Accurate 3D Modeling of User Inputted Molecules Using a Nelder Mead Algorithm Ben Parr Period 6

Introduction Create program to let users easily and intuitively create simple molecules (i.e. not macromolecules)‏ Water (H2O)‏ Benzene (C6H6)‏ Nicotine (C10H14N2)‏ Have the program position the atoms correctly Easy viewing for a better understanding of the geometry of molecules

Background Understanding the geometry of molecules is extremely helpful Buying molecule modeling sets for every student in an introductory chemistry is too costly Some software similar to my project is also costly No real feasible option for beginner chemistry students

Current State All graphics and user interface implemented Nelder Mead Algorithm programmed

Nelder Mead Algorithm Start with original simplex Has N+1 vertices where N = 3 * (# of atoms in model)‏ Multiply by 3 because each atom has a x, y, z Each vertex has 3*N dimensions (contains the x,y,z of each atom in the model)‏ Used to minimize an energy function “energy” of the model Run through the algorithm until the tolerance (max energy of vertex – min energy of vertex) is less than .000001

One Possible Variation

What's Next Program energy function that takes into account: The distance between atoms (maximize)‏ The distance between bonded atoms Make them a defined distance away from each other (values from a text file)‏ Create a better original simplex Current original simplex is just for testing purposes Too small may lead to local search Too large could take too long