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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

Nine conformations of compound (1) found by computational analysis. The number in parenthesis is the relative energy in kcal mol−1.
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fig4: Nine conformations of compound (1) found by computational analysis. The number in parenthesis is the relative energy in kcal mol−1.

Mentions: A computational analysis of ring conformations of compound (1) was carried out using protocols reported earlier (Patel et al., 2013 ▸, 2014 ▸). Conformers were first generated by the stochastic method and minimized in the MMFF94x force field with chloro­form as the solvent to produce nine conformational clusters within 3–5 kcal mol−1 in energy that are distinct in their azepane-ring conformations, Fig. 4 ▸. Representative conformers were then subjected to DFT geometry optimization [SV(P) basis set at the B3LYP level in COSMO solvent chloro­form]. Two of the nine ring geometries (geometries vi and vii, Fig. 4 ▸) found by this computational analysis matched to geometries A and B of compound (1) in the unit cell, respectively. Hence the X-ray structure reported here for (1) validates our conformational analysis methodology as reported earlier (Patel et al., 2013 ▸, 2014 ▸).


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)

Nine conformations of compound (1) found by computational analysis. The number in parenthesis is the relative energy in kcal mol−1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Nine conformations of compound (1) found by computational analysis. The number in parenthesis is the relative energy in kcal mol−1.
Mentions: A computational analysis of ring conformations of compound (1) was carried out using protocols reported earlier (Patel et al., 2013 ▸, 2014 ▸). Conformers were first generated by the stochastic method and minimized in the MMFF94x force field with chloro­form as the solvent to produce nine conformational clusters within 3–5 kcal mol−1 in energy that are distinct in their azepane-ring conformations, Fig. 4 ▸. Representative conformers were then subjected to DFT geometry optimization [SV(P) basis set at the B3LYP level in COSMO solvent chloro­form]. Two of the nine ring geometries (geometries vi and vii, Fig. 4 ▸) found by this computational analysis matched to geometries A and B of compound (1) in the unit cell, respectively. Hence the X-ray structure reported here for (1) validates our conformational analysis methodology as reported earlier (Patel et al., 2013 ▸, 2014 ▸).

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