Theoretical Study On The Interactions Of The Nucleotides With The Metal Lons

It is well known metal ions play a crucial role in organism. Thereforeinteractions between metal ions and biomolecules arouse widespread concern.Nucleotide is the basic structural unit of nucleic acids, which participates in almost allof the biochemical reactions. Nucleotide consists of three parts: a part of phosphoricacid, pentose and base ring. Metal ions can interact with the oxygen atom of thephosphate, the oxygen atom of the pentose and the C, N, O atoms of the heterocyclicbase.We use the density functional theory (DFT) calculations to study the preferentialbinding sites of the Mg²⁺, Mn²⁺, Ca²⁺, Na⁺ and K⁺ on the AMP, GMP, CMP, and TMPat the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) level. Five typical adsorptionmotifs are gotten: central-binding (type I), between phosphate and base (type II),between phosphate and furanose (type III), between furanose and base (type IV), andat the outer edge of base (type V) were obtained and analyzed for the AMP and GMPcompounds. The most stable binding site of metal ion for the AMP is type I, and thatfor the GMP is type II. In the CMP ? and TMP ? metal ion, which have only onecarbon-nitrogen ring, while there are two carbon-nitrogen rings for the AMP andGMP. The most obvious characteristic is the disappearance of the isomers of type III.For the CMP? and TMP?metal ion compounds the most stable binding sites for thebivalent ions Mg²⁺, Mn²⁺ and Ca²⁺ are type I and those for the monovalent ions Na⁺and K+ are type II. The ion binding stability order is Mg²⁺ > Mn²⁺ > Ca²⁺ > Na⁺ > K⁺for all the AMP, GMP, CMP and TMP compounds, and the Mg²⁺ and Mn²⁺ showsome similarities in their structures and interaction energies. As for electronicproperties, we calculated the vertical excitation energies, NBO charges and bondorders of the metal ion nucleotide compounds. The changes of the vertical excitationenergies all attribute to the change of the conjugation in the metal ion nucleotidecompounds. Our work is expected to provide useful information for understanding thestructures and stability of metal ions nucleotide compounds.