The understanding of molecular interactions in controlled assemblies of nanoparticles on different surfaces has potential applications in sensors, biosensors and catalysis. In this presentation we discuss recent findings of a study of the assembly of metal nanoparticles on a surface via interactions of amino acids. The nanoparticle assemblies are characterized using infrared reflectance spectroscopy (IRS) and atomic force microscopy (AFM) techniques. The IRS and AFM characterization results provide important information for determining the structural properties of the assemblies. Interesting correlations are found between the structure of the amino acids and the resulting nanostructure in the assembly. Implications of the findings to understanding of the detailed interactions of amino acids in the nanoparticle assemblies will be discussed.