We used quantum mechanical (QM) electron correlation interactions density functional theory (DFT) methods (i.e. high precision quantum mechanical simulations) to investigate various self-assembled photoactive bioorganic systems of artificial minimal living cells [1-13]. The cell systems studied are based on peptide nucleic acid (PNA) and consisted of up to 360 atoms (not including the associated water or methanol solvent shells) and are up to 3.0-4.2 nm in diameter. The electron correlations interactions originating the hydrogen bonds and Van der Waals weak chemical bonds that increase due to the addition of a polar solvent (water or methanol) molecules, and fatty acid (FA) and precursor fatty acid (pFA) molecules play a critical role in the QM interaction based self-assembly of the photosynthetic center and functioning of the photosynthetic processes of the artificial minimal living cells. The distances between the separated sensitizer, precursor fatty acid, and water or methanol molecules are comparable to Van der Waals and hydrogen bonding radii. As a result these nonlinear quantum interactions compress the overall system resulting in a smaller gap between the HOMO and LUMO electron energy levels and photoexcited electron tunneling occurs from the sensitizer (either a 1,4-bis(N,N-dimethylamino) naphthalene or a [Ru(bpy)2(4,4'-Me-2-2'-bpy)]2+) to pFA molecules (notation used: Me = methyl; bpy = bipyridine).
The electron tunneling and associated light absorption of most intense transitions as calculated by the time dependent density functional theory (TD DFT) method differs from spectroscopic experiments by only 0.3 or 0.2 nm, which is within the value of experiment errors [10]. This agreement implies that the quantum mechanically self-assembled structures of minimal living cells very closely approximate the realistic ones.
One successful example: we have performed calculations using TD DFT PBEPBE model with the 6-31G basis set together with COSMO water solvent model installed on our research group dual processor Opteron servers Linux cluster of the difference of electron charge density (excited-state - ground-state) for the conjugated cytosine-1,4-bis(N,N-dimethylamino)naphthalene supermolecule and six fatty acid, and two pFA molecules, and visualized the electron charge tunneling associated with certain excited state transitions.