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Accession Number ADA559013
Title Modeling Biomolecular-Surface Nonbonded Interactions: Application to Nucleobase Adsorption on Single-Wall Carbon Nanotube Surfaces.
Publication Date 2012
Media Count 9p
Personal Author B. Akdim P. N. Day R. Pachter R. R. Naik S. S. Kim
Abstract In this work we explored the selectivity of single nucleobases towards adsorption on chiral single-wall carbon nanotubes (SWCNTs) by density functional theory calculations. Specifically, the adsorption of molecular models of guanine (G), adenine (A), thymine (T),and cytosine (C), as well as of AT and GC Watson-Crick (WC) base pairs on chiral SWCNT C(6, 5), C(9, 1) and C(8, 3) model structures, was analyzed in detail. The importance of correcting the exchange-correlation functional for London dispersion was clearly demonstrated, yet limitations in modeling such interactions by considering the SWCNT as a molecular model may mask subtle effects in a molecular/macroscopic material system. The trend in the calculated adsorption energies of the nucleobases on same diameter C(6, 5) and C(9, 1) SWCNT surfaces, i.e. G > A > T > C, was consistent with related computations and experimental work on graphitic surfaces, however contradicting experimental data on the adsorption of single- strand short homo-oligonucleotides on SWCNTs that demonstrated a trend of G > C > A > T (Albertorio et al 2009 Nanotechnology 20 395101). A possible role of electrostatic interactions in this case was partially captured by applying the effective fragment potential method, emphasizing that the interplay of the various contributions in modeling nonbonded interactions is complicated by theoretical limitations. Finally, because the calculated adsorption energies for Watson-Crick base pairs have shown little effect upon adsorption of the base pair farther from the surface, the results on SWCNT sorting by salmon genomic DNA could be indicative of partial unfolding of the double helix upon adsorption on the SWCNT surface.
Keywords Adenine
Adsorption
Carbon nanotubes
Consistency
Cytosine
Density functional theory
Deoxyribonucleic acids
Energy
Experimental data
Genome
Molecular structure
Patterns
Structures
Surfaces


 
Source Agency Non Paid ADAS
NTIS Subject Category 99D - Basic & Synthetic Chemistry
Corporate Author Air Force Research Lab., Wright-Patterson AFB, OH. Materials and Manufacturing Directorate.
Document Type Journal article
Title Note Journal article.
NTIS Issue Number 1219
Contract Number N/A

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