Structure and Classification of Organic Molecules

Structure of Organic Molecules

Introduction to Organic Chemistry

Organic chemistry is the branch of chemistry that studies compounds containing carbon. Most organic molecules are characterized by covalent bonding, where atoms share electrons. Carbon is a unique element in organic chemistry because it is tetravalent, meaning it forms four covalent bonds with other atoms.

• Covalent Bond: A chemical bond formed by the sharing of electron pairs between atoms.

• Tetravalency of Carbon: Carbon always forms four bonds, which can be single, double, or triple bonds.

• Example: Ethane ($C_2H_6$) is a simple organic molecule where each carbon forms four single bonds.

Covalent Bonds in Organic Molecules

Types of Covalent Bonds

Carbon atoms can form single, double, or triple covalent bonds by sharing one, two, or three pairs of electrons, respectively, with neighboring atoms.

• Single Bond: Sharing one pair of electrons (e.g., in ethane, $C_2H_6$).

• Double Bond: Sharing two pairs of electrons (e.g., in ethylene, $C_2H_4$).

• Triple Bond: Sharing three pairs of electrons (e.g., in acetylene, $C_2H_2$).

General formulas:

• Ethane: $H_3C-CH_3$

• Ethylene: $H_2C=CH_2$

• Acetylene: $HC\equiv CH$

Geometry of Carbon Bonding

VSEPR Theory and Molecular Shapes

The geometry of a carbon atom in a molecule depends on the number of groups (atoms or lone pairs) attached to it:

• Tetrahedral (4 groups): Bond angle ≈ 109.5°, as in methane ($CH_4$).

• Trigonal Planar (3 groups): Bond angle ≈ 120°, as in ethylene ($C_2H_4$).

• Linear (2 groups): Bond angle = 180°, as in acetylene ($C_2H_2$).

These shapes are predicted by the Valence Shell Electron Pair Repulsion (VSEPR) theory.

Bond Polarity and Representation

Polar Covalent Bonds

When carbon bonds to a more electronegative atom (such as N, O, F, or Cl), the bond becomes polar covalent, resulting in partial charges on the atoms.

• Electronegativity: The ability of an atom to attract shared electrons in a bond.

• Bond Polarity: A bond is polar if the two atoms have different electronegativities.

Bond Representation in 3D

• Solid wedge (▲): Bond coming out of the plane toward the viewer.

• Dashed wedge (▿): Bond going behind the plane away from the viewer.

• Straight line: Bond in the plane of the paper.

Common Bonds in Organic Molecules

Carbon's Bonding Partners

• Hydrogen: Most common bond in organic molecules.

• Nitrogen, Oxygen, Halogens: Carbon often bonds with these atoms, forming a variety of functional groups.

• Examples: $C-N$, $C=O$, $C-O$, $C\equiv N$, $C=O$, $C\equiv N$

Polarity and Solubility of Organic Molecules

Solubility Principles

Most organic compounds are nonpolar and do not dissolve in water unless they contain polar groups or are small in size.

• Nonpolar molecules: Do not dissolve in water (hydrophobic).

• Polar molecules: Dissolve in water if they are small or have many polar groups (hydrophilic).

• Biological relevance: Solubility affects how molecules behave in biological systems.

Functional Groups

Definition and Importance

The chemical behavior of organic molecules is determined by the functional groups they contain. A functional group is a specific group of atoms within a molecule that is responsible for characteristic chemical reactions.

• Family of compounds: Molecules with the same functional group belong to the same family and have similar chemical properties.

• Predictability: The presence of a functional group allows chemists to predict the reactivity of a molecule.

Table: Common Functional Groups

The following table summarizes the main families of organic compounds and their functional groups:

Family	Functional Group Structure	Example	Suffix/Prefix
Alkane	R-H (no functional group)	Propane ($CH_3CH_2CH_3$)	-ane
Alkene	C=C (double bond)	Ethylene ($CH_2=CH_2$)	-ene
Alkyne	C≡C (triple bond)	Acetylene ($HC\equiv CH$)	-yne
Aromatic	Benzene ring	Benzene ($C_6H_6$)	None
Alkyl halide	R-X (X = F, Cl, Br, I)	Ethyl chloride ($CH_3CH_2Cl$)	halo-
Alcohol	R-OH	Ethanol ($CH_3CH_2OH$)	-ol
Ether	R-O-R'	Diethyl ether ($CH_3CH_2OCH_2CH_3$)	ether
Amine	R-NH2	Ethylamine ($CH_3CH_2NH_2$)	-amine
Aldehyde	R-CHO	Acetaldehyde ($CH_3CHO$)	-al
Ketone	R-CO-R'	Acetone ($CH_3COCH_3$)	-one
Carboxylic acid	R-COOH	Acetic acid ($CH_3COOH$)	-oic acid
Ester	R-COOR'	Methyl acetate ($CH_3COOCH_3$)	-oate
Amide	R-CONH2	Acetamide ($CH_3CONH_2$)	-amide
Thiol	R-SH	Ethanethiol ($CH_3CH_2SH$)	-thiol
Sulfide	R-S-R'	Dimethyl sulfide ($CH_3SCH_3$)	sulfide

Hydrocarbons and Isomerism

Hydrocarbon Types

• Alkanes: Only single bonds, general formula $C_nH_{2n+2}$.

• Alkenes: At least one double bond, general formula $C_nH_{2n}$.

• Alkynes: At least one triple bond, general formula $C_nH_{2n-2}$.

• Aromatics: Alternating double bonds in a ring (e.g., benzene).

Isomerism

Isomers are compounds with the same molecular formula but different structures.

• Constitutional (structural) isomers: Differ in the connectivity of their atoms.

• Conformers: Different spatial arrangements of the same molecule due to rotation around single bonds.

Example: Butane ($C_4H_{10}$) and isobutane (2-methylpropane) are constitutional isomers.

Drawing Organic Structures

Structural, Condensed, and Line-Angle Formulas

• Structural formula: Shows all atoms and bonds explicitly.

• Condensed formula: Groups atoms together (e.g., $CH_3CH_2CH_3$ for propane).

• Line-angle (skeletal) structure: Each vertex or line end represents a carbon; hydrogens on carbon are implied.

Guidelines for Line Structures:

• Each line represents a bond between carbons.

• Vertices and line ends are carbon atoms.

• Hydrogens attached to carbon are not shown; other atoms (O, N, halogens) are shown explicitly.

• Neutral carbon forms four bonds; missing bonds are assumed to be to hydrogen.

Practice Problems and Applications

Sample Problems

• Problem 1: Molecule Polarity – Identify polar regions in organic molecules by locating bonds between carbon and more electronegative atoms (e.g., O, N).

• Problem 2: Organic Families – Classify molecules by their functional groups.

• Problem 3: Predicting Structures – Draw possible structures for given molecular formulas (e.g., $C_4H_{10}$, $C_4H_{10}O$, $C_4H_9N$).

• Problem 4: Isomer Drawing – Draw all constitutional isomers for a given formula.

• Problem 5: Condensed Formulas – Write condensed formulas for isomers.

• Problem 6: Line Structures – Convert condensed formulas to line structures and vice versa.

• Problem 7: Conformers – Identify different conformers of the same molecule.

• Problem 8: Conformers or Isomers – Distinguish between conformers (same molecule, different shape) and isomers (different connectivity).

Summary Table: Hydrocarbon Formulas

Type	General Formula	Example
Alkane	$C_nH_{2n+2}$	Methane ($CH_4$), Ethane ($C_2H_6$)
Alkene	$C_nH_{2n}$	Ethylene ($C_2H_4$)
Alkyne	$C_nH_{2n-2}$	Acetylene ($C_2H_2$)

Key Equations

• Alkane formula: $C_nH_{2n+2}$

• Alkene formula: $C_nH_{2n}$

• Alkyne formula: $C_nH_{2n-2}$

Additional info:

• Understanding functional groups is essential for predicting the reactivity and properties of organic molecules.

• Practice converting between different structural representations to develop fluency in organic structure drawing.