Effect of charge redistribution on the binding of DNA nucleotide to carbon nanotube in molecular dynamics. Issue 8 (24th May 2017)

• Record Type: Journal Article
• Authors: Chehelamirani, Morteza; Tang, Tian
• Is Part Of: Molecular simulation. Volume 43:Issue 8(2017)
• Page Start: 610
• Page End: 624
• Publication Date: 2017-05-24
• Subjects: DNA -- nucleotide -- carbon nanotube -- molecular dynamics simulation -- partial atomic charges -- stability; Molecular dynamics -- Computer simulation -- Periodicals; Statistical mechanics -- Computer simulation -- Periodicals; 539.6
• DOI: 10.1080/08927022.2017.1279285
• Languages: English
• ISSNs: 0892-7022

Abstract

Abstract: All-atom molecular dynamics (MD) simulations are performed to study the binding of DNA nucleotides with two carbon nanotubes (CNTs) with similar diameters but different chiralities. Two schemes for assigning partial atomic charges (PACs) are adopted: (I) using PACs obtained from isolated DNA nucleotide and CNT optimised in vacuum, and (II) using PACs obtained from optimising nucleotide-CNT hybrid in solution. The former approach is what most MD simulations have used in the study of DNA-CNT hybrids, while in the latter approach, a redistribution of the PACs has occurred upon the hybridisation. Our results show that the charge redistribution has a profound effect on the dynamics of binding. In particular, PACs obtained from (II) lead to more stable binding structures in the MD simulations. The findings suggest that care should be taken in simulating DNA-CNT interactions using the classical force field approach.