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Chemistry 2131:
Organic Chemistry for the Life Sciences(3)

Introduction to Stereochemistry

• we have already seen a number of different kinds of organic isomers. While studying the alkanes we encountered constitutional isomers. The molecules have the same molecular formula, but the order of attachment of atoms is different. We encountered cis/trans isomers while examining the cycloalkanes. Because of the restricted rotation about the ring C-C bonds, groups can be oriented differently relative to the plane of the ring. This kind of isomer is a kind of stereoisomer. Another stereoisomer that we have seen is the cis/trans isomers of alkenes. Again it is not the order of attachment of atoms, but their orientation is space that differs.
• so, to define: stereoisomers are molecules that differ from each other by the arrangement in space or the geometry of atoms in the molecule.
• this is easiest approached if you have model in front of you. Take one tetrahedral carbon and attach four differently coloured balls to it. Now make another, only put the balls on in a different order. You will find that there are two possible ways to make models, and they are not identical.
• if you try to superimpose the molecules on each other you will find that you can't, no matter how much you rotate them through space.
• you will find that the molecules are mirror images of each other. Two molecules that differ only in that they are mirror images of each other are called enantiomers.
• moleucles which are stereoisomers of each other, but are not mirror images of each other are called diastereomers. It is important to remember that the examples that we have seen to date, cis/trans isomers of cycloalkanes and alkenes, are diastereomers, because the molecules are not mirror images of each other.
• moleucles that are not superimposable on their mirror images are said to be chiral. Another way of looking at it is that the moelcules have a handedness to them.
• any molecules that has a plane of symmetry to it cannot be chiral.
• the most common source of chirality in organic molecules is a carbon atom bonded to four different groups, like the carbon with four different balls on it that we just made. The carbon atom which is chiral is called a stereocentre.
• as an example, let's look at the classic but good example of lactic acid (2-hydroxypropanoic acid). Make both enantiomers of this molecule. Looking at the central carbon atom, it has one methyl group on it, one hydrogen, one hydroxyl group and one carboxyl group on it. There are two ways to make it.

2. The R-S Naming System:

• now that we know that stereoisomers exist how do we name them? We already know how to name stereoisomers of cycloalkanes, with the cis/trans system. And we know how to name stereoisomers of alkenes, using the E,Z system. We use the R-S system to name organic molecules which contain stereocentres.
• the first step is to locate all stereocentres in the molecule. Remember that to be a stereocentre the carbon atom must have four different groups on it.
• then, for each centre, assign a priority to each group exactly as we did for the E,Z system, based on atomic number.
• next, one orients the molecule such that the group of lowest priority is directly away from you and the other group project towards you (not unlike a Newman projection)
• then, you read the groups projecting towards you from highest to lowest priority. If the reading is clockwise, the configuration is designated R, which stands for the latin "rectus", and if the reading is counterclockwise, the configuration is designated S, which stands for "sinister".
• if there are several stereocentres, this must be done for each centre. The designations are clearly numbered 2S, 3R...

3. Drawing Stereocentres and Fischer Projections:

• now that we know how to name a ctereoisomer form its structure (we did it form a model), how do we go about depicting such things on paper? Let's use a simple example, 2-butanol to explore this.
• make both enantiomers of this molecule. First determine for yourself which is R and which is S.
• by convention, we can draw two bonds in the plane of the paper as regular solid lines at an approximately 110 degree angle. The bond going away from you or into the paper if you like is drawn as a dshed line or wedge. The bond coming out of the paper or out towards you is drawn as a solid wedge.
• Let's start with the S enantiomer. For uniformity, let's put the hydroxyl group up and the hydrogen back (as if we were going to read the configuration). In this case the OH is up in the plane, and if we rotate it a little the methyl group can also be in the plane. This puts the ethyl group towards you and the hydrogen away from you.
• you should notice that there are many ways to draw the same molecule, just as there are many ways to hold the molecule.
• this method is great for one stereocentre, but what if you have several? It can get very messy. Another method exists which is much easier to draw, and is much more useful for multiple stereocentre containing molecules, it is called a Fischer projection.
• for Fischer projections, you must orient the molecule such that the vertical bonds are oriented away from you and the horizantal bonds are towards you like handles on a bicycle. For reasons that will become obvious when we study carbohydrates in a few weeks, it is the convention to put the main carbon chain up and down.
• so let's put the main chain up and down for our 2-butanol. With the (S)2-butanol, take the OH in your right hand and the hydrogen in your left hand the methyl group should go up and out and the ethyl group should be down and out.
• we draw the stereocentre as a cross with the groups drawn at the ends. Remember that the only part actually in the plane of the paper is the carbon atom (the stereocentre) itself.
• let's go through the whole thing with the (R)-2-butanol
• how can we tell if two Fischer projections represent the same molecules or not? The only "manipulation" of the drawing that is "allowed" is to rotate the projection 180 degrees in the plane of the paper. To rotate out of the plane changes the molecule. Try this!