Noncovalent Research Articles

Supramolecular assemblies involving unusual N(nitrile)∙∙∙π(fum) and nitrile-nitrile non-covalent contacts in fumarato and succinato bridged polymers of Co(II) and Ni(II): Experimental and theoretical studies

Two new Co(II) and Ni(II) coordination polymers viz. [Co(H2O)2(μ-fum)(3-CNpy)2]n (1) and {[Ni(H2O)2(μ-succ)(4-CNpy)2]·2H2O}n (2) (where, fum= fumarate, CNpy = cyanopyridine, succ = succinate) have been synthesized and characterized using single crystal XRD, elemental analysis, spectroscopic (IR and electronic) techniques and TGA. Compound 1 crystallizes as a fumarato bridged Co(II) polymer; whereas, compound 2 is a succinato bridged Ni(II) polymer. The presence of various non-covalent interactions in the compounds stabilizes the layered assemblies of the compounds. Antiparallel nitrile∙∙∙nitrile interactions are observed in both the crystal structures involving the nitrile moieties of coordinated CNpy which provide rigidity to the compounds. Further analysis reveals that the N-atom of –CN group of 3-CNpy in 1 is involved in unusual N(nitrile)∙∙∙π(fum) interactions with the π-electrons of the C=C bond of fum. Enclathrated (H2O)2 cores within the supramolecular host cavity of compound 2 provides additional reinforcement to the crystal structure. We have also carried out theoretical studies to analyze the π-stacking and H-bonding interactions present in the crystal structure of compound 1 using quantum theory of atoms-in-molecules (QTAIM), non-covalent interaction plot (NCI plot) and molecular electrostatic potential (MEP) surface analysis. The MEP value at the N-atom of the cyano group of 1 is negative and the value is neutral over the double bond of the fum; indicating the possibilities of formation of N(nitrile)∙∙∙π(fum) interactions. Energetic analysis suggests that antiparallel π-stacking observed between the 3-CNpy moieties in 1 is the most dominating force followed by N(nitrile)∙∙∙π(fum) interaction and finally the H-bonds.

Unveiling the Selectivity of Ru(II)-Catalyzed C-H Activation for Defluorinative Cyclization of 2-Arylbenzimidazole and Trifluoromethyl Diazo: A DFT Study.

The synthesis of monofluorinated heterocyclic compounds by C-H activation combined with defluorination is useful. Studies on the reaction mechanism and selectivity have shown that these processes play a positive role in promoting the development of monofluorinated reactions. Density functional theory (DFT) calculations were performed to investigate the mechanism and selectivity of Ru(II)-catalyzed 2-arylbenzimidazole with trifluoromethyl diazo. DFT calculations showed that C-H activation occurs through a concerted metalation/deprotonation (CMD) mechanism. After that, deprotonation and defluorinative cyclization are assisted by acetate and trifluoroethanol (TFE). Further mechanistic insights through noncovalent interaction (NCI) analysis were also obtained to elucidate the origin of the selectivity in the defluorination process.

A remarkably simple dispersion damping scheme and the DH24 double hybrid density functional.

In recent papers, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] and then Becke [J. Chem. Phys. 159, 241101 (2023)] have developed a novel double hybrid density functional, "DH23," whose terms are based on good local physics. Its 12 coefficients are trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.73 kcal/mol for the revDH23 variant). Here, we simplify DH23 by introducing a dispersion damping scheme involving atomic numbers only and one global parameter. The resulting new functional, "DH24," performs as well as its predecessors.

The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis.

Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.

Asymmetric hydrogenation of ketimines with minimally different alkyl groups.

Asymmetric catalysis allows the synthesis of optically active compounds, often requiring the differentiation between two substituents on prochiral substrates1. Despite decades of development of mainly noble metal catalysts, achieving differentiation between substituents with similar steric and electronic properties remains a significant challenge2,3. Here, we introduce a class of earth-abundant manganese catalysts for the asymmetric hydrogenation of dialkyl ketimines to give a range of chiral amine products. These catalysts distinguish between pairs of minimally differentiated alkyl groups bound to the ketimine, such as methyl and ethyl, and even subtler distinctions, like ethyl and n-propyl. The degree of enantioselectivity can be adjusted by modifying the components of the chiral manganese catalyst. This reaction demonstrates a wide substrate scope and achieves a turnover number (TON) of up to 107,800. Our mechanistic studies indicate that the exceptional stereoselectivity arises from the modular assembly of confined chiral catalysts and cooperative non-covalent interactions between the catalyst and the substrate.

Noncovalent Interaction Guided Precise Photoluminescence Regulation of Gold Nanoclusters in Both Isolate Species and Aggregate States

AbstractDesigning luminophores bright in both isolate species and aggregate states is of great importance in many emerging cutting‐edge applications. However, the conventional luminophores either emit in isolate species but quench in aggregate state or emit in aggregate state but darken in isolate species. Here we demonstrate that the precise regulation of noncovalent interactions can realize luminophores bright in both isolate species and aggregate states. It is firstly discovered that the intra‐cluster interaction enhances the emission of atomically precise Au25(pMBA)18 (pMBA=4‐mercaptobenzoic acid), a nanoscale luminophore, while the inter‐cluster interaction quenches the emission. The emission enhancing strategies are then well‐designed by both introducing exogenous substances to block inter‐cluster interaction and surface manipulation of Au25(pMBA)18 at the molecular level to enhance intra‐cluster interaction, opening new possibilities to controllably enhance the luminophore's photoluminescence in both isolate species and aggregate states in different phases including aqueous solution, solid state and organic solvents.

Theoretical and experimental study of a new antioxidant xanthone: Solvent and intramolecular hydrogen bond effects

Free radicals are harmful reactive species that cause various problems in the human body. Antioxidant compounds, such as xanthones found in natural products, can help prevent these effects. This study focuses on the antioxidant behavior of ravenelin (RVL) and ravenelin B (RVLB), a newly discovered xanthone in the Exserohilum rostratum fungus. Both experimental and in silico tests were conducted, comparing them to ascorbic acid, a standard antioxidant. The results showed that RVL has a lower bond dissociation energy (312 kJ/mol) than ascorbic acid (313 kJ/mol), indicating comparable antioxidant performance. This difference is mild but agrees with the experiment that indicates RVL efficiency is equivalent to ascorbic acid at low concentrations. RVLB, however, demands higher dissociation energy (323 kJ/mol) and consequently it has a lower antioxidative efficiency. Thus, antioxidant capacity is found as RVL>ascorbic acid>RVLB. From experimental assays, the RVL performance was confirmed through experimental tests at different solute concentrations. The study also examines the effects of solvents and intramolecular hydrogen bonds. Ravenelin molecules present three hydroxyl groups involved in intramolecular OH⋯O interactions. However, analysis based on the infrared spectra, as well as Bader's theory and non-covalent interactions done in water solvent showed that the two strongest H-bonds (≈−37 kJ/mol) better stabilize the molecular structure, but are not favorable to antioxidant reactions, indicating that hydrogen scavenging occurs at the less hydrogen-bonded hydroxyl group. The solvent also plays an active role first in facilitating hydrogen abstraction besides changing the hydrogen scavenging mechanism according to the environmental polarizability. Additionally, the antioxidant mechanism of ravenelin molecules changes from nonpolar to polar solvents, allowing for hydrogen abstraction.

Noncovalent Interaction Guided Precise Photoluminescence Regulation of Gold Nanoclusters in Both Isolate Species and Aggregate States.

Designing luminophores bright in both isolate species and aggregate states is of great importance in many emerging cutting-edge applications. However, the conventional luminophores either emit in isolate species but quench in aggregate state or emit in aggregate state but darken in isolate species. Here we demonstrate that the precise regulation of noncovalent interactions can realize luminophores bright in both isolate species and aggregate states. It is firstly discovered that the intra-cluster interaction enhances the emission of atomically precise Au25(pMBA)18 (pMBA=4-mercaptobenzoic acid), a nanoscale luminophore, while the inter-cluster interaction quenches the emission. The emission enhancing strategies are then well-designed by both introducing exogenous substances to block inter-cluster interaction and surface manipulation of Au25(pMBA)18 at the molecular level to enhance intra-cluster interaction, opening new possibilities to controllably enhance the luminophore's photoluminescence in both isolate species and aggregate states in different phases including aqueous solution, solid state and organic solvents.

Catechol-induced covalent modifications modulate the aggregation tendency of α-synuclein: An in-solution and in-silico study.

Parkinson's disease (PD) stands as a challenging neurodegenerative condition characterized by the emergence of Lewy Bodies (LBs), intracellular inclusions within dopaminergic neurons. These LBs harbor various proteins, prominently including α-Synuclein (Syn) aggregates, implicated in disease pathology. A promising avenue in PD treatment involves targeting Syn aggregation. Recent findings from our research have shown that 3,4-dihydroxyphenylacetic acid (DOPAC) and 3,4-dihydroxyphenylethanol (DOPET) possess the ability to impede the formation of Syn fibrils by disrupting the aggregation process. Notably, these compounds primarily engage in noncovalent interactions with the protein, leading to the formation of off-pathway oligomers that deter fibril growth. Through proteolysis studies and mass spectrometry (MS) analysis, we have identified potential covalent modifications of Syn in the presence of DOPAC, although the exact site remains elusive. Employing molecular dynamics simulations, we delved into how DOPAC-induced covalent alterations might affect the mechanism of Syn aggregation. Our findings indicate that the addition of a covalent adduct on certain residues enhances fibril flexibility without compromising its secondary structure stability. Furthermore, in the monomeric state, the modified residue fosters novel bonding interactions, thereby influencing long-range interactions between the N- and C-termini of the protein.

Study on the molecular interactions between givosiran and theophylline by surface-enhanced Raman spectroscopy, biolayer interferometry, and visible/fluorescence spectroscopy

Givosiran is a small-interfering ribonucleic acid (siRNA) drug used to treat acute hepatic porphyria. As an exogenous double-stranded RNA, givosiran has a specific spatial conformation. When they coexist, givosiran and small-molecule drugs may interact through non-covalent bonds, which may affect their efficacies. This study aimed to evaluate the molecular interaction between givosiran and three structurally-related small-molecule drugs. We combined surface-enhanced Raman spectroscopy, biolayer interferometry, and visible/fluorescence spectroscopy with a methylene blue probe to study the molecular interaction between givosiran and theophylline, caffeine, and theobromine. Molecular interactions were observed only between theophylline and givosiran, with an affinity constant (KD) of 64.2 μM. The main binding forces were hydrogen bonds and van der Waals forces, and the equilibrium binding constant (KA) was 1.855 × 104 L·mol−1. This study focused on the 5 W (Whether, Where, Why, hoW about the tendency, hoW strong) issues of the molecular interaction between givosiran and small-molecule chemical drugs. Our findings contradict the previous perception that the probability of drug–drug interactions (DDI) between nucleic acid and small-molecular drugs is low. Our study illustrates that a combination of direct and indirect analytical methods will pave a new way for future siRNA-related unknown interactions studies.

The carrier function and inhibition effect on benign prostatic hyperplasia of a glucan from Epimedium brevicornu Maxim

Epimedium, a traditional Chinese medicine commonly used as a dietary supplement, contains polysaccharides and flavonoids as its main bioactive ingredients. In this study, a neutral homogeneous polysaccharide (EPSN-1) was isolated from Epimedium brevicornu Maxim. EPSN-1 was identified as a glucan with a backbone of →4)-α-D-Glcp-(1→, branched units comprised α-D-Glcp-(1→6)-α-D-Glcp-(1→, β-D-Glcp-(1→6)-β-D-Glcp-(1→ and α-D-Glcp-(1→ connected to the C6 position of backbone. The conformation of EPSN-1 in aqueous solution indicated its potential to form nanoparticles. This paper aims to investigate the carrier and pharmacodynamic activity of EPSN-1. The findings demonstrated that, on the one hand, EPSN-1, as a functional ingredient, may load Icariin (ICA) through non-covalent interactions, improving its biopharmaceutical properties such as solubility and stability, thereby improving its intestinal absorption. Additionally, as an effective ingredient, EPSN-1 could help maintain the balance of the intestinal environment by increasing the abundance of Parabacteroides, Lachnospiraceae UGG-001, Anaeroplasma, and Eubacterium xylanophilum group, while decreasing the abundance of Allobaculum, Blautia, and Adlercreutzia. Overall, this dual action of EPSN-1 sheds light on the potential applications of natural polysaccharides, highlighting their dual role as carriers and contributors to biological activity.

A data-driven exploration of the complexity of the phosphorus-centered pnictogen bonds

Phosphorus-centered pnictogen bonds, similar to well-studied halogen bonds, play a vital role in molecular recognition and assembly. This study aims to explain how pnictogen bonds interact with other noncovalent interactions. A model system, phosphines (PH3), which is also present in phosphorus cycles and reduces planetary atmospheres, is examined. The investigation of the phosphorus trifluoride (PF3) molecule explores its substituent effects. To generate a broad spectrum of molecular configurations, a specially tailored protocol for sampling and optimisation was implemented. The configurations were refined to uncover primary interaction patterns, and a clustering algorithm revealed unique interaction patterns. This report presents the energy stability and distribution of all the clusters. Our findings verify the prevalent presence of pnictogen bonds, identified by their geometric characteristics and co-occurrence with hydrogen bonds, which show an almost linear correlation. Another significant discovery is the correlation between various energy decomposition elements, especially regarding the electrostatic energy and overall binding energy. These results are anticipated to significantly contribute towards our comprehension of non-covalent interactions among phosphorus-containing molecules and the formulation of empirical models having physical interpretations.

Mouldable multicomponent low molecular weight supergelators

ABSTRACT A significant drawback of gels formed from low molecular weight gelators (LMWGs) is their typically poor mechanical stability due to the weak non-covalent interactions responsible for forming the gel. Here, we present a rare example of bicomponent gels prepared from LMWGs that show excellent mechanical stability even at <0.7 wt.% gelator loading. The gels can be moulded into any desired shape, without creep deformation. Dynamic diffusion of a guest, like β-carotene, from a spiked gel into its submerged solvent environment is explored through UV–vis spectrophotometry and NMR techniques, showing that the integrity of the gel network remains in the presence of the guest.

Mechanism on microbial transglutaminase and Tremella fuciformis polysaccharide-mediated modification of lactoferrin: Development of functional food

Lactoferrin (LF) with various biological functions demonstrates great application potential. However, its application was restricted by its poor gelation and instability. The aim of this work was to explore the effect of microbial transglutaminase (MTGase) and Tremella fuciformis polysaccharide (TP) on the functional properties of LF. The formation of a self-supporting LF gel could be induced by MTGase through generating covalent crosslinks between the LF protein molecules. Meanwhile, TP was introduced into the gel system to improve the strength of LF-TP composite gels by enhancing non-covalent interactions such as hydrogen bond and electrostatic interactions during gel formation. Additionally, the LF-TP composite gel exhibited outstanding functional characteristics such as gastrointestinal digestive stability and antioxidant property. This work clarified the mechanism on MTGase and TP-mediated modification of lactoferrin, offered a novel strategy to increase the functional characteristics of LF, and enlarged the application range of LF and TP.

Revealing the mechanism, Regio- and stereo selectivity and solvent effects of [3 + 2] cycloaddition reactions involving N-benzyl fluoro nitrone and electron-deficient alkynes

The [3 + 2] cycloaddition reactions (32CA) between N-benzyl fluoro nitrone and electron-deficient dipolarophiles alkynes have been studied using molecular electron density theory at the B3LYP-D3/6-31G(d) level. The findings indicate that, in these 32CA reactions, a one-step mechanism is in play with asynchronous transition states. The topological analyses of these transition states are consistent with the presence of non-covalent interactions at the bonding regions between atoms. The analysis of the energy profile in gas phase and in the presence of solvents indicates a preference for a specific site addition over the others. Parr functions were thus used to justify such regioselectivity. In addition, we show that solvents do not modify the regioselectivity achieved, but it increases the activation energies and reduces the exothermic nature of this 32CA reaction. The present findings are in agreement with the experimental results.

Catalytic Asymmetric Cascade Dearomatization of Indoles via a Photoinduced Pd-Catalyzed 1,2-Bisfunctionalization of Butadienes.

Photoinduced Pd-catalyzed bisfunctionalization of butadienes with a readily available organic halide and a nucleophile represents an emerging and attractive method to assemble versatile alkenes bearing various functional groups at the allylic position. However, enantiocontrol and/or diastereocontrol in the C-C or C-X bond-formation step have not been solved due to the open-shell process. Herein, we present a cascade asymmetric dearomatization reaction of indoles via photoexcited Pd-catalyzed 1,2-biscarbonfunctionalization of 1,3-butadienes, wherein asymmetric control on both the nucleophile and electrophile part is achieved for the first time in photoinduced bisfunctionalization of butadienes. This method delivers structurally novel chiral spiroindolenines bearing two contiguous stereogenic centers with high diastereomeric ratios (up to >20 : 1 dr) and good to excellent enantiomeric ratios (up to 97 : 3 er). Experimental and computational studies of the mechanism have confirmed a radical pathway involving excited-state palladium catalysis. The alignment and non-covalent interactions between the substrate and the catalyst were found to be essential for stereocontrol.

A Simple Organo-electrocatalysis System for the Chlor-related Industry.

Consuming a substantial quantum of energy (~165 TW h), the chlor-alkali industry garners considerable scholarly and industrial interest, with the anode reaction involving the oxidation of chloride ions being a paramount determinant of reaction rates. While the dimensionally stable anode (DSA) displays commendable catalytic activity and longevity, they rely on precious metals and exhibit a non-negligible side reaction in sodium hypochlorite (NaClO) production, underscoring the appeal of metal-free alternatives. However, the molecules and systems currently available are characterized by intricate complexity and are not amenable to large-scale production. Herein, we have successfully developed an economical and highly efficient molecular catalyst, demonstrating superior performance compared with the former organic molecules in the chloride ion oxidation process (COP) for the production of both chlorine gas (Cl2) and NaClO. The molecule of 2N only needs 92 mV to reach a current density of 1000mA cm-2, with a small cost of only 0.002 $ g-1. Furthermore, we propose a novel mechanism underpinned by non-covalent interactions, serving as the foundation for an innovative approach to the design of efficient anodes for the COP.

In-situ noncovalent interaction of ammonium ion enabled C–H bond functionalization of polyethylene glycols

The noncovalent interactions of ammonium ion with multidentate oxygen-based host has never been reported as a reacting center in catalytic reactions. In this work, we report a reactivity enhancement process enabled by non-covalent interaction of ammonium ion, achieving the C–H functionalization of polyethylene glycols with acrylates by utilizing photoinduced co-catalysis of iridium and quinuclidine. A broad scope of alkenes can be tolerated without observing significant degradation. Moreover, this cyano-free condition respectively allows the incorporation of bioactive molecules and the PEGylation of dithiothreitol-treated bovine serum albumin, showing great potentials in drug delivery and protein modification. DFT calculations disclose that the formed α-carbon radical adjacent to oxygen-atom is reduced directly by iridium before acrylate addition. And preliminary mechanistic experiments reveal that the noncovalent interaction of PEG chain with the formed quinuclidinium species plays a unique role as a catalytic site by facilitating the proton transfer and ultimately enabling the transformation efficiently.

Novel Salts of Heterocyclic Polyamines and 5-Sulfosalicylic Acid: Synthesis, Crystal Structure, and Hierarchical Supramolecular Interactions

A series of novel salts of heterocyclic polyamines with 5-sulfosalicylic acid (C4H7N4+)(C7H5O6S−)∙2(H2O) (1), (C4H6ClN4+)(C7H5O6S−)∙H2O (2), (C5H8N3+)(C7H5O6S−)∙H2O (3), (C5H7N6+)(C7H5O6S−)∙H2O (4), (C6H14N22+)(C7H4O6S2−)∙H2O (5), and (C14H19N2+)(C7H5O6S−) (6) have been successfully synthesized. Their crystal structures have been determined by single-crystal X-ray diffraction. Overall, compounds adopt a layered structure with aminium cations and 5-sulfosalicylic anions linked via water molecules. The solid-state architectures of these compounds are dominated by O(N,H)-H⋯O and N-H⋯N hydrogen bonds and stabilized by weak interconnects. C-Cl⋯π and S-O⋯π interactions, apart from π⋯π and C-H(O)⋯π, were reported. Diverse approaches were used to study the effect of substituents in the polyamines in solid-state arrangement. A Hirshfeld surface analysis, with associated 3D Hirshfeld surface maps and 2D fingerprint plots, molecular electrostatic potential, and energy frameworks were used to comprehensively investigate the nature and hierarchy of non-covalent interactions and inspect supramolecular differences. The contact enrichment ratio calculations provided deeper insight into the propensity of interconnects to influence crystal packing. The evaluation of the effects of H-bonding synthons resulting from different substituents in the polyamines on self-assemblies is also presented. In the context of crystal engineering, a specific intramolecular synthon via O-H⋯O observed in nearly all crystals can be employed in the pseudo-cyclic replacement strategy in the design of new molecules.

GEMF: a novel geometry-enhanced mid-fusion network for PLA prediction.

Accurate prediction of protein-ligand binding affinity (PLA) is important for drug discovery. Recent advances in applying graph neural networks have shown great potential for PLA prediction. However, existing methods usually neglect the geometric information (i.e. bond angles), leading to difficulties in accurately distinguishing different molecular structures. In addition, these methods also pose limitations in representing the binding process of protein-ligand complexes. To address these issues, we propose a novel geometry-enhanced mid-fusion network, named GEMF, to learn comprehensive molecular geometry and interaction patterns. Specifically, the GEMF consists of a graph embedding layer, a message passing phase, and a multi-scale fusion module. GEMF can effectively represent protein-ligand complexes as graphs, with graph embeddings based on physicochemical and geometric properties. Moreover, our dual-stream message passing framework models both covalent and non-covalent interactions. In particular, the edge-update mechanism, which is based on line graphs, can fuse both distance and angle information in the covalent branch. In addition, the communication branch consisting of multiple heterogeneous interaction modules is developed to learn intricate interaction patterns. Finally, we fuse the multi-scale features from the covalent, non-covalent, and heterogeneous interaction branches. The extensive experimental results on several benchmarks demonstrate the superiority of GEMF compared with other state-of-the-art methods.