Limits...
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.

Show MeSH

Related in: MedlinePlus

Geometric parameters used for separating the carboxyl syn and anti conformers. The syn conformers are defined by a θ value below 120° (marked by a blue dashed line on the histogram; θ corresponds to the O⋯O—H angle). The anti conformers are defined by a θ value greater than 120°. The histogram has been derived from an ensemble of low R-factor (R ≤ 0.05) carboxylic acid containing structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383392&req=5

fig2: Geometric parameters used for separating the carboxyl syn and anti conformers. The syn conformers are defined by a θ value below 120° (marked by a blue dashed line on the histogram; θ corresponds to the O⋯O—H angle). The anti conformers are defined by a θ value greater than 120°. The histogram has been derived from an ensemble of low R-factor (R ≤ 0.05) carboxylic acid containing structures.

Mentions: Carboxylic acids bear a proton that is commonly found in the syn and more rarely in the anti conformation. In order to distinguish between the syn and anti conformers, we imposed the following criterion on the O⋯O—H angle (θ) (Fig. 2 ▶). The syn conformer corresponds to θ angle values between 0 and 120°; the anti confirmer to θ angle values between 120 and 180°. The relative proportion of these conformers is roughly 9/1 in favour of syn, while negatively charged carboxylate groups represent about 2/3 of the total carboxyl groups (Table 2 ▶). The main geometric features of carboxyl(ate) groups are similar to those reported in an early study (Leiserowitz, 1976 ▶). Our updated values are reported in Table 2 ▶. Note that, due to its partial double-bond character, the C=O bond of carboxyl groups is shorter by ∼ 0.11 Å than the adjacent C—O(H) hydroxyl bond.


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 the carboxyl syn and anti conformers. The syn conformers are defined by a θ value below 120° (marked by a blue dashed line on the histogram; θ corresponds to the O⋯O—H angle). The anti conformers are defined by a θ value greater than 120°. The histogram has been derived from an ensemble of low R-factor (R ≤ 0.05) carboxylic acid containing structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Geometric parameters used for separating the carboxyl syn and anti conformers. The syn conformers are defined by a θ value below 120° (marked by a blue dashed line on the histogram; θ corresponds to the O⋯O—H angle). The anti conformers are defined by a θ value greater than 120°. The histogram has been derived from an ensemble of low R-factor (R ≤ 0.05) carboxylic acid containing structures.
Mentions: Carboxylic acids bear a proton that is commonly found in the syn and more rarely in the anti conformation. In order to distinguish between the syn and anti conformers, we imposed the following criterion on the O⋯O—H angle (θ) (Fig. 2 ▶). The syn conformer corresponds to θ angle values between 0 and 120°; the anti confirmer to θ angle values between 120 and 180°. The relative proportion of these conformers is roughly 9/1 in favour of syn, while negatively charged carboxylate groups represent about 2/3 of the total carboxyl groups (Table 2 ▶). The main geometric features of carboxyl(ate) groups are similar to those reported in an early study (Leiserowitz, 1976 ▶). Our updated values are reported in Table 2 ▶. Note that, due to its partial double-bond character, the C=O bond of carboxyl groups is shorter by ∼ 0.11 Å than the adjacent C—O(H) hydroxyl bond.

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