Synthon preference in O-protonated amide crystals-dominance of short strong hydrogen bonds

Sathyanarayana Reddy Perumalla, Calvin Sun

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Although the amide functional group is weakly ionizable, there have been serendipitous discoveries of amide salts. To facilitate their systematic design, we sought to identify the preference of 12 possible synthons in oxygen protonated amide structures. An analysis of a total of 81 protonated amide crystal structures retrieved from the Cambridge Structural Database and 12 new protonated amide structures prepared by us, revealed that ∼86% of these structures involving charge assisted short strong hydrogen bonds, including ∼54% of the hydrogen bridged dimers formed between protonated and neutral amide. The probability of forming hydrogen bridged dimers increases in the order of primary amide < secondary amide < tertiary amide. The two previously missing synthons, R22(8) and R12(6), in primary amides are realized for the first time in this work. However, the two predicted ring (R) hydrogen bonding synthons, R22(8) and R12(6), for cis secondary amides remain to be discovered.

Original languageEnglish (US)
Pages (from-to)8941-8946
Number of pages6
Issue number44
StatePublished - Nov 28 2013


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