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A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems.

D'Ascenzo L, Auffinger P - Acta Crystallogr B Struct Sci Cryst Eng Mater (2015)

Bottom Line: 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.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 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France.

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.

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Histograms showing the distance distribution between the two O atoms directly involved in the carboxyl(ate)–water hydrogen bond. For clarity, only water molecules positioned in a 1 Å slice above and below the plane defined by the three heavy atoms of the carboxyl(ate) groups are considered. A cut-off of 2.2 Å for d(C=O⋯H—Ow) or d(C—OH⋯Ow) was used. (a) d(C—OH⋯Ow) histogram involving carboxyl groups. (b) d(C=O⋯Ow) histogram involving carboxylate groups. (c) d(C=O⋯Ow) histogram involving carbonyl O atoms of the carboxyl group.
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fig11: Histograms showing the distance distribution between the two O atoms directly involved in the carboxyl(ate)–water hydrogen bond. For clarity, only water molecules positioned in a 1 Å slice above and below the plane defined by the three heavy atoms of the carboxyl(ate) groups are considered. A cut-off of 2.2 Å for d(C=O⋯H—Ow) or d(C—OH⋯Ow) was used. (a) d(C—OH⋯Ow) histogram involving carboxyl groups. (b) d(C=O⋯Ow) histogram involving carboxylate groups. (c) d(C=O⋯Ow) histogram involving carbonyl O atoms of the carboxyl group.

Mentions: The hydrogen-bond length between carboxyl(ate) groups and water molecules is strongly dependent on the acceptor or donor character of the former. When bound to the hydroxyl group, the average d(C—O(H)⋯Ow) distance is 2.59 ± 0.06 Å (Fig. 11 ▶a); when bound to a carboxyl(ate) carbonyl group, the average d(C=O⋯Ow) distance (2.77 ± 0.07 Å) becomes close to water hydrogen-bond distances (Figs. 11 ▶b and c). The shortest reported hydrogen-bond lengths are close to 2.4 Å. Such a short length is found in the CACTUW structure (Vishweshwar et al., 2004 ▶), where the (C=O)O—H⋯Ow distance is close to 2.48 Å and involves an anti conformer (Fig. 9 ▶a). Interestingly, only 44 water molecules establish a hydrogen bond with the lone pair of the carboxyl—OH group either in syn or anti (compared with the ∼ 2800 water molecules found around the other groups), confirming its poor acceptor potential. The associated distances are close to 2.80 Å.


A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems.

D'Ascenzo L, Auffinger P - Acta Crystallogr B Struct Sci Cryst Eng Mater (2015)

Histograms showing the distance distribution between the two O atoms directly involved in the carboxyl(ate)–water hydrogen bond. For clarity, only water molecules positioned in a 1 Å slice above and below the plane defined by the three heavy atoms of the carboxyl(ate) groups are considered. A cut-off of 2.2 Å for d(C=O⋯H—Ow) or d(C—OH⋯Ow) was used. (a) d(C—OH⋯Ow) histogram involving carboxyl groups. (b) d(C=O⋯Ow) histogram involving carboxylate groups. (c) d(C=O⋯Ow) histogram involving carbonyl O atoms of the carboxyl group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383392&req=5

fig11: Histograms showing the distance distribution between the two O atoms directly involved in the carboxyl(ate)–water hydrogen bond. For clarity, only water molecules positioned in a 1 Å slice above and below the plane defined by the three heavy atoms of the carboxyl(ate) groups are considered. A cut-off of 2.2 Å for d(C=O⋯H—Ow) or d(C—OH⋯Ow) was used. (a) d(C—OH⋯Ow) histogram involving carboxyl groups. (b) d(C=O⋯Ow) histogram involving carboxylate groups. (c) d(C=O⋯Ow) histogram involving carbonyl O atoms of the carboxyl group.
Mentions: The hydrogen-bond length between carboxyl(ate) groups and water molecules is strongly dependent on the acceptor or donor character of the former. When bound to the hydroxyl group, the average d(C—O(H)⋯Ow) distance is 2.59 ± 0.06 Å (Fig. 11 ▶a); when bound to a carboxyl(ate) carbonyl group, the average d(C=O⋯Ow) distance (2.77 ± 0.07 Å) becomes close to water hydrogen-bond distances (Figs. 11 ▶b and c). The shortest reported hydrogen-bond lengths are close to 2.4 Å. Such a short length is found in the CACTUW structure (Vishweshwar et al., 2004 ▶), where the (C=O)O—H⋯Ow distance is close to 2.48 Å and involves an anti conformer (Fig. 9 ▶a). Interestingly, only 44 water molecules establish a hydrogen bond with the lone pair of the carboxyl—OH group either in syn or anti (compared with the ∼ 2800 water molecules found around the other groups), confirming its poor acceptor potential. The associated distances are close to 2.80 Å.

Bottom Line: 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.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 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France.

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.

Show MeSH
Related in: MedlinePlus