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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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Rare carboxyl–carboxyl dimers involving the lone pair of the hydroxyl group (‘hydroxyl dimers’). The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue, N atoms are shown in magenta. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) Antiplanar SS-A dimer (CACTUW; R = 0.04). Due to the size of the system, only the interacting fragments are shown. The unusually short carboxyl–Ow distance is given. The red asterisks mark the carboxyl groups involved in the ss-a dimer. (b) Antiplanar sa-s dimer (CAYJAO; R = 0.06). (c) Synplanar sa-s dimer involving two fumaric acid molecules (EMONAW; R = 0.11). The N-containing interacting molecule has been truncated due to its size.
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fig9: Rare carboxyl–carboxyl dimers involving the lone pair of the hydroxyl group (‘hydroxyl dimers’). The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue, N atoms are shown in magenta. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) Antiplanar SS-A dimer (CACTUW; R = 0.04). Due to the size of the system, only the interacting fragments are shown. The unusually short carboxyl–Ow distance is given. The red asterisks mark the carboxyl groups involved in the ss-a dimer. (b) Antiplanar sa-s dimer (CAYJAO; R = 0.06). (c) Synplanar sa-s dimer involving two fumaric acid molecules (EMONAW; R = 0.11). The N-containing interacting molecule has been truncated due to its size.

Mentions: ‘Hydroxyl dimers’: Although the two carboxyl hydroxyl groups could form hydrogen bonds, this interaction occurs rarely. Only two ss-a and six sa-s conformers were characterized (Table 3 ▶; Fig. 9 ▶). None of the two other possible as-a and aa-s conformers were observed. This points to the fact that the lone pairs of carboxyl —OH groups seem to be much less basic and/or accessible to other carboxyl groups than the lone pairs of more common hydroxyl groups.


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)

Rare carboxyl–carboxyl dimers involving the lone pair of the hydroxyl group (‘hydroxyl dimers’). The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue, N atoms are shown in magenta. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) Antiplanar SS-A dimer (CACTUW; R = 0.04). Due to the size of the system, only the interacting fragments are shown. The unusually short carboxyl–Ow distance is given. The red asterisks mark the carboxyl groups involved in the ss-a dimer. (b) Antiplanar sa-s dimer (CAYJAO; R = 0.06). (c) Synplanar sa-s dimer involving two fumaric acid molecules (EMONAW; R = 0.11). The N-containing interacting molecule has been truncated due to its size.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig9: Rare carboxyl–carboxyl dimers involving the lone pair of the hydroxyl group (‘hydroxyl dimers’). The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue, N atoms are shown in magenta. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) Antiplanar SS-A dimer (CACTUW; R = 0.04). Due to the size of the system, only the interacting fragments are shown. The unusually short carboxyl–Ow distance is given. The red asterisks mark the carboxyl groups involved in the ss-a dimer. (b) Antiplanar sa-s dimer (CAYJAO; R = 0.06). (c) Synplanar sa-s dimer involving two fumaric acid molecules (EMONAW; R = 0.11). The N-containing interacting molecule has been truncated due to its size.
Mentions: ‘Hydroxyl dimers’: Although the two carboxyl hydroxyl groups could form hydrogen bonds, this interaction occurs rarely. Only two ss-a and six sa-s conformers were characterized (Table 3 ▶; Fig. 9 ▶). None of the two other possible as-a and aa-s conformers were observed. This points to the fact that the lone pairs of carboxyl —OH groups seem to be much less basic and/or accessible to other carboxyl groups than the lone pairs of more common hydroxyl groups.

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