Binding of nucleobases with graphene and carbon nanotube: A review of computational studies

Journal of Biomolecular Structure and Dynamics

Volumn 33, Issue 7, 2015, Pages 1567-1597

  Chehel Amirani, Morteza ^a   Tang, Tian ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

binding energy; carbon nanotube; density functional theory; graphene; nucleobase

Indexed keywords

CARBON NANOTUBE; DOUBLE STRANDED DNA; GRAPHENE; NUCLEIC ACID BASE; SINGLE STRANDED DNA; GRAPHITE; NUCLEOSIDE;

ARTICLE; BINDING KINETICS; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; HYBRIDIZATION; INTERACTIONS WITH NUCLEIC ACID; MATHEMATICAL COMPUTING; MOLECULAR MECHANICS; NUCLEOBASE BINDING; PRIORITY JOURNAL; QUANTUM MECHANICS; SIMULATION; CHEMISTRY;

GRAPHITE; MODELS, MOLECULAR; NANOTUBES, CARBON; NUCLEOSIDES;

EID: 84928795984     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2014.954315     Document Type: Article

References (197)

1. Akdim, B., Pachter, R., Day, P. N., Kim, S. S., & Naik, R. R. (2012). On modeling biomolecular-surface nonbonded interactions: Application to nucleobase adsorption on single- wall carbon nanotube surfaces. Nanotechnology, 23, 165703-1-165703-6.
2. Akita, S., Nishijima, H., Nakayama, Y., Tokumasu, F., & Takeyasu, K. (1999). Carbon nanotube tips for a scanning probe microscope: Their fabrication and properties. Journal of Physics D: Applied Physics, 32, 1044-1048.
3. Albertorio, F., Hughes, M. E., Golovchenko, J. A., & Branton, D. (2009). Base dependent DNA-carbon nanotube interactions: Activation enthalpies and assembly-disassembly control. Nanotechnology, 20, 395101-1-395101-9.
4. Allen, M., Balooch, M., Subbiah, S., Tench, R., Siekhaus, W., & Balhorn, R. (1991). Scanning tunneling microscope images of adenine and thymine at atomic resolution. Scanning Microscopy, 5, 625-630.
5. Antony, J., & Grimme, S. (2008). Structures and interaction energies of stacked graphene-nucleobase complexes. Physical Chemistry Chemical Physics, 10, 2722-2729.
6. Arnett, C. M., Marsh, C. P., Welch, C. R., Strano, M. S., Han, J.-H., Gray, J. H., & Carlson, T. A. (2010). Enzyme-mediated assimilation of DNA-functionalized single-walled carbon nanotubes. Langmuir, 26, 613-617.
7. Bahr, J. L., & Tour, J. M. (2001). Highly functionalized carbon nanotubes using in situ generated diazonium compounds. Chemistry of Materials, 13, 3823-3824.
8. Bahr, J. L., Yang, J., Kosynkin, D. V., Bronikowski, M. J., Smalley, R. E., & Tour, J. M. (2001). Functionalization of carbon nanotubes by electrochemical reduction of aryl diazonium salts: A bucky paper electrode. Journal of the American Chemical Society, 123, 6536-6542.
9. Balandin, A. A. (2011). Thermal properties of graphene, carbon nanotubes and nanostructured carbon materials. Nature Materials, 10, 569-581.
10. Balasubramanian, K., & Burghard, M. (2005). Chemically functionalized carbon nanotubes. Small, 1, 180-192.
11. Banerjee, S., Hemraj-Benny, T., & Wong, S. S. (2005). Covalent surface chemistry of single-walled carbon nanotubes. Advanced Materials, 17, 17-29.
12. Barisci, J. N., Tahhan, M., Wallace, G. G., Badaire, S., Vaugien, T., Maugey, M., & Poulin, P. (2004). Properties of carbon nanotube fibers spun from DNA-stabilized dispersions. Advanced Functional Materials, 14, 133-138.
13. Barone, V., & Cossi, M. (1998). Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. The Journal of Physical Chemistry A, 102, 1995-2001.
14. Baughman, R. H., Cui, C., Zakhidov, A. A., Iqbal, Z., Barisci, J. N., Spinks, G. M., ... Kertesz, M. (1999). Carbon nanotube actuators. Science, 284, 1340-1344.
15. Baughman, R. H., Zakhidov, A. A., & de Heer, W. A. (2002). Carbon nanotubes - The route toward applications. Science, 297, 787-792.
16. Berland, K., Chakarova-Käck, S. D., Cooper, V. R., Langreth, D. C., & Schröder, E. (2011). A van der Waals density functional study of adenine on graphene: Single-molecular adsorption and overlayer binding. Journal of Physics: Condensed Matter, 23, 135001-1-135001-8.
17. Brahman, P. K., Dar, R. A., & Pitre, K. S. (2013). DNA-functionalized electrochemical biosensor for detection of vitamin B1 using electrochemically treated multiwalled carbon nanotube paste electrode by voltammetric methods. Sensors and Actuators B: Chemical, 177, 807-812.
18. Brameld, K., Dasgupta, S., & Goddard, W. A. (1997). Distance dependent hydrogen bond potentials for nucleic acid base pairs from ab initio quantum mechanical calculations (LMP2/cc-pVTZ). The Journal of Physical Chemistry B, 101, 4851-4859.
19. Brooks, B., Bruccoleri, R., Olafson, D., States, D., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4, 187-217.
20. Chandra Shekar, S., & Swathi, R. S. (2014). Stability of nucleobases and base pairs adsorbed on graphyne and graphdiyne. The Journal of Physical Chemistry C, 118, 4516-4528.
21. Chehel Amirani, M., Tang, T., & Cuervo, J. (2013). Quantum mechanical treatment of binding energy between DNA nucleobases and carbon nanotube: A DFT analysis. Physica E: Low-dimensional Systems and Nanostructures, 54, 65-71.
22. Chen, J., Liu, H., Weimer, W. A., Halls, M. D., Waldeck, D. H., & Walker, G. C. (2002). Noncovalent engineering of carbon nanotube surfaces by rigid, functional conjugated polymers. Journal of the American Chemical Society, 124, 9034-9035.
23. Chen, R. J., Bangsaruntip, S., Drouvalakis, K. A., Wong Shi Kam, N., Shim, M., Li, Y., ... Dai, H. (2003). Noncovalent functionalization of carbon nanotubes for highly specific electronic biosensors. Proceedings of the National Academy of Sciences, 100, 4984-4989.
24. Cho, Y., Min, S. K., Yun, J., Kim, W. Y., Tkatchenko, A., & Kim, K. S. (2013). Noncovalent interactions of DNA bases with naphthalene and graphene. Journal of Chemical Theory and Computation, 9, 2090-2096.
25. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., ... Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117, 5179-5197.
26. Das, A., Sood, A., Maiti, P. K., Das, M., Varadarajan, R., & Rao, C. (2008). Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment. Chemical Physics Letters, 453, 266-273.
27. Debye, P., & Hückel, E. (1923). The theory of electrolytes. i. lowering of freezing point and related phenomena. Physikalische Zeitschrift, 24, 185-206.
28. Dewar, M. J. S., Zoebisch, E. G., Healy, E. F., & Stewart, J. J. P. (1985). Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model. Journal of the American Chemical Society, 107, 3902-3909.
29. Dion, M., Rydberg, H., Schröder, E., Langreth, D. C., & Lundqvist, B. I. (2004). Van der Waals density functional for general geometries. Physical Review Letters, 92, 246401-1-246401-4.
30. Dresselhaus, M. S., Dresselhaus, G., Charlier, J. C., & Hernández, E. (2004). Electronic, thermal and mechanical properties of carbon nanotubes. Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences, 362, 2065-2098.
31. Dwyer, C., Guthold, M., Falvo, M., Washburn, S., Superfine, R., & Erie, D. (2002). DNA-functionalized single-walled carbon nanotubes. Nanotechnology, 13, 601-604.
32. Edelwirth, M., Freund, J., Sowerby, S., & Heckl, W. (1998). Molecular mechanics study of hydrogen bonded self-assembled adenine monolayers on graphite. Surface Science, 417, 201-209.
33. Ehrlich, S., Moellmann, J., & Grimme, S. (2013). Dispersioncorrected density functional theory for aromatic interactions in complex systems. Accounts of Chemical Research, 46, 916-926.
34. Enyashin, A. N., Gemming, S., & Seifert, G. (2007). DNAwrapped carbon nanotubes. Nanotechnology, 18, 245702-1-245702-10.
35. Fang, F., & Choi, H. (2008). Noncovalent self-assembly of carbon nanotube wrapped carbonyl iron particles and their magnetorheology. Journal of Applied Physics, 103, 07A301-07A301-3.
36. Freund, J. E. (1998). Characterization of ordered nucleic acid bases adsorbed on graphite and Ag (111). PhD thesis. Ludwig- Maximilians-Universität, München.
37. Freund, J. E., Edelwirth, M., Kröbel, P., & Heckl, W. M. (1997). Structure determination of two-dimensional adenine crystals on graphite. Physical Review B, 55, 5394-5397.
38. Frischknecht, A. L., & Martin, M. G. (2008). Simulation of the adsorption of nucleotide monophosphates on carbon nanotubes in aqueous solution. The Journal of Physical Chemistry C, 112, 6271-6278.
39. Gao, H., Kong, Y., Cui, D., & Ozkan, C. S. (2003). Spontaneous insertion of DNA oligonucleotides into carbon nanotubes. Nano Letters, 3, 471-473.
40. Georgakilas, V., Kordatos, K., Prato, M., Guldi, D. M., Holzinger, M., & Hirsch, A. (2002). Organic functionalization of carbon nanotubes. Journal of the American Chemical Society, 124, 760-761.
41. Goerigk, L., & Grimme, S. (2011). A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. Physical Chemistry Chemical Physics: PCCP, 13, 6670-6688.
42. Gordon, M. S., Slipchenko, L., Li, H., & Jensen, J. H. (2007). Chapter 10 the effective fragment potential: A general method for predicting intermolecular interactions [volume 3 of Annual Reports in Computational Chemistry]. pp. 177-193. Elsevier.
43. Gowtham, S., Scheicher, R. H., Ahuja, R., Pandey, R., & Karna, S. P. (2007). Physisorption of nucleobases on graphene: Density-functional calculations. Physical Review B, 76, 033401-1-033401-4.
44. Gowtham, S., Scheicher, R. H., Pandey, R., Karna, S. P., & Ahuja, R. (2008). First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes. Nanotechnology, 19, 125701-1-125701-6.
45. Gräfenstein, J., & Cremer, D. (2009). An efficient algorithm for the density-functional theory treatment of dispersion interactions. The Journal of Chemical Physics, 130, 124105-1-124105-16.
46. Grimme, S. (2004). Accurate description of van der Waals complexes by density functional theory including empirical corrections. Journal of Computational Chemistry, 25, 1463-1473.
47. Grimme, S. (2006). Semiempirical GGA-type density functional constructed with a long-range dispersion correction. Journal of Computational Chemistry, 27, 1787-1799.
48. Grimme, S. (2011). Density functional theory with London dispersion corrections. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 211-228.
49. Grimme, S., Antony, J., Ehrlich, S., & Krieg, H. (2010). A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. The Journal of Chemical Physics, 132, 154104-1-154104-19.
50. Grimme, S., Ehrlich, S., & Goerigk, L. (2011). Effect of the damping function in dispersion corrected density functional theory. Journal of Computational Chemistry, 32, 1456-1465.
51. Grimme, S., & Steinmetz, M. (2013). Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase. Physical Chemistry Chemical Physics, 16031-16042.
52. Hasegawa, M., & Nishidate, K. (2004). Semiempirical approach to the energetics of interlayer binding in graphite. Physical Review B, 70, 205431-1-205431-7.
53. He, P., & Bayachou, M. (2005). Layer-by-layer fabrication and characterization of DNA-wrapped single-walled carbon nanotube particles. Langmuir, 21, 6086-6092.
54. Head-Gordon, M., Pople, J. A., & Frisch, M. J. (1988). MP2 energy evaluation by direct methods. Chemical Physics Letters, 153, 503-506.
55. Heckl, W. M., Smith, D. P., Binnig, G., Klagges, H., Hänsch, T. W., & Maddocks, J. (1991). Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy. Proceedings of the National Academy of Sciences, 88, 8003-8005.
56. Hirata, F. (Ed.). (2003). Molecular theory of solvation. Volume 24 of Understanding Chemical Reactivity, Springer.
57. Hirsch, A. (2002). Functionalization of single-walled carbon nanotubes. Angewandte Chemie International Edition, 41, 1853-1859.
58. Hobza, P., Selzle, H. L., & Schlag, E. W. (1996). Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-shaped and parallel-displaced. The Journal of Physical Chemistry, 100, 18790-18794.
59. Hohenberg, P., & Kohn, W. (1964). Inhomogeneous electron gas. Physical Review, 136, B864-B871.
60. Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M055-2X and M06- 2X exchange-correlation functionals for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4, 1996-2000.
61. Hu, C., Zhang, Y., Bao, G., Zhang, Y., Liu, M., & Wang, Z. L. (2005). DNA functionalized single-walled carbon nanotubes for electrochemical detection. The Journal of Physical Chemistry B, 109, 20072-20076.
62. Hu, H., Ni, Y., Montana, V., Haddon, R. C., & Parpura, V. (2004). Chemically functionalized carbon nanotubes as substrates for neuronal growth. Nano Letters, 4, 507-511.
63. Hummer, G., Rasaiah, J., & Noworyta, J. (2001). Water conduction through the hydrophobic channel of a carbon nanotube. Nature, 414, 188-190.
64. Iijima, S. (1991). Helical microtubules of graphitic carbon. Nature, 354, 56-58.
65. Iikura, H., Tsuneda, T., Yanai, T., & Hirao, K. (2001). A longrange correction scheme for generalized-gradient-approximation exchange functionals. The Journal of Chemical Physics, 115, 3540-3544.
66. Jacobs, C. B., Peairs, M. J., & Venton, B. J. (2010). Review: Carbon nanotube based electrochemical sensors for biomolecules. Analytica Chimica Acta, 662, 105-127.
67. Jaffe, R. L., & Smith, G. D. (1996). A quantum chemistry study of benzene dimer. The Journal of Chemical Physics, 105, 2780-2788.
68. Johnson, E. R., Mackie, I. D., & DiLabio, G. A. (2009). Dispersion interactions in density-functional theory. Journal of Physical Organic Chemistry, 22, 1127-1135.
69. Johnson, E. R., Wolkow, R. A., & DiLabio, G. A. (2004). Application of 25 density functionals to dispersion-bound homomolecular dimers. Chemical Physics Letters, 394, 334-338.
70. Johnson, R. R., Johnson, A. T. C., & Klein, M. L. (2008). Probing the structure of DNA-Carbon nanotube hybrids with molecular dynamics. Nano Letters, 8, 69-75.
71. Johnson, R. R., Johnson, A. T. C., & Klein, M. L. (2010). The nature of DNA-base-carbon-nanotube interactions. Small (Weinheim an der Bergstrasse, Germany), 6, 31-34.
72. Jones, R. O., & Gunnarsson, O. (1989). The density functional formalism, its applications and prospects. Reviews of Modern Physics, 61, 689-746.
73. Jurecka, P., Cerný, J., Hobza, P., & Salahub, D. R. (2007). Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. Journal of Computational Chemistry, 28, 555-569.
74. Katz, E., & Willner, I. (2004). Biomolecule-functionalized carbon nanotubes: Applications in nanobioelectronics. Chem- PhysChem, 5, 1084-1104.
75. Kilina, S., Yarotski, D. A., Talin, A. A., Tretiak, S., Taylor, A. J., & Balatsky, A. V. (2011). Unveiling stability criteria of DNA-carbon nanotubes constructs by scanning tunneling microscopy and computational modeling. Journal of Drug Delivery, 2011, 415621-1-415621-9.
76. Kim, S. S., Hisey, C. L., Kuang, Z., Comfort, D. A., Farmer, B. L., & Naik, R. R. (2013). The effect of single wall carbon nanotube metallicity on genomic DNA-mediated chirality enrichment. Nanoscale, 5, 4931-4936.
77. Klimes, J. c. v., Bowler, D. R., & Michaelides, A. (2011). Van der Waals density functionals applied to solids. Physical Review B, 83, 195131-1-195131-13.
78. Kohn, W., & Sham, L. J. (1965). Self-consistent equations including exchange and correlation effects. Physical Review, 140, A1133-A1138.
79. Krishnan, A., Dujardin, E., Ebbesen, T. W., Yianilos, P. N., & Treacy, M. M. J. (1998). Young's modulus of single-walled nanotubes. Physical Review B, 58, 14013-14019.
80. Kristyán, S., & Pulay, P. (1994). Can (semi)local density functional theory account for the London dispersion forces? Chemical Physics Letters, 229, 175-180.
81. Kurita, N., & Sekino, H. (2001). Ab initio and DFT studies for accurate description of van der Waals interaction between He atoms. Chemical Physics Letters, 348, 139-146.
82. Le, D., Kara, A., Schröder, E., Hyldgaard, P., & Rahman, T. S. (2012). Physisorption of nucleobases on graphene: A comparative van der Waals study. Journal of Physics: Condensed Matter, 24, 424210-1-424210-7.
83. 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. The Journal of Physical Chemistry C, 117, 13435-13441.
84. Lee, K., Murray, É. D., Kong, L., Lundqvist, B. I., & Langreth, D. C. (2010). Higher-accuracy van der Waals density functional. Physical Review B, 82, 081101-1-081101-4.
85. Lin, Y., Rao, A. M., Sadanadan, B., Kenik, E. A., & Sun, Y.-P. (2002). Functionalizing multiple-walled carbon nanotubes with aminopolymers. The Journal of Physical Chemistry B, 106, 1294-1298.
86. Lustig, S. R., Jagota, A., Khripin, C., & Zheng, M. (2005). Theory of structure-based carbon nanotube separations by ion-exchange chromatography of DNA/CNT hybrids. The Journal of Physical Chemistry B, 109, 2559-2566.
87. Lv, W. (2011). The adsorption of DNA bases on neutral and charged (8, 8) carbon-nanotubes. Chemical Physics Letters, 514, 311-316.
88. Ma, Y., Ali, S. R., Dodoo, A. S., & He, H. (2006). Enhanced sensitivity for biosensors: Multiple functions of DNAwrapped single-walled carbon nanotubes in self-doped polyaniline nanocomposites. The Journal of Physical Chemistry B, 110, 16359-16365.
89. MacKerel Jr., A., Brooks III, C., Nilsson, L., Roux, B., Won, Y., & Karplus, M. (1998). The energy function and its parameterization with an overview of the program. In R. MacKerel (Ed.), The encyclopedia of computational chemistry, (Vol. 1, pp. 271-277). Chichester: John Wiley.
90. Malysheva, O., Tang, T., & Schiavone, P. (2011). Binding force between a charged wall and a complex formed by a polyelectrolyte and an electronically responsive cylinder. The Journal of Adhesion, 87, 251-271.
91. Manna, A. K., & Pati, S. K. (2013). Theoretical understanding of single-stranded DNA assisted dispersion of graphene. Journal of Materials Chemistry B, 1, 91-100.
92. Manohar, S., Tang, T., & Jagota, A. (2007). Structure of homopolymer DNA-CNT hybrids. Journal of Physical Chemistry C, 111, 17835-17845.
93. Marconnet, A. M., Panzer, M. A., & Goodson, K. E. (2013). Thermal conduction phenomena in carbon nanotubes and related nanostructured materials. Reviews of Modern Physics, 85, 1295-1326.
94. Martin, M. G. (2006). Comparison of the AMBER, CHARMM, COMPASS, GROMOS, OPLS, TraPPE and UFF force fields for prediction of vapor-liquid coexistence curves and liquid densities. Fluid Phase Equilibria, 248, 50-55.
95. Martin, W., Zhu, W., & Krilov, G. (2008). Simulation study of noncovalent hybridization of carbon nanotubes by singlestranded DNA in water. The Journal of Physical Chemistry B, 112, 16076-16089.
96. Mayo, S. L., Olafson, B. D., & Goddard, W. A. (1990). Dreiding: A generic force field for molecular simulations. The Journal of Physical Chemistry, 94, 8897-8909.
97. Meijer, E., & Sprik, M. (1996). A density-functional study of the intermolecular interactions of benzene. Journal of Chemical Physics, 105, 8684-8689. Cited By (since 1996) 196.
98. Meng, S., Maragakis, P., Papaloukas, C., & Kaxiras, E. (2007). DNA nucleoside interaction and identification with carbon nanotubes. Nano Letters, 7, 45-50.
99. Meng, S., Wang, W. L., Maragakis, P., & Kaxiras, E. (2007). Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance. Nano Letters, 7, 2312-2316.
100. Meo, M., & Rossi, M. (2006). Prediction of youngs modulus of single wall carbon nanotubes by molecular-mechanics based finite element modelling. Composites Science and Technology, 66, 1597-1605.
101. Møller, C., & Plesset, M. S. (1934). Note on an approximation treatment for many-electron systems. Physical Review, 46, 618-622.
102. Neihsial, S., Periyasamy, G., Samanta, P. K., & Pati, S. K. (2012). Understanding the binding mechanism of various chiral SWCNTs and ssDNA: A computational study. The Journal of Physical Chemistry B, 116, 14754-14759.
103. Okada, T., Abe, T., & Kaneko, M. (2009). Historical overview and fundamental aspects of molecular catalysts for energy conversion. In T. Okada & M. Kaneko (Eds.), Molecular catalysts for energy conversion, (Vol. 111, pp. 1-36). Springer Series in Materials Science. Berlin Heidelberg: Springer.
104. Ortmann, F., Schmidt, W. G., & Bechstedt, F. (2005). Attracted by long-range electron correlation: Adenine on graphite. Physical Review Letters, 95, 186101-1-186101-4.
105. Panigrahi, S., Bhattacharya, A., Banerjee, S., & Bhattacharyya, D. (2012). Interaction of nucleobases with wrinkled graphene surface: Dispersion corrected DFT and AFM studies. The Journal of Physical Chemistry C, 116, 4374-4379.
106. Pantarotto, D., Partidos, C. D., GraffH, R., Hoebeke, J., Briand, J.-P., Prato, M., & Bianco, A. (2003). Synthesis, structural characterization, and immunological properties of carbon nanotubes functionalized with peptides. Journal of the American Chemical Society, 125, 6160-6164.
107. Park, N., Lim, S., Kim, G., & Jhi, S.-H. (2008). Calculation of hydrogen physisorption affinity to graphene species with Ab-intio and density-functional methods. Journal of the Korean Physical Society, 53, 691-694.
108. Patil, A. J., Vickery, J. L., Scott, T. B., & Mann, S. (2009). Aqueous stabilization and self-assembly of graphene sheets into layered bio-nanocomposites using DNA. Advanced Materials, 21, 3159-3164.
109. Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Physical Review Letters, 77, 3865-3868.
110. Perdew, J. P., & Wang, Y. (1992). Accurate and simple analytic representation of the electron-gas correlation energy. Physical Review B, 45, 13244-13249.
111. Petrosyan, S. A., Rigos, A. A., & Arias, T. A. (2005). Joint density-funationl theory: Ab initio study of cr2o3 surface chemistry in solution. The Journal of Physical Chemistry B, 109, 15436-15444.
112. Prato, M., Kostarelos, K., & Bianco, A. (2008). Functionalized carbon nanotubes in drug design and discovery. Accounts of Chemical Research, 41, 60-68.
113. Premkumar, T., & Geckeler, K. E. (2012). Graphene-DNA hybrid materials: Assembly, applications, and prospects. Progress in Polymer Science, 37, 515-529.
114. Qi, P., Vermesh, O., Grecu, M., Javey, A., Wang, Q., Dai, H., ... Cho, K. J. (2003). Toward large arrays of multiplex functionalized carbon nanotube sensors for highly sensitive and selective molecular detection. Nano Letters, 3, 347-351.
115. Qiu, X., Khripin, C. Y., Ke, F., Howell, S. C., & Zheng, M. (2013). Electrostatically driven interactions between hybrid DNA-carbon nanotubes. Physical Review Letters, 111, 048301-1-048301-5.
116. Ramanathan, T., Fisher, F. T., Ruoff, R. S., & Brinson, L. C. (2005). Amino-functionalized carbon nanotubes for binding to polymers and biological systems. Chemistry of Materials, 17, 1290-1295.
117. Ramraj, A., Hillier, I. H., Vincent, M. A., & Burton, N. A. (2010). Assessment of approximate quantum chemical methods for calculating the interaction energy of nucleic acid bases with graphene and carbon nanotubes. Chemical Physics Letters, 484, 295-298.
118. Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American Chemical Society, 114, 10024-10035.
119. Rastogi, R., Dhindsa, N., Suri, C. R., Pant, B., Tripathi, S., Kaur, I., & Bharadwaj, L. M. (2012). Interfacing of DNA with carbon nanotubes for nanodevice applications. Materials Chemistry and Physics, 135, 268-276.
120. Roxbury, D., Jagota, A., & Mittal, J. (2011). Sequence-specific self-stitching motif of short single-stranded DNA on a single- walled carbon nanotube. Journal of the American Chemical Society, 133, 13545-13550.
121. Roxbury, D., Jagota, A., & Mittal, J. (2013). Structural characteristics of oligomeric DNA strands adsorbed onto singlewalled carbon nanotubes. The Journal of Physical Chemistry B, 117, 132-140.
122. Roxbury, D., Manohar, S., & Jagota, A. (2010). Molecular simulation of DNA β-sheet and β-barrel structures on graphite and carbon nanotubes. The Journal of Physical Chemistry C, 114, 13267-13276.
123. Rutledge, L. R., Durst, H. F., & Wetmore, S. D. (2009). Evidence for stabilization of DNA/RNA-protein complexes arising from nucleobase-amino acid stacking and T-shaped interactions. Journal of Chemical Theory and Computation, 5, 1400-1410.
124. Rutledge, L. R., & Wetmore, S. D. (2010). The assessment of density functionals for DNAprotein stacked and T-shaped complexes. Canadian Journal of Chemistry, 88, 815-830.
125. Saito, R., Dresselhaus, G., & Dresselhaus, M. (1998). Physical properties of carbon nanotube. London: Imperial College Press.
126. Sarmah, A., & Roy, R. K. (2013). Understanding the interaction of nucleobases with chiral semiconducting singlewalled carbon nanotubes: An alternative theoretical approach based on density functional reactivity theory. The Journal of Physical Chemistry C, 117, 21539-21550.
127. Seponer, J., Leszczynski, J., & Hobza, P. (1996). Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. Journal of Computational Chemistry, 17, 841-850.
128. Shankar, A., Jagota, A., & Mittal, J. (2012). DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces. The Journal of Physical Chemistry B, 116, 12088-12094.
129. Shim, M., Shi Kam, N. W., Chen, R. J., Li, Y., & Dai, H. (2002). Functionalization of carbon nanotubes for biocompatibility and biomolecular recognition. Nano Letters, 2, 285-288.
130. Shin, S. R., Lee, C. K., So, I. S., Jeon, J. H., Kang, T. M., Kee, C. W., ... Kim, S. J. (2008). DNA-wrapped singlewalled carbon nanotube hybrid fibers for supercapacitors and artificial muscles. Advanced Materials, 20, 466-470.
131. Shtogun, Y. V., Woods, L. M., & Dovbeshko, G. I. (2007). Adsorption of adenine and thymine and their radicals on single-wall carbon nanotubes. Journal of Physical Chemistry C, 111, 18174-18181.
132. Shukla, M., Dubey, M., Zakar, E., Namburu, R., Czyznikowska, Z., & Leszczynski, J. (2009). Interaction of nucleic acid bases with single-walled carbon nanotube. Chemical Physics Letters, 480, 269-272.
133. Singh, P., Kumar, J., Toma, F. M., Raya, J., Prato, M., Fabre, B., ... Bianco, A. (2009). Synthesis and characterization of nucleobase-carbon nanotube hybrids. Journal of the American Chemical Society, 131, 13555-13562.
134. Singh, R., Pantarotto, D., McCarthy, D., Chaloin, O., Hoebeke, J., Partidos, C. D., ... Kostarelos, K. (2005). Binding and condensation of plasmid DNA onto functionalized carbon nanotubes: Toward the construction of nanotube-based gene delivery vectors. Journal of the American Chemical Society, 127, 4388-4396.
135. Sowerby, S. J., Cohn, C. A., Heckl, W. M., & Holm, N. G. (2001). Differential adsorption of nucleic acid bases: Relevance to the origin of life. Proceedings of the National Academy of Sciences, 98, 820-822.
136. Sowerby, S., Edelwirth, M., & Heckl, W. (1998a). Molecular mechanics simulation of uracil adlayers on molybdenum disulfide and graphite surfaces. Applied Physics A: Materials Science & Processing, 66, S649-S653.
137. Sowerby, S. J., Edelwirth, M., & Heckl, W. M. (1998b). Selfassembly at the prebiotic solid-liquid interface: Structures of self-assembled monolayers of adenine and guanine bases formed on inorganic surfaces. The Journal of Physical Chemistry B, 102, 5914-5922.
138. Sowerby, S., & Heckl, W. (1998). The role of self-assembled monolayers of the purine and pyrimidine bases in the emergence of life. Origins of Life and Evolution of the Biosphere, 28, 283-310.
139. Sowerby, S., Heckl, W., & Petersen, G. (1996). Chiral symmetry breaking during the self-assembly of monolayers from achiral purine molecules. Journal of Molecular Evolution, 43, 419-424.
140. Sowerby, S. J., & Petersen, G. B. (1997). Scanning tunneling microscopy of uracil monolayers self-assembled at the solid|liquid interface. Journal of Electroanalytical Chemistry, 43385-43390.
141. Sowerby, S., Stockwell, P., Heckl, W., & Petersen, G. (2000). Self-programmable, self-assembling two-dimensional genetic matter. Origins of Life and Evolution of the Biosphere, 30, 81-99.
142. Srinivasan, R., & Gopalan, P. (1993). Order and stability of an electrochemically condensed adenine layer on graphite. The Journal of Physical Chemistry, 97, 8770-8775.
143. Srinivasan, R., Murphy, J., Fainchtein, R., & Pattabiraman, N. (1991). Electrochemical STM of condensed guanine on graphite. Journal of Electroanalytical Chemistry and Interfacial Electrochemistry, 312, 293-300.
144. Srinivasan, R., Murphy, J., & Pattabiraman, N. (1992). STM observations of two-dimensional condensed layers on solid electrodes. Ultramicroscopy, 42-44, 453-459.
145. Stepanian, S., Karachevtsev, M., Glamazda, A., Karachevtsev, V., & Adamowicz, L. (2008). Stacking interaction of cytosine with carbon nanotubes: MP2, DFT and Raman spectroscopy study. Chemical Physics Letters, 459, 153-158.
146. Stewart, J. J. P. (1989a). Optimization of parameters for semiempirical methods I. Method. Journal of Computational Chemistry, 10, 209-220.
147. Stewart, J. J. P. (1989b). Optimization of parameters for semiempirical methods II. Applications. Journal of Computational Chemistry, 10, 221-264.
148. Stewart, J. J. P. (1991). Optimization of parameters for semiempirical methods. III extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi. Journal of Computational Chemistry, 12, 320-341.
149. Stewart, J. (2007). Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. Journal of Molecular Modeling, 13, 1173-1213.
150. Strano, M. S., Dyke, C. A., Usrey, M. L., Barone, P. W., Allen, M. J., Shan, H., ... Smalley, R. E. (2003). Electronic structure control of single-walled carbon nanotube functionalization. Science, 301, 1519-1522.
151. Sun, C., & Tang, T. (2009). Structure of a polyelectrolyte around an electronically responsive cylinder. Journal of Colloid and Interface Science, 338, 276-283.
152. Sun, Y.-P., Fu, K., Lin, Y., & Huang, W. (2002). Functionalized carbon nanotubes: Properties and applications. Accounts of Chemical Research, 35, 1096-1104.
153. Tao, N. J., & Shi, Z. (1994). Monolayer Guanine and Adenine on Graphite in NaCl solution: A comparative STM and AFM study. The Journal of Physical Chemistry, 98, 1464-1471.
154. Tkatchenko, A., Robert, A., DiStasio, J., Head-Gordon, M., & Scheffler, M. (2009). Dispersion-corrected Møller-Plesset second-order perturbation theory. The Journal of Chemical Physics, 131, 094106-1-094106-7.
155. Tkatchenko, A., & Scheffler, M. (2009). Accurate molecular Van Der Waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102, 073005-1-073005-4.
156. Torres, E., & DiLabio, G. A. (2012). A (nearly) universally applicable method for modeling noncovalent interactions using B3LYP. The Journal of Physical Chemistry Letters, 3, 1738-1744.
157. Tournus, F., & Charlier, J.-C. (2005). Ab initio study of benzene adsorption on carbon nanotubes. Physical Review B, 71, 165421-1-165421-8.
158. Tsuzuki, S., Uchimaru, T., Matsumura, K., Mikami, M., & Tanabe, K. (2000). Effects of the higher electron correlation correction on the calculated intermolecular interaction energies of benzene and naphthalene dimers: Comparison between MP2 and CCSD(T) calculations. Chemical Physics Letters, 319, 547-554.
159. Uchihashi, T., Okada, T., Sugawara, Y., Yokoyama, K., & Morita, S. (1999). Self-assembled monolayer of adenine base on graphite studied by noncontact atomic force microscopy. Physical Review B, 60, 8309-8313.
160. Umadevi, D., & Sastry, G. N. (2011). Quantum mechanical study of physisorption of nucleobases on carbon materials: Graphene versus carbon nanotubes. The Journal of Physical Chemistry Letters, 2, 1572-1576.
161. Vaart, A. V. D., & Merz Jr., K. M. (2000). Charge transfer in biologically important molecules: Comparison of high-level ab initio and semiempirical methods. International Journal of Quantum Chemistry, 77, 27-43.
162. Varghese, N., Mogera, U., Govindaraj, A., Das, A., Maiti, P. K., Sood, A. K., & Rao, C. N. R. (2009). Binding of DNA nucleobases and nucleosides with graphene. ChemPhysChem, 10, 206-210.
163. Veetil, J. V., & Ye, K. (2007). Development of immunosensors using carbon nanotubes. Biotechnology Progress, 23, 517-531.
164. von Lilienfeld, O. A., Tavernelli, I., Rothlisberger, U., & Sebastiani, D. (2004). Optimization of effective atom centered potentials for london dispersion forces in density functional theory. Physical Review Letters, 93, 153004-1-153004-4.
165. Vovusha, H., Sanyal, S., & Sanyal, B. (2013). Interaction of nucleobases and aromatic amino acids with graphene oxide and graphene flakes. The Journal of Physical Chemistry Letters, 4, 3710-3718.
166. Walther, J. H., Jaffe, R., Halicioglu, T., & Koumoutsakos, P. (2001). Carbon nanotubes in water: Structural characteristics and energetics. The Journal of Physical Chemistry B, 105, 9980-9987.
167. 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. The Journal of Physical Chemistry C, 112, 14297-14305.
168. Wang, Y., & Bu, Y. (2007). Noncovalent interactions between cytosine and SWCNT. The Journal of Physical Chemistry B, 111, 6520-6526.
169. Wang, H., & Ceulemans, A. (2009). Physisorption of adenine DNA nucleosides on zigzag and armchair single-walled carbon nanotubes: A first-principles study. Physical Review B, 79, 195419-1-195419-6.
170. Wang, Y., Iqbal, Z., & Mitra, S. (2005). Microwave-induced rapid chemical functionalization of single-walled carbon nanotubes. Carbon, 43, 1015-1020.
171. Wang, H., Muren, N. B., Ordinario, D., Gorodetsky, A. A., Barton, J. K., & Nuckolls, C. (2012). Transducing methyltransferase activity into electrical signals in a carbon nanotube- DNA device. Chemical Science, 3, 62-65.
172. WenXing, B., ChangChun, Z., & WanZhao, C. (2004). Simulation of Young's modulus of single-walled carbon nanotubes by molecular dynamics. Physica B: Condensed Matter, 352, 156-163.
173. Werder, T., Walther, J. H., Jaffe, R. L., Halicioglu, T., & Koumoutsakos, P. (2003). On the water-carbon interaction for use in molecular dynamics simulations of graphite and carbon nanotubes. The Journal of Physical Chemistry B, 107, 1345-1352.
174. Williams, K. A., Veenhuizen, P. T. M., de la Torre, B. G., Eritja, R., & Dekker, C. (2002). Towards DNA-mediated self assembly of carbon nanotube molecular devices. AIP Conference Proceedings, 633, 444-448.
175. Xiao, S., & Hou, W. (2006). Studies of size effects on carbon nanotubes' mechanical properties by using different potential functions. Fullerenes, Nanotubes, and Carbon Nanostructures, 14, 9-16.
176. Xiao, Z., Wang, X., Xu, X., Zhang, H., Li, Y., & Wang, Y. (2011). Base- and structure-dependent dna dinucleotide- carbon nanotube interactions: Molecular dynamics simulations and thermodynamic analysis. The Journal of Physical Chemistry C, 115, 21546-21558.
177. Xu, Y., Pehrsson, P. E., Chen, L., Zhang, R., & Zhao, W. (2007). Double-stranded DNA single-walled carbon nanotube hybrids for optical hydrogen peroxide and glucose sensing. Journal of Physical Chemistry C, 111, 8638-8643.
178. Yamazaki, T., & Fenniri, H. (2012). Imaging carbon nanotube interaction with nucleobases in water using the statistical mechanical theory of molecular liquids. The Journal of Physical Chemistry C, 116, 15087-15092.
179. Yang, R., Tang, Z., Yan, J., Kang, H., Kim, Y., Zhu, Z., & Tan, W. (2008). Noncovalent assembly of carbon nanotubes and single-stranded DNA: An effective sensing platform for probing biomolecular interactions. Analytical Chemistry, 80, 7408-7413.
180. Yarotski, D. A., Kilina, S. V., Talin, A. A., Tretiak, S., Prezhdo, O. V., Balatsky, A. V., & Taylor, A. J. (2009). Scanning tunneling microscopy of DNA-wrapped carbon nanotubes. Nano Letters, 9, 12-17.
181. Zhang, M., Fang, S., Zakhidov, A. A., Lee, S. B., Aliev, A. E., Williams, C. D., ... Baughman, R. H. (2005). Strong, transparent, multifunctional, carbon nanotube sheets. Science, 309, 1215-1219.
182. Zhang, T., Mubeen, S., Myung, N. V., & Deshusses, M. A. (2008). Recent progress in carbon nanotube-based gas sensors. Nanotechnology, 19, 332001-1-332001-14.
183. Zhang, Y.-B., Kanungo, M., Ho, A. J., Freimuth, P., van der Lelie, D., Chen, M., ... Wong, S. S. (2007). Functionalized carbon nanotubes for detecting viral proteins. Nano Letters, 7, 3086-3091.
184. Zhao, X. (2011). Self-assembly of DNA segments on graphene and carbon nanotube arrays in aqueous solution: A molecular simulation study. The Journal of Physical Chemistry C, 115, 6181-6189.
185. Zhao, X., & Johnson, J. K. (2007). Simulation of adsorption of DNA on carbon nanotubes. Journal of the American Chemical Society, 129, 10438-10445.
186. Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2005). Exchangecorrelation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. The Journal of Chemical Physics, 123, 161103-1-161103-4.
187. Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2006). Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 2, 364-382.
188. Zhao, Y., & Truhlar, D. G. (2005). Benchmark databases for nonbonded interactions and their use to test density functional theory. Journal of Chemical Theory and Computation, 1, 415-432.
189. Zhao, Y., & Truhlar, D. G. (2006a). Density functional for spectroscopy: No long-range self-interaction error, good performance for rydberg and charge-transfer states, and better performance on average than B3LYP for ground states. The Journal of Physical Chemistry A, 110, 13126-13130.
190. Zhao, Y., & Truhlar, D. G. (2006b). A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. The Journal of Chemical Physics, 125, 194101-1-194101-18.
191. Zhao, Y., & Truhlar, D. (2008a). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoretical Chemistry Accounts, 120, 215-241.
192. Zhao, Y., & Truhlar, D. G. (2008b). Density functionals with broad applicability in chemistry. Accounts of Chemical Research, 41, 157-167.
193. Zhao, Y., & Truhlar, D. G. (2011). Applications and validations of the Minnesota density functionals. Chemical Physics Letters, 502, 1-13.
194. Zheng, M., Eom, K., & Ke, C. (2009). Calculations of the resonant response of carbon nanotubes to binding of DNA. Journal of Physics D: Applied Physics, 42, 145408-1-145408-8.
195. Zheng, M., Jagota, A., Semke, E. D., Diner, B. A., Mclean, R. S., Lustig, S. R., ... Tassi, N. G. (2003). DNA-assisted dispersion and separation of carbon nanotubes. Nature Materials, 2, 338-342.
196. Zheng, M., Jagota, A., Strano, M. S., Santos, A. P., Barone, P., Chou, S. G., ... Walls, D. J. (2003). Structure-based carbon nanotube sorting by sequence-dependent DNA assembly. Science, 302, 1545-1548.
197. Zou, J., Liang, W., & Zhang, S. (2010). Coarse-grained molecular dynamics modeling of DNA-carbon nanotube complexes. International Journal for Numerical Methods in Engineering, 83, 968-985.