Introduction to organic chemistry

• Organic Chemistry is the study of carbon chemistry as carbon has an amazing ability to join together in chains, rings, balls etc.

• Pre – petrochemical industry almost all carbon compounds were extracted from living things.  It was Lavoisier in 1784 who first suggested that all compounds extracted from living things contain carbon and hydrogen and are called Hydrocarbons.

• Carbon also joins with other elements easily such as oxygen, hydrogen, nitrogen, phosphorous and the halogens.

• Hydrocarbons make up over 90% of all known compounds.

• Carbon can join in many different ways and shapes.

• Organic compounds also contain other elements giving rise to functional groups (later).

Why carbon and not silicon?

        Carbon compounds frequently contain long chains of carbon atoms

• Silicon does not, it forms a compound made of silicon and oxygen.

Bond energies give us the answers

E(C – C) = 347 KJMol^-1

E(C – H) = 413 KJMol^-1

E(C – O) = 358 KJMol^-1

• All the bond energies are of similar magnitude (strong) which means there is little tendency of one of these bonds being replaced by another.

E(Si – Si) = 226 KJMol^-1

E(Si – H) = 318 KJMol^-1

E(Si – O) = 466 KJMol^-1

• The Si – Si bond is the weakest of the bonds and has a tendency to be replaced by the stronger Si – O bond.

Bonding in organic compounds:

• As carbon is in Gp4 of the periodic table it has 4 single outer shell electrons meaning it forms 4 covalent bonds only.

• Carbon can form more than one bond with itself:

4 bonds only	A double bond and 2 single bonds to hydrogen = 4

Saturated and unsaturated hydrocarbons:

Saturated - is a hydrocarbon with single bonds only	Unsaturated - is a hydrocarbon with carbon carbon multiple bonds

Aliphatic and alicyclic hydrocarbons:

	Aliphatic - is a hydrocarbon in which the carbon atoms are all joined in a straight lines (branched or unbranched)
	Alicyclic - is a hydrocarbon in which the carbon atoms are joined together in a ring structure

Functional groups:

• This is the part of the molecule that is responsible for its chemical properties:

• The OH group in this molecule is the functional group.

• All molecules with the same functional group react in similar ways.

Homologous series:

• This is a family of molecules with the same functional group.

• This means they react in a similar way.

• The differences in the molecules are one carbon (and 2 hydrogens).

The Alkanes:

• This is a homologous series of saturated hydrocarbons:

• All the molecules end in 'ane'

• The alkanes and their names are outlined in the table below:

• The number of carbons represent a name (later):

Questions 1 - 3   P 103

Naming hydrocarbons

Naming organic compounds:

• Because there are so many organic compounds we have to have a systematic way of naming them.

• This is called Nomenclature

• Organic molecules are usually made up from:

Carbon chain

Side chains (alkyl groups)

Functional groups

Stems, prefix and suffix:

Stem        The longest carbon chain - the main name (in the middle)    (carbon chain)

Prefix        Added before the main name - pre - main name                      (side chains)

Suffix        Added after the main name - post - main name                        (functional groups)

Alkyl groups:

• If you remove a hydrogen from an alkane you have a group that has a bond that can join to the main carbon chain.

• Based on the alkanes the ending of these are changed to alkyl

Methane	Methyl

• The first six alkyl side chains are in the table below:

Naming alkanes:-

1)   Look for the longest carbon chain alkane

2)   Look for the functional groups

3)   Look for the position of the functional group and assign a number.  Use the lowest number  possible counting from one end of the carbon chain.

4)   The name goes in reverse order of the 3 points above.

Example:-

1)      Look for the longest straight chain alkane

	The longest carbon chain is in bold.  It is 4 carbons long which makes it butane
____________Butane

2)      Look for the functional groups

	A functional group is any side chain off the straight chain.  CH3 is a derivative of methane (CH4) which we call methyl.  See the table below
_______Methylbutane

3)   Look for the position of the functional group and assign a number.  Use the lowest number possible counting from one end of the carbon chain.

	Numbering from one end we get 3 – Methylbutane.  This is incorrect because if we number from the other end we get a lower number.
	Numbering from the other end we get 2 – Methylbutane.  This is correct because if we get a lower number.
2 – Methylbutane

4)      The name goes in reverse order of the 3 points above.

                                         2       -        Methyl             butane

                                         (3)                 (2)                    (1)

           5)      Additional side chains or stems 

• If there is more than 1 side chain we write the names in alphabetical order:-

3-ethyl 2 methyl pentane

• If there is more than 1 chain on the same carbon we use di, tri, tetra etc:

2,2-dimethyl propane

Naming alkenes

• These contain a C=C, the ending of the name changes to ‘ene’ and we have to put a number to where the double bond is in the carbon chain:-

	But – 1 – ene
	But – 2 – ene

Questions 1-2  P105

Naming compounds with functional groups

• Organic Chemistry is studied in a systematic way because each different group of atoms attached to a carbon atom has its own characteristic set of reactions.

• These are known as Functional groups:-

If a suffix starts with a vowel then the stem has 'an' added

Names for alkanes containing a ring of carbon atoms

• If an alkane is cyclic we use the prefix ‘Cyclo’

                                                                                               cyclohexane

Names for Halogenoalkanes

Names for alcohols

Names for aldehydes

Longest chain = 4C = but Functional group = CHO (suffix starts with a vowel)  = butanal The 'al' does not need a number as all aldehydes are at the end of the molecule.

More than one of the same type of functional group

Longest chain = 4C = but Functional group = Cl on carbon 1 (prefix) = 1 - chloro Functional group = Br on carbon 2 (prefix)n = 2 - bromo Functional groups are named alphabetically:  2 - bromo - 1 - chlorobut No suffix = ane = 2 - bromo - 1 - chlorobutane

Names for 2 different functional groups:

Longest chain = 3C = prop Functional group = OH on carbon 1 (suffix, starts with a vowel so add 'an') = propan - 1 - ol Side chain = CH3 on carbon 2 (prefix) = 2 - methylpropan - 1 - ol

Names for many of the same functional groups:

Longest chain = 2C = eth Functional group = Cl, (2 x on carbon 1) and 2 x on carbon 2 (prefix), numbers first then how many chlorines:  1,1,2,2 - tetrachloroeth No suffix = ane = 1,1,2,2 - tetrachloroethane

Note:  di = 2, tri = 3, tetra = 4

Question 1  P 107

Formulae of organic compounds:

Empirical formula:

                Definition:                    Empirical Formula is the simplest ratio of atoms of elements in a compound. 

Molecular formulae

                Definition:                    Molecular formulae is the actual ratio of atoms of elements in a compound.

• This can be calculated using moles from percentage composition:-

 Recap from Module 1:

Example 1:  A sample of iron oxide was found to have 11.2g of iron and 4.8g of oxygen.  Calculate the formula of this compound:

                                           Fe                                           O

                                         11.2                                        4.8

 Divide by Ar                    11.2/56                                   4.8/16

 Moles                               0.2                                           0.3

 Divide by smallest          0.2/0.2                                    0.3/0.2

 Ratio                                1                           :                  1.5

 Ratio                                2                           :                  3

                                                                  Fe₂O₃

Example 2

A sample of hydrocarbon was found to have 1.20g of carbon and 0.25g of hydrogen.  Calculate the Empirical formula of this compound.  Then find out the molecular formula if the Mr = 58

                                            C                                             H

                                         1.20                                        0.25

 Divide by Ar                    1.2/12                                     0.25/1

 Moles                               0.1                                           0.25

 Divide by smallest          0.1/0.1                                    0.25/0.1

 Ratio                                1                           :                  2.5

 Ratio                                2                           :                  5

 Empirical formula                                C₂H₅        Mr = 29

 Molecular formula                               C₄H_{10        58 / 29 = 2, so double up the numbers of atoms to make the actual ratio}

General Formula:

            Definition:        This is the simplest algebraic formula for a member of a homologous series (of the same functional group)

Displayed formula:

        Definition:        Shows the relative positioning of all the atoms in a molecule, and all the bonds between them

Butane:  All the atoms and bonds are shown	Propan-2-ol:  Even O - H bonds are shown

Questions   1-3  P109

Structural and skeletal formula:

Structural formula:

        Definition:                shows the minimum detail for the arrangement of atoms in a molecule

• Typically we show the ratio of all the atoms attached to each carbon atom in a molecule:

Butane:   CH3CH2CH2CH3	1 - Chloropropane:   CH3CH2CH2Cl

• With many CH₂'s we can put them in brackets:

This can be simplified to:                               CH3(CH2)8COOH

Skeletal formula:

        Definition:        The hydrogen's are removed leaving a carbon skeleton and associated functional groups

• A good way to approach this is to count and number the carbons.  This can then be transposed to the carbon skeleton:

Other examples:

Structural formula:CH3CH2CH2CH3	Structural formula:CH3CH(CH3)CH2CH2CH3

• No carbon or hydrogen atoms are shown

• A carbon atom exists at the ends

• A carbon atom exists at each point

Cyclic compounds:

• Cyclic compounds are usually drawn as skeletal:

Questions:  1-3  P111

Skeletal formulae and functional groups

Unsaturated hydrocarbons:

• Add numbers to the carbons on the skeletal formulae.  This is how many carbons in the molecule.

• Add a double bond between the corresponding carbons from the skeletal to the displayed:

Skeletal formulae:	Fill in the displayed formula:
Pent-2-ene

Compounds with functional groups:

Butan-2-ol:

• Functional groups must be included in skeletal formulae

• The end of the side chain off carbon 2 is now an OH instead of a CH₃

Skeletal formulae:	Fill in the displayed formula:
Butan-2-ol

Pentanoic acid:

• Coming off the final carbon is an =O and an -OH, these must be added to the end carbon:

Skeletal formulae:	Fill in the displayed formula:
pentanoic acid

More complex AS / A2 structures:

	Paracetamol
	Retinol, vitamin A
	Salbutamol

Note:

• If a carbon in the skeletal structure is replaced with another element then we have to write the symbol of that element in its place

Questions:  1-4  P113

Isomerism

Structural isomers: 

Activity 1:

• Use the molymods to make and draw as many molecules as possible using all of  5 carbons and 12 hydrogens, C₅H₁₂. 

• There are 3 different shapes.

SEE MOLECULES OF PENTANE

• All of the molecules above contain the same number of atoms but they are arranged differently.  These are called structural isomers.

• This is one reason why we use a systematic method to name organic molecules.

            Definition:        These are compounds with the same molecular formula but with different structural arrangements of atoms

Activity 2:

• Using the molymods make and draw as many molecules as possible using 3 carbons, 8 hydrogens, and 1 oxygen, C₃H₈O.

• Some of these structures that you have made will be from different homologous groups / have different functional groups.

• This means that although they have the same empirical formula, they will have very different physical and chemical properties.

Steroeisomerism:

Activity 3:

• Build but-2-ene using the molymods. 

• Look at your neighbours model, are they exactly the same?

        Definition:        The same atoms are joined to each other in different spatial arrangements

• There are 2 types of Stereoisomerism:  E/Z and optical (optical is covered in A2):

E/Z Isomerism: (of which cis / trans is one type)

• For this 2 things must be present in a molecule:

        1)    A carbon - carbon double bond, C=C

        2)    Each carbon must be attached to 2 different functional groups:

From GCSE:  Cis / trans - But-2-ene:

        Cis trans is a specific type based upon having a hydrogen and a non hydrogen group on each of the carbons on the C=C:

	No free rotation around the C=C
Trans but-2-ene (E-but-2-ene)		Cis but-2-ene (Z-but-2-ene)

• The easiest way to spot which is which is to place a ruler along the C=C

If the hydrogen's are on different sides of the ruler = TRANS = ACROSS / Trans Atlantic (across Atlantic).

 

If the hydrogen's are on the same side of the ruler = CIS = SAME

Cahn - Ingold - Prelog nomenclature:

• Cis trans isomers are one specific type of stereoisomeism.

• Cis / trans isomers are when you have a hydrogen and another group on each of the carbon atoms.

• This is not always the case as some molecules may not fulfil this criteria:

• This molecule only has one hydrogen on one of the carbons so it does not fall into the Cis / trans category

• It can be solved by introducing a system where the priority is given based upon atomic number.

• Chlorine has the highest atomic number so it is given priority.

• Using you ruler apply the same principle as before:

If the chlorine's are on different sides of the ruler = E = 'ENTGEGEN' = OPPOSITE

 

If the chlorine's are on the same side of the ruler = Z = 'ZUSAMMEN' = TOGETHER

You will be expected to assign E/Z to molecules but not necessarily using CIP nomenclature

 

                ET = across the molecule (ET flew 'across' the galaxy!!)

Questions 1-4  P115    1-5  P143

Organic reagents and their reactions:

Organic reactions

• For a reaction to occur:

        A)  A bond must break.

        B)  The breaking of a bond will form a reagent.

        C)  The reaction must take place

A)  Bond breaking:

• For an organic reaction to occur, a covalent bond must be broken.

• Bond breaking is called fission and it can be broken in one of 2 ways:

        1)  Homolytic fission

        2)  Heterolytic fission

1)  Homolytic fission

• This is when the electrons in the bond go ‘HOME’ to their parent atom.  Each atom is the same.  Homo….

• A half headed arrow represents the movement of 1 electron.  This is because most reactions involve the movement of 2 electrons for which we use a normal headed arrow.

• Free radicals are atoms or groups of atoms with an unpaired electron, they are extremely reactive and are said to be ‘short lived’.

Heterolytic fission

• This is when the electrons in the bond go to one of the atoms.

• A double headed arrow represents the movement of 2 electrons, a pair of electrons.

• The 2 resulting ions have a different number of electrons.

• It gives a positive ion and a negative ion.

• These are different from each other = hetero...

B)  Types of reactants:

• Reactants start a reaction going.

• There are 3 types of reactants:

        1)  Free radicals:  these have an unpaired electron and are extremely reactive (as above)

        2)  Nucleophiles:  these are attracted to electron deficient atom, d+ and donate a pair of electrons to form a new covalent bond

• These are often negative ions but must have a lone pair of electrons as these are donated to form a new covalent bond.

• Br^-, OH^-, H₂O, NH₃

        3)  Electrophiles:  these are attracted to electron rich atom, d- and accept a pair of electrons to form a new covalent bond

• These are often positive ions.

• Br₂, HBr, NO₂⁺

C)  Types of reaction:

1)  Addition reactions

• Involves 2 molecules joining to become 1 molecule

• Bromine has been added to ethene.

2)  Substitution reactions

• Involves an atom (or group of atoms) being replaced by another atom (or group of atoms):

• 2 molecules make 2 (new) molecules

• You can see that the Br is being substituted by OH.

3)  Elimination reactions

• Involves the removal of one molecule from another.

• 1 molecule gives 2 molecules:

• Water has been eliminated from ethanol.