Coupling Reagents for Peptide Chemistry

Published on 02.12.2016

In this news section, we highlight three useful coupling reagents for peptide chemistry: PyCLOCK, PyAOP and HDMA.

Since the inception of peptide chemistry, the efficiency of coupling reagents has seen a constant advancement over the years. In the course of these improvements, chemists have striven to find a balance between reactivity of the coupling reagent, and racemization / other side reactions.
Three of the most useful modern coupling reagents are presented here: PyCLOCK, PyAOP and HDMA.

PyCLOCK is phosphonium salt of the racemization suppressant 6-Cl-HOBt. Unlike aminium-type coupling reagents (such as HBTU, HATU), PyCLOCK does not react with free amino groups and therefore does not terminate chain elongation by forming a guanidine side product with the N-terminus of the growing peptide chain. This property renders PyCLOCK especially useful for slow couplings and for cyclization reactions. Furthermore, unlike aminium coupling reagents, PyCLOCK can be used in excess to assure a complete activation of the incoming building block’s carboxylic acid function.

Cycle of activation, coupling and deprotection during solid-phase peptide synthesis.

PyAOP is the 7-aza derivative of PyBOP. As such, it is the phosphonium salt derivative of HOAt. It facilitates higher coupling yields than BOP and PyBOP. Unlike BOP, no toxic HMPA (hexamethylphosphoramide) is formed during the coupling reaction. Like PyCLOCK, PyAOP does not react with the amino terminus of the growing peptide chain und thus is useful for incorporating hindered amino acids, synthesizing difficult sequences and preparing cyclic peptides.

HDMA is an immonium-type coupling reagent. Due to the presence of the morpholino oxygen, HDMA is more soluble than dimethylamino derivatives such as HATU or HBTU. Moreover, it frequently exhibits better coupling efficiency and lower racemization than said dimethylamino-type coupling reagents.

→ Find many more coupling reagents in our Reagents section!


  • Fast conventional Fmoc solid-phase peptide synthesis: a comparative study of different activators; C. A. Chantell, M. A. Onaiyekan and M. Menakuru; Journal of Peptide Science 2012; 18: 88-91. doi:10.1002/psc.1419
  • Peptide Coupling Reagents, More than a Letter Soup; A. El-Faham and F. Albericio; Chemical Reviews 2011; 111: 6557-6602. doi:10.1021/cr100048w
  • Amide bond formation: beyond the myth of coupling reagents; E. Valeur and M. Bradley; Chemical Society Reviews 2009; 38: 606-631. doi:10.1039/b701677h
  • PyClock, the phosphonium salt derived from 6-Cl-HOBt; R. Subiros-Funosas, J. A. Moreno, N. Bayo-Puxan, K. ABU-RABEAH, A. Ewenson, D. Atias, R. S. Marks and F. Albericio; Chimica oggi 2008; 26: 10-12.
  • Novel Proton Acceptor Immonium-Type Coupling Reagents:  Application in Solution and Solid-Phase Peptide Synthesis; A. El-Faham and F. Albericio; Organic Letters 2007; 9: 4475-4477. doi:10.1021/ol701817u
  • Use of Onium Salt-Based Coupling Reagents in Peptide Synthesis1; F. Albericio, J. M. Bofill, A. El-Faham and S. A. Kates; The Journal of Organic Chemistry 1998; 63: 9678-9683. doi:10.1021/jo980807y
  • On the use of PyAOP, a phosphonium salt derived from HOAt, in solid-phase peptide synthesis; F. Albericio, M. Cases, J. Alsina, S. A. Triolo, L. A. Carpino and S. A. Kates; Tetrahedron letters 1997; 38: 4853-4856. doi: