Raman Spectroscopy Study and First-Principles Calculations of the Interaction between Nucleic Acid Bases and Carbon Nanotubes

Abstract

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

Binding of polynucleotides with single‐walled carbon nanotubes: Effect of temperature

“…The conclusion is based on comparison of the energies obtained by ab initio calculation. In accordance with these calculations, the stacking energy of the adenine dimer is not more than 9 kcal/mol [25], but the energy of p-p stacking between adenine and SWNT (10.0) is 14 kcal/mol [26]. Thus, we believe that the main contribution to the temperature dependence of the hyperchromic coefficient is made with residual selfstacking polymer fragments.…”

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

“…For geometry optimization and subsequent interaction energy calculations, we have selected Truhlar's M05-2X 39 functional and the 6-31G++(2d,2p) basis set 40 . M05-2X is a hybrid meta GGA functional with 56% Hartree-Fock exchange component and is known to perform remarkably well for noncovalently bonded molecules of biological relevance, 41 including nucleobases [42][43][44][45][46][47][48][49] . 6-31G++(2d,2p) is a split valance double ζ type basis set, with two sets of d type polarization function for all non-hydrogen atoms and two sets of p type polarization function for hydrogen atoms, and also include s-p diffused orbitals for non-hydrogen atoms, was used for ground state geometry optimization.…”

Effect of chirality and curvature of single‐walled carbon nanotubes on the adsorption of uracil

“…This work initiated the studies on the noncovalent functionalization of carbon nanotubes. Now several reports are available about the noncovalent functionalization of CNT with biological molecules like DNA 9–14, amino acids 15, and proteins 16. These studies have received considerable research interest because the electronic and mechanical properties of the CNT remain unaltered after functionalization 17.…”

“…Gowtham et al 12 reported the binding strength of DNA and RNA nucleic acid bases with CNT (5,0) and the direct correlation with the molecular polarizabilities of the base molecules. Interactions of nucleic acid bases with carbon nanotube (10,0) and with planar graphene surface were examined using a Raman spectroscopic technique and quantum‐chemical methods with different functionals 13. The Raman studies have shown a spectral down shift of the high‐frequency component of the G band of the SWCNTs.…”