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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o994.
Published online 2010 March 31. doi:  10.1107/S1600536810011438
PMCID: PMC2983938

tert-Butyl N-[(S)-1-hydrazinecarbonyl-2-hydroxy­ethyl]carbamate

Abstract

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 [triangle]).

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Object name is e-66-0o994-scheme1.jpg

Experimental

Crystal data

  • C8H17N3O4
  • M r = 219.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o994-efi1.jpg
  • a = 6.9274 (5) Å
  • b = 5.0074 (4) Å
  • c = 16.2388 (15) Å
  • β = 94.483 (5)°
  • V = 561.57 (8) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 120 K
  • 0.26 × 0.14 × 0.03 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2007 [triangle]) T min = 0.616, T max = 0.746
  • 6687 measured reflections
  • 1428 independent reflections
  • 1168 reflections with I > 2σ(I)
  • R int = 0.062

Refinement

  • R[F 2 > 2σ(F 2)] = 0.046
  • wR(F 2) = 0.149
  • S = 1.23
  • 1428 reflections
  • 154 parameters
  • 6 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.30 e Å−3
  • Δρmin = −0.34 e Å−3

Data collection: COLLECT (Hooft, 1998 [triangle]); cell refinement: DENZO (Otwinowski & Minor, 1997 [triangle]) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810011438/hb5376sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810011438/hb5376Isup2.hkl

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

Acknowledgments

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).

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

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 anomalous scattering effects, 1067 Friedel pairs were averaged in the final refinement.

Figures

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; ...
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 ...

Crystal data

C8H17N3O4F(000) = 236
Mr = 219.25Dx = 1.297 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 10838 reflections
a = 6.9274 (5) Åθ = 2.9–27.5°
b = 5.0074 (4) ŵ = 0.10 mm1
c = 16.2388 (15) ÅT = 120 K
β = 94.483 (5)°Plate, colourless
V = 561.57 (8) Å30.26 × 0.14 × 0.03 mm
Z = 2

Data collection

Nonius KappaCCD diffractometer1428 independent reflections
Radiation source: Enraf–Nonius FR591 rotating anode1168 reflections with I > 2σ(I)
10 cm confocal mirrorsRint = 0.062
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 3.0°
[var phi] and ω scansh = −8→8
Absorption correction: multi-scan (SADABS; Sheldrick, 2007)k = −6→6
Tmin = 0.616, Tmax = 0.746l = −21→18
6687 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.149w = 1/[σ2(Fo2) + (0.0838P)2] where P = (Fo2 + 2Fc2)/3
S = 1.23(Δ/σ)max = 0.001
1428 reflectionsΔρmax = 0.30 e Å3
154 parametersΔρmin = −0.34 e Å3
6 restraintsAbsolute structure: nd
Primary atom site location: structure-invariant direct methods

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
O10.2906 (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*
O30.4633 (4)−0.1207 (6)0.74118 (17)0.0298 (7)
O40.6317 (3)0.2100 (5)0.81155 (14)0.0223 (6)
N10.2779 (4)0.2663 (6)0.42051 (18)0.0223 (7)
H1N0.205 (5)0.414 (5)0.409 (3)0.027*
H2N0.4053 (15)0.288 (9)0.412 (2)0.027*
N20.2663 (4)0.1984 (5)0.50498 (18)0.0198 (6)
H3N0.230 (5)0.033 (3)0.513 (2)0.024*
N30.4237 (4)0.3155 (5)0.70510 (18)0.0207 (6)
H4N0.429 (6)0.485 (2)0.720 (2)0.025*
C10.2715 (4)0.3813 (8)0.5650 (2)0.0181 (7)
C20.2480 (4)0.2659 (8)0.65093 (19)0.0182 (7)
H20.22670.06880.64600.022*
C30.0743 (2)0.3924 (5)0.68777 (11)0.0213 (7)
H3A0.07230.33980.74650.026*
H3B0.08420.58940.68520.026*
C40.5023 (2)0.1141 (5)0.75191 (11)0.0193 (7)
C50.7406 (2)0.0190 (5)0.86737 (11)0.0218 (7)
C60.8669 (2)0.2032 (5)0.92338 (11)0.0317 (9)
H6A0.95670.30010.89040.047*
H6B0.94060.09690.96570.047*
H6C0.78470.33100.95010.047*
C70.6005 (6)−0.1336 (9)0.9179 (2)0.0300 (8)
H7A0.5109−0.00780.94110.045*
H7B0.6735−0.22910.96290.045*
H7C0.5272−0.26200.88230.045*
C80.8656 (5)−0.1602 (7)0.8176 (2)0.0246 (8)
H8A0.7860−0.30460.79220.037*
H8B0.9705−0.23660.85420.037*
H8C0.9207−0.05490.77430.037*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0269 (12)0.0135 (13)0.0271 (14)−0.0025 (11)−0.0007 (10)0.0009 (10)
O20.0192 (12)0.0197 (14)0.0342 (14)0.0009 (10)−0.0008 (10)0.0023 (11)
O30.0372 (13)0.0126 (13)0.0370 (15)−0.0006 (12)−0.0138 (11)0.0009 (11)
O40.0314 (12)0.0113 (12)0.0230 (12)0.0012 (10)−0.0066 (10)0.0013 (10)
N10.0214 (14)0.0213 (17)0.0241 (15)−0.0002 (12)0.0013 (12)−0.0001 (13)
N20.0235 (14)0.0133 (13)0.0225 (15)−0.0017 (12)0.0015 (11)0.0000 (13)
N30.0231 (13)0.0110 (14)0.0272 (15)−0.0018 (12)−0.0031 (12)−0.0014 (13)
C10.0143 (13)0.0129 (16)0.0266 (18)0.0004 (13)−0.0010 (12)0.0017 (15)
C20.0182 (15)0.0140 (17)0.0215 (17)−0.0020 (13)−0.0032 (13)−0.0013 (13)
C30.0225 (15)0.0165 (16)0.0252 (17)−0.0019 (15)0.0030 (13)−0.0005 (14)
C40.0212 (15)0.0121 (17)0.0243 (18)−0.0008 (14)−0.0001 (13)0.0004 (13)
C50.0291 (18)0.0122 (16)0.0231 (18)0.0020 (15)−0.0036 (14)0.0027 (14)
C60.042 (2)0.0165 (18)0.033 (2)0.0034 (17)−0.0155 (17)−0.0002 (17)
C70.0403 (19)0.022 (2)0.028 (2)0.0061 (18)0.0032 (16)0.0026 (16)
C80.0285 (16)0.0156 (19)0.0296 (19)0.0021 (15)0.0011 (14)0.0029 (15)

Geometric parameters (Å, °)

O1—C11.236 (4)C2—H21.0000
O2—C31.416 (3)C3—H3A0.9900
O2—H1O0.84 (3)C3—H3B0.9900
O3—C41.216 (3)C5—C81.523 (4)
O4—C41.355 (3)C5—C61.523 (3)
O4—C51.482 (3)C5—C71.525 (4)
N1—N21.421 (4)C6—H6A0.9800
N1—H1N0.91 (3)C6—H6B0.9800
N1—H2N0.911 (13)C6—H6C0.9800
N2—C11.336 (5)C7—H7A0.9800
N2—H3N0.878 (18)C7—H7B0.9800
N3—C41.352 (3)C7—H7C0.9800
N3—C21.466 (4)C8—H8A0.9800
N3—H4N0.883 (14)C8—H8B0.9800
C1—C21.531 (5)C8—H8C0.9800
C2—C31.523 (4)
C3—O2—H1O102 (3)O3—C4—O4124.9 (2)
C4—O4—C5119.0 (2)N3—C4—O4110.6 (2)
N2—N1—H1N109 (3)O4—C5—C8109.80 (19)
N2—N1—H2N107 (2)O4—C5—C6102.46 (12)
H1N—N1—H2N114 (4)C8—C5—C6110.49 (15)
C1—N2—N1122.7 (3)O4—C5—C7109.8 (2)
C1—N2—H3N122 (3)C8—C5—C7113.7 (2)
N1—N2—H3N114 (3)C6—C5—C7109.99 (17)
C4—N3—C2119.3 (3)C5—C6—H6A109.5
C4—N3—H4N124 (3)C5—C6—H6B109.5
C2—N3—H4N110 (3)H6A—C6—H6B109.5
O1—C1—N2123.9 (3)C5—C6—H6C109.5
O1—C1—C2122.0 (3)H6A—C6—H6C109.5
N2—C1—C2114.0 (3)H6B—C6—H6C109.5
N3—C2—C3109.8 (2)C5—C7—H7A109.5
N3—C2—C1109.9 (3)C5—C7—H7B109.5
C3—C2—C1110.2 (2)H7A—C7—H7B109.5
N3—C2—H2109.0C5—C7—H7C109.5
C3—C2—H2109.0H7A—C7—H7C109.5
C1—C2—H2109.0H7B—C7—H7C109.5
O2—C3—C2109.54 (19)C5—C8—H8A109.5
O2—C3—H3A109.8C5—C8—H8B109.5
C2—C3—H3A109.8H8A—C8—H8B109.5
O2—C3—H3B109.8C5—C8—H8C109.5
C2—C3—H3B109.8H8A—C8—H8C109.5
H3A—C3—H3B108.2H8B—C8—H8C109.5
O3—C4—N3124.4 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O2—H1o···N1i0.84 (3)1.94 (3)2.776 (4)174 (5)
N1—H1n···O2i0.91 (3)2.24 (3)3.121 (4)162 (4)
N1—H2n···O1ii0.911 (13)2.29 (2)3.070 (4)144 (3)
N2—H3n···O1iii0.878 (18)2.183 (18)2.985 (4)152 (3)
N3—H4n···O3iv0.883 (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

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5376).

References

  • Brandenburg, K. (2006). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Hooft, R. W. W. (1998). COLLECT Nonius BV, Delft, The Netherlands.
  • 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.
  • 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.
  • Sheldrick, G. M. (2007). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Westrip, S. P. (2010). publCIF In preparation.

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