Introduction to Pharmaceutical Organic Chemistry

Organic Chemistry

Study of carbon-based compounds and their reactions.

Pharmaceutical Organic Chemistry

Focus on organic compounds in pharmaceuticals.

Functional Groups

Atoms/groups in molecules with predictable properties.

Alcohol

Contains hydroxyl (-OH) group on carbon.

Primary Alcohol

Hydroxyl group on a primary carbon.

Secondary Alcohol

Hydroxyl group on a secondary carbon.

Tertiary Alcohol

Hydroxyl group on a tertiary carbon.

Amine

Contains nitrogen atom(s) bonded to carbon.

Primary Amine

One carbon attached to nitrogen (RNH2).

Secondary Amine

Two carbons attached to nitrogen (R2NH).

Tertiary Amine

Three carbons attached to nitrogen (R3N).

Aldehyde

Contains carbonyl group bonded to hydrogen.

Ketone

Contains carbonyl group bonded to two carbons.

Carboxylic Acid

Contains carboxyl group (-COOH) in structure.

Carboxyl Group

Combination of carbonyl and hydroxyl groups.

Carboxylic Ester

Derived from carboxylic acid, H replaced by alkyl.

Branches of Chemistry

Includes organic, inorganic, analytical, physical, biochemistry.

Wöhler's Experiment

First synthesis of organic compound from inorganic source.

Organic Compounds

Over 10 million known, primarily carbon-based.

Inorganic Compounds

Estimated 1.7 million known, non-carbon based.

Vital Force Theory

Historical belief that living organisms produce organic compounds.

Carbon Structures

Framework for organic compounds, essential for life.

Biological Molecules

Includes proteins, nucleic acids, carbohydrates, lipids.

Chemical Reactions

Processes involving the transformation of substances.

Amide

Derivative of carboxylic acid with —OH replaced.

Structural formula

Depicts atoms and bonds in a molecule.

VSEPR model

Predicts molecular geometry based on electron pairs.

Covalent bond

Chemical bond formed by shared electron pairs.

Atomic number (Z)

Number of protons in an atom's nucleus.

Mass number (A)

Total of protons and neutrons in nucleus.

Isotopes

Atoms with same element, different neutron counts.

Atomic mass

Weighted average mass of isotopes in amu.

Electron cloud

Region around nucleus containing negatively charged electrons.

Wave function

Mathematical description of electron's probable location.

Orbital

Region in space where electrons are likely found.

s orbital

Spherical orbital centered around nucleus.

p orbital

Dumbbell-shaped orbital with two lobes.

Electron shell

Energy level containing one or more orbitals.

Aufbau principle

Lowest-energy orbitals fill before higher ones.

Pauli exclusion principle

No two electrons can have identical quantum states.

Hund's rule

Electrons fill degenerate orbitals singly first.

First shell

Contains one s orbital, holds two electrons.

Second shell

Contains one s and three p orbitals, holds eight electrons.

Third shell

Contains one s, three p, and five d orbitals, holds eighteen electrons.

Node

Region in p orbital with zero electron density.

Quantum mechanics

Describes electron energies and behavior.

August Kekulé

Independently observed carbon always has four bonds.

Archibald Couper

Co-discovered carbon's four bond structure.

Tetrahedron

Shape formed by atoms surrounding carbon.

Jacobus van't Hoff

Proposed specific spatial directions for carbon bonds.

Le Bel

Contributed to understanding carbon bond orientation.

Chemical Bond

Attractive force holding atoms together in compounds.

Ionic Bond

Forms through electron transfer between atoms.

Lewis Structures

Diagrams showing valence electrons as dots.

Valence Electrons

Electrons in the outermost shell of an atom.

Stable Molecule

Achieved when atoms complete their electron shells.

Octet Rule

Atoms are stable with eight valence electrons.

Bond Formation

Atoms bond to achieve greater stability.

Non-bonding Electrons

Valence electrons not involved in bonding.

Valence Bond Theory

Describes how covalent bonds form through orbital overlap.

Bond Energy

Energy released when bonds form, measured in kJ/mol.

Bond Length

Distance between nuclei in a bonded molecule.

sp3 Hybrid Orbitals

Combination of s and p orbitals for bonding.

C-H Bonds in CH4

Identical bonds oriented tetrahedrally around carbon.

Bond Strength

Energy required to break a bond.

Covalent Bond Overlap

Occurs when orbitals from two atoms overlap.

Ammonia (NH3) Bonds

Nitrogen forms three bonds with one lone pair.

Hydrogen Bond Strength

H-H bond strength is 436 kJ/mol.

Hybridization

Mixing atomic orbitals to form new orbitals.

sp3 Hybridization

One s and three p orbitals combine.

Tetrahedral Structure

Shape with bond angles of 109.5°.

C-H Bond Strength (Methane)

Strength of 438 kJ/mol for C-H bond.

C-H Bond Length (Methane)

Length of 110 pm for C-H bond.

Ethane Structure

Contains six C-H bonds from sp3 overlap.

C-C Bond Strength (Ethane)

Strength of 376 kJ/mol for C-C bond.

C-C Bond Length (Ethane)

Length of 154 pm for C-C bond.

sp2 Hybridization

One s and two p orbitals combine.

Ethylene Bond Angles

Bond angles of 120° in ethylene.

C-C Double Bond

Formed by one sigma and one pi bond.

Sigma Bond

Head-on orbital overlap forming a single bond.

Pi Bond

Sideways orbital overlap forming a double bond.

Molecular Orbital (MO)

Region where electrons are likely found.

Bonding MO

Lower energy orbital from additive combination.

Antibonding MO

Higher energy orbital from subtractive combination.

Hybridization of Nitrogen

Nitrogen forms four sp3 orbitals in ammonia.

H-N-H Bond Angle

Bond angle of 107.3° in ammonia.

Hybridization of Oxygen

Oxygen is sp3 hybridized in water.

H-O-H Bond Angle

Bond angle of 104.5° in water.

Covalent Bonds

Electron pairs shared between atoms.

sp hybridization

Two sp orbitals for linear triple bonds.

Polar covalent bond

Unequal sharing of electrons between atoms.

Electronegativity (EN)

Atom's ability to attract shared electrons.

Electronegativity scale

Fluorine (EN=4.0) is most electronegative.

Electronegativity trend

Increases left to right, decreases top to bottom.

Partial positive charge

Indicated by !+; electron-poor atom.

Partial negative charge

Indicated by !-; electron-rich atom.

Electrostatic potential maps

Visual representation of charge distribution in molecules.

Bond polarity

Determined by differences in electronegativity.

Methanol (CH3OH)

C-O bond is polar covalent.

Methyllithium (CH3Li)

C-Li bond is polarized with carbon negative.