S3.2 Functional Groups : Classification of Organic Compounds

S3.2.1 Structural Representations of Organic Compounds :

📌 Definition Table :

TERM	DEFINITION
Molecular Formula	Shows the actual number of atoms of each element present in the compound
Empirical Formula	Shows the simplest whole number ratio of the atoms it contains.
Full Structural Formula	Shows all the atoms and bonds in a molecule
Skeletal Formula	Shows all bonds except CH and omits symbols for C and H
Condensed Structural Formula	Omits bonds where they can be assumed or groups atoms together
Stereochemical Formula	Shows relative positions of atoms around a central carbon in three dimensions

🧠 Examiner’s Tip : Remember, solid wedges go out (of the paper) and dashed wedges go in( to the paper).

S3.2.2 Functional Groups and Classes of Compounds :

📌 Definition Table :

TERM	DEFINITION
Aromatic Compound	Contains phenyl group
Aliphatic Compound	No phenyl group
Homologous Series	Compounds that have the same functional group, each member differs from the next by a common structural unit
Functional Group	Atom/Group of atoms that give a molecules its characteristic chemical properties (reactive part of molecule)

• Organic chemistry is the study of carbon compounds
• Catenation property of carbon allows for carbon atoms to join together to form chains/rings
• Functional groups give characteristic physical and chemical properties to a compound
• Saturated compounds only contain single bonds
• Unsaturated compounds contain double/triple bonds
• Compounds can be classified based on their saturation
• Functional groups on different compounds can react in a specific reaction to form new compounds
  • Eg : Two amino acids can link together in a condensation reaction to form a product called a dipeptide with an amide link
  • As the dipeptide will still have functional groups at both ends of the molecule, it can react with more amino acids to form a polypeptide (also known as a protein)

🧠 Paper 2 Tip : You do not require knowledge of arenes as a class of compounds, but you will be expected to recognize a phenyl group if it is part of a structure.

Class	Functional Group	Bond	IUPAC Suffix	General Formula
Alkane	Alkane	C-C	-ane	CnH2n+2
Alkene	Alkenyl	C=C	-ene	CnH2n
Alkyne	Alkynyl	C≡C	-yne	CnH2n-2
Alcohol	Hydroxyl	OH	-anol	CnH2n+1OH
Ether	Alkoxy	C-O-C	-oxyalkane	CnH2n+2O
Aldehyde	Carbonyl	H-CO-R	-anal	CnH2nO
Ketone*	Carbonyl	R-CO-R’	-anone	CnH2nO
Carboxylic Acid	Carboxyl	H-O-C=O	-oic acid	CnH2n+1COOH
Ester	Carboxyl	O=C-O-R	-anoate	CnH2nO2
Halogenalkane	Halogeno	-X X = F/Cl/Br/I		CnH2n+1X
Amine	Amino	-NH2	-anamine	CnH2n+1NH2
Amide	Amido	O=C-NH2	-anamide	CnH2n+1CONH2
Arebe	Phenyl	C6H5	-benzene

* 🧠 Examiner’s Tip : The difference between an aldehyde and a ketone is that in an aldehyde one of the R chains is an H.

S3.2.3 and S3.2.4 Homologous Series :

• A homologous series is a family of compounds in which successive members differ by a common structural unit
• Members of a homologus series show graduation in physical properties
• As the length of the carbon chain increases, boiling point of these compounds also increases – as the strength of the london dispersion forces are increasing
• Alkanes – increase is not linear as effect is proportionally greater for smaller compounds (steep in the beginning)
• For other homologous series – the increase is linear because stronger molecular forces than LDF are present – owing to their functional groups
• As carbon chain length increases, difference in boiling points between members of different homologous series decreases as the functional group is only a small part of a large molecule (most of the molecule is same)
• Alkanes are insoluble in water
• Solubility of alcohols decreases as length of carbon chain increases – functional group has proportionally smaller effect as molecule size increases

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S3.2.5 IUPAC Nomenclature :

⭐️ IUPAC Nomenclature refers to a set of rules used by the International Union of Pure and Applied Chemistry to apply systematic names to organic and inorganic compounds.

📌 IUPAC Rules :

1. Identify the longest straight chain of carbon atoms. This gives the stem of the name.

Number of Carbon atoms	Stem
1	Meth
2	Eth
3	Prop
4	But
5	Pent
6	Hex
7	Hept
8	Oct
9	Non
10	Dec

🧠 Examiner’s Tip : Note that straight chain means continuous/unbranched chains of carbon, don’t get confused by the 3d appearance of some molecules.

2. Identify the functional group. Ensure to number the carbons so that the functional group occupies the lowest position. This gives the suffix of the name (see S3.2.2).

3. Identify substituent groups. Where two different substituents would have the same number when numbering from different directions, the one that comes first in the alphabet is assigned the lower number. Use a prefix eg – di/tri/tetra to show the number of each substituent present. Arrange in alphabetical order.

• When naming molecules – use commas between numbers and dashes between numbers and letters
• Every substituent must have a number to indicate its position
• Alkenes
  • x-alkene or alk-x-ene
  • Eg. but-2-ene or 2-butene
• Alcohols
  • alkan-x-ol or x-alkanol
  • Lowest number to OH rather than an alkyl substituent (functional group takes precedence)
  • If there is more than one OH group – the ‘e’ is retained
    • Eg. butanediol
• Aldehydes/Ketones
  • Aldehydes : alkanal
  • C of CHO is numbered 1 in aldehydes
  • Ketones : alkan-x-one or x-alkanone
• Carboxylic Acid – alkanoic acid
• Esters
  • R-COOH + R’-OH –> R-COO-R’ + H₂O
  • Alkyl group of alcohol gives the prefix
  • Stem comes from parent acid
  • Eg. methanoic acid and butanol gives butyl methanoate
• Ethers
  • Longer chain gives stem – retains alkane name
  • Shorter chain – alkoxy

🌍 Real World Perspective : Ethers are used in the medical field, especially in anaesthetics. Diethyl ether is a general anaesthetic used to induce unconsciousness during surgery.

S3.2.6 Structural Isomers :

TERM	Definition
Structural Isomers	Same molecular formula, different structural formulas
Chain Isomers	Different carbon skeleton
Position Isomers	Same carbon skeleton but position of functional group differs
Functional Group Isomers	Different functional group, same molecular formula

• More branched an isomer, the lower its boiling point – due to reduced strength of LDF
• Positional isomers can exist in alcohols, halogenalkanes and amines and can be classified as primary/secondary or tertiary

• Naming primary/secondary/tertiary halogenalkanes or alcohols
  • Primary – One C bonded to the C bonded to the halogeno/hydroxyl group
  • Secondary – Two C bonded to the C bonded to the halogeno/hydroxyl group
  • Tertiary – Three C bonded to the C bonded to the halogeno/hydroxyl group
• Naming primary/secondary/tertiary amines
  • If N is attached to 1C – primary
  • If N attached to 2C – secondary
  • If N attached to 3C – tertiary

🧠 Examiner’s Tip : Make note of the difference between naming primary/secondary/tertiary alcohols, halogenalkanes and amines. Don’t let it slip you up!

📌 Structural isomers in disubstituted Benzene [HL] :

• Substituted benzene is formed when a hydrogen atom is replaced by a halogeno atom or a functional group like amino or nitro groups
• No structural isomers are possible for monosubstituted benzenes because all 6 positions in the carbon ring are identical
• In disubstituted benzenes – 3 structural isomers are possible
  • More would be possible if benzene has a straight chain structure – offering more evidence supporting the Kekulé structure of benzene

S3.2.7 Stereoisomers [HL] :

TERM	DEFINITION
Stereoisomers	Same structural formula ad bond connectivities but atoms are arranged differently in space
Cis/trans isomerism	Same structural formula but groups are arranged differently in space around a double bond – exists when there is restricted rotation
Configurational isomerism	Can be interconverted only by breaking covalent bonds
Conformational isomerism	Can be interconverted by free rotation along σ bonds
Chiral Carbon	A chiral carbon is attached to 4 different groups. It is also called asymmetric or a stereocentre.
Optical isomerism	Chirality exists when there is an asymmetric carbon atom

• Cis/trans isomerism
  • Double bonded molecules – π component restricts rotation
  • Position of molecules with respect to plane
  • Cis isomer – same group on same side of plane
  • Trans isomer – same group on different sides of plane
  • Is seen when a molecule contains 2 or more different groups attached to the double bond
  • Also occurs in cyclic molecules (disubstituted benzene)
• Optical isomers
  • Molecules are chiral if their mirror images are non superimposable
  • The non superimposable mirror images of a chiral molecules are called enantiomers
  • Enantiomers have opposite configurations at each chiral centre
  • When a molecule has opposite configurations at more than one but not all chiral centers it is called a diastereomer

🧠 Paper 2 Tip : Enantiomers are mirror images of each other. Diastereomers are not mirror images of one another.

📌 Properties of Enantiomers :

• Optical activity
  • Two enantiomers of chiral compounds rotate plane polarised light in opposite directions
  • Non polarised light runs through a polarising filter to create a plane polarised light
  • If light is passed through samples containing equal moles – it rotates in opposite directions by equal amounts
  • d – clockwise direction, l – counterclockwise
  • Polarimeter can be fixed to 90 where no light passes, then sample can pass through and amount of rotation can be recorded
• Racemic mixture – equimolar mixture of two enantiomers of a chiral compound
• Racemic mixtures have no effect on plane polarised light (optically inactive)
• Physical properties
  • Enantiomers have identical physical properties except for optical activity
• Chemical properties
  • Enantiomers have identical chemical properties
  • Process of resolution – method of separating enantiomers from a racemic mixture
  • Racemic mixture is reacted with single enantiomer to produce different products that have distinctive chemical and physical properties

🌍 Real World Connect : The reactivity of a pair of enantiomers with other chiral molecules is especially significant in medical fields, because our bodies have chiral environments. One example of this occured in the 1960s when the drug thaliomide was used to treat morning sickness in women. Whereas one enantiomer is therapeutic, the other causes defects in the fetus. This event pioneered research into chiral compounds and optical isomers.

S3.2.8 Mass Spectroscopy :

TERM	DEFINITION
Qualitative Analysis	Detection of the presence but not the quantity of substances.
Quantitative Analysis	Measurement of the quantity of a particular substance
Structural Analysis	Description of the way in which atoms are arranged
Mass Spectroscopy	Determines relative atomic and molecular mass. Fragmentation patter can be used as evidence to identify different atoms in the structure.
Infrared Spectroscopy	Used to identify bonds in the molecule
Nuclear Magnetic Resonance Spectroscopy	Used to show chemical environments of certain molecules

• Mass Spectroscopy
  • The sample is vaporised and bombarded with high energy electrons – resultant ions are separated by m/z ratio
  • The fragmentation pattern can provide useful information about what groups and ions are present in the compound
  • The molecular ion/parent ion is the ion that passes through the spectrometer without breaking. It corresponds to the relative molecular mass of the compound.
  • The molecular ion has the highest m/z ratio, therefore it corresponds to the farthest peak
  • Other ions that break are also detected – these peaks can be analysed in terms of the groups that were lost or the groups that remained
    • Eg. If you know that the molecular mass of a compound is 46 and there is another peak at 15 – you know that this could correspond to the loss of a CH₃ group (1+1+1+12). From here, you could subtract 15 from 46 and continue to analyse what groups could produce the leftover (31) eg a CH₂OH group – which means your compound could be CH₃CH₂OH or ethanol.

🧠 Paper 2 Tip : Do not forget to include a positive charge when identifying the fragmented ions. The data booklet will help with some characteristic groups and their corresponding relative atomic masses.

S3.2.9 Infrared Spectroscopy :

• Infrared Spectroscopy
  • Used to identify bonds and functional groups
  • Molecules absorb infrared radiation at characteristic vibrational frequencies
  • $\lambda$ ∝ E (wavelength is proportional to energy)
  • Wavelength is inversely proportional to frequency
  • c = f$\lambda$
  • The region above 1500 on the IR spectrometer – used to identify
  • Region below 1500 (fingerprint region) used to confirm presence of bonds
• Absorbing IR radiation excites the bonds in a molecule
• The ability of a molecule to absorb IR radiation depends on the change in dipole moment that occurs when in vibrates
• A bond in a diatomic molecule will only interfere with IR if it is polar
• The change in vibrational energy causes a corresponding change in the dipole moment of these molecules
• In polyatomic molecules – the absorption causes bending and stretching of the molecules
• Homonuclear diatomic molecules are IR inactive
• Linear molecules symmetric stretch is also IR inactive as it produces no change in dipole moment
• Greenhouse effect
  • Shortwave radiation from the Sun to the Earth is reflected and passed (absorbed at surface)
  • Surface radiates long wave IR which is absorbed by greenhouse gasses – causes increase in kinetic energy and temperature
  • Global warming potential of a greenhouse gas compares amount of IR 1 tonne of the gas would absorb as compared to 1 tonne of CO₂
• Matching bonds with wavelengths
  • Characteristic infrared absorption bands are shown in the data table
  • Some bonds can be identified by the distinctive shape of their signals

S3.2.10 and S3.2.11 Nuclear Magnetic Resonance Spectroscopy :

• Hydrogen atoms have the property of nuclear spin – ability to act like a bar magnet
  • They align with lower energy and against higher energy
• HNMR provides information that can be analysed
  • Number of signals in the spectrum
  • Chemical shift of each signal
  • Size/area under each signal
  • Splitting pattern for each signal
• Signals correspond to groups of protons in different chemical environments
• Area under the signal corresponds to the number of protons in each chemical environment
  • Integration trace gives ratio of protons in each chemical environment
• Chemical shift – horizontal scale measured relative to TMS (tetramethylsilane)
  • TMS
    • 12 protons in the same environment (serves as a baseline)
    • Lower chemical shift than all organic molecules (does not interfere)
    • Non-toxic, inert, volatile and easy to remove
• Protons in the same chemical environment are said to be equivalent as they produce the same trace
• H attached to N/O also produce signals
• The closer the hydrogen atom is to an electronegative atom – the higher the chemical shift (measured in parts per million)
  • Chemical shift data is also available in the data booklet – hydrogen nuclei in particular environments have characteristic chemical shifts
• Splitting occurs due to the H atoms on the adjacent C
• Signal splits into n+1 where n is H atoms on adjacent C
• Singlet means no H on adjacent atom
• This multiplicity is also characteristic of some groups
  • Eg CH₃CH₂ group – signal due to 2H splits into quartet, signal due to 3H splits into a triplet
• Complex multiplet – when non equivalent protons on each side contribute to splitting

Overall structural analysis depends on combination of analytical techniques and cross referencing using multiple data points.