title: Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics.
abstract: A molecular dynamics (MD)-based conformational analysis has been performed on a number of cycloalkanes in order to demonstrate the reliability and generality of MD as a tool for conformational analysis. MD simulations on cyclohexane and a series of methyl-substituted cyclohexanes were performed at temperatures between 400 and 1200 K. Depending on the simulation temperature, different types of interconversions (twist-boat-twist-boat, twist-boat-chair and chair-chair) could be observed, and the MD simulations demonstrated the expected correlation between simulation temperature and ring inversion barriers. A series of methyl-substituted 1,3-dioxanes were investigated at 1000 K, and the number of chair-chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method provided 19 out of the 20 most stable conformations found in the MM2 force field. Finally, the general performance of the MD method for conformational analysis is discussed.
authors.affiliation: Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark.
authors.forename: I T
authors.initials: IT
authors.lastname: Christensen
authors.forename: F S
authors.initials: FS
authors.lastname: Jørgensen
mesh_terms: D002151:Calorimetry; D003510:Cyclohexanes / Q000737:chemistry*; D004146:Dioxanes / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D015203:Reproducibility of Results; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D003510:Cyclohexanes; D004146:Dioxanes