CHE141 - GENERAL CHEMISTRY II
Module developed by: David L. Cedeño and Mark Wirtz at Illinois State University
Bond Polarity and Polarity of Molecules
Introduction
The polarity of a molecule is dependent on the polarity of individual bonds (called bond dipoles)
and the three dimensional arrangement of such bonds (i.e. the molecule). A molecule may have
polar bonds, but that does not guarantee that the molecule will be polar. In this exercise you will
use computational software (called Argus Lab) to build three dimensional models of some
molecules and visualize (via electrostatic maps) the charge distribution in individual bonds and
the entire molecule. The polarity of a molecule is an important property, which defines
characteristics such as solubility and reactivity.
You are encouraged to review the following material in your textbook: Section 8.4 (Bond
polarity), 9.3 (Molecular shape and molecular polarity)
Objectives:
 Part A: To understand how the difference of electronegativity between two atoms
influences the polarity of a chemical bond.
 Part B: To understand how the polarity of a molecule is a function of both the geometry
of the molecule and the polarity of individual chemical bonds.
Materials:
You will need Argus Lab 4.0 to carry out the molecular modeling and calculation of electrostatic
surfaces. Click here to download Argus Lab 4.0.
Once you download Argus, you may want to take a few minutes to go through the tutorial (under
Help tab) sections on Molecule Builder and Surfaces.
This handout provides general instructions to guide you (the warm-up sections) through but
assumes you are already familiar with the basics. The playroom section tells you to build,
calculate, and analyze data for other molecules following similar procedures to the ones learned
in the warm-up.
PART A. Polarity of bond
Warm-up Section
Using Argus Lab 4.0 built the following diatomic molecule: H2
Clean up (click
) the molecule and Save (suggested name: h2)
Now calculate surfaces for electron density and electrostatic potential: Go to Calculation then
Energy, leave everything as defaulted, except for:
QM: PM3
Calculate Properties: Check dipole and Mulliken atomic charges
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Click on Surface Properties and select (check) the Electron Density and Electrostatic
Potential boxes, click OK (twice) and run (click
)
Analysis
An output file is generated named (h2.out). Use a text viewer to open it (click
down towards the end of the file to check the dipole moment length.
). Scroll
Record the Dipole moment length here: _________ Debyes
What does the dipole moment measures?
Why is it zero for the H2 molecule?
Record the atomic charges too:
Atomic Charge H: _________
Should they be equal? Why?
Now create and view the surface: Go to Surfaces.
Select QuickPlot ESP mapped density. This generates an electrostatic potential map on
the total electron density contour of the molecule.
You can make the surface mesh (as shown below) or translucent by right clicking on the surface
and selecting Modify Surface. Note: Make sure to click on Select (
operation.
You should see the something like this (and a color scheme bar to its left):
) before doing this
The color bar indicates the charge distribution, from white (high positive) to red (high negative).
Finally, obtain the H-H bond length. First switch the surface off the screen by right clicking and
doing Hide Surface. Then, right click on the bond (make sure the Select icon is on) and choose
Bond Info:
H-H Bond length: ________ Å (angstroms)
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Playroom:
Now it is time to play. Build, clean and save the following molecules (use same settings for H2):
HF, HCl, HBr and HI
Calculate the dipole moment and atomic charges in each case.
Generate and display the electron density and electrostatic potential surfaces. Create a map of
the electrostatic potential on the electron density (same as you did for H2).
Note: To enhance the differences in the electrostatic potential surfaces, change the Contour Values to 0.0200 (to get
to the contour value setting right click on the surface and click Modify Surface):
How does the charge distributed in these different molecules?
Based on your comparison of charge distributions, which molecule should have the most polar
bond, and which one the least polar? Arrange the molecules in increasing order of polarity.
Now, complete the following table of results:
Property
Calculated dipole (D)
Experimental Dipole (D)
Calculated Bond Length (Å)
Experimental Bond Length (Å)
Atomic Charge H
Atomic Charge halogen
Electronegativity difference
H-H
0.00
0.00
0.699
0.74
0.000
---0.00
H-F
H-Cl
H-Br
H-I
1.82
1.08
0.82
0.44
0.92
1.27
1.41
1.61
1.9
0.9
0.7
0.4
What trends do you see in the properties tabulated? Provide reasonable explanations for these
trends
What kind of correlations can be made from the properties tabulated and the electron density
surfaces?
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There seems to be a discrepancy between the experimental and calculated dipole moments.
Provide a feasible explanation
PART B. Polarity of Molecules
Now you understand how the polarity of a bond is influenced by the difference in
electronegativity of the atoms involved in the bond. Let us take a look at how the polarity of a
molecule is defined by both the polarity of the individual bonds and the geometry of the
molecules.
Warm-up Section:
Use Argus to build methane (CH4). To avoid getting a planar CH4, start building the
molecule by adding two hydrogens to a carbon atom in the same plane. Next turn the
molecule by left-clicking, holding and dragging to turn the molecule and add the other
two hydrogens. The resulting model should look like a pyramid with atoms at the corners
and not like a plus sign.
Clean up (
) and Save (suggested name: ch4)
Go to Calculation then Optimize Geometry. Leave everything as defaulted except the
following:
QM: PM3
Calculate Properties: Check to calculate the dipole moment and Mulliken atomic charges
Run the molecule (it takes seconds)
Now calculate surfaces for electron density and electrostatic potential: Go to Calculation
then Energy, leave everything as defaulted, except for:
QM: PM3
Calculate Properties: Check dipole and Mulliken atomic charges
Print: Molecular orbitals
Click on Surface Properties and select (check) the Electron Density and Electrostatic
Potential boxes, as well as the HOMO and LUMO, click OK (twice) and run (will take
seconds)
Analysis
An output file is generated named (ch4_pm3.out). Use a text viewer to open it. Scroll down to
the end of the file to check the dipole moment.
Record the Dipole moment length here:
_________ Debyes
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What does the dipole moment measures for this molecule?
Why is it zero for the CH4 molecule?
Record the atomic charges too:
Atomic Charge C: _________
H: _________
Now create and view the surface: Go to Properties then Surfaces.
Select Mapped in the center area.
Click on the Electron Density folder on the left and drag the CH4 ElenDen:0 grid (the
icon is a blue cube) to the Main (Grid 1) box in the center area.
Click on the Electrostatic Potential folder on the left and drag the CH4 Esp:0 grid to the
Mapped (Grid 2) box in the center area. Then, click on the Create button.
A mapped surface will be generated and stored in the Mapped Surfaces folder on the
right area.
Display the surface by clicking on the icon and the Toggle Display button (the icon will
get illuminated). Then click OK to finish.
You should see the something like this:
You can make the surface translucent or mesh (as shown) by right clicking on the surface and
selecting Modify Surface. Note: Make sure to click on Select (Yellow Arrow icon) before doing
this operation.
Playroom:
Now it is time to play. Build, clean and save the following molecules:
CH3Cl, CH2Cl2, CHCl3 and CCl4
Optimize and calculate the dipole moment and atomic charges in each case. Again, be sure your
molecules are not planar (i.e. they do not look like crosses or plus signs).
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Generate and display the electron density and electrostatic potential surfaces. Create a map of
the electrostatic potential on the electron density (same as you did for CH4).
Note: To get a readable map of the electrostatic potential on the electron density, use the following Contour Values
for these molecules:
For CH3Cl use the contour value 0.02, for CH2Cl2 and CHCl3 use 0.015, for CCl4 use 0.01
Describe how is the electron density distributed in these different molecules?
Based on your comparison of the electron density distributions, which molecule(s) should be
the most polar, and which one(s) the least polar? Arrange the molecules in increasing order
of polarity.
Now, complete the following table of results:
Property
Calculated dipole (D)
Atomic Charge C
Atomic Charge H
Atomic Charge Cl
CH4
0.00
0.00
0.000
----
CH3Cl
CH2Cl2
CHCl3
CCl4
What trends do you see in the properties tabulated? Provide reasonable explanations for these
trends
What kind of correlations can be made from the properties tabulated and the electron density
surfaces?
What would the polarity of a square planar CH2Cl2? Note that there could be two possible
isomers. Would you be able to differentiate them based on polarity?
Note: If you want to try these: Build the molecule CH4 on screen and leave it in one plane (DON’T turn the
molecule, it will look like the plus sign). Clean the geometry. You will have to create this molecule twice to see
both isomers, so choose which you will look at first (either two chlorine atoms next to each other or across from
each other). Inter change two of the hydrogens with chlorines to see the desired molecule. Note: after creating and
changing to chlorine atoms, DO NOT clean geometry.
Finally, set the bond lengths of the atoms. For the bonds between C and Cl, right click the bond, and select Set
Bond Distance. Use the value 1.79 for distance in angstroms. For the bonds between C and H, use the value 1.09
for distance in angstroms.
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Now you are ready to map your electrostatic potential on the electron density. Go to Calculation and select Energy.
Under Hamiltonian select PM3, under Print select Molecular Orbitals, under Calculate Properties select Dipole
Movements and Mulliken Charges. Finally click Surface properties. Select “Ground State Electron Denisty”,
“Electrostatic Potential”, and in the Click Oribitals Click OK twice. Go to Calculation, and click Run. Create a
electrostatic potential on the electron density map as you did for the other molecules (under surfaces) and use the
Contour Value of 0.01 to see change in color.
Repeat for whichever form of planar CH2Cl2 you did not choose.
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