Investigation of the inclusions of puerarin and daidzin with beta-cyclodextrin by molecular dynamics simulation

Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4-5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange-repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

Regulating the electrical double layer to prevent water electrolysis for wet ionic liquids with cheap salts

Hydrophobic ionic liquids (ILs), broadly utilized as electrolytes, face limitations in practical applications due to their hygroscopicity, which narrows their electrochemical windows via water electrolysis. Herein, we scrutinized the impact of incorporating cheap salts on the electrochemical stability of wet hydrophobic ILs. We observed that alkali ions effectively manipulate the solvation structure of water and regulate the electrical double layer (EDL) structure by subtly adjusting the free energy distribution of water in wet ILs. Specifically, alkali ions significantly disrupted the hydrogen bond network, reducing free water, strengthening the O-H bond, and lowering water activity in bulk electrolytes. This effect was particularly pronounced in EDL regions, where most water molecules were repelled from both the cathode and anode with the disappearance of the H-bond network connectivity along the EDL. The residual interfacial water underwent reorientation, inhibiting water electrolysis and thus enhancing the electrochemical window of wet hydrophobic ILs. This theoretical proposition was confirmed by cyclic voltammetry measurements, demonstrating a 45% enhancement in the electrochemical windows for salt-in-wet ILs, approximating the dry one. This work offers feasible strategies for tuning the EDL and managing interfacial water activity, expanding the comprehension of interface engineering for advanced electrochemical systems.

Preparation, Characterization and Molecular Dynamics Simulation of Rutin-Cyclodextrin Inclusion Complexes

Rutin is a natural flavonoid that carries out a variety of biological activities, but its application in medicine and food is limited by its water solubility. One of the classical methods used to enhance drug solubility is encapsulation with cyclodextrins. In this paper, the encapsulation of different cyclodextrins with rutin was investigated using a combination of experimental and simulation methods. Three inclusions of rutin/beta-cyclodextrin (β-CD), rutin/2-hydroxypropyl beta-cyclodextrin (HP-β-CD) and rutin/2,6-dimethyl beta-cyclodextrin (DM-β-CD) were prepared by the freeze-drying method, and the inclusions were analyzed using Fourier infrared spectroscopy (FTIR), X-ray diffraction analysis (XRD), differential scanning calorimetry (DSC) and ultraviolet-visible spectroscopy (UV) to characterize and demonstrate the formation of the inclusion complexes. Phase solubility studies showed that rutin formed a 1:1 stoichiometric inclusion complex and significantly increased its solubility. β-CD, HP-β-CD, DM-β-CD, rutin and the three inclusion complexes were modeled by using MS2018 and AutoDock 4.0, and molecular dynamics simulations were performed to calculate the solubility parameters, binding energies, mean square displacement (MSD), hydrogen bonding and radial distribution functions (RDF) after the equilibration of the systems. The results of simulation and experiment showed that rutin/DM-β-CD had the best encapsulation effect among the three cyclodextrin inclusion complexes.

Encapsulation Efficiency and Functional Stability of Cinnamon Essential Oil in Modified β-cyclodextrins: In Vitro and In Silico Evidence

Essential oils (EOs) have good natural antioxidant and antimicrobial properties; however, their volatility, intense aroma, poor aqueous solubility, and chemical instability limit their applications in the food industry. The encapsulation of EOs in β-cyclodextrins (β-CDs) is a widely accepted strategy for enhancing EO applications. The complexation of cinnamon essential oil (CEO) with five types of β-CDs, containing different substituent groups (β-CD with primary hydroxyl, Mal-β-CD with maltosyl, CM-β-CD with carboxymethyl, HP-β-CD with hydroxypropyl, and DM-β-CD with methyl), inclusion process behaviors, volatile components, and antioxidant and antibacterial activities of the solid complexes were studied. The CEOs complexed with Mal-β-CD, CM-β-CD, and β-CD were less soluble than those complexed with DM-β-CD and HP-β-CD. Molecular docking confirmed the insertion of the cinnamaldehyde benzene ring into various β-CD cavities via hydrophobic interactions and hydrogen bonds. GC-MS analysis revealed that HP-β-CD had the greatest adaptability to cinnamaldehyde. The CEO encapsulated in β-, Mal-β-, and CM-β-CD showed lower solubility but better control-release characteristics than those encapsulated in DM- and HP-β-CD, thereby increasing their antioxidant and antibacterial activities. This study demonstrated that β-, Mal-β-, and CM-β-CD were suitable alternatives for the encapsulation of CEO to preserve its antioxidant and antibacterial activities for long-time use.

Application of molecular docking in elaborating molecular mechanisms and interactions of supramolecular cyclodextrin

The cyclodextrin (CD)-based supramolecular nanomedicines have attracted growing interest because of their superior characteristics, including desirable biocompatibility, low toxicity, unique molecular structure and easy functionalization. The smart structures of CD impart host-guest interaction for meeting the multifunctional needs of disease therapy. However, it faces challenges in formulation design and inclusion mechanism clarification of the functional supramolecular assemblies owing to the complicated structures and mechanisms. Fortunately, molecular docking helps the researchers to comprehend the interaction between the drug and the target molecule for achieving high-through screening from the database. In this review, we summarized the category and characteristics of molecular docking along with the properties and applications of CD. Significantly, we highlighted the application of molecular docking in elaborating molecular mechanisms and simulating complex structures at molecular levels. The issues and development of CD and molecular docking were also presented to provide beneficial reference and new insights for supramolecular nano-systems.

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes

Cyclodextrins (CDs) are highly respected for their ability to form inclusion complexes via host-guest noncovalent interactions and, thus, ensofance other molecular properties. Various molecular modeling methods have found their applications in the analysis of those complexes. However, as showed in this review, molecular dynamics (MD) simulations could provide the information unobtainable by any other means. It is therefore not surprising that published works on MD simulations used in this field have rapidly increased since the early 2010s. This review provides an overview of the successful applications of MD simulations in the studies on CD complexes. Information that is crucial for MD simulations, such as application of force fields, the length of the simulation, or solvent treatment method, are thoroughly discussed. Therefore, this work can serve as a guide to properly set up such calculations and analyze their results.

Illustration of a computational pipeline for evaluating cyclodextrin host-guest complex formation through conformational capture of bullvalene

Cyclodextrins have a diverse range of applications, including as supramolecular hosts, as enzyme active-site analogs, in improving drug solubility and delivery, and in molecular selection. We have investigated their ability to form stable complexes with bullvalenes, unusual organic cage molecules that spontaneously interconvert between numerous degenerate isomers. The shape-shifting nature of substituted bullvalenes raises the potential for dynamic adaptive binding to biological targets. We tested whether β- and γ-cyclodextrins can capture particular bullvalene isomers and whether the preferred binding mode(s) differ between isomers. We first applied our computational host-guest interaction potential energy profiling to determine the best binding mode(s) of unsubstituted bullvalene and each isomer of methylenehydroxybullvalene to β- and γ-cyclodextrin. Subsequent molecular dynamics simulations of the predicted host-guest complexes showed that while unsubstituted bullvalene has a single, albeit ill-defined, binding mode with either cyclodextrin, each isomer of methylenehydroxybullvalene has two possible modes of binding to β-cyclodextrin but only a single, nebulous mode of binding to γ-cyclodextrin. Experimental determination of the binding free energy of each methylenehydroxybullvalene-cyclodextrin complex showed that methylenehydroxybullvalene is more likely to bind to β-cyclodextrin than to γ-cyclodextrin, despite its smaller cavity. Together, our results suggest that β-cyclodextrin, but not γ-cyclodextrin, shows promise for conformational capture of mono-substituted bullvalenes. More broadly, our computational pipeline should prove useful for rapid characterization of cyclodextrin host-guest complexes, avoiding the need for costly synthesis of guest molecules that are unlikely to bind stably, as well as providing detailed atomic-level insight into the nature of complexation.

Adding salt to expand voltage window of humid ionic liquids

Humid hydrophobic ionic liquids-widely used as electrolytes-have narrowed electrochemical windows due to the involvement of water, absorbed on the electrode surface, in electrolysis. In this work, we performed molecular dynamics simulations to explore effects of adding Li salt in humid ionic liquids on the water adsorbed on the electrode surface. Results reveal that most of the water molecules are pushed away from both cathode and anode, by adding salt. The water remaining on the electrode is almost bound with Li⁺, having significantly lowered activity. The Li⁺-bonding and re-arrangement of the surface-adsorbed water both facilitate the inhibition of water electrolysis, and thus prevent the reduction of electrochemical windows of humid hydrophobic ionic liquids. This finding is testified by cyclic voltammetry measurements where salt-in-humid ionic liquids exhibit enlarged electrochemical windows. Our work provides the underlying mechanism and a simple but practical approach for protection of humid ionic liquids from electrochemical performance degradation.

Designing and preparing supramolecular fluorescent probe based on carminic acid and γ-cyclodextrins and studying their application for detection of 2-aminobenzidazole

Supramolecular fluorescent probe, which was designed and modeled from carminic acid (CA) and γ-cyclodextrins (γ-CDs), was initially qualified and stated comprehensively. Fluorescence intensity of CA could be dramatically enhanced ∼850 a.u. through formation of a supramolecular fluorescent probe CA@γ-CDs. The super-probe was verified by geometric conformation and molecular docking, and subsequently characterized by FT-IR, NMR, XRD and fluorescence lifetime. Furthermore, the CA@γ-CDs probe was proved on the detection of fungicide 2-aminobenzidazole (2-BZ). Finally, fluorescence performance of CA and the application of the probe for molecular recognition were both motivated by γ-CDs significantly, which could facilitate the fluorescence detection of CA more extensively and precisely.

Molecular Insight into the Interaction between Camptothecin and Acyclic Cucurbit[4]urils as Efficient Nanocontainers in Comparison with Cucurbit[7]uril: Molecular Docking and Molecular Dynamics Simulation

Cucurbit[n]urils (CB[n], n = 5, 6, 7, 8, 10, 14) and their derivatives due to the hydrophobic cavities and polar carbonyl portals have been considerably explored for their potential uses as drug delivery systems. It is important to understand how these macrocyclic compounds interact with guests. Camptothecin (CPT), as a natural alkaloid, is a topoisomerase inhibitor with antitumor activity against breast, pancreas, and lung cancers. The application of this drug in cancer therapy is restricted due to its low aqueous solubility and high toxicity. Recently, the complex formation between the cucurbit[7]uril (CB[7])/acyclic cucurbit[4]uril (aCB[4]) nanocontainers and CPT have been evaluated to overcome the potential drawbacks of the related drug. Herein, using computational methods, we identified the interaction mechanism of CPT with CB[7]/aCB[4]s, which consist of benzene and naphthalene sidewalls (aCB[4]_benzene and aCB[4]_naphthalene, respectively) since the experimental approaches have not completely provided information at the molecular level. Our molecular docking and molecular dynamics (MD) simulations show that CB[7] and its two acyclic derivatives form stable inclusion complexes with CPT especially through hydrophobic interactions. We also found that aCB[4]s with the aromatic sidewalls can attach to CPT through π-π interactions. This investigation highlights aCB[4]s due to the structural properties and flexible nature as better nanocontainers for controlled release delivery of pharmaceutical agents in comparison with the CB[7] nanocontainer.

Paclitaxel interaction with cucurbit [7]uril and acyclic Cucurbit[4]uril nanocontainers: A computational approach

Paclitaxel (PTX) is a natural terpenoid compound that has been broadly studied for its antitumor activities and widely used as a chemotherapy medication. The treatment efficacy of PTX is affected by its low aqueous solubility, thus causing a subject of extensive research. In recent years, synthetic molecular containers such as cucurbit[n]urils (CB[n]s) and their derivatives have been significantly developing because of their remarkable ability to bind hydrophobic and cationic drugs. Recent experimental studies have shown that acyclic CB[n]-type containers (aCB[n]s), as new derivatives of the family of CB[n]s, increase the solubility of insoluble pharmaceuticals. However, the nature by which the drug interacts with carriers remains largely unknown. In this study, molecular docking and molecular dynamics (MD) simulation were performed to understand how CB[7] and aCB[4] nanocontainers interact with PTX which affect its aqueous solubility. The results clarify how the flexibility of containers is influenced by their structure and how this affects their interactions with PTX. Our results reveal that although both CB[7] and aCB[4] are capable of binding to PTX, the affinity to aCB[4] is higher than that of CB[7]. It has also been shown that the binding to both CB[7] and aCB[4] is probably an entropy-driven process. This research supports the potential use of the cucurbit[n]urils and their acyclic derivatives as drug delivery systems.

Effect of the Incorporation of Functionalized Cyclodextrins in the Liposomal Bilayer

Liposomes loaded with drug–cyclodextrin complexes are widely used as drug delivery systems, especially for species with low aqueous solubility and stability. Investigation of the intimate interactions of macrocycles with liposomes are essential for formulation of efficient and stable drug-in-cyclodextrin-in-liposome carriers. In this work, we reported the preparation of unilamellar vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) embedded with native β-cyclodextrin and two synthetic derivatives: heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMCD) and heptakis(2,3-di-O-acetyl)-β-cyclodextrin (DACD). We then studied the effect of these macrocycles on the liposomal size, membrane viscosity, and liposomal stability at different temperatures and concentrations. We observed that TMCD and DACD affected vesicle size and the change of size was related to CD concentration. Irrespective of its nature, the macrocycle established interactions with the phospholipidic head groups, preventing cyclodextrins to diffuse into the lipid bilayer, as confirmed by molecular dynamics simulations. Such supramolecular structuring improves liposome stability making these colloid systems promising carriers for biologically active compounds.

Molecular Dynamics Simulation for Mechanism Elucidation of Food Processing and Safety: State of the Art

Molecular dynamics (MD) simulation is a useful technique to study the interaction between molecules and how they are affected by various processes and processing conditions. This review summarizes the application of MD simulations in food processing and safety, with an emphasis on the effects that emerging nonthermal technologies (for example, high hydrostatic pressure, pulsed electric field) have on the molecular and structural characteristics of foods and biomaterials. The advances and potential projection of MD simulations in the science and engineering aspects of food materials are discussed and focused on research work conducted to study the effects of emerging technologies on food components. It is expected by showing key case studies that it will stir novel developments as a valuable tool to study the effects of emerging food technologies on biomaterials. This review is useful to food researchers and the food industry, as well as researchers and practitioners working on flavor and nutraceutical encapsulations, dietary carbohydrate product developments, modified starches, protein engineering, and other novel food applications.

Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-time-scale molecular dynamics (MD) simulations, postanalysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. In addition, our study further interprets experiments. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG = -RT ln(kon·C0/koff), and thermodynamics properties, ΔG = ΔH - TΔS. The water entropy calculations show that the entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of nonpolar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD, and strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driving force of binding. The study deepens our understanding of ligand-receptor recognition and suggests strategies for force field parametrization for accurately modeling molecular systems.

Enhancing both oral bioavailability and brain penetration of puerarin using borneol in combination with preparation technologies

Now there are few good oral preparations of puerarin used in cerebrovascular diseases because of its poor oral absorption caused by the low water solubility and the poor penetration into brain. In this study, three oral formulations of puerarin, nanocrystals suspension (NCS), inclusion compounds solution (ICS) and self-microemulsifying drug delivery system (SMEDDS) were prepared with borneol as an oral brain-targeting enhancer. A rat syngeneic in vitro model of the brain-blood barrier (BBB) was established to investigate effects of borneol on the permeability of puerarin across the BBB. The pharmacokinetics of puerarin in mice after oral administration was investigated by a high performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS) method. The in vitro BBB model study showed the permeability of puerarin was increased significantly (p < 0.05) and the value of transepithelial electrical resistance at 2 h was decreased significantly (p < 0.01) when the concentration of borneol was over 12.5 μg/mL compared with the control group. The pharmacokinetics results indicated borneol with doses of over 50 mg/kg could obviously increase both intestinal absorption and brain penetration of puerarin. With co-administration of borneol (100 mg/kg), the AUC of puerarin both in plasma (AUCplasma) and in brain (AUCbrain) for SMEDDS were significantly higher than those for NCS (p < 0.01) and ICS (p < 0.05). These results suggested borneol in combination with SMEDDS could improve both the oral absorption and the brain penetration of puerarin in mice, which was promising for the development of an oral formulation of puerarin used in cerebrovascular diseases.

Free-energy patterns in inclusion complexes: the relevance of non-included moieties in the stability constants

A MD/PMF-based procedure is designed for quantification of the interaction and respective components, guiding complex formation in water between β-CD and several naphthalene derivatives, highlighting the relevance of substituents.

NMR Study on the Inclusion Complexes of β-Cyclodextrin with Isoflavones

The structure of the inclusion complexes of β-cyclodextrin (β-CD) with daidzein and daidzin in D2O were investigated using NMR spectroscopy. For the β-CD and daidzein system, two types of 1:1 complexes were formed with the daidzein deeply inserted into the CD cavity with different orientations. For the β-CD/daidzin system, a 1:1 complex was formed with the flavonoid part of daidzin entering the CD cavity from the wide rim. The inclusion complexes determined by NMR were constructed using molecular docking. Furthermore, the mixture of puerarin, daidzein and daidzin, which are the major isoflavonoid components present in Radix puerariae, was analyzed by diffusion-ordered spectroscopy (DOSY) alone and upon addition of β-CD in order to mimic chromatographic conditions and compare their binding affinities.

Inclusion complexation of pinostrobin with various cyclodextrin derivatives

Pinostrobin (PNS) is one of the important flavonoids and can be abundantly found in the rhizomes of fingerroot (Boesenbergia rotrunda) and galangal (Alpinia galangal and Alpinia officinarum), the herbal basis of Southeast Asian cooking. Similar to other flavonoids, PNS exhibits anti-oxidative, anti-inflammatory and anti-cancer properties. However, this compound has an extremely low water solubility that limits its use in pharmaceutical applications. Beta-cyclodextrin (βCD) and its derivatives, 2,6-dimethyl-βCD (2,6-DMβCD) and the three hydroxypropyl-βCDs (2-HPβCD, 6-HPβCD and 2,6-DHPβCD), have unique properties that enhance the stability and solubility of such low-soluble guest molecules. In the present study, molecular dynamics simulations were applied to investigate the dynamics and stability of PNS inclusion complexes with βCD and its derivatives (2,6-DMβCD, 2,6-DHPβCD, 2-HPβCD and 6-HPβCD). PNS was able to form complexes with βCD and all four of its derivatives by either the chromone (C-PNS) or phenyl (P-PNS) ring dipping toward the cavity. According to the molecular mechanics-generalized Born surface area binding free energy values, the stability of the different PNS/βCD complexes was ranked as 2,6-DHPβCD>2,6-DMβCD>2-HPβCD>6-HPβCD>βCD. These theoretical results were in good agreement with the stability constants that had been determined by the solubility method.

Self-assembled nanoparticle of common food constituents that carries a sparingly soluble small molecule

A previously reported nanoparticle formed through the self-assembly of common food constituents (amylose, protein, and fatty acids) was shown to have the capacity to carry a sparingly soluble small molecule (1-naphthol) in a dispersed system. Potentiometric titration showed that 1-naphthol locates in the lumen of the amylose helix of the nanoparticle. This finding was further supported by calorimetric measurements, showing higher enthalpies of dissociation and reassociation in the presence of 1-naphthol. Visually, the 1-naphthol-loaded nanoparticle appeared to be well-dispersed in aqueous solution. Molecular dynamics simulation showed that the self-assembly was favorable, and at 500 ns, the 1-naphthol molecule resided in the helix of the amylose lumen in proximity to the hydrophobic tail of the fatty acid. Thus, sparingly soluble small molecules, such as some nutraceuticals or drugs, could be incorporated and delivered by this soft nanoparticle carrier.

In silico understanding of the cyclodextrin-phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes

The explicit-solvent molecular dynamic (MD) simulation and adaptive biased forces (ABF) methods were employed to systemically study the structural and thermodynamic nature of the β-cyclodextrin (βCD) monomer, phenanthrene (Phe) monomer, and their inclusion complexes in both the aqueous and membrane environments, aiming at clarifying the atomic-level mechanisms underlying in the CD-enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria. Simulations showed that βCD and Phe monomers could associate together to construct two distinctive assemblies, i.e, βCD1-Phe1 and βCD2-Phe1, respectively. The membrane-involved equilibrium simulations and the data of potential of mean forces (PMFs) further confirmed that Phe monomer was capable of penetrating through the membranes without confronting any large energy barrier, whereas, the single βCD and βCD-involved assemblies were unable to pass across the membranes. These observations clearly suggested that βCD only served as the carrier to enhance the bioavailability of Phe rather than the co-substrate in the Phe biodegradation process. The Phe-separation PMF profiles indicated that the maximum of the Phe uptake by bacteria would be achieved by the "optimal" βCD:Phe molar ratio, which facilitated the maximal formation of βCD1-Phe1 inclusion and the minimal construction of βCD2-Phe1 complex.

Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes

In the present study, our aim is to investigate the preferential binding mode and encapsulation of the flavonoid fisetin in the nano-pore of β-cyclodextrin (β-CD) at the molecular level using various theoretical approaches: molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The molecular docking suggested four possible fisetin orientations in the cavity through its chromone or phenyl ring with two different geometries of fisetin due to the rotatable bond between the two rings. From the multiple MD results, the phenyl ring of fisetin favours its inclusion into the β-CD cavity, whilst less binding or even unbinding preference was observed in the complexes where the larger chromone ring is located in the cavity. All MM- and QM-PBSA/GBSA free energy predictions supported the more stable fisetin/β-CD complex of the bound phenyl ring. Van der Waals interaction is the key force in forming the complexes. In addition, the quantum mechanics calculations with M06-2X/6-31G(d,p) clearly showed that both solvation effect and BSSE correction cannot be neglected for the energy determination of the chosen system.

Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations

Dimerization of cyclodextrin (CD) molecules is an elementary step in the construction of CD-based nanostructured materials. Cooperative binding of CD cavities to guest molecules facilitates the dimerization process and, consequently, the overall stability and assembly of CD nanostructures. In the present study, all three dimerization modes (head-to-head, head-to-tail, and tail-to-tail) of β-CD molecules and their binding to three isoflavone drug analogues (puerarin, daidzin, and daidzein) were investigated in explicit water surrounding using molecular dynamics simulations. Total and individual contributions from the binding partners and solvent environment to the thermodynamics of these binding reactions are quantified in detail using free energy calculations. Cooperative drug binding to two CD cavities gives an enhanced binding strength for daidzin and daidzein, whereas for puerarin no obvious enhancement is observed. Head-to-head dimerization yields the most stable complexes for inclusion of the tested isoflavones (templates) and may be a promising building block for construction of template-stabilized CD nanostructures. Compared to the case of CD monomers, the desolvation of CD dimers and entropy changes upon complexation prove to be influential factors of cooperative binding. Our results shed light on key points of the design of CD-based supramolecular assemblies. We also show that structure-based calculation of binding thermodynamics can quantify stabilization caused by cooperative effects in building blocks of nanostructured materials.

Interface behaviors of acetylene and ethylene molecules with 1-butyl-3-methylimidazolium acetate ionic liquid: a combined quantum chemistry calculation and molecular dynamics simulation study

Although imidazolium-based ionic liquids (ILs) combined with oxygen-containing anions were proposed as the potential solvents for the selective separation of acetylene (C(2)H(2)) and ethylene (C(2)H(4)), the detailed mechanism at the molecular level is still not well understood. The present work focuses on a most effective IL for removing C(2)H(2) from a C(2)H(4) stream, 1-butyl-3-methylimidazolium acetate ([BMIM][OAc]), aiming at understanding the first steps of the adsorption process of the molecules at the IL surface. We present a combined quantum mechanical (QM) calculation and molecular dynamics (MD) simulation study on the structure and property of the IL as well as its interaction with C(2)H(2) and C(2)H(4) molecules. The calculated results indicate that C(2)H(2) presents a stronger interaction with the IL than C(2)H(4) and the anion of the IL is mainly responsible for the stronger interaction. QM calculations show a stronger hydrogen-binding linkage between an acidic proton of C(2)H(2)/C(2)H(4) and the basic oxygen atom in [OAc](-) anion, in contrast to the relative weaker association via the C-H···π interaction between C(2)H(2)/C(2)H(4) and the cation. From MD simulations, it is observed that in the interfacial region, the butyl chain of cations and methyl of anions point into the vapor phase. The coming molecules on the IL surface may be initially wrapped by the extensive butyl chain and then devolved to the interface or caught into the bulk by the anion of IL. The introduction of guest molecules significantly influences the anion distribution and orientation on the interface, but the cations are not disturbed because of their larger volume and relatively weaker interaction with the changes in the guest molecules. The theoretical results provide insight into the molecular mechanism of the observed selective separation of C(2)H(2) form a C(2)H(4) stream by ILs.

Theoretical investigation on the inclusion of TCDD with β-cyclodextrin by performing QM calculations and MD simulations

The rapid enrichment and detection of trace polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are currently challenging issues in the field of environmental science. In this paper, by performing quantum chemistry (QM) calculations and molecular dynamics (MD) simulations, we studied the inclusion complexation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a representative PCDD molecule, with β-cyclodextrin (β-CD), one of the widely used compounds in supramolecular chemistry. The calculated results reveal that the stable inclusion complex can be formed in both the gas phase and solvent, which proposes that β-CD may serve as a potential substrate enriching TCDD. The calculated vibrational spectra indicate that the infrared (IR) and Raman spectroscopy may be suitable for the detection of β-CD-modified TCDD. The present theoretical results may be informative to environmental scientists who are devoting themselves to developing effective methods for detection and treatment of POPs.

Preparation of highly pure daidzin on oligo-β-cyclodextrin-Sepharose HP and investigation of chromatographic behavior of isoflavones by molecular docking

A novel method using column chromatography on oligo-β-cyclodextrin-Sepharose HP for the preparation of high purity daidzin from crude soybean samples was proposed in this work. The isoflavone of daidzin in sample A and B was purified under the optimum mobile phase composed of methanol/acetic acid/water=20.0/8.0/72.0 (v/v/v) at a flow-rate of 1.0 mL/min in one-step operation with a purity of 97.2% and 98.1%, a recovery of 95.3% and 96.3% respectively. The target products in isolated fraction were detected and characterized by HPLC analysis and ESI-MS spectrum. Preparative separation with sample-load of up to 2.42 mg/mL medium gave satisfactory results for daidzin with the purities over 97% and recoveries approximately 90%. Molecular docking simulations were utilized to help demonstrate the inclusion complexation between β-cyclodextrin and the isoflavones in samples through inclusion geometries and calculations of the binding energies. The prediction of the elution orders with AUTODOCK and SURFLEX-DOCK were validated by the chromatographic results.

NMR studies on puerarin and its interaction with beta-cyclodextrin

The interaction between puerarin and β-cyclodextrin (CD) has been studied in D(2)O, H(2)O/acetone-d(6), acetone-d(6) and DMSO-d(6) solutions by (1)H NMR spectroscopy. The NMR data obtained from hydroxy protons indicate that the formation of the inclusion complex between the two molecules is not stabilized by strong hydrogen bond interactions. The sugar part of puerarin as well as the A ring are outside the β-CD cavity while the B and C rings are located inside the cavity and the interaction is mainly stabilized by hydrophobic interactions. In DMSO at 30°C and in acetone-d(6)/H(2)O at temperature below -5°C, doubling of some signals indicated that, in these solvent systems, free rotation of the C-glycosyl bond was restricted due to the steric hindrance between the phenolic hydroxy group at C-7 and the bulky sugar moiety at C-8. In acetone, fast exchange of phenolic protons on the NMR timescale was observed, showing the effect of the solvent on the hindered rotation.