Single-Molecule Exchange inside a Nanocage Provides Insights into the Origin of π-π Interactions.

The attractive interactions between aromatic rings, also known as π-π interactions, have been widely used for decades. However, the origin of π-π interactions remains controversial due to the difficulties in experimentally measuring the weak interactions between π-systems. Here, we construct an elaborate system to accurately compare the strength of the π-π interactions between phenylalanine derivatives via molecular exchange processes inside a protein nanopore. Based on quantitative comparison of binding strength, we find that in most cases, the π-π interaction is primarily driven by dispersive attraction, with the electrostatic interaction playing a secondary role and tending to be repulsive. However, in cases where electronic effects are particularly strong, electrostatic induction may exceed dispersion forces to become the primary driving force for interactions between π-systems. The results of this study not only deepen our understanding of π-stacking but also have potential implications in areas where π-π interactions play a crucial role.

Precise Modulation of Carbon Activity Sites in Metal-Free Covalent Organic Frameworks for Enhanced Oxygen Reduction Electrocatalysis.

Metal-free carbon-based materials have gained recognition as potential electrocatalysts for the oxygen reduction reaction (ORR) in new environmentally-friendly electrochemical energy conversion technologies. The presence of effective active centers is crucial for achieving productive ORR. In this study, we present the synthesis of two metal-free dibenzo[a,c]phenazine-based covalent organic frameworks (DBP-COFs), specifically JUC-650 and JUC-651, which serve as ORR electrocatalysts. Among them, JUC-650 demonstrates exceptional catalytic performance for ORR in alkaline electrolytes, exhibiting an onset potential of 0.90 V versus RHE and a half-wave potential of 0.72 V versus RHE. Consequently, JUC-650 stands out as one of the most outstanding metal-free COF-based ORR electrocatalysts report to date. Experimental investigations and density functional theory calculations confirm that modulation of the frameworks' electronic configuration allows for the reduction of adsorption energy at the Schiff-base carbon active sites, leading to more efficient ORR processes. Moreover, the DBP-COFs can be assembled as excellent air cathode catalysts for zinc-air batteries (ZAB), rivaling the performance of commercial Pt/C. This study provides valuable insights for the development of efficient metal-free organoelectrocatalysts through precise regulation of active site strategies.

Topological Isomerism in Three-Dimensional Covalent Organic Frameworks.

Although isomerism is a typical and significant phenomenon in organic chemistry, it is rarely found in covalent organic framework (COF) materials. Herein, for the first time, we report a controllable synthesis of topological isomers in three-dimensional COFs via a distinctive tetrahedral building unit under different solvents. Based on this strategy, both isomers with a dia or qtz net (termed JUC-620 and JUC-621) have been obtained, and their structures are determined by combining powder X-ray diffraction and transmission electron microscopy. Remarkably, these architectures show a distinct difference in their porous features; for example, JUC-621 with a qtz net exhibits permanent mesopores (up to ∼23 Å) and high surface area (∼2060 m2 g-1), which far surpasses those of JUC-620 with a dia net (pore size of ∼12 Å and surface area of 980 m2 g-1). Furthermore, mesoporous JUC-621 can remove dye molecules efficiently and achieves excellent iodine adsorption (up to 6.7 g g-1), which is 2.3 times that of microporous JUC-620 (∼2.9 g g-1). This work thus provides a new way for constructing COF isomers and promotes structural diversity and promising applications of COF materials.

Solvation structures of calcium and magnesium ions in water with the presence of hydroxide: a study by deep potential molecular dynamics.

The solvation structures of calcium (Ca2+) and magnesium (Mg2+) ions with the presence of hydroxide (OH-) ion in water are essential for understanding their roles in biological and chemical processes but have not been fully explored. Ab initio molecular dynamics (AIMD) is an important tool to address this issue, but two challenges exist. First, an accurate description of OH- from AIMD needs an appropriate exchange-correlation functional. Second, a long trajectory is needed to reach an equilibrium state for the Ca2+-OH- and Mg2+-OH- ion pairs in aqueous solutions. Herein, we adopt a deep potential molecular dynamics (DPMD) method to simulate 1 ns trajectories for the Ca2+-OH- and Mg2+-OH- ion pairs in water; the DPMD method provides efficient machine-learning-based models that have the accuracy of the SCAN exchange-correlation functional within the framework of density functional theory. The solvation structures of the cations and the OH- in terms of three different species have been systematically investigated. On the one hand, we find that OH- have more significant effects on the solvation structure of Ca2+ than that of Mg2+. We observe that the OH- substantially affects the orientation angles of water molecules surrounding the cation. Through the time correlation functions, we conclude that the water molecules in the first solvation shell of Ca2+ change their preferred orientation faster than those of Mg2+. On the other hand, with the presence of the cation in the first solvation shell of OH-, we find that the hydrogen bonds of OH- are severely altered, and the adjacent water molecules of OH- are squeezed. The two cations have substantially different effects on the solvation structure of OH-. Our work provides new insight into the solvation structures of Ca2+ and Mg2+ in water with the presence of OH-.

Synthesis and biological evaluation of new 2­substituted­4­amino-quinolines and -quinazoline as potential antifungal agents.

Aiming to discover novel antifungal agents, a series of 2­substituted­4­amino-quinolines and -quinazoline were prepared and characterized using IR, 1H NMR, 13C NMR, and HRMS spectroscopic techniques. Their antifungal activities against four invasive fungi were evaluated, and the results revealed that some of the target compounds exhibited moderate to excellent inhibitory potencies. The most promising compounds III11, III14, III15, and III23 exhibited potent and broad-spectrum antifungal activities with MIC values of 4-32 µg/mL. The mechanism studies showed that compound III11 (N,2-di-p-tolylquinolin-4-amine hydrochloride) did not play antifungal potency by disrupting fungal membrane, which was quite different from many traditional membrane-active antifungal drugs. Meanwhile, III11 also demonstrated a low likelihood of inducing resistance, and excellent stability in mouse plasma. In addition, some interesting structure-activity relationships (SARs) were also discussed. These results suggest that some 4­aminoquinolines may serve as new and promising candidates for further antifungal drug discovery.

Structural and dynamic properties of solvated hydroxide and hydronium ions in water from ab initio modeling.

Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water from ab initio molecular dynamics (AIMD) has been a challenging task. The difficulty mainly comes from a lack of accurate and efficient exchange-correlation functional in elucidating the amphiphilic nature and the ubiquitous proton transfer behaviors of the two ions. By adopting the strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation functional in AIMD simulations, we systematically examine the amphiphilic properties, the solvation structures, the electronic structures, and the dynamic properties of the two water ions. In particular, we compare these results to those predicted by the PBE0-TS functional, which is an accurate yet computationally more expensive exchange-correlation functional. We demonstrate that the general-purpose SCAN functional provides a reliable choice for describing the two water ions. Specifically, in the SCAN picture of water ions, the appearance of the fourth and fifth hydrogen bonds near hydroxide stabilizes the pot-like shape solvation structure and suppresses the structural diffusion, while the hydronium stably donates three hydrogen bonds to its neighbors. We apply a detailed analysis of the proton transfer mechanism of the two ions and find the two ions exhibit substantially different proton transfer patterns. Our AIMD simulations indicate that hydroxide diffuses more slowly than hydronium in water, which is consistent with the experimental results.

4-Aminoquinolines Bearing a 1,3-Benzodioxole Moiety: Synthesis and Biological Evaluation as Potential Antifungal Agents.

In search of new environmentally friendly and effective antifungal agents, a series of 4-aminoquinolines bearing a 1,3-benzodioxole moiety were prepared and their structures were fully elucidated by spectroscopic analyses. The antifungal activities of all the target compounds against five phytopathogenic fungi were evaluated in vitro. The results revealed that most of the newly synthesized compounds exhibited obvious inhibitory activities at the concentration of 50 µg/mL. Among them, 6-(furan-2-yl)-N-(4-methylphenyl)-2H-[1,3]dioxolo[4,5-g]quinolin-8-amine hydrochloride (7m) displayed more promising antifungal potency with EC50 values of 10.3 and 14.0 µg/mL against C. lunata and A. alternate, respectively. Particularly, the EC50 value of 7m against C. lunata was 7.3-fold as potent as the standard azoxystrobin. There were some significant morphological alterations in the mycelia of C. lunata when treated with 7m at 50 µg/mL. Additionally, the preliminary structure-activity relationships (SARs) were also discussed. Thus, this study suggests that 4-aminoquinolines bearing a 1,3-benzodioxole moiety are interesting scaffolds for the development of novel antifungal agents.

The Influence of Sodium Iodide Salt on the Interfacial Properties of Aqueous Methanol Solution by a Combined Molecular Simulation and Sum Frequency Generation Vibrational Spectroscopy Study.

Understanding the influence of salt ions on the microscopic properties of liquid interfaces is of both fundamental and practical importance. A large number of previous experimental and theoretical investigations have explored the salt effects on the surfaces of either pure water or neat organic liquid. However, how the salt ions affect the interfacial structures of water/organic liquid mixtures has rarely been studied. Here, the molecular dynamics (MD) simulations and sum frequency generation vibrational spectroscopy (SFG-VS) were carried out to investigate the influence of sodium iodide (NaI) on the air/liquid interfaces of the methanol-water mixtures. The SFG-VS spectral intensities were discovered to increase with the addition of 3 M NaI, while the center frequencies of the C-H stretching vibrations at high methanol concentrations showed a ∼2 cm-1 blue shift compared with those obtained before adding NaI. The MD results indicated that Na+ and I- can only affect Part I (near the bulk phase) but not Part II (near the gas phase) of the interfacial region. It was also found that the average orientations of interfacial methyl groups were constant and not effectively disturbed by the changes of methanol concentrations or the addition of NaI. It is therefore concluded that the changes of the SFG-VS intensities upon the addition of NaI salts were mainly caused by the increasing number of interfacial methanol molecules. Further analysis showed that the existence of NaI affects the surface tensions more for the interfaces with higher bulk methanol concentrations, which is in agreement with the SFG-VS results. It is noteworthy that the maximum number density of methanol molecules with the net nonzero orientations is reached near the Gibbs dividing surface, the reasons of which are worth further investigating.

Floral volatiles identification and molecular differentiation of Osmanthus fragrans by neutral desorption extractive atmospheric pressure chemical ionization mass spectrometry.

RATIONALE: Floral volatiles are commonly present only at trace amounts and can be degraded or lost during vapor collection, which is often challenging from the analytical standpoint. Osmanthus fragrans Lour. is a widely cultivated plant known for the highly distinct fragrance of its flowers. The identification of specific volatile organic compounds (VOCs) and molecular differentiation of O. fragrans without any chemical pretreatment and VOC collection are important. METHODS: Twenty-eight VOCs released by the flowers from ten different cultivars of O. fragrans were identified using neutral desorption extractive atmospheric pressure chemical ionization mass spectrometry (ND-EAPCI-MS) without any chemical pretreatment or VOC collection. Chemical identification was performed by high-resolution MSn analysis and whenever possible was confirmed by the analysis of standards. RESULTS: According to our literature search, nine of the identified VOCs, 3-buten-2-one, cyclohexadiene, 2-methylfuran, 3-allylcyclohexene, cuminyl alcohol, hotrienol oxide, epoxy-linalool oxide, N-(2-hydroxyethyl) octanamide, and 3-hydroxy-dihydro-ß-ionone, have not been reported in O. fragrans in earlier studies. Confident differentiation between ten different cultivars of O. fragrans was achieved by the principal component analysis of the mass spectrometric results. CONCLUSIONS: The results of our ND-EAPCI-MS analysis substantially increase our knowledge about the chemistry of the O. fragrans floral fragrance and demonstrate the power of this technique for direct molecular profiling for plant recognition or in biotechnological applications.

Molecular analysis of semen-like odor emitted by chestnut flowers using neutral desorption extractive atmospheric pressure chemical ionization mass spectrometry.

Knowledge about the chemical composition of floral volatile organic compounds (VOCs) is valuable in biological studies as well as for the flavor, cosmetic, and fragrance industries. The flowers of Chinese chestnut (Castanea mollissima) emit a distinctive semen-like odor; however, the chemical composition and biological role for the semen-like odor of chestnut flowers remain scarcely studied. Herein, we report the floral VOCs and the pollinators of chestnut flowers. A fast method based on a neutral desorption (ND) device coupled to extractive atmospheric pressure chemical ionization mass spectrometry (EAPCI-MS) was developed for the rapid identification of VOCs from freshly collected chestnut flowers without any chemical pretreatment. Chemical identification was performed using high-resolution MS analysis in combination with tandem MS analysis and whenever possible was confirmed by the analysis of standard reference compounds. Twenty volatiles were identified, most of which are nitrogen-containing. Out of the identified volatiles, 1-pyrroline is known to have a semen-like odor and is probably also responsible for the semen-like odor of the chestnut flowers. Four nitrogenous VOCs of chestnut flowers, including 1-pyrroline, 1-piperideine, 2-pyrrolidone, and phenethylamine, were also common in other semen-like odor flowers such as Photinia serrulata, Castanopsis sclerophylla, and Stemona japonica, suggesting similar chemical origin. The main visitors of chestnut flowers were dipteran species, such as Eristalis tenax, Eristalis arvorum, Episyrphus balteatus, Lucilia sericata, Chrysomya megacephala, Chrysochus asclepiadeus, and Adalia bipunctata. Our results suggest that the chestnut flowers and other semen-like odor flowers may present a new type of sapromyophily. This study also indicates that ND-EAPCI-MS provides more sensitive and simpler detection of many VOCs (particularly nitrogen-containing VOCs) than GC-MS and therefore can be used to complement traditional approaches for the higher chemical coverage of VOCs analysis. Graphical abstract ᅟ.

Influence of riboflavin on the oxidation kinetics of unsaturated fatty acids at the air/aqueous interface revealed by sum frequency generation vibrational spectroscopy.

Riboflavin, a common nutrient also known as vitamin B2, is known to potentially play important roles in preventing lipid peroxidations. However, the detailed antioxidant mechanisms, especially the influence of riboflavin on lipid oxidations at biological interfaces, have not yet been fully explored. In the current study, the effect of riboflavin molecules on the oxidation kinetics of monounsaturated cis-11-eicosenoic acid (EA) at the air/water interface was systematically investigated using sum frequency generation vibrational spectroscopy (SFG-VS). It was discovered that the oxidation rates of the interfacial EA molecules can be reduced by about two to three times in the presence of riboflavin in the aqueous subphase. Further SFG-VS measurements under the protection of nitrogen purging gas showed that more tightly packed and ordered monolayer structures were formed by the surface adsorption of riboflavin molecules, making the C[double bond, length as m-dash]C bonds less accessible to the gas phase oxidative species. These results suggested that the antioxidant mechanism for riboflavin in the vicinity of biomembranes may not necessarily involve other reducing agents. They also show the great importance of interfacial molecular structures in biologically relevant chemical reactions.

Machine-Learning-Based Interatomic Potentials for Group IIB to VIA Semiconductors: Toward a Universal Model.

Rapid advancements in machine-learning methods have led to the emergence of machine-learning-based interatomic potentials as a new cutting-edge tool for simulating large systems with ab initio accuracy. Still, the community awaits universal interatomic models that can be applied to a wide range of materials without tuning neural network parameters. We develop a unified deep-learning interatomic potential (the DPA-Semi model) for 19 semiconductors ranging from group IIB to VIA, including Si, Ge, SiC, BAs, BN, AlN, AlP, AlAs, InP, InAs, InSb, GaN, GaP, GaAs, CdTe, InTe, CdSe, ZnS, and CdS. In addition, independent deep potential models for each semiconductor are prepared for detailed comparison. The training data are obtained by performing density functional theory calculations with numerical atomic orbitals basis sets to reduce the computational costs. We systematically compare various properties of the solid and liquid phases of semiconductors between different machine-learning models. We conclude that the DPA-Semi model achieves GGA exchange-correlation functional quality accuracy and can be regarded as a pretrained model toward a universal model to study group IIB to VIA semiconductors.

Natural phytoalexins inspired the discovery of new biphenyls as potent antifungal agents for treatment of invasive fungal infections.

With the aim of discovering novel and effective antifungal agents derived from natural sources, a series of new biphenyls based on natural biphenyl phytoalexins were designed, synthesized and evaluated for their antifungal activities against four invasive fungi. By modifying the two benzene rings of noraucuparin, a well-known biphenyl phytoantitoxin, some promising compounds with remarkable antifungal activity were discovered. Notably, compounds 23a, 23e and 23h exhibited potent activities and a broad antifungal spectrum with low MICs of 0.25-16 µg/mL, which were 8-256-fold more potent than that of the lead compound noraucuparin. Particularly, they displayed comparable potency to the positive control amphotericin B against Cryptococcus neoformans. Some interesting structure-activity relationships have also been discussed. Preliminary mechanism studies revealed that compound 23h might achieve its rapid fungicidal activity by disrupting the fungal cell membrane. Moreover, compound 23h exhibited significant inhibition against some virulence factors of Cryptococcus neoformans, low toxicity to normal human cells, as well as favorable pharmacokinetic and drug-like properties. The above results evidenced that the development of new antifungal candidates derived from natural phytoalexins was a bright and promising strategy.

Electric-Field-Induced Interface Behavior of Dodecyl Sulfate with Large Organic Counterions: A Molecular Dynamics Study.

Dodecyl sulfate with tetramethylammonium counterions has been employed to systematically investigate the influence of different static electric fields on molecular structural properties, surface tension, by adopting molecular dynamics (MD) simulations with IR and sum frequency generation (SFG) spectrum calculations. The results indicated that dodecyl sulfate (DS-) and large organic TMA+ counterions can form a mixed adsorption layer in which one head group of DS- is surrounded by two tetramethylammonium (TMA+) and one water molecule. Additionally, it was observed that the surface tension significantly decreases with the increasing static electric field strength since the surfactant stands straighter at the interface as the electric field increases. The result can be instructively adopted in the manufacturing field to control surface tension. Moreover, it was found that the SFG stretch intensities of methylene decrease and the stretch intensities of the methyl group increase with increasing static electric fields. The result indicated that the static electric fields can make DS- more orderly and upright at the interface.

Liquid/Vapor Interface of Dimethyl Carbonate-Methanol Binary Mixtures Investigated by Sum Frequency Generation Vibrational Spectroscopy and Molecular Dynamics Simulation.

In the present work, the dimethyl carbonate (DMC)-methanol binary mixture was used as a benchmark system to study the molecular structures of the liquid/vapor interface of organic-organic mixtures by sum frequency generation vibrational spectroscopy (SFG-VS) and molecular dynamics (MD) simulations. It was discovered that both the methanol and DMC molecules are anisotropically oriented at the surface, yielding strong SFG-VS signals in the C-H stretching frequency range for both molecules. The detailed analyses of the spectroscopic and MD data reveal that the increase of the methanol bulk concentrations reduces the orientational order of the methyl groups for both the interfacial DMC and methanol molecules but does not significantly affect the orientations of the carbonyl group in DMC. Moreover, no obvious correlations were found between the room-temperature orientations of the surface molecules and the azeotropic mole fraction. The present work paves the road for future investigations on the molecular structures of the liquid/vapor interfaces of other organic-organic mixtures, especially those that are important in industrial separations.

Quantification of 1-hydroxypyrene in undiluted human urine samples using magnetic solid-phase extraction coupled with internal extractive electrospray ionization mass spectrometry.

Polycyclic aromatic hydrocarbons (PAHs) are a group of ubiquitous environmental contaminants raising worldwide concerns due to their carcinogenic effects. In this study, 1-hydroxypyrene (1-OHP, the most widely used biomarker of internal dose of PAHs exposure) in undiluted human urine samples (10 mL) was selectively enriched by polypyrrole-coated Fe3O4 magnetite nanocomposites (termed as Fe3O4@Ppy, 1 mg) and then directly eluted by the electrospraying solvent (acetone/benzene/acetic acid (v/v/v, 90/10/1); 100 uL) biased with -3.5 kV to produce the deprotonated 1-OHP anions for mass spectrometric analysis. The method established here significantly improved the current performance for detection of urinary 1-OHP, providing the speed for a single sample analysis within 4 min, the limits of detection (LOD) of 0.0001 µg L(-1), the linear response range of 0.001-5.000 µg L(-1) (R(2) = 0.9994), recovery rates of 90.6-96.1%, and relative standard deviation (RSD, n = 6) values between 2.9% and 8.0%. Human samples including raw human urine collected from 10 healthy volunteers (5 smokers and 5 nonsmokers) and 7 lung cancer patients have been successfully analyzed, showing that magnetic solid-phase extraction (MSPE) coupled with internal extractive electrospray ionization mass spectrometry (iEESI-MS) is an alternative strategy for high throughput quantitative detection of urinary 1-OHP for health risk assessment of PAHs exposure.

Imaging serotonin transporters with 123I-ADAM brain SPECT in healthy non-human primates.

BACKGROUND: Serotonin transporters (SERTs) play a major role in modulating serotonergic neuronal function and are the target of many antidepressant drugs used in neuro-psychiatric disorders. To gain more information on the temporal distribution of SERTs, 2-([2-([dimethylamino]methyl)phenoxyl]thio)-5-[I]iodophenylamine (I-ADAM) single photon emission computed tomography (SPECT) was utilized in an in vivo imaging study using non-human primates. METHODS: Two female monkeys (Macaca cyclopis) were studied. Eight brain SPECT imaging examinations, each 30 min in duration, were obtained after injection of 185 MBq of I-ADAM. Images were obtained using a dual-head gamma camera equipped with ultra-high resolution fan-beam collimators. In addition to visual inspection, the radio-uptake and specific uptake ratios (SURs) of midbrain (MB), thalamus (TH), striatum (ST), temporal and frontal cortices and the whole brain in reference to the corresponding magnetic resonance image at the eight time points were measured. The SUR of MB, using cerebellum (CB) as the reference tissue, was calculated as (MB - CB)/CB, in mean counts/pixel. The SURs of the other brain regions were similarly measured. RESULTS: There was relatively high uptake of I-ADAM in the MB and TH, moderate uptake in ST, lower uptake in the cerebral cortex, and almost no uptake in the CB. The image of MB could be easily identified at the first 30 min time point. It appeared that the SURs of MB, TH and ST reached equilibrium around 210 min after injection. No adverse reactions of the primates were found during and after imaging. Brain distribution of I-ADAM in the primate appeared consistent with the known distribution of SERTs. CONCLUSION: In conjunction with a high SUR in MB, TH and ST, we speculate that I-ADAM may be a potential radioligand for SPECT studies of serotonin transporters in humans.