Noncovalent Research Articles

Ab initio molecular dynamics study of hydroxyl positioning in butanediol and its impact on deep eutectic solvent structure

Electrolytes play a crucial role in enhancing the performance of energy storage devices, including batteries and supercapacitors. However, traditional electrolytes, such as aqueous solutions, organic solvents, and ionic liquids, exhibit inherent limitations and challenges. Deep eutectic solvents have recently emerged as promising alternatives due to their environmentally friendly nature and favorable properties. Despite their widespread applications in various domains, their potential as electrolytes remains relatively underexplored. This study investigates three distinct types of deep eutectic solvents derived from different isomers of butanediols combined with choline chloride. Ab initio molecular dynamics simulations are employed to analyze the microstructure of these deep eutectic solvents, focusing on non-covalent electrostatic interactions, hydrogen bonding patterns, and vibrational spectra. The results reveal significant differences in the structural configuration of hydrogen bond acceptors and hydrogen bond donors and their interactions within the deep eutectic solvents. Specifically, the positioning of functional groups in hydrogen bond donors significantly impacts the hydrogen bonding network and the interaction with monoatomic ions. Moreover, the vibrational spectra analysis highlights the existence of hydrogen bonds involving stretching modes of the OH group, as evidenced by redshift deviations. Overall, this study provides valuable insights into the unique features of deep eutectic solvents as potential electrolytes for energy storage applications. The comprehensive analysis of their microstructure and vibrational properties enhances our understanding of deep eutectic solvent utilization and opens avenues for further research in sustainable energy storage.

Low-molecular-weight gels from amino acid and peptide derivatives for controlled release and delivery.

Low-molecular-weight (LMW) gelators are a versatile class of compounds able to self-assemble and to form supramolecular materials, such as gels. The use of LMW peptides to produce these gels shows many advantages, because of their wide structure tunability, the low-cost and effective synthesis, and the in vivo biocompatibility and biodegradability, which makes them optimal candidates for release and delivery applications. In addition, in these materials, the binding of the hosts may occur through a variety of noncovalent interactions, which are also the main factors responsible for the self-assembly of the gelators, and through specific interactions with the fibers or the pores of the gel matrix. This review aims to report LMW gels based on amino acid and peptide derivatives used for the release of many different species (drugs, fragrances, dyes, proteins, and cells) with a focus on the possible strategies to incorporate the cargo in these materials, and to demonstrate how versatile these self-assembled materials are in several applications.

Mutual synergistic regulation of chloride anion and cesium cation binding using a new designed macrocyclic multi-functional sites receptor: A case of DFT computational prediction.

The mutual synergistic regulation of the multi-functional sites on a single receptor molecule for ion-binding/recognition is vital for the new receptor design and needs to be well explored from experiment and theory. In this work, a new macrocyclic ion receptor (BEBUR) with three functional zones, including two ether holes and one biurea groups, is designed expecting to mutually enhance the ion-binding performance. The binding behaviors of BEBUR mainly for Cl- and Cs+ are deeply investigated by using density functional theoretical calculations. It is found that Cl-/Cs+ binding can be mutually enhanced and synergistically regulated via corresponding conformational changes of the receptor, well reflecting an electrical complementary matching and mutual reinforcement effect. Moreover, solvent effect calculations indicate that BEBUR may be an excellent candidate structure for Cl--binding with the enhancement of counter ion (Cs+) in water and toluene. In addition, visualization of intermolecular noncovalent interaction is used for analysis on the nature of the binding interactions between receptor and ions.

Synthesis of hydrogels from biomaterials and their potential application in tissue engineering

In this study, a series of hydrogels were synthesized from chitosan(s) that was crosslinking with glutaraldehyde at different concentrations. Ascorbic acid in an acidic medium was used to facilitate non-covalent interactions. The chitosan(s) was obtained from shrimp cytoskeleton; while ascorbic acid was extracted from xoconostle juice. The hydrogel reaction was monitored by UV–vis spectroscopy (550 nm) to determine the reaction kinetics and reaction order at 60 °C. The hydrogels structures were characterized by NMR, FT-IR, HR-MS and SEM, while the degree of cross-linking was examined with TGA-DA. The extracellular matrices were obtained as stable hydrogels where reached maximum crosslinking was of 7 %, independent of glutaraldehyde quantity added. The rheological properties showed a behavior of weak gels and a dependence of crosslinking agent concentration on strength at different temperatures. The cytotoxicity assay showed that the gels had no adverse effects on cellular growth for all concentrations of glutaraldehyde.

Chirality-driven strong thioredoxin reductase inhibition

Overexpression of thioredoxin reductase (TXNRD) plays crucial role in tumorigenesis. Therefore, designing TXNRD inhibitors is a promising strategy for targeted anticancer drug development. However, poor selectivity has always been a challenge, resulting in unavoidable toxicity in clinic. Herein we demonstrate a strategy to develop highly selective chiral metal complexes-based TXNRD inhibitors. By manipulating the conformation of two distinct weakly interacting groups, we optimize the compatibility between the drug and the electrophilic group within the active site of TXNRD to enhance their non-covalent interaction, thus effectively avoids the poor selectivity deriving from covalent drug interaction, on the basis of ensuring the strong inhibition. Detailed experimental and computational results demonstrate that the chiral isomeric drugs bind to the active site of TXNRD, and the interaction strength is well modulated by chirality. Especially, the meso-configuration, in which the two large sterically hindered active groups are positioned on opposite sides of the drug, exhibits the highest number of non-covalent interactions and most effective inhibition on TXNRD. Taken together, this work not only provides a novel approach for developing highly selective proteinase inhibitors, but also sheds light on possible underlying mechanisms for future application.

Selection of organic solvents as reaction media for laccase from Trametes versicolor

The ability of laccases to work effectively in properly selected aqueous-organic solutions significantly expands the scope of their application, making them commercially attractive and more competitive. However, it must be considered that molecules of organic solvent are very aggressive towards enzymes and destroy weak non-covalent interactions that maintain the spatial structure of the protein. In this work, we quantitatively described the influence of the nature of water-miscible organic solvents and their concentration on the activity and stability of Trametes versicolor laccase during the oxidation of ABTS (2,2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)) through the maximum rates and the Michaelis constants KM. The obtained kinetic parameters make it possible to compare the effect of various organic solvents on laccase and select the most optimal one, which minimizes the decrease in enzyme activity, maintains its stability and allows repeated use. Among the solvents studied, polyhydroxy compounds have the least negative effect on laccase activity; however, in all cases, a high concentration of organic solvent (≥30% (v/v)) leads to suppression of enzymatic activity. It has been shown that the longer the alkyl chain (hydrophobic fragment of the structure), the stronger the negative effect of alcohols on enzymes. The most toxic solvent for Trametes versicolor laccase is isopropanol. In addition, numerous examples of various uses of Trametes versicolor in aquatic-organic environments are discussed here.

Electrolyte-Gated Carbon Nanotube Field-Effect Transistor-Based Sensors for Nanoplastics Detection in Seawater: A Study of the Interaction between Nanoplastics and Carbon Nanotubes.

Plastics accumulating in the environment are nowadays of great concern for aquatic systems and for the living organisms populating them. In this context, nanoplastics (NPs) are considered the major and most dangerous contaminants because of their small size and active surface, which allow them to interact with a variety of other molecules. Current methods used for the detection of NPs rely on bulky and expensive techniques such as spectroscopy. Here we propose, for the first time, a novel, fast, and easy-to-use sensor based on an electrolyte-gated field-effect transistor (EG-FET) with a carbon nanotube (CNT) semiconductor (EG-CNTFET) for the detection of NPs in aquatic environments, using polystyrene NPs (PS-NPs) as a model material. In particular, as a working mechanism for the EG-CNTFETs we exploited the ability of CNTs and PS to form noncovalent interactions. Indeed, in our EG-CNTFET devices, the interaction between NPs and CNTs caused a change in the electric double layers. A linear increase in the corrected on current (*ION) of the EG-CNTFETs, with a sensitivity of 9.68 μA/(1 mg/mL) and a linear range of detection from 0.025 to 0.25 mg/mL were observed. A π-π interaction was hypothesized to take place between the two materials, as indicated by an X-ray photoelectron spectroscopy analysis. Using artificial seawater as an electrolyte, to mimic a real-case scenario, a linear increase in *ION was also observed, with a sensitivity of 6.19 μA/(1 mg/mL), proving the possibility to use the developed sensor in more complex solutions, as well as in low concentrations. This study offers a starting point for future exploitation of electrochemical sensors for NP detection and identification.

Supramolecular Assembly Frameworks (SAFs): Shaping the Future of Functional Materials.

Supramolecular assembly frameworks (SAFs) represent a new category of porous materials, utilizing non-covalent interactions, setting them apart from metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). This category includes but is not restricted to hydrogen-bonded organic frameworks and supramolecular organic frameworks. SAFs stand out for their outstanding porosity, crystallinity, and stability, alongside unique dissolution-recrystallization dynamics that enable significant structural and functional modifications. Crucially, their non-covalent assembly strategies allow for a balanced manipulation of porosity, symmetry, crystallinity, and dimensions, facilitating the creation of advanced crystalline porous materials unattainable through conventional covalent or coordination bond synthesis. Despite their considerable promise in overcoming several limitations inherent to MOFs and COFs, particularly in terms of solution-processability, SAFs have received relatively little attention in recent literature. This Minireview aims to shed light on standout SAFs, exploring their design principles, synthesis strategies, and characterization methods. It emphasizes their distinctive features and the broad spectrum of potential applications across various domains, aiming to catalyze further development and practical application within the scientific community.

Detection of Noncovalent Protein-Ligand Complexes by IR-MALDESI-MS.

Native mass spectrometry (MS) is a powerful analytical technique to directly probe noncovalent protein-protein and protein-ligand interactions. However, not every MS platform can preserve proteins in their native conformation due to high energy deposition from the utilized ionization source. Most small molecules approved as drugs and in development interact with their targets through noncovalent interactions. Therefore, rapid methods to analyze noncovalent protein-ligand interactions are necessary for the early stages of the drug discovery pipeline. Herein, we describe a method for analyzing noncovalent protein-ligand complexes by IR-MALDESI-MS with analysis times of ∼13 s per sample. Carbonic anhydrase and the kinase domain of Bruton's tyrosine kinase are paired with known noncovalent binders to evaluate the effectiveness of native MS by IR-MALDESI.

Unveiling the energetic complexity of noncovalent interactions in halogenated dimers

AbstractThe understanding of noncovalent interactions is crucial in explaining critical phenomena such as self‐assembly, chemical reactivity, and crystallization. This work examines the energetic diversity of conformations and local minima for several halogenated dimers, represented as R‐X (R = H, F, CH3, CF3; X = Cl, Br, I). Thousands of configurations are randomly generated and refined through geometric optimizations to yield a diverse set of molecular conformers. Frequency calculations were performed for all optimized conformers to confirm that they are local minima. The noncovalent interactions in optimized dimers of halogen‐containing molecules were analyzed with atom in molecules (AIM) method and symmetry‐adapted perturbation theory (SAPT). Additionally, a protocol for generating machine learning models to recover accurate predictions of the physically meaningful SAPT energy components with minor computational cost is presented. These results deepen our understanding of the intricate energy balance and dedicated equilibrium of different noncovalent interactions in halogenated dimers.

Methylene blue dye removal by adsorption with coconut coir and acid-treated forms: adsorption-desorption study, MPR and modeling using artificial intelligence

A batch study is conducted to remove methylene blue (MB) dye from an aqueous solution using coconut coir and its acid-treated forms. The sulfuric acid-treated coconut coir (SCC), phosphoric acid-treated coconut coir (PCC) and untreated coconut coir (UCC) were prepared. Adsorbents were characterized via BET, SEM, pHPZC, FTIR, and FT-Raman analysis. Adsorbent’s total organic carbon (TOC) and the number of oxygen-containing functional groups like carboxylic, lactonic and phenolic, total acidic, and basic groups were also estimated. FTIR and FT-Raman studies establish functional groups responsible for dye removal. The operating parameters were optimized through experiments. Dye was removed maximally at the lowest temperature, 303K. Langmuir and Temkin isotherm models use linear equations, and the Pseudo-second-order kinetic model uses a nonlinear equation, which fits well. The adsorption capacity of SCC, PCC and UCC adsorbents was 88.18 ± 0.63 mg/g, 92.68 ± 2.74 mg/g and 76.39 ± 0.36 mg/g, respectively, for 303K. Intraparticle diffusion dominated more than film diffusion. Physisorption was estimated by applying the Dubinin-Radushkevich (D-R) isotherm model. Thermodynamic study indicates a spontaneous, favorable, exothermic process. 75% glacial acetic acid and 100% methanol are the best solvents for desorbing dye-loaded adsorbents. Porous coir and non-covalent interactions like hydrogen bonding, van der Waals force and π-π interaction between dye and coir are vital in the dye removal process. The regression equation has been successfully formulated, and the application of a genetic algorithm has predicted the percentage removal of methylene blue dye.

Self-assembled nanoparticles of costunolide and glycyrrhizic acid for enhanced ulcerative colitis treatment

Ulcerative colitis (UC) is a persistent inflammatory condition that specifically targets the colon and rectum. Existing therapies fail to adequately address the clinical requirements of people suffering from this ailment. Despite the acknowledged potential of nanomedicines in the field of anti-inflammatory treatment, their widespread use in clinical settings is impeded by their expensive nature and the uncertainty surrounding their safety profiles. This study illustrates that two naturally occurring phytochemicals, Costunolide (COS) and Glycyrrhizic acid (GA), form carrier-free, multifunctional spherical nanoparticles (NPs) through noncovalent interactions, such as π–π stacking and hydrogen bonding. The COS-GA NPs displayed a synergistic anti-inflammatory effect, providing much more evidently improved therapeutic benefits for dextran sodium sulfate (DSS)-induced UC mice due to more effective reduction in inflammation and oxidative stress than did equal dosages of COS or GA used alone. In addition, COS-GA NPs have biocompatibility and biosafety properties unique to them. This study will serve as affirmation of the potential of COS-GA NPs as innovative natural anti-inflammatory and antioxidant activities and also such agents as drug discovery in UC, leading possibly to better outcomes in people living with this disabling condition.

Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents

Deep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example of such systems is the zinc chloride–urea DES, already used in chemical synthesis, among others. In this paper, the ZnCl2(urea)2 crystal is studied from the point of view of its structure, infrared spectrum, and intermolecular interactions using periodic density functional theory and non-covalent interactions analysis. The two main structural motifs found in the crystal are a strongly hydrogen-bonded urea dimer assisted by chloride anions and a tetrahedral Zn(II) coordination complex. The crystal is composed of two interlocking parallel planes connected via the zinc cations. The infrared spectrum and bond lengths suggest a partially covalent character of the Zn−Cl bonds. The present analysis has far-reaching implications for the liquid ZnCl2–urea DES, explaining its fluidity, expected microstructure, and low conductivity, among others.

Multianalytical Approach to Understand Polyphenol-Mal d 1 Interactions to Predict Their Impact on the Allergenic Potential of Apples.

Interactions between phenolic compounds and the allergen Mal d 1 are discussed to be the reason for better tolerance of apple cultivars, which are rich in polyphenols. Because Mal d 1 is susceptible to proteolytic digestion and allergenic symptoms are usually restricted to the mouth and throat area, the release of native Mal d 1 during the oral phase is of particular interest. Therefore, we studied the release of Mal d 1 under different in vitro oral digestion conditions and revealed that only 6-15% of the total Mal d 1 present in apples is released. To investigate proposed polyphenol-Mal d 1 interactions, various analytical methods, e.g., isothermal titration calorimetry, 1H-15N-HSQC NMR, and untargeted mass spectrometry, were applied. For monomeric polyphenols, only limited noncovalent interactions were observed, whereas oligomeric polyphenols and browning products caused aggregation. While covalent modifications were not detectable in apple samples, a Michael addition of epicatechin at cysteine 107 in r-Mal d 1.01 was observed.

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments.

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.

Revealing the deterioration mechanism in gelling properties of pork myofibrillar protein gel induced by high-temperature treatments: Perspective on the protein aggregation and conformation

The purpose of the present study was to investigate the mechanism of gel deterioration of myofibrillar proteins (MP) gels induced by high-temperature treatments based on the protein aggregation and conformation. The results showed that the gel strength and water holding capacity of MP obviously increased and then decreased as the temperature increased, reaching the maximum value at 80 °C (P < 0.05). The microstructure analysis revealed that appropriate temperature (80 °C) contributed to the formation of a more homogeneous, denser, and smoother three-dimensional mesh structure when compared other treatment temperatures, whereas excessive temperature (95 °C) resulted in the formation of heterogeneous and large protein aggregates of MP, decreasing the continuity of gel networks. This was verified by the rheological properties of MP gels. The particle size (D4,3 and D3,2) of MP obviously increased with larger clusters at excessive temperature, and the surface hydrophobicity of MP decreased (P < 0.05), which has been linked to the formation of soluble or insoluble protein aggregates. Tertiary structure and secondary structure results revealed that the proteins had a tendency to be more stretched under higher temperature treatments, which resulted in a decrease in covalent interactions and non-covalent interactions, fostering the over-aggregation of MP. Therefore, our present study indicated that the degradation of MP gels treated at high temperatures was explained by protein aggregation and conformational changes in MP.

A novel one-dimensional thiocyanate-bridged cobalt(III) complex: synthesis, crystal structure characterization and Hirshfeld surface analysis.

A new one-dimensional thiocyanate-bridged cobalt(III) Schiff base complex, namely, catena-poly[[[4-bromo-2-((Z)-{[2-(thiophen-2-yl)ethyl]imino}methyl)phenolato-κ2N,O]cobalt(III)]-μ-thiocyanato-κ2N:S], [Co(SCN)(C13H11BrNOS)2]n or [Co(μ1,3-SCN)L2]n (1), where HL is 4-bromo-2-((Z)-{[2-(thiophene-2-yl)ethyl]imino}methyl)phenol, a bidentate Schiff base prepared from the condensation reaction of 5-bromosalicylaldehyde and 2-(thiophen-2-yl)ethylamine, has been synthesized by stirring Co(ClO4)2·6H2O, the Schiff base HL and ammonium thiocyanate (in a 1:2:1 molar ratio) in ethanol medium. The complex was characterized by FT-IR, electronic spectra and single-crystal X-ray diffraction (SC-XRD) studies. The SC-XRD data suggest that the compound crystallizes in the orthorhombic space group Pca21. The CoIII ion in 1 adopts a distorted octahedral geometry, the metal sites being six-coordinated by one thiocyanate N atom and one thiocyanate S atom in apical positions, and by two imine N atoms and two phenolate O atoms from two anionic L- ligands which form the basal plane. The thiocyanate ligand acts as a μ-1,3 bridge, joining neighbouring CoIII atoms and forming a uniform zigzag one-dimensional polymeric chain. The crystallographic data were also used in the Hirshfeld surface (HS) analysis, which aimed to investigate the nature and quantitative significance of any noncovalent intermolecular interactions inside the crystal lattice. The crystal void parameters have also been computed and show the molecules to be tightly packed.

Tough Supramolecular Hydrogels Crafted via Lignin-Induced Self-Assembly.

Supramolecular hydrogels are typically assembled through weak non-covalent interactions, posing a significant challenge in achieving ultra strength. Developing a higher strength based on molecular/nanoscale engineering concepts is a potential improvement strategy. Herein, a super-tough supramolecular hydrogel is assembled by gradually diffusing lignosulfonate sodium (LS) into a polyvinyl alcohol (PVA) solution. Both simulations and analytical results indicate that the assembly and subsequent enhancement of the crosslinked network are primarily attributed to LS-induced formation and gradual densification of strong crystalline domains within the hydrogel. The optimized hydrogel exhibits impressive mechanical properties with tensile strength of ≈20MPa, Young's modulus of ≈14MPa, and toughness of ≈50MJm⁻3, making it the strongest lignin-PVA/polymer hydrogel known so far. Moreover, LS provides the supramolecular hydrogel with excellent low-temperature stability (<-60°C), antibacterial, and UV-blocking capability (≈100%). Interestingly, the diffusion ability of LS is demonstrated for self-restructuring damaged supramolecular hydrogel, achieving 3D patterning on hydrogel surfaces, and enhancing the local strength of the freeze-thaw PVA hydrogel. The goal is to foster a versatile hydrogel platform by combining eco-friendly LS with biocompatible PVA, paving the way for innovation and interdisciplinarity in biomedicine, engineering materials, and forestry science.

Enhanced electrochemical oxidation and machine learning-assisted sensing of tetrabromobisphenol A using activated carbon facilitated CoWO4 heterostructures

The escalating levels of environmental pollution, particularly from commercially used products, highlight the imperative of efficient sensor technologies to facilitate timely and effective remediation strategies. Herein, a simple method is proposed to enhance the electrochemical performance of CoWO4 structures by coupling them with activated carbon (AC) for direct tetrabromobisphenol A (TBPA) oxidation. The systematic comparison shows that incorporation of AC with CoWO4 not only improves the overall effective surface area (ESA) of the catalyst by 1.8-fold but also improves the cyclic voltammetry (CV) based irreversible oxidation current by 2.0-fold owing to improved conductivity and surface characteristics. Differential pulse voltammetry (DPV) based optimization of the sensory characteristics confirmed robust electrocatalytic TBPA oxidation within a 0.1 to 1.0 µM concentration range, achieving a 0.024 µM detection limit within PBS (0.1 M) (pH 5.0). Moreover, density functional theory (DFT) analysis confirms the non-covalent interaction favorability between TBPA and CoWO4 surface, validating TBPA’s easy adsorption onto the catalytic surface and, thus, facilitated electron mobility between the molecule and the catalyst during the surface oxidation process. The DPV sensing interpreted using machine learning (ML) algorithms confirmed the detection accuracy of the developed sensor. Among the adopted models, artificial neural networks (ANN) achieved the highest R2 score (0.9659) and the lowest values across Mean Squared Error (MSE), Mean Absolute Error (MAE), and Root Mean Squared Error (RMSE) error matrices confirming its suitability in deciphering DPV correlations.Integrating ANN with DPV based electrocatalytic oxidation sensing underscores machine learning’s potential in analyzing complex electrochemical signatures, thus advancing intelligent sensing for precise environmental monitoring.

Subtle chemical modification around the flavin core to create diverse morphological assembly and sensing application

Herein, an intricate interplay of the non-covalent interactions induced via subtle chemical modification around the flavin core was envisaged to generate a diverse array of morphological features. Three different flavin analogues with the covalently linked carboxylic group, a glycine or proline entity were chosen along with a simple flavin entity and were investigated for their photophysical and morphological behavior. A systematic structural variation around flavin core has resulted in the formation of irregular shaped, fibrous, tapered fibers, sphere shaped and punctured disk shaped self-assembled structures. Interestingly, the carboxylic-flavin analogue was found to differentiate between monovalent alkali versus divalent alkaline earth metal ions. Overall, the present study highlights the importance of subtle structural engineering in regulating the diverse modes for self-assembled structures, which might be playing a role in designing chemical structures for practical applications.