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					Accurate 3D Modeling of User Inputted Molecules

Computer Systems Lab: 2007-2008 Ben Parr Period 6

Goal
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Create program to let users easily and intuitively create simple molecules
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Have the program position the atoms correctly Easy viewing for a better understanding of the geometry of molecules

Water (H2O)‫‏‬ Benzene (C6H6)‫‏‬ Nicotine (C10H14N2)‫‏‬

Background
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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

Nelder Mead Algorithm
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Used to “Auto-Position Atoms” Uses a simplex with N+1 vertices
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N = 3*number of atoms Each vertex represents a model

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Minimizes an energy function Ends when it reaches a tolerance

Energy Function
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Calculates energy of a vertex of the simplex (model)‫‏‬ 3 factors affect energy
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Distance between every non-bonded pair of atoms (maximize)‫‏‬ Distance between bonded atoms (get as close to defined value)‫‏‬ Bond angles (maximize)‫‏‬

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Does not take polarity into account

Current State
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All graphics and user interface implemented and work correctly All components of the Nelder Mead Algorithm are programmed
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Energy function Original simplex Actual algorithm

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Very simple molecules position correctly Larger the molecule, the more incorrect the autopositioning

Auto-Positioning for CO2

Auto-Positioning for Propyne: C3H4

Auto-Positioning of Benzene: C6H6

If I had More Time...
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Create a better original simplex
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Currently using mostly random numbers Works, but could be changed to better suit the problem
Lone pair electrons Current program won’t position atoms of water (H2O) correctly

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Account for polarity
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Refine Nelder Mead algorithm to work better for larger molecules


				
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