The Cationminus signpi Interaction

Visualizing protein breathing motions associated with aromatic ring flipping

Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold1-3. It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1. However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.

Hyper-crosslinked tetraphenylborate as a regenerable sorbent for Cs+ sequestration in aqueous media through cation-π interactions

Practical adsorbents that could efficiently collect radioactive Cesium (Cs⁺) are critically important in achieving proper management and treatment measures for nuclear wastes. Herein, a hyper-crosslinked tetraphenylborate-based adsorbent (TPB-X) was prepared by reacting TPB anions as Cs⁺ binding sites with dimethoxymethane (DMM) as crosslinker. The most efficient TPB-X synthesis was attained at 1:4 TPB/DMM mole ratio with sorbent yield of 81.75%. Various techniques such as FTIR, TGA-DTG, N₂ adsorption/desorption and SEM-EDS reveal that TPB-X is a water-insoluble, thermally stable and highly porous granular sorbent. Its hierarchical pore structure explains its very high BET surface area (1030 m² g^-1). Sequestration of Cs⁺ by TPB-X involves its exchange with H⁺ followed by its binding with the phenyl rings of TPB through cation-π interactions. The Cs⁺ adsorption in TPB-X is endothermic and spontaneous, which adheres to the Hill isotherm model (q_m = 140.58 mg g^-1) and follows pseudo-second order kinetics (k₂ = 0.063 g mg^-1 h^-1). Calculations from the density functional theory reveal that the binding of TPB anion is strongest for Cs⁺. Thus, TPB-X was able to selectively capture Cs⁺ in simulated surface water containing Na⁺, K⁺, Mg²⁺, and Ca²⁺ and in HLLW containing Na⁺, Rb⁺, Sr²⁺, and Ba²⁺. Hyper-crosslinking was found beneficial in rendering TPB-X reusable as the sorbent was easily retrieved from the feed after Cs⁺ capture and was able to withstand the acid treatment for its regeneration. TPB-X exhibited consistent performance with no sign of chemical or physical deterioration. TPB-X offers a practical approach in handling Cs⁺ contaminated streams as it can be repeatedly used to enrich Cs⁺ in smaller volume of media, which can then be purified for Cs⁺ reuse or stored for long-term natural Cs⁺ decay process.

Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence

In silico models based on Deep Neural Networks (DNNs) are promising for predicting activities and properties of new molecules. Unfortunately, their inherent black-box character hinders our understanding, as to which structural features are important for activity. However, this information is crucial for capturing the underlying structure-activity relationships (SARs) to guide further optimization. To address this interpretation gap, "Explainable Artificial Intelligence" (XAI) methods recently became popular. Herein, we apply and compare multiple XAI methods to projects of lead optimization data sets with well-established SARs and available X-ray crystal structures. As we can show, easily understandable and comprehensive interpretations are obtained by combining DNN models with some powerful interpretation methods. In particular, SHAP-based methods are promising for this task. A novel visualization scheme using atom-based heatmaps provides useful insights into the underlying SAR. It is important to note that all interpretations are only meaningful in the context of the underlying models and associated data.

How neocarcerand Octacid4 self-assembles with guests into irreversible noncovalent complexes and what accelerates the assembly

Cram's supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small-molecule guests at room temperature, but how they self-assemble and what accelerates their assembly remain poorly understood. This article reports 81 distinct Octacid4•guest self-assembly pathways captured in unrestricted, unbiased molecular dynamics simulations. These pathways reveal that the self-assembly was initiated by the guest interaction with the cavity portal exterior of Octacid4 to increase the portal collisions that led to the portal expansion for guest ingress, and completed by the portal contraction caused by the guest docking inside the cavity to impede guest egress. The pathways also reveal that the self-assembly was accelerated by engaging populated host and guest conformations for the exterior interaction to increase the portal collision frequency. These revelations may help explain why the presence of an exterior binding site at the rim of the enzyme active site is a fundamental feature of fast enzymes such as acetylcholinesterase and why small molecules adopt local minimum conformations when binding to proteins. Further, these revelations suggest that irreversible noncovalent complexes with fast assembly rates could be developed-by engaging populated host and guest conformations for the exterior interactions-for materials technology, data storage and processing, molecular sensing and tagging, and drug therapy.

Oxidized Forms of Ergothioneine Are Substrates for Mammalian Thioredoxin Reductase

Ergothioneine (EGT) is a sulfur-containing amino acid analog that is biosynthesized in fungi and bacteria, accumulated in plants, and ingested by humans where it is concentrated in tissues under oxidative stress. While the physiological function of EGT is not yet fully understood, EGT is a potent antioxidant in vitro. Here we report that oxidized forms of EGT, EGT-disulfide (ESSE) and 5-oxo-EGT, can be reduced by the selenoenzyme mammalian thioredoxin reductase (Sec-TrxR). ESSE and 5-oxo-EGT are formed upon reaction with biologically relevant reactive oxygen species. We found that glutathione reductase (GR) can reduce ESSE, but only with the aid of glutathione (GSH). The reduction of ESSE by TrxR was found to be selenium dependent, with non-selenium-containing TrxR enzymes having little or no ability to reduce ESSE. In comparing the reduction of ESSE by Sec-TrxR in the presence of thioredoxin to that of GR/GSH, we find that the glutathione system is 10-fold more efficient, but Sec-TrxR has the advantage of being able to reduce both ESSE and 5-oxo-EGT directly. This represents the first discovered direct enzymatic recycling system for oxidized forms of EGT. Based on our in vitro results, the thioredoxin system may be important for EGT redox biology and requires further in vivo investigation.

Detection of weak non-covalent cation-π interactions in NGAL by single-molecule force spectroscopy

Cation-π interaction is an electrostatic interaction between a cation and an electron-rich arene. It plays an essential role in many biological systems as a vital driving force for protein folding, stability, and receptor-ligand interaction/recognition. To date, the discovery of most cation-π interactions in proteins relies on the statistical analyses of available three-dimensional (3D) protein structures and corresponding computational calculations. However, their experimental verification and quantification remain sparse at the molecular level, mainly due to the limited methods to dynamically measure such a weak non-covalent interaction in proteins. Here, we use atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of protein neutrophil gelatinase-associated lipocalin (also known as NGAL, siderocalin, lipocalin 2) that can bind iron through the cation-π interactions between its three cationic residues and the iron-binding tri-catechols. Based on a site-specific cysteine engineering and anchoring method, we first characterized the stability and unfolding pathways of apo-NGAL. Then, the same NGAL but bound with the iron-catechol complexes through the cation-π interactions as a holo-form was characterized. AFM measurements demonstrated stronger stabilities and kinetics of the holo-NGAL from two pulling sites, F122 and F133. Here, NGAL is stretched from the designed cysteine close to the cationic residues for a maximum unfolding effect. Thus, our work demonstrates high-precision detection of the weak cation-π interaction in NGAL.

Electronic Supplementary Material

Supplementary material (additional SDS-PAGE, UV-vis, protein sequences, and more experimental methods) is available in the online version of this article at 10.1007/s12274-021-4065-9.

Promotion of TH3 (T = Si and Ge) group transfer within a tetrel bond by a cation-π interaction

The possibility of the transfer of the TH₃ group across a tetrel bond is considered by ab initio calculations. The TB is constructed by pairing PhTH₃ (Ph = phenyl; T = Si and Ge) with bases NH₃, NHCH₂, and the C₃N₂H₄ carbene. The TH₃ moves toward the base but only by a small amount in these dimers. However, when a Be²⁺ or Mg²⁺ dication is placed above the phenyl ring, the tetrel bond strength is greatly magnified reaching up to nearly 100 kcal mol^-1. This dication also induces a much higher degree of transfer which can be best categorized as half-transfer for the two N-bases and a near complete transfer for the carbene.

Theoretical investigation on the nature of substituted benzene⋯AuX interactions: covalent or noncovalent?

The nature of interactions between AuX (X = F, Cl, Br, CN, NO2, CH3) and aromatic moieties with different electronic properties has been investigated for possible tuning of coinage–metal bonds by varying the substituents.

Recent advances in the 3D printing of ionic electroactive polymers and core ionomeric materials

The recent advances in the 3D printing, or additive manufacturing, of ionic electroactive polymers (EAP) and their future applications.

Formation of sandwich and multidecker complexes between O2 and alkali/alkaline earth metals: A DFT study

Abstract: Feasibility of formation of sandwich and multidecker complexes between O2 molecules and alkali/alkaline earth metal has been analyzed in the light of density functional theory (DFT). High value of...

Si doped T-graphene: a 2D lattice as an anode electrode in Na ion secondary batteries

Heteroatom doping into 2-dimensional lattices of materials such as graphene brings revolutionary reform in the field of materials endowing the parent material with remarkable properties.

Insight into non-covalent interactions in a [Cu(N3)4]2- bridged hetero-pentanuclear copper(II)/sodium complex with special emphasis on the strong CH···π[Cu(N3)4] interactions

The swastika-shaped anion, [Cu(N3)4]2- in the pentanuclear hetero-metallic copper(II)-Sodium complex, [(CuLNa)2(µ-N3)2Cu(N3)2] (1), where H2L = N,N'-bis(3-ethoxysalicylidene)-2,2-dimethylpropane-1,3-diamine (N2O4 donor compartmental Schiff base) is nearly planar and provides a π-basic surface adequate...

Recent Advances in High-strength and High-toughness Polyurethanes Based on Supramolecular Interactions

Recent developments in supramolecular chemistry have generated increasing interest in supramolecular polymers and opened a window for the exploitation of various supramolecular polymeric materials and their multifunctional composites. High-performance polyurethanes,...

Polyphosphazene and Non-Catechol-Based Antibacterial Injectable Hydrogel for Adhesion of Wet Tissues as Wound Dressing

Wound dressings with excellent adhesiveness, antibacterial, self-healing, hemostasis properties, and therapeutic effects have great significance for the treatment of acute trauma. So far, numerous mussel-inspired catechol-based wet adhesives have been reported, opening a pathway for the treatment of acute trauma. However, catechol-based hydrogels are easily oxidized, which limits their applications. Here, the design of a polyphosphazene and non-catechol based antibacterial injectable hydrogel is reported as a multifunctional first aid bandage. Inspired by barnacle cement proteins, a series of dynamic phenylborate ester based adhesive hydrogels are prepared by combining the cation-π structure modified polyphosphazene with polyvinyl alcohol. The inherent antibacterial property (4 h antibacterial rate 99.6 ± 0.2%), anti-mechanical damage, and hemostatic behavior are investigated to confirm multi-functions of wound dressings. In water, the hydrogels firmly adhere to tissue surfaces through cation-π and π-π interactions as well as hydrogen bonding (adhesion strength = 45 kPa). Moreover, in vivo experiments indicate the hydrogels can shorten the bleeding time and reduce the amount of bleeding by 88%, and significantly accelerate the wound healing rate. These hydrogels have a promising application in the treatment of acute trauma, which is in urgent need of anti-infection and hemostasis.

Quantitative determination of cation–π interactions between metal ions and aromatic groups in aqueous media by a hydrogel Donnan potential method

The binding ratios of various metal ions to aromatic groups by cation–π interactions in aqueous media have been quantitatively calculated by using Donnan potential measurements.

Investigations on the role of cation-π interactions in active centers of superoxide dismutase

In this study, we have analysed the influence of cation-? interactions on stability and properties of superoxide dismutase (SOD) active centres. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher in the ? group. The energy contribution resulting from most frequent cation-? interactions was in the lower range of strong hydrogen bonds. The cation-? interactions involving transition metal ions as cation have energy more negative than -418.4 kJ mol-1. Stabilization centres for these proteins showed that all residues involved in cation-? interactions were important in locating one or more of such centres. The majority of the residues involved in cation-p interactions were evolutionarily conserved and might have a significant contribution towards the stability of SOD proteins. The results presented in this work can be very useful for understanding the contribution of cation-? interactions to the stability of SOD active canters.

Clustering of Aromatic Amino Acid Residues around Methionine in Proteins

Short-range, non-covalent interactions between amino acid residues determine protein structures and contribute to protein functions in diverse ways. The interactions of the thioether of methionine with the aromatic rings of tyrosine, tryptophan, and/or phenylalanine has long been discussed and such interactions are favorable on the order of 1–3 kcal mol⁻¹. Here, we carry out a new bioinformatics survey of known protein structures where we assay the propensity of three aromatic residues to localize around the [-CH₂-S-CH₃] of methionine. We term these groups “3-bridge clusters”. A dataset consisting of 33,819 proteins with less than 90% sequence identity was analyzed and such clusters were found in 4093 structures (or 12% of the non-redundant dataset). All sub-classes of enzymes were represented. A 3D coordinate analysis shows that most aromatic groups localize near the CH₂ and CH₃ of methionine. Quantum chemical calculations support that the 3-bridge clusters involve a network of interactions that involve the Met-S, Met-CH₂, Met-CH₃, and the π systems of nearby aromatic amino acid residues. Selected examples of proposed functions of 3-bridge clusters are discussed.

Theoretical Investigation of Carbon Dioxide Adsorption on Li+-Decorated Nanoflakes

Recently, the capture of carbon dioxide, the primary greenhouse gas, has attracted particular interest from researchers worldwide. In the present work, several theoretical methods have been used to study adsorption of CO2 molecules on Li+-decorated coronene (Li+@coronene). It has been established that Li+ can be strongly anchored on coronene, and then a physical adsorption of CO2 will occur in the vicinity of this cation. Moreover, such a decoration has substantially improved interaction energy (Eint) between CO2 molecules and the adsorbent. One to twelve CO2 molecules per one Li+ have been considered, and their Eint values are in the range from -5.55 to -16.87 kcal/mol. Symmetry-adapted perturbation theory (SAPT0) calculations have shown that, depending on the quantity of adsorbed CO2 molecules, different energy components act as the main reason for attraction. AIMD simulations allow estimating gravimetric densities (GD, wt.%) at various temperatures, and the maximal GDs have been calculated to be 9.3, 6.0, and 4.9% at T = 77, 300, and 400 K, respectively. Besides this, AIMD calculations validate stability of Li+@coronene complexes during simulation time at the maximum CO2 loading. Bader's atoms-in-molecules (QTAIM) and independent gradient model (IGM) techniques have been implemented to unveil the features of interactions between CO2 and Li+@coronene. These methods have proved that there exists a non-covalent bonding between the cation center and CO2. We suppose that findings, derived in this theoretical work, may also benefit the design of novel nanosystems for gas storage and delivery.

Water-Soluble Cyclophanes Synthesized via the Zincke Reaction

By taking advantage of the Zincke reaction, we successfully synthesized three macrocycles, each of which contains two bipyridinium units as the electron acceptors. Two of them contain sp²-hybridized atoms exclusively in the ring frameworks, while the third contains two methylene units. The third macrocycle is able to form 1:1 inclusion complexes with guests of complementary sizes. A pair of isomers, namely, phenanthrene and anthracene, could be separated by the third macrocycle.

Enzymatic deamination of the epigenetic nucleoside N6-methyladenosine regulates gene expression

N⁶-methyladenosine (m⁶A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N⁶-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N⁶-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N⁶-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N⁶-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N⁶-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.

Synergistic effect of Cu-nanoparticles and β-cyclodextrin functionalized reduced graphene oxide nanocomposite on the adsorptive remediation of tetracycline antibiotics

Pollution by tetracyclines antibiotics has a great potential risk on human and animal health even at trace levels. Copper nanoparticles immobilized-β-cyclodextrin functionalized reduced graphene oxide (Cu/β-CD/rGO) were successfully prepared as an efficient extractor of tetracycline (TC), oxytetracycline (OTC) and doxycycline (DC) antibiotics from different environmental water samples. Tetracyclines (TCs) are strongly deposited in the matrix of Cu/β-CD/rGO nanocomposite via surface complexation with the Cu-nanoparticles besides the formation of inclusion complexes with β-cyclodextrin and π-π interaction of reduced graphene oxide. The novel nanocomposite was characterized by HRSEM, TEM, TGA, FT-IR, XPS, and XRD. The optimization of variables such as the pH, contact time, ionic strength and TC concentration were successfully analyzed. The maximum adsorption capacity (q_m) of Cu/β-CD/rGO calculated from the Langmuir isotherm was 403.2 mg.g^-1 for TC, 476.2 mg.g^-1 for OTC and 434.8 mg.g^-1 for DC at 298 K. The removal efficiency was decreased by 3.7% after five adsorption-desorption cycles. The Cu/β-CD/rGO nanocomposite was applied for removing TCs from tap water and the Nile River water samples. The novel nanocomposite demonstrated fast and highly efficient removing performance for different TCs with low levels and large sample volume.

Macrocyclic host molecules with aromatic building blocks: the state of the art and progress

Macrocyclic host molecules play the central role in host-guest chemistry and supramolecular chemistry. The highly structural symmetry of macrocyclic host molecules can meet people's pursuit of aesthetics in molecular design, and generally means a balance of design, synthesis, properties and applications. For macrocyclic host molecules with highly symmetrical structures, building blocks, which could be described as repeat units as well, are the most fundamental elements for molecular design. The structural features and recognition ability of macrocyclic host molecules are determined by the building blocks and their connection patterns. Using different building blocks, different macrocyclic host molecules could be designed and synthesized. With decades of developments of host-guest chemistry and supramolecular chemistry, diverse macrocyclic host molecules with different building blocks have been designed and synthesized. Aromatic building blocks are a big family among the various building blocks used in constructing macrocyclic host molecules. In this feature article, the recent developments of macrocyclic host molecules with aromatic building blocks were summarized and discussed.

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.

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E_int) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E_int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E_int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E_int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E_int values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

Trisubstituted 1,3,5-Triazines: The First Ligands of the sY12-Binding Pocket on Chemokine CXCL12

CXCL12, a CXC-type chemokine, binds its receptor CXCR4, and the resulting signaling cascade is essential during development and subsequently in immune function. Pathologically, the CXCL12–CXCR4 signaling axis is involved in many cancers and inflammatory diseases and thus has sparked continued interest in the development of therapeutics. Small molecules targeting CXCR4 have had mixed results in clinical trials. Alternatively, small molecules targeting the chemokine instead of the receptor provide a largely unexplored space for therapeutic development. Here we report that trisubstituted 1,3,5-triazines are competent ligands for the sY12-binding pocket of CXCL12. The initial hit was optimized to be more synthetically tractable. Fifty unique triazines were synthesized, and the structure–activity relationship was probed. Using computational modeling, we suggest key structural interactions that are responsible for ligand–chemokine binding. The lipophilic ligand efficiency was improved, resulting in more soluble, drug-like molecules with chemical handles for future development and structural studies.

Autonomous magnetic microbots for environmental remediation developed by organic waste derived carbon dots

Biodegradable precursors for micro/nanobots development are key requirements for several sustainable applications. In this regard, we propose an innovative solution for water purification at minimum cost and efforts where organic waste is used for the treatment of organic pollutants. Herein, catalytic magnetic microbots were developed by functionalizing iron oxide nanoparticles with carbon dots (C-Dots), which were synthesized by using household waste such as potato peels as precursors. The speed of these autonomously propelling bots indeed is found very promising for large distance swimming even in viscous medium by using hydrogen peroxide as fuel. These microbots catalytically propel and degrade toxic polar as well as sparingly water-soluble industrial dyes without any external agitation. The degradation of dyes was confirmed by mass-spectra analysis. Furthermore, these microbots can efficiently degrade a mixture of dyes and reused without compromising its performance significantly. Additionally, rate constant (K) and activation energy (E_a) were also determined to establish the catalytic nature of the bots. The present microbots acted as nanozyme owing to its synergistic catalytic activity of Fe₃O₄ and C-Dots for degradation of mixture of toxic dyes, essential for large scale water treatment.

Novel 2D CaCl crystals with metallicity, room-temperature ferromagnetism, heterojunction, piezoelectricity-like property and monovalent calcium ions

Under ambient conditions, the only known valence state of calcium ions is +2, and the corresponding crystals with calcium ions are insulating and nonferromagnetic. Here, using cryo-electron microscopy, we report direct observation of two-dimensional (2D) CaCl crystals on reduced graphene oxide (rGO) membranes, in which the calcium ions are only monovalent (i.e. +1). Remarkably, metallic rather than insulating properties are displayed by those CaCl crystals. More interestingly, room-temperature ferromagnetism, graphene-CaCl heterojunction, coexistence of piezoelectricity-like property and metallicity, as well as the distinct hydrogen storage and release capability of the CaCl crystals in rGO membranes are experimentally demonstrated. We note that such CaCl crystals are obtained by simply incubating rGO membranes in salt solutions below the saturated concentration, under ambient conditions. Theoretical studies suggest that the formation of those abnormal crystals is attributed to the strong cation-π interactions of the Ca cations with the aromatic rings in the graphene surfaces. The findings highlight the realistic potential applications of such abnormal CaCl material with unusual electronic properties in designing novel transistors and magnetic devices, hydrogen storage, catalyzers, high-performance conducting electrodes and sensors, with a size down to atomic scale.

Cobalt Coordinated Cyano Covalent-Organic Framework for High-Performance Potassium-Organic Batteries

Potassium ion batteries (PIBs) are expected to become the next large-scale energy storage candidates due to its low cost and abundant resources. And the covalent organic framework (COF), with designable periodic organic structure and ability to organize redox active groups predictably, has been considering as the promising organic electrode candidate for PIB. Herein, we report the facile synthesis of the cyano-COF with Co coordination via a facile microwave digestion reaction and its application in the high-energy potassium ion batteries for the first time. The obtained COF-Co material exhibits the enhanced π-π accumulation and abundant defects originated from the Co interaction with the two-dimensional layered sheet structure of COF, which are beneficial for its energy-storage application. Adopted as the inorganic-metal boosted organic electrode for PIBs, the COF-Co with Co coordination can promote the formation of the π-K⁺ interaction, which could lead to the activation of aromatic rings for potassium-ion storage. Besides, the porous two-dimensional layered structure of COF-Co with abundant defects can also promote the shortened diffusion distance of ion/electron with promoted K⁺ insertion/extraction ability. Enhanced cycling stability with large reversible capacity (371 mAh g^-1 after 400 cycles at 100 mA g^-1) and good rate properties (105 mAh g^-1 at 2000 mA g^-1) have been achieved for the COF-Co electrode.

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.

Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics

Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed Zn‐dependent protease, which plays an important role in regulating endogenous peptide hormones, such as enkephalins or angiotensins. In previous biophysical studies, it could be shown that substrate binding is driven by a large entropic contribution due to the release of water molecules from the closing binding cleft. Here, the design, synthesis and biophysical characterization of peptidomimetic inhibitors is reported, using for the first time an hydroxyethylene transition‐state mimetic for a metalloprotease. Efficient routes for the synthesis of both stereoisomers of the pseudopeptide core were developed, which allowed the synthesis of peptidomimetic inhibitors mimicking the VVYPW‐motif of tynorphin. The best inhibitors inhibit DPP3 in the low μM range. Biophysical characterization by means of ITC measurement and X‐ray crystallography confirm the unusual entropy‐driven mode of binding. Stability assays demonstrated the desired stability of these inhibitors, which efficiently inhibited DPP3 in mouse brain homogenate.

Improved pH-Responsive Release of Phenformin from Low-Defect Graphene Compared to Graphene Oxide

Graphene-based drug carriers provide a promising addition to current cancer drug delivery options. Increased accessibility of high-quality graphene made by plasma-enhanced chemical vapor deposition (PE-CVD) makes it an attractive material to revisit in comparison to the widely studied graphene oxide (GO) in drug delivery. Here, we show the potential of repurposing the metabolic drug phenformin for cancer treatment in terms of stability, binding, and pH-responsive release. Using covalent attachment of poly(ethylene glycol) (PEG) onto pristine (PE-CVD) graphene, we show that PEG stabilized graphene nanosheets (PGNS) are stable in aqueous solutions and exhibit higher binding affinity toward phenformin than GO. Moreover, we experimentally demonstrate an improved drug release from PGNS than GO at pH levels lower than physiological conditions, yet comparable to that found in tumor microenvironments.

Exploration of the Cs Trapping Phenomenon by Combining Graphene Oxide with α-K6P2W18O62 as Nanocomposite

A graphene oxide-based α-K₆P₂W₁₈O₆₂ (Dawson-type polyoxometalate) nanocomposite was formed by using two types of graphene oxide (GO) samples with different C/O compositions. Herein, based on the interaction of GO, polyoxometalates (POMs), and their nanocomposites with the Cs cation, quantitative data have been provided to explicate the morphology and Cs adsorption character. The morphology of the GO-POM nanocomposites was characterized by using TEM and SEM imaging. These results show that the POM particle successfully interacted above the surface of GO. The imaging also captured many small black spots on the surface of the nanocomposite after Cs adsorption. Furthermore, ICP-AES, the PXRD pattern, IR spectra, and Raman spectra all emphasized that the Cs adsorption occurred. The adsorption occurred by an aggregation process. Furthermore, the difference in the C/O ratio in each GO sample indicated that the ratio has significantly influenced the character of the GO-POM nanocomposite for the Cs adsorption. It was shown that the oxidized zone (sp²/sp³ hybrid carbon) of each nanocomposite sample was enlarged by forming the nanocomposite compared to the corresponding original GO sample. The Cs adsorption performance was also influenced after forming a composite. The present study also exhibited the fact that the sharp and intense diffractions in the PXRD were significantly reduced after the Cs adsorption. The result highlights that the interlayer distance was changed after Cs adsorption in all nanocomposite samples. This has a good correlation with the Raman spectra in which the second-order peaks changed after Cs adsorption.

Dual acting oximes designed for therapeutic decontamination of reactive organophosphates via catalytic inactivation and acetylcholinesterase reactivation

A conventional approach in the therapeutic decontamination of reactive organophosphate (OP) relies on chemical OP degradation by oxime compounds. However, their efficacy is limited due to their lack of activity in the reactivation of acetylcholinesterase (AChE), the primary target of OP. Here, we describe a set of α-nucleophile oxime derivatives which are newly identified for such dual modes of action. Thus, we prepared a 9-member oxime library, each composed of an OP-reactive oxime core linked to an amine-terminated scaffold, which varied through an N-alkyl functionalization. This library was screened by enzyme assays performed with human and electric eel subtypes of OP-inactivated AChE, which led to identifying three oxime leads that displayed significant enhancements in reactivation activity comparable to 2-PAM. They were able to reactivate both enzymes inactivated by three OP types including paraoxon, chlorpyrifos and malaoxon, suggesting their broad spectrum of OP susceptibility. All compounds in the library were able to retain catalytic reactivity in paraoxon inactivation by rates increased up to 5 or 8-fold relative to diacetylmonoxime (DAM) under controlled conditions at pH (8.0, 10.5) and temperature (17, 37 °C). Finally, selected lead compounds displayed superb efficacy in paraoxon decontamination on porcine skin in vitro. In summary, we addressed an unmet need in therapeutic OP decontamination by designing and validating a series of congeneric oximes that display dual modes of action.

Mechanisms of melatonin binding and destabilizing the protofilament and filament of tau R3-R4 domains revealed by molecular dynamics simulation

The accumulation of β-amyloid (Aβ) and tau protein is considered to be an important pathological characteristic of Alzheimer's disease (AD). Failure of medicine targeting Aβ has drawn more attention to the influence of tau protein and its fibrillization on neurodegeneration. Increasing evidence shows that melatonin (Mel) can effectively inhibit the formation of tau fibrils and disassemble preformed tau fibrils. However, the underlying mechanism is poorly understood. In this work, we investigated the kinetics of melatonin binding and destabilizing the tetrameric protofilament and octameric filament of tau R3-R4 domains by performing microsecond all-atom molecular dynamics simulations. Our results show that Mel is able to disrupt the C-shaped structure of the tau protofilament and filament, and destabilizes the association between N- and C-termini. Mel predominantly binds to β1 and β6-β8 regions and favors contact with the elongation surface, which is dominantly driven by hydrogen bonding interactions and facilitated by other interactions. The strong π-π stacking interaction of Mel with Y310 impedes the intramolecular CH-π interaction between I308 and Y310, and the cation-π interaction of Mel with R379 interferes with the formation of the D348-R379 salt bridge. Moreover, Mel occupies the protofilament surface in the tetrameric protofilament and prevents the formation of intermolecular hydrogen bonds between residues K331 and Q336 in the octameric filament. Our work provides molecular insights into Mel hindering tau fibrillization or destabilizing the protofilament and filament, and the revealed inhibitory mechanisms provide useful clues for the design of efficient anti-amyloid agents.

Molecular mechanisms of resveratrol and EGCG in the inhibition of Aβ42 aggregation and disruption of Aβ42 protofibril: similarities and differences

The aggregation of amyloid-β protein (Aβ) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aβ aggregation and clearing Aβ fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aβ fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aβ₄₂ aggregation and disrupts Aβ₄₂ protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aβ₄₂ dimers (the early aggregation state of Aβ₄₂) and protofibrils (the intermediate of Aβ₄₂ fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aβ₄₂ monomers and inhibit the dimerization of Aβ₄₂. The binding of RSV with Aβ₄₂ peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aβ₄₂ is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the β-sheet structure and K28-A42 salt bridges, leading to a disruption of Aβ₄₂ protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aβ₄₂ protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aβ₄₂ protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aβ. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.

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.

Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.

Role of PhOH and Tyrosine in Selective Oxidation of Hydrocarbons

Earlier, we established that nickel or iron heteroligand complexes, which include PhOH (nickel complexes) or tyrosine residue (nickel or iron complexes), are not only hydrocarbon oxidation catalysts (in the case of PhOH), but also simulate the active centers of enzymes (PhOH, tyrosine). The AFM method established the self-organization of nickel or iron heteroligand complexes, which included tyrosine residue or PhOH, into supramolecular structures on a modified silicon surface. Supramolecular structures were formed as a result of H-bonds and other non-covalent intermolecular interactions and, to a certain extent, reflected the structures involved in the mechanisms of reactions of homogeneous and enzymatic catalysis. Using the AFM method, we obtained evidence at the model level in favor of the involvement of the tyrosine fragment as one of the possible regulatory factors in the functioning of Ni(Fe)ARD dioxygenases or monooxygenases of the family of cytochrome P450. The principles of actions of these oxygenases were used to create highly efficient catalytic systems for the oxidation of hydrocarbons.