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The Schlegel-Frisch ab initio molecular dynamics (ADMP) (DFT:B3LYP), T = 310 K, is used to study complexation between adenosinetriphosphate (ATP), ATP subsystem, and magnesium cofactor [Mg(H 2 O) 6 ] 2+ , Mg subsystem, in a water pool, modeled with 78 water molecules, in singlet (S) and triplet (T) states. The computations prove that the way of ATP cleavage is governed by the electron spin of Mg. In the S state Mg prefers chelation of --phosphate oxygens (O1-O2), whereas in the T state it chelates --phosphate oxygens (O2-O3) or produces a single-bonded intermediate. Unlike the chelates, which initiate ionic reaction paths, the single-bonded intermediate starts off a free-radical path of ATP cleavage, yielding a highly reactive adenosinemonophosphate ion-radical, •AMP -, earlier observed in the CIDNP (Chemically Induced Dynamic Nuclear Polarization) experiment (A.A. Tulub, 2006). The free-radical path is highly sensitive to Mg nuclear spin, which through a hyperfine interaction favors the production of unpaired electron spins. The unique role of Mg in ATP cleavage comes through its ability to serve as a unique redox center, initially accepting an electron from ATP and then giving it back to products. Redox activity of Mg differs for T and S states and affects the number of coordinated water molecules. The findings give a new insight into the NTP (N = nucleoside) energetics and assembly of NTP-operating molecules, including proteins.

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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.

DFT:B3LYP ab initio molecular dynamics (MD) approach is used to elucidate the properties of the Zundel and Eigen, H5O2+ and H9O4+, proton complexes in the triplet state. The simulation considers the complexes in the gas phase (isolated complexes) and inside the clusters composed of 32, 64, and 128 water molecules, mimicking the behavior of aqueous solutions. MD simulations reveal three distinct periods. For the complex in solutions, the periods are smoothed out. The H5O2+ and H9O4+ complexes in the triplet state undergo structural rearrangements, which eventually result in hydrogen elimination. For the H5O2+, the hydrogen is eliminated from the center of the water cluster, whereas for the H9O4+ it is removed from a near-surface water molecule. The rate of hydrogen elimination decreases with increasing the number of water molecules surrounding the complex.