Background Information

Lewis dot structures are effective at showing connectivity between atoms, but to visualize arrangements in 3D, it is helpful to use molecular modeling software. Avogadro is a free tool (https://avogadro.cc/) to build and manipulate molecular models. It is available for most operating systems. The native functionality of Avogadro can fill out octets of molecules automatically, and optimize molecules on the basis of molecular mechanics (VSEPR and valence bond theories). It can also be used, as we will see next week, as a way of generating input for computational chemistry packages that allow access for better optimizations and better data.

Procedure

Part A: Using Avogadro

1. Read through the instructions for drawing a molecule on the Avogadro website: https://avogadro.cc/docs/getting-started/drawing-molecules/. If you get stuck anywhere, it is good to return to this resource.

2. Open Avogadro and familiarize yourself with the tool bars just under the pull down menus. Besides the typical New, Open, Save, Close, & Quit tools are more important ones that work with your molecules. Hover the mouse over them to see what the Draw tool, Navigation tool, Bond Centric Manipulation tool, Manipulation tool, Selection tool, Auto Rotation tool, Auto Optimization tool, and Measurement tool each does. Click on the Tool Settings and Display Settings buttons to see how the application window changes. When both are unselected, the drawing window is bigger. The tool settings change as you click on the tools, and the display settings help to easily change how molecules are displayed.

3. Make sure that the draw tool is selected. Move your cursor onto the page and click the left mouse button to place the element. The type of atom that is selected in the draw settings will be placed at the cursor. If the Adjust hydrogens box is checked then some hydrogens have also been automatically added as well. This is usually helpful, but not always, so be careful. If you have not already gone through the first three step-by-step walkthroughs on the Avogadro website (Getting Started, Drawing Molecules, & Making Selections), do so now as these cover important skills that you will use frequently in this program. In the third tutorial, ignore the parts about SMILES, SMARTS, Residues, and Project Trees.

4. Now that you know how to build molecules and optimize their geometry, let’s build some. Build a water molecule. Click on the navigation tool and rotate the water molecule to see how this tool works. In the absence of a middle mouse button use shift-up/down arrows for zooming.

5. Skip the Bond Centric Manipulation tool and instead select the Manipulation tool. Click and hold on an atom and move the mouse to see how this affects your molecule. Click and drag in the window but not on an atom to see what happens. You have already played with the select tool in the tutorials. We will skip the auto rotation tool.

6. We have a water molecule but it isn’t very pretty. Its bond lengths and bond angle are incorrect. But that is what Avogadro is for. But before optimizing our molecule, let’s characterize what we have so far. Click on the Measurement tool icon and then select a hydrogen atom, then the oxygen, and finally the second hydrogen. The order is important to match the values that appear on the screen. The first distance is between atoms #1 & #2 and the bond angle has the second atom at its apex. Selecting the atoms in another order would make these measurements meaningless. Download a local copy of the linked Excel spreadsheet and record these values for water under Pre-3D Optimization. Then reset the atom selection by clicking in an empty part of the window and select your three atoms in an odd order to see the distance and angle values that are displayed, and record these as well. Can you see how one needs to be careful? Finally, reset the atom selection and click only on the two hydrogen atoms to measure and record the distance between them.

7. Now to obtain an accurate 3D view; under the Extensions drop down menu select Molecular Mechanics / Setup Force Field. Select MMFF94 as the Force Field and click OK. Again, under Extensions, select Optimize Geometry. Your molecule’s geometry is now optimized and arranged as it would appear in 3-dimensional space. Measure all interatomic distances and its bond angle as above and record in the optimized column of your Excel sheet.

8. With the water molecule in the center of the window, select display settings and explore the Display Types but be prepared to restart the program as several of these options crash it. Notice that the ball & stick rendering (The different ways that a molecule can be displayed are known as renderings.) is the default. Uncheck this type and select each of simple wireframe, stick, Van der Waals spheres, & wireframe renderings. Notice that some display types have wrench icons. That means that some details of their displays can be changed by the user.

9. Use ctrl-backspace to remove your water molecule. Now build each of the following molecules: carbon dioxide (\(\ce{O=C=O}\)), nitrogen (NºN), and ammonia (\(\ce{NH3}\)). Repeat step five for each one to get pre- and post- geometry optimization characteristics as you did for water. Record your measurements.

10. It’s time to compare our theoretical calculations and geometries with experimentally derived ones. A good web site that contains experimental parameters of many molecules is http://cccbdb.nist.gov/. We will come back to this web site later, so it would be a good idea to bookmark it or put it in your favorites for easy access. Click on the “Experimental” tab on the top, select all experimental data for one molecule, and enter water (or \(\ce{H2O}\)) as the molecular formula. Scroll down to the geometry data and record the actual experimental values next to the information you got from Avogadro. Record these in your document. Repeat for the values that you recorded for carbon dioxide, nitrogen, and ammonia.

11. Answer the 3 questions listed below the data tables in the linked spreadsheet directly in Excel.

Remember, we have used a quick geometry optimizer in Avogadro for displaying molecular geometry. It uses a process known as MMFF94 that is a molecular mechanics force field method that has been optimized for organic compounds, specifically drug compounds. It is based upon estimating forces between atoms in a molecule and so is called a force field method. These work well for quick geometry optimizations, but when more accurate geometries are needed for more accurate calculations, they do not produce acceptable results, and we must resort to more complicated methods. Avogadro serves as a front end for these calculations. There are many computational packages that can perform these well, but the free ones are not user friendly. You will submit a few optimized Avogadro molecules and your instructor will run them so that you can see the usefulness of these computations.

Along with the Excel sheet, please submit Avogadro save files for the following molecules. Your instructor will return molecular orbital diagram results for you to use in next week’s lab.

Butadiene Ethene Isoprene Borane