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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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Examples of the eight catemer types identified in the CSD. The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue. The white and red dots mark the position of the connected carboxylic groups in the catemeric chain. The red asterisks mark the carboxyl groups used for naming the catemer. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) SS-S homo-catemer (XONNET); (b) SA-S homo-catemer (ACETAC07); (c) AS-A homo-catemer (GIMRAW); (d) AA-A homo-catemer (DMOXBA01); (e) SS-A·AS-S hetero-catemer (ROZHEU); (f) SS-A·AA-S hetero-catemer (WOKPOC); (g) SA-A·AS-S hetero-catemer (MEKLOE). (h) SA-A·AA-S hetero-catemer (MALIAC12).
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fig12: Examples of the eight catemer types identified in the CSD. The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue. The white and red dots mark the position of the connected carboxylic groups in the catemeric chain. The red asterisks mark the carboxyl groups used for naming the catemer. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) SS-S homo-catemer (XONNET); (b) SA-S homo-catemer (ACETAC07); (c) AS-A homo-catemer (GIMRAW); (d) AA-A homo-catemer (DMOXBA01); (e) SS-A·AS-S hetero-catemer (ROZHEU); (f) SS-A·AA-S hetero-catemer (WOKPOC); (g) SA-A·AS-S hetero-catemer (MEKLOE). (h) SA-A·AA-S hetero-catemer (MALIAC12).

Mentions: Nomenclature: The dimer nomenclature can be adapted without major modifications to the catemer motifs for which two classes can be defined: (i) the homo-catemers involving the formation of a continuous chain of the same dimer and (ii) the hetero-catemers involving two alternating dimer types. In the latter case, we impose the convention that the syn conformer precedes the anti conformer. Thus, the SS-A·AS-S code should be used instead of the AS-S·SS-A code. In the current CSD release, four homo- and four hetero-catemer types were identified (Table 4 ▶ and Fig. 12 ▶).


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)

Examples of the eight catemer types identified in the CSD. The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue. The white and red dots mark the position of the connected carboxylic groups in the catemeric chain. The red asterisks mark the carboxyl groups used for naming the catemer. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) SS-S homo-catemer (XONNET); (b) SA-S homo-catemer (ACETAC07); (c) AS-A homo-catemer (GIMRAW); (d) AA-A homo-catemer (DMOXBA01); (e) SS-A·AS-S hetero-catemer (ROZHEU); (f) SS-A·AA-S hetero-catemer (WOKPOC); (g) SA-A·AS-S hetero-catemer (MEKLOE). (h) SA-A·AA-S hetero-catemer (MALIAC12).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383392&req=5

fig12: Examples of the eight catemer types identified in the CSD. The C and O atoms not belonging to the interacting carboxyl groups are shown in light blue. The white and red dots mark the position of the connected carboxylic groups in the catemeric chain. The red asterisks mark the carboxyl groups used for naming the catemer. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (a) SS-S homo-catemer (XONNET); (b) SA-S homo-catemer (ACETAC07); (c) AS-A homo-catemer (GIMRAW); (d) AA-A homo-catemer (DMOXBA01); (e) SS-A·AS-S hetero-catemer (ROZHEU); (f) SS-A·AA-S hetero-catemer (WOKPOC); (g) SA-A·AS-S hetero-catemer (MEKLOE). (h) SA-A·AA-S hetero-catemer (MALIAC12).
Mentions: Nomenclature: The dimer nomenclature can be adapted without major modifications to the catemer motifs for which two classes can be defined: (i) the homo-catemers involving the formation of a continuous chain of the same dimer and (ii) the hetero-catemers involving two alternating dimer types. In the latter case, we impose the convention that the syn conformer precedes the anti conformer. Thus, the SS-A·AS-S code should be used instead of the AS-S·SS-A code. In the current CSD release, four homo- and four hetero-catemer types were identified (Table 4 ▶ and Fig. 12 ▶).

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