NMR Data Interpretation Explained

Neil E. Jacobsen has been the NMR Facility Manager in the Department of Chemistry and Biochemistry at the University of Arizona for the last 20 years. He teaches an undergraduate course in NMR Spectroscopy (Organic Qualitative Analysis) using a series of unknowns including monoterpenes and steroids, with students acquiring their own 400 MHz 1D and 2D NMR data. He also teaches a graduate course in Organic Synthesis and NMR Spectroscopy that is focused on using the spectrometers and interpreting complex NMR data. He has 30 years of experience working in the field of NMR spectroscopy, and during that time he has authored 46 publications in peer-reviewed journals as well as the 2007 Wiley book NMR Spectroscopy Explained.

Examples xi

Preface xiii

Acknowledgments xv

About the Companion Website xvii

Chapter 1 | Spectroscopy and the Proton NMR Experiment 1

1 What is the Structure of a Molecule? 1

2 Mass Spectrometry 3

2.1 Ionization Methods and Molecular Ions 4

2.1.1 Electron Impact (EI) 4

2.1.2 Soft Ionization 5

2.2 High-Resolution Mass Spectrometry and Exact Mass 5

2.3 Isotope Patterns and the Halogens Br and Cl 7

3 Infrared (IR) Spectroscopy 9

4 Ultraviolet (UV) and Visible Spectroscopy 10

5 A Highly Simplified View of the NMR Experiment 13

Chapter 2 | Chemical Shifts and Splitting Patterns 17

1 Chemical Shifts in the Proton Spectrum 17

2 Splitting: The Effect of One Neighbor: A Doublet 21

3 Splitting: The Effect of Two Neighbors: A Triplet 23

4 Splitting: The Effect of Three Neighbors: A Quartet 25

5 Splitting: The Effect of “n” Neighbors: A Multiplet 30

6 Using Splitting Patterns to Choose from a Group of Isomers 34

7 Peak Intensities (Peak Areas) and the Number of Protons in a Peak 37

8 Publication Format for Proton NMR Data 39

9 Recognizing Common Structure Fragments 41

10 Overlap in Proton NMR Spectra. Example: 1-Methoxyhexane 45

11 Protons Bound to Oxygen: OH Groups. Example: 2-Ethyl-1-Butanol 48

12 Summary of Chemical Shifts and Splitting Patterns 50

Chapter 3 | Proton ( 1H) NMR of Aromatic Compounds 51

1 Benzene: The Aromatic Ring Current and the Shielding Cone 51

2 Monsubstituted Benzene: X-C6H5 52

2.1 Toluene 52

2.2 Aromatic Chemical Shifts: Resonance Structures 54

2.3 Nitrobenzene 55

2.4 Anisole 56

2.5 Substituent Effects on Aromatic Chemical Shifts 58

2.6 Long-Range J Couplings in Aromatic Rings: Protons 4 Bonds Apart 59

3 Disubstituted Benzene: X-C6H4-Y 62

3.1 Symmetrical Disubstituted Benzene: X-C6H4-X 62

3.2 Unsymmetrical Disubstituted Benzene, X-C6H4-Y 72

3.2.1 para (1,4) Disubstituted Benzene: p-X-C6H4-Y 73

3.2.2 meta (1,3) Disubstituted Benzene: m-X-C6H4-Y 78

3.2.3 ortho (1,2) Disubstituted Benzene: o-X-C6H4-Y 87

4 Coupling Between Aromatic Ring Protons and Substitutent Protons; Homonuclear Decoupling 100

4.1 The Methyl Group (CH3) 100

4.2 The Methoxy Substituent (OCH3) 102

4.3 The Formyl (H-CˆO) Substituent 103

5 Trisubstituted Aromatic Rings: The AB2 System 106

6 Other Aromatic Ring Systems: Heteroaromatics, Five-Membered Rings and Fused Rings 110

6.1 Pyridine (C5H5N) 111

6.2 Pyrrole (C4H5N) 112

6.3 Furan (C4H4O) 113

6.4 Naphthalene (C10H8) 115

6.5 Indole (C8H7N) 117

6.6 Quinoline and Isoquinoline (C9H7N) 118

7 Summary of New Concepts: Proton NMR of Aromatic Compounds 120

Chapter 4 | Carbon-13 (13C) NMR 125

1 Natural Abundance and Sensitivity of 13C 125

2 Proton Decoupling—Removing the Splitting Effect of Nearby Protons 126

3 Intensity of 13C Peaks—Symmetry and Relaxation 126

4 Chemical Shifts of Carbon-13 (13C) Nuclei 129

4.1 13C Frequency and Chemical Shift Reference 129

4.2 General Regions of the 13C Chemical Shift Scale 130

4.3 Correlations between 1H and 13C Chemical Shift for a C-H Pair 132

4.4 Quantitation of the Steric Effect for 13C Chemical Shifts 135

4.5 Example of Steric Effects on 13C Chemical Shifts: The “Crowded CH” in Steroids 141

4.6 The γ-gauche Effect: Steric Shifts That Give Stereochemical Information 143

4.7 Inductive Effects in 13C Chemical Shifts: Electronegative Atoms 147

4.8 The Effect of Ring Strain on 13C Chemical Shift of sp3-Hybridized Carbons 150

5 Quaternary Carbons: the Carbonyl Group 151

6 Simple Aromatic Compounds: Substituent Effects on 13C Chemical Shifts 156

7 Highly Oxygenated Benzene Rings and Coumarin 161

8 Fused Rings and Heteroaromatic Compounds 165

8.1 Pyridine (C5H5N) 165

8.2 Pyrrole (C4H5N) 167

8.3 Furan (C4H4O) 168

8.4 Naphthalene (C10H8) 168

8.5 Indole (C8H7N) 170

8.6 Quinoline and Isoquinoline (C9H7N) 173

9 Edited 13C Spectra: DEPT 174

9.1 Non-decoupled 13C Spectra 175

9.2 Edited 13C Spectra 176

9.3 Practical Details of the DEPT Experiment 181

9.3.1 Sensitivity 181

9.3.2 Pulse Calibration 181

9.3.3 J Value Setting 182

9.3.4 Phase Correction 185

10 The Effect of Other Magnetic Nuclei on the 13C Spectrum: 31P, 19F, 2H and 14N 185

10.1 Splitting of 13C Peaks By Deuterium (2H) 185

10.2 Splitting of 13C Peaks by Phosphorus (31P) 186

10.3 Splitting of 13C Peaks by Fluorine (19F) 188

10.4 Splitting and Broadening of 13C Peaks by Nitrogen (14N) 189

11 Direct Observation of Nuclei Other Than Proton (1H) and Carbon (13C) 190

11.1 Phosphorus-31 (31P) NMR 192

11.2 Fluorine-19 (19F) NMR 194

Chapter 5 | Alkenes (Olefins) 198

1 Proton Chemical Shifts of Simple Olefins 199

2 Short-Range (Two and Three Bond) Coupling Constants ( J Values) in Olefins 202

3 The Allylic Coupling: A Long-Range (Four-Bond) J Coupling 205

4 Long-Range Olefin Couplings in Cholesterol: The bis-Allylic Coupling (5J) 209

5 Carbon-13 Chemical Shifts of Hydrocarbon Olefins (Alkenes) 210

6 Resonance Effects on Olefinic 13C Chemical Shifts 214

7 Alkynes 225

Chapter 6 | Chirality and Stereochemistry: Natural Products 227

1 The Molecules of Nature 227

2 Chirality, Chiral Centers, Chiral Molecules, and the Chiral Environment 230

3 The AB System 232

4 Detailed Analysis of the AB Spectrum: Calculating the Chemical Shifts 234

5 The ABX System 237

6 Variations on the ABX Theme: ABX3, ABX2 and ABXY 245

7 The Effect of Chirality on 13C Spectra. Diastereotopic Carbons 249

8 A Closer Look at Chemical Shift Equivalence in an Asymmetric Environment 251

8.1 Chemical Shift Equivalence of CH3 Group Protons 251

8.2 Non-Equivalence of CH2 Group Protons 252

8.3 Chemical Shift Equivalence by Symmetry 252

9 J Couplings and Chemical Shifts in the Rigid Cyclohexane Chair System 255

9.1 Cyclohexene and Cyclohexenone 262

10 A Detailed Look at the Dependence of 3jHH on Dihedral Angle: The Karplus Relation 266

11 Magnetic Non-Equivalence. The X-CH2-CH2-Y Spin System: A2B2 and AA’BB’ Patterns 276

12 Bicyclic Compounds and Small Rings (Three- and Four-Membered) 286

12.1 The Bicyclo[2.2.1] Ring System 286

12.2 The Bicyclo[3.1.0] Ring System 291

12.3 The Bicyclo[3.1.1] Ring System 294

Reference 298

Chapter 7 | Selective Proton Experiments: Biological Molecules 299

1 Sugars: Monosaccharides and Oligosaccharides 299

2 Slowing of OH Exchange in Polar Aprotic Solvents Like DMSO 305

3 Selective TOCSY Applied to the Assignment of the 1H Spectra of Sugars 307

4 The Selective NOE (Nuclear Overhauser Effect) Experiment 319

4.1 Recognizing Artifacts in Selective NOE Spectra 320

4.2 The Relationship Between NOE Intensity and Distance 320

4.3 Magnetization Transfer in the Selective TOCSY and Selective NOE Experiments 321

5 Amino Acids and Peptides 331

6 Nucleic Acids 348

7 Parameter Settings for NMR Experiment Setup and NMR Data Processing 357

Bibliography 358

Chapter 8 | Homonuclear Two-Dimensional NMR: Correlation of One Hydrogen (1H) to Another 359

1 Selective TOCSY Experiments Displayed as a Stacked Plot 359

2 The Two-Dimensional COSY Experiment 365

3 Shape and Fine Structure of COSY Crosspeaks; Contour Plots 370

4 2D-COSY Spectra of Sugars 376

5 2D-COSY Spectra of Aromatic Compounds 391

6 Parameter Settings in the 2D COSY Experiment; The DQF-COSY Experiment 397

7 COSY Spectra of Peptides 399

8 COSY Spectra of Natural Products 405

9 Two-Dimensional (2D) TOCSY (Total Correlation Spectroscopy) 412

10 Two-Dimensional (2D) NOESY (Nuclear Overhauser Effect Spectroscopy) 423

Parameter Settings Used for 2D Spectra in this Chapter 429

Chapter 9 | Heteronuclear Two-Dimensional NMR: Correlation of One Hydrogen (1H) to One Carbon (13C) 430

1 3-Heptanone: A Thought Experiment 430

2 Edited HSQC: Making the CH2 Protons Stand Out 436

3 The 2D-HSQC Spectrum of Cholesterol 443

4 A Detailed Look at the HSQC Experiment 455

5 Parameters and Settings for the 2D-HSQC Experiment 458

5.1 Spectral Window 458

5.2 Acquisition Time 458

5.3 One-Bond J Coupling Value 459

5.4 Number of 1D Spectra Acquired: F1 Resolution 460

5.5 Number of Scans: Sensitivity 460

6 Data Processing: Phase Correction in Two Dimensions 460

7 Long-Range Couplings between 1H and 13C 463

8 2D-HMBC (Heteronuclear Multiple-Bond Correlation) 465

8.1 2D-HMBC Spectra of Aromatic Compounds 467

8.2 HMBC Spectra of Natural Products: Using the Methyl Correlations 475

8.3 HMBC Spectra of Sugars 491

9 Parameters and Settings for the 2D-HMBC Experiment 495

9.1 Spectral Window 495

9.2 Acquisition Time 496

9.3 One-Bond and Long-Range JCH Coupling Values 496

9.4 Number of Scans 496

10 Comparison of HSQC and HMBC 496

11 HMBC Variants 497

Parameter Settings Used for 2D Spectra in this Chapter 497

References 498

Chapter 10 | Structure Elucidation Using 2D NMR 499

1 Literature Structure Problems 500

2 Sesquiterpenoids 501

3 Steroids 522

4 Oligosaccharides 552

5 Alkaloids 574

6 Triterpenes 597

Reference 615

Index 617