Cubane cluster surface for pyrimidine nucleobases relaxation: DFT approach

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 nanostruct...

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Bibliographic Details
Published inInternational journal of nano dimension Vol. 12; no. 2; pp. 135 - 144
Main Authors Mirzaei, Mahmoud, Hadipour, Nasser, Gülseren, Oğuz
Format Journal Article
LanguageEnglish
Published Witney OICC Press 01.04.2021
Subjects
Carbon
Clusters
Cubane
Density functional theory
Energy
Energy gap
Investigations
Optimization
Recognition
Thymine
Uracil
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Summary: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.
ISSN:2008-8868
2228-5059
DOI:10.22034/IJND.2021.678667