Exploring the Mechanism of Ionic Liquids to Improve the Extraction Efficiency of Essential Oils Based on Density Functional Theory and Molecular Dynamics Simulation

Highlights

• According to the design of the experiment (DoE), multivariate analysis models were used to optimize the critical process parameters combined with multi-objective optimization.
• Based on the optimized operating conditions, the MILT-HD method not only enhances the extraction efficiency from Amomi fructus but also reduces energy demands and CO₂ emissions.
• Based on the density functional theoretical (DFT) and molecular dynamics (MD) simulations, the mechanisms for ionic liquids (ILs) to improve the extraction efficiency of essential oil was comprehensively revealed.

AbstractIn this paper, Amomi fructus (Latin) was used to explore the mechanism of ionic liquids (ILs) in improving the extraction efficiency of essential oils. Microwave assisted ionic liquid treatment followed by a hydro-distillation (MILT-HD) process for isolating Amomi fructus essential oil was optimized by multi-objective optimization. Under optimum operating conditions, the IL-assisted extraction method not only enhances extraction efficiency but also reduces energy demands and CO₂ emissions. Since the hydrogen bond structure network of cellulose in the cell wall is an important reason for hindering diffusion of essential oils, the mechanism of ILs was explored by density functional theoretical (DFT) and molecular dynamics (MD) simulations. According to DFT calculations, ILs can facilitate the cleavage of cellulose chains and have strong non-covalent interactions with cellulose. Based on the MD simulations, the degree of destruction of the cellulose hydrogen bond structure was explored. According to the DFT and MD simulations, the ILs can significantly destroy cellulose structure, thereby promoting essential oil release from the plant. These results were confirmed by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). This work is conducive to better understand the MILT-HD process for isolating essential oil and comprehensively understand the mechanism of ILs in the extraction process.     

Oregano Essential Oil Interactions with Photogenerated Singlet Molecular Oxygen

Essential oils are a mixture of volatile compounds, products of the secondary metabolism of plants. Once extracted, they can be deteriorated losing their organoleptic and therapeutic properties due to various environmental factors, being light exposure in aerobic conditions the main cause. In this work, the oregano essential oil extraction and characterization from Origanum vulgare plants grown in the experimental field of the FTU-UNSL and its photodegradation in MeOH:H₂O 60:40 v/v solvent were studied. Characterization by EIMS and NIST Mass Spectrometry indicates the main compounds of oregano essential oil, quantified in the extracted oil by GC-MS, are carvacrol (7.14%) and thymol (47.37%). Degradation of essential oil and its two major components can be caused by reactive oxygen species photogenerated from endogenous sensitizers as riboflavin. Our results suggest degradation occurs involving singlet molecular oxygen. Interaction of carvacrol and thymol with singlet oxygen is mainly a physical process, while essential oil has an important reactive component, which indicates there might be other constituents which could contribute to reactive photoprotection. The effect of simultaneous presence of oregano essential oil and tryptophan amino acid—used as a photooxidizable model under riboflavin-photosensitizing conditions—was studied in order to evaluate the possible photoprotection exerted by the essential oil.     

分子导线的研究进展

随着电子设备和器件的尺寸越来越小,基于分子的器件研究引起了人们的广泛关注。其中分子导线具有小尺寸、多样性、性能可调等优点,因而被赋予了许多潜在的应用前景。本文总结了分子导线的概念和分类,重点介绍了两端为金属配合物和含Ru-Ru金属键单元的共轭炔基分子导线,并对四硫富瓦烯类分子的独特性质和它在分子导线中的应用进行了简单小结。     

Molecular Basis for the Mechanical Response of Sulfa Drug Crystals

Comprehension of the nanomechanical response of crystalline materials requires the understanding of the elastic and plastic deformation mechanisms in terms of the underlying crystal structures. Nanoindentation data were combined with structural and computational inputs to derive a molecular-level understanding of the nanomechanical response in eight prototypical sulfa drug molecular crystals. The magnitude of the modulus, E, was strongly connected to the non-covalent bond features, that is, the bond strength, the relative orientation with the measured crystal facet and their disposition in the crystal lattice. Additional features derived from the current study are the following. Firstly, robust synthons well isolated by weak and dispersive interactions reduce the material stiffness; in contrast, the interweaving of interactions with diverse energetics fortifies the crystal packing. Secondly, mere observation of layered structures with orthogonal distribution of strong and weak interactions is a prerequisite, but inadequate, to attain higher plasticity. Thirdly, interlocked molecular arrangements prevent long-range sliding of molecular planes and, hence, lead to enhanced E values. In a broader perspective, the observations are remarkable in deriving a molecular basis of the mechanical properties of crystalline solids, which can be exploited through crystal engineering for the purposeful design of materials with specific properties.     

Estimation of the Elastic Modulus of Cellulose Crystal by Molecular Mechanics Simulation

The elastic modulus of natural cellulose crystal was estimated by the molecular simulation technique. Values between 124 and 155 GPa were derived for the reasonable cellulose I_β crystal model that were nearly equal to the observed value of 138 GPa. While the second-generation force fields were found to be superior to the first-generation ones for the optimization of cellulose structure, neither of these was good enough to achieve the structural optimization. They were, however, adequate for estimating the mechanical properties of cellulose, especially the second-generation force fields. The lateral (that is, intermolecular) interactions between cellulose chains were found to play an important role in the expression of the mechanical properties of cellulose crystal.     

The Effect of Degradation and Stabilization on the Mechanical Properties of Polymers Using Polypropylene Blends as the Main Example

Degradation can result from a variety of chemical, physical and mechanical mechanisms, most of them involving a reduction of molecular weight and thus a decrease in the mechanical performance of the degraded polymer. A clear understanding and control of these mechanisms is absolutely essential: without stabilization some polymers (e.g. PVC, polyolefins) would not survive their processing undamaged. In this paper an overview of the different degradation mechanisms, their effect on molecular chains, and the methods used to characterize the extent of degradation will be given. Subsequently we establish some fundamental relationships between the microstructure and the mechanical performance (of thermoplastic polymers) using differently aged and stabilized polypropylene (PP) - EPR compounds. In particular we investigate the influence of two types of heat stabilizers (phenolic antioxidants and hindered amine stabilizer HAS) on the degradation behaviour of test specimens thermally aged at 120 and 135°C respectively. From an investigation of the changes with aging time in structure and low-strain properties (yield stress, strain at yield, tensile modulus) and from the differences in the evolution of the fracture properties a molecular model of the chain scission mechanisms and of inter-lamellar connectivity (through tie-chain molecules) has been established, which allowed an explanation of the gradual change of the dominant deformation mechanism from cold drawing to crazing and brittle fracture.     

Heterogeneities in Polymer Structural and Dynamic Properties in Graphene and Graphene Oxide Nanocomposites: Molecular Dynamics Simulations

The effect of graphene (G) and graphene oxide (GO), used as the nanofiller in polymer nanocomposites (NC), on the structural and dynamic properties of polymer chains, has been studied by means of molecular dynamics (MD) simulations. Two polymers, i.e., poly(propylene) and poly(vinyl alcohol), are employed as matrices to cover a wider range of polymer–filler interactions. The local structural properties, e.g., density profile, average R _g, and end‐to‐end distance as well as dynamic properties, e.g., estimated translational and orientational relaxation times, of polymer chains are studied. In addition, the interaction energies are estimated between polymers and nanofillers for different hybrid systems using MD pullout simulations. Strong heterogeneities in polymer structural and dynamic properties have been observed such that chains are more oriented and exhibit slower dynamics in the vicinity of the nanofillers (G and GO) as compared to bulk. It is also found that the orientation of polymer chains at the interface is more influenced by the nanofiller in such a way that the more oriented polymer chains are observed in G‐based NC for both polymers. However, the immobilization of polymer chains at the interface proves to be very much dependent on the polymer–filler interactions.

     

Targeting 3CLpro and SARS-CoV-2 RdRp by Amphimedon sp. Metabolites: A Computational Study

Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from Amphimedon sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (1), 20-hepacosenoic acid (11) and amphimedoside C (12) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds 1 and 12 were selected for molecular dynamics simulation studies. Our results showed Amphimedon sp. to be a rich source for anti-COVID-19 metabolites.     

Molecular brushes with long polyfluorene backbones and polymethacrylic acid side chains: Luminescent properties and self-organization in solutions

A series of molecular brushes with a polyfluorene (PF) backbone and polymethacrylic acid side chains of varying lengths were prepared by atom transfer radical polymerization. The structure and composition of the synthesized compounds were confirmed by ¹H NMR and IR spectroscopy. Effect of the length of the backbone on spectral and conformational parameters of the macromolecules in solutions was analyzed. The grafting density of side chains was about 90%. Spectral methods have been used to determine the dependence of side chain grafting on the luminescent properties of polymer solutions, including quantum yields. It was shown that an optimal length of polymethacrylic acid side chains provides solubility of the polymer brushes. Solutions of PF-graft-polymethacrylic acid complexes with the model substance curcumin were investigated. It was established that the molecular brushes containing curcumin form monomolecular micelles. Molecular brushes with zinc phthalocyanine, potential systems for photodynamic, and photothermal therapy, were studied.     

The Antimicrobial and Toxicity Influence of Six Carrier Oils on Essential Oil Compounds

Essential oil compounds have been identified as alternative antimicrobials; however, their use is limited due to their toxicity on human lymphocytes, skin, and reproduction. Carrier oils can reduce the toxicity of essential oils, which raises the question as to whether such activity would extend to the essential oil compounds. Thus, this study aimed to investigate the antimicrobial and toxicity activity of essential oil compounds in combination with carrier oils. The antimicrobial properties of the essential oil compounds, alone and in combination with carrier oils, were determined using the broth microdilution assay. The toxicity was determined using the brine shrimp lethality assay. Antimicrobial synergy (ΣFIC ≤ 0.50) occurred in 3% of the samples when tested against the ESKAPE pathogens. The compound thymoquinone in combination with the carrier oil Prunus armeniaca demonstrated broad-spectrum synergistic activity and a selectivity index above four, highlighting this combination as the most favorable. The carrier oils reduced the toxicity of several compounds, with Calendula officinalis and P. armeniaca carrier oils being responsible for the majority of the reduced toxicity observed. This study provides insight into the interactions that may occur when adding a carrier oil to essential oil compounds.     

An Experimental and Theoretical Study on Essential Oil of Aethionema sancakense: Characterization,Molecular Properties and RDG Analysis

This study aims to experimentally and theoretically examine the plant Aethionema sancakense, which was determined as a new species and whose essential oil and fatty acid compositions were characterized by GC/GC-MS technique. Linoleic acid (23.1%), α-humulene (19.8%), camphene (13.9%), and heptanal (9.7%) were found to be the major essential oil components of A. sancakense aerial part structures. The quantum chemical calculations of these four molecules that are very important to this plant were performed using the density functional method (DFT)/B3LYP with the 6-31 G (d, p) basis set in the ground state for the gas phase. The molecular structures, HOMO-LUMO energies, electronic properties, Fukui functions, and molecular electrostatic potential (MEP) surfaces of the major constituents of Aethionema sancakense essential oil were calculated and interpreted. Finally, the RDG-NCI analysis of these molecules was performed to determine the non-covalent interactions present within the molecules.     

GC-MS Analysis and Microbiological Evaluation of Caraway Essential Oil as a Virulence Attenuating Agent against Pseudomonas aeruginosa

The emergence of resistant microbes threatens public health on our planet, and the emergence of resistant bacteria against the most commonly used antibiotics necessitates urgent alternative therapeutic options. One way to fight resistant microbes is to design new antimicrobial agents, however, this approach takes decades of research. An alternative or parallel approach is to target the virulence of bacteria with natural or synthetic agents. Active constituents from medicinal plants represent a wide library to screen for natural anti-virulence agents. Caraway is used as a traditional spice and in some medicinal applications such as carminative, antispasmodic, appetizer, and expectorant. Caraway essential oil is rich in terpenes that were previously reported to have antimicrobial activities. In our study, we tested the caraway essential oil in sub-inhibitory concentration as a virulence agent against the Gram-negative bacteria Pseudomonas aeruginosa. Caraway essential oil in sub-inhibitory concentration dramatically blocked protease activity, pyocyanin production, biofilm formation, and quorum sensing activity of P. aeruginosa. The gas chromatography–mass spectroscopy (GC-MS) profile of caraway fruit oil identified 13 compounds representing 85.4% of the total oil components with carvone and sylvestrene as the main constituents. In conclusion, caraway essential oil is a promising virulence-attenuating agent that can be used against topical infections caused by P. aeruginosa.     

In Vitro Anti-Inflammatory Activity of Cotula anthemoides Essential Oil and In Silico Molecular Docking of Its Bioactives

The genus Cotula (Asteraceae) comprises about 80 species, amongst them Cotula anthemoides L. It is a wild plant growing in Egypt that possesses many traditional uses as a headache, colic, and chest cold remedy. In our study, the chemical composition of C. anthemoides essential oils was analyzed using GC-MS spectroscopy. Sixteen components of leave and stem oils and thirteen components of flower oils were characterized. The main components in both essential oil parts were camphor (88.79% and 86.45%) and trans-thujone (5.14% and 10.40%) in the leaves and stems and the flowers, respectively. The anti-inflammatory activity of the oils in lipopolysaccharide-stimulated RAW 264.7 macrophage cells was evaluated. The flower oil showed its predominant effect in the amelioration of proinflammatory cytokines and tumor necrosis factor-α, as well as cyclooxygenase-2. The bornyl acetate showed the highest affinity for the cyclooxygenase-2 receptor, while compound cis-p-menth-2-ene-1-ol had the best affinity for the tumor necrosis factor receptor, according to the results of molecular docking. In addition, the molecule cis-β-farnesene showed promising dual affinity for both studied receptors. Our findings show that essential oils from C. anthemoides have anti-inflammatory properties through their control over the generation of inflammatory mediators. These findings suggest that C. anthemoides essential oils could lead to the discovery of novel sources of anti-inflammatory treatments.     

Some Recent Advances in the Design and Use of Molecular Balances for the Experimental Quantification of Intramolecular Noncovalent Interactions of π Systems

Herein, various molecular balances used for comparing the strengths of intramolecular noncovalent interactions are reviewed. Our overview indicates that considerable quantitative insight into the strength of noncovalent interactions can be gained through the careful design of molecular balances. Many exciting opportunities certainly exist for the design of further new balances to quantify and dissect the relative strengths of noncovalent interactions as a function of solvation and the importance of the many factors that contribute to overall molecular recognition. However, even simple model molecules can show a multiplicity of intramolecular noncovalent interactions acting in a combined fashion. It is therefore essential to undertake a detailed computational analysis to identify all possible noncovalent interactions present in a selected molecular balance prior to a quantitative experimental assessment of the strength of a particular noncovalent interaction. It is also argued that the words “torsion” and “molecular balance” seem to have become inextricably linked and, in consequence, even top pan and seesaw balances have been mistakenly referred to in these terms.     

Molecular Interactions Associated with Coagulation of Organic Pollutants by 2S Albumin of Plant Proteins: A Computational Approach

The removal of organic pollutants is a major challenge in wastewater treatment technologies. Coagulation by plant proteins is a promising technique for this purpose. The use of these proteins has been experimentally investigated and reported in the literature. However, the determination of the molecular interactions of these species is experimentally challenging and the computational approach offers a suitable alternative in gathering useful information for this system. The present study used a molecular dynamic simulation approach to predict the potentials of using Moringa oleifera (MO), Arachis hypogaea, Bertholletia excelsa, Brassica napus, and Helianthus annuus plant proteins for the coagulation of organic pollutants and the possible mechanisms of coagulation of these proteins. The results showed that the physicochemical and structural properties of the proteins are linked to their performance. Maximum coagulation of organic molecules to the proteins is between 50–100%. Among five proteins studied for coagulation, Brassica napus and Helianthus annuus performed better than the well-known MO protein. The amino acid residues interacting with the organic molecules play a significant role in the coagulation and this is peculiar with each plant protein. Hydrogen bond and π—interactions dominate throughout the protein–pollutants molecular interactions. The reusability of the proteins after coagulation derived from their structural quality analysis along with the complexes looks promising and most of them are better than that of the MO. The results showed that the seed proteins studied have good prediction potentials to be used for the coagulation of organic pollutants from the environment, as well as the insights into their molecular activities for bioremediation.     

吲哚并喹啉衍生物与G-四链体相互作用的分子模拟研究

G-四链体是富含鸟嘌呤碱基的DNA序列通过氢键相互作用形成的四链螺旋结构. 通过小分子化合物诱导与稳定端粒G-四链体从而抑制端粒酶活性是一种新的抗癌策略. 为了研究一系列吲哚并喹啉衍生物与端粒G-四链体的相互作用, 探究其相互作用模式, 从而为实现基于G-四链体结构的药物合理设计提供依据, 使用分子对接的方法构建了吲哚并喹啉衍生物与G-四链体复合物结构, 在此基础上进行分子动力学模拟, 并使用线性相互作用能(LIE)方法计算了化合物与G-四链体的结合自由能. 结果表明: 化合物与G-四链体的主要相互作用方式由氢键、静电与π-π堆积作用构成, 侧链末端基团类型和侧链的长短是影响相互作用强弱的重要因素. 通过LIE方法计算的结合自由能与实验结果基本吻合, 相关度达到r²＝0.79. 并且, 基于预测的结合模式, 总结了拥有更高活性的新型吲哚并喹啉衍生物应具有的几个结构特征.     

Visualizing The Future of Molecular Graphics

Abstract

The field of computer graphics has played an important role in the advancement of structural molecular biology and in the development of structure-based drug design. This article will provide a brief background on the development of this technology, and then focus on the current trends and future directions in molecular graphics and how they will impact the practice of molecular modeling and design. Specific areas that will be covered include: 1) the development of surface and volume based representations of molecular properties and interactions; 2) new approaches to modeling flexible and multi-component structures, and 3) the impact of object-oriented graphics-based programming and the rapidly growing use of network based computing.