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The guanine functionalization reaction uses singlet oxygen to covalently link single-wall carbon nanotubes to guanine bases in their ssDNA coatings. This creates shallow but densely spaced exciton traps that modulate nanotube band gaps with energetic and spatial control, giving red-shifted electronic transitions. To better understand guanine functionalization, we used quantum chemical computations to compare the stabilities of several candidate addends in multiple orientations on the nanotube surface. Structures of three possible isomers of guanine peroxide (GPO), the reactive intermediate formed through reaction of 9-methyl guanine with singlet O2, were optimized using the semi-empirical PM3 method. To examine effects of nanotube diameter on adduct stability, we then computed the enthalpy changes for bonding of each GPO isomer to a 6 nm segment of (5,4), (6,5), (7,6) and (8,7) SWCNT. Six orientations of the addend on the SWCNT surface were considered for each (n,m) species, giving a total of 72 adduct structures. The results showed that for all four SWCNTs, the most energetically stable adduct is the 4,5-GPO isomer bonded in the ortho L-30 orientation. This adduct can be considered a derivative of 1,4-dioxane. Subsequent ab initio DFT and TDDFT computations comparing bonding orientations of one guanine addend on a 12 nm long SWCNT segment found that ortho L -30 gives a slightly reduced HOMO-LUMO gap, a mildly localized exciton structure, and a slightly red-shifted E11 optical transition as compared to the pristine SWCNT, in agreement with experiment. We conclude that guanine functionalization of near-armchair SWCNTs leads mainly to 4,5-GPO addends bonded in the ortho L -30 orientation.
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This content will become publicly available on July 10, 2026
Molecular Dynamics Insights into the Guanine Functionalization of Single-Wall Carbon Nanotubes
In the guanine functionalization reaction, single-wall carbon nanotubes (SWCNTs) coated with physisorbed single-stranded DNA become covalently bonded to guanine bases in the DNA. The resulting perturbations to SWCNT electronic and optical properties depend on the spacings between the sites of covalent bonding. To model those spacings, we have used advanced molecular dynamics simulations (replica exchange with solute tempering) to study adsorbed conformations of (GT)10 ssDNA strands and the corresponding distributions of guanine locations prior to reaction. The simulations explored the effects of interstrand interactions, nanotube end effects, solution ionic strength, DNA/SWCNT mass ratio, and SWCNT diameter on conformations and guanine spacings. We analyzed the impacts of such simulation conditions on the spatial distribution of guanine nucleobases along the nanotube axis. Irregularities in those spacings are suggested to cause inhomogeneities in exciton energy landscapes and be a source of spectral broadening in SWCNTs modified by guanine functionalization.
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- Award ID(s):
- 2203309
- PAR ID:
- 10651345
- Publisher / Repository:
- American Chemical Society
- Date Published:
- Journal Name:
- The Journal of Physical Chemistry B
- Volume:
- 129
- Issue:
- 27
- ISSN:
- 1520-6106
- Page Range / eLocation ID:
- 6847 to 6860
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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