Computational studies on the conformations of some large‐ring cyclodextrins (CDn, n = 20, 21, 22, 23)

Abstract

Computational studies were carried out on the conformations of large-ring cyclodextrins with degree of polymerization from 20 to 23. Principal component analysis (PCA) was applied for postprocessing of trajectories from conformational search, based on 100.0 ns molecular dynamics simulations. The dominant PCA modes for concerted motions of the macroring atoms were monitored in a lower-dimensions subspace. The first six lowest indexed principal components contribute more than 90% of the total atomic motions in all cases, with about 70% (CD21) to 83% (CD22) contribution coming from the three highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macrorings were also obtained for the whole simulation and for the ten 10.0 ns time intervals of the simulation. We concluded that resemblance exists of the representative conformations of these four cyclodextrins with the circularized three-turn single helical structure proposed for CD21 from small-angle X-ray scattering, as well as with the representative conformations of CD26.

Past, present, and future developments in enantioselective analysis using capillary electromigration techniques

“…Larger cycles have not been studied as extensively, mainly because they are more difficult to isolate and purify from enzymatically degraded starch than their smaller analogues [70], and due to their reputation of having negligible complex forming capacity due to their increased size and flexibility [65]. However, several studies published over the last 20 years have supported the potential of larger CDs for enantioseparations [70][71][72][73][74][75]. For instance, molecular dynamics studies of ranges of large-ring CDs suggest they can adopt a dominant preferred conformation [72,73], that is, they do not inherently possess a decreased chiral recognition ability due to continuous conformational changes in solution allowed by their supposed highly flexible structure.…”

“…However, several studies published over the last 20 years have supported the potential of larger CDs for enantioseparations [70][71][72][73][74][75]. For instance, molecular dynamics studies of ranges of large-ring CDs suggest they can adopt a dominant preferred conformation [72,73], that is, they do not inherently possess a decreased chiral recognition ability due to continuous conformational changes in solution allowed by their supposed highly flexible structure. Furthermore, micromolar affinities toward larger CDs have been observed for engineered hosts [74].…”

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

“…38 The conformations of some LR-CDs were systematically examined using molecular dynamics simulations as a conformational search protocol. [39][40][41][42][43][44][45][46][47][48][49][50][51] We started our studies by performing 5.0 ns simulations on several LR-CDs with degrees of polymerization in the range from 40 to 100. 39 The results were indicative for a variety of geometries with more than one small cavity.…”