1 what is organic chemistry? vitalism examples of organic molecules what’s the common thread that...
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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. (CO2, CaCO3 and NaHCO3 contain carbon but aren’t considered to be organic.)
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• 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!
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• 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.
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Drawing Organic Molecules
• The three things you can count on…Stable carbon-containing compounds have four bonds to carbon.
CH4 CH3CH3 C C
H
H H
H
C CH H
Methane EthaneEthene(Ethylene)
Ethyne(Acetylene)
Three bonds to nitrogen...
Two bonds to oxygen
N
H
HH
Ammonia
N
H
C
H
Aminomethane(methylamine)
H
H
H
CC
H
H
H
N
Acetonitrile
HO
HH
O C
H
H
H
C
O
HHWater
Methanol Formaldehyde
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These species are not stable, but are reaction intermediates...
C
H
HH
H
CH3
CH3
CH3
CH2
Loss of H+
Loss of H
Loss of H
Loss of H2
Carbanion
Carbocation
Free radicalCarbene
The other elements of row 2...
N
HH
H
HO
H
Loss of H+
Loss of H+
Gain of H+N
H
HH
H
O
HH
H
Gain of H+
HO
N
H
H
Replacement of a hydrogen atom with a carbon-based group gives an amine: an organic derivative of ammonia.
Replacement of a hydrogen atom with a carbon-based group gives an alcohol: an organic derivative of water.
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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 C2H6O. 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:
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• 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.
CC
CC
C
CC
CC
C
H H
H H
H H
H
H H
H
H H
NOT
CH3CH2CH2CH2CH3or or
(structural formula) (condensed structural formula) (line-bond structure)
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Structural Formula Condensed Structural Formula
Line-Bond Structure
C
CC
C
CC
H
HH
HH H
HH
H
H
O
CHCH2ClCH2
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C C N
HH
H
C O
H
H
C
HH
H
Br
Functional Groups: "reactive centers that contain heteroatoms or multiple carbon-carbon bonds.
Heteroatoms: atoms in a molecule other than carbon or hydrogen.
Alkanes Alkenes Alkynes
HC
CC
CC
H
HC
CC
C C C C
HH
HH
H
H H
H H
H H
H HH
H
H
H H
H
H
H
Multiple carbon-carbon bonds: unsaturation.
Arenes
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The Functional Groups
Condensed structure Name Nomenclature Suffix(drop the e and add:)
CCl
O
CH
O
OH
C C
C C
COCl Acid chloride -oyl chloride
OH Alcohol -ol
CHO Aldehyde -al
Alkene -ene
Alkyne -yne
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CN
O
H
H
N
H
H
COH
O
Amide -amide
Amine -amineNH2
CO2H Carboxylic acid -anoic acid
CONH2
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C
O
CO
O
R
O
C N
S
CO2R Ester -anoate
Ether ether
CO Ketone -anone
CN Nitrile -nitrile
Sulfide sulfide
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Things to watch for…Don't be confused by common structural elements. For example
OH
COH
O Both of these contain the hydroxyl group, but they are different functional groups.
C
O
CN
O
H
H Both of these contain the carbonyl group (C=O), but they are different functional groups.
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The "open" bond in these structures is attached to a carbon...
H3CC
CH3
O
H3CC
OH
O
C
C
H
H
H
C
CH3
O
KetoneKetone
Not a ketone
Ether
Ether Not an ether
H3CO
CH3
H3CC
O
O
CH3C
CC
C
CC OCH3
H
H
H
H
H
and, with the exception of alkene/alkyne/arene, this carbon is usually not part of another functional group...
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Identify the functional groups…
CH3
N
O
CH2CH3
CH2CH3
H
O
OC
COH
OH3C
O
O
H
OH
H3C
CH3H2C
CCl3
Cl ClH2N CO2H
OH
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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:
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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. C3H8O has three structural isomers:
• How many structural isomers can you draw for C3H6?
When drawing isomers, all structures must still obey the octet rule!
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Structural Isomers
• How many structural isomers can you draw for C6H14?
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• How many structural isomers can you draw for C3H9N?
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How do you know when molecules are the same?
Molecules are identical if, in equivalent conformations, they are superimposable.
C C
H3C
HH
CH2CH3
C C
H
HH3C
CH2CH3
C C
H
HH3C
CH2CH3
C C
H3C
HH
CH2CH3
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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 CH3 which is, in turn, more important than H.
H
HCH3
CH3
H
HH
HH
CH3
H
H3C
Cl
H H
Cl Cl
H Cl
H
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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.
O
OH
stearic acid (a saturated fatty acid)
O
OH
a trans fatty acid
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C
H
ClCH2CH3
CH3C
H
ClH3CH2C
H3C
Are these molecules the same?
C
H
ClCH2CH3
CH3C
H
ClH3CH2C
H3C C
H
ClCH3
CH2CH3
Rotate 180° around CH bond
C
H
ClCH2CH3
CH3C
H
ClCH3
CH2CH3
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Enantioisomerism
C
H
ClCH2CH3
CH3C
H
ClH3CH2C
H3C
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.
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C
H
ClCH2CH3
CH3C
H
ClH3CH2C
H3C
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.
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• 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:
CH3
CC
CH2
CH3
H
H
Cl
Cl
CH3
CC
CH2
CH3
Cl
ClH
H
and are enantiomers
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e.g. For each of the following molecules, locate the stereocenter(s) and decide whether the molecule is chiral or achiral.
CH3
CH3
OH
OH
CH3 HCH3 H
OH
OH
H CH3CH3 H
CH3
H
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• 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.
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N
O
O
NH
O
O
H
N
O
O
NH
O
O
H
Like many drugs, this anti-nausea drug was sold as a racemic mixture.