Browsing by Author "Hadipour, N."
Now showing 1 - 4 of 4
Results Per Page
Sort Options
Item Unknown Cubane cluster surface for pyrimidine nucleobases relaxation: DFT approach(Danishgah-i Azad-i Islami, 2020-12-27) Mirzaei, M.; Hadipour, N.; Gülseren, OğuzDensity 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.Item Open Access DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs(Elsevier, 2016-08) Mirzaei, M.; Gülseren, O.; Hadipour, N.Atomic scale properties of quadrupole coupling constants (CQ) have been evaluated for singular and paired 5-fluorouracil (FU) models. Structural possibilities and properties for various types of hydrogen bonded (HB) homo pairs of FU have been investigated based on density functional theory (DFT) calculations. The models have been optimized to obtain the minimum energy level structures and only the planar molecular pairs have been considered. Various types of HB interactions have also managed the molecular shapes for the FU pairs. Different types of energies and also electron transferring properties have been investigated by the evaluated optimized properties. The atomic scale results indicated different strengths of HB interactions for FU pairs according to the changes of CQ properties for atoms in the singular and paired systems depending on the strength of interactions.Item Open Access DNA codon recognition by a cubane wire: In silico approach(DergiPark, 2021) Mirzaei, M.; Hadipour, N.; Gülseren, OğuzDNA codons, consisting of triplet nucleotides (NTs), could play important roles for RNA transcription and protein translation in living systems. Therefore, their recognition could be seen important for diagnosis and therapy purposes. Based on triplet sequence formations of Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) NTs, 64 codons were investigated in this work regarding their complexation with a molecular cubane (CUB) wire. To achieve this aim, each of singular 64 codons and CUB were optimized to be prepared for docking processes of complex formations. Hence, 64 complexes of codon-CUB were docked to see the recognition potency of CUB wire versus each of DNA codons. Interestingly, the obtained docking scores indicated that the CUB could work specifically versus the DNA codons, in which G-rich and A-rich triples were seen to be more favorable for complexation with CUB in comparison with other C-rich and T-rich triplet codons. Moreover, the results indicated that not pure G triplet but GAG codon was the most favorable one to be recognized by the CUB wire. However, pure T triplet was the worst one for such complex formations. The results of this work remarkably indicated that the CUB wire could work for recognition process of DNA codons from each other and such recognition could be very much specified for each of G-rich and A-rich codons, in which GAG codon was the best one among all the 64 investigated codons.Item Open Access Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies(Elsevier, 2016-06) Kouchaki, A.; Gülseren, O.; Hadipour, N.; Mirzaei, M.Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si12C8 and Si8C12 are constructed to be counterparts of decorated hybrid structures, FU@Si12C8 and FU@Si8C12, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si12C8 hybrids, whereas non-covalent interactions are seen for FU@Si8C12 ones. The obtained properties indicated that Si12C8 model could be considered as a better counterpart for interactions with FU structures than Si8C12 model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures.