Benzyl N-((S)-2-hydr­oxy-1-{N′-[(E)-2-methoxy­benzyl­idene]hydrazinecarbon­yl}eth­yl)carbamate from synchrotron data

Alessandra C Pinheiro; Marcus V N de Souza; Edward R T Tiekink; James L Wardell; Solange M S V Wardell

doi:10.1107/S1600536810011463

. 2010 Mar 31;66(Pt 4):o1004–o1005. doi: 10.1107/S1600536810011463

Benzyl N-((S)-2-hydroxy-1-{N′-[(E)-2-methoxybenzylidene]hydrazinecarbonyl}ethyl)carbamate from synchrotron data

Alessandra C Pinheiro ^a, Marcus V N de Souza ^a, Edward R T Tiekink ^b,^*, James L Wardell ^c,^‡, Solange M S V Wardell ^d

PMCID: PMC2983774 PMID: 21580568

Abstract

A U-shaped conformation is found in the title compound, C₁₉H₂₁N₃O₅, with the benzene rings lying to the same side of the molecule; the dihedral angle between them is 10.83 (16)°. The dihedral angle formed between the hydrazinecarbonyl and carbamate residues is 68.42 (13)°. The carbonyl groups lie approximately at right angles to each other [O—C⋯C—O pseudo torsion angle of 107.7 (3)°], and the conformation about the C12=N3 bond [1.279 (4) Å] is E. An intramolecular N_cb—H⋯O_hy (cb = carbmate and hy = hydroxy) hydrogen bond occurs, generating an S(6) loop. In the crystal, intermolecular O_h—H⋯O_ca (ca = carbonyl) and N_hz—H⋯O_ca (hz = hydrazine) hydrogen bonds lead to the formation of a supramolecular chain, two molecules thick, which propagates along the a axis; these are connected by C—H⋯O_ca contacts.

Related literature

For background to tuberculosis, see: Cole & Alzari (2007 ▶); Portero & Rubio (2007 ▶). For information on the development of anti-tuberculosis agents, see: Lourenço et al. (2007a ▶,b ▶); Lourenço et al. (2008 ▶); Ferreira et al. (2008 ▶); Costa et al. (2006 ▶); de Souza et al. (2006a ▶,b ▶); Pinheiro et al. (2007 ▶).

Experimental

Crystal data

C₁₉H₂₁N₃O₅
M _r = 371.39
Orthorhombic,
a = 6.002 (6) Å
b = 14.053 (14) Å
c = 21.09 (2) Å
V = 1779 (3) Å³
Z = 4
Synchrotron radiation
λ = 0.6889 Å
μ = 0.06 mm⁻¹
T = 120 K
0.30 × 0.04 × 0.02 mm

Data collection

Rigaku Saturn 724+ detector on Crystal Logics CCD diffractometer
13639 measured reflections
1827 independent reflections
1627 reflections with I > 2σ(I)
R _int = 0.047

Refinement

R[F ² > 2σ(F ²)] = 0.030
wR(F ²) = 0.124
S = 1.29
1827 reflections
257 parameters
3 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Data collection: CrystalClear (Rigaku/MSC, 2008 ▶); cell refinement: APEX2 (Bruker, 2008 ▶); data reduction: APEX2; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and DIAMOND (Brandenburg, 2006 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810011463/hb5379sup1.cif

e-66-o1004-sup1.cif^{(21.1KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810011463/hb5379Isup2.hkl

e-66-o1004-Isup2.hkl^{(88.1KB, hkl)}

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
N1—H1n⋯O3	0.89 (3)	2.44 (3)	2.788 (5)	104 (2)
O3—H3o⋯O4ⁱ	0.85 (2)	2.04 (2)	2.789 (4)	147 (4)
N2—H2n⋯O2ⁱⁱ	0.88 (3)	2.10 (3)	2.974 (5)	177 (3)
C10—H10b⋯O2ⁱ	0.99	2.45	3.439 (5)	175
C16—H16⋯O4ⁱⁱⁱ	0.95	2.55	3.284 (5)	134

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

Acknowledgments

We thank Prof. W. Clegg and the synchrotron component, based at Daresbury, of the EPSRC National Crystallographic Service, University of Southampton, for the data collection. JLW acknowledges support from CAPES and FAPEMIG (Brazil).

supplementary crystallographic information

Comment

Tuberculosis (TB) is once again a major public health problem. The need for better drugs is clear (Cole & Alzari, 2007; Portero & Rubio, 2007). Continuing our studies on potential anti-tuberculosis agents (Lourenço et al., 2007a, 2007b, 2008; Ferreira et al., 2008; Costa et al., 2006; de Souza et al., 2006a, 2006b), including serinyl derivatives (Pinheiro et al., 2007), we have investigated a series of serinyl derivatives, N-(2-hydroxy-1-{N'-[(1E)-(2- methoxyphenyl)methylidene]hydrazinecarbonyl}ethyl)carbamic acid esters and now report the structure of one of these, benzyl N-(2-hydroxy-1-{N'-[(1E)-(2- methoxyphenyl)methylidene] hydrazinecarbonyl}ethyl)carbamate, (I).

Overall, the molecule of (I), Fig. 1, has a U-shaped conformation with the benzene rings lying to the same side of the molecule; the dihedral angle between their least-squares planes is 10.83 (16) °. The dihedral angle formed between the least-squares planes through the hydrazinecarbonyl (r.m.s. deviation of the O4,N2,N3,C11 atoms = 0.0198 Å) and carbamate (r.m.s. deviation of the O1,O2,N1,C8 atoms = 0.0044 Å) is 68.42 (13) °. The carbonyl groups are approximately at right-angles to each other as seen in the pseudo O2–C8···C11–O4 torsion angle of 107.7 (3) °. Each of the N–H groups is anti to the adjacent carbonyl so that the N–H groups also lie to opposite sides of the molecule. The conformation about the C12═N3 bond [1.279 (4) Å] is E. Although the absolute structure could not be determined experimentally, the assignment of the S-configuration at the C2 atom is based on a starting reagent.

There are three acidic H atoms in the molecule of (I) and each of these forms a significant hydrogen bond, Table 1. Whereas the carbamate-N1–H atom forms an intramolecular N–H···O hydrogen bond to the hydroxyl-O3 atom, the hydroxyl-O3–H atom forms an intermolecular O–H···O interaction with the carbonyl-O4 atom, and the hydrazine-N2–H atom likewise forms an N–H···O hydrogen bond with the carbonyl-O2 atom. The intermolecular hydrogen bonds lead to the formation of a supramolecular double-chain along the a direction, Fig. 2, with additional stability to the chain afforded by C–H···O interactions involving the carbonyl-O2 atom, Table 1. The primary interactions between chains are of the type C–H···O and involve the carbonyl-O4 atom, Table 1 and Fig. 3.

Experimental

The compound, phenyl (1S)-2-hydrazino-1-(hydroxymethyl)-2-oxoethylcarbamate, was obtained from L-serine methyl ester hydrochloride on successive reactions with (a) PhCH₂Cl and Et₃N, and (b) N₂H₄.H₂O. To a stirred ethanol solution (10 ml) of phenyl (1S)-2-hydrazino-1-(hydroxymethyl)-2-oxoethylcarbamate (1.0 mmol), at room temperature was added 2-methoxybenzaldehyde (1.05 mmol). The reaction mixture was stirred for 4 hours at 353 K and concentrated under reduced pressure. The residue was purified by washing with cold ethanol (3 × 10 ml), affording the title compound; yield 80%. Solution NMR spectra revealed the presence of (E)- and (Z)-isomers, however, the colourless needles of (I) obtained from MeOH solution were solely the (E)-isomer, m.pt. 453–454 K.

¹H NMR (400 MHz, DMSO-d₆) δ (ppm): 11.48 and 11.36 (1H, s, NHN, E- and Z- isomers), 8.59 and 8.33 (1H, s, N=CH, E- and Z- isomers), 7.83 (d, J = 7.1) and 7.79 (d, J = 7.8), (1H, H5, E- and Z- isomers), 7.45-7.25 (6H, m, Ph and H3), 7.45-7.25 (m) and 7.19 (d, J = 8.4), (1H, NHCH, E and Z- isomers), 7.10 and 7.08 (1H, s, H2, E- and Z- isomers), 7.00 (1H, m, H4), 5.05 and 5.04 (2H, s, CH₂Ph, E- and Z- isomers), 5.01 and 4.11 (1H, m, CH, E- and Z- isomers), 4.97 (t, J = 5.8) and 4.85 (t, J = 5.6), (1H, OH, E- and Z- isomers 3.86 and 3.84 (3H, s, CH₃, E- and Z- isomers), 3.80-3.55 (2H, m, CH₂OH). ¹³C NMR (100 MHz, DMSO-d₆) δ (ppm): 171.2 and 166.7 (COCH, E- and Z- isomers), 157.7 and 157.6 (C1, E- and Z- isomers), 155.9 and 155.8 (COO, E- and Z- isomers), 142.5 and 139.0 (N=CH, E- and Z- isomers), 137.0 and 136.9 (C6', E- and Z- isomers), 131.5, 131.3, 128.3, 127.7, 127.6 and 125.4 (C3, C5, C1', C2', C3', C4' and C5'), 122.2, 122.1 and 120.7 (C4 and C6), 111.8 (C2), 65.5 and 65.3 (CH₂Ph, E- and Z- isomers), 61.5 and 61.1 (CH₂OH, E- and Z- isomers), 56.4 and 54.6 (CH, E- and Z- isomers), 55.7 (CH₃). IR (cm^-1; KBr): 3262 (O—H); 1692 (COCH and COO). EM/ESI: [M+Na]: 370.2.