Nature has developed codon as a tool to manipulate a two-electron spin symmetry (short-living electrons, forming a radical pair, arise from the Mg-bound nucleosidetriphosphate cleavage at the triplet/singlet (T/S) cro...Nature has developed codon as a tool to manipulate a two-electron spin symmetry (short-living electrons, forming a radical pair, arise from the Mg-bound nucleosidetriphosphate cleavage at the triplet/singlet (T/S) crossing), which permits or forbids further nucleotide synthesis (DNA/RNA) and the synthesis of proteins. The thesis is confirmed by conducting DFT:B3LYP (6-311G** basis set) computations (T/S potential energy surfaces) with the model system composed of the template (C-G-C-G-A nucleotide sequence) and the growing chain (G-C-G nucleotide sequence, DNA or RNA). The origin of codon is in hyperfine interaction between a single electron, transferred onto the template, and three 31P nuclei built into the phosphorus fragments of nucleotides. The nuclei, together with the polynucleotide structure, form a spiral twist that is homeomorphic to a triangle patch on the Poincare sphere. Each triangle has unique angle values depending on the nucleotide nature and their position in the codon. The patch tracing produces the Berry phase changing the electron spin orientation from “up” to “down”. The Berry phase accumulation proceeds around the (T/S) conical intersections (CIs). The CIs are a result of complementary recognition between nucleotide bases at distances exceeding the commonly accepted Watson-Crick pairing by 0.17 A. Upon changing spin symmetry, the DNA or RNA chain is allowed to elongate by attaching a newly coming nucleotide. Without complementary recognition between the bases, the chain stops its elongation. The Berry phase accumulation along the patch tracing explains the effect of Crick’s wobbling when the second nucleotide plays a primary role in recognition. The data is directly linked to creation of a quantum computing device.展开更多
A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a ...A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the .AMP- and .O- radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the .OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the .OH radical captures its hydrogen atom. The process is accompanied by producing water and the .AMP radical. The .AMP- and .AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the .AMP-..OH radical pair spin symmetry and the radius of the .OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3’ group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2’ group of ribose (RNA) . a result that nature has developed over evolution.展开更多
文摘Nature has developed codon as a tool to manipulate a two-electron spin symmetry (short-living electrons, forming a radical pair, arise from the Mg-bound nucleosidetriphosphate cleavage at the triplet/singlet (T/S) crossing), which permits or forbids further nucleotide synthesis (DNA/RNA) and the synthesis of proteins. The thesis is confirmed by conducting DFT:B3LYP (6-311G** basis set) computations (T/S potential energy surfaces) with the model system composed of the template (C-G-C-G-A nucleotide sequence) and the growing chain (G-C-G nucleotide sequence, DNA or RNA). The origin of codon is in hyperfine interaction between a single electron, transferred onto the template, and three 31P nuclei built into the phosphorus fragments of nucleotides. The nuclei, together with the polynucleotide structure, form a spiral twist that is homeomorphic to a triangle patch on the Poincare sphere. Each triangle has unique angle values depending on the nucleotide nature and their position in the codon. The patch tracing produces the Berry phase changing the electron spin orientation from “up” to “down”. The Berry phase accumulation proceeds around the (T/S) conical intersections (CIs). The CIs are a result of complementary recognition between nucleotide bases at distances exceeding the commonly accepted Watson-Crick pairing by 0.17 A. Upon changing spin symmetry, the DNA or RNA chain is allowed to elongate by attaching a newly coming nucleotide. Without complementary recognition between the bases, the chain stops its elongation. The Berry phase accumulation along the patch tracing explains the effect of Crick’s wobbling when the second nucleotide plays a primary role in recognition. The data is directly linked to creation of a quantum computing device.
文摘A new radical mechanism of nucleotide polymerization is found. The finding is based on the Car-Parrinello molecular dynamics computations at 310 K with an additional spin-spin coupling term for 31P and 1H atoms and a radical pair spin term included. The mechanism is initiated by a creation of a high-energy spin-separated Mg-ATP complex in a triplet state in which the Mg prefers an uncommon chelation to the O2-O3 oxygens of the ATP. The cleavage of the complex produces the .AMP- and .O- radicals. The latter captures a proton from acidic solution (the Zundel cation) that converts it into the .OH radical. The process agrees with the protoncoupled electron transfer (PCET) mechanism. Through interacting with the HO-C3' group of the deoxyribose/ribose the .OH radical captures its hydrogen atom. The process is accompanied by producing water and the .AMP radical. The .AMP- and .AMP radicals then interact yielding a dimer. The described mechanism is easily generalized for a bigger number of adjoining nucleotides and their type. The radical mechanism is highly sensitive to the .AMP-..OH radical pair spin symmetry and the radius of the .OH diffusion. This confines the operation of the radical mechanism: it is applicable to nucleotide polymerization through the HO-C3’ group of deoxyribose/ribose (DNA/RNA polymerization) and inapplicable through the HO-C2’ group of ribose (RNA) . a result that nature has developed over evolution.
