Molecular dynamics study of the conformational dynamics and energetics of some large‐ring cyclodextrins (CD<i>n</i>, <i>n</i> = 24, 25, 26, 27, 28, 29)

Gotsev, Martin G.; Ivanov, Petko M.; Jaime, Carlos

doi:10.1002/chir.20365

Cited by 20 publications

(49 citation statements)

References 60 publications

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“…Differences were obtained here in comparison with all earlier analyses of hydrogen bond distributions, 41,42,51,52 and these discrepancies resulted from the minor variations introduced in the equilibration stage of the simulation protocol (heating of the system from 0 K to 300 K within the first 10000 time-steps by increasing in ten steps the temperature in portions of 30 degrees, plus 90000 time-steps equilibration at 300 K). It appears that some properties, like intermolecular hydrogen bonds distributions are very sensitive to parameters of the simulation protocol.…”

Section: Analysis Of Hydrogen Bonds Distributioncontrasting

confidence: 55%

“…Up to now, researchers in the field of cyclodextrins have been focusing their attention at the cavities formed by these macrorings, especially the native CDs. However, the results from our previous studies, 51,52 as well as the present one, with large variety of chiral structural shapes, open the possibility of using not the cavities but the whole macroring as a suitable ligand for some large chiral molecules with chirality originating from the symmetry group to which the molecule belongs, not from the existence of chiral atoms. Due to the flipping of about 180º in anti orientation of two diametrically opposed glucoses along the perimeters of the macrorings, the molecular shapes of CD10 and CD14, determined from X-ray analyses, resemble the shape of a butterfly in which the wings are formed by cyclodextrin-like fragments and the conformational band-flips ("flips") are located at the body.…”

Section: Structural Variations Of the Large-ring Cyclodextrins In Solmentioning

confidence: 67%

“…The general appearances of conformations ( Figure 6(j-l)) are analogous to the trends monitored in our previous simulations. 41,51 The most representative structural motifs during the simulation are a helical portion, one or two loops and an arc. The only difference in the results from the previous simulation protocol 41,51,52 (data designated with CD26*) is that the first "flip" did not disappear from the very beginning of the simulation, but survived during the first 3.0 ns.…”

Section: Structural Variations Of the Large-ring Cyclodextrins In Solmentioning

confidence: 99%

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Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

Gotsev¹,

Ivanov²

2007

Arkivoc

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Molecular dynamics simulations in water were performed on the three largest large-ring cyclodextrins (LR-CD) for which X-ray data is available -CD10, CD14 and CD26. The Glycam-04 force field in AMBER and explicit water molecules (TIP3P) were used in the 20.0 ns simulations. Small variations about the starting conformation of CD10 were detected. Different structural motifs were monitored for CD14 that may represent chiral species of particular interest for exploring supramolecular and chiral molecular recognition effects: broadly opened macroring, that resembles the initial geometry of CD10 but in larger scale, a big circular loop with a small helical turn, deformed figure eight conformation, and a symmetrically squeezed open form ("a dumbbell"). The final geometry of CD14 is free of additional strain introduced by band-flips. The preferred conformation of CD26 contains a small helix and an extended helical portion that transforms also to an arc and a loop. Two modifications of the equilibration step of the simulation protocol were tested.

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Section: Analysis Of Hydrogen Bonds Distributioncontrasting

confidence: 55%

Section: Structural Variations Of the Large-ring Cyclodextrins In Solmentioning

confidence: 67%

Section: Structural Variations Of the Large-ring Cyclodextrins In Solmentioning

confidence: 99%

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Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

Gotsev¹,

Ivanov²

2007

Arkivoc

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“…45,46,47,48,50,58 The results provided further support to the hypothesis for the existence of more than one cavity in LRCDs. Recent study was also conducted on CDn (n 5 24, 25, 26, 27, 28, 29) based on reasonably long 50.0 ns MD simulations.…”

supporting

confidence: 83%

“…Our earlier studies on LR-CDs, 45,47,48,58,59,88 as well as the present examination of the conformations of some other LRCDs, provided us with evidences to attempt classification (according to their preferred conformation) of the LR-CDs in the range for degrees of polymerization from 10 to 30. Open bent boat-like macrorings are the representative conformations of CD10 to CD13.…”

Section: ) According To Their Preferred Conformationsmentioning

confidence: 97%

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

Ivanov

2011

Chirality

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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.

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

2020

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Past, present, and future developments in enantioselective analysis using capillary electromigration techniques Enantioseparation of chiral products has become increasingly important in a large diversity of academic and industrial applications. The separation of chiral compounds is inherently challenging and thus requires a suitable analytical technique that can achieve high resolution and sensitivity. In this context, CE has shown remarkable results so far. Chiral CE offers an orthogonal enantioselectivity and is typically considered less costly than chromatographic techniques, since only minute amounts of chiral selectors are needed. Several CE approaches have been developed for chiral analysis, including chiral EKC and chiral CEC. Enantioseparations by EKC benefit from the wide variety of possible pseudostationary phases that can be employed. Chiral CEC, on the other hand, combines chromatographic separation principles with the bulk fluid movement of CE, benefitting from reduced band broadening as compared to pressure-driven systems. Although UV detection is conventionally used for these approaches, MS can also be considered. CE-MS represents a promising alternative due to the increased sensitivity and selectivity, enabling the chiral analysis of complex samples. The potential contamination of the MS ion source in EKC-MS can be overcome using partial-filling and counter-migration techniques. However, chiral analysis using monolithic and open-tubular CEC-MS awaits additional method validation and a dedicated commercial interface. Further efforts in chiral CE are expected toward the improvement of existing techniques, the development of novel pseudostationary phases, and establishing the use of chiral ionic liquids, molecular imprinted polymers, and metalorganic frameworks. These developments will certainly foster the adoption of CE(-MS) as a well-established technique in routine chiral analysis.

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Molecular dynamics study of the conformational dynamics and energetics of some large‐ring cyclodextrins (CDn, n = 24, 25, 26, 27, 28, 29)

Cited by 20 publications

References 60 publications

Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

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

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

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