Electrostatic Calculations Research Articles

Synthesis, Characterization, in silico DFT, Molecular docking, ADMET Profiling Studies and Toxicity Predictions of Ag(I) Complex Derived from 4‐Aminoacetophenone

AbstractThe reaction of the synthesized (E)‐1‐(4‐((2,4‐dihydroxy‐6‐methylphenyl)diazenyl)phenyl)ethan‐1‐one, (DMPDE) ligand with Ag(I) ion at room temperature resulted in the formation of the complex; [Ag(DMPDE)(H2O)2]. 1H NMR, 13C NMR, FTIR, UV‐Vis, mass spectra, elemental analyses, thermal analysis (TGA/DTA), and molar conductance measurements were done to elucidate the structure of synthetic compounds. The results revealed an interesting geometrical variation; tetrahedral for Ag(I) complex. FT‐IR spectra demonstrated that the ligand (DMPDE) under investigation behaves as a bidentate ligand (N,O) through the nitrogen atom of the azo group which is the farthest of the acetophenone moiety and oxygen phenolic for benzene moiety and forms a stable five‐membered chelating ring. The electronic structure, molecular electrostatic potential (MEP) and quantum chemical calculations of the newly synthesized compounds are investigated theoretically at the DFT/B3LYP level of theory. Additionally, the ligand (DMPDE) and Ag(I) complex were screened against the growth of pathogenic bacteria [Actinomycosis (G+), E. Escherichia Coli (G−)] and fungi (Penicillium spp.) compared with the reference antibiotics, Chloramphenicol and Nystatin. Furthermore, 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) was used to evaluate the antioxidant activities of the ligand and its complex, which showed they both possess significant antioxidant properties in comparison with L‐ascorbic acid (Vit. C) as standard. Based on docking studies, (DMPDE) and Ag(I) complex demonstrated a greater affinity for (PDB ID: 3T88), which corresponds to Escherichia coli protein (−6.7818 kcal/mol) and (−6.7928 kcal/mol), respectively. Interestingly, the most active Ag(I) complex inside the active site of cervical cancer receptor (PDB ID: 4XR8) demonstrated a higher binding energy (−6.2631 kcal/mol) than free ligand (−5.8561 kcal/mol). In silico, ADMET displayed that compounds obey the Lipinski rule and the “Veber's rule. Consequently, is likely to exhibit oral bioavailability with good LD50 and a safety profile that includes non‐cytotoxicity, non‐immunotoxicity, and non‐skin sensitization. Finally, the compounds synthesized showed significant anticancer activity in human cervical cancer cell lines HeLa and SiHa compared with positive controls (cisplatin) and normal human hepatic cells (WRL‐68). In the present study, all tested cancer cell lines showed promising activity against Ag(I) complex, whose IC50 value ranged from (61.02 to 71.09) μg/mL.

The Role of Antisolvents with Different Functional Groups in the Formation of Cs4PbBr6 and CsPbBr3 Particles.

Compared to the high-temperature hot injection (HI) technique, the room-temperature supersaturated recrystallization (SR) approach is more hopeful to realize the industrialized production of CsPbX3 (X = Cl, Br, and I) nanomaterials. However, accurate compositional control of the product is still difficult, and the role and underlying mechanism of antisolvents in the reprecipitation process remain unclear. Herein, CsPbBr3 particles and CsPbBr3/Cs4PbBr6 composites with certain proportions are synthesized using different antisolvents with the SR method. By adjustment of the polarity or functional group of antisolvents, it is found that the functional groups of antisolvents have a major impact on the composition of the products. Furthermore, the influential mechanism of different antisolvents on the compositions of products is investigated by combining electrostatic potential calculations and ultraviolet-visible absorption spectroscopy. It suggests that the interaction between functional groups of antisolvents and organic ligands influences the coordination status of the intermediate Pb-complex and further affects the separating rate of the Pb(II)-intermediate, leading to the formation of products with different compositions. A physicochemical mechanism is proposed to explain the formation of Cs4PbBr6 and CsPbBr3. This work deepens the understanding of the formation mechanism of all-inorganic metal halide perovskite-related materials based on the SR method and provides new routes to achieve their controllable preparation.

PMC-IZ: A Simple Algorithm for the Electrostatics Calculation in Slab Geometric Molecular Dynamics Simulations.

Slab geometric systems are widely utilized in molecular simulations. However, an efficient, straightforward, and accurate method for calculating electrostatic interactions in these systems for molecular dynamics (MD) simulations is still needed. This review introduces a PME-like approach called PMC-IZ, specifically designed for slab geometric systems. Traditional approaches for long-range electrostatic interaction calculations in slab geometry typically involve Ewald summation, where the Gaussian charge density is summed within 3D unit cells and then integrated in the 2D periodic space. In the proposed approach here, the Poisson equation was solved for a single Gaussian charge density within 2Dl periodic space, followed by convolution within 3D unit cells using an effective potential as the convolution kernel for summation. The effective potential ensures that the solution within the region of interest adheres strictly to 2D periodic boundary conditions while inherently possessing 3D periodic boundary condition properties. The PMC-IZ method provides for such systems accurate treatment of electrostatic interactions, overcomes limitations associated with finite vacuum layers, and offers improved computational efficiency. We thus postulate that this method provides a valuable tool for studying electrostatic interactions in slab geometric system MD simulations. It has promising applications in various areas such as surface science, catalysis, and materials research, where accurate modeling of slab geometric electrostatic interactions is essential.

Fundamental investigation of micro-nano cellulose and lignin interaction for transparent paper: Experiment and electrostatic potential calculation

Plastic has significant negative consequences for the environment and human health, demanding greener alternatives. Lignocellulose is a sustainable biomass material, and its paper has been considered as a potential material to replace plastics. Micro-nano lignocellulose, derived from natural plants, possesses a small size and abundant hydrogen bonding capacity. However, there is no clear explanation for the interactions between lignin and micro-nano cellulose, and little understanding of how the interaction can affect the papers' structure and optical properties. Electrostatic potential calculation is a reliable tool to explain non-covalent interactions, and can explore the binding between lignin and micro-nano cellulose. In this paper, kenaf – a non-wood fiber raw material – was employed to prepare micro-nano lignocellulose. The resulting slurry facilitated the production of transparent paper via a simple casting method. The prepared transparent micro-nano paper exhibited high transparency (~90 %), UVA resistance (~80 %), and hydrophobicity (~114°). More importantly, the electrostatic potential calculation demonstrates the inherent relationship between structure and performance, providing practical knowledge for constructing film materials.

Supramolecular motifs formed by CH3/Cl-substituted arene groups: evidence for structural differences in thiophosphoramides and similarities in their complexes.

Differences/similarities of supramolecular motifs are discussed in two new thiophosphoramide structures and their Ni molecular complexes: (C2H5O)2P(S)(NHC(S)NHCH2C6H4X) and [{(C2H5O)2P(S)(NC(S)NHCH2C6H4X)}2Ni] (X = Cl/CH3I/II and III/IV). The structures have equal numbers of donor/acceptor sites contributing to classical hydrogen bonds (PS/CS and 2 × NH in ligands and 2 × PS and 2 × NH in the complexes). However, these donor and acceptor sites contribute to inter/intramolecular hydrogen bonding in ligands and intramolecular hydrogen bonding in complexes. In the supramolecular assemblies of the ligands, the classic hydrogen bonds (N-H⋯S[double bond, length as m-dash]C) are restricted in dimer synthons, and the weaker interactions (formed by Cl/CH3 substituents) compete against each other. In the complexes, despite the lack of classic intermolecular hydrogen bond, numerous weak interactions, e.g., C-H⋯Y (Y = S, O, Ni, N, and π), contribute to the molecular assemblies, which do not include the participation of Cl/CH3. Thus, different packing features of ligands, but similar in complexes are observed. Each ligand and the associated complex show nearly equal supramolecular motifs in the slice of the substituted benzyl groups, related to the formation of C-H⋯Cl/π⋯π for the 4-Cl-C6H4CH2 groups in I/III and C-H⋯π for the 4-CH3-C6H4CH2 groups in II/IV. The repeatabilities of the motifs made by 4-Cl-C6H4CH2/4-CH3-C6H4CH2 were checked by surveying 142/844 structures with 178/1482 segments in the CSD, which show that 17% and 12% of the structures exhibited similarities with the title structures. The methods X-ray crystallography, 2D fingerprint plots, electrostatic potential surfaces, QTAIM, and energy framework calculations were applied to present the discussion.

Computational Methods to Target Protein-Protein Interactions.

The chapter emphasizes the importance of understanding protein-protein interactions in cellular mechanisms and highlights the role of computational modeling in predicting these interactions. It discusses sequence-based approaches such as evolutionary trace (ET), correlated mutation analysis (CMA), and subtractive correlated mutation (SCM) for identifying crucial amino acid residues, considering interface conservation or evolutionary changes. The chapter also explores methods like differential ET, hidden-site class model, and spatial cluster detection (SCD) for interface specificity and spatial clustering. Furthermore, it examines approaches combining structural and sequential methodologies and evaluates modeled predictions through initiatives like critical assessment of prediction of interactions (CAPRI). Additionally, the chapter provides an overview of various software programs used for molecular docking, detailing their search, sampling, refinement and scoring stages, along with innovative techniques and tools like normal mode analysis (NMA) and adaptive Poisson-Boltzmann solver (APBS) for electrostatic calculations. These computational and experimental approaches are crucial for unraveling protein-protein interactions and aid in developing potential therapeutics for various diseases.

A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems.

We introduce a simple cutoff-based method for precise electrostatic energy calculations in the molecular dynamics (MD) simulations of point-particle systems. Our method employs a theoretically derived smooth pair potential function to define electrostatic energy, offering stability and computational efficiency in MD simulations. Instead of imposing specific physical conditions, such as dielectric environments or charge neutrality, we focus on the relationship represented by a single summation formula of charge-weighted pair potentials. This approach allows an accurate energy approximation for each particle, enabling a straightforward error analysis. The resulting particle-dependent pair potential captures the charge distribution information, making it suitable for heterogeneous systems and ensuring an enhanced accuracy through distant information inclusion. Numerical investigations of the Madelung constants of crystalline systems validate the method's accuracy.

Bound ion effects: Using machine learning method to study the kinesin Ncd’s binding with microtubule

Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions that are bound or restricted at the Ncd-tubulin dimer binding interfaces. To consider the ion effects, widely used implicit solvent models treat ions implicitly in the continuous solvent environment without focusing on the individual ions’ effects. But highly charged biomolecules such as the Ncd and tubulin dimer may capture some ions at highly charged regions as bound ions. Such bound ions are restricted to their binding sites; thus, they can be treated as part of the biomolecules. By applying multiscale computational methods, including the machine-learning-based Hybridizing Ions Treatment-2 program, molecular dynamics simulations, DelPhi, and DelPhiForce, we studied the interaction between the Ncd motor domain and the tubulin dimer using a hybrid solvent model, which considers the bound ions explicitly and the other ions implicitly in the solvent environment. To identify the importance of treating bound ions explicitly, we also performed calculations using the implicit solvent model without considering the individual bound ions. We found that the calculations of the electrostatic features differ significantly between those of the hybrid solvent model and the pure implicit solvent model. The analyses show that treating bound ions at highly charged regions explicitly is crucial for electrostatic calculations. This work proposes a machine-learning-based approach to handle the bound ions using the hybrid solvent model. Such an approach is not only capable of handling kinesin-tubulin complexes but is also appropriate for other highly charged biomolecules, such as DNA/RNA, viral capsid proteins, etc.

Polymer Coating with Balanced Coordination Strength and Ion Conductivity for Dendrite-Free Zinc Anode.

Decorating Zn anodes with functionalized polymers is considered as an effective strategy to inhibit dendrite growth. However, this normally brings extra interfacial resistance rendering slow reaction kinetics of Zn2+ . Herein, a poly(2-vinylpyridine) (P2VP) coating with modulated coordination strength and ion conductivity for dendrite-free Zn anode is reported. The P2VP coating favors a high electrolyte wettability and rapid Zn2+ migration speed (Zn2+ transfer number, tZn 2+ = 0.58). Electrostatic potential calculation shows that P2VP mildly coordinates with Zn2+ (adsorption energy = -0.94eV), which promotes a preferential deposition of Zn along the (002) crystal plane. Notably, the use of partially (26%) quaternized P2VP (q-P2VP) further reduces the interfacial resistance to 126 Ω, leading to a high ion migration speed (tZn 2+ = 0.78) and a considerably low nucleation overpotential (18mV). As a result of the synergistic effect of mild coordination and partial electrolysis, the overpotential of the q-P2VP-decorated Zn anode retains at a considerably low level (≈46mV) over 1000h at a high current density of 10mA cm-2 . The assembled (NH4 )2 V6 O16 ·1.5H2 O || glass fiber || q-P2VP-Zn full cell reveals a lower average capacity decay rate of only 0.018% per cycle within 500 cycles at 1 A g-1 .

Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT

Sodium-dependent glucose transporters (SGLTs) couple a downhill Na+ ion gradient to actively transport sugars. Here, we investigate the impact of the membrane potential on vSGLT structure and function using sugar uptake assays, double electron-electron resonance (DEER), electrostatic calculations, and kinetic modeling. Negative membrane potentials, as present in all cell types, shift the conformational equilibrium of vSGLT towards an outward-facing conformation, leading to increased sugar transport rates. Electrostatic calculations identify gating charge residues responsible for this conformational shift that when mutated reduce galactose transport and eliminate the response of vSGLT to potential. Based on these findings, we propose a comprehensive framework for sugar transport via vSGLT, where the cellular membrane potential facilitates resetting of the transporter after cargo release. This framework holds significance not only for SGLTs but also for other transporters and channels.

Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives

The utilization of the density functional theory (DFT) methodology has developed as a highly efficient method for investigating molecular structure and vibrational spectra, and it is increasingly being employed in various applications relating to biological systems. This study focuses on conducting investigations, both experimental and computed, to analyze the molecular structure, electronic properties and features of (E)-4-(((9H-purin-6-yl)imino)methyl)-2-methoxyphenol (ANVA). The expression ANVA should be rewritten as follows: the compound is a derivative of adenine (primary amine), specifically a vanillin (aldehyde). The present study reports the synthesis, characterization, DFT, docking and antimicrobial activity of ANVA. The optimization of the molecular structure was conducted, and the determination of its structural features was performed using DFT with the B3LYP/cc-pVDZ method. The vibrational assignments were determined in detail by analyzing the potential energy distribution. A strong correlation was observed between the spectra that were observed and the spectra that were calculated. The calculation of intramolecular charge transfer was performed using natural bond orbital analysis. In addition, several computational methods were employed, including highest occupied molecular orbital–least unoccupied molecular orbital analysis, molecular electrostatic potential calculations, non-linear optical, reduced density gradient, localization orbital locator and electron localization function analysis. This paper examines the present use of adenine derivatives in combatting bacterial and fungal infections, as well as the inclusion of spectral and quantum chemical calculations in the discussion. Communicated by Ramaswamy H. Sarma

Cloning, computational analysis and expression profiling of steroid 5 alpha-reductase 1 (SRD5A1) gene during reproductive phases and ovatide stimulation in endangered catfish, Clarias magur

The cloning and characterization of the complete coding sequence of the Clarias magur SRD5A1 (CmSRD5A1) gene, which encodes an enzyme responsible for regulating steroid levels by converting testosterone into 5α-dihydrotestosterone (DHT), have been successfully achieved. DHT plays a vital role in enabling the complete expression of testosterone's actions in neuroendocrine tissues. The ORF of the full-length cDNA sequence of SRD5A1 was 795 bp, translating into 265 amino acids, with a total length of 836 bp including UTRs. Like other vertebrates, the signal peptide analysis revealed that SRD5A1 is a non-secretory protein, and hydropathy profiles indicated that it is hydrophobic in nature. The 3D structure of CmSRD5A1 sequence generated above was predicted using highly accurate AlphaFold 2 in Google Colab online platform. CmSRD5A1 contains seven transmembrane helices connected by six loops, with the N-termini located on the periplasmic side and C-termini on the cytosolic side. Structural superimposition with known bacterial and human SRD5As showed very high structural similarity. The electrostatic potential calculation and surface analysis of CmSRD5A1 revealed the presence of a large cavity with two openings one highly electropositive towards the cytosolic side and another relatively neutral towards the transmembrane region. The structural comparison revealed that the electropositive side of the cavity should bind to NADPH and the steroid hormone in the hydrophobic environment. Polar residues binding to NADPH are highly conserved and the same as known strictures. The conserved residues involved in hydrogen bonding with the ketone group at C-3 in the steroids hence fevering Δ4 double-bond reduction are identified as E66 and Y101. Our findings showed that SRD5A1 expression was lower during the spawning phase than the preparatory phase in female fish, while the administration of Ovatide (a GnRH analogue) resulted in up-regulation of expression after 6 h of injection in the ovary. In males, the lowest expression was observed during the preparatory phase and peaked at 16 h post- Ovatide injection in the testis. The expression of SRD5A1 in the brain of female fish was slightly higher during the Ovatide stimulation phase than the spawning phase. This study represents the first report on the cloning and characterization of the full-length cDNA of SRD5A1 in Indian catfish.

Crystal packing of structurally similarand strong dimeric subunits of isomeric N/ -(1,3- benzothiazol-2-yl)nitrobenzenesulfonylhydrazides, influenced by the position of the nitro group

Detailed structural analyses, utilizing single crystal X-ray diffraction, Hirshfeld surface analyses, PIXEL and electrostatic potentials calculations, have been carried out on three isomeric N/-(1,3-benzothiazol-2-yl)nitrobenzenesulfonylhydrazides, Bt-NHNHSO2C6H4NO2-o, m and p. These compounds each crystallize from ethanol solution with two independent, but similar, amino tautomers, in the asymmetric units. For all three compounds, similar and dominant dimeric unsymmetric sub-structures are present in the solid state, linked prominently by pairs of N—H(hydrazinyl)···N(thiazolyl) hydrogen bonds and face-to-face π···π interactions: these sub-structures are the motifs I for each compound. A significant consequence of the different positions of the nitro group in the phenyl ring is the presence of the intramolecular N—H(hydrazonyl)···O(nitro) hydrogen bond present in the ortho derivative, but absent in the meta and para isomers. Apart from this, the different sites of the nitro groups have only a small influence on the internal structure of these motifs I, however they do play a major role in their packing and connections with other motifs. Among the interactions connecting the motifs are N—H···O(nitro), C—H···O(nitro), C—H···O(sulfonyl), C—H···π,N = O···π, S = O···π, face-to-face π···π, and S···S interactions. A survey was carried out on the arrangements of (O2)S-NHNHC fragments in R/S(O2)NHNHCOR compounds.

Improving the physicochemical and pharmacokinetic properties of olaparib through cocrystallization strategy

Olaparib (OLA) is the first PARP inhibitor worldwide used for the treatment of ovarian cancer. However, the oral absorption of OLA is extremely limited by its poor solubility. Herein, pharmaceutical cocrystallization strategy was employed to optimize the physicochemical and pharmacokinetic properties. Four cocrystals of OLA with oxalic acid (OLA-OA), malonic acid (OLA-MA), fumaric acid (OLA-FA) and maleic acid (OLA-MLA) were successfully discovered and characterized. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy confirmed the formation of cocrystals rather than salts, and the possible hydrogen bonding patterns were analyzed through molecular surface electrostatic potential calculations. The in vitro and in vivo evaluations indicate that all of the cocrystals demonstrate significantly improved dissolution performance, oral absorption and tabletability compared to pure OLA. Among them, OLA-FA exhibit sufficient stability and the most increased Cmax and AUC0-24h values that were 11.6 and 6.1 times of free OLA, respectively, which has great potential to be developed into the improved solid preparations of OLA.

Synthesis, acaricidal activity, and structure-activity relationships of novel phenyl trifluoroethyl thioether derivatives containing substituted benzyl groups.

To discover and develop novel acaricidal compounds, a series of 2-fluoro-4-methyl/chlorine-5-((2,2,2-trifluoroethyl)thio)aniline/phenol compounds containing N/O-benzyl moieties were synthesized based on lead compound LZ-1. The activity of these compounds against carmine spider mites (Tetranychus cinnabarinus) was determined using the leaf-spray method. Bioassays indicated that most of the designed target compounds possessed moderate to excellent acaricidal activity against adult T. cinnabarinus. The median lethal concentrations of 25b and 26b were 0.683 and 2.448 mg L-1 against adult mites, respectively; exceeding those of bifenazate (7.519 mg L-1 ) and lead compound LZ-1(3.658 mg L-1 ). Compound 25b exhibited 100% mortality in T. cinnabarinus larvae at 10 mg L-1 . Continuing the study of these compounds in field trials, we compared the efficacy of mite killing by compound 25b with the commercial pesticide spirodiclofen and showed that mite control achieved 95.9% and 83.0% lethality at 10 and 22 days post-treatment. In comparison, spirodiclofen showed 92.7% lethality at 10 days and 77.2% lethality at 22 days post-treatment at a concentration of 100 mg L-1 . Results showed that 25b produced more facile and long-lasting control against T. cinnabarinus than the commercial acaricide spirodiclofen. Density functional theory analysis and electrostatic potential calculations of various molecular substitutions suggested some useful models to achieve other highly active miticidal compounds. © 2023 Society of Chemical Industry.

Spectroscopic, Quantum Chemical and Molecular Docking Studies on N-(9H-Purin-6-yl) Benzamide: A Potent Antimalarial Agent

This study presents a comprehensive analysis of N-(9H-purin-6-yl) Benzamide (NPB) using a combination of Density Functional Theory (DFT) calculations and experimental techniques. The molecular configuration of NPB was optimized using DFT/B3LYP method employing the 6-311++G (d,p) basis set. The fundamental frequencies were calculated and assigned, which agree well with the experimental results. The UV-Vis spectroscopic analyses, HOMO-LUMO energy gap assessment, Molecular Electrostatic Potential calculation, and Mulliken charge analysis, Fukui function calculation and Natural bond orbital analysis were performed for the NPB molecule. The UV-Visible spectral analysis, which predicts the transition of bonding and anti-bonding π-electrons from the purine ring to the aromatic ring of the NPB molecule. A smaller energy gap in the HOMO-LUMO analysis reveals that the NPB molecule is more reactive and Mulliken atomic charge distribution analysis indicates that the carbon atoms are highly influenced by their substituents. Natural Bond Orbital (NBO) analysis was employed to investigate the bonding within the NPB molecule. The Fukui function analysis indicates that the biological activity of the NPB molecule. In order to analyze the structure of NPB molecule, the thermodynamic properties in the temperature range 100–1000 K were obtained by thermodynamic analysis software SHERMO calculator. The molecular docking analysis was carried out for antimalarial proteins (5ZNC, 2BMA, 7E27, 7E26) using auto-docking simulations. This computational method confirms the bioactivity and drug-likeness parameters of the NPB molecule. The molecular docking results predicts the formation of hydrogen bonds between the ligand (NPB) and the protein receptors. Based on these findings, this study establishes that the distinctive methodology applied to identify NPB molecule as a potential candidate for an antimalarial drug designing, which is suitable for in vivo and in vitro investigations.

Antimalarial drug discovery against malaria parasites through haplopine modification: An advanced computational approach.

The widespread emergence of antimalarial drug resistance has created a major threat to public health. Malaria is a life-threatening infectious disease caused by Plasmodium spp., which includes Apicoplast DNA polymerase and Plasmodium falciparum cysteine protease falcipain-2. These components play a critical role in their life cycle and metabolic pathway, and are involved in the breakdown of erythrocyte hemoglobin in the host, making them promising targets for anti-malarial drug design. Our current study has been designed to explore the potential inhibitors from haplopinederivatives against these two targets using an in silico approach. A total of nine haplopine derivatives were used to perform molecular docking, and the results revealed that Ligands 03 and 05 showed strong binding affinity compared to the control compound atovaquone. Furthermore, these ligand-protein complexes underwent molecular dynamics simulations, and the results demonstrated that the complexes maintained strong stability in terms of RMSD (root mean square deviation), RMSF (root mean square fluctuation), and Rg (radius of gyration) over a 100 ns simulation period. Additionally, PCA (principal component analysis) analysis and the dynamic cross-correlation matrix showed positive outcomes for the protein-ligand complexes. Moreover, the compounds exhibited no violations of the Lipinski rule, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) predictions yielded positive results without indicating any toxicity. Finally, density functional theory (DFT) and molecular electrostatic potential calculations were conducted, revealing that the mentioned derivatives exhibited better stability and outstanding performance. Overall, this computational approach suggests that these haplopine derivatives could serve as a potential source for developing new, effective antimalarial drugs to combat malaria. However, further in vitro or in vivo studies might be conducted to determine their actual effectiveness.

Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds

The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately − 60 kcal mol−1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.

A 3,5-dinitropyridin-2yl Substituted Flavonol-based Fluorescent Probe for Rapid Detection of H2S in Water, Foodstuff Samples and Living Cells.

A novel flavonol-based fluorescent probe, Fla-DNT, has been synthesized for the rapid and specific detection of H2S. Fla-DNT exhibits excellent selectivity and anti-interference properties, a short response time (4min), large Stokes shift (138nm), and low detection limit (1.357 µM). Upon exposure to H2S, Fla-DNT displays a remarkable increase in fluorescence intensity at 542nm. Meanwhile, the recognizing site of H2S was predicted through Electrostatic potential and ADCH charges calculations, while the sensing mechanism of H2S was determined via HRMS analysis and DFT calculation. More importantly, the probe owes multiple applications, such as a recovery rate ranging from 92.00 to 102.10% for detecting H2S in water samples, and it can be fabricated into fluorescent strips to track H2S production during food spoilage by tracking color changes, thereby enabling real-time monitoring of food freshness. The bioimaging experiments demonstrate the capability of Fla-DNT to detect both endogenous and exogenous H2S in living cells. These results provide a reliable method and idea for H2S detection in complex environments.

Effect of resolution enhancement using metal ion assisted strategy based on electrospray ionization-ion mobility spectrometry: A case study of carbendazim and thiabendazole in fruits

A method for the rapid and simultaneous determination of carbendazim and thiabendazole residues by electrospray ionization-ion mobility spectrometry (ESI-IMS) combined with a metal ion-assisted technique was developed and validated in different fruit matrices. The metal ion assisted strategy was performed instead of tedious pre-separation procedures to overcome the limitation of low resolution of IMS. Four transition metal cations, Co(II), Ni(II), Cu(II), and Zn(II), were screened and their interactions with carbendazim and thiabendazole were investigated. The injection flow rate and metal ion concentration were optimized. The Cu(II) assisted approach helped to achieve well-separated peaks with a peak-to-peak resolution of 3.61. This method was then applied to detect carbendazim and thiabendazole simultaneously in apples, pears, bananas, and mangoes. The limit of detection (LOD) were 0.03 mg kg−1 and 0.13 mg kg−1 for carbendazim and thiabendazole, respectively, while spiked recoveries were 61.5–122.0% and 83.5–119.8%, respectively, with RSDs less than 13.9%. These satisfactory evaluation parameters indicated that the approach was capable of performing quantitative analysis of multi-pesticide residues. In addition, the feasibility of using metal ion assisted-ESI-IMS for the simultaneous detection also was theoretically demonstrated through molecular electrostatic potential analysis and binding energy calculation based on density functional theory (DFT). Both experimental and theoretical results revealed the effectiveness of the metal ion assisted strategy in improving the resolution of ESI-IMS.