3: Project
CHM 2000 Project Sinex
Investigating Chemical Structures using Avogadro II
Download the Avogadro molecular editor at https://avogadro.cc/ .
Build the following molecules, optimize geometry, and then perform an energy minimization. For organic-type molecules (carbon-based), use the MMFF94 force field. Insert an image of each molecule from Avogadro using Snipping Tool in Windows.
1
\(\ce{CH3-CH=CH2}\)
Record the bond lengths for the carbon bonds.
Single bond length Double bond length
2
Benzene, \(\ce{C6H6}\) where the six carbons form a ring. Do a Lewis dot structure!
Record the bond lengths for the carbon bonds. Are they single or double bonds according to length?
What is the geometry of each carbon atom?
3
\(\ce{H2C=C=CH2}\)
Record the bond lengths for the carbon bonds.
How are the hydrogens on the two ends of the molecules arranged (one end compared to other end of the molecule; rotate the molecule to look down the C=C=C axis)?
4
Isomers are compounds with the same molecular formula, but the atoms are arranged differently (different connectivity). Build the two isomers of SCl4F2 and do an energy minimization (use the UFF force field). Are the isomers polar or nonpolar. If polar, retrieve the dipole moment.
Copy and paste the structures of the two isomers.
5
Go to http://materia.fisica.unimi.it/manini/dida/structures.html and retrieve the crystalline structures of diamondcrystal.xyz and graphite.xyz (right click and Save link as…). Import (under the file menu) the structures into Avogadro. They will take some time to load. Do NOT optimize geometry and perform an energy minimization. Copy and paste the structures below. What is the geometry of the carbon in each structure?
Change the display type to van der Waals Spheres (electron cloud or space-filled model). Which structure has the tighter packing? Why?
What holds the layers in graphite together in the crystalline structure?