Visualization of the last one hundred steps of geometry optimization of squarine molecule based micelle done by quantum mechanical methods. Carbon atoms and their associated covalent bonds are shown as grey spheres and sticks, hydrogens are in light grey, oxygens - red, nitrogens - blue.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 1,4-bis(N,N-dimethylamino) naphthalene or a squarine, or a [Ru(bpy)2(4,4'-Me-2-2'-bpy)]2+) to pFA molecules (notation used: Me = methyl; bpy = bipyridine).
With the exception of the fatty acid molecules, the main parts of one of LANL artificial minimal living cell include a PNA double helix molecule which is covalently bonded to the 1,4-bis(N,N-dimethyl-amino)naphthalene sensitizer molecule shown at bottom-left, a pFA molecule (bottom-right), an SH anion molecule (center left). Carbon atoms and their associated covalent bonds are shown as green spheres and sticks, hydrogens are in light grey, oxygens - red, nitrogens - blue, sulfur - gold. Hydrogen bonds are depicted by dashed lines.