Structural characteristics of amylose in solution and basic energetic features of amylose inclusion complexes with synthetic polymers have been investigated by means of molecular modeling techniques and molecular dynamics (MD) simulations. Using a helical model, the dynamic behavior of V-Amylose in mixtures of water and DMSO was simulated, particularly employing the number of the glycans intramolecular hydrogen bonds as an indicator for the structures helix character. The results parallel the assumption that an increasing percentage of DMSO results in increasing helical stability, which can be attributed to the increased steric demand and the inferior H bond capabilities of DMSO molecules as compared to water molecules. However, given a long enough simulation time, the helical structure of amylose is lost in water as well as in DMSO, yielding a random orientation of the polysaccharide strand. In this process, OH6-OH2/OH3 H bonds are preferentially broken as compared to OH2-OH3 H bonds. On the basis of these results the stability of amylose inclusion complexes was investigated by modeling V-amylose complexes with long-chain hydrocarbon molecules of a varying number of included ether groups. The resulting complexes were evaluated by means of molecular dynamics simulations and were rated in terms of their Gibbs energy of complex formation by the approximation method of the linear interaction energy (LIE). The results show an almost linear correlation between the size of the ligands hydrophilic surface area and their free enthalpy of complex formation. In this way, experimental results from Kaneko et al. concerning the polymer series PTHF, PTO, PEO are reproduced demonstrating the accuracy of the employed procedure. The value of the system specific LIE coefficient could approximately be determined in this context.