Theoretical Research On Noncovalent Functionalization Of Carbon Nanotubes

Carbon nanotubes (CNTs) have attracted enormous interest on account of their remarkable electrical, mechanical, and structural properties, offering a wide spectrum of applications in a variety of fields that range from gene delivery to bioimaging. However, their poor solubility and dispersity in aqueous and organic solvents have imposed great limitations to the wide usage of CNTs. Noncovalent functionalization of CNTs can not only overcome this shortcoming, but also potentially preserve the π-conjugated system. Furthermore, noncovalent functionalization can decrease toxicity of CNTs by combining biomolecules as a function of their biocompatibility. However, many aspects of the interactions involved in noncovalent functionalization of CNTs remain poorly understood owing to the lack of atomic-level information. In this dissertation, therefore, noncovalent functionalization of CNTs was probed with the help of molecular simulations to understand the nature of the underlying interactions and the processes of self-assembly. The main contents of the present dissertation include:(1) Helical wrapping of CNTs by polysaccharides is a new strategy of noncovalent functionalization. The wrapping processes of alginic acid, chitosan, and amylose around CNTs was systematically investigated by means of molecular dynamics simulations and free energy calculations. The results show that these polysaccharide chains can spontaneously wrap around CNTs by virtue of van der Waals attractions and hydrophobic interactions. Alginic acid and chitosan form loose helical structures due to the big rigidity while amylose forms compact helical conformation stabilized by an interlaced hydrogen-bond network. Documented experimentally and coined "Great Wall of China" motif, the typical arrangement of alginic acid residues around the tubular structure, is observed in the present simulations. Investigation of metal cations binding to alginic acid suggests that calcium ions can mediate aggregation of alginic acid chains by interacting strongly with the carboxylate groups, thereby leading to reverse unwrapping. Furthermore, the free-energy landscape characterizing the wrapping process of the chitosan chain from a straight conformation to a tight helical one brings to light two energetically favored helical conformations corresponding to distinct pitches. This method can be employed to estimate the pitch of the most stable helical structure, as well as to predict its stability with respect to an extended conformation, which provides a possible route for designing functionalized polymers wrapped on CNTs. At last, the simulations prove that amylose can wrap spontaneously around the tubular surface, starting from the end of the CNTs. Conversely, if wrapping proceeds from the middle of the CNTs, self-organization into a helical structure is not observed. The results reported herein shed meaningful light on the potential of short SWNTs for building ordered and innovative nanostructures.(2) The adsorption of hydrophobin protein named HFBI on the CNT surface can effectively increase the solubility of CNTs, leading to the architecture of ordered and novel nanoscale materials. Atomistic molecular dynamics simulations have been conducted to elucidate the adsorption mechanism of HFBI on the CNT surface in an aqueous environment. Independent simulations starting from three representative initial orientations of HFBI toward the tubular surface were performed, resulting in different adsorption modes. The main secondary structures of the protein in each mode are found to be preserved in the entire course of adsorption due to the four disulfide bonds. The relative binding free energies of the different adsorption modes were calculated, showing that the mode, in which the binding residues of HFBI fully come from its hydrophobic patch, is most energetically favored. Meanwhile, the adsorption behavior of HFBI on polydimethylsiloxane substrates was explored and the same adsorption mechanism was obtained. Moreover, a set of residues consisting of Leul2, Leu24, Leu26, Ile27, Ala66, and Leu68are found to play an important role in the adsorption of HFBI on different hydrophobic substrates, irrespective of the structural features of the surfaces. The results reported herein are consistent with experiments, and provide the theoretical basis for the design of bioactive surfaces.(3) Smith-Lemli-Opitz syndrome, a congenital and developmental malformation disease, is typified by abnormal accumulation of7-dehydrocholesterol (7DHC), the immediate precursor of cholesterol (CHOL), and depletion thereof. Knowledge of the effect of7DHC on the biological membrane is, however, still fragmentary. Large-scale atomistic molecular dynamics simulations have been conducted to elucidate differences in the structural properties of a bilayer membrane due to CHOL and7DHC, which is envisioned to probe the pathogeny of Smith-Lemli-Opitz syndrome from the perspective of computer simulations and provide a preliminary exploration for gene delivery by functionalized CNTs. The present series of results indicate that CHOL and7DHC possess virtually the same ability to condense and order membranes. Furthermore, the condensing and ordering effects are shown to be strengthened at increasing sterol concentrations.