Organic Chemistry I: Structures – Hydrocarbons, Functional Groups, and Isomerism

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Topic 7: Organic Chemistry I – Structures (Ch. 20 & 3)

Overview

This section introduces the foundational concepts of organic chemistry, focusing on the structure and classification of organic molecules, including hydrocarbons, functional groups, and isomerism. Understanding these concepts is essential for further study in organic and general chemistry.

Introduction to Organic Chemistry

Definition and Importance

Organic chemistry is the study of molecules that contain carbon.
Organic compounds are found in a wide variety of substances, including:
- Proteins, sugars, DNA, vitamins, alcohols, pharmaceuticals
- Rubbers, plastics, soaps, gasoline, explosives, artificial flavourings

The Chemistry of Carbon

Unique Properties of Carbon

Carbon can form a diverse array of molecules because:
- It can form long chains (catenation).
- It can form single, double, and triple bonds.
- C–C and C–H bonds are very stable.
Organic molecules are primarily composed of C, H, O, and N.
Functional groups add character and different properties to hydrocarbons.

20.3 Hydrocarbons

Classification and Nomenclature

Hydrocarbons are compounds composed only of carbon and hydrogen.
Greek prefixes are used to indicate the number of carbon atoms:

# of C	Greek prefix	# of C	Greek prefix
1	meth	6	hex
2	eth	7	hept
3	prop	8	oct
4	but	9	non
5	pent	10	dec

Representing Organic Molecules

Common representations include:
- Structural formula: Shows all atoms and bonds explicitly.
- Condensed structural formula: Groups atoms to simplify the structure.
- Carbon skeleton (bond-line) formula: Shows only the carbon backbone and functional groups; hydrogens on carbons are implied.
For large molecules, Lewis structures are cumbersome; bond-line structures are preferred for clarity and simplicity.

Three-Dimensional Structures

Line-dash-wedge notation is used to depict 3D structures:
- Line: Bond in the plane of the page.
- Dash: Bond going into the page (away from viewer).
- Wedge: Bond coming out of the page (towards viewer).

Categories of Hydrocarbons

Aromatic: Contain benzene ring-like structures (e.g., benzene, toluene, phenol).
Aliphatic: All other hydrocarbons (alkanes, alkenes, alkynes).

Alkanes

Alkanes are saturated hydrocarbons (only single bonds).
All carbons are sp3-hybridized.
General formula for non-cyclic alkanes:
General formula for cyclic alkanes:
Can be straight-chain, branched, or cyclic.

Alkenes and Alkynes

Alkenes and alkynes are unsaturated hydrocarbons (contain double or triple bonds).
Alkenes: Contain at least one C=C double bond.
Alkynes: Contain at least one C≡C triple bond.

Aromatic Molecules

Aromatic compounds have benzene-like ring structures, which are especially stable due to resonance.
Examples: benzene, toluene, phenol, benzaldehyde, benzoic acid, aniline, benzamide.

Examples

Drawing line structures for various molecules (e.g., hexane, diethylether, cyclopentanone, 4-ethyl-2-methylhexane).

20.4 Functional Groups

Definition and Importance

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.
They give "character" to organic molecules and are generally the site of chemical reactivity.

Common Functional Groups

Functional group	Structural formula	Condensed formula
Carboxylic acid	RCOOH	RCOOH
Ester	RCOOR'	RCOOR'
Amide	RCONH2	RCONH2
Aldehyde	RCHO	RCHO
Ketone	RCOR'	RCOR'
Alcohol	R–OH	ROH
Amine	RNH2	RNH2
Alkene	RCH=CHR'	RCH=CHR'
Alkyne	RC≡CR'	RC≡CR'
Aromatic	C6H5R	C6H5R
Ether	ROR'	ROR'
Alkyl halide	RX	RX
Alkyl	R	R

Alkyl Halides

Alkanes with a halogen (F, Cl, Br, I) attached: R–X.
Classified as methyl, primary (1°), secondary (2°), or tertiary (3°) based on the number of carbon atoms attached to the carbon bearing the halogen.

Alcohols and Thiols

Alcohols: Contain an –OH group.
Thiols: Contain an –SH group.
Both can be primary, secondary, or tertiary depending on substitution.

Ethers and Thioethers

Ethers: R–O–R'
Thioethers: R–S–R'
These molecules are bent around the O or S atom.

Ketones and Aldehydes

Both contain a carbonyl group (C=O).
Aldehyde: Carbonyl at the end of a chain (R–CHO).
Ketone: Carbonyl in the middle of a chain (R–CO–R').
C=O bond is strongly polar; commonly found in biomolecules.

Esters and Carboxylic Acids

Both contain a carbonyl (C=O) next to an oxygen.
Carboxylic acids are acidic (low pH): R–COOH.
Esters are commonly used as artificial flavourings: R–COOR'.

Amines and Amides

Amines: Nitrogen analogues of alcohols (R–NH2, R2NH, R3N).
Amides: Nitrogen analogues of carboxylic acids (R–CONH2).
Both can be primary, secondary, or tertiary depending on substitution on the nitrogen atom.

Examples

Identification of functional groups in various molecules, including drugs and biomolecules.

20.5 Constitutional Isomerism

Definition and Identification

Isomers: Compounds with the same chemical formula but different arrangements of atoms.
Constitutional isomers (structural isomers): Atoms are connected in a different order.
Can be identified by comparing Lewis structures.
Example: can be either propanol or isopropanol.

20.7 Configurational Isomerism (Stereoisomerism)

Stereoisomers

Stereoisomers have the same connectivity but a different arrangement of atoms in space.
VSEPR (Valence Shell Electron Pair Repulsion) theory is used to distinguish isomers.
Two main types:
- Geometric isomers (diastereomers): Different spatial arrangement, e.g., cis/trans isomers.
- Optical isomers (enantiomers): Non-superimposable mirror images.

Geometric Isomers

Have different spatial arrangement of atoms (e.g., cis/trans or E/Z isomerism).
Example: can have different arrangements of F and Cl atoms.

Optical Isomers (Enantiomers)

Non-superimposable mirror images.
Molecules with enantiomers are chiral.
A carbon with four different groups attached is a chiral centre.
Chiral molecules react differently with other chiral molecules; many drugs are chiral, and often only one enantiomer is biologically active.

Examples and Practice

Identify relationships between isomers (e.g., geometric vs. optical vs. constitutional).
Draw enantiomers and identify chiral centers.
Determine which isomer has a molecular dipole moment.
Practice drawing all possible isomers for a given formula (e.g., ).

Summary Table: Types of Isomers

Type	Description	Example
Constitutional	Different connectivity	Propanol vs. isopropanol
Geometric (diastereomers)	Same connectivity, different spatial arrangement (cis/trans)	cis-2-butene vs. trans-2-butene
Optical (enantiomers)	Non-superimposable mirror images	(R)-carvone vs. (S)-carvone