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1 Peptide Fragmentation/Deletion Side Reactions 1

1.1 Acidolysis of Peptides Containing N-Ac-N-alkyl-Xaa Motif 1

1.2 Des-Ser/Thr Impurities Induced by O-acyl Isodipeptide BocSer/Thr（Fmoc-Xaa）-OH as Building Block for Peptide Synthesis 3

1.3 Acidolysis of-N-acyl-N-alkyl-Aib-Xaa-Bond 6

1.4 Acidolysis of-Asp-Pro-Bond 9

1.5 Autodegradation of Peptide N-Terminal H-His-Pro-Xaa-Moiety 10

1.6 Acidolysis of the Peptide C-Terminal N-Me-Xaa 11

1.7 Acidolysis of Peptides with N-Terminal FITC Modification 12

1.8 Acidolysis of Thioamide Peptide 14

1.9 Deguanidination Side Reaction on Arg 18

1.10 DKP（2，5-Diketopiperazine）Formation 22

References 28

2 β-Elimination Side Reactions 33

2.1 β-Elimination of Cys Sulfhydryl Side Chain 33

2.2 β-Elimination of Phosphorylated Ser/Thr 37

References 41

3 Peptide Global Deprotection/Scavenger-Induced Side Reactions 44

3.1 Tert-Butylation Side Reaction on Trp During Peptide Global Deprotection 44

3.2 Trp Alkylation by Resin Linker Cations During Peptide Cleavage/Global Deprotection 47

3.3 Formation of Trp-EDT and Trp-EDT-TFA Adduct in Peptide Global Deprotection 53

3.4 Trp Dimerization Side Reaction During Peptide Global Deprotection 55

3.5 Trp Reduction During Peptide Global Deprotection 57

3.6 Cys Alkylation During Peptide Global Deprotection 58

3.7 Formation of Cys-EDT Adducts in Peptide Global Deprotection Reaction 59

3.8 Peptide Sulfonation in Side Chain Global Deprotection Reaction 63

3.9 Premature Acm Cleavage Off Cys（Acm）and Acm S→O Migration During Peptide Global Deprotection 67

3.10 Methionine Alkylation During Peptide Side Chain Global Deprotection with DODT as Scavenger 69

3.11 Thioanisole-Induced Side Reactions in Peptide Side Chain Global Deprotection 71

References 73

4 Peptide Rearrangement Side Reactions 77

4.1 Acid Catalyzed Acyl N→O Migration and the Subsequent Peptide Acidolysis 77

4.2 Base Catalyzed Acyl O→N Migration 80

4.3 His-Nim-Induced Acyl Migration 86

References 93

5 Side Reactions Upon Amino Acid/Peptide Carboxyl Activation 95

5.1 Formation of N-Acylurea Upon Peptide/Amino Acid-Carboxyl Activation by DIC 95

5.2 Uronium/Guanidinium Salt Coupling Reagents-Induced Amino Group Guanidination Side Reactions 97

5.3 δ-Lactam Formation Upon Arg Activation Reaction 100

5.4 NCA Formation Upon Boc/Z-Amino Acid Activation 102

5.5 Dehydration of Side Chain-Unprotected Ash/Gln During Carboxyl-Activation 103

5.6 Formation of H-β-Ala-OSu from HOSu-Carbodiimide Reaction During Amino Acid Carboxyl-Activation 105

5.7 Benzotriazinone Ring Opening and Peptide Chain Termination During Carbodiimide/HOOBt Mediated Coupling Reactions 107

5.8 Peptide Chain Termination Through the Formation of Peptide N-Terminal Urea in CDI-Mediated Coupling Reaction 108

5.9 Guanidino or Hydantoin-2-Imide Formation from Carbodiimide and Nα Group on Amino Acid/Peptide 110

5.10 Side Reactions-Induced by Curtius Rearrangement on Peptide Acyl Azide 110

5.11 Formation of Pyrrolidinamide-Induced by Pyrrolidine Impurities in Phosphonium Salt 115

References 116

6 Intramolecular Cyclization Side Reactions 119

6.1 Aspartimide Formation 119

6.1.1 Factors That Influence Aspartimide Formation 121

6.1.2 Solutions for Aspartimide Formation 127

6.2 Asn/Gln Deamidation and Other Relevant Side Reactions 137

6.2.1 Mechanism of Asn/Gln Deamidation 137

6.2.2 Factors Impacting on Asn/Gln Deamidation 140

6.2.3 Influences of Asn/Gln Deamidation on Peptide Chemical Synthesis 142

6.3 Pyroglutamate Formation 144

6.4 Hydantoin Formation 147

6.5 Side Reactions on N-Terminal Cys（Cam）and N-Bromoacetylated Peptide 153

References 156

7 Side Reactions on Amino Groups in Peptide Synthesis 163

7.1 Nα-Acetylation Side Reactions 163

7.2 Trifluoroacetylation Side Reactions 166

7.3 Formylation Side Reactions 171

7.3.1 Trp（For）-Induced Peptide Formylation 172

7.3.2 Formic Acid-Induced Peptide Formylation 173

7.3.3 DMF-Induced Peptide Formylation 175

7.4 Peptide N-Alkylation Side Reactions 179

7.4.1 Chloromethyl Resin Induced Peptide N-Alkylation Side Reactions 179

7.4.2 Peptide N-Alkylation During Deblocking of Nα-Urethane Protecting Group 180

7.4.3 Peptide N-Alkylation During Global Deprotection 183

7.4.4 N-Alkylation Side Reaction on N-Terminal His via Acetone-Mediated Enamination 195

7.5 Side Reactions During Amino Acid Nα-Protection（Fmoc-OSu Induced Fmoc-β-Ala-OH and Fmoc-β-Ala-AA-OH Dipeptide Formation） 196

References 198

8 Side Reactions on Hydroxyl and Carboxyl Groups in Peptide Synthesis 203

8.1 Side Reactions on Asp/Glu Side Chain and Peptide Backbone Carboxylate 203

8.1.1 Base-Catalyzed Asp/Glu（OBzl）Transesterification Side Reaction During the Loading of Chloromethyl Resin 203

8.1.2 Esterification Side Reactions on Asp/Glu Du ring Peptidyl Resin Cleavage and Product Purification 204

8.2 Side Reactions on Ser/Thr Side Chain Hydroxyl Groups 207

8.2.1 Alkylation Side Reactions on Ser/Thr Side Chain Hydroxyl Groups 207

8.2.2 Acylation Side Reactions on Ser/Thr Side Chain Hydroxyl Groups 208

8.2.3 β-Elimination Side Reactions on Ser/Thr 210

8.2.4 N-Terminal Ser/Thr-Induced Oxazolidone Formation Side Reactions 212

8.2.5 Ser/Thr-Induced Retro Aldol Cleavage Side Reaction 214

References 215

9 Peptide Oxidation/Reduction Side Reactions 217

9.1 Oxidation Side Reactions on Cvs 217

9.2 Oxidation Side Reactions on Met 223

9.3 Oxidation Side Reactions on Trp 227

9.4 Oxidation Side Reactions on Other Amino Acids and at Nonsynthetic Steps 228

9.5 Peptide Reduction Side Reactions 230

References 231

10 Redundant Amino Acid Coupling Side Reactions 235

10.1 Dipeptide Formation During Amino Acid Nα-Fmoc Derivatization 235

10.2 Redundant Amino Acid Coupling via Premature Fmoc Deprotection 238

10.2.1 Lvs-Nε-Induced Fmoc Premature Cleavage 239

10.2.2 Nα-Proline-Induced Fmoc Premature Cleavage 242

10.2.3 DMF/NMP-Induced Fmoc Premature Cleavage 245

10.2.4 Residual Piperidine-Induced Fmoc Premature Cleavage 246

10.2.5 DMAP/DIEA-Induced Fmoc Premature Cleavage 247

10.2.6 Hydrogenation-Induced Fmoc Premature Cleavage 248

10.2.7 Fmoc Deblocking in the Starting Material 248

10.3 Redundant Amino Acid Coupling Induced by NCA Formation 249

10.4 His-Nim Promoted Gly Redundant Incorporation 250

10.5 Redundant Coupling Induced by the Undesired Amino Acid-CTC Resin Cleavage 250

10.6 Redundant Amino Acid Coupling Induced by Insufficient Resin Rinsing 252

10.7 Redundant Amino Acid Coupling Induced by Overacylation Side Reaction 253

References 254

11 Peptide Racemization 257

11.1 Peptide Racemization Mechanism 257

11.1.1 Peptide Racemization via Oxazol-5（4H）-one Formation 257

11.1.2 Peptide Racemization via Enolate Formation 258

11.1.3 Peptide Racemization via Direct Hα Abstraction 259

11.1.4 Peptide Racemization via Aspartimide Formation 260

11.1.5 Acid-Catalyzed Peptide Racemization 260

11.2 Racemization in Peptide Synthesis 261

11.2.1 Amino Acids with a High Tendency of Racemization in Peptide Synthesis 261

11.2.2 DMAP-Induced Racemization 267

11.2.3 Microwave Irradiation-Induced Racemization 268

11.2.4 Racemization During Peptide Segment Condensation 268

11.3 Strategies to Suppress Racemization in Peptide Synthesis 269

11.3.1 Amino Acid Nα-Protecting Group 269

11.3.2 Amino Acid Side Chain Protecting Group 274

11.3.3 Coupling Reagent 276

11.3.4 Coupling Tactics 282

11.3.5 Solvent 285

11.3.6 Base 285

11.3.7 Amino Acid Activation Mode 286

11.3.8 Temperature 287

11 3.9 Cu（Ⅱ）Salt Additive 287

References 288

12 Side Reactions in Peptide Phosphorylation 293

12.1 Formation of H-Phosphonate Side Product 293

12.2 Formation of Pyrophosphate Side Product 296

References 297

13 Cys Disulfide-Related Side Reactions in Peptide Synthesis 299

13.1 Disulfide Scrambling via Thiol-Disulfide Exchange 299

13.2 Disulfide Degradation and Consequent Trisulfide and Lanthionine Formation 302

13.2.1 Disulfide Degradation Pattern 302

13.2.2 Trisulfide Formation 303

13.2.3 Lanthionine Formation 308

References 309

14 Solvent-Induced Side Reactions in Peptide Synthesis 311

14.1 DCM-Induced Side Reaction 311

14.2 DMF-Induced Side Reaction 312

14.2.1 DMF-Induced N-Formylpiperidine Formation 312

14.2.2 DMF-Induced Formylation Side Reactions 313

14.2.3 DMF-Induced Acid Chloride Formation Side Reactions 313

14.3 Methanol/Ethanol-Induced Side Reactions 315

14.3.1 Methanol-Induced Esterification Side Reactions 315

14.3.2 Methanol-Induced N-Alkylation Side Reactions in Catalytic Hydrogenation 315

14.4 Acetonitrile-Induced Side Reaction 316

14.5 Acetone-Induced Side Reaction 317

14.6 MTBE-Induced Side Reaction 319

14.7 TFE-Induced Side Reaction 319

References 320

Appendix Ⅰ Molecular Weight Deviation of Peptide Impurity 323

Appendix Ⅱ List of Abbreviations 347

Subject Index 353