Chemistry Unit 4- Basic Organic Chem and Isomerism

Nomenclature- Naming Organic Compounds. Branched alcohol:

1. Count the carbon atoms in the longest chain (chain may be bent)

1=meth, 2=eth, 3=prop, 4=but, 5= pent, 6=hex, 7=hept, 8=oct, 9=non, 10=dec

2. The main functional group of the molecule usually gives you the end of the name (suffix)

Homologous series- series of organic compounds with similar general formula, similar chemical properties due to the same functional group. 

Alkanes---> -ane ---> e.g. propane CH3CH2CH3

Branched alkanes---> -yl ---> methylpropane CH3CH(CH3)CH3

Cycloalkanes ---> cyclo- ---> cyclohexane C6H12

Alkenes ---> -ene ---> propene CH3CH=CH2

Haloalkanes ---> chloro-, bromo-, iodo- ---> chloroethane CH3CH2CI

Alcohols ---> -ol ---> ethanol CH3CH2OH

3. Number the carbons in the longest chain so that the carbon with the main functional group attached has the lowest possible number. If there is more than one chain, pick the one with the most side-chains.

4. Write the carbon number that the functional group is on before the suffix

5. Any side chains or less important functional groups are added as prefixes at the start of the name.Put them in alphabetical order, with the number of the carbon each is attached to. 

6. If there is more than one identical side chain or functional group, use di- (2) tri- (3) or tetra- (4) before that part of the name, but ignore when doing aplhabetical order. 

e.g. longest chain is 5 carbons, main functional group is -OH which is on carbon 2, there's an ethyl group on carbon 3 and methyl groups on carbon 2 and carbon 4.... 

so its called 3-ethyl-2,4-dimethylpentan-2-ol. 

Alcohol has the general formula C n H 2n+1 OH. An alcohol is primary, secondary or tertiary depending on which C atom the hydroxyl group -OH is bonded to. Primary has bonds H, H, R1 and OH around the carbon. Secondary has bonds H, R1, R2 and OH around the C and tertiary has R1, R2, R3 and OH around the carbon. 

Haloalkanes: 

 They are just alkanes where one or more hydrogens have been swapped for halogen, use the process for alcohols. 

Alkenes:

They have at least one double bond in their carbon chain. 

For alkenes with more than three carbons, you need to say which carbon the double bond starts from. 

e.g.1. longest chain has 5 carbons, so the stem of the name is pent-

2. Functional group is C=C so it's pentene

3. The first carbon in the double bond is carbon 2, so this is pent-2-ene

If the alkene has more than two double bonds, the suffix becomes diene and the stem of the name gets an extra "a" too, e.g. buta or penta... numbers may be written first, e.g. 1,3- butadiene

General formula=  An algebraic formula that can describe any member of a family of compounds. Formula for butan-1-ol =     C n H 2n+1 OH (for all alcohols)

Empirical formula=  The simplest ratio of atoms of each element in a compound (cancel the numbers down if possible e.g. ethane, C2H6 has the formula CH3). for butan-1-ol = C4H10 O 

Molecular formula= The actual number of atoms of each element in a molecule, with any functional groups indicated. For butan-1-ol = C4H9OH

Structural formula= Shows the atoms carbon by carbon, with the attached hydrogens and functional groups. For butan-1-ol = CH3CH2CH2CH2OH

Displayed formula- SHows how all the atoms are arranged and all the bonds between them. For butan-1-ol

Skeletal formula- Shows the bonds of the carbon skeleton only, with any functional groups. C and H atoms aren't shown. For butan-1-ol /\/\OH

Chain Isomers:

Have different arrangements of the carbon skeleton. Some are straight chains, and others branched in different ways:

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Positional Isomers:

Same skeletal and the same atoms or groups of atoms attached. The difference is that the functional group is attached to a different carbon atom:

t

tFunctional group Isomers:

Have the same atoms arranged into different functional groups:

t

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Stereoisomers:

Have the same structural formula, but a different arrangement in space

You can twist and rotate around a single bond, but a double bond has a fixed position, so the molecule can't rotate. 

Due to the lack of rotation around the double bond, some alkenes have stereoisomers. 

Stereoisomers happen when each double bonded carbon atom has two different atoms or groups attached to it. Then you get an E isomer or a Z isomer

E isomers:

The same groups are across the double bond. Name = e.g. E-but-2-ene

Z isomers:

The same groups are both above/both below the double bond. e.g Z-but-2-ene

Another type of stereoisomerism (same structural formula, but atoms arranged differently in space). 

A chiral (or asymmetric) carbon atom is one that has four different groups attached to it. Its possible to arrange the groups in two difffernte ways around the carbon atom so that the two different molecules are made- called enantiomers or optical isomers. 

The enantiomers are mirror images and no matter which way you turn them, they can't be superimposed. 

If the molecules can be superimposed, they are achiral- there's no optical isomerism.

Locating the chiral centre- Look for the carbon atom with four different groups attached. 

How to draw: when you've located the chiral centre, draw one enantiomer in a tetrahedral shape, thick line, two thin and a dotted and then draw the mirror image. 

Optical Isomers are optically active- they rotate plane-polarised light (normally light vibrates in all directions, but plane-polarised only vibrates in one direction). 

One enantiomer rotates it in a clockwise direction, the other in an anti-clockwise.

Racemate: (or racemic mixture) contains equal quantities of each enantiomer of an optically active compound. 

racemates don't show any optical activity as the two enantiomers cancel each other's light- rotating effect.

Chemists often react two archiral things together and get a racemic mixture of a chiral product.

This is because when two molecules react together there's an equal chance of forming each of the enantiomers. 

You can modify a reaction to produce a single enantiomer using chemical methods but its difficult and expensive- just find a use for the unwanted enantiomer.

Must only contain a single optical isomer

Drugs work by changing chemical reactions that are taking place in the body

Do this by binding to an active site- usually on an enzyme or a specific receptor molecule

Drug must be exactly the right shape to fit, only one enantiomer will do. The other could fit into a different enzyme and might cause harmful side effects, or have no effect at all. 

So if a drug happens to be chiral, it must be made so that it only contains one enantiomer

1. Developed n 1950's as sedative drug. Early tests showed few side effects

2. Proved as an effective anti-sickness, perscribed to treat morning sickness in pregnant women. 

3. At the same time babies began to be born with malformed limbs- thalidomide shown to be causing the symptoms.

4. Drug had not been tested thoroughly, particularly in relation to it's effect on the developing foetus.

5. Further studies demonstrated the two optical isomers have different effects in the body. One is an effective anti-sickness drug, the other can cause birth defects. In this case, even if a pure dose of the safe isomer is given, the body will convert some of it into the harmful isomer.

6. Thalidomide can be useful for treating other diseases, such as some types of cancer. Patients can now be treated with it, but strict controls are in place.