Vibrational Spectroscopy in Life Science / Edition 1

Vibrational Spectroscopy in Life Science / Edition 1

by Friedrich Siebert, Peter Hildebrandt
     
 

ISBN-10: 3527405062

ISBN-13: 9783527405060

Pub. Date: 12/21/2007

Publisher: Wiley

The authors describe basic theoretical concepts of vibrational spectroscopy, address instrumental aspects and experimental procedures, and discuss experimental and theoretical methods for interpreting vibrational spectra. It is shown how vibrational spectroscopy provides information on general aspects of proteins, such as structure, dynamics, and protein folding.

Overview

The authors describe basic theoretical concepts of vibrational spectroscopy, address instrumental aspects and experimental procedures, and discuss experimental and theoretical methods for interpreting vibrational spectra. It is shown how vibrational spectroscopy provides information on general aspects of proteins, such as structure, dynamics, and protein folding. In addition, the authors use selected examples to demonstrate the application of Raman and IR spectroscopy to specific biological systems, such as metalloproteins, and photoreceptors. Throughout, references to extensive mathematical and physical aspects, involved biochemical features, and aspects of molecular biology are set in boxes for easier reading.
Ideal for undergraduate as well as graduate students of biology, biochemistry, chemistry, and physics looking for a compact introduction to this field.

Product Details

ISBN-13:
9783527405060
Publisher:
Wiley
Publication date:
12/21/2007
Series:
Tutorials in Biophysics Series
Pages:
320
Product dimensions:
6.97(w) x 9.69(h) x 0.80(d)

Table of Contents

Preface IX

1 Introduction 1

1.1 Aims of Vibrational Spectroscopy in Life Sciences 2

1.2 Vibrational Spectroscopy – An Atomic-scale Analytical Tool 3

1.3 Biological Systems 4

1.4 Scope of the Book 7

1.5 Further Reading 9

References 10

2 Theory of Infrared Absorption and Raman Spectroscopy 11

2.1 Molecular Vibrations 12

2.1.1 Normal Modes 15

2.1.2 Internal Coordinates 18

2.1.3 The FG-Matrix 19

2.1.4 Quantum Chemical Calculations of the FG-Matrix 23

2.2 Intensities of Vibrational Bands 25

2.2.1 Infrared Absorption 25

2.2.2 Raman Scattering 28

2.2.3 Resonance Raman Effect 32

2.3 Surface Enhanced Vibrational Spectroscopy 38

2.3.1 Surface Enhanced Raman Effect 39

2.3.2 Surface Enhanced Infrared Absorption 43

References 60

3 Instrumentation 63

3.1 Infrared Spectroscopy 63

3.1.1 Fourier Transform Spectroscopy 64

3.1.1.1 Interferometer 67

3.1.1.2 Infrared Detectors 69

3.1.2 Advantages of Fourier Transform Infrared Spectroscopy 70

3.1.3 Optical Devices: Mirrors or Lenses? 71

3.1.4 Instrumentation for Time-resolved Infrared Studies 72

3.1.4.1 Time-resolved Rapid-scan Fourier Transform Infrared Spectroscopy 72

3.1.4.2 Time-resolved Studies Using Tunable Monochromatic Infrared Sources 74

3.1.4.3 Time-resolved Fourier Transform Infrared Spectroscopy Using the Step-scan Method 74

3.1.5 Time-resolved Pump-probe Studies with Sub-nanosecond Time-resolution 76

3.2 Raman Spectroscopy 79

3.2.1 Laser 80

3.2.1.1 Laser Beam Properties 81

3.2.1.2 Optical Set-up 83

3.2.2 Spectrometer and Detection Systems 84

3.2.2.1 Monochromators 84

3.2.2.2 Spectrographs 86

3.2.2.3 Confocal Spectrometers 87

3.2.2.4 Fourier Transform Raman Interferometers 89

References 97

4 Experimental Techniques 99

4.1 Inherent Problems of Infrared and Raman Spectroscopy in Life Sciences 99

4.1.1 The ‘‘Water’’ Problem in Infrared Spectroscopy 99

4.1.2 Unwanted Photophysical and Photochemical Processes in Raman Spectroscopy 101

4.1.2.1 Fluorescence and Raman Scattering 102

4.1.2.2 Photoinduced Processes 104

4.2 Sample Arrangements 105

4.2.1 Infrared Spectroscopy 106

4.2.1.1 Sandwich Cuvettes for Solution Studies 106

4.2.1.2 The Attenuated Total Reflection (ATR) Method 108

4.2.1.3 Electrochemical Cell for Infrared Spectroscopy 113

4.2.2 Raman and Resonance Raman Spectroscopy 116

4.2.2.1 Measurements in Solutions 116

4.2.2.2 Solid State and Low-temperature Measurements 117

4.3 Surface Enhanced Vibrational Spectroscopy 118

4.3.1 Colloidal Suspensions 119

4.3.2 Massive Electrodes in Electrochemical Cells 120

4.3.3 Metal Films Deposited on ATR Elements 122

4.3.4 Metal/Electrolyte Interfaces 123

4.3.5 Adsorption-induced Structural Changes of Biopolymers 127

4.3.6 Biocompatible Surface Coatings 128

4.3.7 Tip-enhanced Raman Scattering 130

4.4 Time-resolved Vibrational Spectroscopic Techniques 131

4.4.1 Pump–Probe Resonance Raman Experiments 132

4.4.1.1 Continuous-wave Excitation 133

4.4.1.2 Pulsed-laser Excitation 138

4.4.1.3 Photoinduced Processes with Caged Compounds 141

4.4.2 Rapid Mixing Techniques 141

4.4.2.1 Rapid Flow 144

4.4.2.2 Rapid Freeze–Quench 145

4.4.3 Relaxation Methods 146

4.4.4 Spatially Resolved Vibrational Spectroscopy 148

4.5 Analysis of Spectra 149

References 151

5 Structural Studies 155

5.1 Basic Considerations 155

5.2 Practical Approaches 158

5.3 Studies on the Origin of the Sensitivity of Amide I Bands to Secondary Structure 161

5.4 Direct Measurement of the Interaction of the Amide I Oscillators 167

5.5 UV-resonance Raman Studies Using the Amide III Mode 169

5.6 Protein Folding and Unfolding Studies Using Vibrational Spectroscopy 171

References 178

6 Retinal Proteins and Photoinduced Processes 181

6.1 Rhodopsin 183

6.1.1 Resonance Raman Studies of Rhodopsin 185

6.1.2 Resonance Raman Spectra of Bathorhodopsin 188

6.1.3 Fourier Transform Infrared Studies of the Activation Mechanism of Rhodopsin 195

6.1.3.1 Low-temperature Photoproducts 197

6.1.3.2 The Active State Metarhodopsin II (MII) 201

6.2 Infrared Studies of the Light-driven Proton Pump Bacteriorhodopsin 206

6.3 Study of the Anion Uptake by the Retinal Protein Halorhodopsin Using ATR Infrared Spectroscopy 214

6.4 Infrared Studies Using Caged Compounds as the Trigger Source 217

References 222

7 Heme Proteins 227

7.1 Vibrational Spectroscopy of Metalloporphyrins 228

7.1.1 Metalloporphyrins Under D4h Symmetry 228

7.1.2 Symmetry Lowering 231

7.1.3 Axial Ligation 232

7.1.4 Normal Mode Analyses 233

7.1.5 Empirical Structure–Spectra Relationships 234

7.2 Hemoglobin and Myoglobin 236

7.2.1 Vibrational Analysis of the Heme Cofactor 237

7.2.2 Iron–Ligand and Internal Ligand Modes 239

7.2.3 Probing Quaternary Structure Changes 240

7.3 Cytochrome c – a Soluble Electron-transferring Protein 244

7.3.1 Vibrational Assignments 245

7.3.2 Redox Equilibria in Solution 246

7.3.3 Conformational Equilibria and Dynamics 248

7.3.4 Redox and Conformational Equilibria in the Immobilised State 253

7.3.5 Electron Transfer Dynamics and Mechanism 260

7.3.6 The Relevance of Surface-enhanced Vibrational Spectroscopic Studies for Elucidating Biological Functions 267

7.4 Cytochrome c Oxidase 268

7.4.1 Resonance Raman Spectroscopy 268

7.4.2 Redox Transitions 271

7.4.3 Catalytic Cycle 274

7.4.4 Oxidases from Extremophiles and Archaea 277

References 278

8 Non-heme Metalloproteins 283

8.1 Copper Proteins 284

8.2 Iron–Sulfur Proteins 290

8.3 Di-iron Proteins 296

8.4 Hydrogenases 300

References 302

Index 305

Customer Reviews

Average Review:

Write a Review

and post it to your social network

     

Most Helpful Customer Reviews

See all customer reviews >