5 Fundamentals of Chemistry Lab Protocol

Exercise 1: Atomic structure – draw a diagram of an uncharged carbon-12 atom

Read and discuss the following information as a lab group to learn or review basic information about atoms. After reading each bullet point, pause to briefly discuss (answer the indicated questions) with your group mates how the information might help you complete the task.

• Carbon has an atomic number of six (6). This means all atoms with 6 protons in the nucleus are carbon atoms. How many protons are present in one Carbon-12 atom?
• Isotopes are different versions of the same element. Two atoms are isotopes of one another if they contain the same number of protons but have different numbers of neutrons. Therefore, different isotopes of the same element will have a different atomic mass = # of protons + # of neutrons (a proton and a neutron are equal in atomic mass). Carbon-12 refers to a carbon atom with an atomic mass of 12. How many neutrons are in one Carbon-12 atom?
• When thinking about an atom, we will assume that it is uncharged unless we are told otherwise. To be uncharged, the carbon-12 atom must have the same number of electrons as it has protons. How many electrons will be part of the uncharged Carbon-12 atom?
• Atoms can have multiple electron shells. Each shell has a maximum number of electrons that it can hold: the shell closest to the nucleus is the first shell and can hold a maximum of 2 electrons; the second and third shells can each hold a maximum of 8 electrons. Since electrons prefer to be in their lowest possible energy state, the first shell is filled first followed by shell 2 and then shell 3. How many electrons will be part of the first shell in a Carbon-12 atom? How many electrons will be in the second and third shells, respectively?
• Whichever electron shell is the outermost shell containing electrons is called the valence shell of that atom. How many electrons are expected to be in the valence shell of a Carbon-12 atom?
• The valence number of an atom refers to the number of unpaired electrons in the valence shell. Note that this is not the same as the number of valence electrons. The valence number can be determined by placing one electron at a time into the valence shell. If the second or third shell is the valence shell, consider it to have a north, east, south, and west position. You must put one electron into each of these positions before going back and adding a second electron. After you have done this, the number of electrons that are not part of a pair of electrons is called the valence number. (Remember that before placing any electrons in the valence shell, lower-level shells must be filled.) What is the valence number of an uncharged Carbon-12 atom?
• The number of bonds that an atom is expected to make is the same as the valence number of that atom. How many bonds is a Carbon-12 atom expected to make?

Now, complete the task of drawing an uncharged Carbon-12 atom.  Each group member is to draw their own diagram. Include its nucleus and electron shells making sure that the number of protons, neutrons, and electrons are correct and can be clearly counted by the instructor.  Make sure it is clear which valence electrons are paired and which are unpaired.

Using your phone, take a picture of your Carbon-12 atom and insert it into your post-lab assignment.

Exercise 2: Chemical Bonds

Read the following information together with your group.

• Each element has its own properties. All carbon atoms are expected to have the same chemical properties.  Electronegativity is one of the properties that significantly impacts the type of chemical bond forms between two atoms. Electronegativity can be thought of as the greed that elements have for additional electrons. A textbook definition might sound more like, “the tendency of an element to hold electrons near its nucleus when interacting with other atoms.” An electronegativity value has been estimated for each element. The electronegativity value of one element on its own has little meaning. However, the difference in electronegativity values between two interacting atoms is meaningful because it can be used to predict the type of bond by which they interact. Electronegativity values are not usually memorized; however, the relationship between elements often is.

In your own words, how does electronegativity help determine the kind of bond that will form between two atoms?

Using a periodic table, complete the following table.

Complete the following table. Determine the type of bonding (nonpolar covalent, polar covalent, ionic, or none).

Now we are ready to use the models!

Exercise 3: Identify the model elements by color

Different types of atoms make different numbers of covalent bonds. The balls in the chemistry model kit represent different elements and the connectors represent covalent bonds.  Based on the number of holes per ball (which represent unpaired electrons and the potential to make a bond), indicate which color of ball represents each of the following elements:

Phosphorus which makes a whopping 5 covalent bonds:

Carbon:

Hydrogen:

Nitrogen:

Oxygen:

In this model kit, the pieces used to represent single covalent bonds are short and rigid. The pieces used to represent double covalent bonds are long so that they can bend a little bit. Find examples of each in the kit.

Exercise 4: Build functional groups

For each of the following functional groups, build the functional group using the correct elements, then take a photograph of the models you’ve produced. Be sure to look at the post-lab assignment to determine how this photograph should be taken.  Use the information on the next page to help you.

1. Methyl
2. Hydroxyl
3. Carboxyl
4. Carbonyl
5. Amino
6. Phosphate

Below is a table that displays the functional groups to help you accomplish this task. Note that the colors may be different than the model. Focus on the elements used.

Exercise 5: Build an amino acid using functional groups.

There are four components that make up an amino acid:

• A central carbon, including a covalent bond to one hydrogen.
• An amino group.
• A carboxyl group.
• An R group, also known as the amino acid’s side chain. In chemistry, R is used when writing definitions of molecules. It means that almost anything can be in that position on the molecule and the molecule will retain its identity. However, there are only 20 standard amino acids used in life. Non-standard amino acids exist and some of them are used in some organisms.

Using the functional groups you produced in the previous task and other model parts, build the amino acid valine, isoleucine, serine, or asparagine. Below is a table showing the atomic make-up of all standard amino acids.

Take a photograph of your model of the amino acid and submit it as part of your post-lab assignment.

Exercise 6: Build various hydrocarbons

Hydrocarbons are molecules that are composed of only carbon and hydrogen atoms. These molecules are not abundant in life, but most organic molecules are modified hydrocarbons with functional groups attached. Therefore, understanding hydrocarbons helps us understand other organic molecules. Build each of the following hydrocarbons:

• An unbranched chain with 4 carbons and 10 hydrogens (C₄H₁₀)
• A branched hydrocarbon with 4 carbons and 10 hydrogens (C₄H₁₀)
• Chain with 4 carbons and 8 hydrogens (C₄H₈) including one double bond between any two carbon atoms
• A ring with 6 carbons and 12 hydrogens (C₆H₁₂)
• Two different structural isomers of C₄H₉OH

Exercise 7: Demonstrate hydrogen bonding

Build five water molecules (H₂O).

Lay the water molecules on the table. Line up the water molecules so that the oxygen of one water molecule is pointing toward one of the hydrogens of the other water molecule. Take a picture.

What is the name of the attraction between the oxygen of one water molecule and the hydrogen of the other?

Is this a type of covalent bond? Circle one:         Yes                         No

In a single water molecule, electrons across each covalent bond are not shared equally. The electrons spend more time around the oxygen than the hydrogen because oxygen has a higher electronegativity. This uneven of electrons is called a polar covalent bond. Polarity results in a partial negative charge on the oxygen and a partial positive charge on the hydrogen.

How does polarity affect water molecules?

Text adapted from Jacob Broderick