Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules

Research on the dielectric properties of flexible β-CD/PVDF all-organic films

All-organic dielectric polymers are currently a hot topic in the study of dielectric materials. However, it is still challenging to improve the dielectric constant, breakdown strength, and energy storage density of materials simultaneously. This study used PVDF as the matrix, and β-CD/PVDF all-organic composite dielectric films were prepared using a solution blending method. The research found that after the introduction of β-Cyclodextrin (β-CD), the β-phase content of the polymer and the crystallinity of the films were 40.9 % and 48.96 %, respectively, which are 1.1 and 1.4 times that of pure PVDF. Improved microstructure significantly enhanced the dielectric performance and energy density of the composite films with β-CD. The composite films with β-CD with dielectric constant (εr), breakdown strength (Eb), and energy density reaching 12.35, 401.7 MV/m, and 6.11 J/cm3, respectively, which are 1.38, 1.1, and 1.3 times that of pure PVDF. This method provides a new pathway for preparing all-organic dielectric films with high dielectric constant, high breakdown strength, and high energy density.

Liquid Structure Scenario of the Archetypal Supramolecular Deep Eutectic Solvent: Heptakis(2,6-di-O-methyl)-β-cyclodextrin/levulinic Acid

The concept of supramolecular solvents has been recently introduced, and the extended liquid-state window accessible for mixtures of functionalized cyclodextrins (CDs) with hydrogen bond (HB) donor species, e.g., levulinic acid, led to the debut of supramolecular deep eutectic solvents (SUPRA-DES). These solvents retain CD's inclusion ability and complement it with enhanced solvation effectiveness due to an extended HB network. However, so far, these promising features were not rationalized in terms of a microscopic description, thus hindering a more complete capitalization. This is the first joint experimental and computational study on the archetypal SUPRA-DES: heptakis(2,6-di-O-methyl)-β-CD/levulinic acid (1:27). We used X-ray scattering to probe CD's aggregation level and molecular dynamics simulation to determine the nature of interactions between SUPRA-DES components. We discover that CDs are homogeneously distributed in bulk and that HB interactions, together with the electrostatic ones, play a major role in determining mutual interaction between components. However, dispersive forces act in synergy with HB to accomplish a fundamental task in hindering hydrophobic interactions between neighbor CDs and maintaining the system homogeneity. The mechanism of mutual solvation of CD and levulinic acid is fully described, providing fundamental indications on how to extend the spectrum of SUPRA-DES combinations. Overall, this study provides the key to interpreting structural organization and solvation tunability in SUPRA-DES to extend the range of sustainable applications for these new, unique solvents.

Grafting (S)-2-Phenylpropionic Acid on Coordinatively Unsaturated Metal Centers of MIL-101(Al) Metal-Organic Frameworks for Improved Enantioseparation

Chiral metal-organic frameworks (cMOFs) are emerging chiral stationary phases for enantioseparation owing to their porosity and designability. However, a great number of cMOF materials show poor separation performance for chiral drugs in high-performance liquid chromatography (HPLC). The possible reasons might be the irregular shapes of MOFs and the low grafting degree of chiral ligands. Herein, MIL-101-Ppa@SiO₂ was synthesized by a simple coordination post-synthetic modification method using (S)-(+)-2-Phenylpropionic acid and applied as the chiral stationary phase to separate chiral compounds by HPLC. NH₂-MIL-101-Ppa@SiO₂ prepared via covalent post-synthetic modification was used for comparison. The results showed that the chiral ligand density of MIL-101-Ppa@SiO₂ was higher than that of NH₂-MIL-101-Ppa@SiO₂, and the MIL-101-Ppa@SiO₂ column exhibited better chiral separation performance and structural stability. The binding affinities between MIL-101-Ppa@SiO₂ and chiral compounds were simulated to prove the mechanism of the molecular interactions during HPLC. These results revealed that cMOFs prepared by coordination post-synthetic modification could increase the grafting degree and enhance the separation performance. This method can provide ideas for the synthesis of cMOFs.

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.

Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References

A large diversity in the targeted hydration free energies (HFEs) during model parameterization of metal ions was reported in the literature with a difference by dozens of kcal/mol. Here, we developed a series of nonbonded dummy models of the Mg²⁺ ion targeting different HFE references in TIP3P water, followed by assessments of the designed models in the simulations of MgCl₂ solution and biological systems. Together with the comparison of existing models, we conclude that the difference in the targeted HFEs has a limited influence on the model performance, while the usability of these models differs from case to case. The feasibility of reproducing more properties of Mg²⁺ such as diffusion constants and water exchange rates using a nonbonded dummy model is demonstrated. Underestimated activity derivative and osmotic coefficient of MgCl₂ solutions in high concentration reveal a necessity for further optimization of ion-pair interactions. The developed dummy models are applicable to metal coordination with Asp, Glu, and His residues in metalloenzymes, and the performance in predicting monodentate or bidentate binding modes of Asp/Glu residues depends on the complexity of metal centers and the choice of protein force fields. When both the binding modes coexist, the nonbonded dummy models outperform point charge models, probably in need of considering polarization of metal-binding residues by, for instance, charge calibration in classical force fields. This work is valuable for the use and further development of magnesium ion models for simulations of metal-containing systems with good accuracy.

Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin

Recently, β-cyclodextrin (βCD)-based polymers with enhanced adsorption kinetics and high removal capacity of organic micropollutants (OMPs) and uptake rates have been synthesized and tested experimentally. Although the exact physical–chemical mechanisms via which these polymers capture the various types of OMPs are not yet fully understood, it is suggested that the inclusion complex formation of OMPs with βCD is very important. In this study, the inclusion complex formation of OMPs with βCD in an aqueous solution is investigated by using the well-established attach–pull–release method in force field-based molecular dynamics simulations. A representative set of OMPs is selected based on the measured occurrences in surface and ground waters and the directives published by the European Union. To characterize the formation of the inclusion complex, the binding free energies, enthalpies, and entropies are computed and compared to experimental values. It is shown that computations using the q4md-CD/GAFF/Bind3P force field combination yield binding free energies that are in reasonable agreement with the experimental results for all OMPs studied. The binding enthalpies are decomposed into the main contributing interaction types. It is shown that, for all studied OMPs, the van der Waals interactions are favorable for the inclusion complexion and the hydrogen bond formation of the guest with the solvent and βCD plays a crucial role in the binding mechanism. Our findings show that MD simulations can adequately describe the inclusion complex formation of βCD with OMPs, which is the first step toward understanding the underlying mechanisms via which the βCD-based polymers capture OMPs.

Colorimetric Detection of Aliphatic Alcohols in β-Cyclodextrin Solutions

The sensitive, selective, and practical detection of aliphatic alcohols is a continuing technical challenge with significant impact in public health research and environmental remediation efforts. Reported herein is the use of a β-cyclodextrin derivative to promote proximity-induced interactions between aliphatic alcohol analytes and a brightly colored organic dye, which resulted in highly analyte-specific color changes that enabled accurate alcohol identification. Linear discriminant analysis of the color changes enabled 100% differentiation of the colorimetric signals obtained from methanol, ethanol, and isopropanol in combination with BODIPY and Rhodamine dyes. The resulting solution-state detection system has significant broad-based applicability because it uses only easily available materials to achieve such detection with moderate limits of detection obtained. Future research with this sensor system will focus on decreasing limits of detection as well as on optimizing the system for quantitative detection applications.

A molecular dynamics study of conformations of beta-cyclodextrin and its eight derivatives in four different solvents

Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin (βCD) derivatives for pharmaceutical and other applications. The effect of four different solvents on the structures of the native βCD and its hydrophilic (methylated βCD; MEβCD and hydroxypropyl βCD; HPβCD) and hydrophobic derivatives (ethylated βCD; ETβCD) was explored using molecular dynamics (MD) simulations and solvation free energy calculations. The native βCD, 2-MEβCD, 6-MEβCD, 2,6-DMβCD, 2,3,6-TMβCD, 6-HPβCD, 2,6-HPβCD and 2,6-ETβCD in non-polar solvents (cyclohexane; CHX and octane; OCT) were stably formed in a symmetric cyclic cavity shape through their intramolecular hydrogen bonds. In contrast, βCDs in polar solvents (methanol; MeOH and water; WAT) exhibited large structural changes and fluctuations leading to significant deformations of their cavities. Hydrogen bonding with polar solvents was found to be one of the major contributors to this behavior: solvent-βCD hydrogen bonding strongly competes with intramolecular bonding leading to significant changes in the structural stability of βCDs. An exception to this is the hydrophobic 2,6-ETβCD which retained its spherical cavity in all solvents. Based on this, it is proposed that the 2,6-ETβCD can act as a sustained release drug carrier.

Effect of Dimethyl Sulfoxide on the Binding of 1-Adamantane Carboxylic Acid to β- and γ-Cyclodextrins

Most therapeutic targets are proteins whose binding sites are hydrophobic cavities. For this reason, the majority of drugs under development are hydrophobic molecules exhibiting low solubility in water. To tackle this issue, a few percent of cosolvent, such as dimethyl sulfoxide (DMSO), is usually employed to increase drug solubility during the drug screening process. However, the few published studies dealing with the effect of adding DMSO showed that the affinity of hydrophobic ligands is systematically underestimated. To better understand the effect of DMSO, there is a need of studying its effect on a large range of systems. In this work, we used β- and γ-cyclodextrins (made of 6 and 7 α-d-glucopyranoside units, respectively) as models of hydrophobic cavities to investigate the effect of the addition 5% DMSO on the affinity of 1-adamantane carboxylic acid (ADA) to these cyclodextrins. The two systems differ by the size of the cyclodextrin cavity. The evaluation of binding constants was performed using ultrasound velocimetry, nuclear magnetic resonance spectroscopy, and molecular simulations. All techniques show that the presence of 5% DMSO does not significantly modify the affinity of ADA for γ-cyclodextrin, while the affinity is dramatically reduced for β-cyclodextrin. The bias induced by the presence of DMSO is thus more important when the ligand volume better fits the cyclodextrin cavity. Our work also suggests that free energy calculations provide a sound alternative to experimental techniques when dealing with poorly water-soluble drugs.

Validation and Comparison of Force Fields for Native Cyclodextrins in Aqueous Solution

Molecular dynamics simulations of native α-, β-, and γ-cyclodextrin in aqueous solution have been conducted with the goal to investigate the performance of the CHARMM36 force field, the AMBER-compatible q4md-CD force field, and five variants of the GROMOS force field. The properties analyzed are structural parameters derived from X-ray diffraction and NMR experiments as well as hydrogen bonds and hydration patterns, including hydration free enthalpies. Recent revisions of the torsional-angle parameters for carbohydrate systems within the GROMOS family of force fields lead to a significant improvement of the agreement between simulated and experimental NMR data. Therefore, we recommend using the variant 53A6_GLYC instead of 53A6 and 56A6_{CARBO_R} or 2016H66 instead of 56A6_CARBO to simulate cyclodextrins in solution. The CHARMM36 and q4md-CD force fields show a similar performance as the three recommended GROMOS parameter sets. A significant difference is the more flexible nature of the cyclodextrins modeled with the CHARMM36 and q4md-CD force fields compared to the three recommended GROMOS parameter sets.

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.

Towards Rational Chemosensor Design through Improved Understanding of Experimental Parameter Variation and Tolerance in Cyclodextrin-Promoted Fluorescence Detection

We have previously developed a highly efficient fluorescence-based toxicant-detection method that operates in complex environments to detect aromatic toxicants and toxicant metabolites with high sensitivity and selectivity. This method relies on the ability of γ-cyclodextrin to act as a supramolecular scaffold, and uses a variety of non-covalent interactions between the cyclodextrin, toxicant, and fluorophore to enable efficient detection. Reported herein is an investigation of the effect of various experimental parameters, including host concentration, temperature, pH, salt, and solvent, on the observed energy-transfer efficiencies. These results advance our understanding of γ-cyclodextrin-based association complexes and provide crucial information for the development of fluorescence-based sensors using such complexation and the resultant fluorescence-based detection.

Inclusion complexes of propiconazole nitrate with substituted β-cyclodextrins: the synthesis and in silico and in vitro assessment of their antifungal properties

Inclusion complexes with sulfobutylether-β-cyclodextrin, β-cyclodextrin sulphated sodium salt and monochlorotriazinyl-β-cyclodextrin were characterized and assessed for antifungal activity and cytotoxicity.

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.