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Vibrational Spectroscopy in Life Science
Siebert, Friedich
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Últimas novedades
bioquímica
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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.
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Preface.
1 Introduction.
1.1 Aims of Vibrational Spectroscopy in Life Sciences.
1.2 Vibrational Spectroscopy – An Atomic-scale Analytical Tool.
1.3 Biological Systems.
1.4 Scope of the Book.
1.5 Further Reading.
References.
2 Theory of Infrared Absorption and Raman Spectroscopy.
2.1 Molecular Vibrations.
2.1.1 Normal Modes.
2.1.2 Internal Coordinates.
2.1.3 The FG-Matrix.
2.1.4 Quantum Chemical Calculations of the FG-Matrix.
2.2 Intensities of Vibrational Bands.
2.2.1 Infrared Absorption.
2.2.2 Raman Scattering.
2.2.3 Resonance Raman Effect.
2.3 Surface Enhanced Vibrational Spectroscopy.
2.3.1 Surface Enhanced Raman Effect.
2.3.2 Surface Enhanced Infrared Absorption.
References.
3 Instrumentation.
3.1 Infrared Spectroscopy.
3.1.1 Fourier Transform Spectroscopy.
3.1.1.1 Interferometer.
3.1.1.2 Infrared Detectors.
3.1.2 Advantages of Fourier Transform Infrared Spectroscopy.
3.1.3 Optical Devices: Mirrors or Lenses?
3.1.4 Instrumentation for Time-resolved Infrared Studies.
3.1.4.1 Time-resolved Rapid-scan Fourier Transform Infrared Spectroscopy.
3.1.4.2 Time-resolved Studies Using Tunable Monochromatic Infrared Sources.
3.1.4.3 Time-resolved Fourier Transform Infrared Spectroscopy Using the Step-scan Method.
3.1.5 Time-resolved Pump-probe Studies with Sub-nanosecond Time-resolution.
3.2 Raman Spectroscopy.
3.2.1 Laser.
3.2.1.1 Laser Beam Properties.
3.2.1.2 Optical Set-up.
3.2.2 Spectrometer and Detection Systems.
3.2.2.1 Monochromators.
3.2.2.2 Spectrographs.
3.2.2.3 Confocal Spectrometers.
3.2.2.4 Fourier Transform Raman Interferometers.
References.
4 Experimental Techniques.
4.1 Inherent Problems of Infrared and Raman Spectroscopy in Life Sciences.
4.1.1 The ‘‘Water’’ Problem in Infrared Spectroscopy.
4.1.2 Unwanted Photophysical and Photochemical Processes in Raman Spectroscopy.
4.1.2.1 Fluorescence and Raman Scattering.
4.1.2.2 Photoinduced Processes.
4.2 Sample Arrangements.
4.2.1 Infrared Spectroscopy.
4.2.1.1 Sandwich Cuvettes for Solution Studies.
4.2.1.2 The Attenuated Total Reflection (ATR) Method.
4.2.1.3 Electrochemical Cell for Infrared Spectroscopy.
4.2.2 Raman and Resonance Raman Spectroscopy.
4.2.2.1 Measurements in Solutions.
4.2.2.2 Solid State and Low-temperature Measurements.
4.3 Surface Enhanced Vibrational Spectroscopy.
4.3.1 Colloidal Suspensions.
4.3.2 Massive Electrodes in Electrochemical Cells.
4.3.3 Metal Films Deposited on ATR Elements.
4.3.4 Metal/Electrolyte Interfaces.
4.3.5 Adsorption-induced Structural Changes of Biopolymers.
4.3.6 Biocompatible Surface Coatings.
4.3.7 Tip-enhanced Raman Scattering.
4.4 Time-resolved Vibrational Spectroscopic Techniques.
4.4.1 Pump–Probe Resonance Raman Experiments.
4.4.1.1 Continuous-wave Excitation.
4.4.1.2 Pulsed-laser Excitation.
4.4.1.3 Photoinduced Processes with Caged Compounds.
4.4.2 Rapid Mixing Techniques.
4.4.2.1 Rapid Flow.
4.4.2.2 Rapid Freeze–Quench.
4.4.3 Relaxation Methods.
4.4.4 Spatially Resolved Vibrational Spectroscopy.
4.5 Analysis of Spectra.
References.
5 Structural Studies.
5.1 Basic Considerations.
5.2 Practical Approaches.
5.3 Studies on the Origin of the Sensitivity of Amide I Bands to Secondary Structure.
5.4 Direct Measurement of the Interaction of the Amide I Oscillators.
5.5 UV-resonance Raman Studies Using the Amide III Mode.
5.6 Protein Folding and Unfolding Studies Using Vibrational Spectroscopy.
References.
6 Retinal Proteins and Photoinduced Processes.
6.1 Rhodopsin.
6.1.1 Resonance Raman Studies of Rhodopsin.
6.1.2 Resonance Raman Spectra of Bathorhodopsin.
6.1.3 Fourier Transform Infrared Studies of the Activation Mechanism of Rhodopsin.
6.1.3.1 Low-temperature Photoproducts.
6.1.3.2 The Active State Metarhodopsin II (MII).
6.2 Infrared Studies of the Light-driven Proton Pump Bacteriorhodopsin.
6.3 Study of the Anion Uptake by the Retinal Protein Halorhodopsin Using ATR Infrared Spectroscopy.
6.4 Infrared Studies Using Caged Compounds as the Trigger Source.
References.
7 Heme Proteins.
7.1 Vibrational Spectroscopy of Metalloporphyrins.
7.1.1 Metalloporphyrins Under D4h Symmetry.
7.1.2 Symmetry Lowering.
7.1.3 Axial Ligation.
7.1.4 Normal Mode Analyses.
7.1.5 Empirical Structure–Spectra Relationships.
7.2 Hemoglobin and Myoglobin.
7.2.1 Vibrational Analysis of the Heme Cofactor.
7.2.2 Iron–Ligand and Internal Ligand Modes.
7.2.3 Probing Quaternary Structure Changes.
7.3 Cytochrome c – a Soluble Electron-transferring Protein.
7.3.1 Vibrational Assignments.
7.3.2 Redox Equilibria in Solution.
7.3.3 Conformational Equilibria and Dynamics.
7.3.4 Redox and Conformational Equilibria in the Immobilised State.
7.3.5 Electron Transfer Dynamics and Mechanism.
7.3.6 The Relevance of Surface-enhanced Vibrational Spectroscopic Studies for Elucidating Biological Functions.
7.4 Cytochrome c Oxidase.
7.4.1 Resonance Raman Spectroscopy.
7.4.2 Redox Transitions.
7.4.3 Catalytic Cycle.
7.4.4 Oxidases from Extremophiles and Archaea.
References.
8 Non-heme Metalloproteins.
8.1 Copper Proteins.
8.2 Iron–Sulfur Proteins.
8.3 Di-iron Proteins.
8.4 Hydrogenases.
References.
Index.
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