Cubane cluster surface for Pyrimidine nucleobases relaxation: DFT approach

International Journal of Nano Dimension

مقاله 6، دوره 12، شماره 2، تیر 2021، صفحه 135-144   

نوع مقاله: Reasearch Paper

شناسه دیجیتال (DOI): 10.22034/ijnd.2021.678667

نویسندگان

Mahmoud Mirzaei^{* 1، 2}؛ Naser Hadipour³؛ Oğuz Gulseren⁴

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

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

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

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

چکیده

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.

کلیدواژه‌ها

Cluster؛ Cubane؛ DFT؛ Nucleobase؛ Recognition

مراجع

1. Iijima S., (2002), Carbon nanotubes: Past, present, and future. Physica B. 323: 1-5.

2. Mirzaei M., Kalhor H. R., Hadipour N. L., (2011), Covalent hybridization of CNT by thymine and uracil: A computational study. J. Mol. Model. 17: 695-699.

3. Kulnitskiy B. A., Mordkovich V. Z., Karaeva A. R., Urvanov S. A., Blank V. D., (2020), Cubic and tetragonal maghemite formation inside carbon nanotubes under chemical vapor deposition process conditions. Fuller. Nanotube. Carbon Nanostruct. 28: 913-918.

4. Chu D., Liu Y., Li Y., Liu Y., Cui Y., (2020), Journey to the holy grail of coordination saturated Buckyball. Inorg. Chem. Front. 142: 7584-7590.

5. Alijani H., Tayyebi S., Hajjar Z., Shariatinia Z., Soltanali S., (2017), Prediction of the Carbon nanotube quality using adaptive neuro–fuzzy inference system. Int. J. Nano Dimens. 8: 298-306.

6. Biegasiewicz K. F., Griffiths J. R., Savage G. P., Tsanaktsidis J., Priefer R., (2015), Cubane: 50 years later. Chem. Rev. 115: 6719-6745.

7. Li B. T., Jiang J. J., Li L. L., Peng J., (2020), Thermal stability and detonation character of nitroso-substituted derivatives of cubane. Mol. Phys. Article: e1834157.

8. Mansoori G. A., George T. F., Assoufid L., Zhang G., (2007), Molecular Building Blocks for Nanotechnology: From Diamondoids to Nanoscale Materials and Applications. Springer Science & Business Media.

9. Huang H. T., Zhu L., Ward M. D., Wang T., Chen B., Chaloux B. L., Wang Q., Biswas A., Gray J. L., Kuei B., Cody G. D., (2020), Nanoarchitecture through Strained molecules: Cubane-derived scaffolds and the smallest carbon nanothreads. J. Am. Chem. Soc. 142: 17944-17955.

10. Watson J. D., Crick F. H., (1953), Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature. 171: 737-738.

11. Heller C., (2001), Principles of DNA separation with capillary electrophoresis. Electrophores. 22: 629-643.

12. Nikfar Z., Shariatinia Z., (2020), Tripeptide arginyl-glycyl-aspartic acid (RGD) for delivery of Cyclophosphamide anticancer drug: A computational approach. Int. J. Nano Dimens. 11: 312-336.

13. Crick F. H., Watson J. D., (1956), Structure of small viruses. Nature. 177: 473-475.

14. Gelderblom H. R., Hausmann E. H., Özel M., Pauli G., Koch M. A., (1987), Fine structure of human immunodeficiency virus (HIV) and immunolocalization of structural proteins. Virolog. 156: 171-176.

15. Boopathi S., Poma A. B., Kolandaivel P., (2020), Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. J. Biomol. Struct. Dyn. 2020: 1-10.

16. Jiao J., Duan C., Xue L., Liu Y., Sun W., Xiang Y., (2020), DNA nanoscaffold-based SARS-CoV-2 detection for COVID-19 diagnosis. Biosens. Bioelec. 167: 112479-112485.

17. Mirzaei M., Elmi F., Hadipour N. L., (2006), A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: A density functional theory study. J. Phys. Chem. B. 110: 10991-10996.

18. Mirzaei M., Hadipour N. L., Ahmadi K., (2007), Investigation of C–H… OC and N–H… OC hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters. Biophys. Chem. 125: 411-415.

19. Mirzaei M., (2013), Uracil-functionalized ultra-small (n, 0) boron nitride nanotubes (n= 3–6): Computational studies. Superlat. Microstruct. 57: 44-50.

20. Mirzaei M., Kalhor H. R., Hadipour N. L., (2011), Investigating purine-functionalised carbon nanotubes and their properties: A computational approach. IET Nanobiotechnol. 5: 32-35.

21. Faramarzi R., Falahati M., Mirzaei M., (2020), Interactions of fluorouracil by CNT and BNNT: DFT analyses. Adv. J. Sci. Eng. 1: 62-66.

22. Harismah K., Ozkendir O. M., Mirzaei M., (2020), Lithium adsorption at the C20 fullerene-like cage: DFT approach. Adv. J. Sci. Eng. 1: 74-79.

23. Mirzaei M., (2013), Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. Int. J. Nano Dimens. 3: 175-179.

24. Naderi E., Mirzaei M., Saghaie L., Khodarahmi G., Gulseren O., (2017), Relaxations of methylpyridinone tautomers at the C60 surfaces: DFT studies. Int. J. Nano Dimens. 8: 124-131.

25. Mirzaei M., Meskinfam M., Yousefi M., (2012), Covalent hybridizations of carbon nanotubes through peptide linkages: a density functional approach. Comput. Theor. Chem. 981: 47-51.

26. Mirzaei M., (2020), Science and engineering in silico. Adv. J. Sci. Eng. 1: 1-2.

27. Gaussian 09, Revision D.01, Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Petersson G. A., Nakatsuji H., Li X., Caricato M., Marenich A., Bloino J., Janesko B. G., Gomperts R., Mennucci B., Hratchian H. P., Ortiz J. V., Izmaylov A. F., Sonnenberg J. L., Williams-Young D., Ding F., Lipparini F., Egidi F., Goings J., Peng B., Petrone A., Henderson T., Ranasinghe D., Zakrzewski V. G., Gao J., Rega N., Zheng G., Liang W., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Throssell K., Montgomery J. A., Jr., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Keith T., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Millam J. M., Klene M., Adamo C., Cammi R., Ochterski J. W., Martin R. L., Morokuma K., Farkas O., Foresman J. B., Fox D. J., (2016), Gaussian, Inc., Wallingford CT.

28. Nouri A., Mirzaei M., (2009), DFT calculations of B-11 and N-15 NMR parameters in BN nanocone. J. Mol. Struct. Theochem. 913: 207-209.

29. Mirzaei M., (2010), The NMR parameters of the SiC-doped BN nanotubes: A DFT study. Physica E. 42: 1954-1957.

30. Parr R. G., (1980), Density functional theory of atoms and molecules. Horiz. Quant. Chem.23: 5-15.

31. Grimme S., (2006), Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction. J. Comput. Chem. 27: 1787-1799.

32. Partovi T., Mirzaei M., Hadipour N. L., (2006), The C–H...O hydrogen bonding effects on the 17O electric field gradient and chemical shielding tensors in crystalline 1-methyluracil: A DFT study. Z. Naturforsch. A. 61: 383-388.

33. Ozkendir O. M., (2020), Electronic structure study of Sn-substituted InP semiconductor.  Adv. J. Sci. Eng. 1: 7-11.

34. Yaghoobi R., Mirzaei M., (2020), Computational analyses of cytidine and aza-cytidine molecular structures. Lab-in-Silico. 1: 21-25.

35. Mirzaei M., Gülseren O., Hadipour N., (2016), DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs. Comput. Theor. Chem. 1090: 67-73.

36. Gunaydin S., Alcan V., Mirzaei M., Ozkendir O. M., (2020), Electronic structure study of Fe substituted RuO₂ semiconductor. Lab-in-Silico. 1: 7-10.

37. Lashkari M., Arshadi M. R., (2004), DFT studies of pyridine corrosion inhibitors in electrical double layer: Solvent, substrate, and electric field effects. Chem. Phys. 299: 131-137.

38. Rad A. S., Mirabi A., Peyravi M., Mirzaei M., (2017), Nickel-decorated B12P12 nanoclusters as a strong adsorbent for SO2 adsorption: Quantum chemical calculations. Canada. J. Phys. 95: 958-962.

39. Eslami M., Peyghan A. A., (2015), DNA nucleobase interaction with graphene like BC3 nano-sheet based on density functional theory calculations. Thin Solid Films. 589: 52-56.

40. Lee J. H., Choi Y. K., Kim H. J., Scheicher R. H., Cho J. H., (2013), Physisorption of DNA nucleobases on h-BN and graphene: vdW-corrected DFT calculations. J. Phys. Chem. C. 117: 13435-13441.