Solution conformation and hydrogen bonding of α-CD in aqueous solution (CHARMM molecular dynamics simulations).

Cyclodextrins cyclo[D-Glcp α(1→4)]_n with n = 6

Hydration Shell
hsp1	hsp2	hsp3	hsp4	hsh1	hsh2	hsh3	hsh4
Cavity Water
cav1	cav2	cav3	cav4
Hydrogen Bonding Propability
hbo0	hbo1	hbo2	hbo3	hbo4	hbo5	hbo6
Water Distributions
toct	trac	ellp	diff	isoc	den1	den2

Comparison of the natural cyclodextrins with six (α-CD), seven (β-CD), eight (γ-CD), and nine units (δ-CD); all X-ray or neutron-diffraction crystal structures.

Cyclodextrins cyclo[D-Glcp α(1→4)]_n with n = 6-9

α-CD (n = 6)
mlp1	mlp2	mlp3	mlp4	mlp5	mlp6
β-CD (n = 7)
mlp1	mlp2	mlp3	mlp4	mlp5	mlp6
γ-CD (n = 8)
mlp1	mlp2	mlp3	mlp4	mlp5	mlp6
δ-CD (n = 9)
mlp1	mlp2	mlp3	mlp4	mlp5	mlp6

Image Notes
mlp1	View on the 2-OH/3-OH (left) and 6-CH2OH side (right) of the torus; models were rotated bye 180 deg. around a vertical axis. The same scale was applied for all compounds, except δ-CD was reduced by ca. 15%.
mlp2	Orientation according to pictures *mlp1, half opened models
mlp3	View on the 2-OH/3-OH side in closed and bisected form each.
mlp4	View on the 6-CH2OH side in closed and bisected form each.
mlp5,6	Side view models with all 2-OH and 3-OH groups pointing up, and the 6-CH2OH groups pointing down, in closed and bisected form each.

For details see:

Molecular Modeling of Saccharides, Part IX. On the Hydrophobic Characteristics of Cyclodextrins: Computer-Aided Visualization of Molecular Lipophilicity Patterns. F. W. Lichtenthaler and S. Immel, Liebigs Ann. Chem. 1996, 27-37.
Abstract

In the first row, the cyclodextrins with five (left side each) and six glucose units (right side) are shown (all PIMM91-structures). In the second row, the unnatural small ring cyclodextrins with three (upper left), four (upper right), and five (lower left) residues are compared to the natural α-cyclodextrin (lower right); PIMM91-structures respectively. The third row depicts the natural cyclodextrins with six (α-CD, upper left), seven (β-CD, upper right), eight (γ-CD, lower left), and nine units (δ-CD, lower right); all X-ray or neutron-diffraction crystal structures. The forth row display the permethylated α- (left) and β-CD (right), X-ray geometries.

Cyclodextrins cyclo[D-Glcp α(1→4)]_n with n = 3-9

n = 5,6
sld	mlp1	mlp2	mlp3	mlp4	mlp5	mlp6
n = 3-6
sld	mlp1	mlp2	mlp3	mlp4	mlp5	mlp6	mlp7	strain
n = 6-9 (natural α-, β-, γ-, and δ-cyclodextrin)
sld	mlp1	mlp2	mlp3	mlp4	mlp5	mlp6	mlp7
rib1	rib3	rib2	rib4	riba	ribc	ribb	ribd
n = 6,7 (per-O-methylated α- and β-cyclodextrin)
sld	mlp1	mlp2	mlp3	mlp4	mlp5	mlp6

Image Notes
sld	Dreiding models and molecular Surfaces in dotted form, view on the 2-OH and 3-OH side of the torus
mlp1	View on the 2-OH and 3-OH side of the torus
mlp2	View on the 2-OH and 3-OH side, half opened models
mlp3	View on the 6-CH2OH side
mlp4	View on the 6-CH2OH side, half opened models
mlp5	Side view models with all 2-OH and 3-OH groups pointing up, and the 6-CH2OH groups pointing down
mlp6	View as in "*mlp5", with a different depth of slice through the surface
mlp7	View as in "*mlp5", with a different depth of slice through the surface
strain	Cyclo-α(1→4)-glucotrioside: fragmental energetic contributions of angle bending (left), dihedral distortions (center), and van der Waals interactions (right) to the total PIMM91-strain energy (red: high internal strain energies, violet: unstrained molecular fragments, view as in "*sld")

For details see:

Molecular Modeling of Saccharides, Part IX. On the Hydrophobic Characteristics of Cyclodextrins: Computer-Aided Visualization of Molecular Lipophilicity Patterns. F. W. Lichtenthaler and S. Immel, Liebigs Ann. Chem. 1996, 27-37.
Abstract

Molecular Modeling of Saccharides, Part VI. Small Ring Cyclodextrins: their Geometries and Hydrophobic Topographies. S. Immel, J. Brickmann, and F. W. Lichtenthaler, Liebigs Ann. Chem. 1995, 929-942.
Abstract