Arvydas Tamulis

Vilnius University

We have found self-assembly of four neurotransmitter acetylcholine (ACh) molecular complexes in a water molecules environment by using geometry optimization with DFT B97d method. These complexes organizes to regular arrays of ACh molecules possessing electronic spins, i.e. quantum information bits. These spin arrays could potentially be controlled...

Quantum entangled processes are demonstrable contributors to biological systems and their origins. Through specific process analysis of the papers: Quantum entanglement in photoactive prebiotic systems and Quantum Dynamics of Self-Assembly of Minimal Photosynthetic Cells an Integrated Informational Theoretic approach will be applied. Once extended...

Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information...

The dynamics of quantum mechanical self-assembly of two separate supramolecular systems, i.e., two minimal cells each containing two different photosynthetic centres (1) and (2) were investigated by means of semiempirical and density functional theory methods (DFT) using the electron correlation approach. These two bi cellular systems consist of 71...

Electron correlation time dependent density functional theory (TD-DFT) was used to investigate various self-assembled photoactive quantum entangled supramolecular systems. The prebiotic kernel contains provitamin D and sensitizer (1,4-bis(N,N-dimethylamino)naphthalene) attached covalently to a oxo-guanine nucleotide and the precursor of fatty acid...

We read in the Book of Genesis [1:11]: Then God said, "Let the earth put forth vegetation: plants yielding seed, and fruit trees of every kind on earth that bear fruit with the seed in it." And it was so. Let us remind that The Old Testament was written in symbolic language understandable for the readers which lived few thousands years ago. It is i...

The quantum mechanical self-assembly of two separate photoactive supramolecular systems with different open electronic shell photosynthetic centers was investigated by means of density functional theory methods. These photoactive prebiotic kernel systems are based on two different photoactive neutral radical sensitizer molecules: (5-(4-(1-hydroxyet...

This paper contains the review of quantum entanglement investigations in living systems, and in the quantum mechanically modelled photoactive prebiotic kernel systems. We define our modelled self-assembled supramolecular photoactive centres, composed of one or more sensitizer molecules, precursors of fatty acids and a number of water molecules, as...

In this work, a supramolecular quantum mechanical self assembly of two minimal-protocells (micelles) containing 696 atoms is studied using density functional theory and its time dependent version. This two micelles system is initially optimized using semiempirical PM3 method. Their frontier molecular orbitals are analyzed using DFT-PBEPBE/6-311++G(...

Quantum density functional theory studied photosynthetic system consists of photoelectron donor neutral radical molecule (5-(4-(1-hydroxyethyl)phenyl)pentanoic acid (1), a precursor of fatty acid (pFA, 2-oxo-2-phenylethyl ester) molecule and water molecules. The system include an explicitly simulated aqueous environment consisting of some 155 atoms...

The quantum mechanical self-assembly of two separate photoactive supramolecular systems with different photosynthetic centers was investigated by means of density functional theory methods. Quantum entangled energy transitions from one subsystem to the other and the assembly of logically controlled artificial minimal protocells were modeled. The sy...

Density functional theory methods were used to investigate self-assembled photoactive bioorganic system of interest for logically controlled artificial minimal cell. The cell system studied is based on cytosine and noncanonical oxo-guanine nucleobases and consisted of up to 366 atoms and are up to 2.5 nm in diameter. The electron correlation intera...

Quantum chemical ab initio calculations and investigations of trans- and cis-stilbene, Disperse Orange 3 (D03) and several organic photoelectron donor, electron acceptor molecules and their supermolecules connected via the electron insulator bridges were performed using Hartree-Fock (HF) and density functional theory (DFT) methods. The optimized gr...

Quantum mechanical electron correlation density functional theory methods were used to investigate various self-assembled photoactive bioorganic systems of interest for artificial minimal cells. The cell systems studied are based on nucleotides or their compounds and consisted of up to 123 atoms (not including the associated water or methanol solve...

Density functional theory methods were used to investigate various self-assembled photoactive bioorganic systems of interest for artificial minimal cells. The cell systems studied are based on nucleotides or their compounds and consisted of up to 123 atoms (not including the associated water or methanol solvent shells) and are up to 2.5 nm in diame...

We used quantum mechanical nonlocal gradient electron correlation interactions density functional theory methods to investigate various self-assembled photoactive bioorganic systems of artificial minimal living cells. The cell systems studied are based on sensitizer squarine, 8-oxo-guanine, cytosine, fatty acid, water molecules and consisted of aro...

Quantum mechanical based electron correlation interactions among molecules are the source of the weak hydrogen and Van der Waals bonds that are critical to the self-assembly of artificial fatty acid micelles. Life on Earth or elsewhere could have emerged in the form of self-reproducing photoactive fatty acid micelles, which gradually evolved into n...

What is minimal life, how can we make it, and how can it be useful? We present experimental and computational results towards bridging nonliving and living matter, which results in life that is different and much simpler than contemporary life. A simple yet tightly coupled catalytic cooperation between genes, metabolism, and container forms the des...

The first comprehensive general resource on state-of-the-art protocell research, describing current approaches to making new forms of life from scratch in the laboratory. Protocells offers a comprehensive resource on current attempts to create simple forms of life from scratch in the laboratory. These minimal versions of cells, known as protocells,...

Quantum mechanical self-assembly of artificial minimal living cells were studied. These cells are based on peptide nucleic acid and are 3.5-4.5 nanometers in diameter. The electron tunneling and associated light absorption of most intense transitions as calculated by time dependent density functional theory method differs from spectroscopic experim...

Artificial living cells and their substructures are self-assembling due to electron correlation interactions among biological and water molecules which leads to appearing the attraction dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen b...

The calculation data of four systems of two Cm molecules performed using a semiempirical CNDO/S - CI method obtained show three new, additional bands: 342.9 - 364.5, 427.3 - 437.1 and 481.6 - 495.9 nm not found in the calculations of single C60 molecule and charge transfer band in the system of two C60 molecules and two small charges.

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 bo...

Quantum Mechanical Molecular Physics Approach Quantum Modeling of Water and Fatty Acid–Dependent Photoinduced Electron Transfer in PNA-Based Protocells Conclusions References

Neutral radical molecules as qubit systems for quantum information processing are described and the application of quantum chemistry methods in search of suitable radicals is outlined. An exemplifying calculation of the relevant magnetic properties of neutral radicals is presented and the suitability of these compounds as building blocks for a quan...

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 investi...

The quantum mechanical investigations of the one isomer of aza‐fullerene molecules have been performed. The investigation of the NMR spectra indicate that adducts and presence of PyO and HCl molecule leads to separation of NMR spectra.

Quantum mechanical investigations were performed to find a suitable sensitizer to peptide nucleic acid monomer with thymine and cytosine basis. It was found that the 1,4-dihydroquinoxaline and 7,8-dimethylisoalloxazine molecules could be used as a sensitizer. The low quantum yield efficiency could be due to the formation of different geometrical st...

Applying the time-dependent density functional theory (TD-DFT) method the design of molecular logical functions from the dithieno[3,2-b:2,3-d]thiophene (thiophene) and azo-dye Disperse Orange 3 (DO3) molecules joined with various electron-insulator bridges is performed. Based on the results of the investigations, the main design rules for the selec...

The neutral radical of dodecyl syringate is suggested as a can- didate for molecular Electron Spin Resonance (ESR) quantum,computers. The first principle of quantum,chemical calculations indica tes that this mo- lecule with a stable delocalised electron spin may represent a qubit in quan- tum information processing. The spin density analysis exhibi...

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,...

The mechanism and conditions of meso-tetra (4-sulfonatophenyl) porphine (TPPS4) molecular aggregate formation and their geometrical structure are investigated by methods of molecular mechanics and quantum chemistry. J- type aggregates are formed of zwitterionic forms of TPPS4 via interaction of their positively charged porphyrin rings and negativel...

The quantum mechanical investigations of the PyO and aza-fullerne molecules have been performed. The investigation of the NMR spectra indicate enought well separated lines that allow us the aza-fullerene with adducts accepted as derivative generating up to 14 qubits of NMR quantum computer. The PyO molecule properties are exibited as applying for q...

The mechanism and conditions of meso-tetra (4-sulfonatophenyl) porphine (TPPS4) molecular aggregate formation and their geometrical structure are investigated by methods of molecular mechanics and quantum chemistry. J- type aggregates are formed of zwitterionic forms of TPPS4 via interaction of their positively charged porphyrin rings and negativel...

Quantum chemical ab initio investigations with full geometrical optimizations of dianion and monoanion fluorescein molecules in the ground state were performed by applying the density functional theory (DFT) B3PW91/6-311G** model to clarify the difference in the geometrical and electronic structure of the dianion molecule and that of monoanion in i...

Implementation of quantum information processing based on spatially localized electronic spins in stable molecular radicals is discussed. The necessary operating conditions for such molecules are formulated in self-assembled monolayer (SAM) systems. As a model system we start with 1, 3 -diketone types of neutral radicals. Using first principles qua...

Quantum m echanically designed hardware of molecular electronics digital and NMR quantum computers are presented in this article. The results of light induced internal molecular motions in azo-dyes molecules have been used for the design and density functional theory time-dependent (DFT-TD) calculations of light driven logically controlled (OR func...

There are presented several two and three variable 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 [1-3] have been used for the design of light d...

Quantum mechanically designed hardware of molecular NMR and ESR quantum computers are presented. Maximal lengths of these quantum information processing logic gates are no more than few nanometers. There are designed several single supermolecule and supramolecular devices containing biliverdin derivatives and their dimers. Composition of molecular...

The design applying the density functional theory time dependent (DFT-TD) method of molecular OR logical functions from the ditiHeno[3,2-b:2′,3′-d]thiophene and azo-dye Disperse Orange 3 (DO3) molecules joined with various electron-insulator bridges are performed. The obtained results of the geometry optimization indicate the similarity of the spat...

Quantum mechanical investigations of hydrogen and nitrogen atom Nuclear Magnetic Resonance (NMR) values of Cu, Co, Zn, Mn and Fe biliverdin derivatives and their dimers and aza—fallerene C48N12 adducts using ab initio and first principle methods indicate that these modified derivatives should generate from one to seven and eleven, twelve, eighteen,...

Density functional theory time dependent (DFT-TD) model B3PW91/6-311G** calculations of azo-dye Disperse Orange 3 (DO3) molecule show that in radiationless, first and fourth transitions, electron charge moves out from -N=N- bridge, which supports our recently found per linear trans-cis isomerization way. The results of light induced internal molecu...

During the last decade, molecular electronics calls for electronic properties at the molecular level. The molecular device designs may be performed basing on photo-isomerization properties of azo-dye molecules. Various azo-dye derivatives are used in the technology of density optical data storage and when compared with other kinds of storage, they...

The geometrical structure of both the ground and excited state of the azo-dyes: Disperse Orange 3 (DO3) and Ch2- C4H4-N=N-C44/H(subscript 4-CH2 molecules have been investigated applying the Hartree Fock (HF), density functional theory (DFT) methods with the Berny geometry optimization and Ames Laboratory determinant (ALDET)single- double-triple-qua...

The geometrical structure of both the ground and excited state of the azo-dyes: Disperse Orange 3 (DO3) and Ch2- C4H4-N=N-C44/H(subscript 4-CH2 molecules have been investigated applying the Hartree Fock (HF), density functional theory (DFT) methods with the Berny geometry optimization and Ames Laboratory determinant (ALDET)single- double-triple-qua...

Quantum chemical ab initio calculations and investigations of several organic photoelectron donor, electron acceptor molecules and their supermolecules connecting via the electron insulator bridges were performed using Hartree-Fock (HF) and density functional theory (DFT) methods. The optimized ground state geometry was as initial optimizing geomet...

The quantum chemical investigations of the Disperse Orange 3 (D03) molecule isomerization through linear transition state has been assumed and investigated when -N=N- bond broken in the first excited state was not obtained. The one- and many electron energy diagrams have been drawn. It is shown that crossing between active one electron-state takes...

Ab initio quantum chemical investigations of the oxidative P–O coupling of white phosphorus and alcohol have been carried out by the model platinum complexes [PtCl3(CH3OH)(η2-P4)]+ (1), [PtCl3(CH3OH)(η2-P4)]− (2), [PtBr3(CH3OH)(η2-P4)]+ (3), [PtBr3(CH3OH)(η2-P4)]− (4) and [PtClBr2(CH3OH)(η2-P4)]+ (5) applying the B3PW91 model of density functional...

Quantum chemical ab initio calculations along with full geometry optimizations of Disperse Orange 3 (DO3), molecule in the ground state of the trans and cis conformations and carbazole (Cz), phenylenediamine molecules were performed applying the method of density functional theory (DFT). The obtained geometry of the ground state was used as initial...

Geometry and energy of formation of single molecules: fullerene C60, CS2 and tetrathiofulvalene (TTF) and their complexes: C60 +CS2 and C60 +TTF were obtained using Hartree-Fock (HF) and Density Functional Theory methods in various basis sets. Weak chemical interactions were estimated enough well using HF/6-31G for a comparison of various geometric...

Quantum chemical ab initio calculations along with full geometry optimizations of Disperse Orange 3 (DO3), molecule in the ground state of the trans and cis conformations and carbazole (Cz), phenylenediamine molecules were performed applying the method of density functional theory (DFT). The obtained geometry of the ground state was used as initial...

Quantum chemical ab initio investigations of the stability of the non-covalent fullerene complexes: C60 molecule + Li atom, two C60, two C60 + CS2, C60 + CS2, C60 + C6H6 were performed using Hartree-Fock (HF) and Density Functional Theory (DFT) methods in various basis sets. The inclusion of electron correlation effect calculated by using DFT B3PW9...

The molecular implementation of two variable logic functions: OR, NOR, AND, NAND and basic elements of molecular cellular automata and neuromolecular networks was described. The design of the basic elements of molecular computers was based on the semiempirical quantum chemical calculations of organic photoactive electron donor, electron acceptor an...

The quantum mechanical investigations of fullerene C24, C26, C28 molecule conformers are performed in the framework of the point set group theory and semiempirical PM3 configuration interaction and the MNDO, AMI methods. The main criterion of stability of calculated fiillerene molecules we state the lowest total energy of various isomers and confor...

The quantum chemical calculations of the photodonor molecules: carbazole (Cz), dimetilphenylenediamine (DMePhDA), paraphenildiamine (PPhDA), photoacceptor molecules: 2,4,7-trinitro-9fluorenone (TNF), 2,4,5,7-tetranitro-fluorenone (TeNF), 2,4,7-trinitro-9-dicyano-fluorene (TN9(CN)2F), 2,4,5,7-tetranitro-9-dicyano-fluorene (TeN9(CN)2F), 1,2,4,5-tetra...

Quantum chemical investigations of the electronic structure of the design carbazole (Cz) containing supermolecules, supramolecules, single charge donor and acceptor molecules were performed in the framework of the semiempirical neglect of differential overlap (MNDO) method. The data obtained show that it is a small charge redistribution in Cz-(CH2)...

Quantum chemical investigations of the electronic structure of the design carbazole (Cz)-containing supermolecules, supramolecules, oligovinylcarbazole (OVK) and oligoepoxypropylcarbazole (OEPK) were performed in the framework of the semiempirical modified neglect of differential overlap (MNDO) method. The data obtained show that donor-acceptor pro...

Self-formation in molecular nanotechnology is based on interaction between organic and biological molecules. Selection rules of the distinct interactions of the symmetric and topologically similar molecule self-formation are investigated.

Chemical modification of aluminum and copper surfaces and the adsorption of peroxidase (HRPO E.C. 1.11.1.7) onto these surfaces have been investigated using Fourier Transform Infrared Spectroscopy (FT-IR). The pretreatment of an aluminum surface with titanium tetrachloride increases the activity of adsorbed peroxidase by a factor of 7. An additiona...

Two identical molecules with overlapping molecular orbitals are considered in the Hartree-Fock approximation as a single system, that is, the intermolecular orbital of the system is regarded as a linear combination of molecular orbitals belonging to one randomly degenerate level of both molecules. Analysis of the subsystem of equations obtained for...

) Quantum mechanical density functional theory nonlocal gradient electron correlation interactions methods are used for investigations of various self-assembled photoactive fatty acid micelles. The micelle systems studied are based on a photoactive squarine sensitizer, an 8-oxo-guanine electron donor, cytosine, a fatty acid and its precursor (pFA)...

This report results from a contract tasking Institute of Theoretical Physics and Astronomy as follows: The contractor will investigate quantum mechanical design of light-driven, single supermolecular logically-controlled machines and molecular computing devices based on fullerene and photoactive molecules and supermolecules. New two- or three-varia...

Hypothetical qubit system designed for quantum information processing based on spatially ordered organic radicals (S = 1=2) in self-assembled monolayer is described and application of quantum chemistry methods in search of suitable radicals is outlined. Exemplifying calculation of relevant magnetic properties of diketo type neutral radicals is pres...

Artificial minimal living cells and their substructures are quantum mechanically self-assembling due to competition of weak electrostatic forces and weak attraction Van der Waals dispersion forces, and hydrogen bonds originated due to electron correlation interactions among biological and water molecules. The best available method to simulate in mi...