Abstract
Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.
Highlights
Carboxyl and carboxylate [written collectively as carboxyl(ate)] groups are found in a large variety of biomolecular compounds and in drugs and synthetic molecular systems
H-atom disorder is common in carboxylic systems, structures where the H atom could not be unambiguously assigned to a single O atom were not considered (Leiserowitz, 1976; Berkovitch-Yellin & Leiserowitz, 1982; Wilson et al, 1996; Das et al, 2005; Thomas et al, 2010; Hursthouse et al, 2011)
In order to distinguish between the syn and anti conformers, we imposed the following criterion on the OÁ Á ÁO—H angle () (Fig. 2)
Summary
Carboxyl and carboxylate [written collectively as carboxyl(ate)] groups are found in a large variety of biomolecular compounds and in drugs and synthetic molecular systems For the former, the two Asp and Glu amino acids represent $ 2% of the $ 2 million amino acids found in the Protein Data Bank (PDB, November 2014 release; Berman et al, 2000). Despite the fact that carboxyl groups figure among the best investigated hydrogen-bond functionalities (Huggins, 1936; Leiserowitz, 1976; Berkovitch-Yellin & Leiserowitz, 1982; Steiner, 2001, 2002; Das & Desiraju, 2006; RodrıguezCuamatzi et al, 2007), no systematic classification of carboxyl– carboxyl motifs is currently available
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