Molecular Recognition in Different Environments: β-Cyclodextrin Dimer Formation in Organic Solvents

Unveiling cyclodextrin conjugation as multidentate excipients: An exploratory journey across industries

The discovery of branched molecules like dextrin by Schardinger in 1903 marked the inception of cyclodextrin (CD) utilization, catalyzing its journey from laboratory experimentation to widespread commercialization within the pharmaceutical industry. CD, a cyclic oligosaccharide containing glucopyranose units, acts as a versatile guest molecule, forming inclusion complexes (ICs) with various host molecules. Computational studies have become instrumental in elucidating the intricate interactions between β-CD and guest molecules, enabling the prediction of binding energy, forces, affinity, and complex stability. The computational approach has established robust correlations with experimental outcomes, enhancing our understanding of CD-mediated complexation phenomena. This comprehensive review delves into the CD based Inclusion complex (CDIC) formation and a myriad of components, including drug molecules, amino acids, vitamins, and volatile oils. These complexes find applications across diverse industries, ranging from pharmaceuticals to nutraceuticals, food, fragrance, and beyond. In the pharmaceutical realm, β- CDICs offer innovative solutions for enhancing drug solubility, stability, and bioavailability, thus overcoming formulation challenges associated with poorly water-soluble drugs. Furthermore, the versatility of CDs extends beyond pharmaceuticals, with applications in the encapsulation of phytoactive compounds in nutraceuticals and the enhancing flavor, aroma in food and fragrance industries. This review underscores the pivotal role of CDs conjugation in modern drug delivery systems, emphasizing the importance of interdisciplinary approaches that integrate computational modeling with experimental validation. As the pharmaceutical landscape continues to evolve, CDs-based formulations stand poised to drive innovation and address the ever-growing demand for efficacious and patient-friendly drug delivery solutions.

Surprisingly fast self-healing coatings with anti-fog and antimicrobial activities via host-guest interaction

Dual functional coatings with anti-fog and antimicrobial performances greatly enhance the safety and reliability of medical detection devices, but are prone to mechanical damage, resulting in reduced performance and a shorter service lifespan. Herein, a semi-interpenetrating polymer network (SIPN) coating, featuring hydrophobic-hydrophilic balanced copolymers as bulk chains and host-guest inclusion compounds (HGICs) as cross-linkers, is reported, which demonstrates particularly effective anti-fog and antibacterial performances, along with a surprisingly fast self-healing capability under various scenarios. This HGIC-based coating displayed remarkable anti-fog capability over a wide temperature range from -20 ℃ to 85 ℃ and exhibited reliable antibacterial activities (≥98 %) against both gram-positive and gram-negative bacteria. Also, this coating showed extremely high self-healing ability (≥92 % recovery rate) within just 20 s, significantly outperforming traditional self-healing systems. These findings support the development of functional coatings that can highly maintain rapid self-healing performance while also providing anti-fog and antibacterial properties in medical detection devices.

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.

Isomerism of Cyclodextrin Tetramer Induced by Alkali Halide Cluster Ions Observed by Ion Mobility Spectrometry-Mass Spectrometry

Cyclodextrins (CDs) exhibit versatile self-assembly properties due to their hydrophilic and hydrophobic components, with applications such as drug delivery and selective binding. While research on CD self-assembly is extensive, limited studies have explored their aggregation behavior, particularly in interactions with small ionic guests. The present work investigates the structure of β-CD tetramers aggregated with alkali metal chloride clusters using ion mobility spectrometry-mass spectrometry (IMS-MS). The results revealed that diverse structures emerge in the tetramer depending on the alkali metal cluster size. Notably, the doubly charged tetramer exhibits distinct aggregation trends with specific numbers of MCl clusters for Na+ and K+ ions. After initially adopting a bucket-wheel structure with two internal cations, the structure transforms into a new isomer with a tetrahedral configuration upon cluster addition. The formation of the new isomer structure is closely linked to filling the cavity volume with MCl clusters and ionic interactions, which possibly compensate for the weakened hydrogen bonds between CDs. Theoretical calculations further support the structures, showing well-matched collision cross-section (CCS) values compared with the experimental CCS values. This study highlights the role of alkali metal chloride clusters as potential templates, leading to the formation of novel CD assemblies.

Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations

Proteins and enzymes generally achieve their functions by creating well-defined 3D architectures that pre-organize reactive functionalities. Mimicking this approach to supramolecular pre-organization is leading to the development of highly versatile artificial chemical environments, including new biomaterials, medicines, artificial enzymes, and enzyme-like catalysts. The use of β-turn and α-helical motifs is one approach that enables the precise placement of reactive functional groups to enable selective substrate activation and reactivity/selectivity that approaches natural enzymes. Our recent work has demonstrated that helical peptides can serve as scaffolds for pre-organizing two reactive groups to achieve enzyme-like catalysis. In this study, we used CYANA and AmberTools to develop a computational approach for determining how the structure of our peptide catalysts can lead to enhancements in reactivity. These results support our hypothesis that the bifunctional nature of the peptide enables catalysis by pre-organizing the two catalysts in reactive conformations that accelerate catalysis by proximity. We also present evidence that the low reactivity of monofunctional peptides can be attributed to interactions between the peptide-bound catalyst and the helical backbone, which are not observed in the bifunctional peptide.

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.

Exploring Isomerism in Isolated Cyclodextrin Oligomers through Trapped Ion Mobility Mass Spectrometry

Cyclodextrin (CD) macrocycles are used to create a wide range of supramolecular architectures which are also of interest in applications such as selective gas adsorption, drug delivery, and catalysis. However, predicting their assemblies and identifying the possible isomers in CD oligomers have always remained challenging due to their dynamic nature. Herein, we interacted CDs (α, β, and γ) with a divalent metal ion, Cu²⁺, to create a series of Cu²⁺-linked CD oligomers, from dimers to pentamers. We characterized these oligomers using electrospray ionization mass spectrometry and probed isomerism in each of these isolated oligomers using high resolution trapped ion mobility spectrometry. Using this technique, we separated multiple isomers for each of the Cu²⁺-interlinked CD oligomers and estimated their relative population, which was not accessible previously using other characterization techniques. We further carried out structural analysis of the observed isomers by comparing the experimental collision cross sections (CCSs) to that of modeled structures. We infer that the isomeric heterogeneity reflects size-specific packing patterns of individual CDs (e.g., close-packed/linear). In some cases, we also reveal the existence of kinetically trapped structures in the gas phase and study their transformation to thermodynamically controlled forms by examining the influence of activation of the ions on isomer interconversion.

Influence of β-Cyclodextrin Methylation on Host-Guest Complex Stability: A Theoretical Study of Intra- and Intermolecular Interactions as Well as Host Dimer Formation

Understanding the non-covalent interactions in host-guest complexes is crucial to their stability, design and applications. Here, we use density functional theory to compare the ability of β-cyclodextrin (β-CD) and heptakis(2,6-di-O-methyl)-β-cyclodextrin (DM-β-CD) to encapsulate the model guest phenol. For both macrocycles, we quantify the intramolecular interactions before and after the formation of the complex, as well as the intermolecular host-guest and host-host dimer interactions. These are individually classified as van der Waals interactions or hydrogen bonds, respectively. The results show a stronger intramolecular binding energy of β-CD, with the absolute difference being −5.53 kcal/mol relative to DM-β-CD. Consequently, the intermolecular interactions of both cyclodextrins with phenol are affected, such that the free binding energy calculated for the DM-β-CD/phenol complex (−5.23 kcal/mol) is ≈50% more negative than for the complex with β-CD (−2.62 kcal/mol). The latter is in excellent agreement with the experimental data (−2.69 kcal/mol), which validates the level of theory (B97-3c) used. Taken together, the methylation of β-CD increases the stability of the host-guest complex with the here studied guest phenol through stronger van der Waals interactions and hydrogen bonds. We attribute this to the disruption of the hydrogen bond network in the primary face of β-CD upon methylation, which influences the flexibility of the host toward the guest as well as the strength of the intermolecular interactions. Our work provides fundamental insights into the impact of different non-covalent interactions on host-guest stability, and we suggest that this theoretical framework can be adapted to other host-guest complexes to evaluate and quantify their non-covalent interactions.

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

Theoretical Study of Macrocyclic Host Molecules: From Supramolecular Recognition to Self-Assembly

Supramolecular chemistry focuses on molecular recognition and self-assembly of various building blocks through weak non-covalent interactions, including anion-π, hydrogen bond (HB), hydrophobic interactions, van der Waals (vdW) interactions, etc, which...

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.

Diffusivity of α-, β-, γ-cyclodextrin and the inclusion complex of β-cyclodextrin: Ibuprofen in aqueous solutions; A molecular dynamics simulation study

Cyclodextrins (CDs) are widely used in drug delivery, catalysis, food and separation processes. In this work, a comprehensive simulation study on the diffusion of the native α-, β- and γ-CDs in aqueous solutions is carried out using Molecular Dynamics simulations. The effect of the system size on the computed self-diffusivity is investigated and it is found that the required correction can be as much as 75% of the final value. The effect of the water force field is examined and it is shown that the q4md-CD/TIP4P/2005 force field combination predicts the experimentally measured self-diffusion coefficients of CDs very accurately. The self-diffusion coefficients of the three native CDs were also computed in aqueous-NaCl solutions using the Joung and Cheatham (JC) and the Madrid-2019 force fields. It is found that Na+ ions have higher affinity towards the CDs when the JC force field is used and for this reason the predicted diffusivity of CDs is lower compared to simulations using the Madrid-2019 force field. As a model system for drug delivery and waste-water treatment applications, the diffusion of the β-CD:Ibuprofen inclusion complex in water is studied. In agreement with experiments for similar components, it is shown that the inclusion complex and the free β-CD have almost equal self-diffusion coefficients. Our analysis revealed that this is most likely caused by the almost full inclusion of the ibuprofen in the cavity of the β-CD. Our findings show that Molecular Dynamics simulation can be used to provide reasonable diffusivity predictions, and to obtain molecular-level understanding useful for industrial applications of CDs.

Detailed chemical characterization and molecular modeling of serotonin inclusion complex with unmodified β-cyclodextrin

In this study, we analyzed the capability of unmodified β-cyclodextrin (β-CD) to form the stable complex with serotonin hydrochloride (SER), as an important neurotransmitter in the brain. The stable β-CD: SER formulation was prepared and characterized using spectroscopic, thermal, molecular docking, and molecular dynamics techniques, revealing the phenomenon of H-bond formations and the domination of hydrophobic forces between the host molecule and its guest via the amine group of SER and the narrow side of β-CD. The complexation mechanism was mainly enthalpy-driven, representing the improvement in SER photo-stability. Overall, the results highlighted the possibility to use this formulation with improved stability in clinical practice for treatment and prevention of various depressive conditions, such as anxiety disorders.

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.

Succinyl-β-cyclodextrin: Influence of the substitution degree on albendazole inclusion complexes probed by NMR

Succinyl-β-CD derivatives were obtained by green synthesis with degrees of substitution (DS) 1.3 and 2.9. The spray-drying technique was used to obtain albendazole (ABZ):succinyl-β-CD inclusion complexes. Phase solubility diagrams indicated that both succinyl-β-CD derivatives formed 1:1 molar ratio ABZ complexes, but the complex with DS 2.9 has a lower formation constant. The presence of stable inclusion complexes in aqueous solution was confirmed by NMR. For both complexes the aromatic moiety is encapsulated into the host cavity. In the solid-state, ¹³C and ¹⁵N NMR spectral differences between ABZ and ABZ included in spray-dried systems showed that strong structural changes occurred in the systems. At least two different ABZ amorphous species were identified based on DS. ABZ species were stable over more than six months based on spectral data. Finally, the influence of DS in the number and type of the inclusion complexes was elucidated.

Intramolecular deactivation processes of electronically excited Lanthanide(III) complexes with organic acids of low molecular weight

The luminescence of Lanthanide(III) complexes with different model ligands was studied under direct as well as sensitized excitation conditions. The research was performed in the context of studies dealing with deep-underground storages for high-level nuclear waste. Here, Lanthanide(III) ions served as natural analogues for Actinide(III) ions and the low-molecular weight organic ligands are present in clay minerals and furthermore, they were employed as proxies for building blocks of humic substances, which are important complexing molecules in the natural environment, e.g., in the far field of a repository site. Time-resolved luminescence spectroscopy was applied for a detailed characterization of Eu(III), Tb(III), Sm(III) and Dy(III) complexes in aqueous solutions. Based on the observed luminescence the ligands were tentatively divided into two groups (A, B). The luminescence of Lanthanide(III) complexes of group A was mainly influenced by an energy transfer to OH-vibrations. Lanthanide(III) complexes of group B showed ligand-related luminescence quenching, which was further investigated. To gain more information on the underlying quenching processes of group A and B ligands, measurements at different temperatures (77K≤T≤353K) were performed and activation energies were determined based on an Arrhenius analysis. Moreover, the influence of the ionic strength between 0M≤I≤4M on the Lanthanide(III) luminescence was monitored for different complexes, in order to evaluate the influence of specific conditions encountered in host rocks foreseen as potential repository sites.

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.

Elucidating the H-Bonding Environment of Coumarin 102 in a Phenol-Cyclohexane Mixture by Molecular Dynamics Simulation: Implications for H-Bond-Guided Photoinduced Electron Transfer

Recently, we have experimentally demonstrated that the fluorescence intensity of coumarin 102 (C102) modulates anomalously upon hydrogen bonding to phenol in a nonpolar solvent: cyclohexane. The fluorescence intensity is first quenched gradually up to a particular mole fraction (X_PH ≈ 0.013) but thereafter increases with further increases in the phenol mole fraction. These studies speculate about the importance of C102-phenol H-bonding to induce photoinduced electron transfer (PET) and propose a competition between the C102-phenol and phenol-phenol H-bonding to account for the anomalous fluorescence modulation. In this work, we investigate the exact H-bonding environment around the acceptor C102 at various compositions by molecular dynamics simulation and correlate the H-bonding environment to the observed fluorescence quenching. In addition to the 1:1 C102-phenol complex, 1:2 C102-(phenol)₂ complexes with two different types of geometries were also found. Furthermore, density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations were carried out to understand the H-bonding in these complexes in the ground state and in the excited state and their possible contribution to the observed fluorescence quenching.

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.

Molecular dynamics simulation of cyclodextrin aggregation and extraction of Anthracene from non-aqueous liquid phase

Cyclodextrin (CD) extraction is widely used for the remediation of polycyclic aromatic hydrocarbons (PAH) pollution, but it remains unclear about the influence of CD aggregation on the PAH transport from non-aqueous liquid phase to water. The atomistic adsorption and complexation of PAHs (32 anthracenes) by CD aggregates (48 β-cyclodextrins) were studied by molecular dynamics simulations at hundreds of nanoseconds time scale. Results indicated that high temperature promoted the βCD aggregation in bulk oil, which was not found in bulk water. Nevertheless, the fractions of anthracenes entrapped inside the βCDs cavity in both scenarios were significantly increased when temperature increased from 298 to 328K. Free energy calculation for the sub-steps of CD extraction demonstrated that the anthracenes could be extracted when the βCDs arrived at the water-oil interface or after the βCDs entered the bulk oil. The former was kinetic-controlled while the latter was thermodynamic-limited process. Results also highlighted the formation of porous structures by CD aggregates in water, which was able to sequestrate PAH clusters with the size obviously larger than the cavity diameter of individual CD. This provided an opportunity for the extraction of recalcitrant PAHs with molecular size larger than anthracenes by cyclodextrins.

Regioselective self-acylating cyclodextrins in organic solvent

Amphiphilic cyclodextrins have been synthesized with self-acylating reaction using vinyl esters in dimethylformamide. In the present study no base, catalyst, or enzyme was used, and the structural analyses using thin layer chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry show that the cyclodextrin is substituted preferentially by one acyl moiety at the C2 position of the glucose unit, suggesting that cyclodextrin functions as a regioselective catalytic carbohydrate in organic solvent. In the self-acylation, the most acidic OH group at the 2-position and the inclusion complexing ability of cyclodextrin were considered to be significant. The substrate preference was also observed in favor of the long-chain acyl group, which could be attributed to the inclusion ability of cyclodextrin cavity. Furthermore, using the model amphiphilic building block, 2-O-mono-lauryl β-cyclodextrin, the self-organized supramolecular architecture with nano-vesicular morphology in water was investigated by fluorescence spectroscopy, dynamic light scattering and transmission electron microscopy. The cavity-type nano-assembled vesicle and the novel synthetic methods for the preparation of mono-acylated cyclodextrin should be of great interest with regard to drug/gene delivery systems, functional surfactants, and carbohydrate derivatization methods.

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Complexes of peracetylated cyclodextrin in a non-aqueous aprotic medium: the role of residual water

Not all peracetylated cyclodextrins can be completely dried and water protons can be invisible due to the overlapping signals of the acetyl groups. Apparent stability constants of complexes were also calculated.

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.

Experimental and computational study of BODIPY dye-labeled cavitand dynamics

Understanding the distance distribution and dynamics between moieties attached to the walls of a resorcin[4]arene cavitand, which is switchable between an expanded kite and a contracted vase form, might enable the use of this molecular system for the study of fundamental distance-dependent interactions. Toward this goal, a combined experimental and molecular dynamics (MD) simulation study on donor/acceptor borondipyrromethene (BODIPY) dye-labeled cavitands present in the vase and kite forms was performed. Direct comparison between anisotropy decays calculated from MD simulations with experimental fluorescence anisotropy data showed excellent agreement, indicating that the simulations provide an accurate representation of the dynamics of the system. Distance distributions between the BODIPY dyes were established by comparing time-resolved Förster resonance energy transfer experiments and MD simulations. Fluorescence intensity decay curves emulated on the basis of the MD trajectories showed good agreement with the experimental data, suggesting that the simulations present an accurate picture of the distance distributions and dynamics in this molecular system and provide an important tool for understanding the behavior of extended molecular systems and designing future applications.