Molecular Structures

Molecular Structures
Learning Objectives:
- Understand covalent bonding displayed by elements in biological systems
- Apply the octet rule
- Practice converting molecular formulas into molecular structures
- Be able to visualize and draw three dimensional molecular shapes
Introduction:
The octet rule states that most elements will share or exchange valence electrons in order to achieve a similar electron arrangement to the nearest noble gas. This concept is extremely important because it explains why elements bond to form compounds such as water, electrolytes, DNA, proteins and other biologically important substances.
In this lab we will be focusing on a small palette of biologically important elements and studying how they covalently bond. In covalent compounds, the behavior of these elements tends to be consistent and predictable.

Group Electron Arrangement

Number of Bonds and
Lone Pairs

1A
7A

1 bond and no lone pairs

H
X

6A

X = F, Cl, Br or I
O
O
O

6A
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S

1 bond and 3 lone pairs in biological systems
Oxygen generally has 2 bonds and 2 lone pairs, but may have one bond and 3 lone pairs in anions such as hydroxide, or 3 bonds and 1 lone pair in cations such as hydronium.

Sulfur has 2 bonds and 2 lone pairs in biological systems.
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5A

N
Nitrogen generally forms 3 bonds with 1 lone pair, but may form 4 bonds with no lone pairs in cations.

N

5A

3-

O
O

P

O

O

4A
C

Si

In biological systems, phosphorus generally exists as the phosphate ion shown here where it forms 5 bonds with no lone pairs. Outside of biological systems, P sometimes behaves like N by forming 3 bonds with 1 lonepair. Carbon forms 4 bonds and no lone pairs. It is not stable with any other arrangement.
Similarly, silicon is only stable with 4 bonds.

Procedure:
Please draw structures, build models, and draw 3D pictures for each formula given. The first one has been done for you as an example. The structure was determined using the information above. N forms 3 bonds with 1 lone pair in neutral molecules and H forms 1 bond with no lone pairs. Using these rules there is only one stable way to arrange these atoms into a molecule.
The 3D picture is determined using the models in conjunction with Valence Shell
Electron Pair Repulsion theory (VSEPR theory). Despite its intimidating name,
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VSEPR theory is based on a very simple concept. It states that both bonds and lone pairs are made of electrons and occupy spaces. These electrons repel each other due to charge and therefore spread out as far as possible from each other.
The shapes of molecules can be predicted by the number of bonded atoms and lone pairs around the central atom(s). Please see section 5.8 of the textbook for a discussion of the possible molecular shapes along with number of bonded atoms and lone pairs associated with them.
Scientists have a simple method for creating 3D drawings of molecules using dashes and wedges to show perspective. In the 3D drawing, bonds represented by lines are in the plan of the paper, bonds shown as wedges project outwards towards the viewer and bonds shown as dashed line point away from the viewer.

Model

3D Drawing

Tips for using the model kits:
- For most of the central atoms you will want to use a ball with 4 holes.
- Sticks with no balls on the end can be used to represent lone pairs
- Double and triple bonds can be created using the ‘bendy’ sticks.

- When finished, please disassemble the models completely and return all parts to the box.

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Molecular Structures

Practice Draft (for your records)
Lab Day/Time________________

Formula Structure
1.

Name_________________________
Partner’s Name_______________________

3D Drawing and
Molecular Shape

NH3

Trigonal Pyramidal

2.

3.

4.

5.

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6.

7.

8.

9.

10.

11.

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Lab Report (turn in neat copye before you leave) Name___________________
Lab Day/Time________________
Partner’s Name_______________________

Formula Structure
1.

3D Drawing and
Molecular Shape

NH3

Trigonal Pyramidal

2.
2pts
3.
2pts
4.
2pts
5.
2pts

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6.
2pts
7.
2pts
8.
2pts
9.
2pts
10.
2pts
11.
2pts

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Exploratory Section (Extra Credit):
There are 11 possible isomers (different structures possessing the same formula) for C3H6O. See if you can figure out at least 4 of them!

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