Search Results (1,341)

Structure and nonlinear spectra of the basal surface of ice Ih were investigated by molecular dynamics simulations. At a temperature significantly lower than the melting temperature $T_m$, the ice structure at the interface is only weakly perturbed by the presence of surface. The computed nonlinear spectrum of the interface well agrees with the experimental data and the results of the calculations provide the molecular-level interpretation of spectral features. In particular, the ice surface specific positive peaks in the Im[${\chi }^{\left(2\right)}$] spectrum at ∼3180 cm⁻¹ and at ∼3420 cm⁻¹ were found to result from the low- and high-frequency vibrational modes of quadruply H-bonded surface molecules, respectively. The spectrum of the crystalline ice interface is significantly affected by intermolecular interactions. Upon increasing the temperature, the structural disorder extends to the second water bilayer. The thickness of the premelted water layer of 6–8 Å can be estimated at the temperature by ca. 5 K below $T_m$. The increase in the temperature results in a change in the intensity and shape of the nonlinear spectrum of the ice Ih interface. The changes can be explained by the interconversion between different H-bonded surface species and by an increase in disordering of water molecules that reduces strength of intermolecular interactions. Results of the present work contribute to our understanding of the structure–spectrum relationship of the ice/air interface, and shed light on the origins of features in the nonlinear spectra of the system. Full article

The aromaticity of small boron clusters remains under scrutiny due to persistent inconsistencies between magnetic and electronic descriptors. Here, we reexamine B₃⁻, B₃⁺, B₄, B₄²⁺, and B₄²⁻ using a multidimensional approach that integrates Adaptive Natural Density Partitioning, Electron Density of Delocalized Bonds, magnetically induced current density, and the z-component of the induced magnetic field. We introduce a model in which σ-aromaticity arises from two distinct delocalization topologies: a radial 2e⁻ σ-pathway and a tangential multicenter circuit formed by alternating filled and vacant sp² orbitals. This framework accounts for the evolution of aromaticity upon oxidation or reduction, preserving coherence between electronic structure and magnetic response. B₃⁻ features cooperative radial and tangential σ-delocalization, together with a delocalized 2e⁻ π-bond, yielding robust double aromaticity. B₃⁺ retains σ- and π-aromaticity, but only via a tangential 6e⁻ σ-framework, leading to a more compact delocalization and slightly attenuated ring currents. In B₄, the presence of a radial 2e⁻ σ-bond and a 4c–2e π-bond confers partial aromatic character, while the tangential 8e⁻ σ-framework satisfies the 4n rule and induces a paratropic current. In contrast, B₄²⁺ lacks the radial σ-component but retains a tangential 8e⁻ σ-circuit and a 2e⁻ 4c–2e π-bond, leading to a σ-antiaromatic and π-aromatic configuration. Finally, B₄²⁻, exhibits delocalized π- and σ-circuits, yielding consistent diatropic ring currents, which confirms its fully doubly aromatic nature. Altogether, this analysis underscores the importance of resolving σ-framework topology and demonstrates that, when radial and tangential contributions are correctly distinguished, Hückel’s rule remains a powerful tool for interpreting aromaticity in small boron rings. Full article

The hydroesterification of olefins provides a highly efficient way to produce high value-added ester products from simple and abundant olefin feedstocks. In this work, DFT calculation was performed to investigate the detailed reaction mechanism of propene hydroesterification over Rh(II)/Silicalite-2 catalysts. Three possible mechanistic pathways were systematically explored and compared in terms of their adsorption configurations, reaction energies, and transition-state barriers. Among them, the Carbonylation-First pathway exhibited the most favorable energy profile with the lowest overall kinetic barriers, indicating it to be the most likely way for ester formation. A comparison of methyl butyrate and methyl isobutyrate formation revealed that the linear product is energetically more favorable, particularly along the Carbonylation-First pathway. Moreover, the Rh(II) center demonstrates a different catalytic effect over conventional Rh(I) species by significantly lowering the energy barrier for CO insertion, a key step in both hydroformylation and hydroesterification. These findings provide fundamental insight into the role of Rh(II)/zeolite systems in carbonylation reactions and offer theoretical guidance for the design of catalysts. Full article

This study explores how intermolecular interactions govern the composition of saturated solutions of influence flufenamic acid (FlA) in deep eutectic solvents (DESs). Using choline chloride (ChCl) or menthol (Men) as the HBAs and various polyols as the HBDs, FlA solubility was measured in different DES systems. The experimental values along with intermolecular interactions quantified via COSMOtherm-derived Gibbs free energies were used in the determination of component distributions for varying DES formulations. It was inferred that DES systems primarily consist of molecular complexes (dimers and hetero-pairs) rather than monomers due to their high association propensity. In the case of ChCl-based DESs, the HBA–HBD hetero-pairs are favored and strongly dominate. In contrast, Men-based DESs exhibited a strong attraction to HBDs; however, their self-association led to the predominance of HBD dimers. Solubility of FlA correlated with solute-containing hetero-pairs, peaking at optimal HBA–HBD ratios. These insights support in developing a rationale for DES design for pharmaceutical applications. The conclusions of this study were inferred from a novel crafted physically constrained iterative algorithm that reliably determines molecular composition from the equilibrium constants, overcoming the limitations of conventional numerical solvers in highly associated systems. Full article

The experimental IR and Raman vibrational spectra of a hydrated La(III) complex with a 1,2,3-triazole ligand were characterized by using four different Density Functional Theory (DFT) levels and two accurate scaling procedures. In the theoretical calculations, the hydration water in the experimental sample was considered under the Discrete Model (DM) with different numbers of explicit water molecules and different positions around the La(III) ion and the carboxylate groups. The predicted IR spectra at the M06-2X/Lanl2dz level appear to be the closest to the experimental ones. Based on the optimized structures, molecular properties and global chemical descriptors were also calculated, and the findings obtained are discussed in detail herein. Additionally, several photophysical properties were determined in both the free ligand and in several lanthanide complexes, and with the sample in the solid state and in DMSO solution. A blue shift in the fluorescence of the complexes was observed compared to the free ligand, as well as in the solid-state sample compared to the solution. Full article

Despite the widespread use of vaccines against SARS-CoV-2, COVID-19 continues to pose global health challenges, requiring efficient drug screening and repurposing strategies. This study presents a novel hybrid framework that integrates deep learning (DL) with molecular docking to accelerate the identification of potential therapeutics. The framework comprises three crucial steps: (1) a previously developed DL model is employed to rapidly screen candidate compounds, selecting those with predicted interaction scores above a cut-off value of 0.8; (2) AutoDock Vina version 1.5.6 and LeDock version 1.0 are used to evaluate binding affinities, with a threshold of <−7.0 kcal·mol⁻¹; and (3) predicted drug–protein binding sites are evaluated to determine their overlap with known active residues of the target protein. We first validated the framework using four experimentally confirmed COVID-19 drug–target pairs and then applied it to identify potential inhibitors of the SARS-CoV-2 main protease (M^Pro). Among 29 drug candidates selected based on antiviral, anti-inflammatory, or anti-cancer properties, only Enasidenib met all three selection criteria, showing promise as an M^Pro inhibitor. However, further experimental and clinical studies are required to confirm its efficacy against SARS-CoV-2. This work provides an interpretable strategy for virtual screening and drug repurposing, which can be readily adapted to other DL models and docking tools. Full article

The escalating crisis of multidrug resistance, together with the persistence of antibiotic residues in clinical and environmental matrices, demands integrated strategies that couple sensitive detection, efficient decontamination, and controlled delivery. However, current techniques for quantifying avibactam (AVI)—a broad-spectrum β-lactamase inhibitor—such as HPLC-UV lack the sensitivity and specificity required for both therapeutic drug monitoring and environmental surveillance. Encapsulation of AVI within cyclodextrins (CDs) may simultaneously enhance its stability, bioavailability, and detectability, while the high binding affinities of CDs position them as molecular traps capable of scavenging residual AVI. In this study, the inclusion complexation of AVI with various CDs was examined through molecular dynamics (MD) simulations, experimental isothermal titration calorimetry (ITC), and non-covalent interaction (NCI) analysis. Stable 1:1 inclusion complexes were observed between AVI and β-cyclodextrin (β-CD), 2,6-dimethyl-β-cyclodextrin (DM-β-CD), and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), with standard Gibbs free energies of binding (ΔG°) of –3.64, –3.24, and –3.11 kcal/mol, respectively. In contrast, γ-cyclodextrin (γ-CD) exhibited significantly weaker binding (ΔG° = –2.25 kcal/mol). DFT-based NCI analysis revealed that cooperative interaction topology and cavity complementarity, rather than the sheer number of localized contacts, govern complex stability. Combined computational and experimental data establish β-CD derivatives as effective supramolecular hosts for AVI, despite an entropic penalty in the DM-β-CD/AVI complex. These CD–AVI affinities support the development of improved analytical methodologies and pharmaceutical formulations, and they also open avenues for decontamination strategies based on molecular trapping of AVI. Full article

Nanodiamonds in water can generate solvated electrons under ultraviolet (UV) excitation, but UV light constitutes only a small portion of solar energy. To harvest solar energy in the visible range, we investigate band gap reduction via surface amino functionalization and examine its impact on photo-excited charge transfer to water. Adamantane, the smallest nanodiamond, is used as a model due to its electron emission properties. Liquid water is first represented using water dimers and then complete solvation shell structures surrounding the adamantane. By systematically analyzing different functionalized adamantane structures, we find that nitrogen serves as the primary electron donor to nearby water molecules. Furthermore, the negative electron affinity of adamantane, which determines its emission capability, is preserved with half of the amino group functionalization on the surface. Our findings motivate further experimental verification using nanodiamonds with amino-functionalized surfaces. Full article

Drug discovery is an intricate and resource-intensive process in which computational approaches, such as molecular docking, are essential, particularly in the early stages, to identify potential hits. However, docking still has many drawbacks, including problems in managing protein flexibility and the reliability of scoring functions. In this paper, we systematically compared the performance of AutoDock Vina, one of the most widely used open-source docking tools, with GNINA. This advanced evolution integrates convolutional neural networks (CNNs) for pose scoring. The comparison was conducted on ten heterogeneous protein targets, including metalloenzymes, kinases, and G-protein-coupled receptors (GPCRs). With the ability to accurately replicate binding poses and their energy values, GNINA showed outstanding performance in both virtual screening (VS) of active ligands and re-docking steps of co-crystallized ligands. GNINA’s enhanced ability to accurately distinguish between true positives and false positives—a specificity not found with AutoDock Vina—is confirmed by ROC curves and Enrichment Factor (EF) results. Therefore, we propose an integrated GNINA-based workflow that can significantly enhance the quality and reliability of docking results, providing a valuable tool for optimizing the initial stages of drug discovery. Full article

The glucagon-like peptide-1 receptor (GLP-1R), which belongs to the class B1 G protein-coupled receptor (GPCR) family, is an important target for treatment of metabolic disorders, including type 2 diabetes and obesity. The growing interest in GLP-1R-based therapies is driven by the development of various functional agonists as well as the huge commercial market. Thus, understanding the structural details of ligand-induced signaling are important for developing improved GLP-1R drugs. Here, we investigated the conformational dynamics of the receptor in complex with a selection of prototypical functional agonists, including CHU-128 (small molecule-biased), danuglipron (small molecule balanced), and Peptide 19 (peptide balanced), which exhibit unique, distinct binding modes and induced helix packing. Furthermore, our all-atom molecular dynamics (MD) simulations revealed atomic feature how different those ligands led to signaling pathway preference. Our findings offer valuable insights into the mechanistic principle of GLP-1R activation, which are helpful for the rational design of next-generation GLP-1R drug molecules. Full article

Magnetite (Fe₃O₄) provides a protective corrosion layer in the steam generators of nuclear power plants. The presence of monoethanolamine (MEA) in coolant water has a beneficial effect on corrosion processes. In that context, the adsorption of MEA and ethanol–ammonium cation on the {111} surface of magnetite was studied using the molecular dynamics (MD) method. A modified version of the mechanical force field (ClayFF) was used. The systems were simulated at different temperatures (423 K; 453 K; 503 K). Surface coverage data were obtained from adsorption simulations; the root-mean-square deviation (RMSD) of the target molecules were calculated, and their minimum distance to the magnetite surface was traced. The potential and adsorption energies of MEA were calculated as a function of temperature. It has been established that the interaction between MEA and magnetite is due to electrostatic phenomena and the adsorption rate increases with temperature. A comparison was made with existing experimental results and similar MD simulations. Full article

The valence-shell electronic state spectroscopy of β-butyrolactone (CH₃CHCH₂CO₂) is comprehensively investigated by employing experimental and theoretical methods. We report a novel vacuum ultraviolet (VUV) absorption spectrum in the photon wavelength range from 115 to 320 nm (3.9–10.8 eV), together with ab initio quantum chemical calculations at the time-dependent density functional (TD-DFT) level of theory. The dominant electronic excitations are assigned to mixed valence-Rydberg and Rydberg transitions. The fine structure in the CH₃CHCH₂CO₂ photoabsorption spectrum has been assigned to C=O stretching, $v_7^{\prime }\left(a\right)$, CH₂ wagging, $v_{14}^{\prime }\left(a\right)$, C–O stretching, $v_{22}^{\prime }\left(a\right)$, and C=O bending, $v_{26}^{\prime }\left(a\right)$ modes. Photolysis lifetimes in the Earth’s atmosphere from 0 km up to 50 km altitude have been estimated, showing to be a non-relevant sink mechanism compared to reactions with the ^•OH radical. The nuclear dynamics along the C=O and C–C–C coordinates have been investigated at the TD-DFT level of theory, where, upon electronic excitation, the potential energy curves show important carbonyl bond breaking and ring opening, respectively. Within such an intricate molecular landscape, the higher-lying excited electronic states may keep their original Rydberg character or may undergo Rydberg-to-valence conversion, with vibronic coupling as an important mechanism contributing to the spectrum. Full article

Experimental and theoretical studies were applied to investigate the adsorption properties of testagen (KEDG) peptide on copper surfaces in sodium chloride solution and, implicitly, its inhibition efficiency (IE) on metal corrosion. The tetrapeptide synthesized from the amino acids lysine (Lys), glutamic acid (Glu), aspartic acid (Asp), and glycine (Gly), named as H-Lys-Glu-Asp-Gly-OH, achieved an inhibition efficiency of around 86% calculated from electrochemical measurements, making KEDG a promising new copper corrosion inhibitor. The experimental data were best fitted to the Freundlich adsorption isotherm. The standard free energy of adsorption ($\mathsf{\Delta }{\mathrm{G}}_{\mathrm{a}\mathrm{d}\mathrm{s}}^{\mathrm{o}}$) reached the value of −30.86 kJ mol⁻¹, which revealed a mixed action mechanism of tetrapeptide, namely, chemical and physical spontaneous adsorption. The copper surface characterization was performed using optical microscopy and SEM/EDS analysis. In the KEDG presence, post-corrosion, SEM images showed a network surface morphology including microdeposits with an acicular appearance, and EDS analysis highlighted an upper surface layer consisting of KEDG, sodium chloride, and copper corrosion compounds. The computational study based on DFT and Monte Carlo simulation confirmed the experimental results and concluded that the spontaneous adsorption equilibrium establishment was the consequence of the contribution of noncovalent (electrostatic, van der Waals) interactions and covalent bonds. Full article

In this study, three alternating donor–acceptor (D–A) type [12]cycloparaphenylene ([12]CPP) derivatives ([12]CPP 1a, 2a, and 3a) were designed through precise molecular engineering, and their multidimensional photophysical responses and chiroptical properties were systematically investigated. The effects of the alternating D–A architecture on electronic structure, excited-state dynamics, and optical behavior were elucidated through density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The results show that the alternating D–A design significantly reduced the HOMO–LUMO energy gap (e.g., 3.11 eV for [12]CPP 2a), enhanced charge transfer characteristics, and induced pronounced red-shifted absorption. The introduction of an imide-based acceptor ([12]CPP 2a) further strengthened the electron push-pull interaction, exhibiting superior performance in two-photon absorption, while the symmetrically multifunctionalized structure ([12]CPP 3a) predominantly exhibited localized excitation with the highest absorption intensity but lacked charge transfer features. Chiral analysis reveals that the alternating D–A architecture modulated the distribution of chiral signals, with [12]CPP 1a displaying a strong Cotton effect in the low-wavelength region. These findings not only provide a theoretical basis for the molecular design of functionalized CPP derivatives, but also lay a solid theoretical foundation for expanding their application potential in optoelectronic devices and chiral functional materials. Full article

In order to explore the essence of the anticoccidiosis of anticoccidial drugs under bioelectric currents, the intermolecular double-proton transfer and conformational transformation of 4-pyridone-3-carboxylic acid were investigated by quantum chemistry calculations (at the M06-2X/6-311++G**, M06-2X/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels) and finite temperature string (FTS) under external electric fields. The solvent effect of H₂O on the double-proton transfer was evaluated by the integral equation formalism polarized continuum model. The results indicate that the influences of the external electric fields along the direction of the dipole moment on double-proton transfer are significant. The corresponding products are controlled by the direction of the external electric field. Due to the first-order Stark effect, some good linear relationships form between the changes of the structures, atoms in molecules (AIMs) results, surface electrostatic potentials, barriers of the transition state, and the external electric field strengths. From the gas to solvent phase, the barrier heights increased. The spatial order parameters (ϕ, ψ) of the conformational transformation could be quickly converged through the umbrella sampling and parameter averaging, and thus the free-energy landscape for the conformational transformation was obtained. Under the external electric field, there is competition between the double-proton transfer and conformational transformation. The external electric field greatly affects the cooperativity transfer, while it has little effect on the conformational transformation. This study is helpful in the selection and updating of anticoccidial drugs. Full article