Chemistry for Biomedical Engineering

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Topic 0: Preliminary concepts

• Units
• Standard conditions for T and P
• Standard state
• Mass and charge of elemental particles. Atomic mass
• Ions, molecules, mol, Avogadro’s number
• Mass spectrometry
• Molecular formula, empirical formula
• Notation in chemical equations. Mass and charge balance
• Types of chemical reactions
• Gases

Topic 1: Atoms

• Ancient ideas about atoms
• Experiments and concepts that led to Bohr’s model
• Bohr’s model of hydrogen atom
• Foundations of Quantum Mechanics
• Schrödinger equation for hydrogen atom
• Quantum numbers and atomic orbitals
• Probability density
• Multielectronic atoms
• Shortcomings of the Aufbau Principle
• Periodic Table
• Periodicity of chemical properties

• Topic 2: Molecules
• Classification of chemical bonds
• Covalent bond. Lewis structures
• Molecular geometry. VSEPR theory
• Theory of Molecular Orbitals
• Energy diagrams. Bond order
• Coordination compounds
• Hybridization: simple, double and triple bonds
• Bond distance and bond energy
• Ionic character of covalent bonds. Dipole moments
• Intermolecular forces. Classification
• Coulombic interactions
• Polarization interactions
• Hydrogen bonding. Structure of water
• Repulsive potential.

Topic 3: States of Matter

• Classification
• Types of solids
• Gases.
• Liquids.
•  Brownian motion
•  Clausius –Clapeyron equation
•  Equilibrium phase diagrams
• Solutions.
•   Solubility. Temperature dependence. Hydration
•   Units for concentration
•   Colligative properties: freezing point depression, boiling point elevation, osmosis, dialysis

Topic 4: Elementary thermodynamics

• Definitions: systems, variables, state functions
• Heat and Work
• First law of thermodynamics
• Internal energy and enthalpy
• Standard molar enthalpy of reaction
• Thermo-chemistry and Hess law
• Heat capacity: constant pressure and constant volume
• Temperature dependence of enthalpy
• Second law of thermodynamics. Entropy
• Reversible and irreversible processes
• Temperature dependence of entropy
• Reaction entropy
• Third law of thermodynamics
• Absolute entropy
• Gibbs free energy
• Spontaneity in chemical reactions
• Standard Gibbs energy of formation
• Gibbs free energy and equilibrium constant in reactions between gases
• Temperature dependence of reaction constant

Topic 5: Equilibrium Reactions

• Kp and Kc in homogeneous and heterogeneous equilibriums
• Le Chatelier’s principle
• Factors affecting chemical equilibrium: concentration, pressure, volume, inert gases,
• temperature.
• Arrhenius theory of acids and bases.
• Brönsted theory of acids and bases
• Lewis theory of acids and bases
• Conjugated acid-base pairs
• Water self ionization. pH
• Strength of acids and bases
• Polyprotic acids.
• Hydrolysis
• Buffers.
• Acid-base titrations
• Acid-base indicators
• Solubility. Solubility product
• Bio-connections: antacids and buffering in human blood
• Oxidation and reduction reactions
• Oxidation state in inorganic and organic substances
• Balancing redox reactions in acid and basic media
• Galvanic cells. Half reaction
• Conventions about cells
• Standard hydrogen electrode
• Cell potential
• Electrode potential and Gibbs free energy. Nernst equation
• Electrolytic cells. Faraday’s laws

Topic 6: Chemical kinetics

• Definition of reaction rate
• Reaction rate law: rate constant and reaction order
• Integrated kinetic equations
• Reaction mechanisms: elemental process, molecularity, limiting step, reaction intermediate
• Rate constants and equilibrium constants in reversible processes
• Kinetic theories: Collision theory, Arrhenius law and activation energy. Transition state theory,
• activation entropy and activation enthalpy.
• Catalysis. Homogeneous and heterogeneous. Steps of heterogeneous catalysis.
• Enzymatic catalysis: Michaelis-Menten kinetics

Topic 7: Introduction to Organic Chemistry

• Carbon, carbon compounds and hybridization
• Naming, functional group and general rules
• Empirical, structural and molecular formulae
• Isomerism.
• Conformational isomerism: Newman projections. Cyclohexane ring
• Stereoisomerism. Convention rules for naming R/S isomers
• Optical activity. Specific rotation. D/L convention system
• Fisher projections. Diasteromers
• Intermolecular forces and physical properties in organic compounds
• Electronic shifts in s bonds: Inductive effect
• Electronic shifts in p systems: Resonance
• Aromaticity
• Substitution effects in p systems.
• Homolytic and heterolytic breakdown of organic bonds
• Nucleophilic and electrophilic reactives
• Reaction intermediates: radicals. Geometry
• Reaction intermediates: carbocations. Geometry
• Reaction intermediates: carbanions
• Classification of organic reactions: Chain reactions. Electrophilic substitution. Nucleophilic
• substitution. Electrophilic and nucleophilic addition. Elimination. Condensation

Topic 8: Reactions in Organic Chemistry

• Alkanes. Cycloalkanes
• Alkenes. Cycloalkenes. Alkynes
• Benzene and aromatic hydrocarbons.
• Alcohols and phenols. Physical properties
• Acid-base properties of alcohols and phenols
• Naturally occurring alcohols and phenols.
• Reactivity of alcohols: dehydration and oxidation.
• Ethers. Physical properties. Cyclic ethers
• Biologically relevant ethers
• Thiols: acid-base reactions
• Amines.
• Carbonylic compounds. Physical properties and resonance
• Reactivity: oxidation and reduction reactions, nucleophilic addition (acetals).
• Acidity of a-hydrogen. Keto-enol tautomerism
• Natural aldehydes and ketones
• Carboxylic acids.
• Derivatives from carboxylic acids: anhydrides, esters, amides