments.

A H-aggregating fluorescent probe for recognizing both mercury and copper ions based on a dicarboxyl-pyridyl bifunctionalized difluoroboron dipyrromethene

A difluoroboron dipyrromethene fluorescent probe is fabricated for recognizing both Hg²⁺ and Cu²⁺ ions based on an extraordinary ion-induced H-aggregation.

Coordination chemistry of mercury(ii) halide complexes: a combined experimental, theoretical and (ICSD & CSD) database study on the relationship between inorganic and organic units

The coordination sphere can be influenced by many factors of inorganic and organic units. Despite the predominant role of inorganic unit in coordination sphere determination, organic unit can change it via one major or cooperativity of minor effects.

A concerted addition mechanism in [Hmim]Br-triggered thiol–ene reactions: a typical “ionic liquid effect” revealed by DFT and experimental studies

The π⁺–π and H-bond interactions between [Hmim]Br and substrates promote a special one-step addition mechanism in thiol–ene reactions.

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor

Adsorbed mercaptopyridine can sense hydrogen-bonding because the ring breathing mode has a different frequency from bare and protonated species.

Exploiting non-covalent π interactions for catalyst design

Molecular recognition, binding and catalysis are often mediated by non-covalent interactions involving aromatic functional groups. Although the relative complexity of these so-called π interactions has made them challenging to study, theory and modelling have now reached the stage at which we can explain their physical origins and obtain reliable insight into their effects on molecular binding and chemical transformations. This offers opportunities for the rational manipulation of these complex non-covalent interactions and their direct incorporation into the design of small-molecule catalysts and enzymes.

The Cation-π Interaction in Small-Molecule Catalysis

Catalysis by small molecules (≤1000 Da, 10(-9)  m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.

Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F)

Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.

Spatial aromatic fences of metal-organic frameworks for manipulating the electron spin of a fulleropyrrolidine nitroxide radical

The electron spin properties of a fulleropyrrolidine nitroxide radical incarcerated in the pores of MOF-177 and MIL-53 respectively were investigated for the first time. It was found that the spatial confinement effect and intramolecular interactions in these two solid-state spin systems lead to dramatically distinctive spin dynamics.

Cationic CH⋯π interactions as a function of solvation

The energy of a cationic CH⋯π interaction was measured as a function of solvation using molecular torsion balances.

Influence of N-heteroaromatic π–π stacking on supramolecular assembly and coordination geometry; effect of a single-atom change in the ligand

A study on how the polarization of aromatic systems, through the introduction of a nitrogen heteroatom, affects the π–π interactions and crystal packing of mercury coordination compounds.

Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues

Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.