Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests**

Cube-like double four-ring (d4r) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing d4r cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO₂, GeO₂, AlPO₄, GaPO₄) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO₂-AST show significant deformations, with a pyritohedron-like distortion of the d4r cages occurring in GeO₂- and GaPO₄-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO₄- and GaPO₄-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material's properties.     

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding

Aberrant RNA–protein complexes are formed in a variety of diseases. Identifying the ligands that interfere with their formation is a valuable therapeutic strategy. Molecular simulation, validated against experimental data, has recently emerged as a powerful tool to predict both the pose and energetics of such ligands. Thus, the use of molecular simulation may provide insight into aberrant molecular interactions in diseases and, from a drug design perspective, may allow for the employment of less wet lab resources than traditional in vitro compound screening approaches. With regard to basic research questions, molecular simulation can support the understanding of the exact molecular interaction and binding mode. Here, we focus on examples targeting RNA–protein complexes in neurodegenerative diseases and viral infections. These examples illustrate that the strategy is rather general and could be applied to different pharmacologically relevant approaches. We close this study by outlining one of these approaches, namely the light-controllable association of small molecules with RNA, as an emerging approach in RNA-targeting therapy.     

Design,Synthesis and Anticancer Activity of a New Series of N-aryl-N′-[4-(pyridin-2-ylmethoxy)benzyl]urea Derivatives

The development of cancer treatments requires continuous exploration and improvement, in which the discovery of new drugs for the treatment of cancer is still an important pathway. In this study, based on the molecular hybridization strategy, a new structural framework with an N-aryl-N’-arylmethylurea scaffold was designed, and 16 new target compounds were synthesized and evaluated for their antiproliferative activities against four different cancer cell lines A549, MCF7, HCT116, PC3, and human liver normal cell line HL7702. The results have shown seven compounds with 1-methylpiperidin-4-yl groups having excellent activities against all four cancer cell lines, and they exhibited scarcely any activities against HL7702. Among them, compound 9b and 9d showed greatly excellent activity against the four kinds of cells, and the IC₅₀ for MCF7 and PC3 cell lines were even less than 3 μM.     

Exploiting Protein N-Terminus for Site-Specific Bioconjugation

Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.     

Influence of Substitutional Defects in ZIF-8 Membranes on Reverse Osmosis Desalination: A Molecular Dynamics Study

In this study, molecular dynamics simulation is used to investigate the effects of water-based substitutional defects in zeolitic imidazolate frameworks (ZIF)-8 membranes on their reverse osmosis (RO) desalination performance. ZIF-8 unit cells containing up to three defect sites are used to construct the membranes. These substitutional defects can either be Zn defects or linker defects. The RO desalination performance of the membranes is assessed in terms of the water flux and ion rejection rate. The effects of defects on the interactions between the ZIF-8 membranes and NaCl are investigated and explained with respect to the radial distribution function (RDF) and ion density distribution. The results show that ion adsorption on the membranes occurs at either the nitrogen atoms or the defect sites. Complete NaCl rejection can be achieved by introducing defects to change the size of the pores. It has also been discovered that the presence of linker defects increases membrane hydrophilicity. Overall, molecular dynamics simulations have been used in this study to show that water-based substitutional defects in a ZIF-8 structure reduce the water flux and influence its hydrophilicity and ion adsorption performance, which is useful in predicting the type and number of defect sites per unit cell required for RO applications. Of the seven ZIF-8 structures tested, pristine ZIF-8 exhibits the best RO desalination performance.     

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7+O3 Complex in Solution

Infrared (IR) absorption in the 1000–3700 cm⁻¹ range and ¹H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H₇⁺O_3, in acetonitrile. The core H₇⁺O₃ motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H₇⁺O₃ structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H₇⁺O₃ in the OH stretch region, which reaffirms the assignment of the H₇⁺O₃ spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H₇⁺O₃ structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H₇⁺O₃ structures may support proton transport within larger water solvates.     

Dual-Metal Electrolytes for Hybrid-Ion Batteries: Synergism or Antagonism?

The construction of hybrid metal-ion batteries faces a plethora of challenges. A critical one is to unveil the solvation/desolvation processes at the molecular level in electrolytes that ensure efficient transfer of several types of charge carriers. This study reports first results on simulations of mixed-ion electrolytes. All combinations of homo- and hetero-binuclear complexes of Li⁺, Na⁺ and Mg²⁺, solvated with varying number of ethylene carbonate (EC) molecules are modeled in non-polar and polar environment by means of first principles calculations and compared to the mononuclear analogues in terms of stability, spatial organization, charge distribution and solvation/desolvation behavior. The used PF₆⁻ counterion is shown to have minor impact on the geometry of the complexes. The desolvation energy penalty of binuclear complexes can be lowered by the fluoride ions, emerging upon the PF₆⁻ decay. These model investigations could be extended to rationalize the solvation structure and ionic mobility in dual-ion electrolytes.     

Understanding the Effect of Solvent Environment on the Interaction of Hydronium Ion with Biomass Derived Species: A Molecular Dynamics and Metadynamics Investigation

The addition of aprotic solvents results in higher reactivities and selectivities in many key aqueous phase biomass reactions, including the acid-catalyzed conversion of fructose to 5-hydroxyl methyl furfural (HMF). The addition of certain co-solvents inhibits the formation of humins via preferential solvation of key functional groups and can alter reaction kinetics. An important factor in this context is the relative stability of the hydronium ion (the catalyst) in the vicinity of the biomass moiety as compared to that in bulk, as it could determine its efficacy in the protonation step. Hence, in the present work, molecular dynamics (MD) simulations of HMF (the model product) and fructose (the model reactant) in acidic water and water-DMSO mixtures are performed to analyze their interaction with the hydronium ions. We show that the presence of DMSO favors the interaction of the hydronium ion with fructose, whereas it has a detrimental effect on the interaction of hydronium ion with HMF. Well-tempered metadynamics (WT-MTD) simulations are performed to determine the relative stability of the hydronium ion in the immediate vicinity of fructose and HMF, as compared to that in the bulk solvent phase, as a function of solvent composition. We find that DMSO improves the stabilization of the hydronium ions in the first solvation shell of fructose compared to that in the bulk solvent. On the other hand, hydronium ions become less stable in the immediate vicinity of HMF, as the concentration of DMSO increases.     

Phytochemical Profiling of Lavandula coronopifolia Poir. Aerial Parts Extract and Its Larvicidal,Antibacterial, and Antibiofilm Activity Against Pseudomonas aeruginosa

Infections associated with the emergence of multidrug resistance and mosquito-borne diseases have resulted in serious crises associated with high mortality and left behind a huge socioeconomic burden. The chemical investigation of Lavandula coronopifolia aerial parts extract using HPLC–MS/MS led to the tentative identification of 46 compounds belonging to phenolic acids, flavonoids and their glycosides, and biflavonoids. The extract displayed larvicidal activity against Culex pipiens larvae (LC₅₀ = 29.08 µg/mL at 72 h). It significantly inhibited cytochrome P-450 monooxygenase (CYP450), acetylcholinesterase (AChE), and carboxylesterase (CarE) enzymes with the comparable pattern to the control group, which could explain the mode of larvae toxification. The extract also inhibited the biofilm formation of Pseudomonas aeruginosa by 17–38% at different Minimum Inhibitory Concentrations (MICs) (0.5–0.125 mg/mL) while the activity was doubled when combined with ciprofloxacin (ratio = 1:1 v:v). In conclusion, the wild plant, L. coronopifolia, can be considered a promising natural source against resistant bacteria and infectious carriers.     

Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors

A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.