1 Peptide Fragmentation/Deletion Side Reactions

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

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

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

1.4 Acidolysis of-Asp-Pro-Bond

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

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

1.7 Acidolysis of Peptides with N-Terminal FITC Modification

1.8 Acidolysis of Thioamide Peptide

1.9 Deguanidination Side Reaction on Arg

1.10 DKP（2，5-Diketopiperazine）Formation

References

2 β-Elimination Side Reactions

2.1 β-Elimination of Cys Sulfhydryl Side Chain

2.2 β-Elimination of Phosphorylated Ser/Thr

References

3 Peptide Global Deprotection/Scavenger-Induced Side Reactions

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

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

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

3.4 Trp Dimerization Side Reaction During Peptide Global Deprotection

3.5 Trp Reduction During Peptide Global Deprotection

3.6 Cys Alkylation During Peptide Global Deprotection

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

3.8 Peptide Sulfonation in Side Chain Global Deprotection Reaction

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

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

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

References

4 Peptide Rearrangement Side Reactions

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

4.2 Base Catalyzed Acyl O→N Migration

4.3 His-Nim-Induced Acyl Migration

References

5 Side Reactions Upon Amino Acid/Peptide Carboxyl Activation

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

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

5.3 δ-Lactam Formation Upon Arg Activation Reaction

5.4 NCA Formation Upon Boc/Z-Amino Acid Activation

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

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

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

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

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

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

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

References

6 Intramolecular Cyclization Side Reactions

6.1 Aspartimide Formation

6.1.1 Factors That Influence Aspartimide Formation

6.1.2 Solutions for Aspartimide Formation

6.2 Asn/Gln Deamidation and Other Relevant Side Reactions

6.2.1 Mechanism of Asn/Gln Deamidation

6.2.2 Factors Impacting on Asn/Gln Deamidation

6.2.3 Influences of Asn/Gln Deamidation on Peptide Chemical Synthesis

6.3 Pyroglutamate Formation

6.4 Hydantoin Formation

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

References

7 Side Reactions on Amino Groups in Peptide Synthesis

7.1 Nα-Acetylation Side Reactions

7.2 Trifluoroacetylation Side Reactions

7.3 Formylation Side Reactions

7.3.1 Trp（For）-Induced Peptide Formylation

7.3.2 Formic Acid-Induced Peptide Formylation

7.3.3 DMF-Induced Peptide Formylation

7.4 Peptide N-Alkylation Side Reactions

7.4.1 Chloromethyl Resin Induced Peptide N-Alkylation Side Reactions

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

7.4.3 Peptide N-Alkylation During Global Deprotection

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

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

References

8 Side Reactions on Hydroxyl and Carboxyl Groups in Peptide Synthesis

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

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

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

8.2 Side Reactions on Ser/Thr Side Chain Hydroxyl Groups

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

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

8.2.3 β-Elimination Side Reactions on Ser/Thr

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

8.2.5 Ser/Thr-Induced Retro Aldol Cleavage Side Reaction

References

9 Peptide Oxidation/Reduction Side Reactions

9.1 Oxidation Side Reactions on Cvs

9.2 Oxidation Side Reactions on Met

9.3 Oxidation Side Reactions on Trp

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

9.5 Peptide Reduction Side Reactions

References

10 Redundant Amino Acid Coupling Side Reactions

10.1 Dipeptide Formation During Amino Acid Nα-Fmoc Derivatization

10.2 Redundant Amino Acid Coupling via Premature Fmoc Deprotection

10.2.1 Lvs-Nε-Induced Fmoc Premature Cleavage

10.2.2 Nα-Proline-Induced Fmoc Premature Cleavage

10.2.3 DMF/NMP-Induced Fmoc Premature Cleavage

10.2.4 Residual Piperidine-Induced Fmoc Premature Cleavage

10.2.5 DMAP/DIEA-Induced Fmoc Premature Cleavage

10.2.6 Hydrogenation-Induced Fmoc Premature Cleavage

10.2.7 Fmoc Deblocking in the Starting Material

10.3 Redundant Amino Acid Coupling Induced by NCA Formation

10.4 His-Nim Promoted Gly Redundant Incorporation

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

10.6 Redundant Amino Acid Coupling Induced by Insufficient Resin Rinsing

10.7 Redundant Amino Acid Coupling Induced by Overacylation Side Reaction

References

11 Peptide Racemization

11.1 Peptide Racemization Mechanism

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

11.1.2 Peptide Racemization via Enolate Formation

11.1.3 Peptide Racemization via Direct Hα Abstraction

11.1.4 Peptide Racemization via Aspartimide Formation

11.1.5 Acid-Catalyzed Peptide Racemization

11.2 Racemization in Peptide Synthesis

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

11.2.2 DMAP-Induced Racemization

11.2.3 Microwave Irradiation-Induced Racemization

11.2.4 Racemization During Peptide Segment Condensation

11.3 Strategies to Suppress Racemization in Peptide Synthesis

11.3.1 Amino Acid Nα-Protecting Group

11.3.2 Amino Acid Side Chain Protecting Group

11.3.3 Coupling Reagent

11.3.4 Coupling Tactics

11.3.5 Solvent

11.3.6 Base

11.3.7 Amino Acid Activation Mode

11.3.8 Temperature

11 3.9 Cu（Ⅱ）Salt Additive

References

12 Side Reactions in Peptide Phosphorylation

12.1 Formation of H-Phosphonate Side Product

12.2 Formation of Pyrophosphate Side Product

References

13 Cys Disulfide-Related Side Reactions in Peptide Synthesis

13.1 Disulfide Scrambling via Thiol-Disulfide Exchange

13.2 Disulfide Degradation and Consequent Trisulfide and Lanthionine Formation

13.2.1 Disulfide Degradation Pattern

13.2.2 Trisulfide Formation

13.2.3 Lanthionine Formation

References

14 Solvent-Induced Side Reactions in Peptide Synthesis

14.1 DCM-Induced Side Reaction

14.2 DMF-Induced Side Reaction

14.2.1 DMF-Induced N-Formylpiperidine Formation

14.2.2 DMF-Induced Formylation Side Reactions

14.2.3 DMF-Induced Acid Chloride Formation Side Reactions

14.3 Methanol/Ethanol-Induced Side Reactions

14.3.1 Methanol-Induced Esterification Side Reactions

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

14.4 Acetonitrile-Induced Side Reaction

14.5 Acetone-Induced Side Reaction

14.6 MTBE-Induced Side Reaction

14.7 TFE-Induced Side Reaction

References

Appendix Ⅰ Molecular Weight Deviation of Peptide Impurity

Appendix Ⅱ List of Abbreviations

Subject Index