Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

Giuseppina Raffaini,
Fabio Ganazzoli and
Antonino Mazzaglia

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Published 14 Jan 2016

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1. Graphical Abstract
2. Scheme 1: (a) Typical structure of aCD bearing hydrophobic chains (R) at the primary side and hydrophilic cha...
  
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3. Figure 1: The aggregate of eight molecules of the aCD of Scheme 1 with n = 0, obtained from the first trial random ar...
  
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4. Figure 2: The aggregate of eight molecules of the aCD of Scheme 1 with n = 0, obtained from the second trial random a...
  
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5. Figure 3: The first trial starting arrangement of sixty-four molecules within the large cell of 123.0 Å, symm...
  
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6. Figure 4: The second trial starting arrangement of sixty-four molecules within the large cell of 123.0 Å, sym...
  
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7. Figure 5: The first final arrangement of sixty-four molecules within the large periodic cell of 123.0 Å after...
  
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8. Figure 6: The second final arrangement of sixty-four molecules within the large periodic cell of 123.0 Å afte...
  
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9. Figure 7: R_H distribution by CONTIN (and Mie scattering normalization) analysis of SC2OH dispersion (2 mg mL⁻¹...
  
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Beilstein J. Org. Chem. 2016, 12, 73–80, doi:10.3762/bjoc.12.8

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Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

Giuseppina Raffaini,
Antonino Mazzaglia and
Fabio Ganazzoli

Full Research Paper
Published 07 Dec 2015

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1. Graphical Abstract
2. Scheme 1: Structure of an aCD functionalized with hydrophobic thioalkyl C2 (R = C₂H₅) or C6 (R = C₆H₁₃) chain...
  
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3. Figure 1: The final optimized geometry of the aCD molecule in vacuo (panel a) and in explicit water (panel b)...
  
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4. Figure 2: Some relevant PDF’s calculated along the runs for the isolated aCD. a) The PDF of the glycosidic ox...
  
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5. Figure 3: The distance between the oxygen atoms of two water molecules and the c.o.m. of the aCD plotted as a...
  
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6. Figure 4: The PDF of the oxygen and of the hydrogen atoms of the water molecules (in red and in blue, respect...
  
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7. Figure 5: The pairwise initial arrangements of two amphiphilic molecules that face the two hydrophobic H grou...
  
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8. Figure 6: Final optimized geometries at equilibrium after the 30 ns MD runs obtained both in vacuo and in wat...
  
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9. Figure 7: The starting arrangements (a–c) of the four α-CD molecules (top row) and the final arrangement afte...
  
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10. Figure 8: The optimized geometry achieved by four aCD molecules in water by four molecules after the MD run. ...
  
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11. Figure 9: a) The initial random arrangement of eight molecules of the model aCD in a space-filling representa...
  
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12. Figure 10: The two aggregates obtained in water, each comprising three molecules of the model aCD, cluster A (...
  
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13. Figure 11: The PDF of the S atoms of the H groups at the primary rim (black symbols) and of the oxygen atoms o...
  
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14. Figure 12: The time change of the potential energy and of the van der Waals energy due to the dispersion and c...
  
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15. Figure 13: a) The PDF of the eight molecules of the model aCD in water as a function of their distance r from ...
  
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