1.1: Basic Tools
1) Avogadro has built in molecules. To access them, go to the toolbar under Build > Insert > Fragment.
There are various built in molecules and compounds as shown. We are going to start with the simplest but one of the most essential molecule known to mankind H2O! Click on water at the bottom.
2) The molecule should appear as follow, see Figure \(\PageIndex{3}\). The way it may actual appear on your computer varies by what is defaulted by Avogadro when you downloaded it.
3) Because the software is 3D representation of the molecule (xyz), you will have to adjust the position of the molecule to your liking. To do so, select the diamond star button on the ribbon above the display types, see fFgure \(\PageIndex{4}\). You can rotate the molecule about an atom by clicking on the atom, holding the left mouse button, and moving your mouse as needed.
4) As shown in Figure \(\PageIndex{4}\), the whole molecule, that is each individual bond and atom, is highlighted in blue. To unselect all the atoms, click the black arrow button on the ribbon above the Display Type and right click on the black space next to the molecule. If you want to reselect a specific bond or atom select the black arrow button and then click on the desired atom or bond, see figure V. You can select multiple atoms or bonds by holding the CLRT button and clicking on the desired atoms or bonds.
5) To view the bond length between atoms, at the top toolbar, go to View > Properties > Bond Properties . The bond properties will show as below: You can highlight the bond number to know which bond is what. For example, if you wish to know which bond is “Bond 1” and which atoms are forming that bond you simply click on Bond 1 and the bond will then be highlighted in blue. You could also label the atoms by simply selecting the Label check box under the display type box for better visuals. You can also measure bonds by using the Ruler Button and selecting the atoms. Overall you can explore other properties such as Atom Properties or Angle Properties similarly. See figure VI.
6) This is generally the basics as far as handling molecules. We will now continue with on another tool before going into building your own specific molecules. There is the Manipulation Tool (the hand button). The button and functions are shown in Figure \(\PageIndex{7}\). You can “stretch” atoms and bonds with this tool (could be a hassle if you need to build your molecules with a specific bond length and could ruin it if you are not careful). So, please be weary when using this tool. I would suggest just sticking to the black arrow when working with the molecules. Remember though you can always start over
Note: You could fix the stretched water molecule with a method that is introduced in section two.
7) However, the hand button is useful when you are trying to shift the position of the WHOLE MOLECULE . Simply highlight the whole molecule blue (see figure III and step 4), click any part of the highlighted molecule and shift to the position you desire.