Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

Pure carbon nanotubes (CNT) and CNT–polymer composites have many useful properties, ranging from electrical conductivity to superior mechanical strength. However, the full potential of using CNTs as reinforcements (in a polymer matrix, for example) has been severely limited because of complications associated with the dispersion of CNTs. CNTs tend to entangle with each other, forming materials with properties that fall short of expectations. One of the effective ways of dispersing CNTs is the use of short π-conjugated oligomers like oligo­(p-phenylene ethynylene)­s (OPEs) as dispersants. In this study, we provide a comprehensive investigation of the interactions between single-walled CNTs (SWCNTs) and OPEs with two different end groups; aldehyde (ALD) and dithiafulvene (DTF). The hybrid B3LYP and the dispersion (D)- and/or the long-range (LR)-corrected density functional theory (DFT) methods such as B97D, wB97XD, and CAM-B3LYP with the 6-31G­(d) basis set are employed in obtaining electronic structure information (dipole moments and energy levels) for the gas-phase (single) oligomers and the (6,5) SWCNT and their combinations. In addition, the D- and/or LR-corrected DFT methods are used in determining binding energies and intermolecular distances for the OPE/SWCNT combinations. We focus on understanding the roles of oligomer’s end groups and side chains in the dispersion of SWCNTs. In agreement with the experimental observations, the electronic structure and the binding energy results show that OPE-DTF interacts more strongly with the SWCNT than OPE-ALD. This work also provides insight into why OPEs end-capped with DTFs are much more effective in the dispersion of CNTs than OPEs end-capped with ALDs. Furthermore, this computational analysis can be of use in choosing an appropriate D- and/or LR-corrected DFT method when studying properties of systems containing CNTs.

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π-Conjugated oligomers with relatively short molecular backbones can be used effectively in dispersion of carbon nanotubes (CNTs). In this paper, we present a systematic study on interactions between diphenylene-fluorene oligomers (DPFs) and single-walled CNTs (SWCNTs) using density functional theory (DFT) calculations. Four DFT methods are used in this work: the long range (LR)-corrected CAM-B3LYP, the dispersion (D)-corrected B97D, the LR- and D-corrected wB97XD, and the hybrid B3LYP. The DPFs examined in this study contain different functional groups attached to the π-conjugated backbone, including two different end groups, carboxaldehyde (ALD) and dithiafulvenyl (DTF), and three different side chains (SCs), CH, OCH, and SCH. The computational results disclose the effects of end groups, SCs, and DFT methods on structures, dipole moments, and energetics of isolated DPFs and DPF/SWCNT combinations. Consistent with our previous study (involving oligo(p-phenylene ethynylene)s (OPEs)) [Aljohani et al., J. Phys. Chem. C, 2017, 121, 4692-4702], our results herein demonstrate that the type of end group plays a key role in determining the strength of interactions between SWNTs and conjugated oligomers. In particular, DTF-endcapped oligomers have a stronger electrostatic interaction with SWCNT than ALD-endcapped oligomers do. As a result, DTF-endcapped conjugated oligomers become more polarized than ALD-endcapped oligomers after complexing with SWCNTs. The magnitude of binding energy, on the other hand, shows dependence on the orientation of the backbone and side chains of these oligomers relative to the SWCNT which in the case of fluorene-based oligomers is not always favourable for optimal binding. This study indicates that fluorene-based oligomers might not be as good dispersants of SWCNTs as OPEs.

Among different dispersants of single-walled carbon nanotubes (SWCNTs), conjugated organic oligomers have the ability to interact strongly with SWCNTs and allow for effective dispersion in several organic solvents.