Table of contents for Biophysical chemistry / James P. Allen.
Bibliographic record and links to related information available from the Library of Congress catalog
Information from electronic data provided by the publisher. May be incomplete or contain other coding.
0. Basic thermodynamic and biochemical concepts.
0.1 Fundamental thermodynamic concepts.
States of matter.
Volume, mass, and number.
0.2 Properties of gases.
The ideal gas laws.
0.3 Kinetic energy of gases.
0.4 Real Gases.
Liquifying gases for low temperature spectroscopy.
0.5 Molecular Basis for Life.
Classification of amino acids by their side chains.
DNA and RNA.
1. First law of thermodynamics.
First law of thermodynamics.
1.1 Research Direction: Drug design I.
Internal energy for an ideal gas.
Dependence of specific heat on enthalpy.
Derivative box: State Functions described using partial derivatives.
Enthalpy changes of biochemical reactions.
1.2 Research Direction: Global climate change.
2. Second law of thermodynamics.
Entropy changes for reversible and irreversible processes.
The second law of thermodynamics.
Interpretation of entropy.
Third law of thermodynamics.
Relationship between the Gibbs free energy and the equilibrium constant.
2.1 Research Direction: Drug design II.
Gibbs free energy for an ideal gas.
Using the Gibbs free energy.
Carnot cycle and hybrid cars.
Derivative box: Entropy as a state function.
2.2 Research Direction: Nitrogen fixation.
3. Phase diagrams, mixtures and chemical potential.
Substances may exist in different phases.
Phase diagrams and transitions.
Properties of lipids described using the chemical potential.
3.1 Research Direction: lipid rafts.
Determination of micelle formation using surface tension.
3.2 Research Direction: Protein crystallization.
4. Equilibria and reactions involving protons.
Gibbs free energy minimum.
Derivative box:Relationship between the Gibbs energy and equilibrium constant.
Response of the equilibrium constant to condition changes.
Protonation states of amino acid residues.
Buffering in the cardiovascular system.
4.1 Research Direction: Proton coupled electron transfer and pathways.
5. Oxidation/reduction reactions and bioenergetics.
The Nernst Equation:.
Gibbs energy of formation and activity.
5.1 Research Direction: Respiratory chain.
5.2 Research Direction: ATP synthase.
6. Kinetics and enzymes.
The rate of a chemical reaction.
Parallel first-order reactions.
Sequential first order reactions.
The order of a reaction.
Reactions that approach equilibrium.
6.1 Research Direction: Electron transfer I: Energetics.
Derivative box Derivation of Marcus relationship.
Enzymes lower the activation energy.
6.2 Research Directions: Dynamics in enzyme mechanism.
6.3 Research direction: The RNA world.
7. The Boltzmann distribution and statistical thermodynamics.
7.1 Research Direction: Protein folding and prions.
8. Quantum theory: Introduction and principles.
Experimental failures of classical physics.
Principles of quantum theory.
Wave Particle Duality.
General approach for solving Schrödinger’s equation.
Interpretation of quantum mechanics.
Heisenberg Uncertainty Principle.
A quantum mechanical world.
8.1 Research Direction: Schrödinger’s cat.
9. Particle in box and tunneling.
One-dimensional particle in the box.
Properties of the solutions.
Energy and wavefunction.
Average or expectation value.
9.1 Research Direction: Carotenoids.
Two-dimensional particle in a box.
9.2 Research Direction: Probing biological membranes.
9.3 Research Direction: Electron transfer II: Distance dependence.
10. Vibrational motion and infrared spectroscopy.
Simple Harmonic Oscillator: Classical theory.
Potential energy for the simple harmonic oscillator.
Simple Harmonic Oscillator: Quantum theory.
Derivative box: Solving Schrodinger’s equation for the simple harmonic oscillator.
Properties of the wavefunctions.
Energy and wavefunction.
10.1Research Direction: Hydrogenase.
11. Atomic structure: Hydrogen atom and Multi-electron atoms.
Schrodinger’s equation for the hydrogen atom.
Derivative box: Solving Schrodinger’s equation for the hydrogen.
Separation of variables.
Properties of the general solution.
11.1 Research Direction: Hydrogen economy.
Derivative box:Relativistic equations.
Many electron atoms.
Self-consistent field theory (Hartree-Fock).
12. Chemical bonds and protein interactions.
Schrodingers’ equation for the hydrogen molecule.
Interactions in proteins.
Determination of secondary structure using circular dichroism.
12.1 Research Direction: Modeling protein structures.
13. Electronic Transitions and optical spectroscopy.
The nature of light.
The Beer-Lambert law.
Derivation box: Relationship between the Einstein coefficient.
Franck Condon Principle.
The Relationship Between Emission and Absorption Spectra.
The yield of fluorescence.
Fluorescence Resonance Energy Transfer: FRET.
13.1 Research Direction: Probing Energy transfer using 2D optical spectroscopy.
13.2 Research Direction: Single molecule spectroscopy.
14. X-ray diffraction and EXAFS.
Diffraction from Crystals.
Derivative box: Phases of complex numbers.
Experimental measurement of X-ray diffraction.
Examples of protein structures.
14.1 Research Direction: Nitrogenase.
15. Magnetic resonance.
Nuclear magnetic resonance.
Two dimensional NMR:Nuclear Overhauser effect.
NMR spectra of amino acids.
15.1 Research Direction: Development of new NMR techniques.
15.2 Research Direction: Spinal Muscular Atrophy.
Magnetic Resonance Imaging (MRI).
Electron Spin Resonance.
15.3 Research Direction: heme proteins.
15.4 Research Direction: ribonucleotide reductase.
16. Signal transduction.
Biochemical pathway for visual response.
Spectroscopic studies of rhodopsin.
Comparison of rhodopsins from different organisms.
Rhodopsin proteins in visual response.
17. Membrane potentials, transporters, and channels.
Energetics of transport across membranes.
18. Molecular imaging.
Green fluorescent protein,GFP.
Mechanism of chromophore formation.
FRET: fluorescence resonance energy transfer.
Imaging of GFP in cells.
Imaging in organisms.
Positron emission tomography.
Energy transfer and light-harvesting complexes.
Electron transfer, bacterial reaction centers, and photosystem I.
Library of Congress subject headings for this publication: