organic compounds
tert-Butyl N-[(S)-1-hydrazinecarbonyl-2-hydroxyethyl]carbamate
aInstituto de Tecnologia em Farmacos, Fundação Oswaldo Cruz (FIOCRUZ), FarManguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, RJ, Brazil, bInstituto de Tecnologia em Farmacos, Fundação Oswaldo Cruz (FIOCRUZ), FarManguinhos, Rua Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, RJ, Brazil, cCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland, dCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil, and eDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: edward.tiekink@gmail.com
In the title compound, C8H17N3O4, the dihedral angle between the hydrazinecarbonyl and carbamate groups is 44.94 (12)°, and the carbonyl groups are anti to each other. In the crystal, the hydroxy group forms an O—H⋯Na (a = amine) hydrogen bond and each of the four N—H atoms forms an N—H⋯O hydrogen bond; the hydrazinecarbonyl O atom accepts two such bonds. This results in two-dimensional arrays in the ab plane, mediated by the hydrogen bonding, sandwiched by tert-butyl groups.
Related literature
For background to the use of serinyl compounds as potential anti-tuberculosis agents, see: Pinheiro et al. (2007).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; 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).
Supporting information
10.1107/S1600536810011438/hb5376sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810011438/hb5376Isup2.hkl
To a stirred ethanol solution (10 ml) of methyl (2S)-2-[(tert-butoxycarbonyl)amino]-3-hydroxypropanoate (0.3 g, 1.37 mmol), obtained from L-serine methyl ester hydrochloride and (BOC)2O, at room temperature was added N2H4.H2O (80%, 5.5 mmol). The reaction mixture was stirred for 24 hours at room temperature and concentrated under reduced pressure. The residue was columned chromatographed on silica gel using a gradient of 0 to 5% chloroform in methanol, affording the title compound as a white solid in 70% yield. The crystals used in the structural study were grown from EtOH solution, m. pt. 403–404 K. 1H NMR (500 MHz, DMSO-d6) δ (ppm): 9.02 (1H, s, NHNH2), 6.58 (1H, d, J = 8.2, NHCH), 4.81 (1H, t, J = 5.6, OH), 4.19 (2H, s, NHNH2), 3.93 (1H, m, CH), 3.60–3.40 (2H, m, CH2OH), 1.37 (9H, s, (CH3)3C). 13C NMR (125 MHz, DMSO-d6) δ (ppm): 169.7 (COCH), 155.1 (COO), 78.1 ((CH3)3C), 61.9 (CH2OH), 55.5 (CH), 28.2 ((CH3)3C). IR (cm-1, KBr): 3281 (O—H), 1699 (COCH), 1668 (COO). EM/ESI (m/z [M—H]-): 218.1.
The C-bound H atoms were geometrically placed (C–H = 0.98–1.00 Å) and refined as riding with Uiso(H) = 1.2-1.5Ueq(parent atom). The O-bound H atom was refined with the distance restraint O–H = 0.840±0.001, and with Uiso(H) = 1.5Ueq(O). The N-bound H atoms were treated similarly with N–H = 0.880±0.001 and 0.910±0.001 Å, and with Uiso(H) = 1.2Ueq(N). In the absence of significant
effects, 1067 Friedel pairs were averaged in the final refinement.Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); 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).Fig. 1. The molecular structure of (I) showing displacement ellipsoids at the 50% probability level. | |
Fig. 2. A view of a supramolecular array in (I) in the ab plane. The O–H···N and N–H···O hydrogen bonding interactions are shown as orange and blue dashed lines, respectively. Colour code: O, red; N, blue; C, grey; and H, green. | |
Fig. 3. A view of the crystal packing in (I) in projection down the b axis, showing the stacking of layers. The O–H···N and N–H···O hydrogen bonding interactions are shown as orange and blue dashed lines, respectively. Colour code: O, red; N, blue; C, grey; and H, green. |
C8H17N3O4 | F(000) = 236 |
Mr = 219.25 | Dx = 1.297 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 10838 reflections |
a = 6.9274 (5) Å | θ = 2.9–27.5° |
b = 5.0074 (4) Å | µ = 0.10 mm−1 |
c = 16.2388 (15) Å | T = 120 K |
β = 94.483 (5)° | Plate, colourless |
V = 561.57 (8) Å3 | 0.26 × 0.14 × 0.03 mm |
Z = 2 |
Nonius KappaCCD diffractometer | 1428 independent reflections |
Radiation source: Enraf–Nonius FR591 rotating anode | 1168 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.062 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.0° |
ϕ and ω scans | h = −8→8 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | k = −6→6 |
Tmin = 0.616, Tmax = 0.746 | l = −21→18 |
6687 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.046 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.149 | w = 1/[σ2(Fo2) + (0.0838P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.23 | (Δ/σ)max = 0.001 |
1428 reflections | Δρmax = 0.30 e Å−3 |
154 parameters | Δρmin = −0.34 e Å−3 |
6 restraints | Absolute structure: nd |
Primary atom site location: structure-invariant direct methods |
C8H17N3O4 | V = 561.57 (8) Å3 |
Mr = 219.25 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.9274 (5) Å | µ = 0.10 mm−1 |
b = 5.0074 (4) Å | T = 120 K |
c = 16.2388 (15) Å | 0.26 × 0.14 × 0.03 mm |
β = 94.483 (5)° |
Nonius KappaCCD diffractometer | 1428 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | 1168 reflections with I > 2σ(I) |
Tmin = 0.616, Tmax = 0.746 | Rint = 0.062 |
6687 measured reflections |
R[F2 > 2σ(F2)] = 0.046 | 6 restraints |
wR(F2) = 0.149 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.23 | Δρmax = 0.30 e Å−3 |
1428 reflections | Δρmin = −0.34 e Å−3 |
154 parameters | Absolute structure: nd |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.2906 (3) | 0.6236 (5) | 0.55336 (15) | 0.0226 (6) | |
O2 | −0.0983 (3) | 0.3069 (5) | 0.64307 (16) | 0.0245 (6) | |
H1O | −0.149 (6) | 0.452 (5) | 0.627 (3) | 0.037* | |
O3 | 0.4633 (4) | −0.1207 (6) | 0.74118 (17) | 0.0298 (7) | |
O4 | 0.6317 (3) | 0.2100 (5) | 0.81155 (14) | 0.0223 (6) | |
N1 | 0.2779 (4) | 0.2663 (6) | 0.42051 (18) | 0.0223 (7) | |
H1N | 0.205 (5) | 0.414 (5) | 0.409 (3) | 0.027* | |
H2N | 0.4053 (15) | 0.288 (9) | 0.412 (2) | 0.027* | |
N2 | 0.2663 (4) | 0.1984 (5) | 0.50498 (18) | 0.0198 (6) | |
H3N | 0.230 (5) | 0.033 (3) | 0.513 (2) | 0.024* | |
N3 | 0.4237 (4) | 0.3155 (5) | 0.70510 (18) | 0.0207 (6) | |
H4N | 0.429 (6) | 0.485 (2) | 0.720 (2) | 0.025* | |
C1 | 0.2715 (4) | 0.3813 (8) | 0.5650 (2) | 0.0181 (7) | |
C2 | 0.2480 (4) | 0.2659 (8) | 0.65093 (19) | 0.0182 (7) | |
H2 | 0.2267 | 0.0688 | 0.6460 | 0.022* | |
C3 | 0.0743 (2) | 0.3924 (5) | 0.68777 (11) | 0.0213 (7) | |
H3A | 0.0723 | 0.3398 | 0.7465 | 0.026* | |
H3B | 0.0842 | 0.5894 | 0.6852 | 0.026* | |
C4 | 0.5023 (2) | 0.1141 (5) | 0.75191 (11) | 0.0193 (7) | |
C5 | 0.7406 (2) | 0.0190 (5) | 0.86737 (11) | 0.0218 (7) | |
C6 | 0.8669 (2) | 0.2032 (5) | 0.92338 (11) | 0.0317 (9) | |
H6A | 0.9567 | 0.3001 | 0.8904 | 0.047* | |
H6B | 0.9406 | 0.0969 | 0.9657 | 0.047* | |
H6C | 0.7847 | 0.3310 | 0.9501 | 0.047* | |
C7 | 0.6005 (6) | −0.1336 (9) | 0.9179 (2) | 0.0300 (8) | |
H7A | 0.5109 | −0.0078 | 0.9411 | 0.045* | |
H7B | 0.6735 | −0.2291 | 0.9629 | 0.045* | |
H7C | 0.5272 | −0.2620 | 0.8823 | 0.045* | |
C8 | 0.8656 (5) | −0.1602 (7) | 0.8176 (2) | 0.0246 (8) | |
H8A | 0.7860 | −0.3046 | 0.7922 | 0.037* | |
H8B | 0.9705 | −0.2366 | 0.8542 | 0.037* | |
H8C | 0.9207 | −0.0549 | 0.7743 | 0.037* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0269 (12) | 0.0135 (13) | 0.0271 (14) | −0.0025 (11) | −0.0007 (10) | 0.0009 (10) |
O2 | 0.0192 (12) | 0.0197 (14) | 0.0342 (14) | 0.0009 (10) | −0.0008 (10) | 0.0023 (11) |
O3 | 0.0372 (13) | 0.0126 (13) | 0.0370 (15) | −0.0006 (12) | −0.0138 (11) | 0.0009 (11) |
O4 | 0.0314 (12) | 0.0113 (12) | 0.0230 (12) | 0.0012 (10) | −0.0066 (10) | 0.0013 (10) |
N1 | 0.0214 (14) | 0.0213 (17) | 0.0241 (15) | −0.0002 (12) | 0.0013 (12) | −0.0001 (13) |
N2 | 0.0235 (14) | 0.0133 (13) | 0.0225 (15) | −0.0017 (12) | 0.0015 (11) | 0.0000 (13) |
N3 | 0.0231 (13) | 0.0110 (14) | 0.0272 (15) | −0.0018 (12) | −0.0031 (12) | −0.0014 (13) |
C1 | 0.0143 (13) | 0.0129 (16) | 0.0266 (18) | 0.0004 (13) | −0.0010 (12) | 0.0017 (15) |
C2 | 0.0182 (15) | 0.0140 (17) | 0.0215 (17) | −0.0020 (13) | −0.0032 (13) | −0.0013 (13) |
C3 | 0.0225 (15) | 0.0165 (16) | 0.0252 (17) | −0.0019 (15) | 0.0030 (13) | −0.0005 (14) |
C4 | 0.0212 (15) | 0.0121 (17) | 0.0243 (18) | −0.0008 (14) | −0.0001 (13) | 0.0004 (13) |
C5 | 0.0291 (18) | 0.0122 (16) | 0.0231 (18) | 0.0020 (15) | −0.0036 (14) | 0.0027 (14) |
C6 | 0.042 (2) | 0.0165 (18) | 0.033 (2) | 0.0034 (17) | −0.0155 (17) | −0.0002 (17) |
C7 | 0.0403 (19) | 0.022 (2) | 0.028 (2) | 0.0061 (18) | 0.0032 (16) | 0.0026 (16) |
C8 | 0.0285 (16) | 0.0156 (19) | 0.0296 (19) | 0.0021 (15) | 0.0011 (14) | 0.0029 (15) |
O1—C1 | 1.236 (4) | C2—H2 | 1.0000 |
O2—C3 | 1.416 (3) | C3—H3A | 0.9900 |
O2—H1O | 0.84 (3) | C3—H3B | 0.9900 |
O3—C4 | 1.216 (3) | C5—C8 | 1.523 (4) |
O4—C4 | 1.355 (3) | C5—C6 | 1.523 (3) |
O4—C5 | 1.482 (3) | C5—C7 | 1.525 (4) |
N1—N2 | 1.421 (4) | C6—H6A | 0.9800 |
N1—H1N | 0.91 (3) | C6—H6B | 0.9800 |
N1—H2N | 0.911 (13) | C6—H6C | 0.9800 |
N2—C1 | 1.336 (5) | C7—H7A | 0.9800 |
N2—H3N | 0.878 (18) | C7—H7B | 0.9800 |
N3—C4 | 1.352 (3) | C7—H7C | 0.9800 |
N3—C2 | 1.466 (4) | C8—H8A | 0.9800 |
N3—H4N | 0.883 (14) | C8—H8B | 0.9800 |
C1—C2 | 1.531 (5) | C8—H8C | 0.9800 |
C2—C3 | 1.523 (4) | ||
C3—O2—H1O | 102 (3) | O3—C4—O4 | 124.9 (2) |
C4—O4—C5 | 119.0 (2) | N3—C4—O4 | 110.6 (2) |
N2—N1—H1N | 109 (3) | O4—C5—C8 | 109.80 (19) |
N2—N1—H2N | 107 (2) | O4—C5—C6 | 102.46 (12) |
H1N—N1—H2N | 114 (4) | C8—C5—C6 | 110.49 (15) |
C1—N2—N1 | 122.7 (3) | O4—C5—C7 | 109.8 (2) |
C1—N2—H3N | 122 (3) | C8—C5—C7 | 113.7 (2) |
N1—N2—H3N | 114 (3) | C6—C5—C7 | 109.99 (17) |
C4—N3—C2 | 119.3 (3) | C5—C6—H6A | 109.5 |
C4—N3—H4N | 124 (3) | C5—C6—H6B | 109.5 |
C2—N3—H4N | 110 (3) | H6A—C6—H6B | 109.5 |
O1—C1—N2 | 123.9 (3) | C5—C6—H6C | 109.5 |
O1—C1—C2 | 122.0 (3) | H6A—C6—H6C | 109.5 |
N2—C1—C2 | 114.0 (3) | H6B—C6—H6C | 109.5 |
N3—C2—C3 | 109.8 (2) | C5—C7—H7A | 109.5 |
N3—C2—C1 | 109.9 (3) | C5—C7—H7B | 109.5 |
C3—C2—C1 | 110.2 (2) | H7A—C7—H7B | 109.5 |
N3—C2—H2 | 109.0 | C5—C7—H7C | 109.5 |
C3—C2—H2 | 109.0 | H7A—C7—H7C | 109.5 |
C1—C2—H2 | 109.0 | H7B—C7—H7C | 109.5 |
O2—C3—C2 | 109.54 (19) | C5—C8—H8A | 109.5 |
O2—C3—H3A | 109.8 | C5—C8—H8B | 109.5 |
C2—C3—H3A | 109.8 | H8A—C8—H8B | 109.5 |
O2—C3—H3B | 109.8 | C5—C8—H8C | 109.5 |
C2—C3—H3B | 109.8 | H8A—C8—H8C | 109.5 |
H3A—C3—H3B | 108.2 | H8B—C8—H8C | 109.5 |
O3—C4—N3 | 124.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H1o···N1i | 0.84 (3) | 1.94 (3) | 2.776 (4) | 174 (5) |
N1—H1n···O2i | 0.91 (3) | 2.24 (3) | 3.121 (4) | 162 (4) |
N1—H2n···O1ii | 0.91 (1) | 2.29 (2) | 3.070 (4) | 144 (3) |
N2—H3n···O1iii | 0.88 (2) | 2.18 (2) | 2.985 (4) | 152 (3) |
N3—H4n···O3iv | 0.88 (1) | 2.02 (1) | 2.892 (4) | 172 (3) |
Symmetry codes: (i) −x, y+1/2, −z+1; (ii) −x+1, y−1/2, −z+1; (iii) x, y−1, z; (iv) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C8H17N3O4 |
Mr | 219.25 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 120 |
a, b, c (Å) | 6.9274 (5), 5.0074 (4), 16.2388 (15) |
β (°) | 94.483 (5) |
V (Å3) | 561.57 (8) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.26 × 0.14 × 0.03 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2007) |
Tmin, Tmax | 0.616, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6687, 1428, 1168 |
Rint | 0.062 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.046, 0.149, 1.23 |
No. of reflections | 1428 |
No. of parameters | 154 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.30, −0.34 |
Absolute structure | Nd |
Computer programs: , DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H1o···N1i | 0.84 (3) | 1.94 (3) | 2.776 (4) | 174 (5) |
N1—H1n···O2i | 0.91 (3) | 2.24 (3) | 3.121 (4) | 162 (4) |
N1—H2n···O1ii | 0.911 (13) | 2.29 (2) | 3.070 (4) | 144 (3) |
N2—H3n···O1iii | 0.878 (18) | 2.183 (18) | 2.985 (4) | 152 (3) |
N3—H4n···O3iv | 0.883 (14) | 2.015 (12) | 2.892 (4) | 172 (3) |
Symmetry codes: (i) −x, y+1/2, −z+1; (ii) −x+1, y−1/2, −z+1; (iii) x, y−1, z; (iv) x, y+1, z. |
Footnotes
‡Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.
Acknowledgements
The use of the EPSRC X-ray crystallographic service at the University of Southampton, England, and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from CAPES and FAPEMIG (Brazil).
References
Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Hooft, R. W. W. (1998). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
Pinheiro, A. C., Kaiser, C. R., Lourenço, M. C. S., de Souza, M. V. N., Wardell, S. M. S. V. & Wardell, J. L. (2007). J. Chem. Res. pp. 180–184. CrossRef Google Scholar
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Continuing our interests in serinyl compounds as potential anti-tuberculosis agents (Pinheiro et al., 2007), we have prepared the title compound, tert-butyl N-[1(S)-1-(hydrazinecarbonyl)-2-hydroxyethyl]carbamate (I) from L-serine methyl ester hydrochloride, as a precursor of a series of tert-butyl N-(2-hydroxy-1-(S)-{N'-[(1E)-(2-aryl)methylidene]-hydrazinecarbonyl}ethyl)carbamates. We now report the syntheses and structure of (I).
The molecular structure of (I), Fig. 1, is twisted with the dihedral angle formed between the least-squares planes through the hydrazinecarbonyl (r.m.s. deviation = 0.0045 Å) and carbamate (r.m.s. deviation = 0.021 Å) residues being 44.94 (12) °. The carbonyl-O1 and O3 atoms lie to opposite sides of the molecule as seen in the pseudo O1–C1···C4–O3 torsion angle of -176.7 (3) °. Finally, each of the N–H groups is anti to the adjacent carbonyl so that the N–H groups, too, lie to opposite sides of the molecule. Although the absolute structure could not be determined experimentally, the assignment of the S-configuration at the C2 atom is based on the starting reagents. There are five acidic H atoms in the structure, and each of these forms a significant hydrogen bonding interaction, Table 1. The hydroxyl-O2–H forms an O–H···N bond with the amino-N1 atom. The carbonyl-O1 atom accepts two N–H hydrogen bonds, one from the amino-N1 atom and the other from the hydrazine-N2. The second amino-N1–H atom forms a hydrogen bond with the hydroxyl-O2 atom, and, finally, the carbamate-N3–H interacts with the O3-carbonyl atom. The hydrogen bonds cooperate with each other to form a 2-D array in the ab plane, Fig. 2, and these stack along the c axis being sandwiched by the t-butyl groups, Fig. 3.