The coenzyme Q (CoQ) molecule plays a critical role in the biochemical generation of energy in the form of adenosine triphosphate. Various types of CoQ can be classified according to their number of isoprenoid units in the tail. In human beings, CoQ10 is produced and is necessary for the basic functioning of cells. CoQ10 exists in two forms, as ubiquinone (UQ) and as ubiquinol (UQH2), which have different roles in the body. Molecular dynamics (MD) simulations for the analysis of the effects of solvents on the structure of the UQ molecule are presented. Besides, semi-empirical molecular orbital PM3 calculation is applied to obtain structural and electronic properties of both the UQ and the UQH2 molecules. According to the MD simulation, the UQ molecule seems to be flexible both in vacuum and in water. On the other hand, the molecule stays more rigid in methanol. PM3 calculations show that both molecules are quite hydrophobic. Furthermore, UQ is chemically more reactive than UQH2, but the latter is kinetically more stable than the former.