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Crystal structure of (4R,5S,6R)-6-azido-5-benz-yloxy-3,3,4-tri-fluoro-azepan-1-ium 2,2,2-tri-fluoro-acetate from synchrotron data.

Patel AR, Bhadbhade MM, Liu F - Acta Crystallogr E Crystallogr Commun (2015)

Bottom Line: The seven-membered rings adopt different conformations with the principal differences occurring in the CF2CHFCH2 segments of the ring systems.The geminal F atoms on the quaternary C atom exhibit essentially identical bond angles [109 (2) and 106 (2)°] in the two independent mol-ecules.The two mol-ecules associate as a dimeric unit via two C-H⋯F inter-actions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.

ABSTRACT
The structure of the title compound, C15H16F6N4O3, was determined using synchrotron radiation on an extremely small crystal (0.015 × 0.01 × 0.01 mm). Although the diffraction was weak, leading to high residuals and a poor data-to-parameter ratio, the data allowed ready solution and refinement to reveal the entire structure. The solid-state structure is in accordance with the absolute configuration assigned based on that of the known starting material. The compound comprises a highly substituted seven-membered N-heterocyclic cation and a tri-fluoro-methane-sulfonate counter-anion. The title compound crystallizes with two independent cations (A and B) and anions (C and D) in the asymmetric unit. Two geminal F atoms, a single F atom, a benzyl ether and an azide group are substituted on consecutive C atoms between the NH2 and CH2 units of the azepan-1-ium ring system. The seven-membered rings adopt different conformations with the principal differences occurring in the CF2CHFCH2 segments of the ring systems. The geminal F atoms on the quaternary C atom exhibit essentially identical bond angles [109 (2) and 106 (2)°] in the two independent mol-ecules. The two mol-ecules associate as a dimeric unit via two C-H⋯F inter-actions. An extensive series of N-H⋯O, N-H⋯F, C-H⋯O, C-H⋯N, C-H⋯F and C-H⋯π contacts generate a three-dimensional network with cations and anions linked into ABCD repeat columns along a.

No MeSH data available.


Related in: MedlinePlus

Inter­molecular contacts between A cations and C anions viewed along c. Midpoints of the C10A—C11A bonds are shown as coloured spheres.
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fig5: Inter­molecular contacts between A cations and C anions viewed along c. Midpoints of the C10A—C11A bonds are shown as coloured spheres.

Mentions: In the crystal structure, C anions form chains along the a-axis direction through F3C⋯O1C contacts at a distance of 2.78 (2) Å. Each anion further connects to an A cation with O1C accepting three interactions and N1A as a bifurcated donor, leading to the formation of N1A—H1AA⋯O1C, N1A—H1AB⋯O1C and C4A—H4AA⋯O1C hydrogen bonds and generating (4) and (5) ring motifs, respectively (Bernstein et al., 1995 ▸). These contacts generate columns of A mol­ecules along a. These columns are further supported by weak C7A—H7AA⋯Cg2 contacts (Cg2 is the mid-point of the C10A—C11A bond of the C8A–C13A phenyl ring), Fig. 5 ▸. Similarly, B cations are linked to D anions with O2D accepting three interactions and forming N1B—-H1BA⋯O2D, N1B—H1BB⋯O2D and C4B—H4BA⋯O2D hydrogen bonds. Unlike the AC system however, a C4B—H4BA⋯F1D hydrogen bond completes the B⋯D cation–anion contacts. These generate (4) and (5) ring motifs respectively. Weak C7B—H7BA⋯Cg1 contacts (Cg1 is the midpoint of the C10B–C11B bond of the C8B–C13B phenyl ring) link adjacent B mol­ecules, also forming columns of B cations and D anions along the a-axis direction, Fig. 6 ▸. Contacts between the A and B cations are limited to very weak C12B—H12B⋯N4A hydrogen bonds linking adjacent columns of A and B cations, Fig. 7 ▸. This eclectic mixture of contacts generates columns with an ABCD repeat unit in the direction of the a axis, Fig. 8 ▸. Additional N—H⋯O, C—H⋯O and C—H⋯F contacts result in a three-dimensional network of cations and anions stacked along c.


Crystal structure of (4R,5S,6R)-6-azido-5-benz-yloxy-3,3,4-tri-fluoro-azepan-1-ium 2,2,2-tri-fluoro-acetate from synchrotron data.

Patel AR, Bhadbhade MM, Liu F - Acta Crystallogr E Crystallogr Commun (2015)

Inter­molecular contacts between A cations and C anions viewed along c. Midpoints of the C10A—C11A bonds are shown as coloured spheres.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645019&req=5

fig5: Inter­molecular contacts between A cations and C anions viewed along c. Midpoints of the C10A—C11A bonds are shown as coloured spheres.
Mentions: In the crystal structure, C anions form chains along the a-axis direction through F3C⋯O1C contacts at a distance of 2.78 (2) Å. Each anion further connects to an A cation with O1C accepting three interactions and N1A as a bifurcated donor, leading to the formation of N1A—H1AA⋯O1C, N1A—H1AB⋯O1C and C4A—H4AA⋯O1C hydrogen bonds and generating (4) and (5) ring motifs, respectively (Bernstein et al., 1995 ▸). These contacts generate columns of A mol­ecules along a. These columns are further supported by weak C7A—H7AA⋯Cg2 contacts (Cg2 is the mid-point of the C10A—C11A bond of the C8A–C13A phenyl ring), Fig. 5 ▸. Similarly, B cations are linked to D anions with O2D accepting three interactions and forming N1B—-H1BA⋯O2D, N1B—H1BB⋯O2D and C4B—H4BA⋯O2D hydrogen bonds. Unlike the AC system however, a C4B—H4BA⋯F1D hydrogen bond completes the B⋯D cation–anion contacts. These generate (4) and (5) ring motifs respectively. Weak C7B—H7BA⋯Cg1 contacts (Cg1 is the midpoint of the C10B–C11B bond of the C8B–C13B phenyl ring) link adjacent B mol­ecules, also forming columns of B cations and D anions along the a-axis direction, Fig. 6 ▸. Contacts between the A and B cations are limited to very weak C12B—H12B⋯N4A hydrogen bonds linking adjacent columns of A and B cations, Fig. 7 ▸. This eclectic mixture of contacts generates columns with an ABCD repeat unit in the direction of the a axis, Fig. 8 ▸. Additional N—H⋯O, C—H⋯O and C—H⋯F contacts result in a three-dimensional network of cations and anions stacked along c.

Bottom Line: The seven-membered rings adopt different conformations with the principal differences occurring in the CF2CHFCH2 segments of the ring systems.The geminal F atoms on the quaternary C atom exhibit essentially identical bond angles [109 (2) and 106 (2)°] in the two independent mol-ecules.The two mol-ecules associate as a dimeric unit via two C-H⋯F inter-actions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.

ABSTRACT
The structure of the title compound, C15H16F6N4O3, was determined using synchrotron radiation on an extremely small crystal (0.015 × 0.01 × 0.01 mm). Although the diffraction was weak, leading to high residuals and a poor data-to-parameter ratio, the data allowed ready solution and refinement to reveal the entire structure. The solid-state structure is in accordance with the absolute configuration assigned based on that of the known starting material. The compound comprises a highly substituted seven-membered N-heterocyclic cation and a tri-fluoro-methane-sulfonate counter-anion. The title compound crystallizes with two independent cations (A and B) and anions (C and D) in the asymmetric unit. Two geminal F atoms, a single F atom, a benzyl ether and an azide group are substituted on consecutive C atoms between the NH2 and CH2 units of the azepan-1-ium ring system. The seven-membered rings adopt different conformations with the principal differences occurring in the CF2CHFCH2 segments of the ring systems. The geminal F atoms on the quaternary C atom exhibit essentially identical bond angles [109 (2) and 106 (2)°] in the two independent mol-ecules. The two mol-ecules associate as a dimeric unit via two C-H⋯F inter-actions. An extensive series of N-H⋯O, N-H⋯F, C-H⋯O, C-H⋯N, C-H⋯F and C-H⋯π contacts generate a three-dimensional network with cations and anions linked into ABCD repeat columns along a.

No MeSH data available.


Related in: MedlinePlus