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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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Carboxyl–carboxyl dimers involving a syn conformer and the lone pair of a carbonyl group (‘carbonyl dimer’) along with 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 groups are shown in light blue, F and Cl atoms are shown in yellow and green, respectively. (a) Antiplanar SS-S dimer (NAGVUM) and O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SS-A dimer (CBUCDX01) and O1—O2—O3—O4 dihedral angle rotamer histogram. (c) Antiplanar and synplanar SA-S dimers (CLACET01 and ACETAC09) and O1—O2—C3—C4 dihedral angle rotamer histogram. (d) Antiplanar SA-A dimer (MALIAC12) and O1—O2—C3—C4 dihedral angle rotamer histogram.
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fig7: Carboxyl–carboxyl dimers involving a syn conformer and the lone pair of a carbonyl group (‘carbonyl dimer’) along with 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 groups are shown in light blue, F and Cl atoms are shown in yellow and green, respectively. (a) Antiplanar SS-S dimer (NAGVUM) and O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SS-A dimer (CBUCDX01) and O1—O2—O3—O4 dihedral angle rotamer histogram. (c) Antiplanar and synplanar SA-S dimers (CLACET01 and ACETAC09) and O1—O2—C3—C4 dihedral angle rotamer histogram. (d) Antiplanar SA-A dimer (MALIAC12) and O1—O2—C3—C4 dihedral angle rotamer histogram.

Mentions: ‘Carbonyl dimers’: Eight ‘carbonyl dimer’ types were identified (Table 3 ▶). The four types involving the syn conformer of the donor carboxyl group and among them, the SA-S dimers, are well represented. The synplanar rotamers are generally not observed except for the SA-S dimers where they are as prominent as antiplanar rotamers (Fig. 7 ▶). Note that syn- and antiplanar rotamers are defined by inter-dimer dihedral angles with values close to 0 and 180°, respectively (see, for example, Fig. 7 ▶c). The ACETAC09 acetic acid structure seems to be stabilized by a C—H⋯O interaction involving the methyl group, an orientation that is not found for chloroacetic acid in the CLACET01 structure and illustrates how weak interactions participate in structural networks.


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)

Carboxyl–carboxyl dimers involving a syn conformer and the lone pair of a carbonyl group (‘carbonyl dimer’) along with 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 groups are shown in light blue, F and Cl atoms are shown in yellow and green, respectively. (a) Antiplanar SS-S dimer (NAGVUM) and O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SS-A dimer (CBUCDX01) and O1—O2—O3—O4 dihedral angle rotamer histogram. (c) Antiplanar and synplanar SA-S dimers (CLACET01 and ACETAC09) and O1—O2—C3—C4 dihedral angle rotamer histogram. (d) Antiplanar SA-A dimer (MALIAC12) and O1—O2—C3—C4 dihedral angle rotamer histogram.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig7: Carboxyl–carboxyl dimers involving a syn conformer and the lone pair of a carbonyl group (‘carbonyl dimer’) along with 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 groups are shown in light blue, F and Cl atoms are shown in yellow and green, respectively. (a) Antiplanar SS-S dimer (NAGVUM) and O1—O2—O3—O4 dihedral angle rotamer histogram. (b) Antiplanar SS-A dimer (CBUCDX01) and O1—O2—O3—O4 dihedral angle rotamer histogram. (c) Antiplanar and synplanar SA-S dimers (CLACET01 and ACETAC09) and O1—O2—C3—C4 dihedral angle rotamer histogram. (d) Antiplanar SA-A dimer (MALIAC12) and O1—O2—C3—C4 dihedral angle rotamer histogram.
Mentions: ‘Carbonyl dimers’: Eight ‘carbonyl dimer’ types were identified (Table 3 ▶). The four types involving the syn conformer of the donor carboxyl group and among them, the SA-S dimers, are well represented. The synplanar rotamers are generally not observed except for the SA-S dimers where they are as prominent as antiplanar rotamers (Fig. 7 ▶). Note that syn- and antiplanar rotamers are defined by inter-dimer dihedral angles with values close to 0 and 180°, respectively (see, for example, Fig. 7 ▶c). The ACETAC09 acetic acid structure seems to be stabilized by a C—H⋯O interaction involving the methyl group, an orientation that is not found for chloroacetic acid in the CLACET01 structure and illustrates how weak interactions participate in structural networks.

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