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Study of DNA base-Li doped SiC nanotubes in aqueous solutions: a computer simulation study

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Abstract

Due to the importance of soluble nanotubes in biological systems, computational research on DNA base functionalized nanotubes is of interest. This study presents the quantitative results of Monte Carlo simulations of Li-doped silicon carbide nanotubes and its nucleic acid base complexes in water. Each species was first modeled by quantum mechanical calculations and then Monte Carlo simulations were applied to study their properties in aqueous solution. Solvation free energies were computed to indicate the solvation behavior of these compounds. The computations show that solvation free energies of the complexes of DNA bases with Li-doped SiC nanotubes are in the order: thymine > cytosine > adenine > guanine. The results of complexation free energies were also used to study the stability of related structures, which indicate that thymine-Li-doped SiC nanotubes produce the most stable compound among the four DNA base complexes.

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References

  1. Martin CR, Kohli P (2003) The emerging field of nanotube biotechnology. Nat Rev Drug Discov 2:29–37

    Article  CAS  Google Scholar 

  2. Lin Y, Taylor S, Li HP, Fernando KAS, Qu LW, Gu LR, Wang W, Zhou B, Sun YP (2004) Advances toward bioapplicationsofcarbon nanotubes. J Mater Chem 14:527–541

    Article  CAS  Google Scholar 

  3. Bianco A, Kostarelos K, Prato M (2005) Applications of carbonnanotubes in drug delivery. Curr Opin Chem Biol 9(6):674–679

    Article  CAS  Google Scholar 

  4. Kam NWS, Dai HJ (2005) Carbon Nanotubes as intracellular proteintransporters: generality and biological functionality. J Am Chem Soc 127:6021–6026

    Article  CAS  Google Scholar 

  5. Kam NWS, O’Connell M, Wisdom JA, Dai HJ (2005) Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction. Proc Natl Acad Sci USA 102(33):11600–11605

    Article  CAS  Google Scholar 

  6. Wu WWS, Pastorin G, Benincasa M, Klumpp C, Briand JP, Gennaro R, Prato M, Bianco A (2005) Targeted delivery of amphotericinB to cells by using functionalized carbon nanotubes. Angew Chem Int Ed 44(39):6358–6362

    Article  CAS  Google Scholar 

  7. Kam NWS, Liu ZA, Dai HJ (2006) Carbon nanotubes asintracellular transporters for proteins and DNA: an investigation of theuptake mechanism and pathway. Angew Chem Int Ed 45:577–581

    Article  CAS  Google Scholar 

  8. Kuzmany H, Kukovecz A, Simon F, Holzweber M, Kramberger C, Pichler T (2004) Functionalization of carbon nanotubes. Synth Met 141(1):113–122

    Article  CAS  Google Scholar 

  9. Johnston HJ, Hutchison GR, Christensen FM, Peters S, Hankin S, Aschberger K, Stone V (2010) A critical review of the biological mechanisms underlying the in vivo and in vitro toxicity of carbon nanotubes: the contribution of physico-chemical characteristics. Nanotoxicology 4(2):207–246

    Article  CAS  Google Scholar 

  10. Lam CW, James JT, McCluskey R, Arepalli S, Hunter RL (2006) A review of carbon nanotube toxicity and assessment of potential occupational and environmental health risks. Crit Rev Toxicol 36(3):189–217

    Article  CAS  Google Scholar 

  11. Murr LE, Garza KM, Soto KF, Carrasco A, Powell TG, Ramirez DA, Guerrero PA, Lopez DA, Venzor J (2005) Cytotoxicity assessment of some carbon nanotubes and related carbon nanoparticle aggregates and the implications for anthropogenic carbon nanotube aggregates in the environment. Int J Environ Res Public Health 2(1):31–42

    Article  CAS  Google Scholar 

  12. Park EJ, Roh J, Kim SN, Kang MS, Lee BS, Kim Y, Choi S (2011) Biological toxicity and inflammatory response of semi-single-walled carbon nanotubes. PLoS One 6(10):e25892

    Article  CAS  Google Scholar 

  13. Mwangi JN, Wang N, Ritts A, Kunz JL, Ingersoll CG, Li H, Deng B (2011) Toxicity of silicon carbide nanowires to sediment-dwelling invertebrates in water or sediment exposures. Environ Toxicol Chem 30(4):981–987

    Article  CAS  Google Scholar 

  14. Zhang YF, Huang HC (2008) Comput Mater Sci 43:664–669

    Article  CAS  Google Scholar 

  15. Mpournpakis G, Froudakis GE, Lithoxoos GP, Samios J (2006) Nano Lett 6:1581–1583

    Article  Google Scholar 

  16. Zhao MW, Xia YY, Li F, Zhang RQ, Lee ST (2005) Phys Rev B 71:085312-1-7

    Google Scholar 

  17. Cicero G, Galli G (2004) J Phys Chem B 108:16518–16524

    Article  CAS  Google Scholar 

  18. Haeri HH, Ketabi S, Hashemianzadeh SM (2012) J Mol Model 18:3379–3388

    Article  Google Scholar 

  19. Mavrandonakis A, Froudakis GE, Schnell M, Muhlhäuser M (2003) From pure carbon to silicon-carbon nanotubes: an ab-initio study. Nano Lett 3:1481–1484

    Article  CAS  Google Scholar 

  20. Sun XH, Li CP, Wong WK, Wong NB, Lee CS, Lee ST, Teo BK (2002) Formation of silicon carbide nanotubes and nanowires via reaction of silicon (from disproportionation of silicon monoxide) with carbon nanotubes. J Am Chem Soc 124:14464–14471

    Article  CAS  Google Scholar 

  21. Zhao MW, Xia YY, Li F, Zhang RQ, Lee S-T (2005) Strain energy and electronic structures of silicon carbide nanotubes: density functional calculations. Phys Rev B 71:085312.1–085312.6

    Google Scholar 

  22. Miyamoto Y, Yu BD (2002) Computational designing of graphitic silicon carbide and its tubular forms. Appl Phys Lett 80:586–588

    Article  CAS  Google Scholar 

  23. Menon M, Richter E, Mavrandonakis A, Froudakis G, Andriotis AN (2004) Structure and stability of SiC nanotubes. Phys Rev B 69:115322.1–115322.4

    Article  Google Scholar 

  24. Menon M, Richter E, Mavrandonakis A, Froudakis G, Andriotis AN (2004) Phys Rev B69:115322–115334

    Google Scholar 

  25. Mananghaya M, Rodulfo E, Santos GS, Villagracia A (2012) Theoretical investigation on the solubilizationin water of functionalized single-wall carbon nanotubes. J Nanotechnol 2012:1–6

    Google Scholar 

  26. Star A, Liu Y, Grant K, Ridvan L, Stoddart JF, Steuerman DW, Diehl MR, Boukai A, Heath JR (2003) Noncovalent side-wallfunctionalization of single-walled carbon nanotubes. Macromolecules 36(3):553–560

    Article  CAS  Google Scholar 

  27. Chen RJ, Zhang Y, Wang D, Dai HJ (2001) Noncovalentsidewallfunctionalization of single-walled carbon nanotubes for protein immobilization. J Am Chem Soc 123(16):3838–3839

    Article  CAS  Google Scholar 

  28. Dyke CA, Tour JM (2004) Covalent functionalization of single-walled carbon nanotubes for materials applications. J Phys Chem A 108(51):11151–11159

    Article  CAS  Google Scholar 

  29. Prato M, Bianco A (2003) Can carbon nanotubes be considered useful tools for biological applications. Adv Mater 15(20):1765–1768

    Article  Google Scholar 

  30. Huang W, Taylor S, Fu K, Lin Y, Zhang D, Hanks TW, Rao AM, Sun YP (2002) Attaching proteins to carbon nanotubes via diimideactivatedamidation. Nano Lett 4:311–314

    Article  Google Scholar 

  31. Lin Y, Allard LF, Sun YP (2004) Protein-affinity of singlewalledcarbon nanotubes in water. J Phys Chem B 108(12):3760–3764

    Article  CAS  Google Scholar 

  32. Bianco A, Kostarelos K, Partidos CD, Prato M (2005) Chem Commun 5:571–577

    Article  Google Scholar 

  33. Lacerda L, Bianco A, Prato M, Kostarelos K (2008) J Mater Chem 18:17–22

    Article  CAS  Google Scholar 

  34. Lu F, Gu L, Meziani MJ, Wang X, Luo PG, Veca LM, Cao L, Sun YP (2009) Adv Mater 21:139–152

    Article  CAS  Google Scholar 

  35. Gowtham S, Scheicher RH, Pandey R, Karna SP, Ahuja R (2008) Nanotechnology 19:125701-1-6

    Google Scholar 

  36. Zheng M, Jagota A, Semke ED, Diner BA, Mclean RS, Lustig SR, Richardson RE, Tassi NG (2003) Nat Mater 2:338–342

    Article  CAS  Google Scholar 

  37. Wang Y (2008) J Phys Chem C 112:14297–14305

    Article  CAS  Google Scholar 

  38. Varghese N, Mogera U, Govindaraj A, Das A, Maiti PK, Sood AK, Rao CNR (2009) ChemPhysChem 10:206–210

    Article  CAS  Google Scholar 

  39. Zhao C, Peng Y, Song Y, Ren J, Qu X (2008) Small 4:656–661

    Article  CAS  Google Scholar 

  40. Gao X, Xing G, Yang Y, Shi X, Liu R, Chu W, Jing L, Zhao F, Ye C, Yuan H, Fang X, Wang C, Zhao Y (2008) J Am Chem Soc 130:9190–9191

    Article  CAS  Google Scholar 

  41. Umadevi D, Sastry GN (2011) Quantum mechanical study of physisorption of nucleobaseson carbon materials: graphene versus carbon nanotubes. J Phys Chem Lett 2:1572–1576

    Article  CAS  Google Scholar 

  42. Zhong X, Slough WJ, Pandey R, Friedrich C (2012) Interaction of nucleobases with silicon nanowires: a first-principles study. Chem Phys Lett 553:55–58

    Article  CAS  Google Scholar 

  43. Kharisov BI, Kharissova OV, Gutierrez HL, Méndez UO (2009) Ind Eng Chem Res 48:572–590

    Article  CAS  Google Scholar 

  44. Gu Z, Liang F, Chen Z, Sadana A, Kittrell C, Billups WE, Hauge RH, Smalley RE (2005) In situ Raman studies on lithiated single-wall carbon nanotubes in liquid ammonia. Chem Phys Lett 410(4):467–470

    Article  CAS  Google Scholar 

  45. Hashemianzadeh SM, FarajiSh, Amin A, Ketabi S (2008) Theoretical study of the interactions between isolated DNA bases and various groups IA and IIA metal ions by ab initio calculations. Monatshefte fur chemie, chemical monthly 139: 89–100

  46. Leach AR (1996) Molecular modeling—principles and application. Longman, Essex

    Google Scholar 

  47. Redmill PS, Capps SL, Cummings PT, McCabe C (2009) A molecular dynamics study of the Gibbs free energy of solvation of fullerene particles in octanol and water. Carbon 47:2865–2874

    Article  CAS  Google Scholar 

  48. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  49. Jorgensen WL (1981) Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J Am Chem Soc 103:335–340

    Article  CAS  Google Scholar 

  50. Jia Y, Wang M, Wu L (2007) Sep Sci Technol 42:3681–3695

    Article  CAS  Google Scholar 

  51. Lithoxoos GP, Samios J (2008) J Phys Chem C 112:16725–16728

    Article  CAS  Google Scholar 

  52. Aaqvist J (1990) Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem 94(21):8021–8024

    Article  CAS  Google Scholar 

  53. Pranata J, Wierschke SG, Jorgensen WL (1991) J Am Chem Soc 113:2810–2819

    Article  CAS  Google Scholar 

  54. Hansen JP, McDonald IR (1991) Theory of simple liquids. Academic, London

    Google Scholar 

  55. Beveridge DL, Capua D, Annu FM (1989) Rev Biophys Biophys Chem 18:431

    Article  CAS  Google Scholar 

  56. Monajjemi M, Ketabi S, Hashemian Zadeh M, Amiri A (2006) Biochem Mosc 71(1):S1–S8

    Article  CAS  Google Scholar 

  57. Lippert B (2000) Coord Chem Rev 200–202:487–516

    Article  Google Scholar 

  58. Petersson GA, Al-Laham MA (1991) A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms. J Chem Phys 94:6081–6090

    Article  CAS  Google Scholar 

  59. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14:1347–1363

    Article  CAS  Google Scholar 

  60. Metropolis N, Rosenbulth AW, Rosenbulth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1093

    Article  CAS  Google Scholar 

  61. Wang Y (2008) Theoretical evidence for the stronger ability of thymine to disperse SWCNT than cytosine and adenine: self-stacking of DNA bases vs their cross-stacking with SWCNT. J Phys Chem C 112:14297–14305

    Article  CAS  Google Scholar 

  62. Zheng M, Jagota A, Semke ED, Diner BA, Mclean RS, Lustig SR, Richardson RE, Tassi NG (2003) DNA-assisted dispersion and separation of carbon nanotubes. Nat Mater 2(5):338–342

    Article  CAS  Google Scholar 

  63. Das A, Sood AK, Maiti PK, Das M, Varadarajan R, Rao CNR (2008) Chem Phys Lett 453:266–273

    Article  CAS  Google Scholar 

  64. Gowtham S, Scheicher RH, Ahuja R, Pandey R, Karna SP (2007) Phys Rev B 76:033401-1-4

    Article  Google Scholar 

  65. Antony J, Grimme S (2008) Phys Chem Chem Phys 10:2722–2729

    Article  CAS  Google Scholar 

  66. Kollman PA (1993) Chem Rev 93:2395–2417

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, East Tehran Branch, Islamic Azad University, Tehran, Iran

    Sepideh Ketabi

  2. Molecular Simulation Research Laboratory, Departments of Chemistry, Iran University of Science and Technology (IUST), Tehran, Iran

    Seyed Majid Hashemianzadeh & Morteza MoghimiWaskasi

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  1. Sepideh Ketabi
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  2. Seyed Majid Hashemianzadeh
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  3. Morteza MoghimiWaskasi
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Correspondence to Sepideh Ketabi.

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Ketabi, S., Hashemianzadeh, S.M. & MoghimiWaskasi, M. Study of DNA base-Li doped SiC nanotubes in aqueous solutions: a computer simulation study. J Mol Model 19, 1605–1615 (2013). https://doi.org/10.1007/s00894-012-1721-8

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  • DOI: https://doi.org/10.1007/s00894-012-1721-8

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