Molecular Spectroscopy—Experiment and Theory (eBook)

Andrzej Kolezynski is an Associate Professor of Chemistry at AGH University of Science and Technology in Krakow, Poland and has also a PhD in philosophy. In his research, he applies methods of computational chemistry and physics to the periodic and non-periodic solids in order to analyse electronic structure, transport properties and electron density topological properties in relation to structure, chemical bonding and other physical and chemical properties of the compounds of interest. In addition to his research activities, he was a guest editor of several special issues in the Journal of Molecular Structure (2013, 2017), Spectrochimica Acta A (2017) and Vibrational Spectroscopy (2017), a chairman of the organising committees of two international conferences on molecular spectroscopy and served as a member and chair of the expert panels assessing grant applications for two main Polish funding agencies, the National Science Centre and National Centre for Research and Development. Dr. Kolezynski has published more than 40 research papers in international refereed journals and authored a monograph and two book chapters.Magdalena Król is an Assistant Professor at AGH University of Science and Technology. She received her master's degree in Chemical Technology and PhD in Chemistry from the same university. In her research, she applies various spectroscopic methods to study the structure and properties of aluminosilicate materials, with particular emphasis on materials from the zeolites group. In addition to her research activities, she was a guest editor of the special issue in Vibrational Spectroscopy (2017). Dr. Król is a co-author of over 50 articles (including over 30 papers in international refereed journals) and 5 book chapters.

Preface 6
Contents 8
Contributors 10
1 Computational Methods in Spectroscopy 13
Abstract 13
1.1 Introduction 13
1.2 Theoretical Foundations for Modeling of Real Systems and Processes Studied by Spectroscopic Methods 17
1.2.1 Ab Initio Methods 18
1.2.1.1 Schrödinger Equation 18
1.2.1.2 Born–Oppenheimer Approximation, Potential Energy Hypersurface 20
1.2.1.3 Hartree–Fock Method and Post-HF Extensions 22
1.2.1.4 Density Functional Theory 26
1.2.2 Practical Aspects of the Application of Computational Methods in Spectroscopy 34
1.2.2.1 Harmonic Approximation—Vibrational Spectroscopy 34
1.2.2.2 Time-Dependent DFT 38
1.3 The Problem of Computational Complexity and the Resulting Necessary Simplifications and Approximations 43
1.3.1 The Size and Complexity of the System 44
1.3.1.1 Size of the System: Molecules, Clusters, Amorphous and Periodic Solids 45
1.3.1.2 Structure Disorder: Point Defects, Dopants, Vacancies 49
1.3.2 Model Structure Simplifications and Approximations (Theory Level) 52
1.4 Conclusions 53
References 54
2 Scaling Procedures in Vibrational Spectroscopy 61
Abstract 61
2.1 Introduction 63
2.2 Fundamentals 64
2.2.1 Potential Energy Surface 64
2.2.2 One Dimensional Vibrational Problem 66
2.2.3 Wilson–Decius–Cross Method 71
2.3 Scaling Procedures 74
2.3.1 General Strategy 76
2.3.2 Uniform Scaling 77
2.3.2.1 Fundamentals of the Method 77
2.3.2.2 Development of US 80
2.3.3 Wavenumber Linear Scaling 84
2.3.4 Scaled Quantum Mechanical Force Field Method 85
2.3.4.1 Fundamentals of the Method 85
2.3.4.2 Development of SQM 87
2.3.5 Effective Scaling Frequency Factor Method 93
2.3.5.1 Fundamentals of the Method 93
2.3.5.2 Development of ESFF 96
2.3.6 Comparison of Multi-parameter Scaling Procedures 101
2.3.6.1 Quality of the Scaled Frequencies 101
2.3.6.2 Numerical Stability 102
2.3.6.3 Possible Future Applications 102
References 103
3 Quantum Dot and Fullerene with Organic Chromophores as Electron-Donor-Acceptor Systems 108
Abstract 108
3.1 Introduction 109
3.2 Brief History of Photocells Based on Organic Materials 110
3.3 Porphyrins and Phthalocyanies 111
3.4 Phthalocyanine and Porphyrin with Quantum Dots 114
3.5 Corroles and Fullerene 117
3.6 Energy and Electron Transfer 121
3.7 Summarizing 127
Acknowledgements 128
References 128
4 Material Analysis Using Raman Spectroscopy 134
Abstract 134
4.1 Introduction 135
4.2 Experimental 137
4.3 Results and Discussion 138
4.4 Calculation of Young’s Modulus 145
4.5 Conclusions 146
Acknowledgements 146
References 146
5 Ligand-Core NLO-Phores 149
Abstract 149
5.1 Introduction 149
5.2 Atomically Precise Clusters of Gold and Silver: Synthesis, Characterization, and Optical Properties 151
5.2.1 Atomically Precise Clusters of Gold and Silver 151
5.2.2 Atomically Precise Clusters of Gold and Silver—Synthetic Routes 154
5.2.3 Atomically Precise Clusters of Gold and Silver—Optical Properties 155
5.3 Atomically Precise Clusters of Gold and Silver as New NLO Chromophores—Background and Design 156
5.4 Measurement Techniques of Optical Nonlinearities—Two-Photon Absorption/Fluorescence 160
5.5 Case Studies 162
5.5.1 NLO Emission of Ag29(DHLA)12—Playing with Photons and Colors 162
5.5.2 Bulky Counter-Ions—a Simple Route to Enhance the TPEF Efficiencies 164
5.6 Conclusions and Outlooks 165
Acknowledgements 166
References 166
6 Small and Large Molecules Investigated by Raman Spectroscopy 171
Abstract 171
6.1 Molecules of Biomedical Importance—Structure and Interactions 171
6.1.1 The Basis of the Raman Optical Activity (ROA) 172
6.1.2 ROA Research on Chiral Compounds and Its Applications, Now and Over the Years 173
6.1.3 Sophisticated Applications of the ROA Techniques 175
6.1.4 The Basis of Surface-Enhanced Raman Spectroscopy (SERS) 176
6.1.5 Applications of SERS in Structural Studies—A Case of Pharmaceuticals 178
6.2 Application of Raman Spectroscopy to In Vitro Endothelial Cell Cultures 180
6.2.1 Characteristics of Endothelial Cell Cultures 181
6.2.2 In Vitro Cell Models of Pathophysiology of the Endothelium 182
6.2.3 In Vitro Cell Models in Drug Screening 186
6.2.4 Probing of Intracellular Environment by SERS Imaging 187
6.3 Examination of Primary and Cultured Cells 189
6.3.1 Liver Sinusoidal Endothelial Cells (LSECs) 190
6.3.2 Cardiac Microvascular Endothelial Cells (CMECs) 190
6.4 Label-Free and Label Raman Spectroscopic Imaging as a Potential Tool for Diagnosis of Diseases of Affluence in Tissues 193
6.4.1 Label-Free Raman Spectroscopic Imaging 193
6.4.2 Tissue Imaging With Immuno-SERS Microscopy 196
References 198
7 Hydantoins and Mercaptoimidazoles: Vibrational Spectroscopy as a Probe of Structure and Reactivity in Different Environments, from the Isolated Molecule to Polymorphs 209
Abstract 209
7.1 Introduction 209
7.2 Structures and Infrared Spectra of the Isolated Molecules 211
7.2.1 Mercaptoimidazoles 211
7.2.2 Hydantoins 215
7.3 Photochemistry for the Matrix-Isolated Molecules 218
7.3.1 Mercaptoimidazoles 218
7.3.2 Hydantoins 221
7.4 Neat Condensed Phases—Polymorphism and Phase Transitions 222
7.4.1 Mercaptoimidazoles: The Case of the Thioimidazole Dimer 222
7.4.2 Hydantoins: Polymorphism in 1MH and 5MH 225
7.4.3 Hydantoins: The Unusual Conformational Selection in AAH upon Crystallization 228
7.5 Conclusion 229
Acknowledgements 230
References 230
8 Vibrational Spectroscopy in Analysis of Stimuli-Responsive Polymer–Water Systems 233
Abstract 233
8.1 Stimuli-Responsive Polymer Systems 233
8.2 Water and Polymer–Water Systems as Seen by Vibrational Spectroscopy 238
8.3 pH-Sensitive Systems—Polyelectrolytes 245
8.4 Thermo-Responsive Systems—“Non-Ionisable” Polymers 249
8.5 Computer Simulations of Thermo-Responsive Polymer–Water Systems 255
8.6 Outlooks and Perspectives 267
Acknowledgements 270
References 271
9 Mössbauer Spectroscopy of Magnetoelectric Perovskite Oxides 282
Abstract 282
9.1 Introduction 282
9.2 Mössbauer Spectroscopy 283
9.2.1 Hyperfine Interactions 285
9.2.1.1 Isomer Shift 285
9.2.1.2 Magnetic Hyperfine Field (Nuclear Zeeman Splitting) 287
9.2.1.3 Quadrupole Splitting 288
9.2.1.4 Calculation of the Hyperfine Interaction Parameters 289
9.3 Magnetoelectrics 292
9.3.1 ABO3 Perovskites 294
9.3.1.1 BiFeO3 295
9.3.1.2 Pb(Fe0.5Nb0.5)O3 298
9.3.1.3 Bi0.5Pb0.5(Fe0.75Nb0.25)O3 299
B-Site Disorder 300
Magnetic Ordering Temperature 302
Iron Magnetic Moments 303
9.4 Conclusions 305
References 306
10 Vibrational Spectroscopy of Zeolites 310
Abstract 310
10.1 Introduction 310
10.2 Systematics of Zeolite-Type Crystals 311
10.3 Application of QM Methods in Interpretation of Zeolite Spectra 312
10.4 Vibrational Spectra of Silicates 314
10.5 Spectrum Analysis Based on the SBUs 316
10.5.1 SBU Terminated by Protons (Dependence of Framework Type on Characteristic Vibration Modes) 317
10.5.2 Influence of Tetrahedral Substitution on the Spectra Envelope 318
10.5.3 SBU Terminated by Cations 321
10.5.4 Factors Affecting the Position of RO Vibration Band 323
10.6 SBU Versus Periodic Structure 323
10.7 Influence of Extra-Framework Ions on Vibrational Spectra 328
10.7.1 Ion Exchange Versus Spectrum 328
10.7.2 Anions in the Structure of Zeolites 335
10.8 Conclusions 336
Acknowledgements 337
References 338
11 In Situ and Operando Techniques in Catalyst Characterisation and Design 342
Abstract 342
11.1 Introduction 343
11.2 Methods for Real-Time Catalyst Investigation 345
11.2.1 Determination of Active Centres Using Probe Molecules 345
11.2.2 in Situ FTIR Spectroscopy 349
11.2.2.1 Enhanced in Situ FTIR Techniques 353
11.2.2.2 2D Correlation Spectroscopy 354
11.2.3 in Situ Raman Spectroscopy 355
11.2.4 In Situ UV-Vis Spectroscopy 358
11.3 New Trends in in Situ Investigation of Catalysts 359
11.3.1 Conjugated AFM/Raman Spectroscopy 359
11.4 Summary 361
Acknowledgements 363
References 363
12 Application of Spectroscopic Methods in the Studies of Polysiloxanes, Cubic  Oligomeric Silsesquioxanes, and Spherosilicates Modified by Organic Functional Groups via Hydrosilylation 369
Abstract 369
12.1 Introduction 369
12.2 Hydrosilylation Process 371
12.3 Spectroscopic Methods Applied in the Studies of Polysiloxanes, Oligomeric Silsesquioxanes, and Spherosilicates Modified by Hydrosilylation 372
12.4 Polysiloxanes Modified by Organic Functional Groups 373
12.4.1 Modified Polyvinylsiloxanes 374
12.4.2 Modified PHMS and PHMS-DMS Copolymers 375
12.4.2.1 Polymers with Epoxy Side Groups 377
12.4.2.2 Polymers with Ester, Polyether, and Other Oxygen-Containing Side Groups 379
12.4.2.3 Polymers with Fluoroalkyl and Other Fluorine-Containing Side Groups 384
12.4.2.4 Polymers with Nitrogen-Containing Side Groups 387
12.5 Organofunctional Cubic Oligomeric Silsesquioxanes and Spherosilicates 391
12.5.1 {{/hbox{T}}_{8}}^{{/rm H}} and {/hbox{Q}}_{8} {{/hbox{M}}_{8}}^{{/rm H}} Modified by Epoxy Groups 392
12.5.2 {{/hbox{T}}_{8}}^{{/rm H}} and {/hbox{Q}}_{8} {{/hbox{M}}_{8}}^{{/rm H}} Modified by Other Oxygen-Containing Groups 396
12.5.3 {{/hbox{T}}_{8}}^{{/rm H}} and {/hbox{Q}}_{8} {{/hbox{M}}_{8}}^{{/rm H}} Modified by Fluorocarbon Groups 398
12.5.4 {{/hbox{T}}_{8}}^{{/rm H}} and {/hbox{Q}}_{8} {{/hbox{M}}_{8}}^{{/rm H}} Modified by Nitrogen-Containing Groups 399
12.6 Conclusions 401
References 402
13 Spectroscopic Aspects of Polydimethylsiloxane (PDMS) Used for Optical Waveguides 409
Abstract 409
13.1 Introduction 409
13.2 Experiment 411
13.2.1 Polymer Sample Preparation 411
13.2.2 Waveguide Fabrication 411
13.2.3 Optical Measurements 413
13.3 Characterization of the Optical PDMS Materials 414
13.3.1 Refractive Index and Bandwidth 414
13.3.2 Optical Loss Phenomena 417
13.3.2.1 Intrinsic Absorption Loss by Electronic Transitions 418
13.3.2.2 Intrinsic Absorption Loss by Molecular Vibrations 419
13.3.2.3 Assignment and Wavenumber Calculation of Vibrational PDMS Bands 419
13.3.2.4 Absorption Loss for PDMS Core and Cladding due to Molecular Vibrations 421
13.3.2.5 Estimation of Absorption Loss for PDMS Derivatives 424
13.3.2.6 Intrinsic Scattering Loss 426
13.3.2.7 Scattering Loss from Mould Roughness 427
13.3.2.8 Optical Loss Due to Interlayer 428
13.3.3 Optical Insertion Loss of PDMS Waveguides after Fabrication and Ageing 429
13.4 Conclusions 431
Acknowledgements 432
References 432
14 The Luminescent Properties of Photonic Glasses and Optical Fibers 434
Abstract 434
14.1 Introduction 434
14.2 The Effect of the Structure of Antimony-Germanate Glasses Modification on the Luminescent Properties 437
14.3 Plasmon Effect in Antimony-Germanate Glasses 441
14.4 Upconversion Luminescence in the Vis Range of Optical Fibers from Low-Phonon Energy Glasses 450
14.5 Optical Fibers from GeO2–Ga2O3–BaO System 457
14.6 Summary 460
Acknowledgements 461
References 461
15 Spectroscopic Characterization of Silicate Amorphous Materials 464
Abstract 464
15.1 Glassy State Theory 464
15.2 Vibrational Spectroscopy as a Tool to Study of Disordered Structure 470
15.2.1 Decomposition of IR Spectra of Glasses 471
15.3 Glass Structure in the Light of Spectroscopic Studies 474
15.3.1 Model Silica Glass 474
15.3.2 The Influence of Cationic Substitutions on Glass Structure 479
15.4 Conclusions 485
References 486
16 Spectroscopy in the Analysis of Artworks 489
Abstract 489
16.1 Introduction 489
16.2 Raman Spectroscopy 490
16.2.1 Case Studies 497
16.2.1.1 Medieval Manuscripts 497
16.2.1.2 The Provenance Investigation of the Archeological Amber 503
16.3 Vis 506
16.3.1 Microfading Tests 508
16.3.1.1 Description of the Methodology 509
16.3.1.2 Data Processing and Interpretation 510
16.3.1.3 Applications of the MFT Method 513
16.4 Conclusions 514
References 515
Index 524