Probing Interactions in Complex Molecular Systems through Ordered Assembly

Abstract

Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies of three classes of ''super molecular'' nanostructured materials. These included (1) dendrimers, (2) DNA bonded nano-particles, and (3) colloids, all of which form solution-based self-organizing systems. To this end, our goals were, first, to learn how to modify models of epitaxy in small molecule systems so that they are useful, efficient, and applicable to assembly of super-molecular species; and, second, to learn how systematic variations in the structure and bonding of the building blocks affect the surface kinetics and energetics that control the assembly process and the subsequent dynamic behavior of the assembled structures. AFM imaging provided experimental data on morphology and kinetics, while kinetic Monte Carlo (KMC) simulations related these data to molecular-scale processes and features.