On the Importance of Anion–π Interactions in the Mechanism of Sulfide:Quinone Oxidoreductase

Sulfide:quinone oxidoreductase (SQR) is a flavin‐dependent enzyme that plays a physiological role in two important processes. First, it is responsible for sulfide detoxification by oxidizing sulfide ions (S^2? and HS^?) to elementary sulfur and the electrons are first transferred to flavin adenine dinucleotide (FAD), which in turn passes them to the quinone pool in the membrane. Second, in sulfidotrophic bacteria, SQRs play a key role in the sulfide‐dependent respiration and anaerobic photosynthesis, deriving energy for their growth from reduced sulfur. Two mechanisms of action for SQR have been proposed: first, nucleophilic attack of a Cys residue on the C4 of FAD, and second, an alternate anionic radical mechanism by direct electron transfer from Cys to the isoalloxazine ring of FAD. Both mechanisms involve a common anionic intermediate that it is stabilized by a relevant anion–π interaction and its previous formation (from HS^? and Cys‐S‐S‐Cys) is also facilitated by reducing the transition‐state barrier, owing to an interaction that involves the π system of FAD. By analyzing the X‐ray structures of SQRs available in the Protein Data Bank (PDB) and using DFT calculations, we demonstrate the relevance of the anion–π interaction in the enzymatic mechanism.     

Orbital Effect‐Induced Anomalous Anion–π Interactions between Electron‐Rich Aromatic Hydrocarbons and Fluoride

Anion–π interactions generally exist between an anion and an electron‐deficient π‐ring because of the electron‐accepting character of the ring. In this paper, we report orbital effect‐induced anomalous binding between electron‐rich π systems and F^? through anion–π interactions calculated at the MP2/6‐31+G(d,p) and ωB97X‐D/6‐31+G(d,p) levels of theory. We find that anion–π interactions between F^? and electron‐rich π rings increase markedly with increasing number of π electrons and size of the π rings. This is contrary to intuition because anion–π interactions would be expected to gradually decrease because of gradually increasing Coulombic repulsion between the negative charge of the anions and gradually increasing number of π electrons of the aromatic surfaces. Energy decomposition analysis showed that the key to this anomalous effect is the more effective delocalization of negative charge to the unoccupied π* orbitals of larger π rings, which is termed an “orbital effect”.     

Preorganized Anion Traps for Exploiting Anion–π Interactions: An Experimental and Computational Study

1,3‐Bis(pentafluorophenyl‐imino)isoindoline (A^F) and 3,6‐di‐tert‐butyl‐1,8‐bis(pentafluorophenyl)‐9H‐carbazole (B^F) have been designed as preorganized anion receptors that exploit anion–π interactions, and their ability to bind chloride and bromide in various solvents has been evaluated. Both receptors A^F and B^F are neutral but provide a central NH hydrogen bond that directs the halide anion into a preorganized clamp of the two electron‐deficient appended arenes. Crystal structures of host–guest complexes of A^F with DMSO, Cl^?, or Br^? (A^F:DMSO, A^F:Cl^?, and ${{\rm A}{{{\rm F}\hfill \atop 2\hfill}}}$ :Br^?) reveal that in all cases the guest is located in the cleft between the perfluorinated flaps, but NMR spectroscopy shows a more complex situation in solution because of E,Z/Z,Z isomerism of the host. In the case of the more rigid receptor B^F, Job plots evidence 1:1 complex formation with Cl^? and Br^?, and association constants up to 960 M ^?1 have been determined depending on the solvent. Crystal structures of B^F and B^F:DMSO visualize the distinct preorganization of the host for anion–π interactions. The reference compounds 1,3‐bis(2‐pyrimidylimino)isoindoline (A^N) and 3,6‐di‐tert‐butyl‐1,8‐diphenyl‐9H‐carbazole (B^H), which lack the perfluorinated flaps, do not show any indication of anion binding under the same conditions. A detailed computational analysis of the receptors A^F and B^F and their host–guest complexes with Cl^? or Br^? was carried out to quantify the interactions in play. Local correlation methods were applied, allowing for a decomposition of the ring–anion interactions. The latter were found to contribute significantly to the stabilization of these complexes (about half of the total energy). Compounds A^F and B^F represent rare examples of neutral receptors that are well preorganized for exploiting anion–π interactions, and rare examples of receptors for which the individual contributions to the binding energy have been quantified.     

Anion–π Slides for Transmembrane Transport

The recognition and transport of anions is usually accomplished by hydrogen bonding, ion pairing, metal coordination, and anion–dipole interactions. Here, we elaborate on the concept to use anion–π interactions for this purpose. Different to the popular cation–π interactions, applications of the complementary π‐acidic surfaces do not exist. This is understandable because the inversion of the aromatic quadrupole moment to produce π‐acidity is a rare phenomenon. Here, we suggest that π‐acidic aromatics can be linked together to produce an unbendable scaffold with multiple binding sites for anions to move along across a lipid bilayer membrane. The alignment of multiple anion–π sites is needed to introduce a cooperative multi‐ion hopping mechanism. Experimental support for the validity of the concept comes from preliminary results with oligonaphthalenediimide (O‐NDI) rods. Predicted by strongly positive facial quadrupole moments, the cooperativity and chloride selectivity found for anion transport by O‐NDI rods were consistent with the existence of anion–π slides. The proposed mechanism for anion transport is supported by DFT results for model systems, as well as MD simulations of rigid O‐NDI rods. Applicability of anion–π slides to achieve electroneutral photosynthesis is elaborated with the readily colorizable oligoperylenediimide (O‐PDI) rods. To clarify validity, scope and limitations of these concepts, a collaborative research effort will be needed to address by computer modeling and experimental observations the basic questions in simple model systems and to design advanced multifunctional anion–π architectures.     

Competition Between π–π and CH/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy‐Substituted 1,8‐Bis((propyloxyphenyl)ethynyl)naphthalenes

The structural and electronic consequences of π–π and C?H/π interactions in two alkoxy‐substituted 1,8‐bis‐ ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X‐ray crystallography and electronic structure computations. The crystal structure of analogue 4 , bearing an alkoxy side chain in the 4‐position of each of the phenyl rings, adopts a π‐stacked geometry, whereas analogue 8 , bearing alkoxy groups at both the 2‐ and the 5‐positions of each ring, has a geometry in which the rings are splayed away from a π‐stacked arrangement. Symmetry‐adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π‐stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π–π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti‐alignment of C?O bond dipoles, and two C?H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π–π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.     

Molecular Complexes of Simple Anions with Electron‐Deficient Arenes: Spectroscopic Evidence for Two Types of Structural Motifs for Anion–Arene Interactions

Anion–π interactions between a π‐acidic aromatic system and an anion are gaining increasing recognition in chemistry and biology. Herein, the binding features of an electron‐deficient aromatic system (1,3,5‐trinitrobenzene (TNB)) and selected anions (OH^?, Br^?, and I^?) are examined in the gas phase by using the combined information derived from collision‐induced dissociation experiments at variable energy, infrared multiple‐photon dissociation spectroscopy, and quantum chemical calculations. We provide spectroscopic evidence for two different structural motifs of anion–arene complexes depending on the nature of the anion. The TNB–OR^? complexes (R=H, or alkyl groups which were studied earlier) adopt an anionic σ‐complex structure whereby RO^? attacks the aromatic ring with covalent bond formation, and develops a tetrahedral ring carbon bound to H and OR. The halide complexes rather conform to a structure in which the TNB moiety is hardly altered, and the halogen is placed on an unsubstituted carbon atom over the periphery of the ring at a C–X distance that is appreciably longer than a typical covalent bond length. The ensuing structural motif, previously characterized in the solid state and named weak σ interaction, is now confirmed by an IR spectroscopic assay in the gas phase, in which the sampled species are unperturbed by crystal packing or solvation effects.     

Long‐Range Effects in Anion–π Interactions: Their Crucial Role in the Inhibition Mechanism of Mycobacterium Tuberculosis Malate Synthase

The glyoxylate shunt is an anaplerotic bypass of the traditional Krebs cycle. It plays a prominent role in Mycobacterium tuberculosis virulence, so it can be exploited for the development of antitubercular therapeutics. The shunt involves two enzymes: isocitrate lyase (ICL) and malate synthase (GlcB). The shunt bypasses two steps of the tricarboxylic acid cycle, allowing the incorporation of carbon, and thus, refilling oxaloacetate under carbon‐limiting conditions. The targeting of ICL is complicated; however, GlcB, which accommodates the pantothenate tail of acetyl‐CoA in the active site, is easier to target. A catalytic Mg²⁺ unit is located at the bottom of the cavity, and plays a very important role. Recently, the development of effective antituberculosis drugs based on phenyldiketo acids (PDKAs) has been reported. Interestingly, all the crystal structures of GlcB–inhibitor complexes exhibit close contact between the carboxylate of Asp633 and the face of the aromatic ring of the inhibitor. Remarkably, the replacement of the phenyl ring in PDKA by aliphatic moieties yields inactive inhibitors, suggesting that the aromatic moiety is crucial for inhibition. However, the aromatic ring of PDKA is not electron‐deficient, and consequently, the anion–π interaction is expected to be very weak (dominated only by polarization effects). Herein, through a combination analysis of the recent X‐ray structures of GlcB–PDKA complexes retrieved from the protein data bank (PDB) and computational ab initio studies (RI‐MP2/def2‐TZVP level of theory), we demonstrate the prominent role of the Mg²⁺ ion in the active site, which promotes long‐range enhancement of the anion–π interaction.     

Asymmetric Anion–π Catalysis on Perylenediimides

Anion–π catalysis, that is the stabilization of anionic transition states on π‐acidic aromatic surfaces, has so far been developed with naphthalenediimides (NDIs). This report introduces perylenediimides (PDIs) to anion–π catalysis. The quadrupole moment of PDIs (+23.2 B) is found to exceed that of NDIs and reach new records with acceptors in the core (+70.9 B), and their larger surface provides space to better accommodate chemical transformations. Unlike NDIs, the activity of PDI catalysts for enolate and enamine addition is determined by the twist of their π surface rather than their reducibility. These results, further strengthened by nitrate inhibition and circular dichroism spectroscopy, support an understanding of anion–π interactions centered around quadrupole moments, i.e., electrostatic contributions, rather than redox potentials and charge transfer. The large PDI surfaces provide access to the highest enantioselectivities observed so far in anion–π catalysis (96 % ee).     

Enolate Stabilization by Anion–π Interactions: Deuterium Exchange in Malonate Dilactones on π‐Acidic Surfaces

Of central importance in chemistry and biology, enolate chemistry is an attractive topic to elaborate on possible contributions of anion–π interactions to catalysis. To demonstrate the existence of such contributions, experimental evidence for the stabilization of not only anions but also anionic intermediates and transition states on π‐acidic aromatic surfaces is decisive. To tackle this challenge for enolate chemistry with maximal precision and minimal uncertainty, malonate dilactones are covalently positioned on the π‐acidic surface of naphthalenediimides (NDIs). Their presence is directly visible in the upfield shifts of the α‐protons in the ¹H NMR spectra. The reactivity of these protons on π‐acidic surfaces is measured by hydrogen–deuterium (H–D) exchange for 11 different examples, excluding controls. The velocity of H–D exchange increases with π acidity (NDI core substituents: SO₂R>SOR>H>OR>OR/NR₂>SR>NR₂). The H–D exchange kinetics vary with the structure of the enolate (malonates>methylmalonates, dilactones>dithiolactones). Moreover, they depend on the distance to the π surface (bridge length: 11–13 atoms). Most importantly, H–D exchange depends strongly on the chirality of the π surface (chiral sulfoxides as core substituents; the crystal structure of the enantiopure (R,R,P)‐macrocycle is reported). For maximal π acidity, transition‐state stabilizations up to ?18.8 kJ mol^?1 are obtained for H–D exchange. The Brønsted acidity of the enols increases strongly with π acidity of the aromatic surface, the lowest measured pK_a=10.9 calculates to a ΔpK_a=?5.5. Corresponding to the deprotonation of arginine residues in neutral water, considered as “impossible” in biology, the found enolate–π interactions are very important. The strong dependence of enolate stabilization on the unprecedented seven‐component π‐acidity gradient over almost 1 eV demonstrates quantitatively that such important anion–π activities can be expected only from strong enough π acids.     

Enhanced Aerogen–π Interaction by a Cation–π Force

The interaction between a noble gas atom and an aromatic π‐electron system, which mainly originates from the London dispersion force, is very weak and has not attracted enough attention yet. Herein, we reported a type of notably enhanced aerogen–π interaction between cation–π systems and noble gas atoms. The binding strength of a divalent cation–π system with a xenon atom is comparable to a moderate hydrogen bond (up to ca. 7 kcal mol^?1), whereas krypton and argon atoms produce slightly weaker interactions. Energy‐decomposition analysis reveals that the induction interaction is responsible for the stabilization of divalent cation–π?Xe species besides the dispersion interaction. Our results might be helpful to increase the understanding of some unsolved mysteries of aerogens.     

The Effects of Substituents on the Geometry of π–π Interactions

We have designed and utilized a simple molecular recognition system to study the substituent effects in aromatic interactions. Recently, we showed that 3‐ and 3,5‐disubstituted benzoyl leucine diethyl amides with aromatic rings of varying electronic character organized into homochiral dimers in the solid state through a parallel displaced π–π interaction and two hydrogen bonds, but no such homochiral dimerization was observed for the unsubstituted case. This phenomenon supports the hypothesis that substituents stabilize π–π interactions regardless of their electronic character. To further investigate the origin of substituent effects for π–π interactions, we synthesized and crystallized a series of 4‐substituted benzoyl leucine diethyl amides. Surprisingly, only two of the 4‐substituted compounds formed homochiral dimers. A comparison among the 4‐substituted compounds that crystallized as homochiral dimers and their 3‐substituted counterparts revealed that there are differences in regard to the geometry of the aromatic rings with respect to each other, which depend on the electronic nature and location of the substituent. The crystal structures of the homochiral dimers that showed evidence of direct, local interactions between the substituents on the aromatic rings also displayed nonequivalent dihedral angles in the individual monomers. The crystallographic data suggests that such “flexing” may be the result of the individual molecules orienting themselves to maximize the local dipole interactions on the respective aromatic rings. The results presented here can potentially have broad applicability towards the development of molecular recognition systems that involve aromatic interactions.     

Self‐Assembly and Disassembly of Vesicles as Controlled by Anion–π Interactions

Anion–π interactions have been widely studied as new noncovalent driving forces in supramolecular chemistry. However, self‐assembly induced by anion–π interactions is still largely unexplored. Herein we report the formation of supramolecular amphiphiles through anion–π interactions, and the subsequent formation of self‐assembled vesicles in water. With the π receptor 1 as the host and anionic amphiphiles, such as sodium dodecylsulfate (SDS), sodium laurate (SLA), and sodium methyl dodecylphosphonate (SDP), as guests, the sequential formation of host–guest supramolecular amphiphiles and self‐assembled vesicles was demonstrated by SEM, TEM, DLS, and XRD techniques. The intrinsic anion–π interactions between 1 and the anionic amphiphiles were confirmed by crystal diffraction, HRMS analysis, and DFT calculations. Furthermore, the controlled disassembly of the vesicles was promoted by competing anions, such as NO₃^?, Cl^?, and Br^?, or by changing the pH value of the medium.