2: In class Lab
CHM 2000 Lab Activity Sinex
Investigating Chemical Structures using Avogadro
Download the Avogadro molecular editor at https://avogadro.cc/ .
Build the following molecules, select 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, a screen capture program in Windows.
Build ethene, H2C=CH2
What is the geometry of the carbon? What is the H-C-H bond angle?
Is the molecule polar or nonpolar?
Now let’s substitute some chlorine atoms for the hydrogen and re-optimize the structures. Isomers are compounds with the same molecular formula (C2H2Cl2), but the atoms are arranged differently (different connectivity). trans - across or opposite sides cis - same side
| 1,1-dichloroethene | trans-1,2-dichloroethene | cis-1,2-dichloroethene |
|---|---|---|
|
|
Measure the bond angles, Cl-C-Cl in the first one, Cl-C-H in the other two. Record the values.
Calculate the dipole moment and record it for each molecule. Verify the dipole moments by looking them up in the CRC Handbook of Chemistry and Physics .
Since the dichloroethene molecules are planar, draw the dipole arrow on them if appropriate.
Go to http://materia.fisica.unimi.it/manini/dida/structures.html and retrieve the crystalline structure of graphene.xyz, an unusual two-dimensional or atomic layer solid (right click and Save link as…). Import (under the file menu) the structure into Avogadro. It may take a little time to load. DO NOT optimize geometry or minimize energy !!!! Copy and paste the structures below. Change the display type to van der Waals Spheres (electron cloud or space-filled model). Describe the electron cloud produced on the graphene sheet.
Graphene should have alternating single and double carbon-carbon bonds. From the bond lengths, what can you infer?
Graphene has an electrical conductivity comparable to metals such as copper and a strength comparable to steel.
Build a carbyne, which is a chain of carbon atoms with alternating single and triple carbon-carbon bonds. Make your chain with a total of 12 carbon atoms, add the first triple bond starting at the end of the chain, select optimize geometry, and then perform an energy minimization.
What is the geometry of the carbons in the chain?
Measure the bond lengths in your carbyne structure:
triple bond single bond
_______________ _______________
How do the measured lengths compare to typical length of a C-to-C single and triple bonds?
Carbyne, a 1D network covalent material, may be the strongest material known to humankind!
For more info, see Route to Carbyne: Scientists Create Ultra-Long 1D Carbon Chains at
http://www.sci-news.com/othersciences/chemistry/carbyne-ultra-long-1d-carbon-chains-03770.html .