Cubane cluster surface for Pyrimidine nucleobases relaxation: DFT approach

Document Type : Reasearch Paper


1 Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.

2 Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.

3 Department of Chemistry, Tarbiat Modares University, Tehran, Iran.

4 Department of Physics, Bilkent University, Ankara, Turkey.


Density functional theory (DFT) approach was employed to investigate relaxation processes of each of pyrimidine nucleobases (NBs); cytosine (C), thymine (T) and uracil (U), at the Cubane Cluster Surface (CCS). The main idea was about providing a material for recognition of NBs, in which a nanostructure form of cubane (CCS) was first generated by optimization process. In the next step, relaxation processes of each of NBs at the surface were investigated to examine the function of such system for NBs recognition. The results indicated that the electronic based molecular properties could work as proper parameters for recognizing such molecular system, in which energy gap (EG) could be referred for the purpose. Measuring EG could help to recognize the complexes of CCS-C, CCS-T and CCS-U from each other. Strength of such complex formations was investigated using values of binding energy (BE); CCS-U > CCS-C > CCS-T. Total results of EG, BE and additional atomic scale properties indicated that the investigated CCS could work very well to recognize U as the characteristic NB of RNA.


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