Modern Vibrational Spectroscopy and Micro-Spectroscopy

430 Pages·2015·8.169 MB·English

by  Max Diem

Modern Vibrational Spectroscopy and
Micro-Spectroscopy
Modern Vibrational Spectroscopy and
Micro-Spectroscopy
Theory, Instrumentation and Biomedical Applications
MAXDIEM
Northeastern University, USA
Thiseditionfirstpublished2015
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LibraryofCongressCataloging-in-PublicationData
Diem,Max,1947-
Modernvibrationalspectroscopyandmicro-spectroscopy:theory,instrumentation,andbiomedicalapplications/MaxDiem.
pagescm
Includesbibliographicalreferencesandindex.
ISBN978-1-118-82486-3(pbk.)
1.Spectrumanalysis–Diagnosticuse 2.Vibrationalspectra. I.Title.
RC78.7.S65D542015
616.07′54–dc23
2015019354
AcataloguerecordforthisbookisavailablefromtheBritishLibrary.
Setin10/12ptTimesLTStdbySPiGlobal,Chennai,India
1 2015
I would like to dedicate this book to my wife, Mary Jo, who put up with my
hidingawayinmyhomeofficeformanyaneveningandmyabsentmindedness
for 16 months during which this book was written.
I also would liketo acknowledgethe excellent and enthusiastic crewof post-
docs,graduateandundergraduatestudentsinmyresearchlaboratoryatNorth-
easternUniversitywhowasresponsibleforthemajorityoftheworkpresented
here (listed chronologically).
Miloš, Christian, Susie, Melissa, Brian, Tatjana, Jen (I), Ben, Ellen, Kostas,
Antonella, Evgenia, Erin, Jen (II), Christina, Kathleen, and Doug.
Max Diem
Contents
Preface xv
Prefaceto‘IntroductiontoModernVibrationalSpectroscopy’(1994) xix
I MODERNVIBRATIONALSPECTROSCOPYANDMICRO-SPECTROSCOPY:
THEORY,INSTRUMENTATIONANDBIOMEDICALAPPLICATIONS 1
I.1 HistoricalPerspectiveofVibrationalSpectroscopy 1
I.2 VibrationalSpectroscopywithinMolecularSpectroscopy 2
References 4
1 MolecularVibrationalMotion 5
1.1 Theconceptofnormalmodesofvibration 6
1.2 Theseparationofvibrational,translational,androtationalcoordinates 6
1.3 Classicalvibrationsinmass-weightedCartesiandisplacementcoordinates 7
1.4 Quantummechanicaldescriptionofmolecularvibrations 13
1.4.1 Transitionfromclassicaltoquantummechanicaldescription 13
1.4.2 Diatomicmolecules:harmonicoscillator 14
1.4.3 Diatomicmolecules:anharmonicity 19
1.4.4 Polyatomicmolecules 20
1.5 Time-dependentdescriptionandthetransitionmoment 22
1.5.1 Time-dependentperturbationofstationarystatesbyelectromagneticradiation 22
1.5.2 Thevibrationaltransitionmomentforabsorption:harmonicdiatomicmolecules 25
1.5.3 Thevibrationaltransitionmomentforabsorption:anharmonicdiatomicmolecules 27
1.5.4 Thevibrationaltransitionmomentforabsorption:polyatomicmolecules 30
1.5.5 Isotopiceffects:diatomicmolecules 31
1.6 BasicinfraredandRamanspectroscopies 32
1.6.1 Infraredabsorptionspectroscopy 32
1.6.2 Raman(scattering)spectroscopy 35
1.7 Concludingremarks 38
References 38
2 SymmetryPropertiesofMolecularVibrations 39
2.1 Symmetryoperationsandsymmetrygroups 40
2.2 Grouprepresentations 44
2.3 Symmetryrepresentationsofmolecularvibrations 50
2.4 Symmetry-basedselectionrulesforabsorptionprocesses 54
2.5 SelectionrulesforRamanscattering 56
2.6 Discussionofselectedsmallmolecules 57
2.6.1 Tetrahedralmolecules:carbontetrachloride,CCl ,andmethane,CH 57
4 4
viii Contents
2.6.2 Chloroformandmethylchloride 64
2.6.3 Dichloromethane(methylenechloride),CH Cl 67
2 2
2.6.4 Dichloromethane-d (methylenechloride-d ),CHDCl 68
1 1 2
References 69
3 InfraredSpectroscopy 71
3.1 GeneralaspectsofIRspectroscopy 71
3.2 Instrumentation 73
3.2.1 Sourcesofinfraredradiation:blackbodysources 73
3.2.2 Sourcesofinfraredradiation:quantum-cascadelasers,
nonlineardevices 75
3.2.3 Transferoptics 76
3.2.4 Colorsortingdevices:monochromators 76
3.2.5 Colorencodingdevices:interferometers 79
3.2.6 Detectors 82
3.2.7 Read-outdevices 84
3.3 MethodsininterferometricIRspectroscopy 84
3.3.1 Generalinstrumentation 84
3.3.2 Opticalresolution 86
3.3.3 Zerofillingandfouriersmoothing 86
3.3.4 Phasecorrection 88
3.3.5 Apodization 91
3.4 Samplingstrategies 92
3.4.1 Transmissionmeasurement 92
3.4.2 Specularreflection 94
3.4.3 Diffusereflection 95
3.4.4 Attenuatedtotalreflection 97
3.4.5 Infraredreflectionabsorptionspectroscopy(IRRAS) 99
3.4.6 Fouriertransformphotoacousticspectroscopy(FT-PAS) 100
3.4.7 Planararrayinfraredspectroscopy(PA-IRS) 101
3.4.8 Two-dimensionalFTIR 101
3.4.9 Infraredmicrospectroscopy 102
References 102
4 RamanSpectroscopy 103
4.1 GeneralaspectsofRamanspectroscopy 104
4.2 Polarizability 105
4.3 PolarizationofRamanscattering 107
4.4 Dependenceofdepolarizationratiosonscatteringgeometry 111
4.5 AcomparisonbetweenRamanandfluorescencespectroscopy 114
4.6 InstrumentationforRamanspectroscopy 116
4.6.1 Sources 116
4.6.2 DispersiveRamaninstrumentationandmultichanneldetectors 116
4.6.3 InterferometricRamaninstrumentation 121
4.6.4 Ramanmicrospectroscopy 122
References 122
Contents ix
5 ADeeperLookatDetailsinVibrationalSpectroscopy 123
5.1 Fermiresonance 124
5.2 Transitiondipolecoupling(TDC) 128
5.3 Groupfrequencies 129
5.4 Rot-vibrationalspectroscopy 130
5.4.1 Classicalrotationalenergy 130
5.4.2 Quantummechanicsofrotationalspectroscopy 132
5.4.3 Rot-vibrationaltransitions 137
References 141
6 SpecialRamanMethods:Resonance,Surface-Enhanced,andNonlinear
RamanTechniques 143
6.1 ResonanceRamanspectroscopy 144
6.2 Surface-enhancedRamanscattering(SERS) 146
6.3 NonlinearRamaneffects 149
6.3.1 Spontaneous(incoherent)nonlinearRamaneffects 149
6.3.2 Coherentnonlineareffects 152
6.4 Continuouswaveandpulsedlasers 159
6.4.1 Einsteincoefficientsandpopulationinversion 160
6.4.2 Operationofagaslaser 162
6.4.3 Principlesofpulsedlasers 163
6.4.4 Operationofpulsedlasers 163
6.5 Epilogue 164
References 164
7 Time-ResolvedMethodsinVibrationalSpectroscopy 167
7.1 Generalremarks 167
7.2 Time-resolvedFTinfrared(TR-FTIR)spectroscopy 168
7.2.1 Experimentalaspects 168
7.2.2 ApplicationsofTR-FTIRspectroscopy 169
7.3 Time-resolvedRamanandresonanceRaman(TRRR)spectroscopy 171
7.3.1 Instrumentalaspects 171
7.3.2 ApplicationsofTRRR 173
7.3.3 Hemegroupdynamicstudies 173
7.3.4 Rhodopsinstudies 174
References 175
8 VibrationalOpticalActivity 177
8.1 Introductiontoopticalactivityandchirality 177
8.2 Infraredvibrationalcirculardichroism(VCD) 179
8.2.1 Basictheory 179
8.2.2 Excitontheoryofopticalactivity 180
8.3 ObservationofVCD 181
8.4 ApplicationsofVCD 185
8.4.1 VCDofbiologicalmolecules 185
8.4.2 SmallmoleculeVCD 185
x Contents
8.5 Ramanopticalactivity 186
8.6 ObservationofROA 188
8.7 ApplicationsofROA 189
8.7.1 ROAofbiologicalmolecules 189
8.7.2 SmallmoleculesROA 190
References 190
9 ComputationofVibrationalFrequenciesandIntensities 193
9.1 Historicalapproachestothecomputationofvibrationalfrequencies 193
9.2 Vibrationalenergycalculations 194
9.2.1 Classicalapproaches:theWilsonGFmatrixmethod 194
9.2.2 Earlycomputer-basedvibrationalanalysis 197
9.3 Abinitioquantum-mechanicalnormalcoordinatecomputations 197
9.4 Vibrationalintensitycalculations 198
9.4.1 Fixedpartialchargemethodforinfraredintensities 198
9.4.2 QuantummechanicalinfraredandRamanintensities:localizedmolecularorbitals 200
9.4.3 Thefiniteperturbationmethod 200
References 202
II BIOPHYSICALANDMEDICALAPPLICATIONSOFVIBRATIONAL
SPECTROSCOPYANDMICROSPECTROSCOPY 203
10 BiophysicalApplicationsofVibrationalSpectroscopy 205
10.1 Introduction 205
10.2 Vibrationsofthepeptidelinkageandofpeptidemodels 206
10.2.1 Aminoacidsandthepeptidelinkage 206
10.2.2 Thevibrationalmodesofthepeptidelinkage 206
10.3 Conformationalstudiesofpeptidesandpolyaminoacids 210
10.4 Proteinspectroscopy:IR,VCD,Raman,resonanceRaman,andROAspectraofproteins 215
10.5 Nucleicacids 219
10.5.1 Structureandfunctionofnucleicacids 219
10.5.2 Phosphodiestervibrations 222
10.5.3 Ribosevibrations 222
10.5.4 Basevibrations 222
10.6 ConformationalstudiesonDNAandDNAmodelsusingIR,Raman,andVCDspectroscopies 223
10.7 Lipidsandphospholipids 227
10.8 Epilogue 231
References 231
11 VibrationalMicrospectroscopy(MSP) 235
11.1 Generalremarks 235
11.2 Generalaspectsofmicroscopy 236
11.3 Ramanmicrospectroscopy(RA-MSP) 239
11.3.1 Dispersive(singlepoint)systems 240
11.3.2 Micro-Ramanimagingsystems 241
Contents xi
11.4 CARSandFSRSmicroscopy 242
11.5 Tip-enhancedRamanspectroscopy(TERS) 243
11.6 Infraredmicrospectroscopy(IR-MSP) 243
11.6.1 Fourier-transforminfraredimagingsystems 244
11.6.2 QCL-basedsystems 246
11.7 Samplingstrategiesforinfraredmicrospectroscopy 247
11.7.1 Transmissionmeasurement 247
11.7.2 Transflectionmeasurement 247
11.7.3 Attenuatedtotalreflection(ATR) 248
11.8 Infrarednear-fieldmicroscopy 249
References 249
12 DataPreprocessingandDataProcessinginMicrospectralAnalysis 251
12.1 Generalremarks 251
12.2 Datapreprocessing 252
12.2.1 Cosmicrayfiltering(Ramandatasetsonly) 253
12.2.2 Linearwavenumberinterpolation(Ramandatasetsonly) 253
12.2.3 Conversionfromtransmittancetoabsorbanceunits(someinfrareddatasets) 253
12.2.4 Normalization 253
12.2.5 Noisereduction 254
12.2.6 Conversionofspectratosecondderivatives 256
12.3 Reductionofconfoundingspectraleffects 257
12.3.1 Reductionofwatervaporcontributionsincellularpixelspectra 258
12.3.2 MieandresonanceMiescattering 258
12.3.3 Correctionofdispersivebandshapes 260
12.3.4 Standingwaveeffect 262
12.4 Unsupervisedmultivariatemethodsofdatasegmentation 263
12.4.1 Factormethods 264
12.4.2 Datasegmentationbyclusteringmethods 269
12.5 Supervisedmultivariatemethods 272
12.5.1 Discussionofsensitivity,specificity,andaccuracy 272
12.5.2 Softindependentmodelingofclassanalogy(SIMCA) 273
12.5.3 Artificialneuralnetworks(ANNs) 274
12.5.4 Supportvectormachines(SVMs) 275
12.5.5 Randomforests(RFs) 276
12.5.6 Cross-validation 277
12.6 Summaryofdataprocessingformicrospectralanalysis 278
12.7 Two-dimensionalcorrelationmethodsininfraredspectroscopy(2D-IR) 278
References 280
13 InfraredMicrospectroscopyofCellsandTissueinMedicalDiagnostics 283
13.1 Introduction 283
13.2 Spectralhistopathology(SHP) 284
13.2.1 Reviewofclassicalhistopathology 284
13.2.2 Spectralmethodsinhistopathology 285
13.2.3 Infraredabsorptionspectroscopyofcellsandtissue:introductorycomments 285
xii Contents
13.3 MethodologyforSHP 287
13.3.1 Generalapproach 287
13.3.2 Sequenceofstepsinclassicalhistopathology 288
13.3.3 Sequenceofstepsforspectralhistopathology 288
13.4 ApplicationsofSHPfortheclassificationofprimarytumors 294
13.4.1 Cervicaltissueandcervicalcancer 294
13.4.2 Lungcancer 298
13.4.3 Prostatecancer 303
13.4.4 Breastcancer 304
13.5 ApplicationofSHPtowardthedetectionandclassificationofmetastatictumors 304
13.5.1 Detectionofcoloncancermetastasesinlymphnodes 304
13.5.2 Detectionofbreastcancermetastasesinlymphnodes 306
13.5.3 Detectionandclassificationofbrainmetastases 307
13.6 FutureprospectsofSHP 309
13.7 Infraredspectralcytopathology(SCP) 310
13.7.1 Classicalcytopathology 311
13.7.2 Spectralcytopathology 314
13.7.3 MethodsforSCP 314
13.8 SCPresults 316
13.8.1 EarlyresultsofSCP 316
13.8.2 Fixationstudies 317
13.8.3 Spectralcytopathologyofcervicalmucosa 320
13.8.4 Spectralcytopathologyoftheoralmucosa 323
13.8.5 Spectralcytopathologyofesophagealcells 326
13.9 SCPofculturedcells 328
13.9.1 EarlySCPeffortsandgeneralresults 328
13.9.2 SCPofculturedcellstostudytheeffectsofthecellcycleandofdrugsoncells 328
13.10 Infraredspectroscopyofcellsinaqueousmedia 331
13.11 FuturepotentialofSCP 333
References 333
14 RamanMicrospectroscopyofCellsandTissueinMedicalDiagnostics 339
14.1 Introduction 339
14.2 ExperimentalConsiderationforRamanMicrospectroscopy 341
14.3 High-ResolutionRamanSpectralCytopathology 343
14.3.1 Subcellularorganization 343
14.3.2 Subcellulartransportphenomena 345
14.4 Low-ResolutionRamanSCPofCulturedCellsInVitro 349
14.5 RamanSCPinSolution 352
14.5.1 Opticaltweezingofcellsinaqueousmedia 352
14.5.2 Cellstrappedinmicrofluidicchips 353
14.5.3 ResonanceRamanspectroscopyoferythrocytes 353
14.6 RamanSpectralHistopathology(RaSHP) 354
14.7 InVivoRamanSHP 356
14.8 DeepTissueRamanSHP 357
14.8.1 Hardtissuediagnostics 357