BT 304: Organic Chemistry Course

Course Overview

• Course code is BT 304
• The Course Co-ordinator is Dr. Mahera Moin, an Assistant Professor at Dow College of Biotechnology, Dow University of Health Sciences

Course Outline

• Chapter 1: Introduction to Organic Chemistry
• Chapter 2: Properties of Organic Molecules
• Chapter 3: Nomenclature of Organic Compounds
• Chapter 4: Chemistry of Saturated Hydrocarbons
• Chapter 5: Chemistry of Unsaturated Hydrocarbons
• Chapter 6: Chemistry of Halo Alkanes
• Chapter 7: Alcohols
• Chapter 8: Phenols
• Chapter 9: Amines
• Chapter 10: Carboxylic Acids
• Chapter 11: Functional Group Derivatives of Carboxylic Acids

Recommended Books

• Organic Chemistry by John Mc Murry
• Organic Chemistry by Francis A. Carey
• Introduction to Medicinal Chemistry by Graham Patrick
• Organic Chemistry by Solomon

Marks Distribution

• Internal Evaluation: 15 marks
• Mid Term: 15 marks
• Final Exams: 70 marks Note: Subject to change

Learning Objectives

• Recognize scientists' contributions to organic chemistry
• Understand the importance of organic compounds and chemistry in daily life
• Explain general properties of organic vs. inorganic compounds
• Identify different functional groups in organic compounds
• Define and differentiate isomers of organic compounds

Basic Concepts Review

• Organic compounds contain carbon atoms
• Covalent bond: atoms share a pair of electrons
• Covalent bonds uses Lewis structures, with dots representing electrons
• Octet rule: second-row elements bond to achieve noble gas electron configuration
• Lone pair: a pair of unshared electrons
• Formal charge: occurs when atoms don't exhibit the appropriate valence electrons and must be drawn in Lewis structures
• Quantum mechanics describes electrons with wavelike properties
• Wave equation: describes total energy of an electron near a proton
• Solutions to the wave equation are called wavefunctions (ψ), where ψ² is the probability of finding an electron in a location
• Atomic orbitals are represented visually using 3D plots of ψ², where nodes indicate value of ψ is zero
• Occupied orbital: electron density cloud
• Electrons fill orbitals following the Aufbau principle, Pauli exclusion principle, and Hund’s rule
• Degenerate orbitals: orbitals with same energy level
• VSEPR Theory predicts geometry, focusing of small compounds, uses σ bonds and lone pairs exhibited by each atom
• Steric number: total number of electron pairs repelling each other
• Compound geometry depends on number of lone pairs: tetrahedral, trigonal pyramidal, bent, trigonal planar, or linear
• Dipole moments (μ): occur when centers of negative and positive charge are separated by a distance; used to indicate polarity (measured in debyes)
• Percent ionic character determined by dipole moment
• Molecular dipole moment: vector sum of individual dipole moments in a compound
• Physical properties determined by intermolecular forces

Intermolecular forces

• Dipole-dipole interactions: occur between polar molecules
• Hydrogen bonding: a special dipole-dipole interaction where lone pairs of electronegative atoms interact with electron-poor hydrogen
• Compounds with hydrogen bonding: higher boiling points
• London dispersion forces: interaction between transient dipole moments
• Stronger in larger alkanes due to surface area and ability to accommodate more interactions

Organic Chemistry Definitions

• Berzilius Definition: substances derived from living organisms (plants and animals) are 'Organic Compounds' and the branch of chemistry dealing with them is called the 'Organic Chemistry'
• Modern Definition: study of Carbon compounds or the study of hydrocarbons and their derivatives
• Distinguishing characteristic: All organic compounds contain carbon, which is central to living organisms structure and existence on Earth

Exceptions to Organic Compounds

• Carbon monoxide (CO)
• Carbon dioxide (CO₂)
• Carbon disulfide (CS₂)
• Carbonates (e.g., Na₂CO₃)
• Bicarbonates (e.g., NaHCO₃)
• Cyanides (e.g., KCN)
• Cyanates (e.g., KOCN)

Why is Carbon Special?

• Nature chose it to create living organisms
• Carbon atoms form strong bonds to other carbon atoms, creating rings and chains, a self-linking property known as 'catenation'
• Carbon atoms also form strong bonds with elements like hydrogen, nitrogen, oxygen, and sulfur
• These properties allow it to be the base for diverse compounds for living organisms

Bonding in Organic Compounds

• Organic compounds are made of covalent bonds
• Inorganic compounds are made of ionic bonds (e.g., NaCl lattice)

Covalent Bonds

• Nonpolar covalent bonds: electrons are shared equally
• Polar covalent bonds: electrons are not shared; opposite charges attract each other

Properties Comparison- Organic Vs Inorganic Compounds

• Organic compounds: almost entirely covalent, gases/liquids/solids with low melting points (less than 360°C), insoluble in water, soluble in organic solvents, do not conduct electricity in aqueous solutions, almost all burn, slow reactions
• Inorganic compounds: mostly ionic, solids with high melting points, many soluble in water, insoluble in organic solvents, conduct electricity in aqueous solutions, very few burn, reactions are often very fast

Organic Chemistry Importance

• Application in daily life: study of carbon/chemistry of daily life
• Largely shapes world with hardly any walk without using organic compounds
• Foods contain mixtures consisting of organic compounds, such as starch, fats, proteins, and vegetables. The changes these foods undergo inside bodies are organic chemical reactions.
• Clothes that humans wear are organic due to the character/essence, such as leather, cotton, wool, and/or synthetics.

Obtaining Organic Compounds

• Isolation from nature
• Synthesis in the laboratory: Compounds made in the laboratory are identical chemically and physically to those found in nature, assuming each is 100% pure

Combinatorial Chemistry

• Chemists produce as many compounds as possible from building blocks
• Mixtures include two or three drug candidates
• Select biologically active compounds and separating promising candidates for further evaluation
• Cheaper and faster way to produce large libraries of synthetic compounds and "fish out" active ones, it is an automated method of carrying out a large number of in vitro assays on a small scale.

Combinatorial Chemistry vs Organic Chemistry

• Traditional Organic Chemistry: A + B → C (one molecule at a time)

• Combinatorial Chemistry: A1 + B1 → C(1,2,3...n) (many molecules at a time)

Combinatorial Chemistry in Drug Design

• Scaffolds: Molecular core of a drug
• Binding groups(substituents): Are attached as substituents
• Spider-like Scaffold and Tadpole-like Scaffold

Combinatorial Chemistry Advantages

• Conventional: one molecule at a time, Make -> Purity -> Test, hundreds of molecules a month, slower lead generation, high risk of failure
• Combinatorial: many molecule, at a time, Make -> Test -> Purity, thousands of molecules a month, faster leads generation, low risk of failure

Medical Field Uses

• Indispensable compounds are antibiotics, sulpha drugs, alkaloids, aspirin, iodoform, and Organic compounds

Industrial Application

• A necessity in most industries, including food, pharmacy, dyes, paper, sugar, alcohol, synthetic rubber, plastics, fertilizers, and petroleum
• Used for sources of primary energy with petroleum, natural gas, and coal is organic in nature
• Study of Life Processes: Based on carbon's diverse structures and carbon based molecules
• Investigation of tissues, secretions, and constituents of animals/plants
• The vitamins and hormones: organic compounds ensure proper development

History of Organic Chemistry

• Pre-Historic Period: Ancient Romans and Egyptians used organic chemicals as dyes, medicines, and poisons from natural sources
• 1773: Rouelle isolated urea from human urine
• 1742-86: Scheele obtained tartaric, citric, and malic acids from grapes, lemons, and apples
• 1805: Serturner obtained morphine from opium
• 18th Century: natural products included Many organic compounds
• 1807: Berzilius classified compounds as organic and inorganic
• 1828: Wohler made organic urea by heating inorganic ammonium cyanate
• 1860: Kekule proposed theories relating compound's chemical formula to physical structure
• 19th Century: nature of chemical bonding explored
• 20th Century: organic chemistry branched into sub-disciplines of polymer chemistry, pharmacology, bioengineering, and petro-chemistry

Vital Force Theory and Its Decline

• Organic compounds' production was limited to plants/animals with "vital" force
• Lab synthesis from inorganic material: Impossible
• Chemists believed organic compounds couldn't be prepared/manipulated in labs like inorganic
• Early as 1816: Michel Chevreul separated soap (alkali and animal fat) into pure organic fatty acids, without “vital force”
• 1828: Friedrich Wohler converted inorganic ammonium cyanate into organic urea
• Kolbe synthesized acetic acid in the lab, that no special force was needed and that organic compounds could be prepared in the lab

Organic chemistry Separates

• 30 million chemical compounds today, 99%+ contain CARBON
• Carbon's electronic structure and periodic table position make it unique
• Group 4A element: carbon shares 4 electrons, forming 4 covalent bonds
• Catenation: carbon forms immense diversity of compounds, from methane to DNA (100 million carbons)

Functional definition

• Functional Group Classification: Functional Groups determine chemical behavior
• Organic compounds share properties with similar functional groups
• Functional group classification simplifies organic chemistry
• Common elements: H, O, N, S, P, Cl, Br, I

Molecular Isomerism

• Organic molecules with ‘same molecular formula but different structures