Transition state analogues for nucleotidyl transfer reactions: Structure and stability of pentavalent vanadate and phosphate ester dianions

Article Abstract:

The structural and electronic similarities of both the ground state and the transition state (TS) are examined in the framework of the potential energy surfaces of the alkaline methanolysis of [(C[H.sub.3]O).sub.2]P[O.sub.2.sup.-] and [(C[H.sub.3]O).sub.2]V[O.sub.2.sup.-]. The atomic charges of the starting material and the pentavalent dianionic intermediate containing the vanadium(V) and phosphorus central atoms are calculated, which establishes a firm foundation for the design of vanadate-diester-based transition state analogues for nucleic acid synthesis and hydrolysis.

Science & research, Analysis, Electric properties, Structure, Chemical properties, Transition state (Chemistry), Potential energy, Vanadium compounds

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Phosphate ester hydrolysis in aqueous solution: associative versus dissociative mechanisms

Article Abstract:

The first systematic study of the free energy surfaces for the nonenzymatic hydrolysis of monomethyl phosphate in aqueous solution was conducted. In addition, this study examined the energetics of different reaction mechanisms and the structures and charge distributions of analogous reaction intermediates and transition states. Findings revealed that the associative and dissociative reaction pathways possess similar activation barriers for the hydrolysis of the mono- and dianionic methyl phosphates.

Phosphates, Surface energy

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Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: ab initio/Langevin dipoles study

Article Abstract:

Research was conducted to examine the potentials of mean force for the association of adenine, guanine, uracil, purine, thymine and cytosine in aqueous solution using Langevin dipoles solvation model and ab initio MP2/6-31G measurements. Using the linear relationship between entropies and binding enthalpies, the entropy contributions to the free energies for hydrogen bonding and stacking were calculated. Results indicate that pure bases are more stable than their pyrimidine-containing counterparts.

Hydrogen bonding, Hydrogen bonds, Nucleic acids, Thermodynamic potentials

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