Coarse-grain mesoscale modeling of nano-architectures in water

Computational Chemistry has become an area of interest by chemists because it helps to solve chemical problems using the tools of computer science. This project will include the use of software Materials Studio to predict structures of supramolecular structures. One of the main purposes is to simulate a coarse-grained molecular dynamics with a larger-length and longer-time scales to represent a system with details of all atoms involved. In order to achieve this groups of several atoms are transformed in a single bead. The molecular structure of a polymer such as a chain of five monomers of ethylene and five monomers of ethyleneoxide can be represented by a diblock of 5 beads each representing ethylene and ethyleneoxide. There will be a total of 10 beads which represent the polymer and facilitates the analysis. Clicking on a single bead will give us information about that bead such as the molecular weight, size, kind of atoms, etc. When a molecule is not found in the library of the software then it is possible to create the monomer manually where we open a new 3D atomistic screen and draw the molecule with all atoms so we can name it and save it for future use. This simulation has its own forcefield parameterized for the interaction among each kind of bead in the system. With the use of this simulation it is possible to optimize and equilibrate the structure to be able to analyze optimizations of geometries and molecular dynamics to an atomistic level.