Philippine Science High School System Resource Material in Chemistry 3

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Molecular Models I: Organic Compounds
_______________________________________________________________________________ LEARNING
OUTCOMES: At the end of this activity, you should be able: x To use models to visualize structure in organic
molecules x To build and compare isomers having a given molecular formula x To explore the three-dimensional
character of organic molecules
___________________________________________________________________ I N T R OD U C T I O N
Organic Chemistry usually involves carbon-containing compounds, thus it is also called the chemistry of carbon
compounds.
Important Characteristics of Organic Compounds: 1) Carbon forms strong bonds to itself as well as to other elements
such as oxygen, nitrogen, hydrogen and the halogens. 2) Carbon atoms are generally tetravalent. Carbon is usually
bound by four covalent bonds to adjacent atoms. 3) Organic molecules are three-dimensional and bond angles are
discrete: 180, 120, 109.5 corresponding to compounds that have triple bonds, double bonds and single bonds
respectively. 4) Organic compounds have limitless variety in shape and structure. A molecular formula tells the atoms
comprising the compound but tells nothing of the structure: For example: C4H10 which can be represented by butane
and 2methylpropane. Butane 2-methylpropane
Another example is C2H6O, which can be represented as dimethyl ether and ethanol: Dimethyl ether Ethanol The
structures above represent different compounds and each have unique set of physical and chemical properties. The
pairs are called isomers each other.
2EXPERIMENT
The three dimensional character of molecules is expressed by its stereochemistry. Stereochemistry shows the spatial
relationships between atoms on one carbon and atoms on the adjacent carbon atoms. Because rotation can occur
around the carbon-carbon single bonds in open chain molecules, the atoms on adjacent carbons can assume different
spatial relationships with respect to each other. These rotations result to conformations. Conformers cannot be
considered isomers because rotations can happen anytime resulting to just identical molecules.
Conformers may be represented by projections. There are two common projection conventions: Sawhorse projection
and Newman projection. The sawhorse projection views the carboncarbon bond at an angle and all the bonds and
atoms are shown in their spatial arrangements. Newman projection provides a sight directly along the carbon-carbon
bond. In the Newman projection the carbon atoms behind the first are usually not visible.
Sawhorse projection of ethane showing all the bonds and atoms.
Conformers of ethane show only the first carbon atom. The first structure is an eclipsed conformation
while the second one is a staggered conformation.
PROCEDURE
Materials
1) Obtain a set of ball-and-stick molecular models. (Clay may be used as substitute if no molecular models are
available.)
2) The set should contain the following parts (other colored spheres may be substituted just make sure to label the
spheres correctly.)
x 2 black spheres representing tetravalent Carbon atom (4 holes)
x 6 white spheres representing hydrogen (monovalent element, one hole but in some models hydrogen has already a
built in bond stick) x 2 colored spheres representing Chlorine (monovalent, one hole) x 1 blue sphere representing
oxygen (divalent, 2 holes) x 8 sticks to represent the bonds 3) Protractor
Procedure
1) Construct the molecule methane. Methane is a simple hydrocarbon consisting of one carbon and four hydrogens.
 a. Rest the model on the desk and examine the structure. Rotate the molecule so that different set of hydrogen atoms
are viewed from your viewing angle.
b. Is there any difference between the ways that the two structures look?
c. Does the term equivalent adequately describe the four hydrogens of methane?
d. Tilt the molecule so that only two hydrogens are in contact with the desk and all four hydrogen atoms are visible
from view. Draw the way in which the methane molecule would look in a two-dimensional space showing all four
hydrogen atoms.
e. Using a protractor, measure the angle H–C–H on the model.
2) Replace one of the hydrogens of methane model with colored sphere, which represents the halogen chlorine. The
new model is chloromethane, CH3Cl. Position the molecule so that the three hydrogens are on the desk.
a. Grasp the atom and tilt it to the right keeping the two hydrogens on the desk. Take note of this projection and draw
the structure of the projection.
b. Return the model to its original position and then tilt it as before, but this time to the left. Take note of this
projection and draw this projection.
c. While the projection of CH3Cl changes, does the structure of the molecule change?
3) Now replace a second hydrogen with another chlorine sphere. The new molecule is dichloromethane, CH2Cl2.
a. Examine the model as you twist and turn it in space.
b. Draw four possible projections of the molecule. Are the projections isomers of CH2Cl2 or just the same structure
only seen differently in three dimensions?
4) Construct the molecule ethane, C2H6.
a. Write the structural formula for ethane. b. Are all the hydrogens attached to the carbon atoms equivalent?
c. Draw a sawhorse representation of ethane. Draw a staggered and an eclipsed Newman projection of ethane.
d. Replace any hydrogen in your model with chlorine. Draw the structure of the molecule.
e. Twist and turn your model. Draw two Newman projections of the chloroethane molecule.
f. Are the structures isomers or conformers of the same compound? Why?
5) Dichloroethane, C2H4Cl2.
a. From the chloroethane molecule, C2H4Cl, constructed in preceding procedure, remove one hydrogen from the
molecule and replace it with chlorine. Note that this time you now have an option whether to remove hydrogen from
the carbon atom that already has one chlorine atom attached to it or the second carbon atom that has hydrogen atoms
attached to it.
b. First remove the hydrogen atom from the carbon atom that has chlorine atom attached to it. Draw the structure of
the compound. Construct another C2H4Cl2 with the chlorine atoms each attached to the carbon atoms. Draw the
structure and write their IUPAC name. Are these structures similar?
6) Butane
a. Butane has the formula C4H10. With the help from a partner, construct a model of butane by connecting the four
carbons in a series and then adding the needed hydrogens. First orient the model in such a way that the carbons appear
as coplanar or in the same plane from your viewpoint. Next, tilt the model so that the carbons appear as zigzag line.
Then, twist around any of the C–C bond so that a part of the chain is at an angle to the remainder. Draw each of these
structures. Are these structures equivalent or are they isomers? Why?
b. Is it possible to create a staggered and eclipsed Newman projection of butane by aligning all four Carbon atoms?
c. To create a Newman projection Rotate the second carbon atom clockwise by 60 degrees; draw the Newman
projection showing the eclipsed conformation. Continue rotating the second carbon clockwise by 60-degree
increments and observe the changes that take place.
d. Examine the structure of butane. If one hydrogen atom will be replaced with chlorine, how many monochlorobutane
isomers could be obtained? Test your prediction by replacing the hydrogen by chlorine on the models. Draw the
structure of these isomers.
e. Reconstruct the butane system. First, form a threecarbon chain, then connect the fourth carbon to the center carbon
of the chain. Add the necessary hydrogens. Draw the structure of the molecule. Can any manipulation of the model by
twisting or turning of the model or by rotation of any of the bonds give you the same butane system?
f. Examine the structure of 2-methylpropane. Predict how many monochloroisomers of 2-methylproane could be
formed and test your predictions by replacing the hydrogen with chlorine on the model. Draw the structures of these
isomers.
7) C2H6O
a. There are two isomers with the molecular formula C2H6O: ethanol (ethyl alcohol and dimethyl ether. With your
partner, construct both of these isomers. Draw these isomers.
b. Manipulate each model. Can either be turned into the other by a simle twist or turn?
8) Butenes
a. Construct 2 butene, CH3–CH=CH–CH3. There are two isomers for the compound of this formulation: the isomer
with the two –CH3 groups on the same side of the double bond, cis-2-butene; and the isomer with the two –CH3
groups on the opposite side of the double bond, trans-2-butene. Draw these structures.
b. Can you twist, turn, or rotate one model into the other? Explain.
c. How many bonds are connected to any single atom of these structures?
d. With the protractor, measure the C–C=C angle.
e. Construct methylpropene. Can you have a cis- or a trans- isomer in this system?
9) Butynes
a. Construct 2-butyne, CH3–CΞC–CH3. Can you have a cis- or trans- isomer in this system?
b. With the protractor, measure the C–CΞC angle.
c. Construct a second butyne with the molecular models. How does this isomer differ from the one previously made?
Pre-Laboratory Questions
1) How do you define organic chemistry?

2) What are the four most common elements found in organic compounds?

3) Define isomers. Give two examples of isomers and draw their structures.
 4) Use Newman projections to show ethane in the eclipsed conformation and in the staggered conformation. Label
them correctly. How can you convert one into the other?

Report Sheet
1. Methane

2. Chloromethane

3. Dichloromethane

4. Ethane and Chloroethane

5. Dichloroethane

6. Butane

7. C2H6O
8. Butenes

9. Butynes

Post-Laboratory Questions
1. Write the structural formula for the two isomers of chloropropane, C3H7Cl.

2. Draw a staggered and an eclipsed conformer for 1,2dichloroethane, ClCH2CH2Cl.

3. Why can you not convert cis-2-butene