1 What is Organic Chemistry? Vitalism Examples of organic molecules What’s the common thread that ties these molecules together? Organic chemistry is the study of carbon-containing molecules that aren’t minerals. (CO 2, CaCO 3 and NaHCO 3 contain carbon but aren’t considered to be organic.)

2 What do organic chemists do? Drug design Discovery Process Structural determination When a plant/marine/etc. extract is found to have interesting properties, a chemist separates out the different molecules in the extract and uses modern equipment to help them determine the structures of the molecules involved – a lot like solving puzzles. These chemists get to go on great field trips!

3 Energy-related research Petroleum products are organic molecules. So are biofuels. Agricultural Chemicals Design of newer, better, (hopefully) safer herbicides and pesticides is done by organic chemists. Polymers Basic research In every field of science, there are some scientists who do research just for the sake of learning. Because they’re not driven by any particular agenda, they often produce ideas that lead to completely new understanding of our world – and sometimes technology nobody had imagined before.

4 Drawing Organic Molecules The three things you can count on…

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6 Drawing Organic Molecules Connectivity: the sequence of atoms and bonds. Molecules with the same connectivity can often be drawn in many different ways. It is not enough to write C 2 H 6 O. We must show how the atoms are connected: The structures above are structural formulas. They show the location of every atom in the molecule. For very large molecules, structural formulas take a long time to draw and can be confusing to read. Because of this, chemists have developed other methods for drawing structures. In a condensed structural formula, we group hydrogen atoms with the atoms they’re attached to and leave out the single bonds:

7 In a line-bond structures, we do not draw the hydrogen atoms attached to carbon nor do we draw the C symbols. Each line is a bond, and where lines meet or end there is a C atom. If you write the ‘C’, you must write all the atoms bonded to it as well.

8 Structural FormulaCondensed Structural Formula Line-Bond Structure

9 AlkanesAlkenesAlkynesArenes

10 The Functional Groups

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13 Things to watch for…

14 Ketone Not a ketone Ether Not an ether and, with the exception of alkene/alkyne/arene, this carbon is usually not part of another functional group...

15 Identify the functional groups…

16 Isomers Shape is crucial in organic chemistry. A molecule’s shape often determines how it interacts with other molecules. Isomers are compounds that have the same molecular formula but different arrangements of atoms. The term denotes a relationship. Isomers can be divided into two main categories: –Structural isomers have different connectivity. In other words, there will be a difference in which atoms are connected to which: –Stereoisomers have the same connectivity but different structure. We saw an example of this when we looked at cis- and trans- complexes in the co-ordination chemistry section of CHEM 1000:

17 Structural Isomers Structural isomers have different physical properties from each other (melting point, boiling point, etc.). This is also the only kind of isomerism for which the different isomers can have different functional groups. e.g. C 3 H 8 O has three structural isomers: How many structural isomers can you draw for C 3 H 6 ? When drawing isomers, all structures must still obey the octet rule!

18 Structural Isomers How many structural isomers can you draw for C 6 H 14 ?

19 How many structural isomers can you draw for C 3 H 9 N?

20 How do you know when molecules are the same? Molecules are identical if, in equivalent conformations, they are superimposable.

21 Stereoisomerism Stereoisomers can be further divided into different groups: –Geometric isomers have the same connectivity but the distance between atoms is different in each isomer due to a different spatial arrangement. Since carbon is not octahedral or square planar, in order to have geometric isomers in organic chemistry, we need either a double bond with two different groups attached to each atom or a ring with two different groups attached to two different carbon atoms in the ring: The isomer with the two more important* groups on the same side of the ring/double bond is called the cis- isomer while the isomer with the two more important groups on opposite sides of the ring/double bond is called the trans- isomer. * The importance of a group is determined by the atomic number of the first atom. So, Cl is more important than CH 3 which is, in turn, more important than H.

22 Naturally occurring lipids (fats and oils) that contain cis- double bonds tend to exist as liquids (oils). To make solid fats (like margarine), a process called hydrogenation is used to ‘saturate’ the fats with hydrogen: Saturated fats pack together more readily than fats containing cis- double bonds, so they can clog arteries and cause other health problems. Worse yet are trans-fats which contain fatty acids with unnatural trans- double bonds which also pack together easily and which the body doesn’t have the enzymes to break down properly: Trans- fatty acids are a by-product of partial hydrogenation. The conditions used to add hydrogen across some of the natural double bonds allow the remaining double bonds to isomerize.

23 Rotate 180° around CH bond

24 Enantioisomerism Chirality (n) Chiral (adj) Enantiomers... An asymmetric, chiral or stereogenic carbon… Any molecule with a single asymmetric carbon atom... An object is chiral if it is nonsuperimposable on its mirror image. A property of objects such that they are not superimposable on their mirror image. are molecules that are non-superimposable mirror-images of one another. is a tetrahedral carbon with four different substituents. must be chiral.

25 Configuration: What happens when we switch two groups on an asymmetric carbon atom? the actual arrangement in space of the substituents around a given asymmetric atom that can be designated R or S. Also applies to E/Z. We reverse (or invert) its absolute configuration. For a molecule with a single chiral center, we are converting one enantiomer into its opposite enantiomer. We must break bonds to do this.

26 The standard way to draw chiral molecules is to use line-bond structures with wedges and dashes to show stereochemistry: –The longest chain is drawn as a zigzag in the plane of the page. –Wedges are used to show groups coming out of the page toward you. –Dashed lines are used to show groups going into the page away from you. If you find this notation confusing, try a condensed structure using wedges and dashes:

27 e.g. For each of the following molecules, locate the stereocenter(s) and decide whether the molecule is chiral or achiral.

28 Unlike other kinds of stereoisomers, the physical and chemical properties of a pair of enantiomers are identical except for one: Another very important difference between enantiomers is that they interact differently with other chiral species. Time to shake hands… The activity of most drugs is based on their interactions with enzymes, which are themselves chiral. Due to the difficulties in synthesizing a single enantiomer of a compound, many drugs are sold as a 1:1 mixture of enantiomers - known as a racemic mixture.

29 Like many drugs, this anti-nausea drug was sold as a racemic mixture.