The increasing freshwater demand due to population growth, industrial revolution, and climate changes has triggered a critical need for expansion and development of desalination and water treatment industry. Recently, with the rapid advance of nanotechnology, significant improvements have been made to the performance of desalination and water treatment system with the aid from nanomaterials and nanostructures. As the global need for freshwater becomes increasingly important, the search for optimal structural and material design holds a promising potential, which has attracted extensive efforts during the past decade.To optimize the functionality of the nanocompounds, the understanding of the atomistic behaviors needs to be obtained. Since the macroscopic behaviors of the systems can be very different at the nanoscale, precise techniques are often required to monitor the processes. However, experimental methods are costly and, sometimes, incapable of capturing the dynamic evolution. Hence, detailed information into the underlying mechanism has been lacking, and the selection of material and structure is mainly based on empirical experience, which hinders the speed of the progress.In the present study, a novel approach for investigating the nanoscale performance of the compounds using computational molecular dynamics (MD) simulations is proposed. Recently, the development of computer science has witnessed a huge development as the computational power is remarkably fastened with new parallel computing architectures. By utilizing the MD approach, one is able to investigate the nanocompounds during the process at a higher speed and a reduced cost compared to experimental testing. Furthermore, MD simulations can provide atomistic insights into the dynamic behaviors of the compounds and propose reasonable structural and chemical improvements to enhance the performance of the system.