Calculation of the minimum energy conformation of biomolecules using a global optimization technique I. Methodology and application to a model molecular fragment (Normal pentane)

Abstract

The conformational energy of a molecule is minimized with respect to interatomic distances using Bremermann's method of unconstrained global optimization (1970). The optimal set of distances is then used for calculating the preferred conformation of the molecule. A simultaneous optimization of all the dihedral angles is achieved. The classical potential function is used in this study. An illustration of the method is given by applying it to normal pentane, which is a commonly occurring fragment of biomolecules. Results show that, for the standard geometry (bond lengths and bond angles), the all- trans) conformation is the preferred one. However, fluctuations of the geometry within the limits of the vibrational spectra can lead to preferred conformations that are not necessarily all- trans.