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Hutter, J. and Curioni, A. (2005) Car-Parrinello molecular dynamics on massively parallel computers. A European Journal of Chemical Physics and Physical Chemistry, 1, 1-12.

has been cited by the following article:

• TITLE: Spin effects govern DNA/RNA nucleotide polymerization

  AUTHORS: Alexander A. Tulub

  KEYWORDS: Radical Polymerization; Nucleotides

  JOURNAL NAME: Journal of Biophysical Chemistry, Vol.2 No.3, August 9, 2011

  ABSTRACT: 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.