Mechanisms For The Formation Of Thiolate-Gold Nanoparticles And Molecular Dynamics Simulations For DNA-AuNP Self-Assembly

Nanotechnology and nano-materials, especially metal nano-materials, have gained great attention for their great achievements and enormous influence in various fields. Because of their special chemical properties and excellent biocompatibility, Gold nanoparticles have extensive applications in nanotechnology and biomedical fields. Therefore, the preparation and self-assembly of gold nanoparticles, especially the self-assembly of DNA modified gold nanoparticles is a hotspot of current research.1. Brust-Schiffrin two-phase synthesis method has been widely used to prepare oil-soluble gold nanoparticles. Although a large number of experimental studies have been performed, the reaction pathway has not been clear yet. The main reason is that many types of products make it difficulty for experimental determination. This requires computer technology to study the microcosmic reaction mechanisms. Reaction pathways for the formation of thiolate-gold nanoparticles are investigated by Density Functional Theory (DFT) and a new mechanism upon solvent polarity and tetraalkylammonium is obtained. Our results show that the disulfide RSSR and Au(Ⅰ) complex can be obtained via reduction of a gold(Ⅲ) complex [Au(Cl)2(SR)2]- at an addition of 2 equiv of thiol; then the reactions follow two different pathways upon solvents at the addition of 3 equiv of thiol. The precursors of metal ions in the two pathways are also identified, which provides the key information for controlling the reactions. In addition, the presence of tetraalkylammonium ([N(CH3)4]+) will hinder the formation of Au(Ⅰ) thiolates by decreasing the distance between the chloride and gold in the product of [Cl…AuCl(HSR)]. Moreover, the reactions favor thermodynamically and occur faster in solvents with higher polarities and the presence of tetraalkylammonium can decrease the barrier height and reaction energy. These findings offer a systematic analysis on the pathways to thiolate-stabilized nanoparticles and give a favorable explanation by comparison with those in experimental system.2. Since it was first published in 1996, the self-assembly of DNA-functionalized gold nanoparticles (DNA-AuNP) has attracted significant interest and the concept of a nucleic acid-nanoparticle conjugate was introduced that could be used as a "programmable atom equivalent" (PAE) to build higher ordered materials through deliberately designed hybridization events. Recent research focused both on developing these constructs and understanding their fundamental behaviors to establish the design rules. For example, Mirkin and coworkers have shynthesized several kinds of crystal lattices and developed a series of design rules to predict thermaldynamically favored structures. However, the realization of NP crystallization is dependent on several other parameters, such as temperature and the length of DNA linkers. A recent study showed that DNA "bond" properties play a great role in the self-assembly system. Two guidelines for DNA "bond" properties are proposed to design NP superlattice:First, sufficient hybridizations, where by "sufficient" it is meant that the percentage of hybridized sticky ends P(H) in equilibrium has to be considerable. Second, thermally active hybridization, meaning that DNA linkers should be able to easily attachto and detach from their complementary counterparts as a result of thermal fluctuations. Therefore, we have studied the dynamical process of self-assembly of DNA-AuNP by using Molecular Dynamics (MD) simulations. Our simulation results show that temperature (T), DNA chain number (n) and length of linker beads (nl) have obvious influence on DNA "bond" properties, thus affects the process of crystallization. We find that the percentage of hybridization P(H) decreases with the increasing of T beacuse of the high rate of DNA dehybridization. Thus crystallization will be ovserved in a narrow range of temperature. We also find that larger coverage of DNA leads to larger P(H) until saturated. In addition, increasing of is unfovered for NP crystallization because DNA dehybridization is unfavored.3. With the development of DNA-NP self-assembly, a great many crystalline structures have been obtained experimentally and some of them are confirmed with theoretical studies. Recently, MD simulations for DNA-AuNP self-assembly systems have made great progress. However, most of the MD simulations have focused on A-B complementary system, few studies has focused on A-A self complementary system. In this chapter, we simulate both of the two systems (A-A self-complementary system and A-B complementary system) by using MD methods to study their crystallization process. Our simulation results show that DNA-AuNP crystallization is realized under certain conditions, which is in agreement with the results in last chapter. Athough NP crystallization can be realized when chain number is 25, however, the formation of FCC lattice is occured when DNA is 35 for A-A system. For A-B system, DNA-AuNP self-assemble into D-BCC (disordered- BCC) structure firstly, then the D-BCC structure will change to BCC superlattice. In addition, we find that annealing makes the system crystalize more quickly.