The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Journal of the American Chemical Society vol. 126  p. 1654–1665  DOI: 10.1021/ja0356277
PMID/PMCID: 14871095 Published: 2004-02-18 

Kevin Range, Matthew J. McGrath, Xabier Lopez, Darrin M. York [ ]

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Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pKa values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions.