Hydration And Metal Cations Effects On The DNA Base Pairs

The effects of the first hydration shell and the bulk solvation effects on the proton-transfer processes of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are studied based on density functional theory, using the B3LYP method and DZP++basis set. The proton-transfer mechanisms of AT and GC base pairs in bulk solvation are that first single-proton transfer (SPT1) and stepwise double proton transfer coexist. When only the first hydration shell surrounded by five water molecules (AT·5H2O, GC·5H2O), or both the first hydration shell and bulk solvation effects through polarizable continuum model (PCM)(AT·5H2O+PCM, GC·5H2O+PCM) are considered, only the first single-proton-transfer mechanism (SPT1) is found. The proton-transfer activation energies of AT and GC base pairs show that the majority of the hydration effects come from the first hydration shell through hydrogen-bond interactions, therefore the first hydration shell greatly influences the base pair structures and proton-transfer mechanism.Using the same calculation method of AT and GC base pair to calculate the influence of the first hydration shell by one and four water on the proton-transfer processes of adenine-thymine anions (AT) and guanine-cytosine anions (GC). The proton H3transfer reaction is found for all the hydrated adenine-thymine anions (AT)-·H2O and (AT)-·4H2O. The proton H6a is found to transfer for both (AN7T)-·H2O and (An3T)-·H2O. The double-proton transferred pathway is found when one water molecule interacts with the02atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The hydration energy of the (AT)4H2O is approximately four times of the (AT)·HaO. The two single-proton transferred pathways are found in the hydrated guanine-cytosine anions (GC)-·H20and (GC)-·4H2O. The proton H1transferred leads to change in the bonds connected to hydrogen bonds, all of the proton transfer processes are exothermic. After the proton H4a transfer, the significant geometry perturbations occur in cytosine ring and the bonds connected to hydrogen bonds. All of the proton transfer processes are endotermic; the energies of the transition states almost equal the proton transfer products, which is not conducive to the H4a proton transfer. All of the guanine and cytosine moieties maintain the same plane after and before the proton transfer. The reaction energy changes of (AT)·H2O、(AT)·4H2O、(GC)·H20and (GC)·4H2O reveal that the first hydration shell play important roles in the proton transfer reaction. The effects of the metal cations Li+、Be2+and the solvation of Li+、Be2+on the proton-transfer processes of adenine-thymine anion (AT)-and guanine-cytosine anion (GC)-base pairs are studied based on density functional theory, using the B3LYP/6-31++g(d,p) method. The double-proton transferred pathway are found when Li+、(H2O)3Li+、Be2+and (H2O)3Be2+interact with the N7atom of adenine, respectively. This result is different from the proton transfer pathway in the anion (AT)-Compared with the metal cations Li+is added on the N7of adenine, the proton H3transfer reaction is more possible while the metal cations Be2+is adsorbed and the reaction product is more stable. The proton H1transfer reaction is found for all the four structures. The proton H4a is only found to transfer for (H2O)2Li+(GC)-.All of the H1proton transfer processes are exothermic and the reaction products are more stable than the conventional structures. The structural change of guanine-cytosine anion is greater during the H1proton transfer process of (H2O)2Be2+(GC)-...