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Fall 2018
Lab 7: Molecular Modeling
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Data and Calculations
PART 1
Model: 2-butyn-1-ol ESP Map – Circle the polar bond(s). Indicate
bond angle among C1-C2-C3: the charge distribution
for this bond using
δ+ and δ-.

PART 2 Model: ammonia, NH3

Model: methane, CH4 Model sketch:
Model sketch:

Lewis structure: Lewis structure:

(If present, circle polar bonds. Indicate the (If present, circle polar bonds. Indicate the
charge distribution for this bond using δ+ and charge distribution for this bond using δ+ and
δ-.) δ-.)

VSEPR Molecular geometry:

VSEPR Molecular geometry:

bond angle:
(indicate bond measured on sketch)
bond angle:
(indicate bond measured on sketch)
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Fall 2018
Lab 7: Molecular Modeling
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Partner: Day/time:
Model: water, H2O Model: carbon dioxide, CO2
Model sketch: Model sketch:

Lewis structure: Lewis structure:

(If present, circle polar bonds. Indicate the (If present, circle polar bonds. Indicate the
charge distribution for this bond using δ+ and charge distribution for this bond using δ+ and
δ-.) δ-.)

VSEPR Molecular geometry: VSEPR Molecular geometry:

bond angle: bond angle:

(indicate bond measured on sketch) (indicate bond measured on sketch)

Model: nitrogen, N2
Model sketch:

Lewis structure:
(indicate δ+ and δ- if polar)

VSEPR Molecular geometry:

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Fall 2018
Lab 7: Molecular Modeling
Name: Room:
Partner: Day/time:

Extra Credit
Choose one of the following compounds to model or email your instructor with one of your own:
butane 2-butanol 2-methylpropene
pentane 2-methylpropane acetylene
hexane 2-methylbutane 1-butyne
heptane propylamine 2-butyne
octane 1-aminobutane 1-chloropropane
1-propanol 2-aminobutane 2-chloropropane
2-propanol propene 1-chlorobutane
1-butanol 1-butene 2-chlorobutane
Advice:

Use the internet (Wikipedia, NIST webbook, ChemSpider) to get a line drawing of your
structure.
Reading chemical structures
Line or skeletal structures are shorthand notation used by chemists to show the basic
structure of an organic compound. Lines represent bonds (single line = single bond; double
line = double bond; triple line = triple bond). Carbons are shown as either endpoints of a
line or vertices. To read the line structure, you need to remember that always carbon
needs to share 4 electrons to complete its octet. It will form 4 bonds. The following
structures are ALL for the same compound: 3-ethyl-2-methylhexane.

Hybridization

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Fall 2018
Lab 7: Molecular Modeling
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Partner: Day/time:
If you structure doesn’t look like the chemical structure you see on the Internet or the
computer automatically adds the wrong number of hydrogens, you need to correct the
hybridization for the carbons (oxygen or nitrogen).
o Carbons with all single bonds are sp3 hybridized.
o Carbons with one double bond and two single bonds are sp2 hybridized.
o Carbons with one triple bond and one single bond are sp hybridized.
o Cabons with two double bonds are sp hybridized.
o Oxygens and nitrogens with only single bonds are sp3 hybridized.
o Oxygens and nitrogens with a double bond are sp2 hybridized.

Remember to optimize your model. After drawing in your atoms and adding the correct
bonds:

1. In the menu at the top, click Edit >> Clean Hybridization

2. In the top row, there are three buttons labeled “H”. Click on the the Add Hydrogens
button. You should see the appropriate number of hydrogens on each of the carbons
(nitrogen and oxygen if applicable).
a. If you do not see the proper number of hydrogen atoms, right-click on the
atom(s) with the wrong number of hydrogens and select Change atom from the
menu.
b. Select the proper atom type (sp, sp2, or sp3)
c. Click the H-eraser button (“Delete Hydrogens”). Then click on Add
hydrogens again.
3. In the top row, is the Clean geometry button. Click the button. You will be prompted
to save your structure; do so.
4. Optimize the geometry with PM3 semi-empirical QM method.
a. Click the optimize energy button
b. Click the PM3 radio button in the Hamiltonian group box in the upper left of the
dialog box.
c. Increase Maximum steps taken in the Geometry Search box to 2000
d. Click OK
5. Click the Run Calculation button

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Fall 2018
Lab 7: Molecular Modeling
Name: Room:
Partner: Day/time:
Extra Credit
Hard copies can be handed in during class OR at your instructor’s office
No electronic submissions will be accepted. No late assignments will be accepted.

Directions:
You MUST complete this assignment on your own.
Only COMPLETED assignments will be graded.
Failure to complete the entire assignment will result in ZERO extra credit points.
You may need to look up information about the compound. Suggested websites:
o Wikipedia (https://en.wikipedia.org/wiki/Main_Page)
o NIST Chemistry WebBook (http://webbook.nist.gov/chemistry/)
o ChemSpider (http://www.chemspider.com/)

A complete assignment includes the following:

1. This page of the packet with the following table completed.
2. A printout of your model (ball and stick).
3. A printout of the ESP map for your compound.

IUPAC Name:
Formula:

Other Name Molecular

(if available): Weight:

Chemical
Structure:

Measured bond Polar or

angle: Nonpolar?

1. On the line drawing, highlight the bond angle that you measured. Record the measured
bond angle from your optimized model in the last row of the table.
2. Using the ESP map, determine if your model is polar (asymmetrical) or nonpolar
(symmetrical).

STAPLE a printout of your model and the ESP map to this page.

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