Investigating Organic Structures and Isomerism
Through Molecular ModelBuilding
Introduction
A molecular formula for a compound tells us the number of atoms of each element in the compound, but rarely indicates the chemical structure, namely the connectivity of the individual atoms to each other in the molecule. Chemists are interested in that structure because it often allows them to predict many physical and chemical propertiesof the compound.
The main goals of our recent discussions of Lewis Diagrams and VSEPR theory were to determine the most likely structure of relatively simple moleculesand then predict their three-dimensional shape, both of which are critical in determining how they behave.
Using Lewis diagrams for more complexstructures such as those found in organic compounds, however, is less convenient. To aid in accurately representingthese structures, molecular model kits arevery helpful.
As you recall from our discussions in class, one of the reasons for the great variety and complexity of carbon compounds is the phenomenon of isomerism. Isomers are different compounds (often having quite different chemical and physical properties)with the same chemical formula. Isomers can come in different varieties depending on how those compounds with the same formula are different, and model kits are extremely beneficial in discovering and depicting these differences.
Two of the different categories of isomers are Constitutional isomers and Stereoisomers.
Constitutional isomers are compounds with the same molecular formula, but a different connectivity (or order of attachment) of their atoms.An example of this can be seen in the molecular formula C4H10. As we have discussed in class, there are two possible orders of attachment of these atoms. As shown below, structure (1) has four carbon atoms attached in a chainand is named butane. In structure (2), three carbon atoms are connected in a chain and the fourth carbon is a branch on that chain connected to the middle carbon. This is a different compound and is called methylpropane.
Structure (1) CH3—CH2—CH2—CH3 (butane)
CH3
|
Structure (2) CH3—CH—CH3 (methylpropane)
Stereosiomers have the same molecular formula and the same connectivity, but different orientations of their atoms in space. As you recall, we have already discussed one type of stereoisomer in class: Geometric (also called cis-trans)isomers arise when substituents across a double bond or on a ring are locked into their orientation in space with respect to one another. An example is shown below. In Structure (1), where both hydrogens exist on the same side of the carbon-carbon double bond, the prefix “cis-“ is used in the name. In Structure(2), the prefix “trans-“ indicates that the two hydrogens are “locked” on opposite sides of the doublebond.
H H
| |
Structure (1) CH3—C==C—CH3 (cis-2-butene)
H
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Structure (2) CH3—C==C—CH3 (trans-2-butene)
|
H
As you can see in the above diagrams, due to restricted rotation about the carbon-carbon double bond, it is not possible (without breaking bonds) to manipulate Structure (1) so as to allow it to be superimposed upon Structure (2) in such a way that all of atoms or groups line up. The two compounds are, therefore, different.
This is the criterion to determine if any two structures are really the same molecule, or, as is the case in the above example, different, and represent isomers of each other.
Another type of stereoisomer is called an Enantiomer. Enantiomersare stereoisomers that are nonsuperimposable “mirror images” of each other. This is a fascinating and important aspect of structural chemistry. These isomers are also called “optical isomers” based on the fact that each member of a pair of enantiomers is “optically active”, meaning they rotate the plane of polarized light, in this case, either to the left or to the right. A detailed discussion of enantiomers and their systematic naming is beyond the scope of this course. However, as you may discover several examples of such isomers during this investigation, explaining how to determine if a particular structure that you build (or any object for that matter) does or does not have a nonsuperimposable mirror image is helpful.
One way to make this determination is to find a carbon atom in the molecule that is bonded to four different groups. An example is shown below using the compound
2-chlorobutane. The dashed vertical line represents the reflecting plane of a mirror between the two isomers. Consider the italicized carbon shown in bold print in each structure. Note that it is connected to four different groups, namely a chlorine atom, a hydrogen atom, a carbon attached to three hydrogens, and a carbon attached to two hydrogens. This carbon is called a stereocenter and its existence in a molecule means that the mirror image of that molecule is a different compound because the two cannot be superimposed on each other such that all the atoms or groups line up.
CH3 CH3
| | |
Cl ► C ◄ H H ►C ◄ Cl
| | |
CH2 CH2
| | |
CH3 CH3
|
MIRROR
PLANE
Anotherway to determine if the molecule does or does not have a nonsuperimposable mirror image is to see if the molecule has a plane of symmetry. This is an imaginary flat surface or plane slicing the molecule in half such that one half is the reflection of the other half. If the structure has at least one plane of symmetry, then it does not have an isomer which is a nonsuperimposable mirror image. If you look again at the two structures on shown on the bottom of the previous page, you will notice that neither possesses a plane of symmetry.
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This investigation will call upon you to employ the systematicnomenclature rules we have discussed in class for naming alkanes, alkenes, alkynes and cycloalkanes. Accordingly, you may find it helpful to review your notes on that material.
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Objectives
1. Using a model kit, to construct a variety of molecular models for simple
organic compounds and represent their structures with appropriate diagrams.
2. To employ IUPAC nomenclature protocols in naming all of the structures built and
then drawn over the course of the investigation.
3. To investigate the variety of isomers that may exist for different chemical formulas by
building, drawing, and naming their structures.
Materials
One MolymodTM student organic model kit per pair of students working as a group.
Procedure
1. Obtain one molecular model kit and note the number indicated on both the bottom and
the cover of that kit. This is the kit number you and your partner will use over the
course of this investigation. On the label pasted onto the model cover is a list of the
contents of the kit. Each kit contains a collection of coloured spheres representing the
atoms of different elements and various grey and white connectorsrepresenting bonds
for the atoms. Before you begin this investigation, ensure that your model kit is not
missing any items. If it is, let me know and I will replace those items.
2. Using the model kit, construct models for the first three compounds in the alkane
series. Diagram and name each of these.
3. Construct models for all the possible isomers having each of the following formulas:
a. C4H10 b. C5H12 c. C6H14
Diagram and name each of the isomers.
What do you notice about the number of isomers possible for each formula as the
number of carbon atoms in the formula increases?
4. Construct models for all possible isomers having each of the following formulas:
a. C3H6 b. C4H8
Diagram and name each of the isomers.
Are all of the isomers alkenes? What can you say about the nature of the possible
isomers for any hydrocarbonhaving the general formula CnH2n?
5. Construct models for as many of the possible isomers having the formula C6H12 as you
can find. Many isomers exist for this formula and a minimum of 20 isomers is
required. Diagram and systematically name each of the isomers and number them for
easier reference. Remember to consider the possibility of the different types of isomers
listed above.
Note: If you and your partner are trying to decide if two models are actually the same
molecule or represent different isomers, then do the following:
Attempt to manipulate the models without breaking bonds in such a way that the two
can be superimposed on each other with all of the atoms or groupslining up. If that
isn’t possible, then the two structures represent different isomers.
Having applied the criteria for enantiomers, if you and your partner believe you have
found two nonsuperimposable mirror-image isomers, diagram the two side-by-side
as reflections of each other. Separate the two diagrams by a vertical dashed line
drawn between them (representing a mirror) as was done in the Introduction above.
As we haven’t discussed systematic rules for naming such isomers, you needn’t
attempt to name these.
For each legitimate isomer you discover beyond the minimum 20, a ½ bonus
mark will be awarded to your group when the report is graded. You will also receive
an additional ½ bonus mark for each pair of enantiomers you discover. However, for
each isomer you present that is identical to one already mentioned in your list, a
deductionof ½ mark will occur.
6. Construct models for all of the possible alkynes having the formula C5H8.
Diagram and name each of the isomers.
Are cis and trans isomers possible for alkynes?
For Further Study
1. Without using a model kit, diagram the two isomers that exist for the formula C2H6O
Which of the two might you expect to have the higher boiling point and why?
2. Use a reference source to learn what “trans fats” are, how they are produced, and what
potential health risk they represent.
3. Use a reference source to investigate how the cis- and trans- isomers of a compound in
our eyes called Retinal are involved in the process that allows us to see.
4. Try to find common objects that you encounter in your daily life that might have
nonsuperimposable mirror images. Shoes and gloves (which means something about
your feet and hands), the spiral binding on a notebook, the thread on a metal screw,
and a ship’s propeller are examples. The next time you visit one of
Vancouver’s beaches, try to find sea shells that have a helical twist. Do the shells you
find have mostly a right or a left-handed spiral, or can you find an equal number of
each?
5. Use a reference source to learn how scientists detect the optical activity of enantiomers
in the laboratory.
6a. Use a reference source to investigate the different biological effects of the “left”
and “right” handed versions of the following compounds:
(i) Thalidomide (ii) Ethambutol (iii) Methorphan (iv) Naproxen
(v) Carvone (vi) Methamphetamine
b. When therapeutic drugs have optical isomers that may not be as effective or may
even be harmful if ingested, research how pharmaceutical companies are able to
produce only the beneficial form of those isomers.
Conclusion
Based on this activity, attempt to summarize some of your thoughts regarding the complexity and variety of organic compounds resulting from isomerism.
References
1. Brown, W; Foote, C. Organic Chemistry Third Edition. Philadelphia: Harcourt. 2002
2. Silberberg, M. Principles of General Chemistry. New York: McGraw-Hill. 2007
3. Morrison, D.; Scodellaro, D. Essential Experiments for Chemistry. Vancouver: SMG
Lab Books. 2005
4. Zumdahl, S.; Zumdahl, S. Chemistry Fifth Edition. Boston: Houghton Mifflin. 2000