Anion−π Interactions: Generality, Binding Strength, and Structure

Spontaneous Transition between Multiple Conductance States and Rectifying Behaviors in an Artificial Single-Molecule Funnel

It has long been an aspirational goal to create artificial channel structures that replicate the feat achieved by ion channel proteins. Biological ion channels occasionally demonstrate multiple conductance states (known as subconductance), remaining a challenging property to achieve in artificial channel molecules. We report a funnel-shaped single-molecule channel constructed by an electron-deficient macrocycle and two electron-deficient aromatic imide arms. Planar lipid bilayer measurements reveal distinct current recordings, including a closed state, two conducting states, and spontaneous transitions between the three states, resembling the events seen in biological ion channels. The transitions result from conformational changes induced by chloride transport in the channel molecule. Both opening states show a non-linear and rectifying I-V relationship, indicating voltage-dependent transport due to the asymmetrical channel structure. This work could enhance our understanding of ion permeation and channel opening mechanism.

Synthesis of Inherently Chiral Homo-heteracalixaromatics

There is a resurgence of research interest in inherently chiral calixarenes and heteracalixaromatics. However, the examples of macrocyclic ring-expanded homocalixarenes and heterocalixaromatics of inherent chirality are not known. Here we report an efficient method to construct inherently chiral N2,O2-linked homo-heteracalixaromatics from reductive amination reactions between bis-aldehydes and aliphatic diamines. Examples of post-macrocyclization derivatization were also demonstrated. Enantiomers were obtained from resolution and did not undergo racemization at an elevated temperature. This study provides a new strategy to design novel and functional inherently chiral macrocycles that have potential applications in supramolecular chemistry.

Oxoanion complexation of nitroisophthalamide receptors: Insights from the DFT calculations

Amide derivative receptors have been designed to investigate the oxoanion complexation ability via hydrogen and halogen bond interactions. Structural, energetic and electronic properties of nitroisophthalamide receptors, i.e., di(benzyl)- (R1), di(hexafluoro)- (R2), di(chloro-,tetrafluoro)- (R3), di(hexachloro)-(R4), di(fluoro-,tetrachloro)-nitroisophthalamide (R5), and their complexes with C2H3O2-, C7H5O2-, NO3-, H2PO4-, and ClO4- oxoanions were computed and obtained using the density functional theory calculations at the B3LYP/6-31G(d,p) theoretical level in gas phase. According to the computed results, all of oxoanions can form the stable complexes with amide receptors R1-R5 via exothermic process in which receptor R1 is found to interact with oxoanions through hydrogen bonds whereas the receptors R2-R5 are found to interact with oxoanion through both of hydrogen and halogen bonds. It is clearly seen that acetate ion displays the strongest complexation interaction with all receptors compared to the other oxoanions. In addition, electronic properties of receptors R1-R5 in both gas and DMSO phases are modified after complexation with oxoanions. Therefore, the designed amide receptors may be potentially used for oxoanion sensing application.

Anion-π interaction with alkenes: persistent complexes vs. irreversible reactions of anions with tetracyanoethylene

The interaction of the tetracyanoethylene (TCNE) π-acceptor with oxo- and fluoro-anions (BF4-, PF6-, ClO4-, NO3-) led to the formation of anion-π complexes in which these polyatomic anions were located over the face of alkenes, with multiple contacts being shorter than the van der Waals separations. The anion-π associations of TCNE with halides were delimited by the electron-donor strengths and nucleophilicity of the anions. Specifically, while bromides formed persistent anion-π associations with TCNE in the solid state and in solutions, only transient anion-π complexes with iodides and chlorides were observed. In the case of iodide (strong 1e reducing agent), the formation of anion-π complexes was followed by the reduction of the π-acceptor to the TCNE-˙ anion-radical. The interaction of TCNE with Cl- (and F-) anions (which are better nucleophiles in the aprotic solvents) led to the formation of 1,1,2,3,3-pentacyanoprop-2-en-1-ide anions. Thermodynamics, UV-Vis spectra, and structures, as well as contributions of electrostatics, orbital interactions, and dispersion to the interaction energies in the complexes of TCNE with various anions were closely related to the characteristics of the corresponding associations with the aromatic and p-benzoquinone acceptors. This points out the general equivalence of the interactions in the anion-π complexes with different π-acceptors and the critical role of the nature of the anions in these bindings.

A grape seed protein-tannic acid powder to transform various non-adhesive hydrogels into adhesive gels

Realizing adhesion between wet materials remains challenging because of the interfacial water. Current strategies depend on complicated surface modifications, resulting in limited functions. Herein, a facile strategy based on the powder of grape seed protein and tannic acid (GSP-TA) was reported to endow various non-adhesive hydrogels adhesion without chemical modifications for both hydrogels and adherents. The GSP-TA powder has the capability to absorb interfacial water, form an adhesive layer on the hydrogel surface, diffusion into the underneath hydrogel matrix, and establish the initial adhesion within 5 s. By forming multiple non-covalent interactions between powders and substrates, the GSP-TA powder served as an efficient surface treating agent, enabling robust adhesion to solid substrates (wood, cardboard, glass, iron, and rubber) and wet tissues (pigskin, muscle, liver and heart). The adhesive strength for wood, cardboard, glass, iron, and rubber was 145.92 ± 5.93, 123.93 ± 15.98, 66.24 ± 7.67, 98.22 ± 4.13, and 80.83 ± 7.48 kPa, respectively. Because of reversible interactions, the adhesion was also repeatable. Due to the merits of grape seed protein and plant polyphenol, it could be completely degraded within 11 days. Bearing several merits, this strategy has promising applications in wound patches, tissue repair, and sensors.

Proposed molecular mechanism of non-competitive inhibition using molecular dynamics simulations between α-glucosidase enzyme and mangostin compound as antidiabetic

CONTEXT

Further understanding of the molecular mechanisms is necessary since it is important for designing new drugs. This study aimed to understand the molecular mechanisms involved in the design of drugs that are inhibitors of the α-glucosidase enzyme. This research aims to gain further understanding of the molecular mechanisms underlying antidiabetic drug design. The molecular docking process yielded 4 compounds with the best affinity energy, including γ-Mangostin, 1,6-dimethyl-ester-3-isomangostin, 1,3,6-trimethyl-ester-α-mangostin, and 3,6,7-trimethyl-ester-γ-mangostin. Free energy calculation with molecular mechanics with generalized born and surface area solvation indicated that the 3,6,7-trimethyl-γ-mangostin had a better free energy value compared to acarbose and simulated maltose together with 3,6,7-trimethyl-γ-mangostin compound. Based on the analysis of electrostatic, van der Waals, and intermolecular hydrogen interactions, 3,6,7-trimethyl-γ-mangostin adopts a noncompetitive inhibition mechanism, whereas acarbose adopts a competitive inhibition mechanism. Consequently, 3,6,7-trimethyl-ester-γ-mangostin, which is a derivative of γ-mangostin, can provide better activity in silico with molecular docking approaches and molecular dynamics simulations.

METHOD

This research commenced with retrieving protein structures from the RCSB database, generating the formation of ligands using the ChemDraw Professional software, conducting molecular docking with the Autodock Vina software, and performing molecular dynamics simulations using the Amber software, along with the evaluation of RMSD values and intermolecular hydrogen bonds. Free energy, electrostatic interactions, and Van der Waals interaction were calculated using MM/GBSA. Acarbose, used as a positive control, and maltose are simulated together with test compound that has the best free energy. The forcefields used for molecular dynamics simulations are ff19SB, gaff2, and tip3p.

Mimicking the Shape and Function of the ClC Chloride Channel Selective Pore by Combining a Molecular Hourglass Shape with Anion-π Interactions

ClC is the main family of natural chloride channel proteins that transport Cl- across the cell membrane with high selectivity. The chloride transport and selectivity are determined by the hourglass-shaped pore and the filter located in the central and narrow region of the pore. Artificial unimolecular channel that mimics both the shape and function of the ClC selective pore is attractive, because it could provide simple molecular model to probe the intriguing mechanism and structure-function relevance of ClC. Here we elaborated upon the concept of molecular hourglass plus anion-π interactions for this purpose. The concept was validated by experimental results of molecular hourglasses using shape-persistent 1,3-alternate tetraoxacalix[2]arene[2]triazine as the central macrocyclic skeleton to control the conductance and selectivity, and anion-π interactions as the driving force to facilitate the chloride dehydration and movement along the channel.

Illuminating a Solvent-Dependent Hierarchy for Aromatic CH/π Complexes with Dynamic Covalent Glyco-Balances

CH/π interactions are prevalent among aromatic complexes and represent invaluable tools for stabilizing well-defined molecular architectures. Their energy contributions are exceptionally sensitive to various structural and environmental factors, resulting in a context-dependent nature that has led to conflicting findings in the scientific literature. Consequently, a universally accepted hierarchy for aromatic CH/π interactions has remained elusive. Herein, we present a comprehensive experimental investigation of aromatic CH/π complexes, employing a novel approach that involves isotopically labeled glyco-balances generated in situ. This innovative strategy not only allows us to uncover thermodynamic insights but also delves into the often less-accessible domain of kinetic information. Our analyses have yielded more than 180 new free energy values while considering key factors such as solvent properties, the interaction geometry, and the presence and nature of accompanying counterions. Remarkably, the obtained results challenge conventional wisdom regarding the stability order of common aromatic complexes. While it was believed that cationic CH/π interactions held the highest strength, followed by polarized CH/π, nonpolarized CH/π, and finally anionic CH/π interactions, our study reveals that this hierarchy can be subverted depending on the environment. Indeed, the performance of polarized CH/π interactions can match or even outcompete that of cationic CH/π interactions making them a more reliable stabilization strategy across the entire spectrum of solvent polarity. Overall, our results provide valuable guidelines for the selection of optimal interacting partners in every chemical environment, allowing the design of tailored aromatic complexes with applications in supramolecular chemistry, organocatalysis, and/or material sciences.

Reversible Hydrosulfide (HS-) Binding Using Exclusively C-H Hydrogen-Bonding Interactions in Imidazolium Hosts

H2S is a physiologically important signaling molecule with complex roles in biology and exists primarily as HS- at physiological pH. Despite this anionic character, few investigations have focused on the molecular recognition and reversible binding of this important biological anion. Using a series of imidazole and imidazolium host molecules, we investigate the role of preorganization and charge on HS- binding. Using a macrocyclic bis-imidazolium receptor, we demonstrate the unexpected 2:1 host-guest binding of HS-, which was characterized both in solution and by X-ray crystallography. To the best of our knowledge, this is the first example of this binding stoichiometry for HS- binding. Moreover, the short C-H···S distances of 2.53, 2.54, 2.76, and 2.79 Å are well within the sum of the van der Waals radii of the interacting atoms, which is consistent with strong C-H···S interactions.

Arsenate Anion-π Interactions on Amine-Modified Polydivinylbenzene in Aqueous Systems: Experimental and Theoretical Investigation

Anion-π interactions aiding in the adsorption of anions in the solution phase, though challenging to quantify, have attracted a lot of attention in supramolecular chemistry. We present the design of a polymer adsorbent that quantifies the adsorption of arsenate ions experimentally by optimizing anion-π interactions in a purely aqueous system and use density functional theory to compare these results with theoretical data. Arsenate anions are removed from water by amine-functionalized polydivinylbenzene using the comonomer 1-vinyl-1,2,4-triazole, which was cross-linked with divinylbenzene via radical polymerization in a hydrothermal procedure. The amine-functionalized polydivinylbenzene successfully removed arsenate anions from water with a capacity of 46 mg g-1, a 70% increase compared to the nonfunctionalized polydivinylbenzene (27 mg g-1) capacity under the same conditions. Adsorption is best described by the Sips isotherm model with a correlation coefficient R2 factor of 0.99, indicating that adsorption sites are homogeneous, and adsorption occurred by forming a monolayer. Kinetic studies indicated that adsorption is second order in the amine-functionalized polydivinylbenzene. Computational studies using density functional theory showed that the 1-vinyl-1,2,4-triazole comonomer improved the thermodynamic stability of the anionic-π interactions of polydivinylbenzene with arsenate anions. Electrostatic interactions dominate the mechanism of adsorption in polydivinylbenzene compared to the anion-induced interactions that dominate adsorption in amine-functionalized polydivinylbenzene.

Anion Recognition in Solution: Insights from Thermodynamics and Ultrafast Structural Dynamics

Anion recognition through noncovalent interactions stands as an emerging field in supramolecular chemistry, exerting a profound influence on the regulation of biological functions. Herein, the thermodynamics of complexation between sodium cyanate (NaOCN) and calix[4]pyrrole was systematically investigated by linear and nonlinear IR spectroscopy, highlighting enthalpy changes as the dominant driving force. The overall orientational relaxation of bound anion can be described by an Arrhenius-type activated process, yielding an activation energy of 15.0 ± 1.0 kJ mol-1. The structural dynamics of contact ion pairs (CIPs) formed between Na+ and OCN- in solution showed a negligible temperature effect, suggesting entropy changes as the principal governing factor. Further analysis revealed that anion recognition in solution is mediated by conformational changes of the receptor and collective rearrangement of hydrogen bond dynamics. This study, framed within the paradigms of thermodynamics and ultrafast structural dynamics, substantially advances our comprehension of the microscopic mechanisms underlying anion recognition in the realm of supramolecular chemistry.

Anion-π Interactions: What's in the Name?

The studies of the anion-π interactions advanced during the last two decades from the discussion of the mere existence of this counter-intuitive bonding to its utilization for anion recognition and transport, catalysis, and other applications. Yet, there are substantial differences in the interpretation of nature and the driving forces of anion-π bonding. Most surprisingly, there are still different opinions about the meaning of this term (i. e., which associations can be considered anion-π complexes). After a brief overview of the studies in this area (including early examples of such complexes), we suggested that anion-π bonding occurs when there is evidence of a net attraction between a (close-shell) anion and the face of an electrophilic π-system. This definition encompasses fundamentally similar supramolecular complexes comprising diverse π-systems and anions and its general acceptance would facilitate a discussion of the nature and distinct driving forces of this fascinating interaction.

An anomalous anion transfer order in graphene oxide membranes induced by anion-π interactions

Selective transport of anions across membranes has become an important goal in chemistry and biology. Here, we found an anomalous anion transfer order within the graphene oxide membrane: Cl^- > Br^- > F^- > I^-. This is at odds with the conventional ranking of the transfer order, which usually decreases as the radii of the anions increase, i.e., F^- > Cl^- > Br^- > I^-. The abnormal transportation of F^- can be ascribed to the strong anion-π interactions between F^- and graphene oxide sheets. Such unexpectedly strong anion-π interaction resulted in the lower movement of F^- in the graphene oxide membrane and caused the anomalous anion transfer order. Our findings not only provide experimental evidence of anion-π interactions, but also improve our understanding of anion-π interactions in the selective transport of anions across a two-dimensional membrane.

Highly Tunable MOF Luminophores Featuring Anthracene Directed Assembly and Fluorescence Regulation

Metal-organic frameworks (MOFs) have been recognized as a potential platform for the development of tunable luminophores owing to their highly modulable structures and components. Herein, two MOF luminophores based on Cd(II) ions, 1,3,5-tri(4-pyridinyl)benzene (TPB), and 1,4-dicarboxybenzene (H₂BDC) were constructed. The directed assembly of the metal ions and organic linkers results in [Cd₂(BDC)₂(TPB)(H₂O)]·x(solvent) (MOF-1) featuring TPB-based blue fluorescence centered at 425 nm. By introducing anthracene as the structure directing agent (SDA) for assembly regulation, [Cd₂(BDC)(TPB)₂(NO₃)₂]·x(solvent) (MOF-2) was obtained, which reveals anthracene feeding-dependent high tunable emission in the 517-650 nm range. Detailed components, photophysical properties, and structural characteristics investigations of MOF-2 indicate the TPB and NO₃^- interactions as the origin of its redshifted emission compared with that of MOF-1. Furthermore, the fluorescence of MOF-2 was found to be regulatable by the anthracene feeding based on the SDA-determined crystallinity of the crystalline sample. All these results provided a unique example of the structural and fluorescence regulation of MOF luminophores.

Molar-Ratio-Dependent Coordination Assembly of Organoiridium(III)-Octatungstate Complexes in Aqueous Solution

We scrutinized the speciation of Cp*Ir-containing tungsten oxide clusters (Cp* is pentamethylcyclopentadienyl anion) in aqueous mixtures of [(Cp*IrCl)₂(μ-Cl)₂] and Na₂WO₄ in varying molar ratios. ¹H nuclear magnetic resonance (NMR) spectroscopy revealed the formation of three distinct Cp*Ir-polyoxotungstate species in the reaction solution, and they were isolated as Na₄[(Cp*Ir)₂(μ-OH)₃]₂[(Cp*Ir)₂H₂W₈O₃₀] (1), [(Cp*Ir)₂(μ-OH)₃]₂[(Cp*Ir)₂{Cp*Ir(OH₂)}₂H₂W₈O₃₀] (2), and [(Cp*Ir)₂{Cp*Ir(OH₂)}₂{Cp*Ir(OH₂)₂}₂H₂W₈O₃₀](NO₃)₂ (3) from the mixtures in which iridium concentration is less than, equal to, and more than the tungsten concentration, respectively. These results show the octatungstate [H₂W₈O₃₀]^10- anion is the major polyoxotungstate species in the presence of {Cp*Ir}²⁺ cations, and it has high nucleophilicity enough to bind up to six {Cp*Ir}²⁺ cations on its surfaces producing a cationic Cp*Ir-octatungstate complex. The octatungstate anion was also generated from the reaction of [(Cp*IrCl)₂(μ-Cl)₂] and methylammonium paratungstate-B, (CH₃NH₃)₁₀[H₂W₁₂O₄₂], and was isolated as a methylamine-coordinated complex (CH₃NH₃)₂[(Cp*Ir)₂{Cp*Ir(NH₂CH₃)}₂H₂W₈O₃₀] (4), indicating {Cp*Ir}²⁺ cations function as a structure-directing agent that converts tungsten species into octatungstate anions in aqueous solution. In addition, the coordination environment of {Cp*Ir}²⁺ can be further modified by coordination with pyridine forming [{Cp*Ir(NC₅H₅)}₂(μ-OH)₂][(Cp*Ir)₂{Cp*Ir(NC₅H₅)}₂H₂W₈O₃₀] (5).

The nature of π-hole interactions between iodide anions and quinoid rings in the crystalline state

The investigated co-crystal of 3-chloro-N-methylpyridinium iodide with tetrabromoquinone (3-Cl-N-MePy·I·Br4Q) reveals a π-hole interaction between an iodide anion and a quinoid ring involving an n → π* charge transfer. The quinoid ring has a partial negative charge (estimated to be in the range 0.08-0.11e) and a partial radical character, which is related to the black colour of the crystals (crystals of neutral tetrabromoquinone are yellow). A detailed X-ray charge density study revealed two symmetry-independent bond critical points between the iodide anions and carbon atoms of the ring. Their maximum electron density of 0.065 e Å-3 was reproduced by quantum chemical modelling. The energy of the interaction is estimated to be -11.16 kcal mol-1, which is comparable to the strength of moderate hydrogen bonding (about -10 kcal mol-1); it is dominantly electrostatic in nature, with a considerable dispersion component.

The dominant component of strong π-hole interactions: electrostatic attraction versus charge transfer

A long-asked question concerning the dominant component of strong π-hole interactions is addressed.

Anion-π interaction inside the polyanionic Mo132O372 cage with hydrophobic inner space

In this paper, we provide experimental evidence to indicate that the polyanionic Mo₁₃₂O₃₇₂ cage with a hydrophobic inner nanospace has a unique capability to participate in anion-π interactions by showing a preference for electron-deficient mono-substituted benzenes over non-electron-deficient guests in inclusion.

Evaluation of the use of biochar to stabilize polycyclic aromatic hydrocarbons and phthalates in sediment

Three types of biochar (BC) (mulberry biochar (MB), wheat straw biochar, and pine tree sawdust biochar) were prepared and used to stabilize hydrophobic organic compounds (HOCs) in contaminated sediment. The kinetics of HOC adsorption to the BCs had two distinct stages. The second stage adsorption process was longer for MB than the other BCs, presumably because MB contained large pores, mesopores, and micropores. The adsorption isotherms for the three BCs were described well by the Freundlich model. The adsorption capacities of MB, WS and PT for HOCs ranged between 106.7 and 1202 μg/g, 135.1 and 1002 μg/g, and 255.6 and 909 μg/g, respectively. The apparent HOC adsorption coefficients (K_BC-w) for the three BCs were determined from the isotherm data and were similar. The HOC logK_OW values correlated well with the logK_BC-w values. In sediment slurry experiments, HOCs were much more effectively stabilized by MB than wheat straw and pine tree sawdust biochar. This was probably because of the MB pore characteristics that favored adsorption of HOCs of various molecular sizes. The Fourier-transform infrared and Raman spectra indicated that the main binding mechanisms were hydrogen boding, hydrophobic interactions, and π-π interactions. MB was found to be a possible agent for stabilizing HOCs in contaminated sediment. HOCs in sediment slurry continued to become adsorbed to MB for a long time, indicating that relatively long reaction times should be allowed for in situ remediation using MB.

Orientation of carbonyl groups in inclusion crystals formed from ketones with aromatic diimide-based macrocycles

Inclusion crystals were formed from ketones with aromatic diimide-based macrocycles possessing adamantane units, where the oxygen atoms of guests interacted with the electron-deficient π-surfaces of the aromatic diimides through CO⋯π contacts.

[2+3] Amide Cages by Oxidation of [2+3] Imine Cages – Revisiting Molecular Hosts for Highly Efficient Nitrate Binding

The pollution of groundwater with nitrate is a serious issue because nitrate can cause several diseases such as methemoglobinemia or cancer. Therefore, selective removal of nitrate by efficient binding to supramolecular hosts is highly desired. Here we describe how to make [2+3] amide cages in very high to quantitative yields by applying an optimized Pinnick oxidation protocol for the conversion of corresponding imine cages. By NMR titration experiments of the eight different [2+3] amide cages with nitrate, chloride and hydrogen sulfate we identified one cage with an unprecedented high selectivity towards nitrate binding vs. chloride (S=705) or hydrogensulfate (S>13500) in CD₂Cl₂/CD₃CN (1 : 3). NMR experiments as well as single‐crystal structure comparison of host‐guest complexes give insight into structure‐property‐relationships.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

Comparative study of the unbinding process of some HTLV-1 protease inhibitors using unbiased molecular dynamics simulations

The HTLV-1 protease is one of the major antiviral targets to overwhelm this virus. Several research groups have developed protease inhibitors, but none has been successful. In this regard, developing new HTLV-1 protease inhibitors to fix the defects in previous inhibitors may overcome the lack of curative treatment for this oncovirus. Thus, we decided to study the unbinding pathways of the most potent (compound 10, PDB ID 4YDF, Ki = 15 nM) and one of the weakest (compound 9, PDB ID 4YDG, Ki = 7900 nM) protease inhibitors, which are very structurally similar. We conducted 12 successful short and long simulations (totaling 14.8 μs) to unbind the compounds from two monoprotonated (mp) forms of protease using the Supervised Molecular Dynamics (SuMD) without applying any biasing force. The results revealed that Asp32 or Asp32′ in the two forms of mp state similarly exert powerful effects on maintaining both potent and weak inhibitors in the binding pocket of HTLV-1 protease. In the potent inhibitor’s unbinding process, His66′ was a great supporter that was absent in the weak inhibitor’s unbinding pathway. In contrast, in the weak inhibitor’s unbinding process, Trp98/Trp98′ by pi-pi stacking interactions were unfavorable for the stability of the inhibitor in the binding site. In our opinion, these results will assist in designing more potent and effective inhibitors for the HTLV-1 protease.

Solvent and Ionic Atmosphere Effects in Anion-π Interactions: Complexes of Halide Anions with p-Benzoquinones

The interplay between the solvent polarity and ionic atmosphere in anion-π association was evaluated via an experimental and a computational study of the BQ·X^- complexes between benzoquinones (BQ) and halide anions (X^-). The UV-Vis spectral measurements showed that these complexes are characterized by the strong absorption bands in the 300-450 nm range and their effective formation constants, K_eff, measured in dichloromethane in the absence (or at low concentrations) of the supporting electrolyte, Bu₄NPF₆, were higher than those in acetonitrile. The experimental data were consistent with the results of the computations, which showed that magnitudes of the interaction energy, ΔE, between BQ and X^- decreased considerably with the increase in the polarity of the media. The addition of auxiliary electrolytes (e.g., Bu₄NPF₆) led to a decrease in the concentration of the BQ·X^- complexes. These changes were related to the competing associations of the π-acceptors with halides and PF₆^- anions (since the interaction energies between BQ acceptors and common non-halide anions, e.g., PF₆^-, BF₄^-, and NO₃^-, were comparable to those in the BQ·X^- complexes) and to the increased ionic strength of the solutions. The variations in strength of anion-π interactions with the solvent polarity and ionic atmosphere were related to the higher effective ionic radii of the complexes. Due to the larger effects of the auxiliary electrolytes in dichloromethane, the formation constants for the BQ·X^- complexes measured at high ionic strength in this solvent were lower than those in more polar acetonitrile or propylene carbonate. Such a combination of the effects of the solvent and ionic atmosphere should be taken into account when comparing experimental data with the results of the calculations and in design of the systems for molecular recognition and catalysis.

Chemical insights into flexizyme-mediated tRNA acylation

A critical step in repurposing the cellular translation machinery for the synthesis of polymeric products is the acylation of transfer RNA (tRNA) with unnatural monomers. Toward this goal, flexizymes, ribozymes capable of aminoacylation, have emerged as a uniquely adept tool for charging tRNA with ever increasingly diverse substrates. In this review, we present a library of monomer substrates that have been tested for tRNA acylation with the flexizyme system. From this mile-high view, we provide insights for understanding the chemical factors that influence flexizyme-mediated tRNA acylation. We conclude that flexizymes are primitive esterification catalysts that display a modest binding affinity to the monomer's aromatic recognition element. Together, these robust, yet flexible, flexizyme systems provide researchers with unprecedented access for preparing unnatural acyl-tRNA and the opportunity to repurpose the translation machinery for the synthesis of novel biologically derived structures beyond native proteins and peptides.

Cooperative Effect of Noncovalent Interactions on Tetrel Bonding in Halogenated Silanes

Tetrel bond, a weak noncovalent interaction between the  σ -hole of a Group IV element (Silicon in our case) and the cloud of an electronegative element (Oxygen in our case) is the focus of current work. The percentage strengthening of tetrel bond has been investigated by optimising 16 binary complexes of halogenated silane and water of general formula SiX n H 4 - n  - H 2 O and 16 ternary complexes, of general formula NaX - SiX n H 4 - n  -H 2 O, where X =F, Cl, Br and I and n = 1, 2, 3 and 4 at various levels of theory defined within the formalism of density functional theory (DFT). With the addition of NaX, tetrel bond between Si and O in SiX n H 4 - n  - H 2 O gets strengthened up to 49%, owing to cooperativity effect exerted by hydrogen bonding between X and H in the ternary complex NaX - SiX n H 4 - n  - H 2 O. In the series of complexes studied here, overall stabilization due to cooperativity lies between 10 kJ/mol to 170 kJ/mol. This large extent of reinforcement due to cooperativity has never been showcased before. The exceptional stabilization and reinforcement owe its genesis to the transformation of the ternary complex into a cluster orchestrated by the H-bonding in most of the cases and covalent bonding in few of the cases.

Theoretical Study of Macrocyclic Host Molecules: From Supramolecular Recognition to Self-Assembly

Supramolecular chemistry focuses on molecular recognition and self-assembly of various building blocks through weak non-covalent interactions, including anion-π, hydrogen bond (HB), hydrophobic interactions, van der Waals (vdW) interactions, etc, which...

Mining anion-aromatic interactions in the Protein Data Bank

Mutual positioning and non-covalent interactions in anion–aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion–aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A – over the ring, B – over the ring-substituent bonds, and C – roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion–aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion–π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion–π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search.

The comprehensive analysis of non-redundant PDB macromolecular structures investigating anion distributions around all aromatic molecules in available biosystems is presented.

Photochromic Polyoxometalate/Perylenediimide Donor-Acceptor Hybrid Crystals with Interesting Luminescent Properties

The self-assembly of electron-deficient protonated N, N'-dipyridyltetrachloroperylenediimide (4Cl-DPPDI) and electron-rich polyoxometalate acids H_nXM₁₂O₄₀ (POMs; X = P or Si; M = W or Mo) resulted in four isomorphous donor-acceptor hybrid crystals 1-4 with segregated POM anions and one-dimensional racemic hydrogen-bonded 4Cl-DPPDI networks as electron-donor and -acceptor components, respectively. Because of the compact contacts between the POM anions and 4Cl-DPPDI tectons induced by anion-π interactions, besides enhanced photochromism, these four unique isostructural hybrids exhibited unusual room-temperature phosphorescence (RTP) emissions. More interestingly, owing to the facial compact contacts of two racemic 4Cl-DPPDI tectons induced by lone pair-π-assisted π-π interactions, they also showed unprecedented photon upconversion by triplet-triplet annihilation (TTA).

π-Face Promoted Catalysis in Water: From Electron-deficient Molecular Cages to Single Aromatic Slides

Exploiting noncovalent π-interactions particularly emerging anion-π interactions to drive efficient catalysis is fascinating. Even with exciting progresses, can anion-π activation operate in water remains elusive. Here we report the design, synthesis and catalytic studies of a class of water-soluble electron-deficient molecular cages and relevant aromatic slide compounds. The prism-like cages contain three divided, long, cationic aromatic walls which constitute three highly electron-deficient V-shape cavities. They were efficiently synthesized in two steps from a parent triformyl cage in gram-scale. Crystal structure showed the π-walls bind to the counter bromide through strong anion-π interactions. Just 5 mol% of cages were effective in catalyzing decarboxylative Aldol reactions of aldehydes and malonic acid half thioesters in water but not in organic solvents, showing a pronounced hydrophobic amplification effect. Meantime, a series of single π-slides resembling the π-wall of the cage performed equally well, while those lacking an extended π-surface were ineffective, highlighting the essential role of electron-deficient π-face on promoting the conversion.

Being positive is not everything - experimental and computational studies on the selectivity of a self-assembled, multiple redox-state, receptor that binds anions with up to picomolar affinities

The interaction of the self-assembled trinuclear ruthenium bowl 1 3+ , that displays three other accessible oxidation states, with oxo-anions is investigated. Using a combination of NMR and electrochemical experimental data, estimates of the binding affinities of 1 4+ , 1 5+ , and 1 6+ for both halide and oxo-anions were derived. This analysis revealed that, across the range of oxidation states of the host, both high anion binding affinities (>10 9 M -1 for specific guests bound to 1 6+ ) and high selectivities (a range of >10 7 M -1 ) were observed. As the crystal structure of binding of the hexafluorophosphate anion revealed that the host has two potential binding sites (named the α and β pockets), the host-guest properties of both putative binding sites of the bowl, in all of its four oxidation states, were investigated through detailed quantum-based computational studies. These studies revealed that, due to the interplay of electrostatically assisted hydrogen-bonding and anion-π interactions, binding to the α pocket is generally preferred, except for the case of the relatively large and lipophilic hexafluorophosphate anionic guest and the host in the highest oxidation states, where the β pocket becomes relatively favourable. This analysis confirms that host-guest interactions involving structurally complex supramolecular architectures are driven by a combination of non-covalent interactions and, even in the case of charged binding pairs, electrostatics alone cannot accurately define these recognition processes.

Putting Anion-π Interactions at Work for Catalysis

Since its discovery two decades ago, anion-π interaction has been increasingly recognized as an important driving force. Extensive theoretical and experimental efforts on the ground-state anion-π binding and recognition have laid the bases for exploring its relevance in catalysis. Accordingly, the concept of "anion-π catalysis" that employing an electron-deficient π surface (π-acidic surface) for anionic reaction intermediate and transition state stabilization has emerged. This article shortly reviews the emergence and development of this concept, aiming to provide an emphasis on the general concept and key progress in this exciting area. To highlight the essential contribution of anion-π interactions, the contents are organized according to their role engaged in catalytic process, for example from both ground-state and transition-state stabilization to solely transition-state stabilization, mainly by a single π-face, and to cooperative π-face activation. A concluding remark and outlook on future development of this field is also given.

Cation-chloride cotransport mediated by an ion pair transporter

Ion transport mediated by an ion pair receptor 1 bearing both cation and anion binding sites is presented. The ion pair binding property was revealed by means of ¹H NMR titrations in organic solutions and X-ray analysis in the solid state. Single crystal structures demonstrated that 1 and CaI₂ formed a solvent-separated ion-pair complex with two iodides each interacting with a triazine ring through anion-π interactions, whereas the calcium ion is bound by a pentaethylene glycol moiety. The ion transport activity was studied by monitoring the efflux of ions from salt-loaded EYPC large unilamellar vesicles (EYPC-LUVs) using ion selective electrodes. Chloride transport across the membrane mediated by the ion pair receptor through K⁺/Cl^- or Na⁺/Cl^- cotransport with a selectivity towards the K⁺/Cl^- symport was realized.

Exploiting Anion-π Interactions for Efficient and Selective Catalysis with Chiral Molecular Cages

Exploiting anion-π interactions in catalyst design is a fascinating direction to develop new and fundamental catalysis. For the appealing yet flexible π-face activation, can two or more π-acidic surfaces be manipulated for cooperative activation to achieve efficient transformation and particularly selectivity control is highly desirable. Here, we demonstrate a supramolecular π-catalysis strategy by establishing cooperative π-face activation in a confined electron-deficient cage cavity. The catalysts have a triazine based prism-like cage core and pendant chiral base sites. Only 2 mol % of cage catalyst efficiently catalyzed the decarboxylate Mannich reactions of sulfamate-headed cyclic aldimines and a series of malonic acid half thioesters in nearly quantitative yields and up to 97 % ee, enabling an unprecedent organocatalytic approach. The supramolecular π-cavity is essential in harnessing cooperative anion-π interactions for the efficient activation and excellent selectivity control.

The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane

The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.

Exploring the structure-property schemes in anion-π systems of d-block metalates

Anion-π based compounds, materials, and processes have gained significant interest due to the diversity of their aesthetic non-covalent synthons, and thanks to their significance in biological systems, catalytic processes, anion binding and sensing, or the supramolecular organization of hierarchical architectures. While systems based on typical inorganic anions or organic residues have been widely reviewed in recent years, those involving anionic d metal comlexes as the main components have been treated with a rather secondary interest. However, actively exploring the new systems of the latter type we have recognized systematic advances in the field. As a result, in the current review we describe the landscape that has recently emerged. Focusing on the established groups of π-acidic species, i.e. polycarbonitirles, polyazines, polyazine N-oxides, diimide derivatives, fluoroarenes, and nitroarenes, we explore and discuss anion-π crystal engineering together with the structure-property schemes important from the standpoint of charge transfer (CT) and electron transfer (ET), magnetism, luminescence, reactivity and catalysis, and the construction of core-shell crystalline composites.

Anion binding properties of a hollow PdL-cage

The hollow [PdL][BArF]2 complex 1 of a tetra-pyridyl (py) ligand (L) has a [Pd(py)4]2+ coordination environment. Addition of coordinating anions resulted in the formation of a neutral species with Pd(py)2(anion)2 coordination environment (12A). These species bind further to the coordinating anions in the order Cl- > N3- > Br- > I- > AcO- with Ka1 : 1 ≤ 414 M-1. With relatively non-coordinating anions 1 remains intact and displays 1 : 2 binding behaviour dominated by the 1 : 1 stoichiometry in the order NO3- (∼105 M-1) » ClO4- and BF4- (∼103 M-1). As evidenced by crystal structure data, DFT calculations and {1H-19F}-HOESY NMR with BF4-, the anions are bound by charge assisted [C-H]+···anion interactions.