Molecular Modeling - Avogadro

Molecular Modeling - Avogadro - Molecular Modeling Using...

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Molecular Modeling Using Avogadro Freeware As part of the Pre-lab exercise, follow the instructions below to get familiar with the Avogadro program by investigating simple molecules. Answer the questions on the Pre-lab Sheet (see last page). Avogadro software is available on any PC in any of the Hamline computer labs. You can also download it for free from Part I - The Effects of Lone Electron Pairs on Structure Step 1: Drawing a Simple Molecule To start the program from a Hamline campus computer, click on the Start icon and select All Programs > Avogadro > Avogadro. The program opens up as a black drawing panel (occupying most of your screen) where you can ‘draw’ different structures. The default choices (on the left of the drawing panel) should be Carbon for the element, Single for the bond order and Adjust Hydrogen s. The first molecule that you will draw is methane, CH 4 . To do so, all you need is to left click once in the drawing area. You should see something like Figure 1, in which a dark gray carbon atom is surrounded by four white hydrogen atoms. This is the structure of methane! Figure 1. Methane
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You may only see three of the four hydrogen atoms (one being hidden from the view by going backward from the screen surface). Rotate the molecule (even if you got to see all four hydrogen atoms). Click on the Rotate button, , then click and hold the left mouse button, and move the mouse to see the molecule from different angles. Step 2: Minimizing the Structure Before measuring bond angles and distances within the methane molecule that you have drawn, you need to make sure that it is, indeed, the correct structure. Since the correct
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