(S)-2,2′-Dihy­droxy-N,N′-(6-hy­droxy­hexane-1,5-di­yl)dibenzamide

Sabine Wilbrand; Christian Neis; Kaspar Hegetschweiler

doi:10.1107/S1600536813000354

. 2013 Jan 12;69(Pt 2):o223. doi: 10.1107/S1600536813000354

(S)-2,2′-Dihydroxy-N,N′-(6-hydroxyhexane-1,5-diyl)dibenzamide

Sabine Wilbrand ^a, Christian Neis ^a, Kaspar Hegetschweiler ^a,^*

PMCID: PMC3569758 PMID: 23424504

Abstract

In the title compound, C₂₀H₂₄N₂O₅, the dihedral angle between the two roughly planar salicylamide fragments [r.m.s. deviations = 0.043 (2) and 0.149 (2) Å] is 25.50 (5)°. The molecular conformation is stabilized by intramolecular O—H⋯O hydrogen bonds involving phenol –OH groups and amide O atoms. Intermolecular hydroxymethyl–amide O—H⋯O and amine–hydroxymethyl N—H⋯O hydrogen bonds form infinite chains along the b axis. These chains are further interlinked by amine–amide N—H⋯O and phenol–phenol O—H⋯O interactions, thus giving layers parallel to (001).

Related literature

For the isolation and physico-chemical properties of myxochelin A, see: Kunze et al. (1989 ▶). For the crystal structure of N,N′-(pentane-1,5-diyl)bis(3-methoxysalicylamide), see: Huang et al. (1995 ▶). For metal complex formation with linear bis-catechol amides and linear bis-salicylamides, see: Duhme et al. (1996 ▶); Huang et al. (1995 ▶); Cappillino et al. (2009 ▶); Stoicescu et al. (2009 ▶). For the treatment of H atoms in SHELXL, see: Müller et al. (2006 ▶). graphic file with name e-69-0o223-scheme1.jpg

Experimental

Crystal data

C₂₀H₂₄N₂O₅
M _r = 372.41
Monoclinic,
a = 9.5934 (7) Å
b = 9.2266 (7) Å
c = 10.3565 (7) Å
β = 96.172 (4)°
V = 911.39 (11) Å³
Z = 2
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 123 K
0.26 × 0.21 × 0.04 mm

Data collection

Bruker Nonius X8 APEX diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2010 ▶) T _min = 0.975, T _max = 0.996
10366 measured reflections
2111 independent reflections
1943 reflections with I > 2σ(I)
R _int = 0.028

Refinement

R[F ² > 2σ(F ²)] = 0.031
wR(F ²) = 0.076
S = 1.05
2111 reflections
259 parameters
6 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2012 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

Click here for additional data file.^{(21KB, cif)}

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813000354/yk2084sup1.cif

e-69-0o223-sup1.cif^{(21KB, cif)}

Click here for additional data file.^{(103.8KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813000354/yk2084Isup2.hkl

e-69-0o223-Isup2.hkl^{(103.8KB, hkl)}

Click here for additional data file.^{(7.3KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536813000354/yk2084Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O6—H6O⋯O7	0.88 (2)	1.70 (2)	2.530 (2)	155 (3)
N8—H8N⋯O14ⁱ	0.87 (2)	2.21 (2)	3.051 (2)	163 (2)
O14—H14O⋯O16ⁱⁱ	0.85 (2)	2.03 (2)	2.858 (2)	165 (3)
N15—H15N⋯O7ⁱⁱⁱ	0.86 (2)	2.25 (2)	3.046 (2)	154 (2)
O22—H22O⋯O16	0.84 (2)	1.95 (2)	2.648 (2)	140 (3)
O22—H22O⋯O6^iv	0.84 (2)	2.19 (2)	2.776 (2)	127 (2)

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

The authors thank Dr Volker Huch (Universität des Saarlandes) for the collection of the data set.

supplementary crystallographic information

Comment

Myxochelin A ((S)-N,N'-(6-hydroxyhexane-1,5-diyl)bis(2,3-dihydroxybenzamide)) belongs to the family of siderophores (Kunze et al., 1989) and is well known for its selective complex formation with iron(III). In a neutral medium, metal binding probably occurs via the two catecholate groups (Huang et al., 1995; Duhme et al., 1996). However, myxochelin A also forms stable ferric complexes in an acidic medium around pH 2–3. Under such conditions, a complete deprotonation of all four phenolic hydroxy groups is unfavourable and, alternatively, metal binding may rather occur in a bis-bidentate fashion via the two ortho-hydroxy-benzamide moieties (Cappillino et al., 2009; Stoicescu et al., 2009). For a direct investigation of such a coordination mode, we prepared dideoxy-myxochelin A as a model ligand and report here its crystal structure. The structure elucidation of a related achiral derivative, which is devoid of the hydroxymethyl group, has been reported by Huang et al. (1995).

The crystal structure of the title compound exhibits an all-staggered zigzag arrangement of the O14—C14—C13—C12—C11—C10—C9 chain with corresponding torsional angles of 172–179°. With regard to this chain, the two ortho-hydroxybenzamide moieties adopt a gauche conformation with C—C—C—N torsional angles of 54.2 (2) and -63.9 (2)°. The two phenyl rings are aligned roughly parallel (the angle between the two mean planes is 23°). Inspection of interatomic distances revealed, however, that the interaction between the two aromatic moieties should be interpreted in terms of simple van der Waals contacts rather than π–π stacking. The amide groups and the corresponding phenyl rings are almost, but not fully, coplanar. The angle between the mean planes defined by C1–C6 and N8, C7, O7, C1 or C17–C22 and N15, C16, O16, C17 is 5° or 19°, respectively. Both aromatic hydroxy groups are involved in intramolecular O—H···O(carbonyl) hydrogen bonding, forming a six-membered ring structure which is quite often observed for salicylamides. Additionally, the aliphatic hydroxy group (O14) donates its proton to the carbonyl O atom O16 of a neighbour, and the amide moiety N8—H8N donates its proton to a further aliphatic hydroxy group (O14). The two types of interactions occur along 2₁ screws and result in the formation of infinite chains, aligned parallel to the crystallographic b axis. Interlinking of these chains occurs via N15—H15N···O7 bonding. In addition, H22O is bifurcated; beside the above-mentioned intramolecular O22—H22O···O16 bond, an intermolecular O22—H22O···O6 bond generates further interlinking along the crystallographic a axis. Altogether, the various types of intermolecular hydrogen bonding interactions resulted in the generation of layers, oriented parallel to the ab plane. Between these layers, only weak van der Waals contacts can be observed.

Experimental

2-Hydroxybenzoic acid was allowed to react with benzyl bromide in acetone yielding 2-benzyloxy-benzoic acid, which was further transformed into (S)-2,6-bis(2-benzoxybenzamido)-hexan-1-ol in a two-step procedure, using thionyl chloride and subsequently (S)-2,6-diaminohexan-1-ol. The protecting benzoxy groups were then removed with ammonium formate and Pd/C. Off-white single crystals were grown from MeOH. Elemental analysis calculated for C₂₀H₂₄N₂O₅ (%): C 64.50, H 6.50, N 7.52; found (%): C 64.19, H 6.35, N 7.50. ¹H NMR (DMSO-d₆): δ (p.p.m.) = 1.38 (m, 2H), 1.62 (m, 4H), 3.30 (dt, 2H), 3.48 (m, 2H), 4.04 (m, 1H), 6.89 (m, 4H), 7.40 (m, 2H), 7.84 (dd, 1H), 7.94 (dd, 1H), 8.47 (d, NH), 8.85 (t, NH). ¹³C NMR (DMSO-d₆): δ (p.p.m.) = 23.1, 28.7, 30.1, 38.8, 51.0, 62.9, 115.0, 115.4, 117.2, 117.3, 118.3, 127.4, 127.9, 133.4, 133.5, 160.0, 160.2.