Molecular Structural Features Research Articles

Experimental and theoretical studies on (2E,5E)-2,5-bis(2-methoxybenzylidene)cyclopentanone: Structural, electrochemical, spectroscopic features, solid-state interactions, molecular docking and adsorption studies onto 2D carbon nanomaterials

A monocarbonyl analog of curcumin, (2E,5E)-2,5-bis(2-methoxybenzylidene)-cyclopentanone (B2MBCP), was prepared and characterized via spectroscopic methods (NMR, UV-Vis, FT-IR, and MS). Furthermore, density functional calculations were implemented to study the molecular structure and spectroscopic features, as well as adsorption properties. In addition, Hirshfeld surface and NBO theoretical analysis were carried out. The reduced density gradient (RDG) analysis via non-covalent interactions (NCI) and interaction region indicator (IRI) indicate the presence of extensive Van der Waals interactions. These interactions are classified in different contributions and energy stabilization from Hirshfeld surface analysis where the dominant type of contacts are H···H contacts. The molecular docking studies of B2MBCP with DNA revealed cooperative interactions that led to intercalation. The results from the cyclic voltammetry (CV) measurements agreed with the calculated energies of the frontier orbitals and the compound structure. Theoretical studies indicated that the relatively flat B2MBCP is adsorbed onto a graphene surface, with a significant adsorption energy of –41.19 kcal/mol. The results of this study provide a better overall picture of the properties of MAC with a cyclopentanone core and can be taken as a useful guide in the search for new biologically active compounds and new possible means of delivery.

Ligational behavior of a hydrazone ligand towards Co(II) ion: Synthesis, physicochemical characterization, antitumor, DFT and molecular docking studies

New cobaltous complexes of a hydrazone ligand (HQinAx) containing quinoline and alloxan nuclei were synthesized. The composition and structure of the produced Co(II)-HQinAx complexes were successfully determined using spectroscopic and analytical techniques. Molar conductivity tests showed the neutral characters of Co-HQinAx complexes. The results illustrated that HQinAx behaves as a neutral/mono-, bi- and tri-anionic bi-, tri- and penta-dentate chelating agent. The obtained complexes have octahedral and square-planar geometries. Thermodynamic parameters were effectively calculated after investigating the thermal decomposition patterns of Co-HQinAx complexes in relation to structure. Density functional theory (DFT) level at B3LYP/6-311G(d,p) and LanL2dz level was used to evaluate the molecular structural features of HQinAx and its Co(II) complexes. Co-HQinAx complexes showed an anticancer action against Ehrlich Ascites Carcinoma. A molecular docking investigation was performed to verify the recorded biological activity of the new compounds by determining how they interact with EFP inhibitor with CDK-2 (PDB ID: 3IG7).

Reverse-degree-based topological indices of two-dimensional coronene fractal structures

Researchers are still drawn to research the physical molecular and chemical structure of benzenoid hydrocarbons, unsaturated, fully conjugated compounds with hexagonal arrangements that exhibit remarkable features in relation to aromaticity. For chemical graphs in many dimensions, structures, or networks, topological indices or numerical descriptors have been employed for decades to link key physicochemical parameters with crucial molecular structural features including melting, boiling point, enthalpy, and cyclicity. For this work, the inverse degrees of the molecular or chemical structure or graphs being studied are used to calculate the reverse-degree-based topological indices. In molecular graph theory, reverse-degree-based topological descriptors are a relatively new method for analyzing chemical networks and structures. In this study, we suggest a reverse-degree-based topological representation. We computed particular types of descriptors of two-dimensional (2-D) coronene fractal formations with a variety of reverse-degree-based topological indices, such as the reverse-degree-based topological index of the first, second, and hyper Zagreb, forgotten, geometric arithmetic, atom-bond-connectivity, and the Randic index.

Natural-Product-Inspired Discovery of Trimethoxyphenyl-1,2,4-triazolosulfonamides as Potent Tubulin Polymerization Inhibitors.

An approach of natural product-inspired strategy and incorporation of an NP-privileged motif has been investigated for the discovery of new tubulin polymerization inhibitors. Two series, N-Arylsulfonyl-3-arylamino-5-amino-1,2,4-triazole derivatives, and their isomers were considered. The compounds were synthesized by construction of the N-aryl-1,2,4-triazole-3,5-diamine motif and sulfonylation. Although the chemo- and regioselectivity in sulfonylation were challenging due to multiple ring-tautomerizable-NH and exocyclic NH2 functionalities present in the molecular motifs, the developed synthetic method enabled the preparation of designed molecular skeletons with biologically important motifs. The approach also led to explore interesting molecular regio- and stereochemical aspects valuable for activity. The X-ray crystallography study indicated that the hydrogen bonding between the arylamine-NH and the arylsulfonyl-"O" unit and appropriate molecular-functionality topology allowed the cis-locking of two aryls, which is important for tubulin-binding and antiproliferative properties. All synthesized compounds majorly showed characteristic antiproliferative effects in breast cancer cells (MCF-7), and four compounds exhibited potent antiproliferative activity. One compound potently bound to tubulin at the colchicine site and inhibited tubulin polymerization in vitro. The compound significantly depolymerized microtubules in MCF-7 cells, arrested the cells at the G2/M phase, and induced cell death. This study represents the importance of the design strategy in medicinal chemistry and the molecular structural features relevant to anticancer anti-tubulin properties. The explored molecules have the potential for further development.

Exploring the novel aryltellurium(IV) complexes: Synthesis, characterization, antioxidant, antimicrobial, antimalarial, theoretical and ADMET studies

The current research study is focused on biological efficacy of newly synthesized Schiff base ligand 1,1′-(ethane-1,2-diylbis(azanylylidene))bis(methanylylidene))bis(naphthalen-2-ol) (HNED) and its aryltellurium(IV) complexes. The synthesized compounds were comprehensively characterized by physical and spectral investigations such asmolar conductance, Powder-XRD, EDAX, elemental, TGA-DTG analysis, mass, FT-IR, UV–Vis, 13C NMR and 1H NMR spectroscopy. The molecular and electronic structural characteristics of the synthesized compounds were explored by theoretical chemical estimations which was based on density functional theory (DFT). The outcome of the spectroscopic and theoretical data revealed that the Schiff base HNED was coordinated with tellurium ion through oxygen and nitrogen atoms, suggesting distorted octahedral geometry of complexes. The compounds displayed mild to strong antimicrobial activity against numerous microbial species, with the growth inhibitory activities of the complexes being greater than those of the Schiff base. Complexes 6c and 6f exhibited the highest scavenging ability. Complex 6a exhibited the highest efficiency in inhibiting malarial malformation. In silico molecular docking was executed to explore the binding interaction and binding energies of compound against the active site of the various receptors (3MZF, 4DXD, 3Q70 and 2GHU). The ADMET results indicated that the synthesized compounds have favorable drug-like behavior. This study suggest that the complexes may act as promising candidates for infection ailments.

Efficient degradation of ciprofloxacin in wastewater by CuFe2O4/CuS photocatalyst activated peroxynomosulfate

In this study, CuFe2O4/CuS composite photocatalysts were successfully synthesized for the activation of peroxynomosulfate to remove ciprofloxacin from wastewater. The structural composition and morphology of the materials were analyzed by XRD, SEM, TEM, and Raman spectroscopy. The electrochemical properties of the samples were tested by an electrochemical workstation. The band gap of the samples was calculated by DFT and compared with the experimental values. The effects of different catalysts, oxidant PMS concentrations, and coexisting ions on the experiments were investigated. The reusability and stability of the photocatalysts were also investigated. The mechanism of the photocatalytic degradation process was proposed based on the free radical trapping experiment. The results show that the p-p heterojunction formed between the two contact surfaces of the CuFe2O4 nanoparticle and CuS promoted the charge transfer between the interfaces and inhibited the recombination of electrons and holes. CuFe2O4-5/CuS photocatalyst has the best catalytic activity, and the removal rate of ciprofloxacin is 93.7%. The intermediates in the degradation process were tested by liquid chromatography-mass spectrometry (LC-MS), and the molecular structure characteristics of ciprofloxacin were analyzed by combining with DFT calculations. The possible degradation pathways of pollutants were proposed. This study reveals the great potential of the photocatalyst CuFe2O4/CuS in the activation of PMS for the degradation of ciprofloxacin wastewater.

Potential energy surface, effect of solvents in molecular level, experimental spectra (FTIR, Raman, UV–visible & NMR), electronic, and dynamics simulation of isobavachalcone –Anti tuberculosis agent

The spectroscopic characteristics, molecular structure, and biological characteristics of the Isobavachalcone (IBC) structure have been studied using computational techniques utilizing the usual B3LYP/6-311++G (d,p). PED (Potential Energy Distribution) is used throughout process of assigning the fundamental wave-numbers of IBC. In this work, we have reported the correlation between experimental and computed examination of molecular configuration, FT:IR & Raman, UV–Visible absorption, and NMR (Nuclear Magnetic Resonance) spectrum of the title compound. Potential energy scan (PES) analysis of IBC was enhanced in the initial stage with same basis set. FMO (Frontier Molecular Orbital), MEP (Molecular Electrostatic Potential), local reactivity and quantum chemical descriptors has also been analyzed. Furthermore, drug-likeness and ADMET predictions of the present ligand shows good pharmacological activity. ELF (Electron Localised Function), LOL (Localised Orbital Locator) and RDG (Reduced Density Function) enacted for both the gas and solvents phases. A docking simulation performed with the 2FUM receptor using the Auto Dock software showed that the IBC compound has inhibitory activity against Mycobacterium tuberculosis disease. All our results suggest that the IBC molecule could have a great effect in the treatment of tuberculosis disease. MD simulations been executed over 100 ns to predict the RMSD, RMSF, and the radius-of gyration analyses.

AutoMSR: Auto Molecular Structure Representation Learning for Multi-label Metabolic Pathway Prediction.

It is significant to comprehend the relationship between metabolic pathway and molecular pathway for synthesizing new molecules, for instance optimizing drug metabolization. In bioinformatics fields, multi-label prediction of metabolic pathways is a typical manner to understand this relationship. Graph neural networks (GNNs) have become an effective method to extract molecular structure's features for multi-label prediction of metabolic pathways. Though GNNs can effectively capture structural features from molecular structure graphs, building a well-performed GNN model for a given molecular structure data set requires the manual design of the GNN architecture and fine-tuning of the hyperparameters, which are time-consuming and rely on expert experience. To address the above challenge, we design an end-to-end automatic molecular structure representation learning framework named AutoMSR that can design the optimal GNN model based on a given molecular structure data set without manual intervention. We propose a multi-seed age evolution (MSAE) search algorithm to identify the optimal GNN architecture from the GNN architecture subspace. For a given molecular structure data set, AutoMSR first uses MSAE to search the GNN architecture, and then it adopts a tree-structured parzen estimator to obtain the best hyperparameters in the hyperparameters subspace. Finally, AutoMSR automatically constructs the optimal GNN model based on the best GNN architecture and hyperparameters to extract the molecular structure features for multi-label metabolic pathway prediction. We test the performance of AutoMSR on the real data set KEGG. The experiment results show that AutoMSR outperforms baseline methods on different multi-label classification evaluation metrics.

Inhibition and structural insights of leishmanial glutamyl-tRNA synthetase for designing potent therapeutics

Aminoacyl-tRNA synthetases (aaRSs), essential components of the protein synthesizing machinery, have been often chosen for devising therapeutics against parasitic diseases. Due to their relevance in drug development, the current study was designed to explore functional and structural aspects of Leishmania donovani glutamyl-tRNA synthetase (LdGluRS). Hence, LdGluRS was cloned into an expression vector and purified to homogeneity using chromatographic techniques. Purified protein showed maximum enzymatic activity at physiological pH, with more binding capacity towards its cofactor (Adenosine triphosphate, 0.06 ± 0.01 mM) than the cognate substrate (L-glutamate, 9.5 ± 0.5 mM). Remarkably, salicylate inhibited LdGluRS competitively with respect to L-glutamate and exhibited druglikeness with negligible effect on human macrophages. The protein possessed more α-helices (43 %) than β-sheets (12 %), whereas reductions in thermal stability and cofactor-binding affinity, along with variation in mode of inhibition after mutation signified the role of histidine (H60) as a catalytic residue. LdGluRS could also generate a pro-inflammatory milieu in human macrophages by upregulating cytokines. The docking study demonstrated the placement of salicylate into LdGluRS substrate-binding site, and the complex was found to be stable during molecular dynamics (MD) simulation. Altogether, our study highlights the understanding of molecular inhibition and structural features of glutamyl-tRNA synthetase from kinetoplastid parasites.

Effect of torrefaction pretreatment on the selectivity improvement of lignin pyrolysis products

Pre-regulating the molecular composition and structural characteristics of lignin before pyrolysis is of great significance for the lignin valorization. In this work, torrefaction pretreatment of softwood kraft lignin (SKL) is carried out at different temperatures, and the characterization results show that torrefaction pretreatment is beneficial for removing oxygen element from SKL, which increases the high heating value of torrefied lignins (TLs). In addition, torrefaction pretreatment has a destructive effect on Cβ-O-C4 linkages, and reduces the molecular weight of TLs. Torrefaction pretreatment also removes the thermally unstable components from SKL and increases the release rate of pyrolysis volatiles. Furthermore, torrefaction pretreatment degrades the methoxy group (-OCH3) in SKL into phenolic hydroxyl group, which reduces the yield of guaiacyl type phenols in TLs pyrolysis products, and significantly increases the yield of catechol type phenols from 23.59% in SKL to 47.50% in TL300.

Effects of aging and diabetes on the deformation mechanisms and molecular structural characteristics of collagen fibrils under daily activity

Crosslinking plays an important role in collagen-based tissues since it affects mechanical behavior and tissue metabolism. Aging and diabetes affect the type and density of crosslinking, effectively altering tissue properties. However, most studies focus on these effects under large stress rather than daily activities. We focus on the deformation mechanisms and structural change at the binding sites for integrins, proteoglycans, and collagenase in collagen fibrils using a fully atomistic model. We show that high-connectivity enzymatic crosslinking (our “HC” model, representing normal tissues) and advanced-glycation end-products (our “Glucosepane” model, which increase in diabetes) result in uniform deformation under daily activity, but low-connectivity enzymatic crosslinking (our “LC” model, representing aging tissues) does not. In particular, the HC model displays more sliding, which may explain the ability of healthy tissues to absorb more strain energy. In contrast, AGEs induce instability in the structures near the binding sites, which would affect the tissue metabolism of the collagen molecule. Our results provide important insights into the molecular mechanisms of collagen and a possible explanation for the role of crosslinking in tissues undergoing daily activity.

Chemical Structure Evaluations of Amine Hardeners to Ensure and Predict the Performance of Wet Adhesion of Epoxies

Abstract The relationship between the chemical structure and performance of a water-sorbed epoxy adhesive (wet adhesion) provides fundamental data for epoxy adhesives for application in wet and underwater environments. However, data on the effect of the chemical structure on wet adhesion remains insufficient. This study systematically examined the wet adhesion strengths of epoxies comprising bisphenol A diglycidyl ether and various amines. The use of numerical parameters quantifying the features of the chemical structure and physicochemical properties via theoretical calculations to analyze the correlation between wet adhesion and the chemical structure of amine yielded clear linear relationships. This enabled the extraction of the amine molecular structural features that were superior in wet adhesion, in addition to quantification of the certainties of the features contributing to the physical properties. Furthermore, a prediction model for wet adhesive strength was prepared using machine-learning least absolute shrinkage and selection operator regression analysis. The model exhibited a reasonable accuracy, even using only 14 experimental values, and its effectiveness was verified experimentally. This process facilitates the rational design and selection of amine hardeners for preparing epoxies with excellent performance in wet conditions and underwater environments.

Research progress on structure, structure-activity relationship, and biological activity of Aconiti Lateralis Radix Praeparata polysaccharides

Aconiti Lateralis Radix Praeparata polysaccharides(AP) are a class of bioactive macromolecules extracted from the herbs of Aconiti Lateralis Radix Praeparata and its various processed products. Since the AP was first separated in 1986, its pharmacological effects include immune regulation, anti-tumor, anti-depression, organ protection, hypoglycemia, and anti-inflammatory had been found. In recent years, with the development of polysaccharide extraction, separation, and structure identification technologies, more than 20 kinds of AP have been separated from Aconiti Lateralis Radix Praeparata and its processed products, and they have ob-vious differences in relative molecular weight, monosaccharide composition, glycosidic bond, structural characteristics, and biological activities. In particular, AP may be dissolved, degraded, or allosteric under the complex processing environment of fermentation, soaking, cooking, etc., leading to the diversified structure of AP, which provides a possibility for further understanding of the structure-activity relationship of AP. Therefore, this study systematically reviewed the research progress on the structure and structure-activity relationship of AP, summarized the biological activity and potential action mechanism of AP, and discussed the technical challenges in the development and application of AP, so as to promote the quality control and further development and utilization of AP.

An autocatalytic Fe(III)/H2O2 Fenton-like process triggered by tetracycline: The overlooked effect of quinone intermediates

The conventional Fe(III)/H2O2 system is of low efficiency on the removal of most organic pollutants. However, we discovered that the Fe(III)/H2O2 system was robust on remediating tetracycline (TC) in water (0.109 min−1 for the pseudo-first kinetic constant), and the reaction was even slightly faster than that in the conventional Fe(II)/H2O2 system (0.105 min−1). The addition of TC could also initiate the degradation of other refractory pollutants in the Fe(III)/H2O2 system. Complexation between Fe(III) and TC with the stoichiometric ratio of 1:1 was observed. Electron transfer from TC to Fe(III) gave rise to the slight production of Fe(II), which served as the initiator of the following Fenton reaction. •OH was ascertained as the main reactive species through quenching experiments, EPR tests and the probe method, while O2•−/HO2• was also a subsidiary contributor. Hydroquinone intermediates were proved to be generated through the hydroxylation of the benzene ring of the TC molecule by •OH and thus facilitate the reductive transformation of Fe(III) to Fe(II). This study analyzes the relationship between molecular structural features of TC and the catalytic efficiency of ferric Fenton-like reactions. We expect to shed light on new mechanistic insights on autocatalysis in the Fenton-like catalytic processes.

QSPR Analysis of Diverse Drugs Using Linear Regression for Predicting Physical Properties

The study focused on QSPR (Quantitative Structure-Property Relationship) analysis using a variety of topological indices on the medications Mefloquinone, Sertraline, Niclosamide, Tizoxanide, PHA-690509, Ribavirin, Emricasan, and Sofosbuvir. Through the use of computational modeling approaches, the study sought to determine how these medications’ chemical structures relate to their individual qualities. The discovered results provided information on the quantitative correlations between structural characteristics and pharmacological qualities, allowing for better comprehension and forecast of their behavior. The results of this study make a positive contribution to the field of medication discovery and design by offering important knowledge about the structure-property correlations of these medicinal molecules. In this article, we focus on using topological indices and a linear regression model to successfully predict various pharmacological features. This method enables more effective drug discovery and development by providing insights into the connection between molecular structure and pharmacological characteristics. We can improve our comprehension of drug behavior and assist targeted drug design by utilizing topological indices and regression analysis.

Prediction of organic molecular optical absorption energy based on deep learning using mordred descriptor features

Organic molecules have several characteristics based on optical absorption. A molecule absorbs a specific light wavelength that represents electronic energy in the material. The absorption wavelength is also related to atomic binding of molecules that interact with material during light exposure producing electronic instability in the material. Molecular absorption can be measured using several optical spectrometer configurations that contain a light source, optical path, and light detector. The measurements of molecular optical absorption have been reported in several research and have been collected into a material database. In this paper, we developed a model for predicting organic molecular optical absorption using deep learning. The model can predict molecular absorption energy based on extracted features of molecular structure using Mordred descriptor features extraction. Our model used 1625 molecules of absorption in several solvent datasets that split into 80% training and 20% testing dataset. The result show that our model has a good agreement with experimental data with correlation coefficient 0.96 and mean average error 0.172 eV.

Structural characterization analysis and macromolecular model construction of coal from Qinggangping coal mine

Understanding the molecular structure characteristics of coal at the molecular level is of great significance to realize the rational utilization and efficient conversion of coal. This paper gives insights into the acquisition of characterization parameters of coal molecular microstructure by testing and analyzing the long flame coal from Qinggangping (QGP) Coal Mine through proximate analysis, ultimate analysis, vitrinite reflectance determination, fourier transform infrared Spectroscopy test (FTIR), X-ray photoelectron epectroscopy test (XPS), carbon nuclear magnetic resonance (13C-NMR) and X-ray diffraction (XRD). The results show that benzene rings in the QGP coal are mainly connected in a disubstituted way, accounting for 36.48%. Oxygen atoms mainly exist in the oxygen-containing functional groups such as the ether C–O, C=O and –COO. Aliphatic hydrocarbons in the aliphatic group are mainly of symmetrical -CHx stretching vibration. Hydroxyl groups are mainly composed of OH–OH and OH–O hydrogen bonds, accounting for 29.21% and 21.53%, respectively. Nitrogen atoms exist in the form of C4H5N. The coal molecular is mainly of aromatic carbon structure, where the ratio of bridge aromatic carbon to peripheral carbon is 0.198. There are benzene, naphthalene and anthracene in the coal molecular structure, and the former two chemicals play a dominating role. According to the analysis results, the molecular formula of the QGP coal is finally determined as C205H181O29N3S. On this basis, the two-dimensional and three-dimensional macromolecular models are constructed with the assistance of simulation software. In addition, the 13C-NMR spectra and densities of the constructed molecular models are calculated, which verifies the rationality of the models. The macromolecular structure model of bituminous coal constructed in this study provides a theoretical model basis for the optimal surfactant.

Unexpected Emission Behaviors of Rhodamine Derivatives in PVA After UV‒Green Light Excitation

AbstractRhodamine derivatives are a class of common fluorescent dyes and are usually co‐doped with room temperature phosphorescence (RTP) polymers for tuning colors; here, their unusual luminescence properties in polyvinyl alcohol are first disclosed. The doped polyvinyl alcohol (PVA) films are photo‐excited for 0.5‒1 min and emit orange and red afterglows with lifetimes of over 1 s at room temperature. More unexpectedly, the respective prompt and delayed room temperature emission colors and spectra are identical, and the red‐shifted afterglows are observed in liquid nitrogen, indicating that room temperature afterglow is thermally activated delayed fluorescence (TADF). Their molecular structure features and quantum chemical calculations support this inference. Impressively, the room temperature afterglows are visible light excitable up to 540 nm since the maximal and strong absorption bands are in green regions. Hence, this work discloses unknown excitation and emission properties of rhodamine derivatives and provides the really visible light excited yet intrinsic red TADF afterglows for the first time.

Feasibility assessment of palmitamide derived from waste edible oil as a warm mix asphalt additive

The disposal of waste edible oil (WEO) has become a global challenge with both environmental and economic issues. To provide a novel strategy for the refinement recycling of WEO, this work investigated the feasibility of palmitamide derived from WEO as a warm mix asphalt (WMA) additive. The molecular structure and thermodynamic characteristics of palmitamide were first determined. Following, WMA binders with different palmitamide contents were prepared and their temperature sensitivity and rheological properties were evaluated. Additionally, the engineering performance of WMA mixtures was explored and the environmental benefits of WEO-derived palmitamide were assessed using the gas chromatography-mass spectrometry. The results demonstrate that the phase transition temperature of WEO-derived palmitamide is 98.87 °C, which shows great potential as a WMA additive. Palmitamide provides asphalt workability suitable for construction at relatively low temperatures through reducing the flow activation energy of asphalt. In addition, the moisture damage resistance and deformation resistance of WMA is also improved due to the hydrophobicity and filling effect of palmitamide, respectively. While it is inevitable that palmitamide slightly weakens the fatigue and low-temperature performance of WMA. Moreover, the application of WEO-derived palmitamide can reduce the volatile organic compounds of asphalt in the mixing stage and compaction stage by 40.3% and 30.8%, respectively. The findings contribute to the sustainable development of road engineering and the circular of waste resources.

Th22 cells and the intestinal mucosal barrier.

T-helper 22 (Th22) cells represent a novel subset of CD4+ T cells that exhibit distinctive characteristics, namely the secretion of IL-22 while abstaining from secreting IL-17 and interferon-γ (IFN-γ). These cells serve as the primary source of IL-22, and both Th22 cells and IL-22 are believed to play a role in maintaining intestinal mucosal homeostasis in inflammatory bowel disease (IBD). However, the precise functions of Th22 cells and IL-22 in this context remain a subject of debate. In this work, we aimed to elucidate their impact on the integrity of the intestinal mucosal barrier by presenting an overview of the molecular structure characteristics and functional effects of Th22 cells and IL-22. Furthermore, we would explore targeted treatment approaches and potential therapeutic strategies focusing on the Th22 and IL-22 pathways.