Iryna Belskaya

Partner: Katherine Belfer

Lab Instructor: Budimir Zdravkovic
October 5th, 2018
Experiment 5. How can we build molecules? “Models to the rescue”

Introduction:
The shape and structure of chemical molecules, and the way atoms are linked together are of
high importance, since it determines the chemical and physical properties of the compounds.
Some molecules can be built in more than one way, depending on their formula and the way
atoms connect together. The theory used to predict the geometry of individual molecules is
called VSEPR (Valence Shell Electron Pair Repulsion), and it is based on the number of electron
pairs surrounding the central atoms of the molecules. The idea of VSEPR is that the valence
electron pairs surrounding an atom tend to repeal each other, and therefore, they “choose” the
arrangement that minimizes the repulsion, and thus, it determines the molecular geometry. The
number of electron pairs in the valence shell of a central atom is determined after drawing
the Lewis structure of the molecule, and expanding it to show all bonding groups as well as lone
pairs of electrons. In this lab we are using the software Gaussian to build molecular models of
several chemical elements and compounds given their chemical formula. We get familiar with
the program, and use it for practicing and for visualizing molecular shapes and structures, and to
answer several focus questions.

Materials:
Lab manual
Gaussian program
Computer

Observations and Experimental:

There is no experimental part in this lab. We followed prescribed steps in the Gaussian program.
In part 1 we learnt how to build the H2 molecule and explored GaussView. In the second part we
practiced the building of molecules in the software. We practiced on building SF6 molecule. The
bond length of our molecule was 1.59. The angles were 90 and 180 degrees. The third part is
dedicated to building molecules and geometry optimization. For the molecules of water,
ammonia and methane we predicted 109.5 degree bond angles. The water molecule bond length
(O-H) was 0.96 for both bonds. We also measured the bond angles and length of the bonds for
methane and ammonia, we tabulated this information in the post-lab assessment question. Please,
see the table. Finally, we visualized molecular orbitals in the 4th part, and compared them to the
ones we know from literature and lectures. We also looked at the N2 molecule and measured the
bond length between two atoms, which was equal to 1.13384. We attached the pictures we
derived by using the software at the end of the lab report. Please, see attachments.

Discussion and Conclusion:

In this experiment we learned how to construct molecule models by using the Gaussian Program
on the laptop. This program allowed us to look and explore molecules more closely, as well as
to make calculations related to the molecular structure and dynamics.
Elements are chemically the simplest substances and hence cannot be broken down using
chemical methods. They can only be changed into other elements using nuclear methods. A
molecule is the smallest particle in a chemical element or compound that has the chemical
properties of that element or compound. They are made up of atoms that are held together by
chemical bonds; these bonds form as a result of the sharing or exchange of electrons among
atoms. Furthermore, using a chemical formula you can construct a model of a molecule. This is
done by being able to first determine what elements and how many of them are in the
molecule. Then by finding out its electron configuration we can determine its orbitals, which
would lead to the drawing of the structure of the molecule.
Using the Gaussian Program in part 4, we looked closer at the molecule N2 in order to review
orbitals, wave functions, nodes, molecular orbital (MO) theory, and to see a practical application
of MO theory to understanding the reactivity of molecules. After building the diatomic nitrogen
molecule we measured the bond length which was found to be B=1.13384. Then we viewed the
energy level diagram, which demonstrated 10 molecular orbitals. The diagram listed the orbitals
by increasing energy but shows no degeneracy. In these sections we also answered focus
questions:
Do these images look like what you expected?
Yes, they did look as expected due to knowing their molecular formulas and therefore
determining they were tetrahedrals, which would give the images shown.

Focus Questions:
Part 1.
1. What is an element?
Element is each of more than one hundred substances that cannot be chemically interconverted
or broken down into simpler substances and are primary constituents of matter. Each element is
distinguished by its atomic number, i.e., the number of protons in the nuclei of its atoms.

2. What is a molecule?
Molecule is a group of atoms bonded together, representing the smallest fundamental unit of a
chemical compound that can take part in a chemical reaction.

3. How can you construct a model of a molecule based on a chemical formula?

To construct a model of a molecule we start with a Lewis structure. When looking at a chemical
formula, each letter represents an element. We know how much of each element is present by
looking at the subscript number. Using the rules of building a Lewis structure we can get the back
bone of a molecule and we can also learn about the bonds holding the atoms in the molecule
together. Using our knowledge of molecular geometry, we can estimate what a molecule would
look like in a 3D plane as well as estimate the bond lengths and bond angles.

Part 4.
1. Do these images look like what you expected (i.e. compared to the images you have seen
in lecture or in your textbook)?
Yes. The images looked like I expected. The angles were more precise in the computer program, but
we know that VSEPR does not predict actual angles adopted by molecule. The difference between
literature and experimental angles was up to several degrees.
 2. What does such a picture of an orbital represent? Explain this as clearly and concisely as
you can.

Pictures of orbitals represent types of bonds that are present, the amount of nodes (areas, where
there no electrons can found), we also can see areas (orbitals themselves), where electrons are most
likely to be found.

References:
Lecture notes from CHEM 102 course
Lab Manual
Chemistry dictionary

Post-Lab Assessment Questions:

1. Fill in the following table using data calculated by GaussView in the lab:

Compounds Angle VSEPR Angle after Angle after Angle Bond length Bond length
predicted “cleanup” ab initio (literature after after ab initio
(i.e. 109.5, (.gif file) Optimization value) “cleanup” optimization
<109.5) (.chk file) (.gif file) (.chk file)

Water 109.5 109.471 106.46527 104.5 0.96 0.94786

Ammonia 109.471 109.471 107.9678 107 1.00 1.00231
Methane 109.47 109.471 109.47122 109.5 1.07 1.08402

2. Do you see a trend for water, ammonia, and methane bond angles? Explain in terms of
their VSEPR structures.
All the bond angles are around 109.471 degrees, which means they are all have a tetrahedral
molecular geometry.
 3. What is the main idea behind VSEPR theory?

The VSEPR theory is based on the number of electron pairs surrounding the central atoms of the
molecules. The idea of VSEPR is that the valence electron pairs surrounding an atom tend to
repeal each other, and therefore, they “choose” the arrangement that minimizes the repulsion,
and thus, it determines the molecular geometry. The number of electron pairs in the valence shell
of a central atom is determined after drawing the Lewis structure of the molecule, and expanding
it to show all bonding groups as well as lone pairs of electrons.

4. Which bond angle after “cleanup” or “lab initio optimization” was the closest to the
literature value? Explain your answer.
“Cleanup” was closest to experimental bond angle as opposed to ab initio
optimization. Ammonia and water showed some difference between the ab initio optimization
and experimental bond angle. Ammonia and water should be at an angle close enough to
109.471 to keep it being a tetrahedral but instead it was 107.97 and 106.47.

5. What is the bond order in the nitrogen molecule as predicted by MO theory? Is this in
agreement with the Lewis structure?
The bond order is 3. It is the most stable form for the molecule N2. It agrees with the Lewis
structure.