CAChe Lab: Molecular Shape and Polarity
Created by: Rebecca A. Kruse
Pre-lab Assignment:
Read “Introduction to Using CAChe.” Draw a Lewis structure and predict the molecular shape for each
molecule listed in the Data Table; enter this information in the Data Table before coming to class. If you wish, you
may predict the molecular polarity for each molecule before coming to class and use your collected data for
reflection and revision.
Pre-lab Discussion:
Valence electrons play an active role in chemical reactions. Lewis structures, or dot diagrams, are commonly
used as a simple way of showing the valence electrons of atoms or ions in a molecule or compound. Predicting
the electron geometry and molecular shape is also of importance as they often help chemists determine whether
or not reactions will occur and/or what the products of a chemical reaction might be.
The valence-shell electron-pair repulsion model, or VSEPR for short, provides a way to predict the shapes of
molecules. In VSEPR, the general organization of atoms around the central atom is determined by first drawing a
Lewis structure. Next, each pair (whether shared or unshared) is considered to repel all the other electron pairs
around the atom, causing each electron pair to take a position around the central atom as far away as possible
from the other electron pairs. The electron geometry is the arrangement of all electron pairs around the central
atom. Once the electron geometry is determined, the molecular shape is simply the arrangement of the shared
electron pairs around the central atom.
Covalent bonds form when one or more pairs of valence electrons are shared between atoms to achieve an
octet. Nonpolar covalent bonds occur when electrons are shared equally such that electron density is found at a
point midway between the two atoms in the bond. Polar covalent bonds occur when electrons are shared
unequally, that is to say electron density is displaced toward one atom in the bond. Differences in
electronegativities of atoms is often used to predict whether a bond non-polar covalent or polar covalent.
Molecules can be either nonpolar or polar. If bonds are nonpolar, the molecule is nonpolar. If bonds are polar,
molecules can still be nonpolar if the charge distribution throughout the molecule is symmetrical. A molecule’s
symmetry depends on its shape as determined using VSEPR. Polar molecules, or dipoles, behave as if one end
were negative and the opposite end positive. The presence of these oppositely charged ends (denoted - and +)
produce forces of attraction between polar molecules that are much greater than the forces of attraction between
similar nonpolar molecules.
In this lab you will use your knowledge of Lewis structures and CAChe to investigate molecular shape and polarity
with computer-based molecular models.
Purpose:
In this exercise you will 1) draw Lewis structures and build energy minimized molecules in CAChe to determine
molecular shapes then 2) will generate 3-D EonD surface maps of selected molecules to determine molecule
polarity. EonD surface maps show electrostatic potential (shows regions of charge in a molecule) mapped
onto electron density (shows the volume or shape of electron cloud).
Lab Procedure:
1. Open CAChe and follow the directions provided in “Building Molecules with CAChe” to do the following:
b. Build each molecule listed below (don’t forget to BEAUTIFY the entire structure!)
c. Use Figure 15-29 on page 409 in your textbook to help you assign molecular shape.
2. Open CAChe and follow the directions provided in “Calculating Electron Density and Electrostatic Potential
with CAChe” to do the following:
a. Perform experiments to calculate EonD surfaces for each molecule.
b. Open the structure, then apply the EonD surface for each molecule listed below.
c. Use the EonD surfaces and legends to help you assign molecular polarity.
3. Complete the data table provided on this page. Use your data to assign molecular polarities. Leave space to
attach computer images that will be provided.
Data Table:
Name, Formula
Lewis
Structure
Predicted
Molecular Shape
Computer
Image
Molecular Polarity
(polar/nonpolar)
a. Hydrogen, H2
_______________
_______________
b. Methane, CH4
_______________
_______________
c. Ammonia, NH3
_______________
_______________
d. Water, H2O
_______________
_______________
e. Hydrogen fluoride, HF
_______________
_______________
f. Carbon dioxide, CO2
_______________
_______________
g. Nitrogen, N2
_______________
_______________
h. Ethylene, CH2CH2
_______________
_______________
i. Methanol, CH3OH
_______________
_______________
j. Hydrogen sulfide, H2S
_______________
_______________
Questions:
1. Calculate the difference in electronegativities between atoms in the following bonds:
a. H-H
f. C-O
b. H-C
g. N-N
c. H-N
h. C-C
d. H-O
i. C-Cl
e. H-F
j. H-S
2. Which of these bonds are polar covalent? nonpolar covalent?
Use your data to help answer the following questions:
3. Which molecule(s) were nonpolar because all bonds were nonpolar?
4. Which molecule(s) had polar covalent bonds but were nonpolar because of symmetry?
5. Which shape(s) appeared to produce polar molecules?
Suggestions for Further Work/Inquiry
Follow the directions provided in “Building Molecules with CAChe” to select a class of drugs from the CAChe
Fragment Library. Drugs are denoted by name, followed by their specific function (i.e. Drugs-antibiotics). Once
you have chosen a particular class of drugs, view some of the molecular structures contained within to complete
the following:
a. Print out a single molecule from your selected class of drugs and label the molecular shape around
each central atom.
b. Do the molecules in your selected class of drugs appear to have a common (portion of) structure that
may be responsible for their function? If so, identify this common (portion of) structure on the
molecule you have printed out.
c. Do the molecules in your selected class of drugs appear to have a common region of polarity? If so,
identify this region on the molecule you have printed out.
d. What do molecular structure and molecular polarity have to do with a drug’s activity? (Hint: Use the
Internet or other resource texts to find a general scheme for drug-receptor site interactions.)