Introduction to Organic Chemistry

Functional groups, nomenclature, isomerism, and reaction types

Functional Groups

Organic chemistry is organized around functional groups — specific arrangements of atoms that determine a molecule's chemical reactivity and properties.

Functional Group	General Formula	Example	Properties
Alkane	$C_nH_{2n+2}$	Methane CH₄	Saturated; low reactivity
Alkene	$C_nH_{2n}$	Ethylene C₂H₄	C=C double bond; addition reactions
Alkyne	$C_nH_{2n-2}$	Acetylene C₂H₂	C≡C triple bond; linear geometry
Alcohol	R–OH	Ethanol C₂H₅OH	H-bonding; polar
Carboxylic Acid	R–COOH	Acetic acid CH₃COOH	Weak acid; H-bonding dimers
Amine	R–NH₂	Methylamine CH₃NH₂	Basic; H-bonding

IUPAC Nomenclature

The IUPAC system provides a systematic way to name organic compounds:

Find the longest continuous carbon chain (parent chain)
Number the carbons from the end nearest to the first substituent
Name and number each substituent (methyl, ethyl, etc.)
Use the appropriate suffix for the functional group (-ane, -ene, -yne, -ol, -al, -one, -oic acid)
Assemble: substituents (alphabetical) + parent name + suffix

Carbon Chain Prefixes

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

Isomerism

Isomers share the same molecular formula but differ in structure or spatial arrangement:

Structural Isomers

Different connectivity of atoms. Example: butane and isobutane (2-methylpropane) both have formula C₄H₁₀.

Geometric (cis/trans)

Same connectivity but different arrangement around a double bond or ring.cis-2-butene has both methyl groups on the same side; trans on opposite sides.

Optical (Enantiomers)

Non-superimposable mirror images due to a chiral center (typically a carbon with 4 different substituents). They rotate plane-polarized light in opposite directions.

Reaction Types & Hybridization

Substitution

One atom or group replaces another. Sₙ1 (unimolecular) and Sₙ2 (bimolecular) mechanisms.

Elimination

Atoms removed from adjacent carbons to form a double bond. E1 and E2 mechanisms.

Addition

Atoms add across a double or triple bond, reducing unsaturation. Markovnikov vs anti-Markovnikov selectivity.

Hybridization

$sp^3$: tetrahedral (109.5°), $sp^2$: trigonal planar (120°),$sp$: linear (180°). Determines molecular geometry.

Degree of Unsaturation (DoU)

Also called the index of hydrogen deficiency, DoU counts the total number of rings plus double bonds in a molecule:

$$\text{DoU} = \frac{2C + 2 + N - H - X}{2}$$

where C, H, N are atom counts and X is the total number of halogen atoms. Oxygen and sulfur do not affect DoU. Each ring or double bond contributes 1; each triple bond contributes 2.

Python: Molecular Property Calculator

Computes the degree of unsaturation and molar mass for a set of organic molecules from their molecular formulas.

Degree of Unsaturation Calculator

Python

Computes DoU and molar mass for various organic molecules from molecular formula

script.py81 lines

import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
# ─────────────────────────────────────────────────────────
# Molecular Property Calculator
# Degree of unsaturation (DoU) from molecular formula
# DoU = (2C + 2 + N - H - X) / 2
# where X = halogens (F, Cl, Br, I)
# ─────────────────────────────────────────────────────────

def degree_of_unsaturation(C, H, N=0, O=0, X=0):
    """Compute degree of unsaturation (index of hydrogen deficiency).
    X = total halogen count (F + Cl + Br + I)
    O does not affect DoU."""
    return (2*C + 2 + N - H - X) / 2

def molar_mass(C, H, N=0, O=0, F=0, Cl=0, Br=0, I=0, S=0):
    """Compute molar mass from atomic counts."""
    masses = {'C': 12.011, 'H': 1.008, 'N': 14.007, 'O': 15.999,
              'F': 18.998, 'Cl': 35.453, 'Br': 79.904, 'I': 126.904,
              'S': 32.065}
    return (C*masses['C'] + H*masses['H'] + N*masses['N'] +
            O*masses['O'] + F*masses['F'] + Cl*masses['Cl'] +
            Br*masses['Br'] + I*masses['I'] + S*masses['S'])

# Test molecules
molecules = [
    ('Ethane (C2H6)',         2, 6, 0, 0, 0),
    ('Ethylene (C2H4)',       2, 4, 0, 0, 0),
    ('Acetylene (C2H2)',      2, 2, 0, 0, 0),
    ('Benzene (C6H6)',        6, 6, 0, 0, 0),
    ('Acetic acid (C2H4O2)',  2, 4, 0, 2, 0),
    ('Aniline (C6H7N)',       6, 7, 1, 0, 0),
    ('Chloroform (CHCl3)',    1, 1, 0, 0, 3),
    ('Caffeine (C8H10N4O2)',  8, 10, 4, 2, 0),
    ('Aspirin (C9H8O4)',      9, 8, 0, 4, 0),
    ('Naphthalene (C10H8)',  10, 8, 0, 0, 0),
]

print(f"{'Molecule':<28} {'Formula':>12} {'DoU':>5} {'M (g/mol)':>10}")
print("-" * 60)

dou_values = []
names_short = []

for name, C, H, N, O, X in molecules:
    dou = degree_of_unsaturation(C, H, N, O, X)
    mm = molar_mass(C, H, N, O)
    formula = f"C{C}H{H}"
    if N > 0: formula += f"N{N}"
    if O > 0: formula += f"O{O}"
    if X > 0: formula += f"X{X}"
    print(f"{name:<28} {formula:>12} {dou:>5.1f} {mm:>10.2f}")
    dou_values.append(dou)
    names_short.append(name.split('(')[0].strip())

print()
print("DoU interpretation:")
print("  DoU=0: fully saturated")
print("  DoU=1: one double bond or one ring")
print("  DoU=2: one triple bond, or two double bonds, or two rings, etc.")
print("  DoU=4: benzene ring (3 double bonds + 1 ring)")

# Plot
fig, ax = plt.subplots(figsize=(10, 5))
colors = plt.cm.plasma(np.linspace(0.2, 0.9, len(dou_values)))
bars = ax.barh(range(len(names_short)), dou_values, color=colors, edgecolor='white', linewidth=0.5)
ax.set_yticks(range(len(names_short)))
ax.set_yticklabels(names_short, fontsize=11)
ax.set_xlabel('Degree of Unsaturation (DoU)', fontsize=12)
ax.set_title('Degree of Unsaturation for Various Organic Molecules', fontsize=14)
ax.grid(True, axis='x', alpha=0.3)

for i, v in enumerate(dou_values):
    ax.text(v + 0.15, i, f'{v:.0f}', va='center', fontsize=10, color='white')

plt.tight_layout()
plt.savefig('output.png', dpi=150, bbox_inches='tight')
print("\nPlot saved.")

Click Run to execute the Python code

Code will be executed with Python 3 on the server

Fortran: Molecular Formula Properties

Computes molar mass and degree of unsaturation for a set of organic molecules.

Molecular Formula Properties

Fortran

Computes molar mass and degree of unsaturation from molecular formula

mol_properties.f9045 lines

program mol_properties
  implicit none
  integer, parameter :: dp = selected_real_kind(15)
  integer, parameter :: n_mol = 8

character(len=30) :: names(n_mol)
  integer :: C(n_mol), H(n_mol), N(n_mol), O(n_mol), X(n_mol)
  real(dp) :: molar_mass, dou
  integer :: i

! Atomic masses
  real(dp), parameter :: mC = 12.011_dp, mH = 1.008_dp
  real(dp), parameter :: mN = 14.007_dp, mO = 15.999_dp

! Define molecules: name, C, H, N, O, X(halogens)
  names(1) = 'Methane';       C(1)=1;  H(1)=4;  N(1)=0; O(1)=0; X(1)=0
  names(2) = 'Ethylene';      C(2)=2;  H(2)=4;  N(2)=0; O(2)=0; X(2)=0
  names(3) = 'Benzene';       C(3)=6;  H(3)=6;  N(3)=0; O(3)=0; X(3)=0
  names(4) = 'Acetic acid';   C(4)=2;  H(4)=4;  N(4)=0; O(4)=2; X(4)=0
  names(5) = 'Glycine';       C(5)=2;  H(5)=5;  N(5)=1; O(5)=2; X(5)=0
  names(6) = 'Caffeine';      C(6)=8;  H(6)=10; N(6)=4; O(6)=2; X(6)=0
  names(7) = 'Aspirin';       C(7)=9;  H(7)=8;  N(7)=0; O(7)=4; X(7)=0
  names(8) = 'Naphthalene';   C(8)=10; H(8)=8;  N(8)=0; O(8)=0; X(8)=0

write(*,'(A)') '========================================================'
  write(*,'(A)') '  Molecular Formula Properties: Molar Mass & DoU'
  write(*,'(A)') '========================================================'
  write(*,'(A)') ''
  write(*,'(A20, A12, A8, A15)') 'Molecule', 'Formula', 'DoU', 'M (g/mol)'
  write(*,'(A)') '-------------------------------------------------------'

do i = 1, n_mol
    molar_mass = C(i)*mC + H(i)*mH + N(i)*mN + O(i)*mO
    dou = (2.0_dp*C(i) + 2.0_dp + N(i) - H(i) - X(i)) / 2.0_dp

write(*,'(A20, A1,I1,A1,I2,A1,I1,A1,I1, F6.1, F12.2)') &
      names(i), 'C', C(i), 'H', H(i), 'N', N(i), 'O', O(i), dou, molar_mass
  end do

write(*,'(A)') ''
  write(*,'(A)') 'DoU = (2C + 2 + N - H - X) / 2'
  write(*,'(A)') 'Each ring or double bond = 1 DoU'
  write(*,'(A)') 'Each triple bond = 2 DoU'
  write(*,'(A)') 'Benzene ring = 4 DoU (3 C=C + 1 ring)'
end program mol_properties

Click Run to execute the Fortran code

Code will be compiled with gfortran and executed on the server

Video Lectures

Lecture 34: Introduction to Organic Chemistry

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