Homodromic hydrogen bonds in low-energy conformations of single molecule cyclodextrins

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.

Structures and stabilities of naturally occurring cyclodextrins: a theoretical study of symmetrical conformers

A molecular modeling study of symmetrical conformers of α-, β-, and γ-cyclodextrins in the gas and aqueous phases was carried out using the M06-2X density functional method, with SMD employed as an implicit solvation model. Eight symmetrical conformers were found for each cyclodextrin. Values of geometrical parameters obtained from the modeling study were found to agree well with those obtained from X-ray diffraction structures. A vibrational analysis using harmonic frequencies was performed to determine thermodynamic quantities. The GIAO method was applied to determine proton and carbon-13 NMR chemical shifts, which were then compared with corresponding chemical shifts reported in the literature. Hydrogen-bonding patterns were analyzed using geometrical descriptors, and quantum chemical topology was explored by QTAIM analysis. The results of this study indicated that four of the eight conformers studied for each cyclodextrin are the most populated in aqueous solution. These results provide the foundations for future studies of host-guest complexes involving these cyclodextrins. Graphical abstract δΔG_solvation: variation of free Gibss energy of solvation.

Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin-water non-covalent complexes

We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.