Structural, energetic, and dynamical properties of rotaxanes constituted of α-cyclodextrins and an azobenzene chain

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 1, 2007, Pages 104-116

  Briquet, Ludovic ^a   Staelens, Nicolas ^a   Leherte, Laurence ^a   Vercauteren, Daniel P ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

Azobenzene; Cyclodextrin; Energy profile; Molecular dynamics; Molecular mechanics; Rotaxane

Indexed keywords

COMPUTER SIMULATION; CYCLODEXTRINS; ENERGY BARRIERS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; SYNTHESIS (CHEMICAL);

DECOMPLEXATION; ENERGY PROFILE; ROTAXANE;

AZOBENZENE;

ALPHA CYCLODEXTRIN; AZOBENZENE DERIVATIVE; MOLECULAR MOTOR; ROTAXANE;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATION; ENERGY TRANSFER; ISOMER; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SUPRAMOLECULAR CHEMISTRY;

ALPHA-CYCLODEXTRINS; AZO COMPOUNDS; COMPUTER SIMULATION; HYDROGEN BONDING; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; ROTAXANES; SOLVENTS; THERMODYNAMICS;

EID: 34250878435     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.10.001     Document Type: Article

References (57)

1. Balzani V., Credi A., Raymo F.M., and Stoddart J.F. Artificial molecular machines. Angew. Chem. Int. Ed. 39 (2000) 3348-3391
2. Harada A. Cyclodextrin-based molecular machines. Acc. Chem. Res. 34 (2001) 456-464
3. Schalley C.A., Beizai K., and Vögtle F. On the way to rotaxane-based molecular motors: studies in molecular mobility and topological chirality. Acc. Chem. Res. 34 (2001) 465-476
4. Clemente-León M., Marchioni F., Silvi S., and Credi A. Photoactive pseudorotaxanes and rotaxanes as artificial molecular machines. Synth. Met. 139 (2003) 773-777
5. Anelli P.L., Spencer N., and Stoddart J.F. A molecular shuttle. J. Am. Chem. Soc. 113 (1991) 5131-5133
6. Ashton P.R., Ballardini R., Balzani V., Credi A., Dress K.R., Ishow E., Kleverlaan C.J., Kocian O., Preece J.A., Spencer N., Stoddart J.F., Venturi M., and Wenger S. A photochemically driven molecular-level abacus. Chem. Eur. J. 6 (2000) 3558-3574
7. Jun S.I., Lee J.W., Sakamoto S., Yamaguchi K., and Kim K. Rotaxane-based molecular switch with fluorescence signaling. Tetrahedron Lett. 41 (2000) 471-475
8. Elizarov A.M., Chiu S.-H., and Stoddart J.F. An acid-base switchable [2]rotaxane. J. Org. Chem. 67 (2002) 9175-9181
9. Stanier C.A., Alderman S.J., Claridge T.D.W., and Anderson H.L. Unidirectional photoinduced shuttling in a rotaxane with a symmetric stilbene dumbbell. Angew. Chem. Int. Ed. 41 (2002) 1769-1772
10. Qu D.H., Wang Q.C., Ren J., and Tian H. A light-driven rotaxane molecular shuttle with dual fluorescence addresses. Org. Lett. 6 (2004) 2085-2088
11. Stewart D.R., Ohlberg D.A.A., Beck P.A., Chen Y., Williams R.S., Jeppesen J.O., Nielsen K.A., and Stoddart J.F. Molecule-independent electrical switching in Pt/organic monolayer/Ti devices. Nano Lett. 4 (2004) 133-136
12. Murakami H., Kawabuchi A., Matsumoto R., Ido T., and Nakashima N. A multi-mode-driven molecular shuttle: photochemically and thermally reactive azobenzene rotaxanes. J. Am. Chem. Soc. 127 (2005) 15891-15899
13. Anderson S., Claridge T.D.W., and Anderson H.L. Azo-dye rotaxanes. Angew. Chem. Int. Ed. 36 (1997) 1310-1313
14. Craig M.R., Claridge T.D.W., Hutchings M.G., and Anderson H.L. Synthesis of a cyclodextrin azo dye [3]rotaxane as a single isomer. Chem. Commun. 16 (1999) 1537-1538
15. Michels J.J., O'Connell M.J., Taylor P.N., Wilson J.S., Cacialli F., and Anderson H.L. Synthesis of conjugated polyrotaxanes. Chem. Eur. J. 9 (2003) 6167-6176
16. Szejtli J. Cyclodextrin Technology (1988), Kluwer, Dordrecht
17. In: Davies J.E.D. (Ed). Spectroscopic and Computational Studies of Supramolecular Systems (1992), Kluwer, Dordrecht
18. Lipkowitz K.B. Applications of computational chemistry to the study of cyclodextrins. Chem. Rev. 98 (1998) 1829-1874
19. Cramer F., Saenger W., and Spatz H.-C. Inclusion compounds. XIX. The formation of inclusion compounds of α-cyclodextrin in aqueous solutions. Thermodynamics and kinetics. J. Am. Chem. Soc. 89 (1967) 14-20
20. Kaifer A.E. Interplay between molecular recognition and redox chemistry. Acc. Chem. Res. 32 (1999) 62-71
21. Pose-Vilarnovo B., Perdomo-López I., Echezarreta-López M., Schroth-Padro P., Estrada E., and Tores-Labandeira J.J. Improvement of water solubility of sulfamethizole through its complexation with β- and hydroxypropyl-β-cyclodextrin-characterization of the interaction in solution and in solid state. Eur. J. Pharm. Sci. 13 (2001) 325-331
22. Leherte L., Latour T., and Vercauteren D.P. Topological analysis of electron density maps for chiral cyclodextrin-guest complexes: a steric interaction evaluation. Supramol. Sci. 2 (1995) 209-217
23. Wu A., Shen X., and He Y. Investigation on γ-cyclodextrin nanotube induced by N,N′-diphenylbenzidine molecule. J. Colloid Interf. Sci. 297 (2006) 525-533
24. Topchieva I.N., Tonelli A.E., Panova I.G., Matuchina E.V., Kalashnikov F.A., Gerasimov V.I., Rusa C.C., Rusa M., and Hunt M.A. Two-phase channel structures based on α-cyclodextrin-polyethylene glycol inclusion complexes. Langmuir 20 (2004) 9036-9043
25. Bonnet P., Jaime C., and Morin-Allory L. Structure and thermodynamics of α-, β-, and γ-cyclodextrin dimers. Molecular dynamics studies of the solvent effect and free binding energies. J. Org. Chem. 67 (2002) 8602-8609
26. Nascimento Jr. C.S., Anconi C.P.A., Dos Santos H.F., and De Almeida W.B. Theoretical study of the α-cyclodextrin dimer. J. Phys. Chem. A 109 (2005) 3209-3219
27. Bortolus P., and Monti S. Cis-trans photoisomerization of azobenzene-cyclodextrin inclusion complexes. J. Phys. Chem. 91 (1987) 5046-5050
28. Sanchez A.M., and de Rossi R.H. Effect of β-cyclodextrin on the thermal cis-trans isomerization of azobenzenes. J. Org. Chem. 61 (1996) 3446-3451
29. * transitions in some hydroxyazo guests having a naphtalene nucleus. J. Chem. Soc., Perkin Trans. 2 2 (1999) 379-386
30. Liu Y., Zhao Y.-L., Chen Y., and Guo D.-S. Assembly behavior of inclusion complexes of β-cyclodextrin with 4-hydroxyazobenzene and 4-aminoazobenzene. Org. Biomol. Chem. 3 (2005) 584-591
31. Briquet L., Vercauteren D.P., Perpète E.A., and Jacquemin D. Is solvated trans-azobenzene twisted or planar?. Chem. Phys. Lett. 417 (2006) 190-195
32. Barbiric D.J., Castro E.A., and de Rossi R.H. A molecular mechanics study of 1:1 complexes between azobenzene derivatives and β-cyclodextrin. J. Mol. Struct. (Theochem.) 532 (2000) 171-181
33. Barbiric D.J., de Rossi R.H., and Castro E.A. Inclusion complexes of 1:2 stoichiometry between azobenzenes and cyclodextrins: a molecular mechanics study. J. Mol. Struct. (Theochem.) 537 (2001) 235-243
34. Sohlberg K., Sumpter B.G., and Noid D.W. Semi-empirical study of a prototype rotaxane-based molecular shuttle. J. Mol. Struct. (Theochem.) 491 (1999) 281-286
35. Castruonovo G., Elia V., Fessas D., Velleca F., and Viscardi G. Thermodynamics of the interaction of α-cyclodextrin with monocarboxylic acids in aqueous solutions: a calorimetric study at 25 °C. Carbohydr. Res. 287 (1996) 127-138
36. Gadre A., Rüdiger V., Schneider H.-J., and Connors K.A. Binding of cyclodextrins to alicyclic and aromatic substrates: complex formation of α-, β-, and γ-cyclodextrins with substituted cyclohexanecarboxylic acids and phenylalkanoic acids. J. Pharm. Sci. 86 (1997) 236-243
37. Lino A.C.S., Takahata Y., and Jaime C. α- and β-cyclodextrin complexes n-alkyl carboxylic acids and n-alkyl p-hydroxy benzoates. A molecular mechanics study of 1:1 and 1:2 associations. J. Mol. Struct. (Theochem.) 594 (2002) 207-213
38. Faucci M.T., Melani F., and Mura P. Computer-aided molecular modeling techniques for predicting the stability of drug-cyclodextrin inclusion complexes in aqueous solutions. Chem. Phys. Lett. 358 (2002) 383-390
39. Choi Y., and Jung S. Molecular dynamics simulations for the prediction of chiral discrimination of n-acetylphenylalanine enantiomers by cyclomaltoheptaose based on the MM-PBSA approach. Carbohydr. Res. 339 (2004) 1961-1966
40. Grabuleda X., and Jaime C. Molecular shuttles. A computational study (MM and MD) on the translational isomerism in some [2]rotaxanes. J. Org. Chem. 63 (1998) 9635-9643
41. Grabuleda X., Ivanov P., and Jaime C. Computational studies on pseudorotaxanes by molecular dynamics and free energy perturbation simulations. J. Org. Chem. 68 (2003) 1539-1547
42. Grabuleda X., Ivanov P., and Jaime C. Shuttling process in [2]rotaxanes. Modeling by molecular dynamics and free energy perturbation theory. J. Phys. Chem. B 107 (2003) 7582-7588
43. Tinker 4.0, User's Guide (2003), J.W. Ponder
44. Allen F.H. The Cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr. B 58 (2002) 380-388
45. Klar B., Hingerty B., and Saenger W. Topography of cyclodextrin inclusion complexes. XII. Hydrogen-bonding in the crystal structure of α-cyclodextrin hexahydrate: the use of multicounter detector in neutron diffraction. Acta Crystallogr. B 36 (1980) 1154-1165
46. Freeman H.S., Mc Intoch S.A., and Singh P. X-ray crystal structure of diazo dyes. Part 2. Derivatives of C.I. disperse yellow 23 and C.I. disperse orange 29. Dye Pigm. 35 (1997) 149-164
47. Materials Studio, Getting Started, Version 2.2 (2002), Accelrys Inc., San Diego
48. Allinger N.L., Yuh Y.H., and Lii J.H. Molecular mechanics. The MM3 force field for hydrocarbons, 1. J. Am. Chem. Soc. 111 (1989) 8551-8566
49. 2. Acta Crystallogr. C 39 (1983) 1121-1123
50. Mostad A., and Roemming C. Refinement of the crystal structure of cis-azobenzene. Acta Chem. Scand. 25 (1971) 3561-3568
51. Fliegl H., Köhn A., Hättig C., and Ahlrichs R. Ab initio calculation of the vibrational and electronic spectra of trans- and cis-azobenzene. J. Am. Chem. Soc. 125 (2003) 9821-9827
52. Stepanić V., Baranović G., and Smrečki V. Structure and vibrational spectra of conjugated acids of trans- and cis-azobenzene. J. Mol. Struct. 569 (2001) 89-109
53. Czerminski R., and Elber R. Reaction path study of conformational transitions in flexible systems: applications to peptides. J. Chem. Phys. 92 (1990) 5580-5601
54. Nakamura S., Hirose H., Ikeguchi M., and Doi J. Conformational energy minimization using a two-stage method. J. Phys. Chem. 99 (1995) 8374-8378
55. Eisenberg D., and McLachlan A.D. Solvation energy in protein folding and binding. Nature 319 (1986) 199-203
56. Desiraju G.R., and Steiner T. The Weak Hydrogen Bond (1999), Oxford Science Publication
57. Jeffrey G.A., and Saenger W. Hydrogen Bonding in Biological Structures (1994), Springer, Berlin