Physical Methods for Inorganic Biochemistry

This volume is intended for students and professionals in diverse areas of the biological and biochemical sciences. It is oriented to those who are unfamiliar with the use of physical methods in studies of the biological elements. We hope the reader will find the material a helpful reference for other volumes of this series as well as the general literature, and some may see ways to adopt these techniques in their own pursuits. Every effort has been made to avoid an abstruse presentation. It should be clear that one individual cannot be expert in all the disciplines considered here (and the authors recognize that fact with sin­ cere humility). As may be expected of an introductory reference, most of our attention was focused on the commonly used methods. To balance this, we have included a few examples of approaches which are promising but relatively undeveloped at this time. Also, an emphasis has been placed on element selectivity. It is impossible to envision the course of future events, and a volume which deals with instrumentation is especially prone to become outdated. Nevertheless, any valid approach to a scientific question should be applicable indefinitely.

1. Introduction.- 1.1 Physical Methods.- 1.1.1 Nuclei.- 1.1.2 Electrons.- 1.1.3 Bonding Framework.- 1.1.4 Whole Molecule Methods.- 1.1.5 Kinetic Methods.- 1.2 Probable Future Trends in Physical Instrumentation.- 1.2.1 Double Resonance Methods.- 1.2.2 Dedicated Computers.- References.- 2. Nuclear Magnetic Resonance (Nmr).- 2.1 The Phenomenon.- 2.2 Multinuclear Nmr.- 2.3 Nmr Phenomena Related to Molecular Structure.- 2.3.1 Chemical Shifts.- 2.3.2 Linewidths.- 2.3.3 Spin-Spin Coupling Patterns and Coupling Constants (J).- 2.4 Instrument Characteristics.- 2.4.1 Dispersion.- 2.4.2 Resolution.- 2.4.3 Sensitivity.- 2.4.4 Data Acquisition.- 2.5 Sample Manipulation (Two-Way Communication).- 2.5.1 Multiple Resonance Methods.- 2.5.2 Nuclear Overhauser Effect.- 2.5.3 High-Resolution Nmr Measurements in Crystalline and Liquid Crystalline Phases.- 2.5.4 Spin System Manipulation with Multiple RF Pulses and Cross Polarization.- 2.5.5 Spinning at the “Magic Angle”.- 2.5.6 Other Line-narrowing Methods.- 2.6 Biological Considerations.- 2.6.1 Sample Preparation.- 2.6.2 Strong Field Effects.- 2.7 Applications of Nmr to the Biological Elements.- 2.7.1 Nonmetal and Main Group Elements.- 2.7.2 Metal Ions.- 2.7.3 Nmr Spectra of Small Molecules in Binding Interactions with Biopolymers.- 2.7.4 Newer Developments in Nmr.- References.- Appendix A: Correlation Nmr.- Appendix B: Mathematical Symbols Used in Chapter 2.- 3. Nuclear Quadrupole Resonance (Nqr).- 3.1 Properties of Nqr.- 3.2 Relationship to Mössbauer, Esr, and Nmr Spectroscopy.- 3.3 Instrumentation.- 3.4 Applications.- 3.4.1 17O-Nqr.- 3.4.2 Nqr/Infrared Double Resonance.- 3.4.3 Nqr Studies with 14N and 127I.- 3.4.4 Biologically Oriented Studies with 35C1.- 3.4.5 Other Potential Applications of Nqr.- References.- 4. Mössbauer Spectroscopy.- 4.1 Instrumentation.- 4.2 Conversion Electron Detection.- 4.3 Sample Considerations.- 4.4 Mössbauer Effect and the Chemical Environment.- 4.4.1 Isomer Shifts, ? (Also Known as Chemical Shifts).- 4.4.2 Magnetic Effects.- 4.4.3 Quadrupole Splitting (?EQ).- 4.4.4 Linewidth and Lineshape.- 4.5 Biological Applications of 57Fe.- 4.5.1 Iron Porphyrin Structures.- 4.5.2 Nonheme Iron.- 4.5.3 More Complex Entities.- 4.6 Mössbauer Isotopes Other than 57Fe.- 4.7 Mössbauer Emission Spectra.- 4.8 Bragg Scattering Effects.- References.- 5. Electron Spin Resonance (Esr).- 5.1 Introduction.- 5.2 Theory.- 5.2.1 Esr and Molecular Structure.- 5.2.2 Hyperfine Splitting Effects.- 5.2.3 The g-Tensor.- 5.2.4 High-Spin and Low-Spin Complexes.- 5.2.5 Linewidth Effects.- 5.3 Esr Instrumentation.- 5.3.1 Double Resonance Methods: ENDOR.- 5.3.2 ELDOR.- 5.4 Applications.- 5.4.1 Naturally Occurring Ions and Radicals.- 5.4.2 Copper Proteins.- 5.4.3 Esr Studies of Iron: Heme Iron.- 5.4.4 Esr Properties of an Oxidoreductase Containing Both Heme and Nonheme Iron.- 5.4.5 Manganese.- 5.4.6 Isotope Substitutions Which Identify Elements Associated with Paramagnetism.- 5.4.7 Metal Ion Replacements.- 5.4.8 ENDOR Applications.- 5.4.9 Biological Studies with Spin Labels.- 5.4.10 Esr Trends.- References.- 6. X-ray Diffraction Methods for the Analysis of Metalloproteins.- 6.1 Introduction.- 6.1.1 Perspective.- 6.1.2 Scope.- 6.2 Theoretical Basis.- 6.2.1 Crystal Properties.- 6.2.2 Diffraction Theory.- 6.2.3 Structure Factor Equation.- 6.2.4 Electron Density Equation.- 6.3 Experimental Procedures.- 6.3.1 Crystallization.- 6.3.2 Preparation of Heavy-Atom Derivatives.- 6.3.3 Data Measurement.- 6.4 Structural Analysis.- 6.4.1 Phase Determination.- 6.4.2 Map Interpretation and Model Building.- 6.4.3 Refinement.- 6.5 Applications.- References.- 7. Electron Energy Levels: Electron Spectroscopy and Related Methods.- 7.1 Electron Spectroscopy for Chemical Analysis (ESCA) and Ultraviolet Photoelectron Spectroscopy (UPS).- 7.1.1 Instrumentation for Producing Photoelectron Spectra.- 7.1.2 Koopmans’ Theorem.- 7.1.3 Empirical Correlations between Atomic Type and Inner Shell Ionization Energy.- 7.1.4 The “Direction” of Binding Energy Shifts in ESCA.- 7.1.5 Correlations between Photoelectron, Nmr, and Mössbauer Chemical Shifts.- 7.1.6 Lineshapes of Photoelectron Energy Levels.- 7.1.7 Sample Requirements for ESCA and UPS.- 7.1.8 Biological Applications of Photoelectron Spectroscopy.- 7.1.9 Core Electron Energies and Shifts in Biomolecules.- 7.1.10 Satellite Peaks.- 7.1.11 Line Intensities.- 7.1.12 Calibration Standards.- 7.1.13 Signal Improvement Methods.- 7.2 Auger (Secondary Electron) Spectroscopy.- 7.2.1 Loss Peaks.- 7.2.2 Auger Electrons.- 7.2.3 Auger Instrumentation.- 7.2.4 Potential Biological Applications of Auger Spectroscopy.- 7.2.5 Auger Imaging Methods (Scanning Auger Microscopy, SAM).- References.- 8. Laser Applications: Resonance Raman (RR) Spectroscopy and Related Methods.- 8.1 Perspective.- 8.2 Resonance Raman (RR) Spectroscopy.- 8.3 Sample Considerations.- 8.4 Symmetry and the Intensity of Vibrational Absorptions.- 8.5 Vibrational Energy Levels.- 8.6 Applications.- 8.6.1 Conventional Raman Spectroscopy (Excitation Away from Absorption Bands).- 8.6.2 Resonance Raman Applications.- 8.7 Newer Methods Which Minimize Fluorescence Interference.- 8.7.1 Coherent Anti-Stokes Raman Spectroscopy (CARS) or Four-Wave Mixing Spectroscopy.- 8.7.2 Time-Resolved Raman Spectroscopy.- References.- 9. Circular Dichroism (CD) and Magnetic Circular Dichroism (MCD).- 9.1 The Relationship between ORD, CD, MORD, and MCD.- 9.1.1 Optical Rotatory Dispersion (ORD).- 9.1.2 Circular Dichroism (CD).- 9.1.3 Magnetic Optical Rotatory Dispersion (MORD) and Magnetic Circular Dichroism (MCD).- 9.2 Sample Considerations.- 9.3 Effects Observed in MCD Spectra.- 9.3.1 A-Term Spectra.- 9.3.2 B-Term Spectra.- 9.3.3 C-Term Spectra.- 9.3.4 MCD Spectra of Optically Active Chromophores.- 9.4 Biochemical Applications.- 9.4.1 Sample Preparations.- 9.4.2 MCD and Heme Structures.- 9.4.3 Iron-Sulfur Cluster Proteins.- 9.4.4 d-Electron Transitions in the Blue Copper Proteins.- 9.4.5 Extrinsic Probes and MCD Effects.- 9.4.6 MCD Studies of Systems Which Do Not Contain Paramagnetic Metal Ions.- References.- 10. Kinetic Methods.- 10.1 Introduction.- 10.2 Methods.- 10.2.1 Flow Techniques.- 10.2.2 Flash Photolysis and Related Techniques.- 10.2.3 Chemical Relaxation Methods.- 10.2.4 Spectroscopic Line Broadening and Lineshape Effects Related to Species Lifetime, the Uncertainty Principle, and Exchange Equilibria.- 10.2.5 Other Kinetic Methods.- 10.2.6 Choice of Detection Methods.- 10.3 Applications.- 10.3.1 Enzyme Kinetics.- 10.3.2 Blue Copper Enzymes.- 10.3.3 In Vivo Kinetic Studies of the Role of Elements.- 10.3.4 Substitution Experiments.- 10.3.5 Paramagnetism.- 10.3.6 Inhibitors.- 10.3.7 Temperature Jump Characterizations.- 10.3.8 Circular Dichroism.- 10.3.9 Chelators.- References.- 11. Bioinorganic Topochemistry: Microprobe Methods of Analysis.- 11.1 Electron Probe Microanalysis.- 11.1.1 Introduction.- 11.1.2 Applications.- 11.2 Ion, Laser, and Proton Microprobe Analysis of Elements.- References.- 12. Neutron Activation Analysis.- 12.1 Introduction.- 12.2 Applications and Examples of Neutron Activation.- References.