Search Results (206)

A comparative study was carried out using density functional theory of the adsorption of phenol and p-chlorophenol on two molecular models of biopolymers in aqueous medium: a chitosan dimer and cellobiose. Twelve adsorbent–adsorbate complexes with three initial orientations per system were optimized, and their structural, electronic, and non-covalent properties were analyzed using boundary orbitals, molecular electrostatic potential, NCI/RDG, and QTAIM. In all four systems, the most stable geometry corresponded to the anchoring of the contaminant hydroxyl group to an adsorbent hydroxyl group, identifying O–H···O as the guiding motif of molecular recognition. However, conformational selectivity was strongly dependent on the adsorbent and the aromatic substituent. For phenol, the alternative orientations were 2.7 and 21.2 kcal mol⁻¹ in chitosan and 6.6 and 48.9 kcal mol⁻¹ in cellobiose. For p-chlorophenol, chitosan showed a much more severe discrimination, with penalties of 43.6 and 46.44 kcal mol⁻¹. In contrast, in cellobiose, the alternative orientations remained close to the minimum, with differences of 5.1 and 3.5 kcal mol⁻¹. The effect of Cl was also reflected in the electron topology: PC increased from 3.2 × 10⁻² to 6.34 × 10⁻² a.u. in chitosan and from 3.2 × 10⁻² to 4.2 × 10⁻² a.u. in cellobiose, while |V|/G went from 3.6 to 7.5 in chitosan and from 3.00 to 3.1 in cellobiose. Overall, the results show that p-chlorophenol interacts more intensely and selectively with chitosan, whereas cellobiose favors a more flexible, less topologically differentiated adsorption. These results clarify how a para-chloro substituent reorganizes hydrogen-bond-driven adsorption on two biopolymer microenvironments with different functional heterogeneity. Full article

In this work, three 3-carboxamidecoumarin derivatives (3b, 3c, and 4) were synthesized and characterized by NMR, IR, and single-crystal X-ray. All compounds maintain an essentially planar coumarin scaffold stabilized by an intramolecular N–H⋯O hydrogen bond (S(6) motif), though compound 4 exhibits a more complex bifurcated S₃²(11)[S(6)S(6)S(5)] network that enhances its conformational rigidity. The crystal packing analysis reveals that while all derivatives form one-dimensional (1D) supramolecular tapes through C–H⋯O interactions, their 3D architectures differ significantly: 3b and 3c rely on a diverse combination of π⋯π stacking and lone pair⋯π contacts, whereas 4 is governed by highly directional stacking between the pyran and pyridine rings. Hirshfeld surface analysis and CE-B3LYP energy framework calculations quantified the balance between intermolecular forces, showing that 3b is dispersion-dominated (H⋯H, 43.5%), while 3c achieves a balanced electrostatic–dispersion regime due to the nitro group, which increases O⋯H/H⋯O contacts to 37.1% and yields the highest stabilization energy (−69.1 kJ/mol). These results demonstrate that the electronic nature of the substituents at the 3- and 6-positions drastically modulates the hierarchy of non-covalent interactions, providing key insights for the crystal engineering of coumarin-based supramolecular systems. Full article

Intermolecular interactions play an important role in the formation and stability of co-crystals. In this study, the interaction behaviour of theophylline in co-crystal structures was systematically analysed using data from the Cambridge Structural Database. A total of fifty-three theophylline co-crystal structures were investigated and classified according to their intermolecular interaction motifs. A structured interaction scheme was developed to describe the accessible interaction sites of theophylline, including classical and non-classical hydrogen bonds, as well as halogen bonds and π∙∙∙π interactions. The study revealed theophylline’s high versatility in forming intermolecular interactions, resulting in twenty interaction patterns. Three dominant motifs were identified as occurring most frequently. The results indicate that steric effects influence the accessibility of specific interaction sites, particularly limiting interactions at the carbonyl group located between the two methyl groups. Hirshfeld surface analysis revealed that O∙∙∙H and H∙∙∙H interactions contribute most significantly to the intermolecular interactions in the analysed structures. Full article

Background: Neglected diseases caused by protozoan parasites remain a major public health burden, particularly in low- and middle-income countries. Among the chemical motifs explored in antiparasitic drug discovery, guanidine-containing compounds have attracted considerable attention due to their strong cationic character, high capacity for hydrogen bonding, and versatility in interacting with biological targets. Methodology: This review summarizes advances reported in the last decade regarding guanidine derivatives with activity against pathogens associated with Chagas disease, human African trypanosomiasis, Leishmaniasis, tuberculosis, toxoplasmosis, dengue and schistosomiasis. Results: Evidence gathered from synthetic, natural, and drug-repurposing studies indicates that the guanidine, guanidine-containing and guanidine-related compounds contribute to modulating biological activity by changing electrostatic interactions, hydrogen-bonding networks, and physicochemical properties, with enzymes, nucleic acids, and membrane-associated targets essential for parasite survival. Across the analyzed studies, several emerging structure–activity relationship trends were identified, including the contribution of polycationic or dicationic architectures, the influence of halogenated or lipophilic substituents, and the dependence of biological activity on the complete molecular framework, including heterocyclic systems, macrocycles, peptide conjugates, hybrid scaffolds, and repurposed drugs. In addition to direct antiparasitic effects, certain guanidine-containing and guanidine-related compounds demonstrate immunomodulatory or host-protective properties, expanding the therapeutic relevance of this class. Despite promising in vitro results, protonation trapping, efflux pump susceptibility, and pharmacokinetic limitations such as poor oral absorption, high polarity, plasma protein binding and limited membrane permeability remain significant challenges for clinical translation. Nonetheless, the integration of medicinal chemistry, computational modeling, and biological screening continues to accelerate the identification of optimized scaffolds. Conclusions: Overall, guanidine-based compounds constitute a promising scaffold for the development of new therapeutic strategies targeting neglected parasitic diseases, and further structural optimization may enable the emergence of candidates with improved efficacy, selectivity, and drug-like properties. Full article

4-Methyl- (1) and 4-ethyl-8-hydroxyquinoline (2) crystallize from a mixture of diethyl ether and chloroform in the triclinic space group P$\overline{1}$. X-ray analysis reveals that both compounds form discrete molecular dimers stabilized by intermolecular O-H∙∙∙N and C-H∙∙∙O hydrogen bonds, resulting in $R_2^2\left(5\right)$ cyclic synthons. This pattern of hydrogen bonds is further stabilized by intramolecular O-H∙∙∙N bonds so that the quinoline nitrogen atom acts as a bifurcated binding site. The dimers exhibit a planar geometry and arrange into layer-like structures held together by π∙∙∙π stacking and van der Waals forces. While the fundamental bonding motifs are similar, the increased steric demand of the ethyl group in compound 2 induces a shift in the crystallographic orientation of the layers and alters the degree of π-overlap compared to the methyl-substituted analogue 1. Full article

Protein recognition underpins advances in drug discovery, immunoassays, clinical diagnostics and biosensing. As a biomimetic alternative to natural receptors, molecularly imprinted polymers (MIPs) have been developed to emulate antibody–antigen complementarity by generating binding cavities that mirror the size, shape and functionality of target macromolecules through template-directed polymerization and subsequent template removal. However, protein imprinting has historically been hampered by low imprinting efficiency and limited selectivity, rendering conventional protein-imprinted polymers (PIPs) inadequate for many contemporary biomedical applications. Functional ionic liquids (ILs)—a class of designer solvents and materials distinguished by tunable structures, exceptional physicochemical properties and favorable biocompatibility—have emerged as versatile additives to address the principal limitations of traditional PIPs, including poor selectivity, sluggish mass transfer and destabilization of protein conformation. Here, we provide a systematic review of the multifaceted roles that ILs play within protein-imprinting systems, delineating their employment as template-anchoring motifs, functional monomers, cross-linkers, porogens and structural stabilizers, and evaluating the consequent effects on polymer architecture and recognition performance. We further probe the multiplicity of non-covalent interactions between ILs and template proteins—highlighting the synergistic modulation afforded by electrostatic forces, hydrogen bonding, hydrophobic interactions and π-π stacking—and consider how such interplay can be harnessed to fine-tune binding-site fidelity. Consolidating recent progress, we summarize IL-enabled PIP applications in protein-specific recognition, biosensor development and analysis of complex real-world samples, and we critically examine the prevailing technical challenges and prospects for translation. The evidence indicates that ILs, by furnishing abundant interaction sites, accelerating mass transport and stabilizing native protein conformations, can markedly enhance PIP adsorption capacity, target specificity and recyclability, positioning them as a cornerstone for next-generation protein separation and enrichment materials and paving the way toward industrial deployment of protein-imprinting technologies. Full article

Ten compounds have been prepared among them six different dioxido(pyridine-2,6-dicarboxylato)vanadate(V) compounds with piperazinium (H₂pip²⁺) (1·6H₂O), methylpiperazinium (H₂mepip²⁺) (2·5H₂O), ethylpiperazinium (H₂etpip²⁺) (3·3H₂O), isopropylpiperazinium (H₂isopip²⁺) (4·H₂O), phenylpiperazinium (Hphepip⁺) (5∙H₂O) and thiomorpholinium 1-oxide (HtmorO⁺) (6·2,6-H₂pydc·2H₂O) cations as counterions as well as methylpiperazinium (H₂mepip²⁺) salt of a mixed valence vanadium [VO(2,6-pydc)-(μ-O)-VO(H₂O)(2,6-pydc)]⁻ complex (7), thiomorpholin-4-ium vanadate (Htmor)VO₃ (8), hexa(thiomorpholin-4-ium) decavanadate hexahydrate (Htmor)₆[V₁₀O₂₈]·6H₂O (9·6H₂O) and organic salt cocrystal thiomorpholin-4-ium 6-carboxypicolinate pyridine-2,6-dicarboxylic acid (Htmor)⁺(2,6-Hpydc)⁻∙(2,6-H₂pydc)·2H₂O (10·2H₂O) via different pathways starting either from pyridine-2,6-dicarboxylic acid or its esters, and were structurally characterized by single-crystal X-ray diffraction. Extended hydrogen bonding interactions are present due to the presence of organic cations as well as due to the diverse roles of water molecules in the hydrogen bonding network. Centrosymmetric hydrogen bonding was found to be an important motif, and diverse supramolecular patterns were also observed due to a wide variety of C–H···O and π···π interactions stabilizing the crystal lattices. Full article

Background/Objectives: Protein kinases play a crucial role in cancer initiation, progression, and therapeutic resistance by regulating signalling pathways involved in tumour growth and survival. Consequently, they represent major targets in anticancer drug discovery. Among heterocyclic scaffolds explored in kinase inhibitor design, benzimidazole has emerged as a privileged structure due to its strong hydrogen-bonding capability and structural resemblance to purine moieties. Triazole motifs are also widely incorporated into bioactive molecules because of their metabolic stability, favourable electronic properties, and ability to establish key interactions within kinase active sites. This review aims to summarise and critically discuss benzimidazole- and triazole-based kinase inhibitors, both as individual scaffolds and as hybrid systems, with emphasis on their kinase targets and multitarget potential. Methods: The relevant literature was surveyed from major scientific databases focusing on studies describing the synthesis, biological evaluation, and molecular modelling of benzimidazole- and triazole-containing kinase inhibitors. Results: Numerous studies demonstrate that both benzimidazole and triazole scaffolds exhibit significant kinase inhibitory activity against oncogenic targets, including EGFR, cyclin-dependent kinases (CDKs), and components of the PI3K/Akt/mTOR signalling pathway. Hybrid molecules combining these pharmacophores frequently enhance binding interactions and facilitate the development of multitarget kinase inhibitors. Structure–activity relationship trends indicate that pharmacophore accessibility, substitution patterns, and linker architecture influence inhibitory potency and selectivity. Conclusions: Overall, benzimidazole- and triazole-based scaffolds represent promising platforms for developing next-generation multitarget anticancer agents and provide valuable insights for the rational design of improved kinase inhibitors. Full article

Water exhibits unique interfacial properties that arise from the collective organization of its hydrogen-bond network. Establishing clear links between molecular-scale interactions and macroscopic observables remains a central challenge in understanding the behavior of liquid water. In this work, we combine experimental measurements of the contact angle of sessile water drops with quantum-chemical modeling of small water clusters (H₂O)_n (n = 2–6) to explore multiscale effects of hydrogen-bond cooperativity. The cluster calculations reveal a nonlinear, saturating evolution of hydrogen-bond geometries with increasing cluster size, reflecting the onset of cooperative many-body effects. Experimentally, the evolution of the apparent contact angle during evaporation is quantified using both conventional geometry and a non-invasive geometrical-optical method based on analysis of the dark refractive ring, which provides independent validation against conventional goniometric measurements. The evaporation dynamics are further interpreted within the diffusion-limited framework of the Popov model, indicating that the temporal evolution of the apparent contact angle is primarily consistent with geometry-controlled mass loss under diffusion-limited conditions, rather than requiring variations in intrinsic surface energy. By combining macroscopic contact-angle measurements with molecular-level cluster analysis, this study offers a qualitative multiscale perspective in which minimal cooperative hydrogen-bond motifs provide molecular context for interpreting interfacial behavior, without implying direct quantitative prediction of macroscopic interfacial observables. Full article

Cyclotides are exceptionally stable plant peptides whose biological activity is widely attributed to interactions with lipid membranes, yet the molecular mechanisms underlying these interactions remain incompletely resolved. Here, we employ microsecond-scale (1 μs) all-atom molecular dynamics simulations to investigate the membrane association of the cyclotide kalata B1 with phospholipid bilayers of distinct headgroup composition, including POPC, POPE, and POPG. This extended timescale enables full bilayer equilibration and allows observation of slower peptide-induced membrane responses that are not accessible in shorter simulations. Across all systems, kalata B1 rapidly adsorbs to the membrane surface and remains predominantly surface-associated throughout the simulations, while the cyclic cystine knot motif remains structurally intact, confirming the exceptional robustness of the cyclotide fold during membrane engagement. Lipid-dependent differences arise primarily from variations in peptide orientation, conformational flexibility, and interfacial dynamics rather than deep bilayer insertion or pore formation. Zwitterionic POPC membranes favor compact, upright peptide configurations, whereas POPE and POPG bilayers promote enhanced lateral spreading and dynamic reorganization driven by hydrogen bonding and electrostatic interactions, respectively. Leaflet-resolved analyses of lipid contacts, membrane thickness, and area per lipid reveal localized, asymmetric perturbations confined to the peptide-exposed leaflet, with no evidence of sustained bilayer thinning or global destabilization. Together, these results support an interfacial, headgroup-dependent mechanism of cyclotide membrane activity and reconcile previous experimental observations. This work provides molecular-level insight into lipid selectivity and early-stage cyclotide–membrane interactions that may inform future design of cyclotide-based bioactive agents. Full article

Chiral and racemic forms of a pyridyl ligand (R-L and rac-L, respectively), containing urea groups at their core and synthesised by the condensation of 3-aminopyridine and α-methylbenzylisocyante, were incorporated into silver complexes. The resulting species depend on the enantiopurity of the ligand alongside an influence from the counter-anion. The enantiopure ligand generated isomorphous, one-dimensional polymeric compounds [Ag(R-L)X] (where X = NO₃, CF₃SO₃) or [Ag(R-L)]X (where X = BF₄, PF₆). The polymeric chains, connected by N and O coordination of the ligands, have outwards facing urea groups that form hydrogen bonds to the counter-anions, which play little role in determining the overall structure. Despite all syntheses containing an excess of Ag(I) salt, the racemic ligand formed only discrete complexes of [Ag(rac-L)₂]⁺ in the presence of each of the above anions. Three of these complexes contain ligands of the same chirality (i.e., complexes with R,R and S,S ligand pairs within the centrosymmetric structures) with only the PF₆-containing compound being different. The anions play a role in dictating the structure of hydrogen-bonded chains, although PF₆⁻ is unique with urea···urea interactions present between complexes. Overall, this system highlights the nuances associated with predicting the structure, and even speciation, of related chiral/achiral systems in addition to influences of counter-anions on structural motifs. Full article

Eight H-bonded salts of arsenic acid and nitrogen bases (2,4,6-trimethylpyridine, pyridine-2,6-diamine, pyridin-4-ol, 4-methoxypyridine, 4-methoxyaniline, 1,3,5-triazine-2,4,6-triamine, diethylamine and N¹,N¹,N²,N²-tetraethylethane-1,2-diamine) were studied in the solid state by single crystal X-ray diffraction technique and DFT calculations. In all cases quite short (≤2.65 Å) OHO bonds were found in the self-assembled supramolecular ribbons or 2D networks of dihydrogen arsenates, constituting a repertoire of five different H-bonding patterns (motifs). The electron localization function maps revealed the spots of the nucleophilic sites on oxygen atoms that determine the preferable directions for H-bonding of H₂AsO₄⁻ anions observed in the crystal packing. Analysis of the electrostatic potential maps for isolated species has demonstrated that upon H-bonding between H₂AsO₄⁻ anions and protonated nitrogen bases, NH⁺⋯⁻OAsO(OH)₂, the redistribution of electron density within the anion provides otherwise virtually non-existent electrophilic sites on hydrogen atoms, which balances the Coulomb repulsion and allows for the anion⋯anion pairing within the crystal. The topological analysis of the calculated crystalline electron density after relaxation of the hydrogen atoms’ positions was used to classify the OHO bonds as moderately strong ones (with an interaction energy up to 65 kJ/mol) and revealed a high degree of ionicity of molecular moieties within ion pairs (with an absolute charge up to 0.87 e). For the strongest OHO and NHO bonds, the noticeable covalent character was shown by using the crystal orbital Hamiltonian population analysis. Full article

The aza-Michael reaction is a fundamental transformation for carbon–nitrogen bond formation, providing efficient access to β-amino carbonyl compounds, nitriles, and related nitrogen-containing building blocks of broad importance in medicinal chemistry and organic synthesis. Over the past two decades, ionic liquids (ILs) have attracted considerable attention as alternative reaction media, promoters, and catalysts for aza-Michael reactions, owing to their distinctive physicochemical properties and tunable structures. This review presents a comprehensive and critical overview of ionic-liquid-mediated aza-Michael reactions, emphasizing the evolution of IL design from early imidazolium-based systems to modern task-specific, supported, and bio-derived ionic liquids. Conventional room-temperature ionic liquids are discussed as non-innocent solvents capable of stabilizing charged intermediates and enhancing electrophilicity, thereby enabling catalyst-free or metal-assisted aza-Michael additions. Subsequent sections focus on task-specific ionic liquids incorporating Brønsted acidic, basic, hydrogen-bond-donating, or bifunctional motifs, highlighting how rational structural design translates into improved activity, selectivity, and substrate scope. Particular attention is devoted to guanidine-, DABCO-, and DBU-based ionic liquids, where mechanistic studies reveal cooperative activation modes rather than simple acid–base catalysis. Recent advances in supported and polymeric ionic liquids are also reviewed, demonstrating effective strategies to combine IL-like reactivity with enhanced recyclability and operational simplicity. Overall, this review clarifies the diverse roles of ionic liquids in aza-Michael chemistry and outlines current challenges and future perspectives toward more sustainable and efficient C–N bond-forming methodologies. Full article

Fyn is a Src-family tyrosine kinase implicated in synaptic dysfunction and neuroinflammation across multiple neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). Saracatinib (AZD0530) is a potent Src-family inhibitor that has been explored as a repurposed therapeutic; however, its clinical utility is limited by poor kinase selectivity caused by high sequence conservation within Src-family ATP-binding sites. Here, we combine surface plasmon resonance (SPR) and X-ray crystallography to define saracatinib recognition by the Fyn kinase domain (KD). SPR single-cycle kinetics shows that saracatinib binds the isolated Fyn KD and full-length Fyn with low-nanomolar affinity, whereas dasatinib binds with subnanomolar affinity and markedly slower dissociation. We determined the crystal structure of the Fyn KD-saracatinib complex at 2.22 Å resolution. The kinase adopts an active-like conformation with the DFG motif and αC-helix in the ‘in’ state and a conserved β3 αC Lys-Glu salt bridge. Saracatinib occupies the adenine and ribose pockets, and engages the hinge through direct and water-mediated hydrogen bonding while complementing a hydrophobic back pocket by van der Waals contacts. Comparison with reported saracatinib-bound structures of other kinases suggests that the active-state geometry observed for Fyn creates a pocket not observed in inactive-like complexes, providing a structural handle for designing Fyn-selective inhibitors. Comparison with all saracatinib-bound kinase co-structures currently available in the PDB (ALK2 and PKMYT1) indicates a conserved monodentate hinge binding mode but kinase-dependent αC-helix conformations, providing a structural rationale for designing Fyn-selective analogues. Full article

The RNA Recognition Motif (RRM) domain of the Ewing sarcoma (EWS) protein plays a pivotal role in RNA binding and gene regulation, being crucial for its function. However, its structural dynamics are yet to be revealed. Herein, we performed 5.5 μs cumulative molecular dynamics (MD) simulations to investigate the unfolding pathways of the EWS-RRM domain in urea and DMSO across 300–500 K. The unfolding process was characterized by using free-energy landscape (FEL) analysis, hydrogen-bond occupancy, and Gaussian Mixture Model (GMM) clustering. At lower temperatures (300–350 K), the RRM largely retained its native conformation, while extensive unfolding occurred between 400 and 450 K. Results revealed multiple conformational ensembles: native (N), native-like intermediate (I_N), intermediate (I), and unfolded (U) states, underlying the unfolding pathway of RRM. In urea at 400 K, a long-lived I-state dominated, with transient N and I_N-populations, whereas in DMSO, the I_N-state appeared more stable, that transitioned into tightly packed I-states, reflecting a stepwise unfolding via compact intermediates. At 450 K, the protein reached the U-state in both solvents, though unfolding occurred more readily in urea. This study highlights the solvent-dependent unfolding mechanisms and heterogeneous I-states of EWS-RRM, providing insight into its stability, misfolding, and potential relevance to Ewing sarcoma pathogenesis. Full article