Computational Investigation on Structural Properties of Carbon Nanotube Binding to Nucleotides According to the QM Methods

محورهای موضوعی : فصلنامه نانوساختارهای اپتوالکترونیکی

Nima Karachi ¹ (Department of Chemistry, Marvdasht Branch, Islamic Azad University, Marvdasht , Iran)
Masoomeh Emadi ² (Department of Chemistry, Marvdasht Branch, Islamic Azad University, Marvdasht , Iran)
Mojtaba Servatkhah ³ (Department of Physics, Marvdasht Branch, Islamic Azad University, Marvdasht , Iran)

تاریخ دریافت : 1397/11/25 تاریخ پذیرش : 1398/01/02 تاریخ انتشار : 1397/10/11

کلید واژه: Single Walled Carbon Nanotube (SWCNT), Density Functional Theory (DFT), Hartree-Fock ( HF),

چکیده مقاله :

The interaction between nucleotides and carbon nanotubes (CNTs) is a subject
of many investigations for treating diseases but there are many questions in this field that
remain unanswered. Because of experimental methods involve assumptions and
interpretation besides limitations, there are many problems that the best study for them is
using theoretical study. Consequently, theoretical methods have become a competitive
alternative to experiments for biochemical investigations. In order to search about the
response of SWCNTs in binding to DNA, the interaction between 3 different sequences
of B-form single-strand DNA (ssDNA) and outer surface of single-walled carbon
nanotubes (SWCNTs) is considered. So we studied the interaction between (5`-ATC-
3`,5`-TCA-3`,5`-TCG-3`) and SWCNT by using Molecular Mechanic(MM) ,Hartree-
Fock(HF) and Density Functional Theory(DFT,B3LYP) methods in gas phase. The basis
sets used were STO-3G, 6–31G.In current interest, energy, dipole moment, total atomic
charges and NMR parameters calculated to obtain information about the molecular
structures and stability of these combinations. Our results revealed the effect of DNA base
and the sequence of nucleotides on the interaction of DNA/SWCNTs systems. So, we can
predict that diseases with special mutation are the better aim for Gene therapy. Therefore,
the outcome reported in this paper indicates that theoretical data can give us essential
insights into the nature of molecular structures interacted to nanotubes.

منابع و مأخذ:

[1] S. M. Moghimi, A.C. Hunter, and J. C. Murray. Nanomedicine: current status
and future prospects. FASEB J. 19 (2005) 311. Available:
https://www.ncbi.nlm.nih.gov/pubmed/15746175
[2] M. Masoudzadeh, N. Karachi, Enhanced removal of humic acids (HAs) from
aqueous solutions using MWCNTs modified by N-(3-nitro-benzylidene)-Ntrimethoxysilylpropyl-
ethane-1,2-diamine on Equilibrium, thermodynamic
and kinetics. J. Phys .Theo Chem, 14 (3) (2017) 270. Available:
https://eng.noormags.ir/.../1339981/enhanced-removal-of-humic-acids-hasfrom-
aqueous.
[3] T.Belin and F. Epron. Carbon nanotubes due to their specific (TEM) are often
used to study CNTs Mater. Sci. Eng. B. 119 (2005) 105.
Available:
https://www.sciencedirect.com/science/article/pii/S0921510705001315
[4] M. Sarafbidabad, Z. Parsaee, Z. Noor Mohammadi,N. Karachi , R Razavie,
Novel double layer film composed of reduced graphene oxide and Rose
Bengal dye: design, fabrication and evaluation as an efficient chemosensor
for silver(I) detection. New J. Chem., 42, (2018) 13674.
Available: https://pubs.rsc.org/en/content/articlelanding/2018/nj/c8nj01796d
[5] E. Herzog, A. Casey, F. M. Lyng , G. Chambers, H. J. Byrne, and M. Davoren,
A new approach to the toxicity testing of carbon-based nanomaterials--the
clonogenic assay. Toxico. Lett., 174 (2007), 49.
Available:https://www.ncbi.nlm.nih.gov/pubmed/17920791
[6] C. Zhao, L. Ji, H. Liu, G. Hu, S. Zhang, M. Yang, and Z. Yang, Functionalized
carbon nanotubes containing isocyanate groups. J. Solid. State. Chem. 177,
(2004). 4394.
Computational Investigation on Structural Properties of Carbon Nanotube *121
Available: https://www.sciencedirect.com/journal/journal-of-solid-statechemistry/
vol/177/issue/12
[7] R. H.Baughman, R. H.Zakhidov, W. A.de Heer, Carbon nanotubes-the route
toward applications Science 297, 787 (2002) science. Available:
sciencemag.org/content/297/5582/787.
[8] Z. Parsaee, N. Karachi, S. M. Abrishamifar,M. R. Rezaei Kahkha, R. Razavi,
Silver-choline chloride modified graphene oxide: Novel nanobioelectrochemical
sensor for celecoxib detection and CCD-RSM model.
Ultrason- Sonochem 45 (2018),106. Available:
https://www.ncbi.nlm.nih.gov/pubmed/29705303
[9] L. Zhou,H. Kamyab,A. Surendar, A. Maseleno, A. Z. Ibatova, S.shivadasa,
N. Karachi, n. Chelliapan, Z. Parsaee, Novel Z-scheme composite
Ag2CrO4/NG/polyimide as high performance nano catalyst for
photoreduction of CO2: Design, fabrication, characterization and
mechanismj photochem. Journal of Photochemistry and Photobiology A:
Chemistry 368(2018).364.
Available:
https://www.sciencedirect.com/science/article/pii/S1010603018305550
[10] M, Nayeri, p, keshavarzian, M. Nayer, A Novel Design of Penternary Inverter
Gate Based on Carbon Nano Tube, Journal of Optoelectronical
Nanostructure,3(1)(2018) 15.
[11] T. Zhou, C. Xu, X. Zhang, C. Cheng, L. Chen, and Y. Xu, A Simple
Theoretical Model for Ring and Nanotube Radial Breathing Mode Acta.
Physic. Chimica. Sinica. 24 (2008), 1579.
Available: https://www.sciencedirect.com/journal/acta-physico-chimicasinica/
vol/24/issue/9
[12] X. Li, Y. Peng, and X. Qu, A new approach to the toxicity testing of carbonbased
nanomaterials--the clonogenic assay. Nucleic Acids Res. 13 (2006),
3670.
Available: https://academic.oup.com/nar/issue/34/13
[13] M. Masoudzadeh,N.Karachi, Removal of Cadmium Ion from Waste Water
Using Carboxylated Nanoporous Graphene (G-COOH). Eurasian J. Anal.
Chem.4 (2018). ,18
Available: www.eurasianjournals.com/Author-Nima-Karachi/74721
[14] G. Lu, P. Maragakis, and E. Kaxiras, , Carbon nanotube interaction with
DNA Nano Lett. 5 (2005). , 897.
Available: https://pubs.acs.org/doi/abs/10.1021/nl050354u
[15] X. Zhao and J. K. Johnson, Simulation of Adsorption of DNA on Carbon
Nanotubes J. Am. Chem. Soc. 34 (2007) , 10438. Available:
https://pubs.acs.org/doi/10.1021/ja071844m
[16] T. Ramanathan, F. T. Fisher, R. S. Ruoff, and L. C. Brinson, Amino-
Functionalized Carbon Nanotubes for Binding to Polymers and Biological
Systems Chem.Mater. 17 (2005). 1290.
Available: https://pubs.acs.org/doi/10.1021/cm048357f
[17] S. Meng, W. L. Wang, P. Maragakis, and E. Kaxiras, Determination of DNABase
Orientation on Carbon Nanotubes through Directional Optical
Absorbance Nano. Lett.8 (2007), 2312.
Available: https://pubs.acs.org/doi/10.1021/nl070953w
[18] A. Star, E. Tu, J. Niemann, J. Christophe, P. Gabriel, C. S. Joiner,and C.
Valcke, Label-free detection of DNA hybridization using carbon nanotube
network field-effect transistors. PNAS 41, (2006). 921.
[19] C. Hu, Y. Zhang, G. Bao, M. Liu, and Z. L. Wang, DNA Functionalized
Single-Walled Carbon Nanotubes for Electrochemical Detection J.
Phys.Chem B 43, (2005). 20072.
Available: https://pubs.acs.org/doi/abs/10.1021/jp0550457
[20] M. E. Hughes, E. Brandin, and J. A. Golovchenko, Optical Absorption of
DNA−Carbon Nanotube Structures Nano. Lett.5 (2007), 1191. Available:
pubs.acs.org/doi/abs/10.1021/nl062906u
[21] S. Meng, P. Maragakis, C. Papaloukas, and E. Kaxiras, Tuning the
Performance of Layer-by-Layer Assembled Organic Light Emitting Diodes
by Controlling the Position of Isolating Clay Barrier Sheets Nano. Lett.1,
(2007). 45. Available: https://pubs.acs.org/doi/abs/10.1021/nl005514a
[22] G. Rink, Y. Kong, and T. Koslowski, Theory and simulation of charge
transfer through DNA – nanotube contacts Chem. Phys. 327, (2006). 98.
Available:
https://www.sciencedirect.com/science/article/abs/pii/S0301010406002382
[23] H. Gao, Y. Kong, and D. Cui, Spontaneous Insertion of DNA
Oligonucleotides into Carbon Nanotubes Nano. Lett. 3 (2003). , 471.
Available: https://pubs.acs.org/doi/10.1021/nl025967a
[24] W. Yang, M. J. Moghaddam, S. Taylor, B. Bojarski, and L. Wieczorek,
Single-walled carbon nanotubes with DNA recognition Chem. Phys. Lett.
443 (2007). , 169.
Available:
https://www.sciencedirect.com/science/article/pii/S0009261407008251
[25] S. Daniel, T. P. Rao, K. S. Rao, S. U. Rani, G. R. K. Naidu, H. Y.Lee, and
T. Kawai, A review of DNA functionalized/grafted carbon nanotubes and
their characterization Sens. Actuators, B 122 (2007) , 672. Available:
https://www.sciencedirect.com/science/article/pii/S0925400506004527
[26] S. Gowtham, R. H. Scheicher, R. Ahuja, R. Pandey, and S. P. Karna ,
Physisorption of nucleobases on graphene: Density-functional calculations
Phys. Rev. B 76, (2007)3401.
Available: https://link.aps.org/doi/10.1103/PhysRevB.76.033401
[27] H, Bahramiyan, S, Bagheri, Linear and nonlinear optical properties of a
modified Gaussian quantum dot: pressure, temperature and impurity effect.
Journal Optoelectronical Nanostructure 3(3) (2018), 79. Available:
jopn.miau.ac.ir/author.index?vol=418&vl=Volume%203%20(2018)
[28] M. J. Moghaddam, S. Taylor, M. Gao, S. Huang, L. Dai, and J. McCall,
Highly Efficient Binding of DNA on the Sidewalls and Tips of Carbon
Nanotubes Using Photochemistry Nano. Lett. 4(1), (2004)89,
Available: pubs.acs.org/doi/full/10.1021/nl034915y
[29] Y, Abed, F Mostaghni, Polarizability and Hyperpolarizability of Schiff Base
Salen-H2 as Judged as UV-vis Spectroscopy and Simulation Analysis Journal
Optoelectronical Nanostructure 3(1)(2018) 27,
Available:
jopn.miau.ac.ir/article_2821_c4ebdfdacf10e9e15d084b7180970784.pdf
[30] M. Zheng, K. Eom and Ch. Ke. Calculations of the resonant response of
carbon nanotubes to binding of DNA, J. Phys. D: Appl. Phys. 42 (2009).
145408
[31] Z. Parsaee, N. Karachi, S. M. Abrishamifar,M. R. Rezaei Kahkha, R. Razavi,
Silver-choline chloride modified graphene oxide: Novel nanobioelectrochemical
sensor for celecoxib detection and CCD-RSM model
Ultrasonics - Sonochemistry 45 (2018). ,106–115.
Available:
https://www.sciencedirect.com/science/article/pii/S1350417718304310
[32] M, Riahinasab, E, Darabi Analytical Investigation of Frequency Behavior in
Tunnel Injection Quantum Dot VCSEL Journal Optoelectronical
Nanostructure 3( 2) (2018) 65.
Available:
jopn.miau.ac.ir/article_2876_3ac61163b777771c8c771cc5f808bb45.pdf
[33] S. J, Mousavi The effect of preparation method and presence of impurity on
structural properties and morphology of iron oxide Journal Optoelectronical
Nanostructure 2( 4)(2017) 1.
Available:
jopn.miau.ac.ir/article_2195_53c324065a22d87f49373f7ca13e4f95.pdf
[34] A.E. Ozel, S. Celik, and S. Akyuz, Vibrational spectroscopic investigation
of free and coordinated 5-aminoquinoline: The IR, Raman and DFT studies
J. Mol. Struct. 925 (2009) 523.
Available:
https://www.sciencedirect.com/science/article/abs/pii/S0022286009000210
[35] N. Karachi,A. Boshra, Alkali endohedrals of C24(BN)12 heterofullerenes: A
DFT aqueous phase study Heteroatom Chemistry,29 (4) (2018) e21435.
Available: https://onlinelibrary.wiley.com/doi/abs/10.1002/hc.21435
[36] N. Karachi , O. Azadi , R. Razavi , A. Tahvili , Z. Parsaee, Combinatorial
experimental and DFT theoretical evaluation of a nano novel thiodicarboxaldehyde
based Schiff base supported on a thin polymer film as a
chemosensor for Pb2+ detection j photochem and photobio A. 360 , (2018).
152. Available:
https://www.sciencedirect.com/science/article/pii/S1010603018303496
[37] A. Maiti, Multiscale modeling with carbon nanotubes Microelectronics 39
(2008), 208.
Available:
https://www.sciencedirect.com/science/article/pii/S0026269206001200
[38] A.J.D .Melinda, A.J.D. Solid state NMR spectroscopy; Principles and
Applications, Cambridge University Press,UK( 2003).
Available:
https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470999394.fmatter