Molecular orbital computations on lipids: modular numbering

Abstract

Ab initio molecular orbital calculations have been carried out on selected phospholipids models to explore their structural properties. A modular numbering of constituent molecular components has been employed to effectively model all MDCA-predicted conformers. This system defines a phospholipid into five fragments consisting of the glycerol, the phosphate group (for phospholipids) and three substituents (X-group and two fatty acid chains). Each fragment is converted into distinct section of an internal coordinates matrix. The relative spatial orientation of all atoms in a given fragment will all be defined in an explicit manner. With a multi-lipid system, several of these modules may be used as a macro-module representing one lipid molecule. Subsequently, several macro-modules may be assembled into a lipid bilayer model. All macro-modules may then be combined to create an internal coordinate matrix describing a multi-lipid system without the loss of an explicit definition of every 3N-6 degree of freedom as well as intermolecular coupling and interaction. Molecular orbitals computations are completed on four selected conformations of glycerol. The results reveal that the dihedral values are not ideal as predicted by MDCA, implying that dihedrals properties are coupled to other inter-atomic interactions within the glycerol module.