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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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The four carboxyl–carboxylate dimer types and their rotamer distribution around the interlinking hydrogen bond for structures with R ≤ 0.05. The C and O atoms not belonging to the interacting carboxyl or carboxylate groups are shown in light blue, N atoms are shown in magenta. (a) (Left) Antiplanar SS dimer involving two fumaric acid molecules (HUSSUJ). (Middle) Synplanar SS dimer (JEDPUE). An NH4+ molecule links the carboxyl(ate) groups. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (Right) O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SA dimer involving two fumaric acid molecules (CLEMAS) and O1—O2—C3—C4 dihedral angle rotamer histogram. (c) Antiplanar AS dimer involving two fumaric acid molecules (SEGSAZ) and O1—O2—O3—O4 dihedral angle rotamer histogram. (d) Antiplanar AA dimer involving two fumaric acid molecules (BAHLEC) and C1—C2—C3—C4 dihedral angle rotamer histogram.
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fig10: The four carboxyl–carboxylate dimer types and their rotamer distribution around the interlinking hydrogen bond for structures with R ≤ 0.05. The C and O atoms not belonging to the interacting carboxyl or carboxylate groups are shown in light blue, N atoms are shown in magenta. (a) (Left) Antiplanar SS dimer involving two fumaric acid molecules (HUSSUJ). (Middle) Synplanar SS dimer (JEDPUE). An NH4+ molecule links the carboxyl(ate) groups. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (Right) O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SA dimer involving two fumaric acid molecules (CLEMAS) and O1—O2—C3—C4 dihedral angle rotamer histogram. (c) Antiplanar AS dimer involving two fumaric acid molecules (SEGSAZ) and O1—O2—O3—O4 dihedral angle rotamer histogram. (d) Antiplanar AA dimer involving two fumaric acid molecules (BAHLEC) and C1—C2—C3—C4 dihedral angle rotamer histogram.

Mentions: The SS dimer, involving a hydrogen bond between a syn hydroxyl group and a syn carboxylate lone pair, is the most prevalent carboxyl–carboxylate dimer in the CSD (Table 3 ▶). The antiplanar SS dimer is frequently observed while dimers close to the synplanar orientation are much less represented (Fig. 10 ▶). Some rare occurrences of the synplanar orientation stabilized by intervening groups (such as NH4+ in JEDPUE; see Fig. 10 ▶) are reported. In those instances, the distances between the O atoms not involved in the hydrogen bond exceed 3.0 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)

The four carboxyl–carboxylate dimer types and their rotamer distribution around the interlinking hydrogen bond for structures with R ≤ 0.05. The C and O atoms not belonging to the interacting carboxyl or carboxylate groups are shown in light blue, N atoms are shown in magenta. (a) (Left) Antiplanar SS dimer involving two fumaric acid molecules (HUSSUJ). (Middle) Synplanar SS dimer (JEDPUE). An NH4+ molecule links the carboxyl(ate) groups. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (Right) O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SA dimer involving two fumaric acid molecules (CLEMAS) and O1—O2—C3—C4 dihedral angle rotamer histogram. (c) Antiplanar AS dimer involving two fumaric acid molecules (SEGSAZ) and O1—O2—O3—O4 dihedral angle rotamer histogram. (d) Antiplanar AA dimer involving two fumaric acid molecules (BAHLEC) and C1—C2—C3—C4 dihedral angle rotamer histogram.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig10: The four carboxyl–carboxylate dimer types and their rotamer distribution around the interlinking hydrogen bond for structures with R ≤ 0.05. The C and O atoms not belonging to the interacting carboxyl or carboxylate groups are shown in light blue, N atoms are shown in magenta. (a) (Left) Antiplanar SS dimer involving two fumaric acid molecules (HUSSUJ). (Middle) Synplanar SS dimer (JEDPUE). An NH4+ molecule links the carboxyl(ate) groups. The light blue spheres indicate that the molecule has been truncated for visualization purposes. (Right) O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SA dimer involving two fumaric acid molecules (CLEMAS) and O1—O2—C3—C4 dihedral angle rotamer histogram. (c) Antiplanar AS dimer involving two fumaric acid molecules (SEGSAZ) and O1—O2—O3—O4 dihedral angle rotamer histogram. (d) Antiplanar AA dimer involving two fumaric acid molecules (BAHLEC) and C1—C2—C3—C4 dihedral angle rotamer histogram.
Mentions: The SS dimer, involving a hydrogen bond between a syn hydroxyl group and a syn carboxylate lone pair, is the most prevalent carboxyl–carboxylate dimer in the CSD (Table 3 ▶). The antiplanar SS dimer is frequently observed while dimers close to the synplanar orientation are much less represented (Fig. 10 ▶). Some rare occurrences of the synplanar orientation stabilized by intervening groups (such as NH4+ in JEDPUE; see Fig. 10 ▶) are reported. In those instances, the distances between the O atoms not involved in the hydrogen bond exceed 3.0 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