Browsing by Author "Alizadehmojarad, Ali A."

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    Covalent and Non-Covalent Functionalization of ssDNA-Wrapped Single-Wall Carbon Nanotubes: Computational and Experimental Studies
    (2023-04-13) Alizadehmojarad, Ali A.; Weisman, Bruce; Kolomeisky, Anatoly
    Single-wall nanotubes (SWCNTs) are nanomaterials with a wide range of optical and electronic properties that depend on their physical structure, which is indexed by a pair of integers (n,m). The discovery and interpretation of nanotube fluorescence has taken SWCNT research to a new level by enabling novel studies of structure-specific reactions and processes. These require the suspension of individualized SWCNTs in liquids through non-covalent functionalization by dispersants such as polymers, conventional surfactants, and single-stranded DNA (ssDNA). Understanding the specific interactions between nanotubes and coatings is important for advancing both basic and applied research. Both computational and experimental investigations have been conducted to understand the mechanism of separation and sorting of specific (n,m) species coated by DNA oligonucleotides. In addition to non-covalent SWCNT functionalization, covalent functionalization has also added a new research dimension and the ability to modify important properties of pristine nanotubes. In this thesis, novel computational and experimental methods were developed to further understand non-covalent and covalent functionalization of SWCNTs dispersed in DNA oligonucleotides and in a conventional surfactant. Computational studies were performed to understand how a DNA oligo distinguishes two enantiomers of an (n,m) species. Replica exchange molecular dynamics (REMD) simulations revealed that this recognition is directly correlated with the nanotube surface area exposed to the environment when wrapped by a DNA oligo. In the case of covalent functionalization of guanine nucleobases to SWCNTs, steered MD (SMD) simulations showed that the nucleotides in the middle of a DNA strand are found in closer proximity to nanotube surface than those at the strand end. These observations are aligned with experimental findings suggesting that a greater degree of guanine functionalization is achieved with 31-nucleotide DNA oligos containing only one guanine in the middle than DNA oligos with one guanine near the end of a DNA strand. A novel experimental method was developed to measure extinction coefficient of SWCNTs in the UV region. These results have enabled the simple determination of total SWCNT concentrations in aqueous dispersions. The DNA/SWCNT mass ratio was then quantitatively evaluated to provide an important parameter for understanding conformations of DNA oligos wrapped around SWCNTs. Through this method, the dependence of DNA/SWCNT mass ratio on DNA oligo base sequence was experimentally determined. Those conformations around different (n,m) species were then further explored using standard MD simulations. In this way, the strength of interactions between nanotubes and DNA oligos was investigated, revealing that thymine-rich DNA oligos interact with nanotube surfaces more strongly than cytosine-rich oligos. The guanine functionalization of SWCNTs was conducted using excitation of metalloporphyrin photosensitizers with violet light. Guanine functionalization of nanotubes was monitored by red-shifts in their absorption and fluorescence spectra. The great advantage of using metalloporphyrin dyes instead of rose bengal as a photosensitizer is that they are more photostable and cause less interference with SWCNT absorption and fluorescence spectra. Consequently, kinetic studies of guanine functionalization of SWCNTs were performed to find the correlation between kinetic parameters and either dye concentration or guanine contents of the DNA oligos. Quantum chemistry methods were used to predict find the most stable product of covalent attachment of guanine to SWCNT side walls and to correlate the formation enthalpy of each adduct with nanotube diameter. The semi-empirical quantum chemistry results show that 4,5-guanine peroxide (GPO) attached to either ortho L30 or ortho L-30 positions on the nanotubes’ surface give the most energetically stable products of guanine functionalization. Excited state calculations then predict that 4,5-GPO attached at the ortho L30 positions results in the most red-shifted (6,5) absorption peak compared to other adducts. In a separate experimental study, the first structure-selective guanine functionalization of SWCNTs was achieved using near-infrared or visible photochemistry. Specific (n,m) SWCNT species were excited by monochromatic excitation at their characteristic E11 or E22 transitions. Energy transfer to dissolved O2 then generated singlet oxygen, which led to formation of guanine peroxide (GPO) and its bonding to SWCNT side walls. The guanine functionalization was selective for the excited nanotubes. Finally, MD simulations were used to investigate the noncovalent adsorption of the surfactant sodium dodecyl sulfate (SDS) on SWCNT surfaces. This study uncovered four different SDS morphologies, characterized their structures, and found the combinations of SDS concentrations and nanotube diameters leading to the different morphologies.
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    Dye Quenching of Carbon Nanotube Fluorescence Reveals Structure-Selective Coating Coverage
    (American Chemical Society, 2020) Zheng, Yu; Alizadehmojarad, Ali A.; Bachilo, Sergei M.; Kolomeisky, Anatoly B.; Weisman, R. Bruce; Smalley-Curl Institute
    Many properties and applications of single-wall carbon nanotubes (SWCNTs) depend strongly on the coatings that allow their suspension in aqueous media. We report that SWCNT fluorescence is quenched by reversible physisorption of dye molecules such as methylene blue, and that measurements of that quenching can be used to infer structure-specific exposures of the nanotube surface to the surrounding solution. SWCNTs suspended in single-stranded DNA oligomers show quenching dependent on the combination of nanotube structure and ssDNA base sequence. Several sequences are found to give notably high or low surface coverages for specific SWCNT species. These effects seem correlated with the selective recognitions used for DNA-based structural sorting of nanotubes. One notable example is that dye quenching of fluorescence from SWCNTs coated with the (ATT)4 base sequence is far stronger for one (7,5) enantiomer than for the other, showing that coating coverage is associated with the coating affinity difference reported previously for this system. Equilibrium modeling of quenching data has been used to extract parameters for comparative complexation constants and accessible surface areas. Further insights are obtained from molecular dynamics simulations, which give estimated contact areas between ssDNA and SWCNTs that correlate with experimentally inferred surface exposures and account for the enantiomeric discrimination of (ATT)4.