Predictive design of functional molecules and nanomaterials using ab initio molecular dynamics and electronic structure theories


Student thesis: Doctoral Thesis

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  • Yu LI


Awarding Institution
Award date15 Jul 2013


It has been widely accepted that rational design of nanostructures is a key to various potential applications, such as nanosensors, nanodetectors and nanoswitches. From isolated molecular systems to extended surfaces or solids, their specific geometries, defects or reconstructions produce fascinating electronic, physical and chemical properties, and open a door of vast potential applications. In conventional experimental investigations, special environmental condition is usually required as well as samples of high cost, which make abundant experiments difficult. In addition, although the previous experimental observations provided examples and results, they gave scarce or insufficient information of atomic structure. Therefore, understanding of the attractive physical phenomena based on experimental observations is obscure. All these factors give reasons to the necessity of computer simulations. On the other hand, the simulation results can guide us on design of experiments to achieve desired applications. Thus, computer simulations can complement the theoretical and experimental approaches, relying on the highly-developed computation resources. As more and more novel nanomaterials have been designed according to computer modeling and subsequently validated by experiments, it is necessary to explore more applications of computer simulation in achieving rational design of functional materials, specifically at the nanoscale. As an important role towards a rational design of nanostructures, atomic modeling, ab initio electronic structure theory based geometric optimization and ab initio molecular dynamics (AIMD) have been used intensively. For multiple dimensional nanostructures, Density Functional Theory (DFT) is able to simulate experiments by generating comparable results with experimental observations and even give accurate predictions and guidance for experiments. DFT-based geometry optimization and electronic structure analysis are the main routines to study local stable structures on the potential energy surfaces, while the MD simulation is more efficient in searching global minima and studying dynamic behavior with various environmental conditions involved. The MD results not only offer a test route for thermal stability of a system but also uncover possible phase changes and atomic reconstructions, leading to novel structures. A combination of these tools enables reliable and comprehensive investigations of novel structures. In this thesis, three systems are selected as typical examples of functional materials for applications of AIMD and electronic structure theories in rational designs. In Chapter 3, an isolated molecule is fully investigated. Special interest is focused on its potential application as a rotor, in light of conformations and potential profiles. In addition, vibrational modes of the molecule are carefully studied and assumed favorable for intermolecular rotation. As a validation of such an assumption, MD simulations allow direct observation of rotational behavior. Detailed discussions based on these results have been performed, specifically on the rotational character and excitation nature of this rotor. In Chapters 4-6, graphene containing extended line defects (ELDs) is systematically discussed, from the formation design of various types of ELDs to chemical functionalization of their magnetic and electronic properties. Formation of ELDs has been assumed in two separate ways: one is from mismatch of two halves of graphene lattices (comparable to one reported 585 ELD-graphene) and the other is induced by linear adsorption of Carbon and Nitrogen atoms upon intrinsic graphene. Both of these assumptions have been approved by optimizations and AIMD simulations. All the simulation studies are closely related to available experimental results. A novel 4-ring ELD has been relaxed via the first route; a further MD simulation reveals that this 4 ELD will spontaneously transform to 747 and 585 ELDs at various high temperatures. Feasibility of the linear adsorption mechanism is discussed combined with temperature, adsorption density and pattern. Thus, AIMD simulation can be considered not only as a justification of thermal stability, but also a global search for phase transformation. After design of 4-ELD and 585-ELD, more researches are conducted on the modulation of magnetic properties of the 585-ELD. The magnetism, as one significant application of this ELD in spintronics, was revealed to be fragile to local structures. Accordingly, by introducing nitrogen chemisorption in an isolated/extended way respectively, the overall magnetism is able to be enhanced or eliminated, as desired. Various electronic structure analyses are involved to explain the resulting magnetism, and confirmed as reliable and powerful methods for property-related studies. Chapter 7 is focused on the stability of a ZnO (0001) polar surface. Compensation mechanism of polarity has no consistent answers so far. The main drawback in experimental studies is the difficulty of observing the evolution processes of such polar surface. Because reconstructions of this polar surface usually occur very fast and complicated, most experimental observations only present dramatically-reconstructed surfaces, partly due to experimental treatments. To uncover an insight of the dynamic reconstruction, we employ a combination application of AIMD, geometry optimization and polarity analysis. In MD simulations at high temperature, sufficient thermal energy contributes to a high mobility of surface atoms to overcome local barriers. Potential atomic reconstructions can thus be revealed. Although various configurations are observed during the MD trajectory, a systematic energetic analysis is followed to select the most favorable structure, based on relaxations and total energy calculations. The dynamic behavior leading to a reasonable compensation result reveals useful information which is difficult to find in real experimental observations. In the last chapter, a comprehensive conclusion is given for each part, justifying the effective applications of AIMD and local optimization in rational design of not only functional molecules but also extended systems.

    Research areas

  • Nanostructured materials, Molecules, Molecular dynamics