Conformational properties of the bacterial polyester poly(3-hydroxy-5,8-decadienoate)

Molecular dynamics simulations under different conditions and rotational isomeric states calculations are performed to understand the local and global conformational properties of the bacterial polyester poly(3-hydroxy-5,8-decadienoate). The rotational isomeric state model is incorporated with Monte Carlo simulations to calculate the dimensions and the characteristic ratio of the infinitely long chain. These calculations, performed in a vacuum, predict a Gaussian distribution for the end-to-end vector with a nonzero mean and a value of 5.5 for the characteristic ratio. Molecular dynamics simulations predict the characteristic ratio of the single chain in good solvent as 23. The role of temperature on the overall dimensions and on the distribution of dihedral angles is discussed. Radii of gyration and helix formation propensities at different temperatures and in different media are compared. The chain in solution is found to have the largest persistence length with the highest helical persistence. Results are compared with experimental and theoretical studies conducted on poly(3-hydroxybutyrate), which has the same backbone structure but a different type of side chain.