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Theoretical Studies of the Interaction and Protection Mechanism between Carbon-based Nanomaterials and Biomolecules

Author SunWenMing
Tutor BuYuXiang
School Shandong University
Course Theoretical and Computational Chemistry
Keywords nanotube fullerene redox properties oxidative damage solvent effect
Type PhD thesis
Year 2011
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The interaction of biomolecules with carbon-based nanomaterials has generated a great deal of interest in the past few years. There are concerns about the biological safety, activity and compatibility of carbon-based nanomaterials. Such issues are relevant to the proposed applications of nanomaterials in drug or gene delivery and protective agent. However, fundamental understanding of how the nanomaterial interacts with a biomolecule at atomic/molecular level still remains as an open question. Given the complexity of the interested systems, it is challenging to probe these properties by experiment. A promising alternative approach is theoretical modeling. Thus, in the present dissertation, density functional theory and dispersion-corrected DFT methods have been performed to investigate the interactions such as glycine with intrinsic/B-doped single walled carbon nanotubes, and nucleic acid bases with C60 and its derivatives. We expect that these findings would offer new strategy for designing new functional nanodevices. We carried out a series of significative work and obtained some valuable results on these issues. The primary innovations are related as follows.(1) Interaction between glycine molecule/radical and intrinsic/B-doped SWCNT. The adsorptions of a glycine molecule as well as dehydrogenated radicals on the side walls of both intrinsic and boron-doped (B-doped) single-walled (8,0) carbon nanotubes (SWCNTs) were investigated by a density functional theory. A glycine molecule tends to physically adsorb on intrinsic SWCNT, yet chemically adsorb on B-doped SWCNT as a result of a somewhat chemical bond between the electron-rich nitrogen atom of the glycine molecule and the electron-scarce boron atom of the doped SWCNT. Opposite to the previous report (J. Phys. Chem. B 2006, 110,6048-6050), it is found in the present study that both the N-centered and C-centered glycine radicals can form quite stable complexes with intrinsic as well as B-doped (8,0) SWCNTs. When the B-doped SWCNT interacts with glycine radicals, although there is a competition between B and the neighbour C in the nanotube axis direction, glycine radicals preferentially bind to the C site. The encapsulations of a glycine molecule into SWCNTs with various diameters are also discussed. We find that the encapsulation process is endothermic for (8,0) and (9,0) SWCNTs, while it is exothermic for (10,0) SWCNT, indicating that the critical diameter of the zigzag SWCNT for the encapsulation is 7.83 A, the diameter of (10,0).(2).Redox properties of nanotubes. Density functional theory was used to investigate redox properties, such as ionization potentials (IP), electron affinities (EA), electronegativities (x) and Fermi levels (Ef) for infinite length armchair single-walled carbon nanotubes (SWNT) (n, n) (n=3-16), zigzag SWNT (n,0) (n=5-16), as well as double-walled carbon nanotubes (DWNT) (n, n)@(n+5, n+5) (n=3,5 and 6). These properties show a strong and different diameter dependence. With increasing diameters, IPs of armchair SWNTs (n, n) decrease monotonically, while EAs increase monotonically. Although IPs of zigzag SWNTs (n,0) also generally decrease, there is an increase occurring just after (3k,0) (k=2,3,4, and 5) and shows a group behaviour, in which every three neighbourhood (3k,0), (3k-1,0) and (3k-2,0) form a group. However, opposite to the armchair SWNTs, the EAs of zigzag SWNTs decrease rapidly with increasing diameter till (11,0) and then gently increase. EAs of the zigzag SWNTs also exhibit a group behaviour, yet are not synchronous with IPs. With increasing diameters, the IPs and EAs of both the armchair and zigzag SWNTs approach to approximately 4.7 and 3.9eV. For the armchair SWNTs electronegativity (x) and Fermi level (-Ef) change very slightly with diameters, while for the zigzag they decrease rapidly till (9,0) and then gently oscillate to the similar levels to those of the armchair. The IPs and EAs for (n, n)@ (n+5, n+5) DWNTs have the same trend as armchair SWNTs. It was also found that these DWNTs characterize better redox properties than their constituents. These interesting findings are important for redox chemistry based on NTs and may offer a new strategy for separation of NTs.(3). Interaction between NAB and C60 in the gas phase. The major objective of this part is to address a controversial binding sequence between nucleic acid bases (NABs) and C6o by investigating adsorptions of NABs and their cations on C6o fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2X and M06-2X, as well as a dispersion-corrected density functional, PBE-D. PBE-D provides result in the following sequence, G>A>T>C, which is the same as the hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2X or even the M06-2X method. The results indicated that PDE-D performs better than M06-2X for the observed NAB@C60π-stacked complexes. To discuss whether C6o could prevent NABs from oxidative damage, ionization potentials of NABs and C6o, and frontier molecular orbitals of the complexes NABs@C6o and (NABs@C6o)+ are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C6o for T and C complexes, while for G and A the hole delocalized over the entire complex, rather than a localization on the C6o moiety. The interesting finding might open a new strategy for protecting DNA from oxidative damage and offer a new idea for designing C60-based antioxidative drugs.(4). Solvation effect on the interaction between NAB and C6o. Solvation effect was involved to investigate the feasibility of C6o act as the protective agent. Results indicated that in the aqueous phase, C6o has a larger IP value than NAB. These results revealed that when an electron escapes from the complexes, the hole was preferentially created in NAB parts, not in C60 moiety. In this sense, the absent of C6o in the aqueous phase could not protect NAB from oxidative damage. This part is not only a supplement to the former exploration, but also offers a new strategy of designing new C60-based protective agent.(5). Interaction between NAB and Li/Na@C60.The binding trend of neutral NAB and Li@C6o decreases in the sequence G>C>A>T, while the binding in cationic state exhibit a distinct sequence of C>G>A>T. These two binding trends are different with their counterparts in NAB-C60 complexes, indicating that the encapsulating of Li atom could affect the binding orders. Regarding its lower IP, Li@C6o could protect NABs from oxidative damage, which produces a better performance than intrinsic C60. We also investigated the performance of different charge population scheme upon our complexes. It was suggested that ESP could obtain reasonable charge population results in the describing of intermolecular properties of these complexes. Besides providing detailed information of the equilibrium distances, binding energies, charge transfer and frontier orbitals about the interaction, the noncovalent interaction was also identifying and visualization based on Yang’s approach. Since Li@C6o has a lower IP than NAB, especially in the aqueous phase, it could protect NAB from oxidative damage both in the gas and aqueous phase.The series of systemic investigations will offer new statregies for the fields such as the CNT-based molecular device design, the application of CNT in electrochemistry, the separation of CNTs and the biomedical engineering application of fullerene-based materials.

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