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Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes.

ABSTRACT: Molecular dynamics simulations were used to characterize the self-assembly of single-stranded DNA (ssDNA) on a (6,5) single-walled carbon nanotube (SWCNT) in aqueous solution for the purpose of gaining an improved theoretical understanding of separation strategies for SWCNTs using ssDNA as a dispersant. Four separate ssDNA sequences, ((TAT)₄, TTA(TAT)₂ATT, C₁₂, (GTC)₂GT), at various levels of loading, were chosen for study based on published experimental work showing selective extraction of particular SWCNT species based on the ssDNA dispersant sequence. We develop a unique workflow based on free energy perturbation (FEP) and use this to determine the relative solubility of these complexes due to the adsorption of the ssDNA on the SWCNT surface, and hence, rank the favorability of separations observed during experiments. Results qualitatively agree with experiments and indicate that the nucleobase sequence of the adsorbed ssDNA greatly affects the free energy of complex solvation which ultimately drives SWCNT separation. Further, to elucidate the underlying physics governing the ssDNA-SWCNT solubility rankings, we also present calculations for four structural characteristics of ssDNA adsorption. We demonstrate that a unique type of intra-strand hydrogen bonding is the most important factor contributing to the stability of the ssDNA-SWCNT complexes and show how these adsorption characteristics are coupled with the FEP results.

SUBMITTER: Hinkle KR

PROVIDER: S-EPMC8204635 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Microbial electrochemical systems (MESs) rely on the microbes' ability to transfer charges from their anaerobic respiratory processes to electrodes through extracellular electron transfer (EET). To increase the generally low output signal in devices, advanced bioelectrical interfaces tend to augment this problem by attaching conducting nanoparticles, such as positively charged multiwalled carbon nanotubes (CNTs), to the base carbon electrode to electrostatically attract the negatively charged bacterial cell membrane. On the other hand, some reports point to the importance of the magnitude of the surface charge of functionalized single-walled CNTs (SWCNTs) as well as the size of functional groups for interaction with the cell membrane, rather than their polarity. To shed light on these phenomena, in this study, we prepared and characterized well-solubilized aqueous dispersions of SWCNTs functionalized by either positively or negatively charged cellulose-derivative polymers, as well as with positively charged or neutral small molecular surfactants, and tested the electrochemical performance of Shewanella oneidensis MR-1 in MESs in the presence of these functionalized SWCNTs. By simple injection into the MESs, the positively charged polymeric SWCNTs attached to the base carbon felt (CF) electrode, and as fluorescence microscopy revealed, allowed bacteria to attach to these structures. As a result, EET currents continuously increased over several days of monitoring, without bacterial growth in the electrolyte. Negatively charged polymeric SWCNTs also resulted in continuously increasing EET currents and a large number of bacteria on CF, although SWCNTs did not attach to CF. In contrast, SWCNTs functionalized by small-sized surfactants led to a decrease in both currents and the amount of bacteria in the solution, presumably due to the detachment of surfactants from SWCNTs and their detrimental interaction with cells. We expect our results will help researchers in designing materials for smart bioelectrical interfaces for low-scale microbial energy harvesting, sensing, and energy conversion applications.

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Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes.

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