Modern Vibrational Spectroscopy and Micro-Spectroscopy

Max Diem Northeastern University, USA

Preface xv

Preface to ‘Introduction to Modern Vibrational Spectroscopy’ (1994) xix

I Modern Vibrational Spectroscopy and Micro-spectroscopy: Theory, Instrumentation and Biomedical Applications 1

I. 1 Historical Perspective of Vibrational Spectroscopy 1

I. 2 Vibrational Spectroscopy within Molecular Spectroscopy 2

References 4

1 Molecular Vibrational Motion 5

1.1 The concept of normal modes of vibration 6

1.2 The separation of vibrational, translational, and rotational coordinates 6

1.3 Classical vibrations in mass-weighted Cartesian displacement coordinates 7

1.4 Quantum mechanical description of molecular vibrations 13

1.4.1 Transition from classical to quantum mechanical description 13

1.4.2 Diatomic molecules: harmonic oscillator 14

1.4.3 Diatomic molecules: anharmonicity 19

1.4.4 Polyatomic molecules 20

1.5 Time-dependent description and the transition moment 22

1.5.1 Time-dependent perturbation of stationary states by electromagnetic radiation 22

1.5.2 The vibrational transition moment for absorption: harmonic diatomic molecules 25

1.5.3 The vibrational transition moment for absorption: anharmonic diatomic molecules 27

1.5.4 The vibrational transition moment for absorption: polyatomic molecules 30

1.5.5 Isotopic effects: diatomic molecules 31

1.6 Basic infrared and Raman spectroscopies 32

1.6.1 Infrared absorption spectroscopy 32

1.6.2 Raman (scattering) spectroscopy 35

1.7 Concluding remarks 38

References 38

2 Symmetry Properties of Molecular Vibrations 39

2.1 Symmetry operations and symmetry groups 40

2.2 Group representations 44

2.3 Symmetry representations of molecular vibrations 50

2.4 Symmetry-based selection rules for absorption processes 54

2.5 Selection rules for Raman scattering 56

2.6 Discussion of selected small molecules 57

2.6.1 Tetrahedral molecules: carbon tetrachloride, CCl4 , and methane, CH4 57

2.6.2 Chloroform and methyl chloride 64

2.6.3 Dichloromethane (methylene chloride), CH2 Cl2 67

2.6.4 Dichloromethane-d1 (methylene chloride-d1), CHDCl2 68

References 69

3 Infrared Spectroscopy 71

3.1 General aspects of IR spectroscopy 71

3.2 Instrumentation 73

3.2.1 Sources of infrared radiation: black body sources 73

3.2.2 Sources of infrared radiation: quantum-cascade lasers, nonlinear devices 75

3.2.3 Transfer optics 76

3.2.4 Color sorting devices: monochromators 76

3.2.5 Color encoding devices: interferometers 79

3.2.6 Detectors 82

3.2.7 Read-out devices 84

3.3 Methods in interferometric IR spectroscopy 84

3.3.1 General instrumentation 84

3.3.2 Optical resolution 86

3.3.3 Zero filling and fourier smoothing 86

3.3.4 Phase correction 88

3.3.5 Apodization 91

3.4 Sampling strategies 92

3.4.1 Transmission measurement 92

3.4.2 Specular reflection 94

3.4.3 Diffuse reflection 95

3.4.4 Attenuated total reflection 97

3.4.5 Infrared reflection absorption spectroscopy (IRRAS) 99

3.4.6 Fourier transform photoacoustic spectroscopy (FT-PAS) 100

3.4.7 Planar array infrared spectroscopy (PA-IRS) 101

3.4.8 Two-dimensional FTIR 101

3.4.9 Infrared microspectroscopy 102

References 102

4 Raman Spectroscopy 103

4.1 General aspects of Raman spectroscopy 104

4.2 Polarizability 105

4.3 Polarization of Raman scattering 107

4.4 Dependence of depolarization ratios on scattering geometry 111

4.5 A comparison between Raman and fluorescence spectroscopy 114

4.6 Instrumentation for Raman spectroscopy 116

4.6.1 Sources 116

4.6.2 Dispersive Raman instrumentation and multichannel detectors 116

4.6.3 Interferometric Raman instrumentation 121

4.6.4 Raman microspectroscopy 122

References 122

5 A Deeper Look at Details in Vibrational Spectroscopy 123

5.1 Fermi resonance 124

5.2 Transition dipole coupling (TDC) 128

5.3 Group frequencies 129

5.4 Rot-vibrational spectroscopy 130

5.4.1 Classical rotational energy 130

5.4.2 Quantum mechanics of rotational spectroscopy 132

5.4.3 Rot-vibrational transitions 137

References 141

6 Special Raman Methods: Resonance, Surface-Enhanced, and Nonlinear Raman Techniques 143

6.1 Resonance Raman spectroscopy 144

6.2 Surface-enhanced Raman scattering (SERS) 146

6.3 Nonlinear Raman effects 149

6.3.1 Spontaneous (incoherent) nonlinear Raman effects 149

6.3.2 Coherent nonlinear effects 152

6.4 Continuous wave and pulsed lasers 159

6.4.1 Einstein coefficients and population inversion 160

6.4.2 Operation of a gas laser 162

6.4.3 Principles of pulsed lasers 163

6.4.4 Operation of pulsed lasers 163

6.5 Epilogue 164

References 164

7 Time-Resolved Methods in Vibrational Spectroscopy 167

7.1 General remarks 167

7.2 Time-resolved FT infrared (TR-FTIR) spectroscopy 168

7.2.1 Experimental aspects 168

7.2.2 Applications of TR-FTIR spectroscopy 169

7.3 Time-resolved Raman and resonance Raman (TRRR) spectroscopy 171

7.3.1 Instrumental aspects 171

7.3.2 Applications of TRRR 173

7.3.3 Heme group dynamic studies 173

7.3.4 Rhodopsin studies 174

References 175

8 Vibrational Optical Activity 177

8.1 Introduction to optical activity and chirality 177

8.2 Infrared vibrational circular dichroism (VCD) 179

8.2.1 Basic theory 179

8.2.2 Exciton theory of optical activity 180

8.3 Observation of VCD 181

8.4 Applications of VCD 185

8.4.1 VCD of biological molecules 185

8.4.2 Small molecule VCD 185

8.5 Raman optical activity 186

8.6 Observation of ROA 188

8.7 Applications of ROA 189

8.7.1 ROA of biological molecules 189

8.7.2 Small molecules ROA 190

References 190

9 Computation of Vibrational Frequencies and Intensities 193

9.1 Historical approaches to the computation of vibrational frequencies 193

9.2 Vibrational energy calculations 194

9.2.1 Classical approaches: the Wilson GF matrix method 194

9.2.2 Early computer-based vibrational analysis 197

9.3 Ab initio quantum-mechanical normal coordinate computations 197

9.4 Vibrational intensity calculations 198

9.4.1 Fixed partial charge method for infrared intensities 198

9.4.2 Quantum mechanical infrared and Raman intensities: localized molecular orbitals 200

9.4.3 The finite perturbation method 200

References 202

II Biophysical and Medical Applications of Vibrational Spectroscopy and Microspectroscopy 203

10 Biophysical Applications of Vibrational Spectroscopy 205

10.1 Introduction 205

10.2 Vibrations of the peptide linkage and of peptide models 206

10.2.1 Amino acids and the peptide linkage 206

10.2.2 The vibrational modes of the peptide linkage 206

10.3 Conformational studies of peptides and polyamino acids 210

10.4 Protein spectroscopy: IR, VCD, Raman, resonance Raman, and ROA spectra of proteins 215

10.5 Nucleic acids 219

10.5.1 Structure and function of nucleic acids 219

10.5.2 Phosphodiester vibrations 222

10.5.3 Ribose vibrations 222

10.5.4 Base vibrations 222

10.6 Conformational studies on DNA and DNA models using IR, Raman, and VCD spectroscopies 223

10.7 Lipids and phospholipids 227

10.8 Epilogue 231

References 231

11 Vibrational Microspectroscopy (MSP) 235

11.1 General remarks 235

11.2 General aspects of microscopy 236

11.3 Raman microspectroscopy (RA-MSP) 239

11.3.1 Dispersive (single point) systems 240

11.3.2 Micro-Raman imaging systems 241

11.4 CARS and FSRS microscopy 242

11.5 Tip-enhanced Raman spectroscopy (TERS) 243

11.6 Infrared microspectroscopy (IR-MSP) 243

11.6.1 Fourier-transform infrared imaging systems 244

11.6.2 QCL-based systems 246

11.7 Sampling strategies for infrared microspectroscopy 247

11.7.1 Transmission measurement 247

11.7.2 Transflection measurement 247

11.7.3 Attenuated total reflection (ATR) 248

11.8 Infrared near-field microscopy 249

References 249

12 Data Preprocessing and Data Processing in Microspectral Analysis 251

12.1 General remarks 251

12.2 Data preprocessing 252

12.2.1 Cosmic ray filtering (Raman data sets only) 253

12.2.2 Linear wavenumber interpolation (Raman data sets only) 253

12.2.3 Conversion from transmittance to absorbance units (some infrared data sets) 253

12.2.4 Normalization 253

12.2.5 Noise reduction 254

12.2.6 Conversion of spectra to second derivatives 256

12.3 Reduction of confounding spectral effects 257

12.3.1 Reduction of water vapor contributions in cellular pixel spectra 258

12.3.2 Mie and resonance Mie scattering 258

12.3.3 Correction of dispersive band shapes 260

12.3.4 Standing wave effect 262

12.4 Unsupervised multivariate methods of data segmentation 263

12.4.1 Factor methods 264

12.4.2 Data segmentation by clustering methods 269

12.5 Supervised multivariate methods 272

12.5.1 Discussion of sensitivity, specificity, and accuracy 272

12.5.2 Soft independent modeling of class analogy (SIMCA) 273

12.5.3 Artificial neural networks (ANNs) 274

12.5.4 Support vector machines (SVMs) 275

12.5.5 Random forests (RFs) 276

12.5.6 Cross-validation 277

12.6 Summary of data processing for microspectral analysis 278

12.7 Two-dimensional correlation methods in infrared spectroscopy (2D-IR) 278

References 280

13 Infrared Microspectroscopy of Cells and Tissue in Medical Diagnostics 283

13.1 Introduction 283

13.2 Spectral histopathology (SHP) 284

13.2.1 Review of classical histopathology 284

13.2.2 Spectral methods in histopathology 285

13.2.3 Infrared absorption spectroscopy of cells and tissue: introductory comments 285

13.3 Methodology for SHP 287

13.3.1 General approach 287

13.3.2 Sequence of steps in classical histopathology 288

13.3.3 Sequence of steps for spectral histopathology 288

13.4 Applications of SHP for the classification of primary tumors 294

13.4.1 Cervical tissue and cervical cancer 294

13.4.2 Lung cancer 298

13.4.3 Prostate cancer 303

13.4.4 Breast cancer 304

13.5 Application of SHP toward the detection and classification of metastatic tumors 304

13.5.1 Detection of colon cancer metastases in lymph nodes 304

13.5.2 Detection of breast cancer metastases in lymph nodes 306

13.5.3 Detection and classification of brain metastases 307

13.6 Future prospects of SHP 309

13.7 Infrared spectral cytopathology (SCP) 310

13.7.1 Classical cytopathology 311

13.7.2 Spectral cytopathology 314

13.7.3 Methods for SCP 314

13.8 SCP results 316

13.8.1 Early results of SCP 316

13.8.2 Fixation studies 317

13.8.3 Spectral cytopathology of cervical mucosa 320

13.8.4 Spectral cytopathology of the oral mucosa 323

13.8.5 Spectral cytopathology of esophageal cells 326

13.9 SCP of cultured cells 328

13.9.1 Early SCP efforts and general results 328

13.9.2 SCP of cultured cells to study the effects of the cell cycle and of drugs on cells 328

13.10 Infrared spectroscopy of cells in aqueous media 331

13.11 Future potential of SCP 333

References 333

14 Raman Microspectroscopy of Cells and Tissue in Medical Diagnostics 339

14.1 Introduction 339

14.2 Experimental Consideration for Raman Microspectroscopy 341

14.3 High-Resolution Raman Spectral Cytopathology 343

14.3.1 Subcellular organization 343

14.3.2 Subcellular transport phenomena 345

14.4 Low-Resolution Raman SCP of Cultured Cells In Vitro 349

14.5 Raman SCP in Solution 352

14.5.1 Optical tweezing of cells in aqueous media 352

14.5.2 Cells trapped in microfluidic chips 353

14.5.3 Resonance Raman spectroscopy of erythrocytes 353

14.6 Raman Spectral Histopathology (Ra SHP) 354

14.7 In Vivo Raman SHP 356

14.8 Deep Tissue Raman SHP 357

14.8.1 Hard tissue diagnostics 357

14.8.2 Deep tissue imaging of breast tissue and lymph nodes 358

References 359

15 Summary and Epilogue 363

Appendix A The Particle in a Box: A Demonstration of Quantum Mechanical Principles for a Simple, One-Dimensional, One-Electron Model System 365

A. 1 Definition of the Model System 365

A. 2 Solution of the Particle-in-a-Box Differential Equation 367

A. 3 Orthonormality of the Particle-in-a-Box Wavefunctions 370

A. 4 Dipole-Allowed Transitions for the Particle in a Box 370

A. 5 Real-World PiBs 371

Appendix B A summary of the Solution of the Harmonic Oscillator (Hermite) Differential Equation 373

Appendix C Character Tables for Chemically Important Symmetry Groups 377

C. 1 The nonaxial groups 377

C. 2 The Cn groups 377

C. 3 The Dn groups 379

C. 4 The Cnv groups 379

C. 5 The Dnh groups 382

C. 6 The Dnd groups 384

C. 7 The Sn groups 385

C. 8 The cubic groups 386

C. 9 The groups C∞, and D∞h for linear molecules 387

C. 10 The icosahedral groups 388

Appendix D Introduction to Fourier Series, the Fourier Transform, and the Fast Fourier Transform Algorithm 389

D. 1 Data Domains 389

D. 2 Fourier Series 390

D. 3 Fourier Transform 392

D. 4 Discrete and Fast Fourier Transform Algorithms 393

References 395

Appendix E List of Common Vibrational Group Frequencies (cm−1) 397

Appendix F Infrared and Raman Spectra of Selected Cellular Components 399

Index 405