Noncovalent Research Articles

Kohn-Sham fragment energy decomposition analysis.

We introduce the concept of Kohn-Sham fragment localized molecular orbitals (KS-FLMOs), which are Kohn-Sham molecular orbitals (MOs) localized in specific fragments constituting a generic molecular system. In detail, we minimize the local electronic energies of various fragments, while maximizing the repulsion between them, resulting in the effective localization of the MOs. We use the developed KS-FLMOs to propose a novel energy decomposition analysis, which we name Kohn-Sham fragment energy decomposition analysis, which allows for rationalizing the main non-covalent interactions occurring in interacting systems both in vacuo and in solution, providing physical insights into non-covalent interactions. The method is validated against state-of-the-art energy decomposition analysis techniques and with high-level calculations.

Protein-tannin interactions towards fabricating flame-retardant, UV-resistance, antibacterial and mechanical-reinforced PA66 fabric

The “Protein-polyphenol interactions” is a hot research topic in the field of interaction between biological macromolecules. Strong interactions between biomass polyphenolic tannins and proteins can be generated through covalent and non-covalent bonds. Inspired by this, keratin (Ker) and oxidized tannin (TA) was co-deposited on polyamide 66 (PA66) fabric to fabricate OTA/Ker coated PA66 fabric (PA66@OTA/Ker), which was then chelated with Fe3+ to prepare fire resistance and anti-dripping PA66 fabric (PA66@OTA/Ker@Fe). The results showed that the total heat release rate (THR), peak heat release rate (pHRR) and total smoke production (TSP) of PA66@OTA/Ker@Fe were reduced by 51 %, 57 % and 52 %, respectively. PA66@OTA/Ker@Fe had a residue char of 21.6 % at 800 °C under N2 atmosphere. In addition, the LOI of PA66@OTA/Ker@Fe increased from 20.5 % of the control sample to 28.5 % and reached a UL-94 V-0 rating. Besides, PA66@OTA/Ker@Fe exhibited excellent UV resistance, good mechanical and anti-bacterial properties. This work provides an eco-friendly strategy for developing multifunctional PA66 fabrics.

Stereoisomeric separation and chiral recognition mechanism study of star cyclodextrin polymer as the chiral stationary phase

BackgroundAs the derivatives of cyclodextrin (CD), cyclodextrin polymers (CDPs) effectively increase the concentration of CD units and construct supramolecular structures with unique stereoselectivity by the structure design. CDPs have shown significant potential in chiral separation, however, the process of stereoselective interactions on chiral stationary phases (CSPs) and the specific contribution of intermolecular forces are still a challenge issue. A comprehensive understanding of the chiral recognition mechanism of CDPs will help to optimize chiral separation conditions and design new CSPs. ResultsThe star CDP with a supermolecular structure was synthesized by grafting β-CD onto the external 6-position hydroxyl groups using β-CD as the parent nucleus. The enhanced host-guest recognition ability of CD supramolecular polymer structure provided better inclusion interaction and increased chiral recognition of the isomers. The Star-CD CSP with star CDP as a chiral ligand performed satisfactory stereoisomer separation ability with the separation factor (α) up to 2.0 for various quinoline alkaloid isomers and 1.89 for catechins. To elucidate its chiral separation mechanism, molecular docking was used to construct the three-dimensional visual models of the binding sites and the contribution of non-covalent interactions between Star-CD CSP and quinoline alkaloid isomers. In addition, the formation sites of non-covalent interactions on the CD monomers of the polymer side chains were confirmed from the actual geometric structure by analyzing the NMR chemical shift changes before and after the formation of complexes between Star-CD polymers and isomers. Combined with the mutual evidence of molecular simulation and chiral NMR, the specific recognition mechanism of selector-selectand complexes was comprehensively expounded. SignificanceThe multi-mode CSP based on cyclodextrin supramolecular structure provides new ideas for the stereoisomeric separation of complex chiral components with multiple chiral centers in natural products. Not limited to the macroscopic performance of the chromatographic separation, molecular docking explored the theoretical model of chiral recognition from the molecular level. The chiral NMR analysis confirmed the credibility of the model from the geometry structure, and then the recognition mechanism of multi-mode CSP was fully elaborated combining the above three aspects.

A Recyclable Ionogel with High Mechanical Robustness Based on Covalent Adaptable Networks.

Ionogels are an emerging class of soft materials for flexible electronics, with high ionic conductivity, low volatility, and mechanical stretchability. Recyclable ionogels are recently developed to address the sustainability crisis of current electronics, through the introduction of non-covalent bonds. However, this strategy sacrifices mechanical robustness and chemical stability, severely diminishing the potential for practical application. Here, covalent adaptable networks (CANs) are incorporated into ionogels, where dynamic covalent crosslinks endow high strength (11.3MPa tensile strength), stretchability (2396% elongation at break), elasticity (energy loss coefficient of 0.055 at 100% strain), and durability (5000 cycles of 150% strain). The reversible nature of CANs allows the ionogel to be closed-loop recyclable for up to ten times. Additionally, the ionogel is toughened by physical crosslinks between conducting ions and polymer networks, breaking the common dilemma in enhancing mechanical properties and electrical conductivity. The ionogel demonstrates robust strain sensing performance under harsh mechanical treatments and is applied for reconfigurable multimodal sensing based on its recyclability. This study provides insights into improving the mechanical and electrical properties of ionogels toward functionally reliable and environmentally sustainable bioelectronics.

Online ligand screening for cytochrome C from herbal medicines through “four-in-one” measurement

Affinity-oriented online ligand screening with LC coupled to different detectors is widely popular to capture active compounds from herbal medicines (HMs). However, false-positive extensively occurs because insufficient information is recorded for the existence and stability of ligand-protein complex. Here, efforts were made to advance the hit confidences via configuring post-column infusion-LC–energy-resolved-affinity MS (PCI-LC–ER-AMS) to achieve “four-in-one” monitoring of: 1) response decrement of potential ligands; 2) response decrement of protein; 3) ions relating to ligand-protein complexes; and 4) ligand-protein binding strength. Ligand fishing for Cyt C from HMs was conducted as a proof-of-concept. For utility justification, a mimic sample containing twelve well-defined ligands and two negative controls underwent LC separation and met Cyt C prior to Qtof-MS measurements. Compared to Cyt C- or ligand-free assay, twelve ligands instead of negative controls showed response decrements that were consistent with twelve negative peaks observed at retention times corresponding to the ligands in Cyt C ion current chromatogram. Serial ions correlating to each ligand-Cyt C complex were observed. After recording breakdown graphs, optimal collision energy (OCE) corresponding to the non-covalent bond dissociation was positively correlated with binding strength. Two HMs including Scutellariae Radix (SR) and Aconiti Lateralis Radix Preparata were investigated. Consequently, 24 compounds were merely fished from SR, and particularly, flavonoid glycosides exhibited greater OCEs and also binding strengths over aglycones. Affinity assays and cellular evaluations consolidated the significant interactions between each captured compound and Cyt C. Overall, PCI-LC–ER-AMS is eligible for confidence-enhanced online ligand screening for Cyt C from HMs through “four-in-one” measurement.

Metal-Based Drug-DNA Interactions and Analytical Determination Methods.

DNA structure has many potential places where endogenous compounds and xenobiotics can bind. Therefore, xenobiotics bind along the sites of the nucleic acid with the aim of changing its structure, its genetic message, and, implicitly, its functions. Currently, there are several mechanisms known to be involved in DNA binding. These mechanisms are covalent and non-covalent interactions. The covalent interaction or metal base coordination is an irreversible binding and it is represented by an intra-/interstrand cross-link. The non-covalent interaction is generally a reversible binding and it is represented by intercalation between DNA base pairs, insertion, major and/or minor groove binding, and electrostatic interactions with the sugar phosphate DNA backbone. In the present review, we focus on the types of DNA-metal complex interactions (including some representative examples) and on presenting the methods currently used to study them.

A HABA dye-based colorimetric assay to detect unoccupied biotin binding sites in an avidin-containing fusion protein.

Avidin-biotin binding, the most robust non-covalent protein-ligand interaction occurring in nature, has wide-ranging applications in biotechnology. A frequent challenge in these applications is accurately determining the number of unoccupied biotin binding sites in avidin-containing fusion proteins. We delineate a novel assay protocol in miniaturized format to quantify available biotin binding sites based on the affinity of the anionic dye 4'-hydroxyazobenzene-2-carboxylic acid for biotin binding sites within avidin. We apply this assay as a quality control assay to evaluate the number of available biotin binding sites in different fusion protein production batches. This method offers a streamlined alternative to fluorescence-based assays commonly employed to assess biotin binding, is less time-consuming than other methods and is applicable to diverse fusion proteins.

Development and Evaluation of Bis-benzothiazoles as a New Class of Benzothiazoles Targeting DprE1 as Antitubercular Agents.

Benzothiazole-bearing compounds have emerged as potential noncovalent DprE1 (decaprenylphosphoryl-β-d-ribose-2'-epimerase) inhibitors active against Mycobacterium tuberculosis. Based on structure-based virtual screening (PDB ID: 4KW5), a focused library of thirty-one skeletally diverse benzothiazole amides was prepared, and the compounds were assessed for their antitubercular activity against M.tb H37Ra. Most potent compounds 3b and 3n were further evaluated against the M.tb H37Rv strain by the microdilution assay method. Among the compounds evaluated, bis-benzothiazole amide 3n emerged as a hit molecule and demonstrated promising antitubercular activity with minimum inhibitory concentration (MIC) values of 0.45 μg/mL and 8.0 μg/mL against H37Ra and H37Rv, respectively. Based on the preliminary hit molecule (3n), a focused library of 12 more bis-benzothiazole amide derivatives was further prepared by varying the substituents on either side to obtain new leads and generate a structure-activity relationship (SAR). Among these compounds, 6a, 6c, and 6d demonstrated remarkable antitubercular activity with MIC values of 0.5 μg/mL against H37Ra and 1.0, 2.0, and 8.0 μg/mL against H37Rv, respectively. The most active compound, 6a, also displayed significant efficacy against four drug-resistant tuberculosis strains. Compound 6a was assessed for in vitro cytotoxicity against the HepG2 cell line, and it displayed insignificant cytotoxicity. Furthermore, time-kill kinetic studies demonstrated time- and dose-dependent bactericidal activity of this compound. The GFP release assay revealed that compound 6a targets the inhibition of a cell wall component. SNPs in dprE-1 gene assessment revealed that compound 6a binds to tyrosine at position 314 of DprE1 and replaces it with histidine, causing resistance similar to that of standard TCA1. In silico docking studies further suggest that the strong noncovalent interactions of these compounds may lead to the development of potent noncovalent DprE1 inhibitors.

N-Heterocyclic Carbene-Catalyzed Asymmetric SN2 Alkylation via Noncovalent Activation.

The field of asymmetric catalysis has been developed by exploring noncovalent interactions, particularly within N-heterocyclic carbene-mediated processes. Despite challenges due to the limited number of compatible electrophiles (predominantly π-acceptors), this study introduces the first asymmetric α-alkylation of 3-aryl oxindoles using Csp3 electrophiles. The innovative protocol integrates diverse oxindoles and alkyl, allyl, and propargyl electrophiles, achieving high yields and enantioselectivities. Preliminary mechanistic explorations support a noncovalent catalytic mechanism, enhancing the tool kit for constructing complex chiral molecules with potential applications.

Carrier-Free Nanoagent Interfering with Cancer-Associated Fibroblasts' Metabolism to Promote Tumor Penetration for Boosted Chemotherapy.

Elevated production of extracellular matrix (ECM) in tumor stroma is a critical obstacle for drug penetration. Here we demonstrate that ATP-citrate lyase (ACLY) is significantly upregulated in cancer-associated fibroblasts (CAFs) to produce tumor ECM. Using a self-assembling nanoparticle-design approach, a carrier-free nanoagent (CFNA) is fabricated by simply assembling NDI-091143, a specific ACLY inhibitor, and doxorubicin (DOX) or paclitaxel (PTX), the first-line chemotherapeutic drug, via multiple noncovalent interactions. After arriving at the CAFs-rich tumor site, NDI-091143-mediated ACLY inhibition in CAFs can block the de novo synthesis of fatty acid, thereby dampening the fatty acid-involved energy metabolic process. As the lack of enough energy, the energetic CAFs will be in a dispirited state that is unable to produce abundant ECM, thereby significantly improving drug perfusion in tumors and enhancing the efficacy of chemotherapy. Such a simple drug assembling strategy aimed at CAFs' ACLY-mediated metabolism pathway presents the feasibility of stromal matrix reduction to potentiate chemotherapy.

Sensitive Coatings Based on Molecular-Imprinted Polymers for Triazine Pesticides' Detection.

Triazine pesticide (atrazine and its derivatives) detection sensors have been developed to thoroughly check for the presence of these chemicals and ultimately prevent their exposure to humans. Sensitive coatings were designed by utilizing molecular imprinting technology, which aims to create artificial receptors for the detection of chlorotriazine pesticides with gravimetric transducers. Initially, imprinted polymers were developed, using acrylate and methacrylate monomers containing hydrophilic and hydrophobic side chains, specifically for atrazine, which shares a basic heterocyclic triazine structure with its structural analogs. By adjusting the ratio of the acid to the cross-linker and introducing acrylate ester as a copolymer, optimal non-covalent interactions were achieved with the hydrophobic core of triazine molecules and their amino groups. A maximum sensor response of 546 Hz (frequency shift/layer height equal to 87.36) was observed for a sensitive coating composed of 46% methacrylic acid and 54% ethylene glycol dimethacrylate, with a demonstrated layer height of 250 nm (6.25 kHz). The molecularly imprinted copolymer demonstrated fully reversible sensor responses, not only for atrazine but also for its metabolites, like des-ethyl atrazine, and structural analogs, such as propazine and terbuthylazine. The efficiency of modified molecularly imprinted polymers for targeted analytes was tested by combining them with a universally applicable quartz crystal microbalance transducer. The stable selectivity pattern of the developed sensor provides an excellent basis for a pattern recognition procedure.

Extraction and detection of sulfonamide antibiotics in milk using magnetic solid-phase adsorbent based on molecular mechanics and DFT calculations

Based on the foundation of calculations in molecular mechanics and density functional theory (DFT) for in-depth mechanistic studies, this paper proposes the sample multi-residue analysis method of five common sulfonamide antibiotics (SAs) in milk. Fe3O4 nanoparticles modified magnetic graphene oxide nanoribbons (Mag-GONRs) with superior dispersibility and dispersion stability, were developed and firstly utilized to rapidly extract residual SAs from milk. Therefore, various SAs in complex samples could be simultaneously determined solely by high performance liquid chromatography-ultraviolet detector (HPLC-UV) without the need for complicated pretreatment processes. In order to obtain satisfactory extraction efficiency, indispensable investigation and optimization were conducted on some parameters influencing the extraction efficiency. And the extracted SAs were determined by. Good linearity for all analytes was achieved with appropriate correlation coefficients (R2 higher than 0.9978). The limits of detection ranged from 0.060 to 0.075 ng·mL−1. Recoveries of the sulfonamides in spiked milk samples were between 79.6 % and 114.6 %, with relative standard deviations within 12 %. Interestingly, with the assistant of computational chemistry, the efficient extraction of Mag-GONRs onto SAs has been validated at the molecular and quantum levels, further elucidating the adsorption mechanism based on non-covalent interactions. In the context of theoretical research and experimental results mutually supporting each other, a practical detection method with actual application value has been proposed in monitoring the residual sulfonamides in milk by the common devices.

Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors.

Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed as targeted covalent inhibitors that have some selectivity for and covalently inhibit cyclin-dependent kinase 12 (CDK12). CDK12 is involved in the transcription of elongated RNA sections that results in the DM1 condition. The covalent bond is achieved after nucleophilic addition to a Michael acceptor warhead. Previous studies of the conformational preferences of thio-Michael additions have focused on characterizing the reaction profile based on the distance between the sulfur and β-carbon atoms. Rotamerism, however, has not been investigated extensively. Here, we use high-level quantum chemistry calculations, up to coupled cluster with single, double, and perturbative triple excitations [CCSD(T)], to characterize the nucleophilic addition of an archetypal nucleophile, methanethiolate, to various nitrogen-containing Michael acceptors which are representative of the small-molecule covalent inhibitors. By investigating the structural, energetic, and electronic properties of the resulting enolates, as well as their reaction profiles, we show that synclinal additions are generally energetically favored over other additions due to the greater magnitude of attractive noncovalent interactions permitted by the conformation. The calculated transition states associated with the addition process indicate that synclinal addition proceeds via lower energetic barriers than antiperiplanar addition and is the preferred reaction pathway.

Efficient Encapsulation of β-Lapachone into Self-Immolative Polymer Nanoparticles for Cyclic Amplification of Intracellular Reactive Oxygen Species Stress.

The selective upregulation of intracellular oxidative stress in cancer cells presents a promising approach for effective cancer treatment. In this study, we report the integration of enzyme catalytic amplification and chemical amplification reactions in β-lapachone (Lap)-loaded micellar nanoparticles (NPs), which are self-assembled from reactive oxygen species (ROS)-responsive self-immolative polymers (SIPs). This integration enables cyclic amplification of intracellular oxidative stress in cancer cells. Specifically, we have developed ROS-responsive SIPs with phenylboronic ester triggering motifs and hexafluoroisopropanol moieties in the side chains, significantly enhancing Lap loading efficiency (98%) and loading capacity (33%) through multiple noncovalent interactions. Upon ROS activation in tumor cells, the Lap-loaded micellar NPs disassemble, releasing Lap and generating additional ROS via enzyme catalytic amplification. This process elevates intracellular oxidative stress and triggers polymer depolymerization in a positive feedback loop. Furthermore, the degradation of SIPs via chemical amplification produces azaquinone methide intermediates, which consume intracellular thiol-related substrates, disrupt intracellular redox hemostasis, further intensify oxidative stress, and promote cancer cell apoptosis. This work introduces a strategy to enhance intracellular oxidative stress by combining enzymatic and chemical amplification reactions, providing a potential pathway for the development of highly efficient anticancer agents.

RAFT polymerization assisted P(NIPAm-co-AAc)-AEMR integrated PVA hydrogels: Dual responsive features, texture analysis, and cytotoxicity studies

Modified P(NIPAm-co-AAc) copolymers are prepared using Radical Addition Fragmentation Chain Transfer (RAFT) copolymerization by varying the concentration of castor oil sourced acrylated epoxy methyl ricinoleate (AEMR). Subsequently, hydrogels are prepared by integrating copolymers with polyvinyl alcohol (PVA) via freeze-thaw process. The employment of RAFT polymerization yielded copolymers with dispersity (D) value of 1.2–1.3 revealing the formation of structurally well controlled polymer chains. The lower critical solution temperature (LCST) of the copolymers (∼30–35 °C) are tuned to the range of physiological temperature (∼37 °C) in PVA hydrogel system. Temperature dependent viscoelastic properties indicated that the characteristics of copolymeric solutions and hydrogels are composition dependent while undergoing noncovalent interactions and the conformational changes and the samples showed extremely elastic behaviour beyond LCST. Swelling ratio of hydrogels are also found to be pH dependent, which displayed higher swelling ratio in alkaline and reduced swelling ratio in acidic medium. Cytotoxicity studies with L929 cells showed that the copolymers and hydrogels exhibited desirable biocompatibility, which gets improved with AEMR concentrations. Thus, these dual responsive PA-AEMR-PVA smart hydrogels can be used as a viable functional material for possible bio-medical applications.

Influence of nitrogen exchange in the core-shell structure of naphthalenediimide molecules on the advancement of quantum electronic properties

This study explores how nitrogen substitution and gold electrodes collectively influence the electronic characteristics of naphthalenediimide (NDI) molecules (M = 1, 2, and 3) through theoretical analysis. Utilizing ELF, LOL, QTAIM, and NCI analyses, we reveal significant alterations in NDI's electronic structure and interactions upon bonding with gold electrodes (Au-M-Au). Both ELF and LOL analyses demonstrate increased electron localization and delocalization on the NDI surface due to gold electrodes, with a stronger effect on nitrogen-doped molecules (M = 2, 3). QTAIM analysis confirms favorable non-covalent interactions, including evident hydrogen bonding, between NDI molecules and gold electrodes, notably intensified in doped molecules, especially the Au…O interaction. NCI analysis provides insight into the diverse interactions within the molecular system. Overall, this research highlights the crucial role of gold electrodes and nitrogen substitution in fine-tuning NDI molecules' electronic properties. The observed modulation of electron behavior and formation of beneficial interactions with gold electrodes hint at promising applications for doped NDI-gold systems requiring efficient charge transport mechanisms.

Supramolecular gels: a versatile crystallization toolbox.

Supramolecular gels are unique materials formed through the self-assembly of molecular building blocks, typically low molecular weight gelators (LMWGs), driven by non-covalent interactions. The process of crystallization within supramolecular gels has broadened the scope of the traditional gel-phase crystallization technique offering the possibility of obtaining crystals of higher quality and size. The broad structural diversity of LMWGs allows crystallization in multiple organic and aqueous solvents, favouring screening and optimization processes and the possibility to search for novel polymorphic forms. These supramolecular gels have been used for the crystallization of inorganic, small organic compounds of pharmaceutical interest, and proteins. Results have shown that these gels are not only able to produce crystals of high quality but also to influence polymorphism and physicochemical properties of the crystals, giving rise to crystals with potential new bio- and technological applications. Thus, understanding the principles of crystallization in supramolecular gels is essential for tailoring their properties and applications, ranging from drug delivery systems to composite crystals with tunable stability properties. In this review, we summarize the use of LMWG-based supramolecular gels as media to grow single crystals of a broad range of compounds.

Strategies and Mechanisms of First-Row Transition Metal-Regulated Radical C-H Functionalization.

Radical C-H functionalization represents a useful means of streamlining synthetic routes by avoiding substrate preactivation and allowing access to target molecules in fewer steps. The first-row transition metals (Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) are Earth-abundant and can be employed to regulate radical C-H functionalization. The use of such metals is desirable because of the diverse interaction modes between first-row transition metal complexes and radical species including radical addition to the metal center, radical addition to the ligand of metal complexes, radical substitution of the metal complexes, single-electron transfer between radicals and metal complexes, hydrogen atom transfer between radicals and metal complexes, and noncovalent interaction between the radicals and metal complexes. Such interactions could improve the reactivity, diversity, and selectivity of radical transformations to allow for more challenging radical C-H functionalization reactions. This review examines the achievements in this promising area over the past decade, with a focus on the state-of-the-art while also discussing existing limitations and the enormous potential of high-value radical C-H functionalization regulated by these metals. The aim is to provide the reader with a detailed account of the strategies and mechanisms associated with such functionalization.

High-intensity ultrasound-modified Jerusalem artichoke leaf protein for stabilizing corn oi-in-water emulsion and Enhacing curcumin delivery

Jerusalem artichoke leaf protein (JALP) has limited applications because of its dark color, even though Jerusalem artichoke is a cash crop. This study utilized high-intensity ultrasound (HIUS) (≤ 600 W) to modify the physicochemical characteristics and functional properties of JALP. Compared with the JALP, all the HIUS-treated JALP (UJALP) samples had a lighter brown color, higher absolute ζ-potential value, lower Z-average size, higher surface hydrophobicity, higher water solubility, lower turbidity, more -SH group, and higher water-holding, oil-holding, emulsifying and foaming capacities. The HIUS treatment disrupted certain non-covalent and SS bonds, promoted protein depolymerization, change protein secondary structures, causing partial unfolding of protein and exposure of some charged groups, hydrophobic groups and chromophores (like tryptophan and tyrosine). The UJALP-stabilized corn oil-in-water emulsions (UJALPEs) were more stable than the JALP-stabilized emulsion (JALPE). The bioaccessibility of curcumin in the JALPE (56.38 %) was significantly lower than in the UJALPE-600 W (64.59 %).

Computational Design of Ligands for the Ir-Catalyzed C5-Borylation of Indoles through Tuning Dispersion Interactions.

The indole moiety is ubiquitous in natural products and pharmaceuticals. C-H borylation of the benzenoid moiety of indoles is a challenging task, especially at the C5 position. We have combined computational and experimental studies to introduce multiple noncovalent interactions, especially dispersion, between the substrate and catalytic ligand to realize C5-borylation of indoles with high reactivity and selectivity. The successful computational predictions of new ligands should be suitable for ligand design in other transition-metal catalyzed reactions.