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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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Related in: MedlinePlus

Geometric parameters used for separating carboxyl–carboxylate dimers involving syn or anti lone pairs. The histogram has been drawn for a sub-ensemble of SS and SA dimers. The syn conformers are defined by a φ value below 130° marked by a blue dashed line on the histogram; φ corresponds to the O(H)⋯O⋯O angle. The anti conformers are defined by a φ value greater than 130°.
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fig5: Geometric parameters used for separating carboxyl–carboxylate dimers involving syn or anti lone pairs. The histogram has been drawn for a sub-ensemble of SS and SA dimers. The syn conformers are defined by a φ value below 130° marked by a blue dashed line on the histogram; φ corresponds to the O(H)⋯O⋯O angle. The anti conformers are defined by a φ value greater than 130°.

Mentions: As noted above (Fig. 2 ▶), simple geometric criteria can be used to filter the carboxyl syn and anti conformers. It was less obvious how to discriminate dimers based on their syn or anti lone pair bonding types. After having tried several options, we found that the histograms showing the φ angle that corresponds to the O(H)⋯O⋯O angle involving the hydrogen-bond donor O atom and the two carboxylate O atoms are the most helpful to achieve such a goal. The histogram drawn for the carboxyl–carboxylate dimers is unambiguous and prompted us to use a 130° cut-off for isolating the SS and AA from the SA and AS carboxyl–carboxylate dimers, respectively (Fig. 5 ▶). Although a clear partition is difficult to identify on the SS-S dimer histogram (data not shown), a visualization of these dimers confirmed the soundness of the defined criteria. As is often the case, borderline conformations are observed and are difficult to eliminate but do not alter the inferred landscape.


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)

Geometric parameters used for separating carboxyl–carboxylate dimers involving syn or anti lone pairs. The histogram has been drawn for a sub-ensemble of SS and SA dimers. The syn conformers are defined by a φ value below 130° marked by a blue dashed line on the histogram; φ corresponds to the O(H)⋯O⋯O angle. The anti conformers are defined by a φ value greater than 130°.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: Geometric parameters used for separating carboxyl–carboxylate dimers involving syn or anti lone pairs. The histogram has been drawn for a sub-ensemble of SS and SA dimers. The syn conformers are defined by a φ value below 130° marked by a blue dashed line on the histogram; φ corresponds to the O(H)⋯O⋯O angle. The anti conformers are defined by a φ value greater than 130°.
Mentions: As noted above (Fig. 2 ▶), simple geometric criteria can be used to filter the carboxyl syn and anti conformers. It was less obvious how to discriminate dimers based on their syn or anti lone pair bonding types. After having tried several options, we found that the histograms showing the φ angle that corresponds to the O(H)⋯O⋯O angle involving the hydrogen-bond donor O atom and the two carboxylate O atoms are the most helpful to achieve such a goal. The histogram drawn for the carboxyl–carboxylate dimers is unambiguous and prompted us to use a 130° cut-off for isolating the SS and AA from the SA and AS carboxyl–carboxylate dimers, respectively (Fig. 5 ▶). Although a clear partition is difficult to identify on the SS-S dimer histogram (data not shown), a visualization of these dimers confirmed the soundness of the defined criteria. As is often the case, borderline conformations are observed and are difficult to eliminate but do not alter the inferred landscape.

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