Electronic properties of carbon nanotubes complexed with a DNA nucleotide

Abstract

Electronic properties of carbon nanotubes (CNTs) play an important role in their interactions with nano-structured materials. In this work, interactions of adenosine monophosphate (AMP), a DNA nucleotide, with metallic and semi-conducting CNTs are studied using the density functional tight binding (DFTB) method. The electronic structure of semi-conducting CNTs was found to be changed as they turned to metallic CNTs in a vacuum upon interaction with the nucleotide while metallic CNTs remain metallic. Specifically, the band gap of semi-conducting CNTs was decreased by 0.79 eV on average while nearly no change was found in the metallic tubes. However, our investigations showed that the presence of explicit water molecules prevents the metallicity change and only small changes in the CNT band gap occur. According to our charge analysis, the average negative charge accumulated on CNTs upon interaction with the AMP was determined to be 0.77 e in a vacuum while it was 0.03 e in solution. Therefore, it is essential to include explicit water molecules in simulating complexes formed by DNA nucleotides and CNTs which were ignored in several past studies performed using quantum mechanical approaches.

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

“…Interestingly, ab initio calculations shows that single-nucleotide or amino acid contacts with the carbon nanotube are sufficient to impact its electronic structure, even though charge transfer with the nanotube is very small. 38,40,42 In the case of nucleotides, the negatively charged phosphate group has a central role in this effect by locally polarizing the nanotube.…”

“…37 A more recent work also indicates that adenosine monophosphate (AMP) changes the band-gap of semi-conducting SWCNT, but not that of metallic SWCNT, mainly due to the negatively charged phosphate group. 38 On single amino acid-SWCNT interaction, ab initio calculations also indicate that aromatic amino acids (Phe, His, Tyr and Trp) form p-p interactions with SWCNT and affect the electronic spectra. 39,40 Hybrid QM/MM calculations were also performed to explicitly consider water molecules revealing a strong adsorption of the bases on SWCNT (stronger than in vacuum), a small charge transfer from SWCNT to the base and an electrostatic potential dominated by the phosphate group.…”

RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

“…Although RM1 has been initially developed with an eye to organic, biochemistry and drug research, it is also being intensively used in materials science. [279][280][281][282][283][284][285][286][287][288][289][290][291][292][293][294][295] For example, Duong et al 291 studied the molecular organization in 2D and 3D co-crystallizations of compounds of the type pyridylsubstituted diaminotriazines. The authors noted: "This method is expected to yield models of 2D organization that are qualitatively reliable.…”

“…The applicability of RM1 to materials science also included: structural properties, and dipole moments of Langmuir-Blodgett films; 293,294 an evaluation of the imidazole derivatives inhibition of mild steel corrosion in 1 M HCl; 292 geometry optimizations of the self-assembly of diblock copolymers MePEG-b-PAAm into micellar structures; 290 processing of 3-dimensional carbon nanostructures; 289 prediction of the enthalpy of formation of the species involved in the self-assembly from oxidation steps to obtain from nanorods to microspheres; 288 structural and vibrational properties of polycyclic aromatic hydrocarbons to carry out nanovehicles equipped with triptycene wheels; 287 energetic properties of a set of 16 molecules that span the most significant families of explosive compounds; 286 an investigation of mesophase behavior of binary mixtures of bent-core and calamitic compounds; 285 tip-based nanofabrication of diamondoid structures; 284 conformational possibilities of a set of 1,1,2-trichloroethane in faujasite (FAU)-type zeolites; 283 nanocrystal clusters that were carried out by biomineralization synthesis; 282 structural properties of a set of coordination polymer phases carried out by the extraction of trivalent lanthanide ions by the bis(2-ethylhexyl)phosphoric acid; 281 the oxidation of the surface of graphene layers; 280 a study of the electronic properties of carbon nanotubes that were complexed with a DNA nucleotide; 295 computational strategies to simulate electronic polarization effects; 296,297 binding and relative energies of the (H 2 O) 16 and (H 2 O) 17 clusters; 298 and conformational structures of trans-1,2-dichlorocyclohexane adsorbed in zeolites. 299…”