Pre lab summary
Roheen Sahebzada
a) Building and Drawing Molecules:
1. Launch Avogadro and click "File" > "New" to start a new project.
2. To draw atoms, click on the "Draw" tool (pencil icon) in the toolbar.
3. Choose the desired element from the periodic table by clicking "Elements" > "Select
Element."
4. Left-click within the workspace to place atoms, and click and drag between atoms to
create bonds.
5. Adjust bond types (single, double, etc.) by clicking on the bond and selecting the
appropriate type.
b) Navigating and Manipulating Molecules:
1. To zoom in and out, scroll the mouse wheel or use the "+" and "-" keys.
2. To move a molecule, select the "Navigate" tool (hand icon) and left-click and drag within
the workspace.
3. To rotate a molecule, hold the right mouse button and drag or use the "Rotate" tool
(circular arrow icon).
c) Optimizing Molecular Energy:
1. To optimize a molecule, click "Extensions" > "Optimize Geometry" or use the "Auto
Optimize" tool (wand icon).
2. Monitor the progress and stop the optimization by clicking "Stop" in the optimization
dialog.
3. Save the optimized structure by clicking "File" > "Save As."
d) Measuring Bond Angles, Lengths, etc.:
1. To measure bond lengths, click the "Measure" tool (ruler icon) and then click on two
atoms to measure the distance.
2. To measure bond angles, click on three atoms sequentially, with the middle atom being
the vertex.
3. To measure dihedral angles, click on four atoms in sequence.
4. All measurements will be displayed in the measurement table.
e) Viewing Properties (Atoms, Bonds - Angles, Lengths):
1. To view atom properties, click "View" > "Properties" > "Atom Properties."
2. To view bond properties, click "View" > "Properties" > "Bond Properties."