Conformations of some lower-size large-ring cyclodextrins derived from conformational search with molecular dynamics and principal component analysis

Quantitative determination of the binding capabilities of individual large-ring cyclodextrins in complex mixtures

Large-ring cyclodextrins (CDs) are a comparatively unexplored family of macrocycles. We use high-resolution 1H-13C HSQC NMR experiments to resolve the anomeric signals of at least 13 different size CDs in a mixture. Using a single titration experiment, we can quantify the individual binding capabilites of these structurally-related hosts, avoiding the need for cumbersome isolation.

On the multivalency of large-ring cyclodextrins

The inclusion complexes of several large-ring cyclodextrins with a number of monovalent ligands (five or six adamantane molecules; CDn/mADA; n = 11, 12, 13, 14, 21, 26; m = 5 (for n = 11 to 14) or 6 (for n = 21, 26)) were examined with molecular dynamics simulations. The results demonstrate the high affinity of the LR-CDs to accommodate in their cavities this hydrophobic test particle. Most of the simulation time two guest molecules associate with the CD11 macrocycle. Two to four guest molecules are included in the cavities of CD12, CD13 and CD14 for the total of about 50% to 75% of the simulation time. Higher order associates of CD21 and CD26 with three to five adamantane substrates, comprise more than 40.0% of the snapshots taken from the simulation trajectories, and they still have remaining unoccupied binding sites that could accommodate even more adamantane molecules. Cluster analyses were performed with the k-mean and the bottom up agglomerative hierarchical methods. These LR-CDs, with theirs more than one docking sites are suitable candidates as multivalent receptors for specifically designed multivalent ligands.

Formation and molecular dynamics simulation of inclusion complex of large-ring cyclodextrin and 4-terpineol

In the present study, the formation and structure of the inclusion compound of large-ring cyclodextrin and 4-terpineol were obtained through different experiments and molecular dynamics (MD) simulation. The analysis of FTIR, ¹ H-NMR, and thermodynamic results confirmed the formation of clathrates. Analysis of molecular structure (root-mean-square deviation and radius of gyration), solubility, and interaction energy (Coul, H bond) based on MD simulations further clarified the nature of the clathrate and the conformational changes caused by guest molecules as well as inclusion complexes process trends. The inclusion complex reportedly has a new crystal structure with improved thermal stability. PRACTICAL APPLICATION: This is the first work to demonstrate the complex formation between 4-terpineol and large-ring cyclodextrin by molecular dynamics simulation. Molecular dynamics simulation confirmed the formation of inclusion complexes theoretically. Conformational changes of the molecules and the formation of complexes with improved thermal stability were observed. Complexing with large-ring cyclodextrin can be used as an effective means to encapsulate the aroma/flavor compounds.

Catalytic reduction of 4-nitrophenol with gold nanoparticles stabilized by large-ring cyclodextrins

Au NP, stabilized by large-ring cyclodextrins, proved to be efficient for the catalytic reduction of 4-nitrophenol.

High-affinity host-guest chemistry of large-ring cyclodextrins

The host-guest chemistry of large-ring cyclodextrins (LRCDs) has been largely unexplored due to the lack of suitable guest molecules that bind with significant affinities to enable potential applications. Herein, we report their complexation with dodecaborate anions (B12X12(2-)), a novel class of guest molecules. The binding constants of the inorganic guests (10(4)-10(6) M(-1)) allow their classification as the first tight binders for LRCDs.

Factor Analysis of Conformations and NMR Signals of Rotaxanes: AIMD and Polarizable MD Simulations

The interlocked ⟨rod | ring⟩ structures of pseudorotaxanes and [2]rotaxanes are usually maintained by the complex hydrogen-bonding (H-bonding) network between the rod and ring. Ab initio molecular dynamics (AIMD) using generalized energy-based fragmentation approach and polarizable force field (polar FF)-based molecular dynamics (MD) simulations were performed to investigate the conformational changes of mechanically interlocked systems and to obtain the ensemble-averaged NMR chemical shifts. Factor analysis (FA) demonstrates that the ring H-donor (2,6 pyridinedicarboxamide group) plays an important role in the ring-rod recognition. In comparison to the conventional fixed-charge force field, the polarization effect is crucial to account for the H-bonding interactions in supramolecular systems. In the hybrid scheme, the polar FF-based MD simulations are used to generate different initial states for the AIMD simulations, which are able to give better prediction of ensemble-averaged NMR signals for chemically equivalent amide protons. The magnitude of the deshielding shift of NMR signal is correlated with the length of hydrogen bond. The polar FF model with variable charges shows that the dipole-dipole interactions between the flexible diethylene glycol chain of ring and polar solvents induce the upfield shifts of NMR signals of rod H-donors and the directional distribution of the neighboring CH3CN solvents.

Computational study on the intramolecular self-organization of the macrorings of some ‘giant’ cyclodextrins (CDn, n = 40, 70, 85, 100)

A limited number of modes determine the overall deformations of the macrorings, which may have more than one cavity. Accordingly, they have the potential to accommodate more than one substrate molecule.