Synthesis and antimicrobial bioassays of 1,3,4-thiadiazole sulfone derivatives containing amide moiety: A study based on molecular dynamics (MD) simulations,MM/GBSA,and molecular docking

The backbone structure (1,3,4-thiadiazole sulfone derivatives containing amide moiety) of target compounds was determined by modification and optimization of the theoretical design based on commercial chemical carboxin, including molecular docking, scaffold hopping, ligand expansion, etc.In this paper, 23 target compounds were synthesized by the combination of theoretical design and chemical synthesis, and characterized by ¹H NMR, ¹³C NMR and HR MS. Addtionally, the antibacterical bioassay showed that most target compounds performed excellent inhibition on Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzae (Xoo) in vitro. Meanwhile, molecular docking, molecular dynamics (MD) simulations, and studies on ligand/protein (carboxin/2FBW and 4n/2FBW) complex systems were displayed, and the interaction patterns of ligand/protein complex system were predicted by molecular docking. Besides, the ligand/protein complex system was subject to MD simulation. The analysis of molecular dynamics such as RMSD values suggested that compound/2FBW complexes were stable. MM/GBSA (Molecular mechanics generalized born surface area) dynamic binding affinity results revealed that the active residues (TYR58, HIS26, ARG43, SER39, etc.) played an essential part in the binding of the compound(s) to form a stable low-energy ligand/protein complex, while the MD trajectories demonstrated that the interactions of drugs with 2FBW affected the tertiary structure and increased the stability of protein. Besides, compound 4n also showed control efficacies (curative and protective) on Xoo in vivo, where the curative efficacy was 35.91% and the protective efficacy was 18.97%. In a word, this study showed that 1,3,4-thiadiazole sulfone derivatives containing amide moiety designed based on the structure of carboxin were promising agricultural antibacterial agents, featuring certain stability of binding affinity to proteins and carboxin.     

Enhanced energy transfer from diolefinic laser dyes to meso-tetrakis (4-sulfonatophenyl) porphyrin immobilized on silver nanoparticles: DFT,TD-DFT and spectroscopic studies

Porphyrin derivatives are known singlet oxygen sensitizers in photodynamic therapy (PDT). Energy transfer from a class of diolefinic laser dyes (DOLDs) as energy donors to the sodium salt of meso-tetrakis (4-sulfonatophenyl) porphyrin (TPPS) as the accepter of energy would extend the range of photon harvesting down to the UV-region. Energy transfer was substantially enhanced in the presence of metallic silver nanoparticles (AgNPs), as revealed by steady-state emission spectroscopy, lifetimes, and quantum mechanics. DOLDs under investigation are 2,5-distyrylpyrazine (DSP), 1,4-bis (β-pyridyl-2 vinyl) benzene (P2VB), and 1,4 bis (2-methylstyryl) benzene (MSB) as efficient donors of intense absorption in the UV-region. AgNPs enhance the rate of energy transfer from DOLDs to TPPS via bringing donor and acceptor into close- proximity with a concomitant increase in dipole–dipole interaction between excited state donor and ground-state acceptor. The DOLDs molecular structures were optimized using the DFT/CAM-B3LYP/6-311G++ (d, p) level of theory. The calculated electronic absorption spectra for the studied DOLDs in the gaseous phase and methanol solvent were studied using the time-dependent density functional theory (TD-DFT) at M06-2X/6-311G++ (2d,2p) level. The calculated absorption/emission spectra for DSP laser dye in methanol are obtained at the TD/ M06-2X/6-311G++(2d, 2p) method. Notably, all theoretical results of the molecular structures under study highly agreed with the practical optical results. Energy transfer rate constants (k_ET) amid energy donor/acceptor pairs were determined by Stern-Volmer constants (KSV) and donors' lifetime measurements. The KSV values indicate an enhanced Fluorescence Resonance Energy Transfer (FRET) efficiencies in the presence of negatively charged AgNPs. The critical transfer distances R_o were determined from the spectral overlap between the emission spectrum of donor and absorption spectrum of TTPS. These outcomes propose the application of designed metal-enhanced FRET for energy-transfer-based assays and photodynamic therapy (PDT) applications.     

CO Oxidation Catalytic Effects of Intrinsic Surface Defects in Rhombohedral LaMnO3

There is an ongoing effort to replace rare and expensive noble-element catalysts with more abundant and less expensive transition metal oxides. With this goal in mind, the intrinsic defects of a rhombohedral perovskite-like structure of LaMnO₃ and their implications on CO catalytic properties were studied. Surface thermodynamic stability as a function of pressure (P) and temperature (T) were calculated to find the most stable surface under reaction conditions (P=0.2 atm, T=323 K to 673 K). Crystallographic planes (100), (111), (110), and (211) were evaluated and it was found that (110) with MnO₂ termination was the most stable under reaction conditions. Adsorption energies of O₂ and CO on (110) as well as the effect of intrinsic defects such as Mn and O vacancies were also calculated. It was found that O vacancies favor the interaction of CO on the surface, whereas Mn vacancies can favor the formation of carbonate species.     

Comparison of Nitrogen Activation on Trinuclear Niobium and Tungsten Sulfide Clusters Nb3Sn and W3Sn (n=0–3): A DFT Study

The reaction of N₂ with trinuclear niobium and tungsten sulfide clusters Nb₃S_n and W₃S_n (n=0–3) was systematically studied by density functional theory calculations with TPSS functional and Def2-TZVP basis sets. Dissociations of N−N bonds on these clusters are all thermodynamically allowed but with different reactivity in kinetics. The reactivity of Nb₃S_n is generally higher than that of W₃S_n. In the favorite reaction pathways, the adsorbed N₂ changes the adsorption sites from one metal atom to the bridge site of two metal atoms, then on the hollow site of three metal atoms, and at that place, the N−N bond dissociates. As the number of ligand S atoms increases, the reactivity of Nb₃S_n decreases because of the hindering effect of S atoms, while W₃S and W₃S₂ have the highest reactivity among four W₃S_n clusters. The Mayer bond order, bond length, vibrational frequency, and electronic charges of the adsorbed N₂ are analyzed along the reaction pathways to show the activation process of the N−N bond in reactions. The charge transfer from the clusters to the N₂ antibonding orbitals plays an essential role in N−N bond activation, which is more significant in Nb₃S_n than in W₃S_n, leading to the higher reactivity of Nb₃S_n. The reaction mechanisms found in this work may provide important theoretical guidance for the further rational design of related catalytic systems for nitrogen reduction reactions (NRR).     

Tuning the Structure and Properties of N-doped Positively Charged Polycyclic Aromatic Hydrocarbons

A detailed study of the geometry, aromatic character, electronic and magnetic properties for a series of positively charged N-doped polycyclic aromatic hydrocarbons (PAHs) was performed. Magnetic properties of the examined molecules were analyzed by means of the magnetically induced current density calculated using the diamagnetic-zero version of the continuous transformation of origin of current density (CTOCD-DZ) method. The comparative study of the local aromaticity of the studied molecules was performed using several different indices: energy effect (ef), harmonic oscillator model of aromaticity (HOMA) index, six centre delocalization index (SCI) and nucleus independent chemical shifts (NICS). The presence of N-atoms in the inner rings was found to cause a planarity distortion in the studied N-doped systems. The geometric changes and charged nature of the studied N-doped systems do not significantly influence the current density and the local aromaticity distribution in comparison with the corresponding parent benzenoid hydrocarbons. The present study demonstrates how quantum chemical calculations can be used for rational design of novel PAHs and for fine tuning of their properties.     

Insights and Activation Energy Surface of the Dehydrogenation of C2HxO Species in Ethanol Oxidation Reaction on Ir(100)

Dehydrogenation of an organic compound is the first and the most fundamental elementary reaction in many organic reactions. In ethanol oxidation reaction (EOR) to form CO₂, there are a total of 46 pathways in C₂H_xO (x=1–6) species leading to the removal of all six hydrogen atoms in five C−H bonds and one O−H bond. To investigate the degree of dehydrogenation in EOR under operando conditions, we performed density function theory (DFT) calculations to study 28 dehydrogenation steps of C₂H_xO on Ir(100). An activation energy surface was then constructed and compared with that of the C−C bond cleavages to understand the importance of the degree of dehydrogenation in EOR. The results show that there are likely 28 dehydrogenations in EOR under fuel cell temperatures and the last two hydrogens in C₂H₂O are less likely cleaved. On the other hand, deep dehydrogenation including 45 dehydrogenations can occur under ethanol steam reforming conditions.     

Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling,Molecular Docking,and Molecular Dynamics Simulation

Six phthalate acid esters(PAEs) priority pollutants[dimethyl phthalate(DMP), diethyl phthalate(DEP), dibutyl phthalate (DBP or DNBP), di-n-octyl phthalate(DNOP), di 2-ethyl hexyl phthalate(DEHP), and butyl benzyl phthalate(BBP)] were opted as the research object. PAE-degrading esterase CarEW(PDB ID:1C7I) isolated from Bacillus subtilis acting as a template and an iterative saturation mutation strategy was adopted to modify key amino acids to attain efficient PAE-degrading esterase substitutes with a reasonable structure constructed by homology modeling method. Present study designed a total of 285 unit-site and multi-site substitutions of PAE-degrading esterase using the homology modeling method. Among them, 207 PAE-degrading esterase substitutions, which contained the 6-site PAE-degrading esterase substitute 1C7I-6-9 with 84.21% enhancement intensity of degradation ability revealed better degradability to all the 6 PAEs after modification. Moreover, molecular dynamics simulation based on the Taguchi method reported the optimal external application environment for PAE-degrading esterase substitutes as follows:pH=6, T=35℃, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H₂O₂ was 50 mg/L, and the voltage gradient was 1.5 V/cm. The degradation ability of PAE-degrading esterase substitutes was found to be elevated by 13.04% as compared to that of the blank control under the optimal condition. Moreover, 11 highly efficient PAE-degrading esterase substitutes with thermal stability were designed.     

Progress on High Voltage PEO-based Polymer Solid Electrolytes in Lithium Batteries

Polymer electrolytes have attracted great interest for next-generation lithium-based batteries on account of safety and high energy density. In this review, we assess recent progress on the design of poly(ethylene oxide)(PEO)-based solid polymer electrolytes in high voltage lithium batteries and identify possible side reactions between PEO-based electrolytes and existing cathodes. We provide an overview of the ways to enhance high voltage resistance of PEO-based electrolytes. Those include components blend, molecular design and interface modification. With these efforts, we want to present new insights into rational design of PEO-based electrolytes to develop solid-state lithium batteries for advanced performance.     

Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation

The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.     

Theoretical insights into the mechanism of photocatalytic reduction of CO2 over semiconductor catalysts

Photocatalytic reduction of CO₂ is one important approach to alleviate greenhouse gas emission and energy crisis, which has gained huge attention in the past decades. However, the lack of understanding complex reaction mechanism impedes new catalysts design. It is also very difficult to understand the mechanism by using only experimental approaches. For this concern, theoretical calculations can effectively supplement the experimental deficiency and thus play an important role. Recently theoretical calculations have been performed on adsorption, migration and reduction of CO₂ molecule on the photocatalyst surface, leading to useful information that have contributed greatly to this field. This review summarizes recent advances in first-principles calculations about CO₂ photoreduction over various semiconductor photocatalysts like metal oxides, sulfides and g-C₃N₄. The methods, models, adsorption and reaction pathways have been discussed in detail. The perspective about future investigation on the photocatalytic reduction of CO₂ using first principles calculations is also presented.