Molecular Models

The document provides instructions for a lab activity on molecular models. It discusses Lewis structures, molecular geometry, hybridization, and molecular polarity. Students are asked to predict structures, geometries, and polarities for various molecules using an online simulation or molecular modeling kits.

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Molecular Models

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An Ho Xuan

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Lab Activity: Molecular Models.

Lewis Structures
When atoms interact to form a chemical bond, only their outer shell (aka valence) electrons
are involved in bonding. To keep track of these valence electrons, a Lewis dot symbolism is used
which consists of the symbol of the element and one dot for each valence electron in the atom
(never group more than a pair of electrons together – there are limits imposed by quantum
chemistry laws). It is simple to remember the number of valence electrons is equal to the
group number of the element in the periodic table.
At all times, atoms “strive” to get surrounded by 8 electrons (except for H and He, they need
only 2 electrons).
• Many times this can be easily achieved, and stable compounds can be obtained.
• Sometimes, this can’t be achieved (just not enough electrons around, e.g., in BF3) and an
incomplete octet results – many of such substances can be isolated but often times they
are quite reactive.
• Sometimes, elements get more than 8 electrons around them. While it is not even possible
for 2nd row elements (Li, Be, B, C, N, O, F, Ne), it is permissible for all subsequent elements
(e.g., P, S, Br, I) because they have more valence orbitals (d-orbitals) available to
accommodate all the electrons. Since each bond (line) is a sharing of two electrons, H
never forms more than one bond, 2nd row elements never form more than four bonds, but
later elements can form more bonds (up to 8).

Sometimes sharing is done “fairly”, and sometimes it isn’t. To keep track of the “fairness”,
chemists use a fictional concept of formal charges. These may or may not be the actual charges
in the molecule, but they surely help to keep track of the electrons. The sum of all formal charges
in a neutral molecule must be zero. The sum of all formal charges in an ion must equal the
charge of the ion. When determining the best Lewis structure (or predominant resonance
structure) for a molecule, the structure is chosen such that the formal charge on each of the
atoms is as close to zero as possible.

Molecular Geometry and Hybridization

Based on a drawn Lewis Structure, you can predict a geometry of your molecule (that is,
how atoms are arranged in space relative to one another).
For every atom, count number of its lone pairs and neighbors (do not worry if some
neighbors are connected to an atom with a single bond, and some with a double or triple bond).
Do not count the following: unpaired electrons, neighbors that are not connected by covalent
bonds (lines).
Based on the number obtained you can predict the molecular geometry using a simple
principle (VSEPR) that neighbors (and lone pairs) repel each other, so the molecule arranges
itself in such a way as to minimize such a repulsion.
You can notice from the table above that the total number of atom’s neighbors (including
lone pairs, this total number is usually called number of electron groups) corresponds to an
atom’s hybridization in a very straightforward way. Try to deduce this relationship yourself.
Regardless of its physical meaning, chemists often communicate molecule’s geometry using
hybridization terms (rather than number of electron groups).
Molecular Dipole (Polar/Nonpolar)

Depending on symmetry of the molecule (which is usually quite obvious from its geometry),
it is possible to predict whether the molecule possesses a molecular dipole, in other words,
whether the molecule is polar:

1) Bonds made from two different elements are polar. How polar depends on their
difference in electronegativity, C-O, O-H, and B-F bonds are much more polar than C-H
bonds.

2) If your central atom is being connected in opposite directions (e.g., 180 o by two equal
atoms, or 120o by three equal atoms), their bond dipoles will cancel and result in a zero
net molecular dipole. An example of such a molecule is CO2, or BF3. However, if the
geometry is such that the dipoles don’t cancel, the molecule is said to be polar, that is, it
behaves as a tiny magnet (gets attracted to other tiny magnets).
Class Activity
You will be assigned (individually or as a group) to predict various molecules’ Lewis
structure, geometry, hybridization of atoms, and presence or absence of a molecular dipole. This
activity will replace the lab report format used in the other labs of this course. Use molecular
modeling kits and the Phet virtual platform to perform following activities.

Part 1
1. Go to https://phet.colorado.edu/en/simulations/molecule-shapes/about. Click
on the picture of the simulation to launch it.
1. Open “Model” simulation. Build models with given number of bonds and
lone pairs and fill the chart. (5 points)

Number Number Electron Molecular Bond

of Bonds of Lone Geometry Geometry Angles Drawing
Pairs

2 0 Linear Linear 1800

3 0

2 1

4 0

3 1

2 2

5 0

4 1
3 2

2 3

6 0

5 1

4 2

2. Draw Lewis diagrams of the following molecules. Predict their three-dimensional shape from
the drawing you make and from what you have learned in doing this activity. Build a model of
each compound in the simulator (or find it on the Real Molecules screen). Confirm or correct
each of your predictions.
CO2, HF, SO2, NH3, H2O, PCl5, SF4, ClF3, SF6, BrF5, XeF4

Fill below table for all the above individual molecular structures. (10 points)

Molecule: _____CO2____________________
Total electron regions Drawing / screen capture

Bonding regions 2
Lone pair regions 2
Electron geometry Linear
Molecular geometry Linear

Molecular Models.
Molecule: _________________________
Total electron regions Drawing / screen capture