Max DiemNortheastern University, USA

“Graduate students who are entering the complex and rapidly developing field of vibrational biospectroscopy or microscopy would find this book useful. Experienced scientists and instructors in vibrational spectroscopy and microspectroscopy will also find this book a valuable reference for their work.”  (Optics & Photonics News, 1 January 2016)

• Preface xvPreface to ‘Introduction to Modern Vibrational Spectroscopy’ (1994) xixI Modern Vibrational Spectroscopy and Micro-spectroscopy: Theory, Instrumentation and Biomedical Applications 1I. 1 Historical Perspective of Vibrational Spectroscopy 1I. 2 Vibrational Spectroscopy within Molecular Spectroscopy 2References 41 Molecular Vibrational Motion 51.1 The concept of normal modes of vibration 61.2 The separation of vibrational, translational, and rotational coordinates 61.3 Classical vibrations in mass-weighted Cartesian displacement coordinates 71.4 Quantum mechanical description of molecular vibrations 131.4.1 Transition from classical to quantum mechanical description 131.4.2 Diatomic molecules: harmonic oscillator 141.4.3 Diatomic molecules: anharmonicity 191.4.4 Polyatomic molecules 201.5 Time-dependent description and the transition moment 221.5.1 Time-dependent perturbation of stationary states by electromagnetic radiation 221.5.2 The vibrational transition moment for absorption: harmonic diatomic molecules 251.5.3 The vibrational transition moment for absorption: anharmonic diatomic molecules 271.5.4 The vibrational transition moment for absorption: polyatomic molecules 301.5.5 Isotopic effects: diatomic molecules 311.6 Basic infrared and Raman spectroscopies 321.6.1 Infrared absorption spectroscopy 321.6.2 Raman (scattering) spectroscopy 351.7 Concluding remarks 38References 382 Symmetry Properties of Molecular Vibrations 392.1 Symmetry operations and symmetry groups 402.2 Group representations 442.3 Symmetry representations of molecular vibrations 502.4 Symmetry-based selection rules for absorption processes 542.5 Selection rules for Raman scattering 562.6 Discussion of selected small molecules 572.6.1 Tetrahedral molecules: carbon tetrachloride, CCl4 , and methane, CH4 572.6.2 Chloroform and methyl chloride 642.6.3 Dichloromethane (methylene chloride), CH2 Cl2 672.6.4 Dichloromethane-d1 (methylene chloride-d1), CHDCl2 68References 693 Infrared Spectroscopy 713.1 General aspects of IR spectroscopy 713.2 Instrumentation 733.2.1 Sources of infrared radiation: black body sources 733.2.2 Sources of infrared radiation: quantum-cascade lasers, nonlinear devices 753.2.3 Transfer optics 763.2.4 Color sorting devices: monochromators 763.2.5 Color encoding devices: interferometers 793.2.6 Detectors 823.2.7 Read-out devices 843.3 Methods in interferometric IR spectroscopy 843.3.1 General instrumentation 843.3.2 Optical resolution 863.3.3 Zero filling and fourier smoothing 863.3.4 Phase correction 883.3.5 Apodization 913.4 Sampling strategies 923.4.1 Transmission measurement 923.4.2 Specular reflection 943.4.3 Diffuse reflection 953.4.4 Attenuated total reflection 973.4.5 Infrared reflection absorption spectroscopy (IRRAS) 993.4.6 Fourier transform photoacoustic spectroscopy (FT-PAS) 1003.4.7 Planar array infrared spectroscopy (PA-IRS) 1013.4.8 Two-dimensional FTIR 1013.4.9 Infrared microspectroscopy 102References 1024 Raman Spectroscopy 1034.1 General aspects of Raman spectroscopy 1044.2 Polarizability 1054.3 Polarization of Raman scattering 1074.4 Dependence of depolarization ratios on scattering geometry 1114.5 A comparison between Raman and fluorescence spectroscopy 1144.6 Instrumentation for Raman spectroscopy 1164.6.1 Sources 1164.6.2 Dispersive Raman instrumentation and multichannel detectors 1164.6.3 Interferometric Raman instrumentation 1214.6.4 Raman microspectroscopy 122References 1225 A Deeper Look at Details in Vibrational Spectroscopy 1235.1 Fermi resonance 1245.2 Transition dipole coupling (TDC) 1285.3 Group frequencies 1295.4 Rot-vibrational spectroscopy 1305.4.1 Classical rotational energy 1305.4.2 Quantum mechanics of rotational spectroscopy 1325.4.3 Rot-vibrational transitions 137References 1416 Special Raman Methods: Resonance, Surface-Enhanced, and Nonlinear Raman Techniques 1436.1 Resonance Raman spectroscopy 1446.2 Surface-enhanced Raman scattering (SERS) 1466.3 Nonlinear Raman effects 1496.3.1 Spontaneous (incoherent) nonlinear Raman effects 1496.3.2 Coherent nonlinear effects 1526.4 Continuous wave and pulsed lasers 1596.4.1 Einstein coefficients and population inversion 1606.4.2 Operation of a gas laser 1626.4.3 Principles of pulsed lasers 1636.4.4 Operation of pulsed lasers 1636.5 Epilogue 164References 1647 Time-Resolved Methods in Vibrational Spectroscopy 1677.1 General remarks 1677.2 Time-resolved FT infrared (TR-FTIR) spectroscopy 1687.2.1 Experimental aspects 1687.2.2 Applications of TR-FTIR spectroscopy 1697.3 Time-resolved Raman and resonance Raman (TRRR) spectroscopy 1717.3.1 Instrumental aspects 1717.3.2 Applications of TRRR 1737.3.3 Heme group dynamic studies 1737.3.4 Rhodopsin studies 174References 1758 Vibrational Optical Activity 1778.1 Introduction to optical activity and chirality 1778.2 Infrared vibrational circular dichroism (VCD) 1798.2.1 Basic theory 1798.2.2 Exciton theory of optical activity 1808.3 Observation of VCD 1818.4 Applications of VCD 1858.4.1 VCD of biological molecules 1858.4.2 Small molecule VCD 1858.5 Raman optical activity 1868.6 Observation of ROA 1888.7 Applications of ROA 1898.7.1 ROA of biological molecules 1898.7.2 Small molecules ROA 190References 1909 Computation of Vibrational Frequencies and Intensities 1939.1 Historical approaches to the computation of vibrational frequencies 1939.2 Vibrational energy calculations 1949.2.1 Classical approaches: the Wilson GF matrix method 1949.2.2 Early computer-based vibrational analysis 1979.3 Ab initio quantum-mechanical normal coordinate computations 1979.4 Vibrational intensity calculations 1989.4.1 Fixed partial charge method for infrared intensities 1989.4.2 Quantum mechanical infrared and Raman intensities: localized molecular orbitals 2009.4.3 The finite perturbation method 200References 202II Biophysical and Medical Applications of Vibrational Spectroscopy and Microspectroscopy 20310 Biophysical Applications of Vibrational Spectroscopy 20510.1 Introduction 20510.2 Vibrations of the peptide linkage and of peptide models 20610.2.1 Amino acids and the peptide linkage 20610.2.2 The vibrational modes of the peptide linkage 20610.3 Conformational studies of peptides and polyamino acids 21010.4 Protein spectroscopy: IR, VCD, Raman, resonance Raman, and ROA spectra of proteins 21510.5 Nucleic acids 21910.5.1 Structure and function of nucleic acids 21910.5.2 Phosphodiester vibrations 22210.5.3 Ribose vibrations 22210.5.4 Base vibrations 22210.6 Conformational studies on DNA and DNA models using IR, Raman, and VCD spectroscopies 22310.7 Lipids and phospholipids 22710.8 Epilogue 231References 23111 Vibrational Microspectroscopy (MSP) 23511.1 General remarks 23511.2 General aspects of microscopy 23611.3 Raman microspectroscopy (RA-MSP) 23911.3.1 Dispersive (single point) systems 24011.3.2 Micro-Raman imaging systems 24111.4 CARS and FSRS microscopy 24211.5 Tip-enhanced Raman spectroscopy (TERS) 24311.6 Infrared microspectroscopy (IR-MSP) 24311.6.1 Fourier-transform infrared imaging systems 24411.6.2 QCL-based systems 24611.7 Sampling strategies for infrared microspectroscopy 24711.7.1 Transmission measurement 24711.7.2 Transflection measurement 24711.7.3 Attenuated total reflection (ATR) 24811.8 Infrared near-field microscopy 249References 24912 Data Preprocessing and Data Processing in Microspectral Analysis 25112.1 General remarks 25112.2 Data preprocessing 25212.2.1 Cosmic ray filtering (Raman data sets only) 25312.2.2 Linear wavenumber interpolation (Raman data sets only) 25312.2.3 Conversion from transmittance to absorbance units (some infrared data sets) 25312.2.4 Normalization 25312.2.5 Noise reduction 25412.2.6 Conversion of spectra to second derivatives 25612.3 Reduction of confounding spectral effects 25712.3.1 Reduction of water vapor contributions in cellular pixel spectra 25812.3.2 Mie and resonance Mie scattering 25812.3.3 Correction of dispersive band shapes 26012.3.4 Standing wave effect 26212.4 Unsupervised multivariate methods of data segmentation 26312.4.1 Factor methods 26412.4.2 Data segmentation by clustering methods 26912.5 Supervised multivariate methods 27212.5.1 Discussion of sensitivity, specificity, and accuracy 27212.5.2 Soft independent modeling of class analogy (SIMCA) 27312.5.3 Artificial neural networks (ANNs) 27412.5.4 Support vector machines (SVMs) 27512.5.5 Random forests (RFs) 27612.5.6 Cross-validation 27712.6 Summary of data processing for microspectral analysis 27812.7 Two-dimensional correlation methods in infrared spectroscopy (2D-IR) 278References 28013 Infrared Microspectroscopy of Cells and Tissue in Medical Diagnostics 28313.1 Introduction 28313.2 Spectral histopathology (SHP) 28413.2.1 Review of classical histopathology 28413.2.2 Spectral methods in histopathology 28513.2.3 Infrared absorption spectroscopy of cells and tissue: introductory comments 28513.3 Methodology for SHP 28713.3.1 General approach 28713.3.2 Sequence of steps in classical histopathology 28813.3.3 Sequence of steps for spectral histopathology 28813.4 Applications of SHP for the classification of primary tumors 29413.4.1 Cervical tissue and cervical cancer 29413.4.2 Lung cancer 29813.4.3 Prostate cancer 30313.4.4 Breast cancer 30413.5 Application of SHP toward the detection and classification of metastatic tumors 30413.5.1 Detection of colon cancer metastases in lymph nodes 30413.5.2 Detection of breast cancer metastases in lymph nodes 30613.5.3 Detection and classification of brain metastases 30713.6 Future prospects of SHP 30913.7 Infrared spectral cytopathology (SCP) 31013.7.1 Classical cytopathology 31113.7.2 Spectral cytopathology 31413.7.3 Methods for SCP 31413.8 SCP results 31613.8.1 Early results of SCP 31613.8.2 Fixation studies 31713.8.3 Spectral cytopathology of cervical mucosa 32013.8.4 Spectral cytopathology of the oral mucosa 32313.8.5 Spectral cytopathology of esophageal cells 32613.9 SCP of cultured cells 32813.9.1 Early SCP efforts and general results 32813.9.2 SCP of cultured cells to study the effects of the cell cycle and of drugs on cells 32813.10 Infrared spectroscopy of cells in aqueous media 33113.11 Future potential of SCP 333References 33314 Raman Microspectroscopy of Cells and Tissue in Medical Diagnostics 33914.1 Introduction 33914.2 Experimental Consideration for Raman Microspectroscopy 34114.3 High-Resolution Raman Spectral Cytopathology 34314.3.1 Subcellular organization 34314.3.2 Subcellular transport phenomena 34514.4 Low-Resolution Raman SCP of Cultured Cells In Vitro 34914.5 Raman SCP in Solution 35214.5.1 Optical tweezing of cells in aqueous media 35214.5.2 Cells trapped in microfluidic chips 35314.5.3 Resonance Raman spectroscopy of erythrocytes 35314.6 Raman Spectral Histopathology (Ra SHP) 35414.7 In Vivo Raman SHP 35614.8 Deep Tissue Raman SHP 35714.8.1 Hard tissue diagnostics 35714.8.2 Deep tissue imaging of breast tissue and lymph nodes 358References 35915 Summary and Epilogue 363Appendix A The Particle in a Box: A Demonstration of Quantum Mechanical Principles for a Simple, One-Dimensional, One-Electron Model System 365A. 1 Definition of the Model System 365A. 2 Solution of the Particle-in-a-Box Differential Equation 367A. 3 Orthonormality of the Particle-in-a-Box Wavefunctions 370A. 4 Dipole-Allowed Transitions for the Particle in a Box 370A. 5 Real-World PiBs 371Appendix B A summary of the Solution of the Harmonic Oscillator (Hermite) Differential Equation 373Appendix C Character Tables for Chemically Important Symmetry Groups 377C. 1 The nonaxial groups 377C. 2 The Cn groups 377C. 3 The Dn groups 379C. 4 The Cnv groups 379C. 5 The Dnh groups 382C. 6 The Dnd groups 384C. 7 The Sn groups 385C. 8 The cubic groups 386C. 9 The groups C∞, and D∞h for linear molecules 387C. 10 The icosahedral groups 388Appendix D Introduction to Fourier Series, the Fourier Transform, and the Fast Fourier Transform Algorithm 389D. 1 Data Domains 389D. 2 Fourier Series 390D. 3 Fourier Transform 392D. 4 Discrete and Fast Fourier Transform Algorithms 393References 395Appendix E List of Common Vibrational Group Frequencies (cm−1) 397Appendix F Infrared and Raman Spectra of Selected Cellular Components 399Index 405