Vilnius University research group used quantum mechanical (QM) nonlocal
gradient electron correlation interactions density functional theory
(DFT) methods to investigate various self-assembled photoactive
bioorganic systems of artificial minimal living cells. 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. This agreement implies that the quantum mechanically self-assembled structures of minimal living cells very closely approximate the realistic ones.
Quantum mechanical electron correlation experiments of self-assembly of above described artificial minimal living cells show that these cells are complex systems because only entire ensemble of PNA, and sensitizer, and pFA, and FA and water molecules is stable and perform quantum photosynthetic processes. Removing the small part of nucleobase, FA and water molecules leads to the structural changes in comparison with realistic structures and difference in comparison with the spectroscopic values of photoexcited electron tunneling from sensitizer (1,4-bis(N,N-dimethylamino)naphthalene to pFA molecules. QM electron correlation experiments of self-assembly of artificial minimal living cells removing the main part of nucleobase, and FA and water molecules leads to the degradation of these cells. We can state what the inclusion of ever more water, and fatty acid, and pFA molecules, and waste pieces of the pFA molecules and nucleobase molecules in the different artificial minimal living cells results in a shift of the absorption spectrum to the red for the artificial protocell photosynthetic centre, leading to an ever closer approach to the real experimental value and indicates the measure of the complexity of this quantum complex system, i.e. a minimal protocell. It is important to say that only QM electron correlation TD-DFT experiments with minimal living cells gives results exactly comparable with spectroscopic results and all other more simplified QM methods such as local gradient DFT or ab initio Hartree-Fock gives structures and spectra far from the experimentally measured.
The corresponding of experimental absorption spectra peaks and our QM calculated confirm that our chosen method of designing single electron nano photocells might be useful not only for artificial living organisms but also for wide implementation in the nano photodevices, and molecular computers.
We have created molecular electronics logic gates regulating the photosynthesis, growing and dividing of artificial living cells and nanobiorobots. It was performed the study of G-C self-assembling energies in various H2O molecules clusters correlating these energies with the G-C dehybridization energies due to charge transfer in the H2O molecules clusters surrounded the photosynthetic center of artificial minimal living cell controlled by the last chain of genome, i.e. hydrogen bonded G-C supramolecule.
Implementation of quantum information bits based on spatially localized electron spins in stable molecular radicals was investigated by unrestricted time dependent functional theory methods. The g-tensor shift calculations of neutral radical molecules was performed for beta-diketone and syringate. beta-diketone neutral radical moiety with an attached hydrocarbon chain. Beta-diketone is suitable for construction of quantum computing processing devices because the qubit is relatively stable due to the small magnitude of g-tensor shift component that is aligned with the external magnetic field, i.e. the direction of hydrocarbon chain which provide the self-assembled monolayer an attachment of the molecule to a substrate.
TD DFT simulations of the artificial minimal living cells with implemented molecular electronics and spintronics gates done using self-assembled neutral radical molecules beta-diketone and syringate show that it is possible to construct more general ContrlNOT and NAND logic functions suitable for the production of the nanobiorobots. Analysis of time dependent density functional theory method calculated absorption spectrum and images of electron transfer trajectories in the different excited states allow to separate two different logically controlled functions of molecular device consisting of guanine-cytosine-PNA-1,4-dihydroquinoxaline-1,4-bis(N,N-dimethylamino)naphthalene supermolecule and Van der Waals bonded precursor of fatty acid molecule. These two different logically controlled functions of artificial minimal living cells are: 1) initiation of metabolic fatty acid production in five excited states or 2) initiation of gene dehybridization in one excited state. This designed supermolecule works in the artificial minimal cell as molecular electronics classic OR logic function (Boolean logics OR gate). Designed of variety of the molecular spintronics devices will regulate photosynthesis and growth of artificial minimal living cells in the conditions of external magnetic fields, while also providing a perspective of the requirements for success in the synthesis of new forms of artificial living organisms.
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. This agreement implies that the quantum mechanically self-assembled structures of minimal living cells very closely approximate the realistic ones.
Quantum mechanical electron correlation experiments of self-assembly of above described artificial minimal living cells show that these cells are complex systems because only entire ensemble of PNA, and sensitizer, and pFA, and FA and water molecules is stable and perform quantum photosynthetic processes. Removing the small part of nucleobase, FA and water molecules leads to the structural changes in comparison with realistic structures and difference in comparison with the spectroscopic values of photoexcited electron tunneling from sensitizer (1,4-bis(N,N-dimethylamino)naphthalene to pFA molecules. QM electron correlation experiments of self-assembly of artificial minimal living cells removing the main part of nucleobase, and FA and water molecules leads to the degradation of these cells. We can state what the inclusion of ever more water, and fatty acid, and pFA molecules, and waste pieces of the pFA molecules and nucleobase molecules in the different artificial minimal living cells results in a shift of the absorption spectrum to the red for the artificial protocell photosynthetic centre, leading to an ever closer approach to the real experimental value and indicates the measure of the complexity of this quantum complex system, i.e. a minimal protocell. It is important to say that only QM electron correlation TD-DFT experiments with minimal living cells gives results exactly comparable with spectroscopic results and all other more simplified QM methods such as local gradient DFT or ab initio Hartree-Fock gives structures and spectra far from the experimentally measured.
The corresponding of experimental absorption spectra peaks and our QM calculated confirm that our chosen method of designing single electron nano photocells might be useful not only for artificial living organisms but also for wide implementation in the nano photodevices, and molecular computers.
We have created molecular electronics logic gates regulating the photosynthesis, growing and dividing of artificial living cells and nanobiorobots. It was performed the study of G-C self-assembling energies in various H2O molecules clusters correlating these energies with the G-C dehybridization energies due to charge transfer in the H2O molecules clusters surrounded the photosynthetic center of artificial minimal living cell controlled by the last chain of genome, i.e. hydrogen bonded G-C supramolecule.
Implementation of quantum information bits based on spatially localized electron spins in stable molecular radicals was investigated by unrestricted time dependent functional theory methods. The g-tensor shift calculations of neutral radical molecules was performed for beta-diketone and syringate. beta-diketone neutral radical moiety with an attached hydrocarbon chain. Beta-diketone is suitable for construction of quantum computing processing devices because the qubit is relatively stable due to the small magnitude of g-tensor shift component that is aligned with the external magnetic field, i.e. the direction of hydrocarbon chain which provide the self-assembled monolayer an attachment of the molecule to a substrate.
TD DFT simulations of the artificial minimal living cells with implemented molecular electronics and spintronics gates done using self-assembled neutral radical molecules beta-diketone and syringate show that it is possible to construct more general ContrlNOT and NAND logic functions suitable for the production of the nanobiorobots. Analysis of time dependent density functional theory method calculated absorption spectrum and images of electron transfer trajectories in the different excited states allow to separate two different logically controlled functions of molecular device consisting of guanine-cytosine-PNA-1,4-dihydroquinoxaline-1,4-bis(N,N-dimethylamino)naphthalene supermolecule and Van der Waals bonded precursor of fatty acid molecule. These two different logically controlled functions of artificial minimal living cells are: 1) initiation of metabolic fatty acid production in five excited states or 2) initiation of gene dehybridization in one excited state. This designed supermolecule works in the artificial minimal cell as molecular electronics classic OR logic function (Boolean logics OR gate). Designed of variety of the molecular spintronics devices will regulate photosynthesis and growth of artificial minimal living cells in the conditions of external magnetic fields, while also providing a perspective of the requirements for success in the synthesis of new forms of artificial living organisms.