skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.

Abstract

Single-wall carbon nanotubes (SWNTs) have shown great promise in novel applications in molecular electronics, biohazard detection, and composite materials. Commercially synthesized nanotubes exhibit a wide dispersion of geometries and conductivities, and tend to aggregate. Hence the key to using these materials is the ability to solubilize and sort carbon nanotubes according to their geometric/electronic properties. One of the most effective dispersants is single-stranded DNA (ssDNA), but there are many outstanding questions regarding the interaction between nucleic acids and SWNTs. In this work we focus on the interactions of SWNTs with single monomers of nucleic acids, as a first step to answering these outstanding questions. We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We find that the binding energies are generally favorable, of the order of a few kcal/mol. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides.more » We use electronic structure (Density Functional Theory (DFT) and Moller-Plesset second order perturbation to uncorrelated Hartree Fock theory (MP2)) methods to complement the classical force field study. With judicious choices of DFT exchange correlation functionals, we find that DFT, MP2, and classical force field predictions are in qualitative and even quantitative agreement; all three methods should give reliable and valid predictions. However, in one important case, the interactions between ions and metallic carbon nanotubes--the SWNT polarization-induced affinity for ions, neglected in most classical force field studies, is found to be extremely large (on the order of electron volts) and may have important consequences for various SWNT applications. Finally, the adsorption of NMPs onto single-walled carbon nanotubes were studied experimentally. The nanotubes were sonicated in the presence of the nucleotides at various weight fractions and centrifuged before examining the ultraviolet absorbance of the resulting supernatant. A distinct Langmuir adsorption isotherm was obtained for each nucleotide. All of the nucleotides differ in their saturation value as well as their initial slope, which we attribute to differences both in nucleotide structure and in the binding ability of different types or clusters of tubes. Results from this simple system provide insights toward development of dispersion and separation methods for nanotubes: strongly binding nucleotides are likely to help disperse, whereas weaker ones may provide selectivity that may be beneficial to a separation process.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Sandia National Laboratories
Sponsoring Org.:
USDOE
OSTI Identifier:
922755
Report Number(s):
SAND2007-6163
TRN: US200806%%250
DOE Contract Number:  
AC04-94AL85000
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; ADSORPTION; ADSORPTION ISOTHERMS; AFFINITY; AQUEOUS SOLUTIONS; BINDING ENERGY; CARBON; COMPOSITE MATERIALS; DETECTION; DNA; ELECTRONIC STRUCTURE; ELECTRONS; FUNCTIONALS; MONOMERS; NANOTUBES; NUCLEIC ACIDS; NUCLEOTIDES; PHOSPHATES; SODIUM IONS; SORTING; Carbon.; Electronic apparatus and appliances-Thermal properties.; Nanotubes.

Citation Formats

Robinson, David B, Leung, Kevin, Rempe, Susan B, Dossa, Paul D, Frischknecht, Amalie Lucile, and Martin, Marcus Gary. Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.. United States: N. p., 2007. Web. doi:10.2172/922755.
Robinson, David B, Leung, Kevin, Rempe, Susan B, Dossa, Paul D, Frischknecht, Amalie Lucile, & Martin, Marcus Gary. Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.. United States. doi:10.2172/922755.
Robinson, David B, Leung, Kevin, Rempe, Susan B, Dossa, Paul D, Frischknecht, Amalie Lucile, and Martin, Marcus Gary. Mon . "Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.". United States. doi:10.2172/922755. https://www.osti.gov/servlets/purl/922755.
@article{osti_922755,
title = {Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.},
author = {Robinson, David B and Leung, Kevin and Rempe, Susan B and Dossa, Paul D and Frischknecht, Amalie Lucile and Martin, Marcus Gary},
abstractNote = {Single-wall carbon nanotubes (SWNTs) have shown great promise in novel applications in molecular electronics, biohazard detection, and composite materials. Commercially synthesized nanotubes exhibit a wide dispersion of geometries and conductivities, and tend to aggregate. Hence the key to using these materials is the ability to solubilize and sort carbon nanotubes according to their geometric/electronic properties. One of the most effective dispersants is single-stranded DNA (ssDNA), but there are many outstanding questions regarding the interaction between nucleic acids and SWNTs. In this work we focus on the interactions of SWNTs with single monomers of nucleic acids, as a first step to answering these outstanding questions. We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We find that the binding energies are generally favorable, of the order of a few kcal/mol. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides. We use electronic structure (Density Functional Theory (DFT) and Moller-Plesset second order perturbation to uncorrelated Hartree Fock theory (MP2)) methods to complement the classical force field study. With judicious choices of DFT exchange correlation functionals, we find that DFT, MP2, and classical force field predictions are in qualitative and even quantitative agreement; all three methods should give reliable and valid predictions. However, in one important case, the interactions between ions and metallic carbon nanotubes--the SWNT polarization-induced affinity for ions, neglected in most classical force field studies, is found to be extremely large (on the order of electron volts) and may have important consequences for various SWNT applications. Finally, the adsorption of NMPs onto single-walled carbon nanotubes were studied experimentally. The nanotubes were sonicated in the presence of the nucleotides at various weight fractions and centrifuged before examining the ultraviolet absorbance of the resulting supernatant. A distinct Langmuir adsorption isotherm was obtained for each nucleotide. All of the nucleotides differ in their saturation value as well as their initial slope, which we attribute to differences both in nucleotide structure and in the binding ability of different types or clusters of tubes. Results from this simple system provide insights toward development of dispersion and separation methods for nanotubes: strongly binding nucleotides are likely to help disperse, whereas weaker ones may provide selectivity that may be beneficial to a separation process.},
doi = {10.2172/922755},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2007},
month = {10}
}

Technical Report:

Save / Share: