The cation-π interaction

AncPhore: A versatile tool for anchor pharmacophore steered drug discovery with applications in discovery of new inhibitors targeting metallo-β-lactamases and indoleamine/tryptophan 2,3-dioxygenases

We herein describe AncPhore, a versatile tool for drug discovery, which is characterized by pharmacophore feature analysis and anchor pharmacophore (i.e., most important pharmacophore features) steered molecular fitting and virtual screening. Comparative analyses of numerous protein–ligand complexes using AncPhore revealed that anchor pharmacophore features are biologically important, commonly associated with protein conservative characteristics, and have significant contributions to the binding affinity. Performance evaluation of AncPhore showed that it had substantially improved prediction ability on different types of target proteins including metalloenzymes by considering the specific contributions and diversity of anchor pharmacophore features. To demonstrate the practicability of AncPhore, we screened commercially available chemical compounds and discovered a set of structurally diverse inhibitors for clinically relevant metallo-β-lactamases (MBLs); of them, 4 and 6 manifested potent inhibitory activity to VIM-2, NDM-1 and IMP-1 MBLs. Crystallographic analyses of VIM-2:4 complex revealed the precise inhibition mode of 4 with VIM-2, highly consistent with the defined anchor pharmacophore features. Besides, we also identified new hit compounds by using AncPhore for indoleamine/tryptophan 2,3-dioxygenases (IDO/TDO), another class of clinically relevant metalloenzymes. This work reveals anchor pharmacophore as a valuable concept for target-centered drug discovery and illustrates the potential of AncPhore to efficiently identify new inhibitors for different types of protein targets.

Regio- and diastereoselective Pd-catalyzed aminochlorocyclization of allylic carbamates: scope, derivatization, and mechanism

The regio- and diastereoselective synthesis of oxazolidinones via a Pd-catalyzed vicinal C-N/C-Cl bond-forming reaction from internal alkenes of allylic carbamates is reported. The oxazolidinones are obtained in yields of 44 to 95% with high to excellent diastereoselectivities (from 6 : 1 to >20 : 1 dr) from readily available precursors. This process is scalable, and the products are suitable for the synthesis of useful amino alcohols. A detailed theoretical and experimental mechanistic study was carried out to describe that the reaction proceeds through an anti-aminopalladation of the alkene followed by an oxidative C-Pd(ii) cleavage with retention of the carbon stereochemistry to yield the major diastereomer. The role of Cu(ii) in a C-Cl bond-forming mechanism step has also been proposed.

Unveiling Polymerization Mechanism in pH-regulated Supramolecular Fibers in Aqueous Media

An amine functionalized C₃‐symmetric benzotrithiophene (BTT) monomer has been designed and synthetized in order to form pH responsive one‐dimensional supramolecular polymers in aqueous media. While most of the reported studies looked at the effect of pH on the size of the aggregates, herein, a detailed mechanistic study is reported, carried out upon modifying the pH to trigger the formation of positively charged ammonium groups. A dramatic and reversible change in the polymerization mechanism and size of the supramolecular fibers is observed and ascribed to the combination of Coulombic repulsive forces and higher monomer solubility. Furthermore, the induced frustrated growth of the fibers is further employed to finely control the one‐dimensional supramolecular polymerisation and copolymerization processes.

Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues

Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ₁, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.

Sulfuroxygen interaction-controlled (Z)-selective anti-Markovnikov vinyl sulfides

The sulfur oxygen (SO) interaction was used herein to obtain (Z)-selective anti-Markovnikov vinyl sulfides from the addition of thiyl radicals to terminal alkynes. DFT calculations predicted that SO interaction originated from the delocalization of the lone-pair of the carbonyl oxygen to the adjacent σ* orbital of the S atom of C-S.

Prospects of ultraviolet resonance Raman spectroscopy in supramolecular chemistry on proteins

Ultraviolet resonance Raman scattering (UVRR) has been frequently used for studying peptide and protein structure and dynamics, while applications in supramolecular chemistry are quite rare. Since UVRR offers the additional advantages of chromophore selectivity and high sensitivity compared with conventional non-resonant Raman scattering, it is ideally suited for label-free probing of relatively small artificial/supramolecular ligands exhibiting electronic resonances in the UV. In this perspective article, we first summarize results of UVRR spectroscopy in supramolecular chemistry in the context of peptide/protein recognition. We focus on selected artificial ligands which were rationally designed as selective carboxylate binders (guanidiniocarbonyl pyrrole, GCP, and guanidiniocarbonyl indole, GCI) and selective lysine binder (molecular tweezer, CLR01), respectively, via a combination of non-covalent interactions involving electrostatics, hydrogen bonding, and hydrophobic effects/van der Waals forces. Current limitations of applying UVRR as a universally applicable method for label-free and site-specific probing of molecular recognition between supramolecular ligands and proteins are highlighted. We then propose solutions to overcome these limitations for transforming UVRR spectroscopy into a generic tool in supramolecular chemistry on proteins, with an emphasis on mono- and multivalent GCP- and GCI-based ligands. Finally, we outline specific cases of supramolecular ligands such as molecular tweezers where alternative approaches such as laser-based mid-IR spectroscopy are required since UVRR can intrinsically not provide the required molecular information.

(Z)-Selective Hydrosilylation and Hydroboration of Terminal Alkynes Enabled by Ruthenium Complexes with an N-Heterocyclic Carbene Ligand

Metal-catalyzed trans-1,2-hydrosilylations and hydroborations of terminal alkynes that generate synthetically valuable (Z)-alkenylsilanes and (Z)-alkenylboranes remain challenging due to the (E)-selective nature of the reactions and the formation of the thermodynamically unfavorable (Z)-isomer. The development of new, efficient catalytic systems for the (Z)-selective hydrosilylation and hydroboration of terminal alkynes is thus highly desirable from a fundamental perspective as it would deepen our understanding of the metal-catalyzed (Z)-selective hydrosilylation and hydroboration of terminal alkynes. This personal account describes our research for developing a ruthenium complex that can efficiently catalyze the hydrosilylation and hydroboration of terminal alkynes, and for exploring the factors controlling (Z)-selectivity of the reactions. Our effort into the activation of B-protected boronic acids, R-B(dan) (dan=naphthalene-1,8-diaminato), that was believed not to participate in Suzuki-Miyaura cross-coupling, is also discussed.

Selectivity and efficiency of electromembrane extraction of polar bases with different liquid membranes-Link to analyte properties

In the present fundamental study, selectivity and efficiency of electromembrane extraction of 50 polar basic substances (-6.7 < log P < +1.0) was systematically studied for ten different supported liquid membranes. For each model substance, 23 molecular descriptors were collected and these were investigated as potential parameters for understanding of extraction efficiency and selectivity by means of partial least squares regression. Overall, a highly aromatic deep eutectic solvent composed of coumarin and thymol with addition of 2% ionic carrier (di(2-ethylhexyl) phosphate) provided the highest extraction efficiency with an average extraction yield of 69% from pure water samples, 55% from plasma, and 62% from urine. With this solvent system, ionic, cation-π, and π-π interactions between the supported liquid membrane and analytes were dominant. Supported liquid membranes without aromaticity, however, operated primarily based on hydrogen-bonding interactions. This is the first time the relationship between analyte properties, solvent composition, and extraction yield has systematically been studied for polar bases in electromembrane extraction. This new knowledge represents a first step toward enabling future development and optimization of electromembrane extraction systems for polar bases based on rational design, rather than trial-and-error approaches.

Coordination of Redox Ions within a Membrane-Binding Peptide: A Tale of Aromatic Rings

The amino-terminal-copper-and-nickel-binding (ATCUN) motif, a tripeptide sequence ending with a histidine, confers important functions to proteins and peptides. Few high-resolution studies have been performed on the ATCUN motifs of membrane-associated proteins and peptides, limiting our understanding of how they stabilize Cu²⁺/Ni²⁺ in membranes. Here, we leverage solid-state NMR to investigate metal-binding to piscidin-1 (P1), a host-defense peptide featuring F1F2H3 as its ATCUN motif. Bound to redox ions, P1 chemically and physically damages pathogenic cell membranes. We design ¹³C/¹⁵N correlation experiments to detect and assign the deprotonated nitrogens produced and/or shifted by Ni²⁺-binding. Occupying multiple chemical states in P1-apo, H3 and the neighboring H4 respond to metalation by populating only the τ-tautomer. H3, as a proximal histidine, directly coordinates the metal, compared to the distal H4. Density functional theory calculations reflect this noncanonical arrangement and point toward cation-π interactions between the F1/F2/H4 aromatic rings and metal. These structural findings, which are relevant to other ATCUN-containing membrane peptides, could help design new therapeutics and materials for use in the areas of drug-resistant bacteria, neurological disorders, and biomedical imaging.

Anion-π interaction at the solid/water interfaces

Anion-π interaction has been found to play a key role in interfacial phenomena. In this study, we evaluated the anion-π interactions at the solid/water interface. Anion adsorption originating from anion-π interaction at the interfaces followed the hydration energy and the presence of conjugated systems of the anions by the QCM measurements. Force curve measurements revealed that the single-molecule force of anion-π interaction between an NDI unit and the negatively charged surface of the cantilever was ∼40 pN. To the best of our knowledge, this is the first example of obtaining a single-molecule force for anion-π interactions.

Large-scale visualization of the dispersion of liquid-exfoliated two-dimensional nanosheets

An ultrafast, non-invasive and large-scale visualization method has been developed to evaluate the dispersion of two-dimensional nanosheets in aqueous solution with a fluorescence microscope by the formation of excimers from the improvement of cation-π interactions.

Host-guest binding in water, salty water, and biofluids: general lessons for synthetic, bio-targeted molecular recognition

Synthetic molecular recognition systems are increasingly being used to solve applied problems in the life sciences, and bio-targeted host-guest chemistry has rapidly arisen as a major field of fundamental research. This tutorial review presents a set of fundamental lessons on how host-guest molecular recognition can be programmed in water. The review uses informative examples of aqueous host-guest chemistry organized around generalizable themes and lessons, building towards lessons focused on molecular recognition in salty solutions and biological fluids. It includes selected examples of macrocyclic host systems that work well, as well as common pitfalls and how to avoid them. The review closes with a survey of the most important and inspirational recent advances, which involve host-guest chemistry in living cells and organisms.

Revealing the Dynamic Process of Ion Pair Recognition by Calix[4]pyrrole: A Case Study of Cesium Chloride

Ion pair receptors based on meso-octamethylcalix[4]pyrrole (CP) have been extensively investigated over recent years. However, the nature of their ion pair recognition has barely been reported, even for CP itself. Herein, cesium chloride was used as a guest ion pair to investigate the dynamic process of ion pair recognition by CP, and the "capture-bind" mechanism for this process is proposed for the first time. The results reveal that Cs⁺ can be first captured by Cl^- at long distances, and then it is bound to the cavity through almost equal contributions of Cl^- and CP. Although the effective charge of Cl^- is obviously reduced by charge-transfer, the electrostatic interactions between Cl^- and Cs⁺ are still strong even at long distances in the presence of CP.

Removal of Cd from aqueous solution by chitosan coated MgO-biochar and its in-situ remediation of Cd-contaminated soil

In this study, magnesium oxide biochar-chitosan composite (MgO-BCR-W) prepared through modification with MgCl₂ and chitosan was investigated as an adsorbent for the removal of Cd from the aquatic and soil environment. Kinetic and thermodynamics revealed that the Cd(II) adsorption onto MgO-BCR-W was well fitted by pseudo-second-order and the Langmuir adsorption isotherm. The adsorption capacities of rice husk biochar (BCR) and MgO-BCR-W for Cd(II) reached 11.09 mg/g and 59.66 mg/g, respectively. Attractively, the computed values of R_L ranged between 0 and 1, suggesting that the adsorption of Cd(II) onto MgO-BCR-W is favourable. Characterisations of the adsorbents revealed that the synergistic effect of surface complexation and precipitation mechanisms played a major role in the removal of Cd. In soil incubation experiment, the addition of MgO-BCR-W at the level of 2% was most effective in Cd stabilization compared to the control, which reduced the content of bioavailable Cd by 22.32%. Furthermore, it reduced the acid extractable Cd by 24.77%, while increased the residual Cd content by 22.24%. The results demonstrated that MgO-BCR-W could be used as an effective and eco-friendly adsorbent for Cd remediation in both water and soil environment.

Glycine rich segments adopt polyproline II helices: Implications for biomolecular condensate formation

Many intrinsically disordered proteins contain Gly-rich regions which are generally assumed to be disordered. Such regions often form biomolecular condensates which play essential roles in organizing cellular processes. However, the bases of their formation and stability are still not completely understood. Based on NMR studies of the Gly-rich H. harveyi "snow flea" antifreeze protein, we recently proposed that Gly-rich sequences, such as the third "RGG" region of Fused in Sarcoma (FUS) protein, may adopt polyproline II helices whose association might stabilize condensates. Here, this hypothesis is tested with a polypeptide corresponding to the third RGG region of FUS. NMR spectroscopy and molecular dynamics simulations suggest that significant populations of polyproline II helix are present. These findings are corroborated in a model peptide Ac-RGGYGGRGGWGGRGGY-NH₂, where a peak characteristic of polyproline II helix is observed using CD spectroscopy. Its intensity suggests a polyproline II population of 40%. This result is supported by data from FTIR and NMR spectroscopies. In the latter, NOE correlations are observed between the Tyr and Arg, and Arg and Trp side chain hydrogens, confirming that side chains spaced three residues apart are close in space. Taken together, the data are consistent with a polyproline II helix, which is bent to optimize interactions between guanidinium and aromatic moieties, in equilibrium with a statistical coil ensemble. These results lend credence to the hypothesis that Gly-rich segments of disordered proteins may form polyproline II helices which help stabilize biomolecular condensates.

NADES-based surfactant-free microemulsions for solubilization and extraction of curcumin from Curcuma Longa

A choline chloride + lactic acid (1:1) natural deep eutectic solvent (NADES) is used as an adjuvant to ethanol/triacetin mixtures to solubilize and extract curcumin from Curcuma Longa. The obtained NADES/ethanol/triacetin mixtures are homogeneous, transparent and of low viscosity even in the absence of water. Dynamic light scattering revealed significant nanostructures, typical of surfactant-free microemulsions. A twofold increase of curcumin solubility and remarkable extraction power (yield of ~90%) can be achieved in the ternary system including the NADES, although curcumin is hydrophobic and the used NADES are very polar. Due to the elevated solubility of curcumin, more extraction cycles can be made than in the previously published aqueous systems with the same amount of solution. As a result, less solvent is required to achieve the same extraction yield.

Discovery of Novel Cyclic Salt Bridge in Thermophilic Bacterial Protease and Study of its Sequence and Structure

The plausible explanation behind the stability of thermophilic protein is still yet to be defined more clearly. Here, an in silico study has been undertaken by investigating the sequence and structure of protease from thermophilic (tPro) bacteria and mesophilic (mPro) bacteria. Results showed that charged and uncharged polar residues have higher abundance in tPro. In extreme environment, the tPro is stabilized by high number of isolated and network salt bridges. A novel cyclic salt bridge is also found in a structure of tPro. High number of metal ion-binding site also helps in protein stabilization of thermophilic protease. Aromatic-aromatic interactions also play a crucial role in tPro stabilization. Formation of long network aromatic-aromatic interactions also first time reported here. Finally, the present study provides a major insight with a newly identified cyclic salt bridge in the stability of the enzyme, which may be helpful for protein engineering. It is also used in industrial applications for human welfare.

Unprecedented Role of the N73-F124 Pair in the Staphylococcus equorum MnSOD Activity

Background:

Bacterial manganese superoxide dismutase (MnSOD) occurs as a dimer, which is responsible for its activity and stability. Therefore, increasing the dimeric strength would increase the stability of the enzyme while maintaining its activity.

Objective:

An N73F substitution was introduced to strengthen interactions between the monomers at the dimer interface. This substitution would introduce a π-stacking interaction between F73 of one monomer to F124 from the other monomers.

Methods:

Site-directed mutagenesis was carried out to substitute N73 with phenylalanine. The activity of the mutant was qualitative- and quantitatively checked while the stability was evaluated with a fluorescence- based thermal-shift assay. Finally, the structure of the mutant was elucidated by means of Xray crystallography.

Results:

The N73F mutant activity was only ~40% of the wild type. The N73F mutant showed one TM at 60+1°C while the wild type has two (at 52-55°C and 63-67°C). The crystal structure of the mutant showed the interactions between F73 from one monomer to F124 from the other monomer. The N73F structure presents an enigma because of no change in the enzyme structure including the active site. Furthermore, N73 and F124 position and interaction are conserved in human MnSOD but with a different location in the amino acid sequence. N73 has a role in the enzyme activity, likely related to its interaction with F124, which resides in the active site region but has not been considered to participate in the reaction.

Conclusion:

The N73F substitution has revealed the unprecedented role of the N73-F124 pair in the enzyme activity.

Syntheses and solid-state structures of two cofacial (bis)dipyrrin dichromium complexes in different charge states

The dichromium Pacman complex (^tBudmx)Cr₂Cl₂·C₄H₁₀O (1) [(^tBudmx)H₂ is a dimethylxanthene-bridged cofacial (bis)dipyrrin, C₄₉H₅₈N₄O] was synthesized by salt metathesis using anhydrous CrCl₂ and previously reported (^tBudmx)K₂. Treatment of 1 with two equivalents of the reductant potassium graphite afforded K₂(^tBudmx)Cr₂Cl₂(thf)₃·0.5C₄H₁₀O·0.5C₄H₈O (thf is tetrahydrofuran, C₄H₈O) (2), with both potassium ions intercalated between the pyrrolic subunits. Comparison of the solid-state structures for 1 and 2 reveals minimal changes in the primary coordination sphere of each Cr ion, with notable elongation of the dipyrrin C-C and C-N bonds upon reduction, consistent with computational support for a ligand-based reduction.

Spectroscopic Signatures and the Cation-π Interaction in Conformational Preferences of the Neurotransmitter Dopamine in Aqueous Solution

The precise determination of the neurotransmitter dopamine's conformational preferences in aqueous solution is crucial for understanding its neurobiological function. The first principle Møller-Plesset perturbation theory (MP2) and dispersion corrected density functional theory (DFT-D3) methods, employing the basis set aug-cc-pVDZ(/pVTZ), are used to reinvestigate the nine lowest-energy (isolated) structures of protonated dopamine (DAH⁺) in both gas and aqueous phases. DAH⁺ trans isomer t₁ is found higher in energy than lowest-energy gauche isomer g⁺¹ (g + 1) by 6.4 and 5.7 kJ mol^-1, at the MP2 and B3LYP-D3 levels of theory, respectively, in the aqueous environment within the polarizable continuum model (PCM). We found that the solvated cation, NH₃⁺, retains its attractive character, which supports the previous report that agonist DAH⁺ can be involved in cation (NH₃⁺)-π interaction in the active states of the D2 dopamine receptor. The dispersion corrected DFT evaluation of anharmonicity allows us to confirm the most experimental frequencies and suggest some new interpretations. The IR and Raman spectra's influential band for both gauche and the trans conformers observed at 1287/1288 cm^-1 were enhanced in aqueous solution. The experimental Raman spectrum for dopamine was compared with the conformer-specific computed Raman spectrum of protonated dopamine (DAH⁺). The intense Raman band at 1451 cm^-1 indicates the necessity of DAH⁺ calculated values in interpreting the Raman spectra. The most intense Raman band at 750 cm^-1 arises due to the trans DAH⁺, t₁, revealed by MP2/aug-cc-pVDZ Raman spectra, indicating trans DAH⁺ dominance in the bulk DAH⁺ of extracellular fluid.

Conserved amino acids in the region connecting membrane spanning domain 1 to nucleotide binding domain 1 are essential for expression of the MRP1 (ABCC1) transporter

Multidrug resistance protein 1 (MRP1) (gene symbol ABCC1) is an ATP-binding cassette (ABC) transporter which effluxes xeno- and endobiotic organic anions including estradiol glucuronide and the pro-inflammatory leukotriene C₄. MRP1 also confers multidrug resistance by reducing intracellular drug accumulation through active efflux. MRP1 has three membrane spanning domains (MSD), and two nucleotide binding domains (NBD). MSD1 and MSD2 are linked to NBD1 and NBD2 by connecting regions (CR) 1 and CR2, respectively. Here we targeted four residues in CR1 (Ser⁶¹², Arg⁶¹⁵, His⁶²², Glu⁶²⁴) for alanine substitution and unexpectedly, found that cellular levels of three mutants (S612A, R615A, E624A) in transfected HEK cells were substantially lower than wild-type MRP1. Whereas CR1-H622A properly trafficked to the plasma membrane and exhibited organic anion transport activity comparable to wild-type MRP1, the poorly expressing R615A and E624A (and to a lesser extent S612A) mutant proteins were retained intracellularly. Analyses of cryogenic electron microscopic and atomic homology models of MRP1 indicated that Arg⁶¹⁵ and Glu⁶²⁴ might participate in bonding interactions with nearby residues to stabilize expression of the transporter. However, this was not supported by double exchange mutations E624K/K406E, R615D/D430R and R615F/F619R which failed to improve MRP1 levels. Nevertheless, these experiments revealed that the highly conserved CR1-Phe⁶¹⁹ and distal Lys⁴⁰⁶ in the first cytoplasmic loop of MSD1 are also essential for expression of MRP1 protein. This study is the first to demonstrate that CR1 contains several highly conserved residues critical for plasma membrane expression of MRP1 but thus far, currently available structures and models do not provide any insights into the underlying mechanism(s). Additional structures with rigorous biochemical validation data are needed to fully understand the bonding interactions critical to stable expression of this clinically important ABC transporter.

Double Orthogonal Click Reactions for the Development of Antimicrobial Peptide Nanotubes

A new class of amphipathic cyclic peptides, which assemble in bacteria membranes to form polymeric supramolecular nanotubes giving them antimicrobial properties, is described. The method is based on the use of two orthogonal clickable transformations to incorporate different hydrophobic or hydrophilic moieties in a simple, regioselective, and divergent manner. The resulting cationic amphipathic cyclic peptides described in this article exhibit strong antimicrobial properties with a broad therapeutic window. Our studies suggest that the active form is the nanotube resulted from the parallel stacking of the cyclic peptide precursors. Several techniques, CD, FTIR, fluorescence, and STEM, among others, confirm the nanotube formation.

Distinct Tetracyanoquinodimethane Derivatives: Enhanced Fluorescence in Solutions and Unprecedented Cation Recognition in the Solid State

Tetracyanoquinodimethane (TCNQ) is known to react with various amines to generate substituted TCNQ derivatives with remarkable optical and nonlinear optical characteristics. The choice of amine plays a crucial role in the outcome of molecular material attributes. Especially, mono/di-substituted TCNQ's possessing strong fluorescence in solutions than solids are deficient. Furthermore, cation recognition in the solid-state TCNQ derivatives is yet undetermined. In this article, we present solution-enhanced fluorescence and exclusive solid-state recognition of K⁺ ion achieved through the selection of 4-(4-aminophenyl)morpholin-3-one (APM) having considerable π-conjugation and carbonyl (C=O) functionality, particularly in the ring. TCNQ when reacted with APM, in a single-step reaction, resulted in two well-defined distinct compounds, namely, 7,7-bis(4-(4-aminophenyl)morpholin-3-ono)dicyanoquinodimethane (BAPMDQ [1], yellow) and 7,7,8-(4-(4-aminophenyl)morpholin-3-ono)tricyanoquinodimethane (APMTQ [2], red), with increased fluorescence intensity in solutions than their solids. Crystal structure investigation revealed extensive C-H-π interactions and strong H-bonding in [1], whereas moderate to weak interactions in [2]. Surprisingly, simple mechanical grinding during KBr pellet preparation with [1, 2] triggered unidentified cation recognition with a profound color change (in ∼1 min) detected by the naked eye, accompanied by a drastic enhancement of fluorescence, proposed due to the presence of carbonyl functionality, noncovalent intermolecular interactions, and molecular assemblies in [1, 2] solids. Cation recognition was also noted with various other salts as well (KCl, KI, KSCN, NH₄Cl, NH₄Br, etc.). Currently, the recognition mechanism of K⁺ ion in [1, 2] is demonstrated by the strong electrostatic interaction of K⁺ ion with CO and simultaneously cation-π interaction of K⁺ with the phenyl ring of APM, supported by experimental and computational studies. Computational analysis also revealed that a strong cation-π interaction occurred between the K⁺ ion and the phenyl ring (APM) in [2] than in [1] (ΔG _binding calculated as ∼16.3 and ∼25.2 kcal mol^-1 for [1] and [2], respectively) providing additional binding free energy. Thus, both electrostatic and cation-π interactions lead to the recognition. Scanning electron microscopy of drop-cast films showed microcrystalline "roses" in [1] and micro/nano "aggregates" in [2]. Optical band gap (∼3.565 eV) indicated [1, 2] as wide-band-gap materials. The current study demonstrates fascinating novel products obtained by single-pot reaction, resulting in contrasting optical properties in solutions and experiencing cation recognition capability exclusively in the solid state.

Anode carbonaceous material recovered from spent lithium-ion batteries in electric vehicles for environmental application

Recycling opportunities for graphitic carbon from lithium-ion battery (LIB) anodes have been neglected owing to the relative low value of application. In this study, the potential methods for removing toxic metals (lead, barium, and cadmium) and organic compounds (2,4-dinitrotoluene [DNT], 2,4,6-trinitrotoluene [TNT], hexahydro-1,3,5-trinitro-1,3,5-triazine [RDX], and 2,4-dichlorophenol [DCP]) with anode carbonaceous material (ACM) obtained from the anodes of spent LIBs were evaluated. The sorption ability of ACM for lead is higher (the maximal sorption capacity is 43.5 mg/g) than for barium and cadmium. Similarly, the maximal sorption capacity of ACM for DCP is 6.5 mg/g, which is higher than those for TNT and DNT (2.6 and 2.3 mg/L, respectively). As a catalyst, ACM significantly enhances oxidation by persulfate with zero-valent iron and reduction by dithiothreitol (DTT) and hydrogen sulfides for nitro compounds. In addition, the graphitic properties enhance the redox reactions. The results suggest that ACM from spent LIBs may be an effective sorbent and catalyst in redox processes for the remediation of contaminated water and soil.

A novel modified method for the efficient removal of Pb and Cd from wastewater by biochar: Enhanced the ion exchange and precipitation capacity

The purpose of this research was to improve the sorption ability of Pb and Cd by promoting the ion exchange and precipitation capacity of biochar. The adsorption performance and mechanisms of Pb and Cd in wastewater using coconut shell biochar modified with magnesium were investigated. After modification, the total adsorption capacity (Q_t) of Pb and Cd on Mg-coated biochar (MgBC400) increased by 20 and 30 times compared with the unmodified biochar (BC400), respectively. The removal of Pb and Cd to biochar was attributed to ion exchange (Q_e), mineral precipitation (Q_p), interaction with oxygen functional groups (OFGs) [(Q_f)], and metal-π electron coordination (Q_π). Compared with the BC400, the adsorption capacity of the four fractions of MgBC400 increased especially the ion exchange and precipitation. The Q_e values of MgBC400 were almost 49 and 59 times that of BC400 in the adsorption of Pb and Cd, respectively. The Q_p values of MgBC400 increased by 214.4 and 81.7 mg/g, respectively. Ion exchange and mineral precipitation dominated the adsorption of Pb and Cd by MgBC400.

Underappreciated Chemical Interactions in Protein-Ligand Complexes

Non-covalent interactions lie at the bases of the molecular recognition process. In medicinal chemistry, understanding how bioactive molecules interact with their target can help to explain structure-activity relationships (SAR) and improve potency of lead compounds. In particular, computational analysis of protein-ligand complexes can help to unravel key interactions and guide structure-based drug design.The literature describing protein-ligand complexes is typically focused on few types of non-covalent interactions (e.g., hydrophobic contacts, hydrogen bonds, and salt bridges). Stacking interactions involving aromatic rings are also relatively well known to medicinal chemistry practitioners. Potency optimization efforts are often focused on targeting these interactions. However, a variety of underappreciated interactions were shown to have a relevant effect on the stabilization of protein-ligand complexes. This chapter aims at listing selected non-covalent interactions and discuss some examples on how they can impact drug design.

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

G-protein-coupled receptors (GPCRs) have enormous physiological and biomedical importance, and therefore it is not surprising that they are the targets of many prescribed drugs. Further progress in GPCR drug discovery is highly dependent on the availability of protein structural information. However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum mechanics (QM) approaches are often too computationally expensive to be of practical use in time-sensitive situations, but the fragment molecular orbital (FMO) method offers an excellent solution that combines accuracy, speed, and the ability to reveal key interactions that would otherwise be hard to detect. Integration of GPCR crystallography or homology modelling with FMO reveals atomistic details of the individual contributions of each residue and water molecule toward ligand binding, including an analysis of their chemical nature. Such information is essential for an efficient structure-based drug design (SBDD) process. In this chapter, we describe how to use FMO in the characterization of GPCR-ligand interactions.

Molecular Recognition in Water Using Macrocyclic Synthetic Receptors

Molecular recognition in water using macrocyclic synthetic receptors constitutes a vibrant and timely research area of supramolecular chemistry. Pioneering examples on the topic date back to the 1980s. The investigated model systems and the results derived from them are key for furthering our understanding of the remarkable properties exhibited by proteins: high binding affinity, superior binding selectivity, and extreme catalytic performance. Dissecting the different effects contributing to the proteins' properties is severely limited owing to its complex nature. Molecular recognition in water is also involved in other appreciated areas such as self-assembly, drug discovery, and supramolecular catalysis. The development of all these research areas entails a deep understanding of the molecular recognition events occurring in aqueous media. In this review, we cover the past three decades of molecular recognition studies of neutral and charged, polar and nonpolar organic substrates and ions using selected artificial receptors soluble in water. We briefly discuss the intermolecular forces involved in the reversible binding of the substrates, as well as the hydrophobic and Hofmeister effects operating in aqueous solution. We examine, from an interdisciplinary perspective, the design and development of effective water-soluble synthetic receptors based on cyclic, oligo-cyclic, and concave-shaped architectures. We also include selected examples of self-assembled water-soluble synthetic receptors. The catalytic performance of some of the presented receptors is also described. The latter process also deals with molecular recognition and energetic stabilization, but instead of binding ground-state species, the targets become elusive counterparts: transition states and other high-energy intermediates.

Evaluation of aromatic amino acids as potential biomarkers in breast cancer by Raman spectroscopy analysis

The scope of the work undertaken in this paper was to explore the feasibility and reliability of using the Raman signature of aromatic amino acids as a marker in the detection of the presence of breast cancer and perhaps, even the prediction of cancer development in very early stages of cancer onset. To be able to assess this hypothesis, we collected most recent and relevant literature in which Raman spectroscopy was used as an analytical tool in the evaluation of breast cell lines and breast tissue, re-analyzed all the Raman spectra, and extracted all spectral bands from each spectrum that were indicative of aromatic amino acids. The criteria for the consideration of the various papers for this study, and hence, the inclusion of the data that they contained were two-fold: (1) The papers had to focus on the characterization of breast tissue with Raman spectroscopy, and (2) the spectra provided within these papers included the spectral range of 500-1200 cm-1, which constitutes the characteristic region for aromatic amino acid vibrational modes. After all the papers that satisfied these criteria were collected, the relevant spectra from each paper were extracted, processed, normalized. All data were then plotted without bias in order to decide whether there is a pattern that can shed light on a possible diagnostic classification. Remarkably, we have been able to demonstrate that cancerous breast tissues and cells decidedly exhibit overexpression of aromatic amino acids and that the difference between the extent of their presence in cancerous cells and healthy cells is overwhelming. On the basis of this analysis, we conclude that it is possible to use the signature Raman bands of aromatic amino acids as a biomarker for the detection, evaluation and diagnosis of breast cancer.

Dual-Site Binding of Quaternary Ammonium Ions as Internal K+-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction

A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K⁺-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.

Evolution of ribosomal protein network architectures

To perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom's r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.

Theoretical study of chloride complexes with hybrid macrocycles

Macrocycle receptors are investigated from DFT calculations to simultaneously recognize two Cl⁻ anions, which show several applications in the environment.

Anion-dependent structural variations and charge transport property analysis of 4′-(3-pyridyl)-4,2′:6′,4′′-terpyridinium salts

Anion-dependent structural variations and charge transport analysis of three 4′-(3-pyridyl)-4,2′:6′,4′′-terpyridinium salts are reported. They exhibit pronounced photosensing behavior when illuminated using visible light.

Photoreactive salt cocrystal: N+–H⋯N hydrogen bond and cation–π interactions support a cascade-like photodimerization of a 4-stilbazole

Hydrogen bonds (i.e., N⁺–H⋯N) in combination with cation⋯π interactions enable a cascade-like [2 + 2] photodimerization of 4-stilbazole in a salt cocrystal.

Beyond hydrogen bonding: recent trends of outer sphere interactions in transition metal catalysis

The implementation of interactions beyond hydrogen bonding in the 2^nd coordination sphere of transition metal catalysts is rare. However, it has already shown great promise in last 5 years, providing new tools to control the activity and selectivity as here reviewed.

The role of CuI in the siloxane-mediated Pd-catalyzed cross-coupling reactions of aryl iodides with aryl lithium reagents

Experiments indicate that a catalytic amount of CuI plays an important role in the siloxane-mediated Pd-catalyzed cross-coupling reactions with the direct use of organolithium reagents. Addition of organolithium to the siloxane transfer agent generates an organosilicon intermediate. DFT calculations indicate that CuI initially accelerates the Si-Pd(II) transmetalation of the organosilicon intermediate by the formation of CuI2 -. Subsequently, CuI2 - works as a shuttle between the Si-Cu(I) and Cu(I)-Pd(II) transmetalation processes.

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.

Naphthobox: a selective molecular box for planar aromatic cations

A molecular box with an electron-rich cavity, namely naphthobox, was contructed and showed selective binding to planar aromatic cations.

Hydrogen adsorption on inorganic benzenes decorated with alkali metal cations: theoretical study

Hydrogen adsorption on different benzenes, both organic and inorganic, decorated with Li cations (Li+) was systematically studied by using quantum chemistry techniques. Our calculations demonstrate that Li+-decoration enhances the hydrogen storage ability of the complexes. MP2 calculations reveal that one to five hydrogen molecules per Li+ have high adsorption energies (Ead), up to -4.77 kcal mol-1, which is crucial for effective adsorption/desorption performance. The assessed hydrogen capacity of studied complexes is in the range of 10.0-10.6 wt%. SAPT2 calculations confirmed that induction and electrostatic interactions play the major role for H2 adsorption of the investigated systems, whereas London dispersion contributes to Ead moderately only in the cases of large number of hydrogen molecules adsorbed. Independent gradient model (IGM) analysis showed that there exists non-covalent bonding between Li+ and H2. The obtained van't Hoff desorption temperatures substantially exceed the temperature of liquid nitrogen. Ab initio molecular dynamics simulations confirmed the stability of the studied complexes. Our investigations establish the high potential of the studied complexes for usage in systems for hydrogen storage.

The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol

Terpene synthases generate terpenes employing diversified carbocation chemistry, including highly specific ring formations, proton and hydride transfers, and methyl as well as methylene migrations, followed by reaction quenching. In this enzyme family, the main catalytic challenge is not rate enhancement, but rather structural and reactive control of intrinsically unstable carbocations in order to guide the resulting product distribution. Here we employ multiscale modeling within classical and quantum dynamics frameworks to investigate the reaction mechanism in the diterpene synthase CotB2, commencing with the substrate geranyl geranyl diphosphate and terminating with the carbocation precursor to the final product cyclooctat-9-en-7-ol. The 11-step in-enzyme carbocation cascade is compared with the same reaction in the absence of the enzyme. Remarkably, the free energy profiles in gas phase and in CotB2 are surprisingly similar. This similarity contrasts the multitude of strong π-cation, dipole-cation, and ion-pair interactions between all intermediates in the reaction cascade and the enzyme, suggesting a remarkable balance of interactions in CotB2. We ascribe this balance to the similar magnitude of the interactions between the carbocations along the reaction coordinate and the enzyme environment. The effect of CotB2 mutations is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, pointing the way for future terpene synthase design.

The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series

The interaction potential energy surfaces (IPESs) of four alkaline metal cations (Na+, K+, Rb+ and Cs+) complexed with phenol and catechol were explored by accurate ab initio calculations to investigate the interplay of different noncovalent interactions and their behavior along the alkali metal series and upon -OH substitution. Selected one-dimensional interaction energy curves revealed two different minimum energy configurations for all phenol- and catechol-metal complexes, characterized either by cation-π or σ-type interactions. For each investigated complex several two-dimensional IPES maps were also computed, exploiting the computational advantages of the MP2mod approach. The size of the alkali cation was found to play a similar role in modulating both kinds of complexes, as the interaction strength always decreases along the metal series, from Na+ to Cs+. Conversely, the number of hydroxyl substituents markedly affected cation-π complexes vs. σ-type ones. As a most relevant finding, in catechol-metal complexes the strength of cation-π interactions is around half that of the σ-type ones. It is argued that the combined effect of cation dimensions and hydroxyl substitution in catechol-Na+ complexes makes σ-type configurations remarkably more stable and easily accessible than cation-π ones. Besides shedding new light on the origin of biological phenomena connected with underwater adhesion, the quantum mechanical interaction energy database provided herein may offer a useful reference for tuning accurate force fields, suitable for molecular dynamics simulations, where environmental effects might be also taken into account.

Effects of electrostatic drag on the velocity of hydrogen migration - pre- and post-transition state enthalpy/entropy compensation

Ab initio molecular dynamics calculations were used to explore the underlying factors that modulate the velocity of hydrogen migration for 1,2 hydrogen shifts in carbocations in which different groups interact noncovalently with the migrating hydrogen. Our results indicate that stronger electrostatic interactions between the migrating hydrogen and nearby π-systems lead to slower hydrogen migration, an effect tied to entropic contributions from the hydrogen + neighboring group substructures.

Perturbation of 1JC,F Coupling in Carbon-Fluorine Bonds on Coordination to Lewis Acids: A Structural, Spectroscopic, and Computational Study

A lithiated m-terphenyl ligand bearing fluorine atoms at the ortho positions of the flanking aryl rings was synthesized and characterized using single crystal X-ray diffraction, variable-temperature multinuclear NMR spectroscopy, and computational methods. Changes in ¹J_C,F on coordination to lithium as a spectroscopic observable parametrizing the strength of the C-F···Li interaction are described, and a general, qualitative relationship between C-F bond lengths, Δ¹J_C,F values, and the extent of C-F bond activation as a result of Lewis acid coordination is proposed.

Direct Measurements of the Forces between Silver and Mica in Humic Substance-Rich Solutions

Deposition of engineered nanoparticles onto porous media from flowing suspensions is important for soil and groundwater quality. The deposition mechanism is controlled by interaction forces between particles and collectors. We investigated the origin and magnitude of opposing forces between silver and mica surfaces (representing nanosilver and sand grains) in solutions relevant to agricultural soils with direct measurements using a surface force apparatus. Solutions of variable NaNO₃, Ca(NO₃)₂, and humic acid (HA) concentrations were used to differentiate individual contributing forces and quantify surface properties. The measured Hamaker constant for silver-water-mica was consistent with Lifshitz theory. Our results indicate that HA forms an adsorbed surface layer, but its charge, thicknesses, compressibility, and mass are significantly larger on mica than silver. Ca²⁺ primarily reduced the differences between the initially adsorbed HA layer properties on each surface, making them more similar. Force-distance profiles indicate that, when silver-mica systems were exposed to HA, osmotic-steric, electrostatic, and van der Waals forces dominate. Soft particle theory was deemed inappropriate for this system. Derjaguin's approximation was utilized to translate force measurements into interaction energy between nanosilver particles and mica collectors. We propose attachment efficiency estimates from measured surface properties, which suggest high particle mobility when nanosilver is applied to HA-rich agricultural soils with modest ionic strength.