Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0-4.2 nm in diameter. The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent density functional theory method, differs from spectroscopic experiments by only 0.2-0.3 nm, which is within the value of experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living cells very closely approximate realistic ones.
In order to support the creation of both artificial living organisms in the USA LANL "Protocell Assembly" project and programmable nano-biorobots in the EU "Programmable Artificial Cell Evolution" project, we used quantum mechanical (QM), density functional theory (DFT), the semiempirical PM3 method, and molecular mechanics (MM) software to investigate various complex photosynthetic systems based on peptide nucleic acid (PNA) in a water environment. Quantum mechanical DFT PBEPBE simulations, including electron correlations, confirm that water molecules that surround all the photosynthetic complex of the LANL protoorganism are main constructing factors and stabilize this system consisting of: PNA fragment attached by covalent bond sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule, lipid precursor molecule and fragment of lipid molecules mono layer. The absorption spectrum shift to the red wavelengths in the complex artificial protocell photosynthetic center might be used as the measure of the complexity of this system. The electron pi-pi* transitions in the first and third excited states are from HOMO and HOMO-1 located on the conjugated water molecules and sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO of the lipid precursor molecule as calculated using the time dependent (TD) PBEPBE/6-31G model. Electron charge tunneling in the first and third excited states should induce metabolic photodissociation of the lipid precursor molecule because of localization of the transferred electron cloud on the head (waste) of the lipid precursor molecule. TD electron correlation PBEPBE/6-31G calculations show that in the different energies of excitation, the charge transfer tunneling is from sensitizer to lipid precursor and cytosine molecules. One should note that in a water solvent, the electron charge transfer pi-pi* transition in the fifth and sixth excited state is from the HOMO and HOMO-1 located on the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO+2 located on the cytosine-PNA fragment molecule. Investigation results indicate that strong back electron tunneling from the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the cytosine molecule in the LANL artificial photosynthetic system exists.
There are presented logic gates of molecular electronics digital computers. Maximal length of these molecular electronics digital logic gates are no more than four nanometers and maximal width 2.5 nm. The results of light induced internal molecular motions in azo-dyes molecules have been used for the design of light driven logically controlled (OR, AND) molecular machines composed from organic photoactive electron donor dithieno[3,2-b:2',3'-d]thiophene and ferrocene molecules, electron accepting tetracyano-indane molecule, and moving azo-benzene molecular fragment. Density functional theory (DFT) B3PW91/6-311G model calculations were performed for the geometry optimization of these molecular electronics logical gates. Applied DFT time dependent (DFT-TD/B3PW91) method and our visualization program give absorption spectra of designed molecular gates and show from which fragments electrons are hopping in various excited states. Quantum mechanical investigations of proton Nuclear Magnetic Resonance (NMR) values of Cu, Co, Zn, Mn and Fe biliverdin derivatives and their dimers using ab initio Hartree-Fock (HF) and DFT methods indicate that these modified derivatives should generate from one to twelve Quantum Bits (QuBits). The chemical shifts are obtained as the difference of the values of the tetramethylsilane (Si(CH3)4) molecule Gauge-Independent Atomic Orbital (GIAO) nuclear magnetic shielding tensor on the hydrogen atoms and that of the magnetically active molecules. There are designed several single supermolecule and supramolecular devices containing molecular electronics digital logic gates, photoactive molecular machines and elements of molecular NMR quantum computers that allowed to design several supramolecular Control NOT NMR quantum computing gates. Self-assembling simulations of these molecular quantum computing gates induced idea of self-assembled molecular quantum supercomputer and molecular quantum computing life.
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