Physical Chemistry for the Biosciences

Raymond Chang
Williams College


Table of Contents

Chapter 1  Introduction

1.1  Nature of Physical Chemistry 

1.2  Units 

1.3  Atomic Mass, Molecular Mass, and the Chemical Mole

 Chapter 2  Properties of Gases

2.1  Some Definitions 

2.2  An Operational Definition of Temperature 

2.3  Ideal Gases 

      • Charles' and Gay-Lussac's Law  • Avogadro's Law  • The Ideal-Gas Equation  • Dalton's             Law of Partial Pressures

2.4  Real Gases 

       • The van der Waals Equation  • The Virial Equation of State

2.5  Condensation of Gases and the Critical State

2.6  Kinetic Theory of Gases 

       • The Model   • Pressure of a Gas  • Kinetic Energy and Temperature

2.7  The Maxwell Distribution Laws 

2.8  Molecular Collisions and the Mean Free Path

2.9  Graham's Laws of Diffusion and Effusion

 Chapter 3  The First Law of Thermodynamics

3.1  Work and Heat 

        • Work  • Heat

3.2  The First Law of Thermodynamics 

        • Enthalpy  • A Comparison of ∆U with ∆H

3.3  Heat Capacities 

        • Constant-Volume and Constant-Pressure Heat Capacities  • Molecular Interpretation     of Heat Capacity  • A Comparison of CV with CP

3.4  Gas Expansion 

        • Isothermal Expansions  • Adiabatic Expansions

3.5  Calorimetry

       • Constant-Volume Calorimetry  • Constant-Pressure Calorimetry  • Differential                 Scanning Calorimetry 

3.6  Thermochemistry

        • Standard Enthalpy of Formation  • Dependence of Enthalpy of Reaction on         Temperature

3.7  Bond Energies and Bond Enthalpies 

       • Bond Enthalpy and Bond Dissociation Enthalpy

 Chapter 4  The Second Law of Thermodynamics

4.1  Spontaneous Processes

4.2  Entropy

        • Statistical Definition of Entropy  • Thermodynamic Definition of Entropy  • The    Carnot Heat Engine

4.3  The Second Law of Thermodynamics

4.4 Entropy Changes

        • Entropy Change due to Mixing of Ideal Gases  • Entropy Change due to Phase   Transitions

4.5  The Third Law of Thermodynamics

        • Third Law or Absolute Entropies  • Entropy of Chemical Reactions  • The Meaning        of Entropy 

4.6  Gibbs Energy

        • The Meaning of Gibbs Energy

4.7  Standard Molar Gibbs Energy of Formation (∆f o)

4.8  Dependence of Gibbs Energy on Temperature and Pressure

       • Dependence of G on Temperature  • Dependence of G on Pressure

4.9  Phase Equilibria

       • The Clapeyron and the Clausius-Clapeyron Equations  • Phase Diagrams  • The   Phase Rule

4.10  Thermodynamics of Rubber Elasticity

 Chapter 5  Solutions

5.1  Concentration Units

       • Percent by Weight  •  Mole Fraction  • Molarity (M)  • Molality (m)

5.2  Partial Molar Quantities

       • Partial Molar Volume  • Partial Molar Gibbs Energy  • The Meaning of Chemical             Potential

5.3  The Thermodynamics of Mixing 

5.4  Binary Mixtures of Volatile Liquids

       • Raoult's Law  • Henry's Law

5.5  Real Solutions

       • The Solvent Component  • The Solute Component

5.6  Colligative Properties

       • Vapor-Pressure Lowering  • Boiling-Point Elevation  • Freezing-Point Depression  •        Osmotic Pressure 

5.7  Electrolyte Solutions

       • A Molecular View of the Electrolyte Solution Process  • Thermodynamics of Ions in         Solution  • Enthalpy, Entropy, and Gibbs Energy of Formation of Ions in Solution

5.8  Ionic Activity

       Debye-Hόckel Theory of Electrolytes  • The Salting-In and Salting-Out Effects

5.9  Colligative Properties of Electrolyte Solutions

       • The Donnan Effect

5.10  Biological Membranes

         • Membrane Transport

Appendix 5.1  Notes on Electrostatics

Chapter 6  Chemical Equilibrium

6.1  Chemical Equilibrium in Gaseous Systems 

        • Ideal Gases  • A Closer Look at Equation 6.7  • A Comparison of ∆rG° with ∆rG  • Real            Gases

6.2  Reactions in Solutions 

6.3  Heterogeneous Equilibria 

6.4  The Influence of Temperature, Pressure, and Catalysts on the Equilibrium Constant 

       • The Effect of Temperature  • The Effect of Pressure  • The Effect of a Catalyst

6.5  Binding of Ligands and Metal Ions to Macromolecules

       • One Binding Site per Macromolecule  • n Equivalent Binding Sites per Macromolecule 

       • Experimental Studies of Binding Equilibria 

  6.6  Bioenergetics

       • The Standard State in Biochemistry  • ATP - The Currency of Energy  • Principles of       Coupled Reactions  • Glycolysis  • Some Limitations of Thermodynamics in Biology

 Chapter 7  Electrochemistry

7.1  Electrochemical Cells 

7.2  Single Electrode Potentials

7.3  Thermodynamics of Electrochemical Cells

       • The Nernst Equation  • Temperature Dependence of EMF

7.4  Types of Electrochemical Cells

       • Concentration Cells  • Fuel Cells

7.5  Applications of EMF Measurements

       • Determination of Activity Coefficients  • Determination of pH 

7.6  Biological Oxidation

       • The Chemiosmotic Theory of Oxidative Phosphorylation 

7.7  Membrane Potential

       • The Goldman Equation  • The Action Potential 

Chapter 8  Acids and Bases

8.1  Definitions of Acids and Bases 

8.2  Acid-Base Properties of Water

       • pH - A Measure of Acidity

8.3  Dissociation of Acids and Bases 

       • The Relationship Between the Dissociation Constant of an Acid and Its Conjugate            Base  • Salt Hydrolysis

8.4  Diprotic and Polyprotic Acids  

8.5  Buffer Solutions

        • The Effect of Ionic Strength and Temperature on Buffer Solutions  •  Preparing a             Buffer Solution with a Specific pH  • Buffer Capacity  

8.6  Acid-Base Titrations

       • Acid-Base Indicators

8.7  Amino Acids

       • Dissociation of Amino Acids  • The Isoelectric Point (pI)  • Titration of Proteins

8.8  Maintaining the pH of Blood

Appendix 8.1  A More Exact Treatment of Acid-Base Equilibria

 

 Chapter 9  Chemical Kinetics

9.1  Reaction Rates

9.2  Reaction Order

       • Zero-Order Reactions  • First-Order Reactions  • Second-Order Reactions 

       • Determination of Reaction Order

9.3  Molecularity of a Reaction

       • Unimolecular Reactions  • Bimolecular Reactions  • Termolecular Reactions 

9.4  More Complex Reactions

       • Reversible Reactions  • Consecutive Reactions  • Chain Reactions

9.5  The Effect of Temperature on Reaction Rates

       • The Arrhenius Equation

9.6  Potential Energy Surfaces 

9.7  Theories of Reaction Rates

       • Collision Theory  • Transition-State Theory  • Thermodynamic  Formulation of     Transition-State Theory

9.8  Isotope Effects in Chemical Reactions 

9.9  Reactions in Solution

9.10  Fast Reactions in Solution 

       • The Flow Method  • The Relaxation Method 

9.11  Oscillating Reactions 

Chapter 10  Enzyme Kinetics

10.1  General Principles of Catalysis

         • Enzyme Catalysis

10.2  The Equations of Enzyme Kinetics

         • Michaelis-Menten Kinetics  • Steady-State Kinetics  • The Significance of KM and        Vmax 

10.3  Chymotrypsin: A Case Study 

10.4  Multisubstrate Systems

         • The Sequential Mechanism  • The Nonsequential or "Ping-Pong" Mechanism

10.5  Enzyme Inhibition

         • Reversible Inhibition  • Irreversible Inhibition 

10.6  Allosteric Interactions

         • Oxygen Binding to Myoglobin and Hemoglobin  • The Hill Equation  • The         Concerted Model  • The Sequential Model  • Conformational Changes in Hemoglobin          Induced by Oxygen Binding 

10.7  The Effect of pH on Enzyme Kinetics

 Chapter 11  Quantum Mechanics and Atomic Structure

11.1  The Wave Theory of Light 

11.2  Planck's Quantum Theory 

11.3  The Photoelectric Effect 

11.4  Bohr's Theory of the Hydrogen Emission Spectrum 

11.5  de Broglie's Postulate 

11.6  The Heisenberg Uncertainty Principle 

11.7  The Schrφdinger Wave Equation 

11.8  Particle in a One-Dimensional Box 

         • Electronic Spectra of Polyenes

11.9  Quantum-Mechanical Tunneling 

11.10  The Schrφdinger Wave Equation for the Hydrogen Atom 

11.11  Many-Electron Atoms and the Periodic Table

            • Electronic Configurations  • Variations in Periodic Properties 

Chapter 12  The Chemical Bond

12.1  Lewis Structures 

12.2  Valence Bond Theory 

12.3  Hybridization of Atomic Orbitals 

12.4  Electronegativity and Dipole Moment 

12.5  Molecular Orbital Theory 

12.6  Diatomic Molecules

         • Homonuclear Diatomic Molecules of the Second-Period Elements  • Heteronuclear        Diatomic Molecules of the Second-Period Elements

12.7  Resonance and Electron Delocalization 

12.8  Coordination Compounds 

         • Crystal Field Theory  • Molecular Orbital Theory  • Valence Bond Theory

12.9  Coordination Compounds in Biological Systems

         • Copper  • Cobalt, Manganese and Nickel  • Toxic Heavy Metals

 Chapter 13  Intermolecular Forces

13.1  Intermolecular Interactions 

13.2  The Ionic Bond 

13.3  Types of Intermolecular Forces 

         • Dipole-Dipole Interaction  • Ion-Dipole Interaction  • Ion-Induced Dipole and Dipole-   Induced Dipole Interactions  Dispersion, or London, Forces  • Repulsive and Total   Interactions  • The Role of Dispersion Forces in Sickle-Cell Anemia

13.4  Hydrogen Bonding

13.5  The Structure and Properties of Water

         • The Structure of Ice  • The Structure of Water  • Some Physiochemical Properties of     Water

13.6  Hydrophobic Interaction

 Chapter 14  Spectroscopy

14.1  Vocabulary 

         • Absorption and Emission  • Units  • Regions of the Spectrum  • Line Width 

         • Resolution  • Intensity  • Selection Rules  • Signal-to-Noise Ratio  • The Beer-Lambert Law

14.2  Microwave Spectroscopy 

14.3  Infrared Spectroscopy 

         • Simultaneous Vibrational and Rotational Transitions

14.4  Electronic Spectroscopy 

         • Organic Molecules  • Transition Metal Complexes  • Molecules that Undergo Charge-   Transfer Interactions  • Application of the Beer-Lambert Law

14.5  Nuclear Magnetic Resonance 

         • Chemical Shifts  • Spin-Spin Coupling  • NMR and Rate Processes  • NMR of Nuclei   Other than 1H • Magnetic Resonance Imagine (MRI)

14.6  Electron Spin Resonance 

14.7  Fluorescence and Phosphorescence 

         • Fluorescence  • Phosphorescence

14.8  Lasers 

         • Properties and Applications of Laser Light

14.9  Optical Rotatory Dispersion and Circular Dichroism

         • Molecular Symmetry and Optical Activity  • Polarized Light and Optical Rotation 

         • Optical Rotatory Dispersion (ORD) and Circular Dichroism (CD)

 Chapter 15  Photochemistry and Photobiology

15.1  Introduction 

         • Thermal Versus Photochemical Reactions  • Primary Versus Secondary Processes 

         • Quantum Yields  • Measurement of Light Intensity  • Action Spectrum

15.2  Photosynthesis 

         • The Chloroplast  • Chlorophyll and Other Pigment Molecules  • The Reaction Center 

         • Photosystems I and II

15.3  Vision 

         • Structure of Rhodopsin  • Mechanism of Vision  • Rotation About the C=C Bond

15.4  Biological Effects of Radiation

         • Sunlight and Skin Cancer  • Photomedicine

 Chapter 16  Macromolecules

16.1  Methods for Determining Size, Shape, and Molar Mass of Macromolecules 

         • Molar Mass of Macromolecules   • Sedimentation in the Ultracentrifuge  • Viscosity 

         • Electrophoresis

16.2  Structure of Synthetic Polymers 

         • Configuration and Conformation  • The Random-Walk Model

 16.3  Structure of Proteins and DNA

       • Proteins  • DNA

16.4  Protein Stability

         • Hydrophobic Interaction  • Denaturation  • Protein Folding

 

        Appendices

         Glossary

         Answers to Even-Numbered Computational Problems

         Index