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Ueda, Hitoshi; Wakisaka, Masahiro; Nagase, Hiromasa; Takaha, Takeshi; Okada, Shigetaka

doi:10.1023/a:1023063718215

Cited by 27 publications

(11 citation statements)

References 5 publications

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“…Physicochemical properties such as solubility in water for LR-CDs with 9-50 D-glucopyranose units also have been presented to date (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). The existence of LR-CDs with up to several hundred D-glucopyranose units has also been revealed (21)(22)(23)(24)(25)(26)(27).…”

Section: B Physicochemical Properties and Molecular Structures Of Lr-cdmentioning

confidence: 99%

“…i) HPLC analysis is used as purity test for LR-CD (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). When it is carried out, the use of at least two kinds of columns with different separation modes, such as an ODS column and amino column, is required due to the contamination of branched CD.…”

Section: Saccharomyces Cerevisiaementioning

confidence: 99%

“…Refractive index and electrochemical detectors are usually used. ii) Molecular weight is measured by fast atom bombardment(FAB) mass spectrometry using glycerin or Magic bullet as matrix (10)(11)(12)(13)(14), matrix assisted laser desorption/ionization (MALDI) time-offlight (TOF) mass spectrometry using 2,5-dihydroxy benzoic acid (gentisic acid) as matrix (16)(17)(18)(19)(20)81), and electrospray (ESI) TOF mass spectrometry (83). iii) The structure of the macrocycle is determined by 1 H, 13 C and two-dimensional NMR (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20).…”

Section: Saccharomyces Cerevisiaementioning

confidence: 99%

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Large-ring Cyclodextrins

Endō¹

2011

TIGG

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Cyclodextrin (CD) is the common name for cyclic α-1,4-glucans; α-, β-and γ-CD, which are composed of 6, 7, 8 D-glucopyranose units, are well-known. However, most scientists have not recognized large-ring cyclodextrins (LRCDs) composed of more than 9 D-glucopyranose units until recently, although the existence of LR-CDs containing 9-13 D-glucopyranose units in macrocycle was reported about a half century ago. The characteristics of LR-CDs have been studied for the last quarter century, and they are still relatively new materials. In this minireview, the unique characteristics of LR-CDs, including molecular structure, physicochemical properties and inclusion complex formation ability, are discussed. Preparation and purification methods are also reviewed.

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Section: B Physicochemical Properties and Molecular Structures Of Lr-cdmentioning

confidence: 99%

Section: Saccharomyces Cerevisiaementioning

confidence: 99%

Section: Saccharomyces Cerevisiaementioning

confidence: 99%

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Large-ring Cyclodextrins

Endō¹

2011

TIGG

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“…A new class of compounds, the large‐ring cyclodextrins (LR‐CDs) 1 attracted attention in recent years. Advances were marked by the study of their physicochemical properties 2, in spite of existing difficulties in their synthesis 3–5, isolation, and purification 6–8. LR‐CDs were first prepared by French et al 9.…”

Section: Introductionmentioning

confidence: 99%

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Gotsev

Ivanov

2006

Int J of Quantum Chemistry

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Molecular dynamics (MD) simulations in water solution were performed on six large ring cyclodextrins (LR-CDs) with a degree of polymerization (DP) 24,25, 27,28,29, and 30, using as starting structures geometries derived from CD26, which was studied previously by MD. The present research was aimed at further extending our knowledge on the structural dynamics and the energetics of this new class of compounds, focusing on several representatives flanking CD26, the largest LR-CD for which X-ray data are available. The most recent parameterization for carbohydrates, Glycam-04, and explicit water molecules (TIP3P) were used in the 10.0-ns simulations. Preceding 10.0-ns simulations of CD26, with the AMBER parm99 force field, revealed that the overall shape of the macromolecule did not change significantly during the last 5.0-ns simulations. We now further test for the probability of prevalence of this conformation by using a different force field and by examining the effect of the size of the macro-ring on the preferred conformations of LR-CDs with DP within a range of 24 -30. Indeed, we found CD26-like geometries present for CD25, CD27, and CD28, which could be interpreted as an indication for an enhanced stability of the CD26 conformation in water solution. Again, we witnessed high flexibility of the macrocycles, and different local structural motifs were detected: twisted helical double parallel strand (CD25, CD30), single helix of three turns (CD29), a spiral (CD25, CD27, CD30), open-shaped loops and helical turns (CD28; "CD26-like geometry"), a rectangular cavity (CD24), a triple-lobe fragment (CD29) or a portion shaped like a jaw (CD24, CD27), and an overall shape of the macromolecule that resembled a butterfly (CD27) or "X" (CD28). Thus, we conclude that the same conformation of CD26 could be also the preferred conformation in water solution of other LR-CDs with DP in the close vicinity of 26. Wiley Periodicals, Inc. Int J Quantum Chem 107: 1657-1672, 2007 Key words: cyclodextrins; molecular dynamics; conformational analysis; AMBER Introduction A new class of compounds, the large-ring cyclodextrins (LR-CDs) [1] attracted attention in recent years. Advances were marked by the study of their physicochemical properties [2], in spite of existing difficulties in their synthesis [3][4][5], isolation, and purification [6 -8]. LR-CDs were first prepared by French et al. [9]. The crystal structure determinations of the CDs composed by 9 [10], 10 [11], 14 [7, 11a], and 26 [12] glucose units provided information on the conformations of these molecules in the crystal lattice. New structural motifs were detected, and it became evident that their geometries differ considerably from the native CDs (i.e., those composed of 6, 7, and 8 glucose units). More recently, the thermal and structural characterization of ␦-CD, -CD, and -CD have been carried out [13], and references to CDs with more than 60 [14] and several hundred [15] glucose units have been made. The 13 C nuclear magnetic resonance (NMR) spectra in D 2 O at...

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“…The large-ring cyclodextrins (LR-CDs; CDs with a degree of polymerization (DP) higher than eight), [1][2][3][4][5] have attracted attention in recent years, and advances were marked in the study of their physicochemical properties, [6][7][8][9][10][11][12][13][14][15] in spite of existing difficulties in their synthesis, isolation and purification. The existence of LR-CDs has been proven by the isolation of these products from the action of 4-α-glucanotransferases on amylose and amylopectin, 2 almost a century after the first evidence for the existence of cyclodextrins.…”

Section: Introductionmentioning

confidence: 99%

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

2015

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The conformations of some 'giant' cyclodextrins (CDn, n = 40, 70, 85, 100) were examined by molecular dynamic simulations using the Glycam06 force field. CD14 and CD26, the largest cyclodextrins, for which crystallographic data are available, were also studied as reference structures. Principal component analysis was used for the analyses of the simulation trajectories. In cases where band-flips were not present in the starting geometry (e.g. CD40), flips appeared later during the conformational search. The results for CDn (n = 14, 26, 40) confirmed an interesting observation for the distribution of band-flips along the perimeters of the macrorings, namely, band-flips separate portions of lengths of about six or twelve glucoses. This allows the formation of energetically favorable small loops of six-seven glucoses or the creation of short two-turns single helices that further enhance the stability of the structures. It was found that flip dihedrals define distributions of fragment lengths 12-6, 12-12, and 12-12-6 residues in the larger CDs (CD70, CD85, CD100). Contributions from 77% (CD40) to 88% (CD26) are from the first three highest-eigenvalue principal components, i.e., a limited number of modes determine the overall deformations of the macrorings. The flexibility of the macrorings increases, going from CD40 to the CDs, with higher degrees of polymerization. CD14 and CD26 present interesting cases - CD26 manifests domination of one deformation mode (ca. 72%), whereas CD14 demonstrates significantly higher flexibility. These results confirm our earlier conclusion, namely, LR-CDs may have more than one cavity. Thus they have the potential to accommodate more than one substrate molecule, as well as larger species by an 'induced fit' mechanism.

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Cited by 27 publications

References 5 publications

Large-ring Cyclodextrins

Large-ring Cyclodextrins

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

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

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