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Conformation and crystal structures of 1-amino-cyclo-hexa-neacetic acid (β(3,3)Ac6c) in N-protected derivatives.

Ahmad Wani N, Gupta VK, Kant R, Aravinda S, Rai R - Acta Crystallogr Sect E Struct Rep Online (2014)

Bottom Line: The backbone torsion angles (ϕ, θ) for β(3,3)-Ac6c-OH are restricted to gauche conformations in all the derivatives, with a chair conformation of the cyclo-hexane ring.In the crystal structure of (I), the packing of mol-ecules shows both carb-oxy-lic acid R 2 (2)(8) O-H⋯O and centrosymmetric R (2) 2(14) N-H⋯O hydrogen-bonding inter-actions, giving rise to chains along the c-axis direction.In the case of compound (III), carb-oxy-lic acid O-H⋯Npyrazine hydrogen bonds give rise to zigzag ribbon structures extending along the c-axis direction.

View Article: PubMed Central - HTML - PubMed

Affiliation: Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India.

ABSTRACT
N-Protected derivatives of 1-amino-cyclo-hexa-neacetic acid (β(3,3)-Ac6c), namely Valeroyl-β(3,3)-Ac6c-OH [2-(1-pentanamidocyclohexyl)acetic acid, C13H23NO3], (I), Fmoc-β(3,3)-Ac6c-OH [2-(1-{[(9H-fluoren-9-yloxy)carbonyl]amino}cyclohexyl)acetic acid, C23H25NO4], (II), and Pyr-β(3,3)-Ac6c-OH {2-[1-(pyrazine-2-amido)cyclohexyl]acetic acid, C13H17N3O3}, (III), were synthesized and their conformational properties were determined by X-ray diffraction analysis. The backbone torsion angles (ϕ, θ) for β(3,3)-Ac6c-OH are restricted to gauche conformations in all the derivatives, with a chair conformation of the cyclo-hexane ring. In the crystal structure of (I), the packing of mol-ecules shows both carb-oxy-lic acid R 2 (2)(8) O-H⋯O and centrosymmetric R (2) 2(14) N-H⋯O hydrogen-bonding inter-actions, giving rise to chains along the c-axis direction. In (II), centrosymmetric carb-oxy-lic acid R 2 (2)(8) O-H⋯O dimers are extended through N-H⋯O hydrogen bonds and together with inter-ring π-π inter-actions between Fmoc groups [ring centroid distance = 3.786 (2) Å], generate a layered structure lying parallel to (010). In the case of compound (III), carb-oxy-lic acid O-H⋯Npyrazine hydrogen bonds give rise to zigzag ribbon structures extending along the c-axis direction.

No MeSH data available.


Related in: MedlinePlus

ORTEP view of the mol­ecular conformation with the atom-labelling scheme. for Valeroyl-β3,3-Ac6c-OH (I), (b) Fmoc-β3,3-Ac6c-OH (II) and (c) Pyr-β3,3-Ac6c-OH (III). The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
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fig2: ORTEP view of the mol­ecular conformation with the atom-labelling scheme. for Valeroyl-β3,3-Ac6c-OH (I), (b) Fmoc-β3,3-Ac6c-OH (II) and (c) Pyr-β3,3-Ac6c-OH (III). The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.

Mentions: The mol­ecular conformations of Valeroyl-β3,3-Ac6c-OH (I), Fmoc-β3,3-Ac6c-OH (II) and Pyr-β3,3-Ac6c-OH (III) are shown in Fig. 2 ▶. The backbone torsion angles (ϕ, θ) (C0′—N1—C1B —C1A and N1—C1B—C1A—C1′) adopt a gauche conformation in all three compounds [ϕ = 61.9 (3)°, θ = 57.2 (3)° for (I); ϕ = 56.7 (3)°, θ = 66.1 (3)° for (II) and ϕ = 65.5 (2)°, θ = 55.0 (2)° for (III). The torsional angle ψ restricts the extended (trans) conformation for (I) [166.9 (2)°] and (III) [157.9 (2)°]. In the case of (II), it is restricted to a gauche conformation [i.e. ψ = −63.6 (3)°]. In a 3,3-disubstituted β-amino acid residue, β3,3-Ac6c-OH, the cyclo­hexane ring imposes a restriction on the torsion angles ϕ and θ. The protecting groups at the N-terminus of (I) adopts a trans geometry [ω0 (C4—C0′—N1—C1B) = 177.4 (2) for (I), ω0 (O—C0′—N1—C1B) = −175.64 (19) for (II) and ω0 (C6—C0—N1— C1A) = −170.04 (17)° for (III)]. In the case of the N-protected tert-butyl­oxycarbonyl (Boc) group, the protecting group adopts a cis geometry with ω0 = 14.50° (Vasudev et al., 2008 ▶). The cyclo­hexane ring adopts a chair conformation with axial amino and equatorial CH2CO groups in all the derivatives. In Pyr-β3,3-Ac6c-OH (III), an intra­molecular N—H⋯N inter­action is observed between NH of the β3,3-Ac6c-OH residue and N3 of the pyrazine ring as shown in Fig. 3 ▶c. There are no intra­molecular hydrogen bonding inter­actions observed in the crystal structures of derivatives (I) and (II).


Conformation and crystal structures of 1-amino-cyclo-hexa-neacetic acid (β(3,3)Ac6c) in N-protected derivatives.

Ahmad Wani N, Gupta VK, Kant R, Aravinda S, Rai R - Acta Crystallogr Sect E Struct Rep Online (2014)

ORTEP view of the mol­ecular conformation with the atom-labelling scheme. for Valeroyl-β3,3-Ac6c-OH (I), (b) Fmoc-β3,3-Ac6c-OH (II) and (c) Pyr-β3,3-Ac6c-OH (III). The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4257263&req=5

fig2: ORTEP view of the mol­ecular conformation with the atom-labelling scheme. for Valeroyl-β3,3-Ac6c-OH (I), (b) Fmoc-β3,3-Ac6c-OH (II) and (c) Pyr-β3,3-Ac6c-OH (III). The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
Mentions: The mol­ecular conformations of Valeroyl-β3,3-Ac6c-OH (I), Fmoc-β3,3-Ac6c-OH (II) and Pyr-β3,3-Ac6c-OH (III) are shown in Fig. 2 ▶. The backbone torsion angles (ϕ, θ) (C0′—N1—C1B —C1A and N1—C1B—C1A—C1′) adopt a gauche conformation in all three compounds [ϕ = 61.9 (3)°, θ = 57.2 (3)° for (I); ϕ = 56.7 (3)°, θ = 66.1 (3)° for (II) and ϕ = 65.5 (2)°, θ = 55.0 (2)° for (III). The torsional angle ψ restricts the extended (trans) conformation for (I) [166.9 (2)°] and (III) [157.9 (2)°]. In the case of (II), it is restricted to a gauche conformation [i.e. ψ = −63.6 (3)°]. In a 3,3-disubstituted β-amino acid residue, β3,3-Ac6c-OH, the cyclo­hexane ring imposes a restriction on the torsion angles ϕ and θ. The protecting groups at the N-terminus of (I) adopts a trans geometry [ω0 (C4—C0′—N1—C1B) = 177.4 (2) for (I), ω0 (O—C0′—N1—C1B) = −175.64 (19) for (II) and ω0 (C6—C0—N1— C1A) = −170.04 (17)° for (III)]. In the case of the N-protected tert-butyl­oxycarbonyl (Boc) group, the protecting group adopts a cis geometry with ω0 = 14.50° (Vasudev et al., 2008 ▶). The cyclo­hexane ring adopts a chair conformation with axial amino and equatorial CH2CO groups in all the derivatives. In Pyr-β3,3-Ac6c-OH (III), an intra­molecular N—H⋯N inter­action is observed between NH of the β3,3-Ac6c-OH residue and N3 of the pyrazine ring as shown in Fig. 3 ▶c. There are no intra­molecular hydrogen bonding inter­actions observed in the crystal structures of derivatives (I) and (II).

Bottom Line: The backbone torsion angles (ϕ, θ) for β(3,3)-Ac6c-OH are restricted to gauche conformations in all the derivatives, with a chair conformation of the cyclo-hexane ring.In the crystal structure of (I), the packing of mol-ecules shows both carb-oxy-lic acid R 2 (2)(8) O-H⋯O and centrosymmetric R (2) 2(14) N-H⋯O hydrogen-bonding inter-actions, giving rise to chains along the c-axis direction.In the case of compound (III), carb-oxy-lic acid O-H⋯Npyrazine hydrogen bonds give rise to zigzag ribbon structures extending along the c-axis direction.

View Article: PubMed Central - HTML - PubMed

Affiliation: Medicinal Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180 001, India.

ABSTRACT
N-Protected derivatives of 1-amino-cyclo-hexa-neacetic acid (β(3,3)-Ac6c), namely Valeroyl-β(3,3)-Ac6c-OH [2-(1-pentanamidocyclohexyl)acetic acid, C13H23NO3], (I), Fmoc-β(3,3)-Ac6c-OH [2-(1-{[(9H-fluoren-9-yloxy)carbonyl]amino}cyclohexyl)acetic acid, C23H25NO4], (II), and Pyr-β(3,3)-Ac6c-OH {2-[1-(pyrazine-2-amido)cyclohexyl]acetic acid, C13H17N3O3}, (III), were synthesized and their conformational properties were determined by X-ray diffraction analysis. The backbone torsion angles (ϕ, θ) for β(3,3)-Ac6c-OH are restricted to gauche conformations in all the derivatives, with a chair conformation of the cyclo-hexane ring. In the crystal structure of (I), the packing of mol-ecules shows both carb-oxy-lic acid R 2 (2)(8) O-H⋯O and centrosymmetric R (2) 2(14) N-H⋯O hydrogen-bonding inter-actions, giving rise to chains along the c-axis direction. In (II), centrosymmetric carb-oxy-lic acid R 2 (2)(8) O-H⋯O dimers are extended through N-H⋯O hydrogen bonds and together with inter-ring π-π inter-actions between Fmoc groups [ring centroid distance = 3.786 (2) Å], generate a layered structure lying parallel to (010). In the case of compound (III), carb-oxy-lic acid O-H⋯Npyrazine hydrogen bonds give rise to zigzag ribbon structures extending along the c-axis direction.

No MeSH data available.


Related in: MedlinePlus