Quantum Mechanical Modeling of Self-Assembly and Photoinduced Electron Transfer in PNA-Based Artificial Living Organisms

Abstract

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.

Computational Modeling of Photoexcitation in DNA Single and Double Strands

“…3.3). Photoinduced electron transfer in a synthetic artificial mimic of DNA strands -peptide nucleic acid -was studied computationally, since it may play a key role in the evolution of life [282,356]. Making use of the excited-state properties of DNA strands, theoretical chemists have attempted to design photodriven molecular motors [357,358].…”

Molecular Spintronics Control of Photosynthesis in Artificial Cell

“…Quantum mechanical electron correlation interaction density functional theory (DFT) methods i.e., high precision quantum mechanical simulations were used to investigate various self-assembled photoactive bioorganic systems of artificial minimal living cells. [13][14][15][16][17][18][19][20][21][22] The cell systems studied in these articles are based on peptide nucleic acid (PNA) and consist of up to 400 atoms (not including the associated water solvent shells) and are about 4.5 nm in diameter.…”

“…Due to the rapid development of computers and quantum mechanical methods and program packages (such as quantum molecular dynamics), possibilities also exist to simulate the main processes of self-assembly and photosynthesis of minimal artificial cells consisting of up to 2000 atoms. [13][14][15][16][17][18][19][20][21][22] Newly synthesized programmable artificial cells or nanobiorobots are planned to be used for nanomedicine, nanoecology, and for future emerging new information technologies. Despite the really useful benefits of these artificial living technologies, one can foresee also some possible dangerous events in case such newly created artificial living cells might self-mutate and escape into the biosphere.…”

“…Due to this small size, all the active processes, including the self-assembly from component molecules, the absorption of light, and the metabolism should in principle be investigated using quantum (wave) theory. [13][14][15][16][17][18][19][20][21][22] The entire minimal cell might be considered to be a molecular electronics device that self-assembles according to quantumbased electron interaction potentials and that absorbs light and carries on its metabolism according to quantum electron excitation and tunneling equations. Therefore in this picture, the photo-induced electron charge transfer in the minimal cell may be viewed as a quantum particle-wave trace.…”

Quantum processes in 8-Oxo-Guanine-Ru(bipyridine)32+ photosynthetic systems of artificial minimal cells

“…Due to its small size, all its processes, including its self-assembly from component molecules, its absorption of light, and its metabolism, should in principle be investigated using quantum (wave) theory [4][5][6][7][8]. The entire minimal cell might be considered to be a molecular electronics device that self-assembles according to quantum-based electron interaction potentials and that absorbs light and carries on its metabolism according to quantum electron excitation and tunnelling equations.…”