Host-guest interactions influence stability of the rebek "tennis ball" dimer complex

Journal of Organic Chemistry

Volumn 63, Issue 22, 1998, Pages 8027-8030

  Evans, David A ^a   Evans, John Spencer ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 2142816275     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo9809581     Document Type: Article

References (15)

1. Rebek J., Jr. Chem. Soc. Rev. 1996, 255.
2. Whitesides, G. M.; Mathias, J. P.; Seto, C. T. Science 1991, 254, 1312.
3. Branda, N.; Wyler, R.; Rebek, J., Jr. Science 1994, 265, 1267.
4. Branda, N.; Grotzfeld, R. M.; Valdes, C.; Rebek., J., Jr. J. Am. Chem. Soc. 1995, 117, 85.
5. Allen, M. P.; Tildesley, D. J. In Computer Simulation of Liquids; Oxford Science Publications: Oxford, 1987; p 71.
6. Fox, T.; Thomas, B. E., IV; McCarrick, M.; Kollman, P. A. J. Phys. Chem. 1996,100, 10779.
7. -4 kcal/ mol. Point charges were assigned using the standard methodology for the CVFF force field. This results in the chloroform molecule having an appropriate dipole moment, and negatively charged chlorine atoms and positively charged carbon and hydrogen atoms as described elsewhere (Jorgensen, W. L.; Briggs, J. M.; Contreras, M. L. J. Phys. Chem. 1990, 94, 1683;
8. Kovacs, H.; Kowalewski, J.; Laarksonen, A. J. J. Phys. Chem. 1990, 94, 7378;
9. 6 where the chlorine atoms are positively charged. Solvation was performed by placing the dimer complex in the center of a pre-equilibrated box of chloroform molecules (box dimensions: X=Y = Z = 40 Å, α = β= γ = 90°), and then removing any contacts closer than 3 Å.
10. BIOSYM/Molecular Simulations Inc, San Diego, CA, 1995.
11. Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. Proteins: Structure Function and Genetics 1988, 4, 31.
12. Molecular dynamics simulations were performed for a period of 500 ps, with a time step of 1 fs, using periodic boundary conditions. The coupling constant for the temperature bath was 200 fs. System information, coordinates, velocities, and energetic properties were recorded every 20 fs. A spherical cutoff of 15 Å was applied to the nonbond forces with a 17 Å cutoff used to calculate the neighbor list. The dimer cavity diameter is within these cutoffs (i.e., 12.5 Å). Equilibration runs were performed on each system prior to the final simulations as follows. "E-dimer" system (100 ps total equilibration time): for the first 50 ps interval, the dimer was constrained and the solvent was allowed to move. In the second 50 ps interval, all constraints were removed. "C-dimer" and "n-dimer" systems (200 ps total equilibration time): for the first 50 ps interval, the host-guest complex was constrained and the solvent was permitted to move. For the second 50 ps interval, the guest was permitted to move, but the solvent and host were constrained. For the third 50 ps interval, the host-guest complex was allowed to move, but the solvent was constrained. For the final 50 ps interval, all constraints were removed.
13. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
14. Osguthorpe, D. J.; Dauber-Osguthorpe, P. ,7. Mol. Graph. 1992, 10, 178.
15. Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946.