Functionalization Of SWNT And Conformation Transition Of DNA

Since the first discovery of single walled carbon nanotube (SWNT) in 1991, accompanying with the rapid progress of nanotechnology, people have accumulated much rational knowledge on SWNTs. We have known that, SWNTs formed by rolling up graphene sheets into tubular structures exhibit unique quasi one-dimensional characteristics. SWNTs also have unique mechanical and electronic properties, so they have great potential in many areas of nanotechnological applications. Among all kinds of investigations on SWNTs, functionalization of SWNTs is one of the most interesting subjects, because people have found that the properties of SWNT, especially their electronic properties, can be tailored by a variety of functionalization methods. This will provide very important opportunity for tailoring nanoblocks to build nanodevices. Particularly, recently, researchers have tried to use biomolecules to functionalize SWNTs. The interactions of SWNTs with protein, DNA, and ligand, respectively, have been investigated to explore possible application of this new kind of bio-nanomaterials in assembly of nanodevices. Some results indicate that, the DNA functionalized SWNTs may exhibit self-assembly properties due to the hydrogen bonds interactions between the bases of DNA, and some groups have fabricated "filed-effect transistors" by using such a scheme, which is called the "bottom-up" method.DNA carries the genetic information of the lives, which is crucial to the heredity and growth. So it has always been the most interesting object to study for biologists and chemists. They have used various experimental and theoretical methods to investigate the conformations of DNA, the damage and repair of DNA, and the interactions between DNA and other biomolecules. At the same time, due to its regular double helix structure, many physicists looked it as a kind of quasi-one dimensional materials and performed a lot of experiments to investigate its mechanical properties and electric conductivity. They want to see whether DNA can be utilized as nanowires in nanotechnology. Besides experiments, people also used theoretical methods, including density functional theory (DFT) calculations and molecular dynamics (MD) simulations to investigate the mechanical and electronic properties of DNA. Many meaningful results, in this light, have been obtained. Due to the limitation of the experimental method, many problems about nanomaterials and biomolecules can only be solved by theoretical methods. At present, computational methods have become one of the most important pathways that can be used to investigate the micromechanisms in nano scale. In general, there are two kinds of methods for using to study nanomaterials: one is the so-called ab initio calculations (or first principle calculations), such as density functional theory (DFT) calculation; the other one is the empirical or semi-empirical molecular dynamics simulations. With the rapid development of supercomputers and computational resources, of course, ab initio MD simulation codes are also available.In this dissertation, DFT calculation and MD simulations are combined to be used in the studies of the properties of SWNTs and DNA. There are five chapters listed as follows:Chapter I. SWNTs and DNA.In this chapter, we will give an introduction about SWNTs and DNA. We will describe the structural, mechanical, and electronic properties of SWNTs. We will also give a brief description for the structure and function of DNA.Chapter II. DFT calculation and MD simulation.In this chapter, the basic theories of DFT calculation and MD simulation are introduced. At present, DFT calculation is one of the most important investigation methods that can describe the structural, mechanical, electronic, magnetic, and optic properties of small systems, without need of any empirical parameters. However, due to its large computational demands, we can only deal with the small systems which contain no more than hundreds of atoms. As for the larger systems, we can only rely on the empirical methods. Classical MD simulation can deal with a system containing ten thousands of atoms, but only the conformational, mechanical, and thermodynamic properties of the system can be obtained. So we are trying to combine the two methods together to obtain as much as information as possible concerning the system under study.Chapter III. Sidewall functionalization of SWNTs with DNA bases and their relevantself-assembly behavior.The functionalization of SWNTs is one of the most interesting research subjects, which means modifying the physical, chemical and electronic or optoelectronic properties of SWNTs by using the methods, such as adsorption of foreign atoms or molecules on the extra- or intra-wall of the SWNT, doping the SWNT with foreign atoms, filling the SWNT with atomic or molecular species, etc. It provides a great potential of tailoring the properties of the SWNTs to meet the needs of application in nanotechnology. Functionalization of carbon nanotubes, either by attaching various molecules or molecular complexes to its extra-wall, intra-wall or tube-end, and by stuffing smaller nanoparticles/molecules into its hollow interior, has been extensively studied due to its potential in facilitating applications in nanodevices and energy storage. In this chapter, we use DFT calculations to investigate the sidewall functionalization of SWNTs with DNA bases. The results indicate that, the electronic structures of the SWNTs can be drastically changed by the sidewall functionalization. The functionalized SWNT exhibits doped degenerated semiconducting properties independent of the initial charity of the SWNT. This may be utilized for band structure engineering. Also, we have performed MD simulations to explore the self-assembly mechanism and the possibility of its potential applications. We have found a stable "ladder" structure which is similar to the stretched dsDNA. Some distorted configurations recover the stable "ladder" structure owing to the hydrogen bond interactions between the base pairs. Such interactions may act as a key role in the self-assembly process.Chapter IV. The controllable sidewall decoration of SWNT by using Si-doping method.Silicon atom is different from carbon atom, because it prefers sp3 bonding very much than sp~2 bonding. That's also the reason why we have not synthesized the single walled silicon nanotube. If we use silicon atom to substitute carbon atom on SWNT, maybe we can improve the reaction activity of the SWNT at the doping site. In this chapter, we investigated the effect of Si doping on the structural and electronic properties of SWNTs, and the decoration of DNA base on the Si-doped SWNT at the doping site. The results indicate that Si-doping can drastically change the electronic properties of SWNTs and improve the reaction activity of the SWNTs at the doping site. This may provide an efficient pathway for the further controllable sidewall decoration.Chapter V. The conformation transition processes of DNA in salt solution.The conformations adopted by DNA and the transition between them are related to the biological functions, such as the interactions between DNA and RNA, DNA and protein, etc. The main conformations(A and B form) depend on the sequence, ionic environment and hydration conditions. Ions play an important role in DNA structures by shielding the phosphate charges in the DNA backbone and affecting water activity around DNA. Increased salt concentrations favor the formation of A-DNA and Z-DNA over B-DNA. A-DNA conformations have been found in solutions with 1 M salt and above, whereas in the case of salt concentrations below 1 M, B-DNA is usually prevalent. In this chapter, we use MD simulations to investigate the effect of salt concentration on the DNA conformation transition processes. The results indicate that, as many people have discovered, AMBER is successful in simulating DNA in solution and has given many meaningful results in DNA study. We have seen a clear A→B conformation transition process and got a stable B structure as others have done. We have also seen an obvious slowered A→B conformation transition in higher salt concentration solution. But we think there are still some artifacts in Cornell force field, for example, the overstabilization of B-DNA and misbalance of the ion parameters, leading to the unexpected result that the final stable structures in different salt concentration solution are all the B-DNA-like conformation. This is a deviation from the experiment, and it may be not appropriate to simulate DNA evolution in high salt concentration solution using Cornell force field.Chapter VI. The electronic structure evolution of DNA during its conformationtransition.Recently, the electronic structure and conductivity of DNA have attracted much interest due to their importance to both molecular biology and nanotechnology. Chemists and Biologists believe that the electronic structure of DNA is relevant to its biological functions, and physicists are interested in the conductivity of DNA due to its potential application as nanowires in nanotechnology. In this chapter, we combined classical molecular dynamics (MD) simulations with ab initio calculations to study the electronic structure evolution of DNA during its conformation transition process. By using MD simulations, we obtained the conformation transition trajectory of an oligonucleotide poly(dC)-poly(dG), from which we selected a series of representative conformations and then performed ab initio calculations for these conformations to reveal their electronic structures. The results indicate that during the conformation transition process of DNA, fluctuation plays a more important role than conformation parameters in affecting the electronic structure of DNA. And we notice that, the natural fluctuating DNA has very different electronic structures from that of canonical crystal DNA. For example, the natural DNA has smaller energy gaps than the canonical crystal DNA, but their HOMO and LUMO distributions are much localized. The localized HOMO and LUMO jump from one location to another accompanying with the fluctuation process. We believe that the fluctuation assisting electronic hopping mechanism dominates charge transportation behavior in natural DNA.