Non-bonded Interaction Energy Research Articles

Study on the properties of nano-Fe3O4 modified asphalt materials based on molecular dynamics

Asphalt possesses the inherent ability to self-heal microcracks, with enhanced healing observed under active heating conditions. Nanomaterials have the capacity to alter the microstructure of asphalt blends, offering certain advantages in terms of asphalt performance. In this study, models of nano-Fe3O4 clusters and nano-Fe3O4/asphalt blending systems with varying particle sizes were established. Molecular dynamics simulations were employed to investigate the physical properties of nano-Fe3O4 and asphalt molecules at different temperatures, simulating the microwave heating process within a temperature range of 303 K to 373 K. The findings revealed that the diffusion coefficient of Fe3O4 clusters decreased with increasing particle size. Nonbonding interaction energy predominantly governed the binding between Fe3O4 clusters and asphalt molecules. The incorporation of nano-Fe3O4 was found to enhance the physical properties of asphalt. Peak values of the radius of gyration for asphaltene and aromatics indicated increased density, while asphaltene, colloids, and aromatics exhibited greater extensibility with the addition of nano-Fe3O4.

Investigation of Phe-tRNA interaction with EF-Tu in GDP/GTP nucleotide bound states: a molecular dynamics simulation study

Elongation factor Tu (EF-Tu) is an important class of translational GTPases (trGTPases) involved in the elongation process. EF-Tu functions by forming the tight complex with the aminoacyl-tRNA (aa-tRNA: transfer RNA carrying an amino acid) in the GTP-bound active state and subsequently transports the aa-tRNA to the A-site (aminoacyl-site) of the ribosome. The correct interaction between mRNA's codon and aa-tRNA anticodon triggers GTP hydrolysis, resulting in the transition of EF-Tu from the active state to the inactive state (EF-Tu bound to GDP). This, in turn, results in the dissociation of EF-Tu:GDP from the tRNA and ribosome. However, the conformational changes and interactions responsible for the tight complex formation between EF-Tu and aa-tRNA in the GTP-bound state and the disruption of the interaction between EF-Tu and aa-tRNA in the GDP-bound state are not well understood. Therefore, to explore the conformational changes in the EF-Tu:Phe-tRNA complex and to get insight into the interaction between Phe-tRNA (tRNA carrying Phenylalanine) and EF-Tu in GDP/GTP nucleotide bound state, 200 ns MD (molecular dynamics) simulation have been carried out. The RMSD, RMSF, cluster, and DSSP analyses suggest that the GTP-bound state attains a more favorable conformation, which may facilitate EF-Tu’s interactions with the tRNA and ribosome. Further investigation of the non-bonded interaction energy calculation revealed the significance of domainII in interaction with the Phe-tRNA in a GTP-bound state. In addition, the H-bonds calculated between the tRNA’s Phe (Phenylalanine attached to the tRNA is considered) and domainII highlights the contribution of Val285 in recognizing tRNA’s Phe by forming an H-bond throughout the simulation time in the GTP bound state. Overall these results provide insight into how GTP nucleotide influences the interaction between EF-Tu and Phe-tRNA.

Molecular dynamics study of the thermodynamic properties of triglyceride/methanol mixtures in the presence of cosolvent

Biodiesel is a renewable source of energy that has the potential to replace fossil fuel-based resources. It is produced via the transesterification reaction in which a triglyceride reacts with methanol in the presence of a catalyst. Cosolvents are usually added to the reactants in transesterification to improve the mutual solubility of methanol and triglycerides and to create a single phase. The commonly used cosolvents in transesterification include tetrahydrofuran (THF) and diethyl ether (DEE). Understanding the thermodynamic properties of this system is important in the selection of cosolvent. In this study, molecular dynamics simulations were used to study the mixing behavior between the components of ternary mixtures of triolein/methanol/THF and triolein/methanol/DEE via the application of Flory-Huggins theory of solutions. A simple approach to calculation of the Flory-Huggins interaction parameters is used in which the mixing energy is derived from averaged non-bonded pair interaction energies. Apart from pure triolein, these ternary systems resemble the experimentally studied ternary systems employing various plant-based oils. The binary interaction parameters, Gibbs Free energy and chemical potentials of the components were calculated to study the mixing behavior. Our results show that along the experimental phase boundary the binary interaction parameters remain relatively unchanged with a deviation observed at the highest volume fractions of triolein where the highest binary interactions were observed indicating the possibility of phase separation. The Gibbs energy of mixing for the systems changed from positive to negative as one moves from two phase to single phase part of the ternary system as expected and in agreement with experimental data. The chemical potentials of the ternary mixture components were calculated from the partial derivatives of the Gibbs free energy of mixing. The activities calculated from Flory-Huggins chemical potentials were compared to those calculated using the UNIFAC model. There is good agreement between the two, with both able to predict a single and biphasic mixture. However, disagreements are noted at low and high concentrations of triolein.

Theoretical study on formation mechanism of acetic acid associating configurations and their distributions under saturated conditions.

The vapor-liquid equilibrium (VLE) properties of acetic acid systems generally behave strong non-ideality due to the associating interaction among acetic acid molecules. Theoretical study of the associating mechanism will provide guidance for the VLE property prediction, which is crucial for the designing on the separation process of the acetic acid systems. In this work, the association conformers and their distribution on acetic acid molecules in saturated gas and liquid phase were firstly studied. The proportions of the acetic acid monomer and multimers were obtained, which will contribute to the foundation for the vapor-liquid equilibrium simulations. The association mechanism on acetic acid molecules was then investigated by comparing among the structures and non-bonded interaction energies of different dimers. The structure of the cyclic dimer containing two OC-HO hydrogen bonds, may be found probably when acetic acid molecules approached. Electronic properties of different acetic acid dimers showed that the electrons around carbonyl oxygen atoms were deflected by the attraction of hydrogen atoms in the other molecule, which polarized the acetic acid molecules when the hydrogen bonds between acetic acid molecules were formed, providing theoretical basis for the polarized acetic acid molecular model. In this work, the molecular dynamics (MD) simulations and DFT calculations were conducted through the software GROMACS and Gaussian 09, respectively. For the MD simulations, the OPLS-AA force field was used as the atomic force field, with the cubic simulation cells constructed by Packmol program. For the DFT calculations, the M06-2X functional was employed for the optimization of the associating structures with the 6-311G** basis sets. Hydrogen bonding energies of dimers were corrected for the basis set superposition error (BSSE) and the deformation energies of monomers. Furthermore, the energy decomposition analysis was conducted at DFT/M06-2X/def-tzp level by the ADF software, and the wave function analysis was conducted by the Multiwfn software including the atom in molecule (AIM) topology analysis, the electronic potential analysis, and the electron density difference analysis.

An Assessment of Dispersion-Corrected DFT Methods for Modeling Nonbonded Interactions in Protein Kinase Inhibitor Complexes.

Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quantifying the strengths of these key protein-ligand interactions. However, the accuracy of DFT methods can vary substantially depending on the choice of exchange-correlation functionals and associated basis sets. In this study, a comprehensive benchmarking of nine widely used DFT methods was carried out to identify an optimal approach for quantitative modeling of nonbonded interactions, balancing both accuracy and computational efficiency. From a database of 2139 kinase-inhibitor crystal structures, a diverse library of 49 nonbonded interaction motifs was extracted, encompassing CH-π, π-π stacking, cation-π, hydrogen bonding, and salt bridge interactions. The strengths of nonbonded interaction energies for all 49 motifs were calculated at the advanced CCSD(T)/CBS level of theory, which serve as references for a systematic benchmarking of BLYP, TPSS, B97, ωB97X, B3LYP, M062X, PW6B95, B2PLYP, and PWPB95 functionals with D3BJ dispersion correction alongside def2-SVP, def2-TZVP, and def2-QZVP basis sets. The RI, RIJK, and RIJCOSX approximations were used for selected functionals. It was found that the B3LYP/def2-TZVP and RIJK RI-B2PLYP/def2-QZVP methods delivered the best combination of accuracy and computational efficiency, making them well-suited for efficient modeling of nonbonded interactions responsible for molecular recognition of protein kinase inhibitors in their targets.

Insights from in silico study of receptor energetics of SARS-CoV-2 variants.

The emergence of new variants of the novel coronavirus SARS-CoV-2 with increased infectivity, superior virulence, high transmissibility, and unmatched immune escape has demonstrated the adaptability and evolutionary fitness of the virus. The subject of relative order of the binding affinity of SARS-CoV-2 variants with the human ACE2 (hACE2) receptor is hotly debated and its resolution has implications for drug design and development. In this work, we have investigated the energetics of the binding of receptor binding domain (RBD) of SARS-CoV-2 variants of concern (VOCs): Beta (B.1.351), Delta (B.1.617.2), Omicron (B.1.1.529), variant of interest (VOI): Kappa (B.1.617.1), and Delta Plus (B.1.617.2.1) variant with the human ACE2 receptor by using the umbrella sampling (US) method. Our work indicates that Delta and Delta Plus variants have greater values of the US binding free energy than Wild-type (WT), whereas Beta, Kappa, and Omicron variants have lower values. Further analysis of hydrogen bonding, salt bridges, non-bonded interaction energy, and contact surface area at the RBD-hACE2 interface establish Delta as the variant with the highest binding affinity among these variants.

Adsorption of zwitterionic oligomer-grafted silica nanoparticles on rock surface in enhanced oil recovery studied by molecular dynamics simulations

The application of surface-functionalized nanoparticles (NPs) in enhanced oil recovery (EOR) has been rapidly increasing. Adsorption of NPs on the rock surface is the key step. In this study, we systematically investigated the adsorption and desorption mechanisms of various brush-like zwitterionic oligomers functionalized silica NPs on the hydrophilic rock surface in an aqueous solution using molecular dynamics simulations. Our simulations show that the adsorption is primarily influenced by the oligomer chains, while the neutral silica NP core contributes very weakly only when it has direct contact with the rock surface at the grafting density of 5 or below. The interactions from SO3⁻ groups located at the tail of zwitterionic side chains account for more than 72% of the non-bonded interaction energy Enb between the NPs and the rock. The adsorption becomes stronger for NPs with shorter (4 monomer units) oligomer chains but slightly weaker for NPs with longer (9 monomer units) oligomer chains when increasing the grafting density, which is well explained by the change in the number of adsorbed SO3⁻ groups. Desorption simulations with the umbrella sampling method indicate that the free energy of desorption decreases with increasing the grafting density. The silica NPs grafted with longer oligomer chains (9 monomer units) require higher free energies of desorption than the ones with shorter oligomer chains. The adsorption of NPs on the rock surface enhances surface hydrophilicity, and the effect of longer oligomer chains is more profound than that of short oligomer chains. This research provides valuable insights into the adsorption and desorption mechanisms of surface-modified silica NPs on the rock surface at the molecular level and thus gives hints to the design of nanofluids.

Molecular dynamics investigation on the interaction of nitrile-based ionic liquids in the separation of azeotropic refrigerant R-513A

The reclamation of mixed refrigerants stands as a potent measure to substantially mitigate the emission of fluorinated gases (F-gases). In the separation of the azeotropic refrigerant R-513A (comprising 56 wt% R-1234yf, 2,3,3,3-Tetrafluoropropene, and 44 wt% R-134a, 1,1,1,2-Tetrafluoroethane), the extractive distillation process using ionic liquids (ILs) was employed. The molecular structure of nitrile-based ILs ([C4C1im][SCN], [C4C1im][N(CN)2], [C4C1im][C(CN)3], [C4C1im][B(CN)4]) exerts a regular impact on the solubility of refrigerants, thereby necessitating molecular dynamics simulation to ascertain the law of refrigerant solubility in ILs concurrent with the augmentation in the number of –CN in the anion. Additionally, an analysis was conducted to elucidate the mechanism underlying the high selectivity of nitrile-based ILs. The results revealed pronounced interactions between R-1234yf and R-134a, predominantly occurring between carbon atoms (-CF3 groups in R-134a and R-1234yf), and chiefly van der Waals interactions. An enhancement in the number of –CN in anion led to the fortification of the van der Waals interaction between R-134a/R-1234yf and the anion. The stronger nonbonding interaction energy between R-134a and the anion, as well as the higher radial distribution function (RDF) peak height between R-134a and the anion, signified a more robust interaction between R-134a and the anion compared to R-1234yf and the anion. Concurrently, the variance in the RDFs in the anion-C atom (-CH2F group in R-134a and -CF group in R-1234yf) revealed the selectivity of the four ILs to R-134a and R-1234yf. Among the four anions, [B(CN)4]− exhibited the most interaction sites with R-134a. This investigation contributes significantly to comprehending the interaction mechanism of azeotropic refrigerants and the interaction mechanism between refrigerants and nitrile-based ILs.

Effect of sliding velocity on the nanoscale friction behaviour of articular cartilage contact interface: insights from all-atom molecular dynamics investigation

ABSTRACT This study employs molecular dynamics simulations to explore nanoscale friction behaviour as a function of varying loading and sliding speeds on a developed top-layer articular cartilage contact interface atomistic model. To investigate nanotribological behaviour, sliding speed variations on the normal force, friction force, non-bonded interaction energy and interface temperature is obtained at the inter-cartilage interface. Analysis conducted at high velocity in a simplified tissue-like hydrated environment revealed ice-like dynamic smooth sliding behaviour of protein chains when cartilage interfaces are even 3.8 Å apart. With an increase in velocity, the coefficient of friction (COF) increases significantly in a hydrated environment. Additionally, at lower loads, the effect of sliding velocity is more pronounced than at higher loads. However, results show that articular cartilage adapts to higher load and speed sliding conditions exhibiting lower friction (COF-0.03–1.17) by means of interfacial water rearrangements and protein side-chain non-bonded interactions reducing heavy shear deformation. This is attributed to an alteration in the load-bearing and friction mechanism owing to water rearrangement and adsorption at nanoconfined biointerfaces. This study provides mechanistic insights into friction mechanisms at the cartilage interface which could lead to wear-like conditions under physiological sliding contact conditions, thereby facilitating the design of better implants.

Molecular study on diffusion behavior and performance recovery of aged asphalt binder containing functional rejuvenators

In hot in-place recycling (HIR) technology, there are many shortcomings and challenges such as low mixing temperature, short mixing time and less virgin asphalt binder, demanding multifunctional rejuvenators with higher diffusion rates. Therefore, there is an urgent need to develop a rejuvenator that balances diffusion rate and performance recovery. In this study, molecular dynamics (MD) simulation was employed to establish the basic structure of oil fractions, including chain alkanes, cycloalkanes and aromatic hydrocarbons. To improve the diffusion rate of rejuvenators, functional groups in penetrants and surfactants, such as hydroxyl, carboxyl, amide, ether, and ester groups, were incorporated into the basic structure for artificial design and enhancement. The diffusion rates of the primary and enhanced structures were investigated, and the internal factors for diffusion were analyzed. Furthermore, two rejuvenation methods for rejuvenators were proposed based on the changes in non-bond interaction energy in different asphalt binder systems. Moreover, the performance recovery of different rejuvenators were investigated. The results show that the diffusion rate of chain alkanes in the basic structure is the fastest, while that of aromatic hydrocarbons is the slowest. When ether and ester groups are used as enhanced structures, the diffusion rates of chain alkanes increase by 34.7% and 61.1%, respectively. Regarding performance recovery, chain alkanes exhibit the best performance recovery effect, which is further enhanced when ether and ester groups are employed as enhanced structures.

Experimental and molecular dynamics study of fuel desulfurization process using deep eutectic solvent

The sulfur-containing compounds in China's crude oil mainly exist in the form of thiophene (TPs). More than 80% of TPs are composed of dibenzothiophene (DBT). The combustion of sulfur-containing fuel oil pollutes the air. Studies have shown that DES, as a new solvent similar to ionic liquids, has the advantages of simple preparation, easy availability of raw materials and high extraction rate. In this paper, experiments on DES synthesis were carried out to screen DES with the best extraction efficiency, and the effects of extraction operation temperature and initial sulfur concentration of raw oil on DES extraction and desulfurization were explored. The DES separation mechanism for DBT extraction from n-heptane-DBT was used as the simulated oil. Quantum chemistry was calculated for 9 commonly used DES, and the hydrogen bonding between DES-DET-n-heptane was analyzed by using the obtained σ-Profiles map information, and the selected DES was compared with the auxiliary experiment from the perspective of quantum chemistry. Then, the molecular dynamics (MD) simulation between different DES and raw oil was carried out, that is, the non-bond interaction energy, radial distribution function, spatial distribution function and mean square shift results of DBT-Heptane-DES calculated by molecular dynamics were used to deeply analyze the microscopic separation mechanism of DES extraction desulfurization. The results show that the DES composed of choline chloride/diethylene glycol can theoretically perform more efficient desulfurization operations, and this theoretical analysis method can provide a strong basis for the desulfurization of other types of DES and the separation of other systems.

Inhibitory action of indanone-carbamate hybrid molecules on the aggregation of Aβ16−22 peptides and their translocation across POPC lipid bilayer

The aggregation of Aβ peptides leads to Alzheimer's Disease (AD), the most common kind of dementia. This neurodegenerative disease has no permanent cure to date. Drug design for Alzheimer's is, therefore, a major challenge to the scientific community. A recent experimental study showed the potency of two indanone-carbamate-based molecules to act as drugs against AD. However, the central molecular mechanism of action of these inhibitors is unknown. For knowing the mechanism of amyloid aggregation and the role of these novel molecules as inhibitors, an extensive all-atom molecular dynamics simulation of the Aβ16−22 peptides is performed. A variety of analyses are carried out to explore the structural change of the peptides in an aqueous medium in the absence and presence of inhibitors viz. secondary structure analysis, solvent accessible surface area calculation, residue-wise and Cα atom-wise contact mapping. In order to identify the peptide's residues associated with amyloid aggregation and interaction with the inhibitor, nonbonding interaction energies, radial distribution functions, coordination number, hydrogen bonds, and potential of mean forces are estimated. The central hydrophobic core, more importantly, the aromatic phenylalanine residues are found to play a substantial role in the formation of toxic amyloid oligomers. All the analyses demonstrate diminishing interpeptide interactions in presence of the inhibitors thereby checking amyloid aggregation. The molecules are also found to destabilize preformed amyloid fibrils. Furthermore, permeation properties of these small molecule inhibitors are investigated across a model POPC lipid bilayer, revealing their biocompatibility and translocation mechanisms.

Prediction of co-amorphous formation using non-bonded interaction energy: Molecular dynamic simulation and experimental validation

Co-amorphous (CA) formulation is a promising strategy to improve the solubility of poorly water-soluble drugs, however, effective prediction of a CA system is a challenge. In this study, a modified non-bonded interaction energy (ΔEnon-bonded) model was developed based on 105 solvent-based cases of 13 drugs chosen from the literature to predict CA formation by solvent-based methods using molecular dynamic simulation. With the cut-off value of −3500 kJ·mol−1, the model hit 5 gefitinib CAs and 4 erlotinib CAs, validating its feasibility. The quadratic relationship between co-former proportion (xco-former) and ΔEnon-bonded was analyzed using polynomial regression, indicating the xco-former is most likely to render CA when ΔEnon-bonded reaches its extreme value. Hydrogen bonds between the NH group of active pharmaceutical ingredient and sulfonamide group of co-former were confirmed experimentally and computationally. Typical CA samples showed remarkable improved solubility (12.1 and 9.3 times) in PBS solution and good physical stability under room conditions.

Functionalization of Metal–Organic Framework Nanochannels for Water Transport and Purification

Artificial water nanochannels (AWCs) have drawn great attention due to their potential use in water purification. Herein, we propose an AWC design, which is based on coordinatively functionalizing unsaturated metal sites found in metal–organic frameworks (MOFs) with one-dimensional nanochannels. As a computational demonstration, we consider two MOFs, namely, Ni-CPO-27 and Ni-CPO-54, and graft proline, imidazolecarboxylic acid, imidazolecarboxaldehyde, pyrazolecarboxylic acid, and pyrazole carbaldehyde molecules into the MOF nanochannels. To assess the strength of the molecule-metal binding, binding energies were calculated using density functional theory. The results indicate that the MOFs containing either proline or 2-imidazolecarboxylic acid form water-stable AWCs with binding energies twice that of the binding energy of water. To shed light on the water diffusion mechanism in the proline-Ni-CPO-27/54 and 2-imidazolecarboxylic-Ni-CPO-27/54 AWCs, molecular dynamics simulations were performed to calculate the mean-squared displacement of water molecules and nonbonded interaction energies between select pairs of atoms in water and coordinated molecules were analyzed. It was found that the fastest water diffusion occurs in proline-Ni-CPO-54 with a self-diffusion coefficient of 7.2 ± 0.5 × 10–8 cm2/s. In comparison, the fastest water self-diffusion coefficient reported in a carbon nanotube-based AWC is 9 × 10–6 cm2/s. Nonbonded interactions between specific atom pairs regulate water diffusion in the functionalized MOF nanochannels. In particular, the change in water mean-squared displacement with changing water loading correlates well with the nonbonded energies between the partially positively charged hydrogen atoms in water and the partially negatively charged oxygen and nitrogen atoms in the proline and 2-imidazolecarboxylic acid molecules. The results presented herein indicate that water-stable MOFs could perform well as AWCs, thereby lending support to the further design and synthesis of MOF-based AWCs for water purification.

Decontamination of enoxacin containing aqueous phase through hydrophobic deep eutectic solvents: Solvent regeneration and quantum chemical insights

The current work addresses the extraction of a drug (enoxacin) from an aqueous environment by liquid-liquid extraction using three hydrophobic deep eutectic solvents (DES) namely, (a) dl-menthol: decanoic acid (1:1), (b) dl-menthol: dodecanoic acid (2:1), and (c) dodecanoic acid: decanoic acid (1:2). The experiments were conducted at varying mass ratios of DES/ water phase at ambient condition followed by quantum chemical (QC) analysis. Within the batch process with a single cycle, the extraction efficiency and the distribution ratio of 82 % and 4.75 respectively, were reported with the DES; dl-menthol: decanoic acid (1:1). Different initial drug concentrations (5 to 20 ppm) were introduced to observe the extraction performance at various contamination levels. Followed by the batch-type extraction experiments, three different recycling schemes have been implemented to assess the reuse and recovery of DESs. A 90 % percentage extraction was achieved by recycling the DES phase with purification through activated carbon (AC) which allowed it to maintain its continuity of the aqueous phase. The higher hydrophobicity of the DES phase with relatively high drug solubility proved to be the driving force of the enhanced DES-drug interaction. This was supported by the QC analysis as comparably higher non-bonded interaction energy was obtained for the DES-enoxacin complex suggesting stronger interaction and compactness. The charge transfer (CT) process confirmed the magnitude of charge transfer between DES and the drug through natural bonding orbital (NBO) charge analysis. Non-bonded interactions with dispersion effect were confirmed by the structural arrangement analysis of the complex supported by frontier molecular orbital (FMO) analysis. The quantum theory of atom in molecules and the non covalent interaction (QTAIM & NCI) analysis suggest hydrogen bonding and dispersion interactions (van der Waals) as the basis of interaction between the molecular groups.

Assessment of the properties of natural-based chiral deep eutectic solvents for chiral drug separation: insights from molecular dynamics simulation.

The structural and physicochemical properties of chiral deep eutectic solvents (DESs) consisting of racemic mixtures of menthol and acetic acid (DES1), racemic mixtures of menthol and lauric acid (DES2), and racemic mixtures of menthol and pyruvic acid (DES3) for enantioselective extraction processes are investigated. Structural results, such as the radial distribution function (RDF) and the combined distribution function (CDF), indicate that the hydroxyl hydrogen of menthol has a dominant interaction with the carbonyl oxygen of the acids in the considered DESs. The number of hydrogen bonds and non-bonded interaction energies formed between S-menthol and HBDs are larger than those with R-menthol, resulting in the self-diffusion coefficient of S-menthol being larger than that of R-menthol. Therefore, it can be said that the proposed DESs are good candidates for the separation of drugs with S chirality. The effects of acid type on the density and isothermal compressibility of DESs show the behaviour of DES2 > DES3 > DES1 and DES1 > DES3 > DES2, respectively. Our results provide a better perspective on new chiral DESs at the molecular level for enantioselective processes.

Mechanism analysis of liquid-liquid extraction separation for dimethyl carbonate and methanol by choline-based DESs as extractants

Dimethyl carbonate (DMC) is a widely used chemical raw material and chemical product with excellent performance. In this manuscript, based on electrostatic potential (ESP), reduced density gradient (RDG) function, non-bond interaction energy, radial distribution function (RDF), spatial distribution function (SDF) and self-diffusion coefficient, the separation of DMC / methanol (MeOH) by four deep eutectic solvents (DESs) was studied. The results of ESP analysis showed that the hydrogen bond receptor played a leading role in the separation process, and the urea in the four hydrogen bond donors was more likely to form a stable structure with MeOH. The weak interaction region between different DESs and azeotropes was studied by RDG function. Based on the non-bond interaction energy, it can be seen that Cl− can form a very strong interaction with MeOH, and Electrostatic energy (Eelec) plays a leading role in the separation process. The charge density around the central atom can be observed by RDF and SDF, so as to determine the interaction between azeotrope and DESs. The diffusion rate of azeotrope in different DESs was studied by self-diffusion coefficient. The results showed that MeOH moved the slowest in the DES composed of urea and choline chloride (CHCl). The effect of DES structure on the liquid level of methanol dimethyl carbonate system was clarified by analyzing the experimental liquid-liquid equilibrium data. In this study, based on quantum chemistry (QC) calculation and molecular dynamics (MD) simulation, this study analyzed the liquid-liquid extraction and separation mechanism of DMC and MeOH. The extraction effect of DES composed of CHCl+urea is the best, which has certain theoretical guiding significance for liquid-liquid extraction to realize the green and efficient separation of DMC and MeOH.

An in-silico study to gain a comprehensive understanding of the effects of glucosylation on quercetin properties

In order to gain a molecular understanding of why quercetin characteristics are altered by glucosylation, DFT calculations and MD simulations were utilized. According to DFT findings, glucosylation of quercetin altered its structural stability, molecular polarity, molecular polarizability, and Gibbs free energy of transfer, which gives a molecular explanation for the observed alterations in the aqueous solubility and lipophilicity of derivatives. The outcomes of MD simulations also demonstrated how the various hydroxyl groups of quercetin interact with solvent molecules and how glucosylation can have an impact on that. Additionally, it was shown that glucosylation often increased the number of hydrogen bonds and the nonbonded interaction energies between the molecules of the solvent and the solute. The solubility behavior of glucosylated derivatives in water and alcoholic solvents can be reasonably interpreted molecularly using these results, which could suggest approaches for improving the features of these kinds of bioactive compounds.

Anthracene separation from analogous polycyclic aromatic hydrocarbons using the naphthalene-based solvents

Tricyclic aromatic hydrocarbons are difficult to be separated due to similar characteristics and boiling points, particularly anthracene and its isomer phenanthrene. The structural properties of anthracene and phenanthrene have been analyzed to identify the structural distinctions serving as critical factors to select a suitable solvent. Naphthalene-based solvents with electron-withdrawing substituent have been used to recognize phenanthrene molecules via electrostatic interaction. The separation performances of naphthalene-based solvents have been compared by the partition coefficient, purity, and yield, emphasizing the superior performance of acetylnaphthalene. The separation of anthracene is effective with a higher purity of 99.3 wt% and yield of 70.2 wt%, at room temperature and lower viscosity, economic cost savings of more than ten times, and beneficial by using the environment-benign back extractant. It also shows a better separation effect on real coal tar. In addition, the nonbonded interaction energy was further decomposed to illustrate the separation mechanism of naphthalene-based solvents from the energy perspective because the electrostatic interaction between phenanthrene and acetylnaphthalene plays a vital role. This work not only provides a new perspective on the selection of extractants but also promotes the application of intermolecular interaction in the separation and purification technology of analogous polycyclic aromatic hydrocarbons.

Multiscale mechanism exploration and experimental optimization for rosmarinic acid extraction from Rosmarinus officinalis using natural deep eutectic solvents

This study aimed at efficient rosmarinic acid (RA) extraction from rosemary ( Rosmarinus officinalis L.) using natural deep eutectic solvents (NADESs). Quantum chemical calculations and molecular dynamics simulation were used to dissect the microscopic mechanisms. Three choline chloride (ChCl) based NADESs and ethanol (traditional extractant as reference) were investigated. The σ -profiles of RA and each solvent were analyzed. The infinite dilution activity coefficient ( γ ∞ ) of RA in different solvents, the total non-bonded interaction energy and the average H-bond number were calculated, to predict the RA solubility, understand the bond type and strength in each system. Among the solvents studied, ChCl/LA (lactic acid) exhibited wider complementary σ -profile with that of RA, as well as lower ln γ ∞ , higher H-bond number and predominant electrostatic-interaction. Moreover, self-diffusion coefficients revealed that RA had better compatibility with ChCl/LA. Additionally, with different solvents as extractant, ChCl/LA outperformed the others by exhibiting the highest RA extraction yield. Based on results from single factor experiments, Box-Behnken design with response surface methodology was performed for further process optimization. The regressed model obtained was reliable from the ANOVA analysis of variances. RA extraction yield was 6.10% under optimal conditions of 69 °C, 5.6 h, liquid to solid ratio 34 and water content 13.5% (w/w). The combination of simulation and experiment in this study can shed light on the exploration of natural product extraction with high efficiency using green and novel NADESs. • Efficient rosmarinic acid extraction from rosemary with natural deep eutectic solvents. • Solvent evaluation for extractability by molecular simulation and experiment. • Response surface methodology was used for extraction optimization. • Optimal rosmarinic acid yield 6.10% was obtained with Choline chloride/Lactic acid. • Multiscale mechanism exploration inspires solvent screening& design for extraction.