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Acta Crystallogr Sect E Struct Rep Online. 2010 August 1; 66(Pt 8): o2023–o2024.
Published online 2010 July 14. doi:  10.1107/S1600536810027273
PMCID: PMC3007287

Benzyl N-{(1S)-2-hy­droxy-1-[N′-(2-nitro­benzyl­idene)hydrazinylcarbon­yl]eth­yl}carbamate

Abstract

The carbamate and hydrazone groups in the title compound, C18H18N4O6, are approximately orthogonal [dihedral angle = 83.3 (4)°], and the carbonyl groups are effectively anti [O=C(...)C=O torsion angle = −116.2 (7)°]. The conformation about the imine bond [1.295 (11) Å] is E. The crystal packing is dominated by O—H(...)O and N—H(...)O hydrogen bonding, which leads to two-dimensional arrays in the ab plane.

Related literature

For background to the anti-tumour potential of l-serine derivatives, see: Jiao et al. (2009 [triangle]); Yakura et al. (2007 [triangle]); Takahashi et al. (1988 [triangle]); Sin et al. (1998 [triangle]). For background of the anti-tumour potential of N-acyl­hydrazone l-serine derivatives, see: Rollas & Küçükgüzel (2007 [triangle]); Terzioğlu & Gürsoy (2003 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2023-scheme1.jpg

Experimental

Crystal data

  • C18H18N4O6
  • M r = 386.36
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2023-efi1.jpg
  • a = 4.6675 (7) Å
  • b = 5.7001 (7) Å
  • c = 16.645 (3) Å
  • α = 90.457 (9)°
  • β = 92.087 (7)°
  • γ = 97.319 (9)°
  • V = 438.90 (11) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 120 K
  • 0.20 × 0.07 × 0.01 mm

Data collection

  • Nonius KappaCCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2007 [triangle]) T min = 0.624, T max = 1.000
  • 7083 measured reflections
  • 1791 independent reflections
  • 1243 reflections with I > 2σ(I)
  • R int = 0.093

Refinement

  • R[F 2 > 2σ(F 2)] = 0.089
  • wR(F 2) = 0.190
  • S = 1.14
  • 1791 reflections
  • 262 parameters
  • 6 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.32 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/S1600536810027273/zs2049sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810027273/zs2049Isup2.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 (Brazil).

supplementary crystallographic information

Comment

Several L-serine derivatives have been found to have potential in anti-cancer therapy, for example, conagenin, a naturally occurring serine derivative, was shown to improve the anti-tumour efficacy of adriamycin and mitomycin C against murine leukemias (Jiao et al., 2009; Yakura et al., 2007). Other L-serine derivatives reported as potential new anti-tumour agents include the antibiotic thrazarine, which sensitizes tumour cells to macrophage-mediated cytolysis (Takahashi et al., 1988), and eponemycin, an immunomodulator, which plays a crucial role in tumour progression and metastases by supplying essential nutrients to B16 melanoma cells (Sin et al., 1998).

Following on from such reports, we have synthesized some N-acylhydrazone L-serine derivatives from L-serine to screen for anti-tumour activity. The choice of N-acylhydrazonyl derivatives was suggested by publications indicating that compounds with such groups can aid anti-tumour activities (Rollas & Küçükgüzel, 2007; Terzioğlu & Gürsoy, 2003). We now report the structure of the title compound (I). While the solid, isolated by recrystallization from methanol, was purely in the E-form, NMR spectra in DMSO-d6 solution indicated that both E and Z forms are produced.

Significant twists are evident in the molecular structure of (I) (Fig. 1). The twisting is most pronounced about the central methine link with the dihedral angle formed between the least-squares planes through the carbamate group (N1,C1,O1,O2; r.m.s. = 0.0028 Å) and the hydrazone group (N2,N2,C4,O4; r.m.s. = 0.0202 Å) being 83.3 (4)°. The dihedral angle O2–C2···C4–O4 is -116.2 (7)° indicating an anti disposition for the carbonyl-O2 and O4 atoms. While the benzyl-benzene ring is approximately co-planar with the carbamate group [the O1–C1–C12–C13 torsion angle is -171.3 (8)°], the benzene ring adjacent to the hydrazone residue is not [N3–C5–C6–C7 = -137.9 (9) °]; the dihedral angle formed between the terminal benzene rings is 67.8 (4) °. The conformation about the imine C5═N3 bond [1.295 (11) Å] is E.

The crystal packing is dominated by O–H···O and N–H···O hydrogen bonding (Table 1). The hydroxyl group hydrogen bonds with the carbonyl-O2 to form a chain along the b axis. Each N–H hydrogen-bonds to an O atom, N1–H to the hydroxy-O3 atom to form a chain along the a axis, and N3–H to a carbonyl-O4 atom to form an amide-type tape along the a axis. The net result of the hydrogen bonding is the formation of two-dimensional arrays in the ab plane (Fig. 2), that stack along the c axis (Fig. 3).

Experimental

An ethanolic solution of 2-nitrobenzaldehyde (1.05 mmol) and PhCH2O(CO)NHCH(CH2OH)CONHNH2, prepared from L-serine and hydrazine hydrate, (1.0 mmol) was refluxed for 4 h. After rotary evaporation, the residue was washed with cold ethanol (3 x 10 ml), and recrystallized from methanol. The crystals used in the structure determination were grown from methanol solution, m.p. 428–429 K.

1H NMR (500 MHz, DMSO-d6) δ (p.p.m.): 11.88 and 11.71 (1H, s, NHN, (E/Z)-diastereomer), 8.66 and 8.39 (1H, s, N═CH, (E/Z)-diastereomer), 8.07 (2H, m, H3 and H6), 7.80 (1H, m, H5), 7.67 (1H, m, H4), 7.44 (d, J = 7.8) and 7.34 (m), (1H, NHCH, (E/Z)-diastereomer), 7.38–7.30 (5H, m, Ph), 5.05 and 5.04 (2H, s, CH2Ph, (E/Z)-diastereomer), 5.03 (m) and 4.89 (t, J = 5.9), (1H, OH, (E/Z)-diastereomer), 5.03 and 4.15 (1H, m, CH, (E/Z)-diastereomer), 3.80–3.60 (2H, m, CH2OH). 13C NMR (125 MHz, DMSO-d6) δ (p.p.m.): 171.7, 167.4, 156.0, 148.2, 148.1, 142.4, 138.8, 137.0, 136.9, 133.8, 133.6, 130.6, 130.5, 128.7, 128.4, 128.0, 127.8, 127.7, 124.7, 124.6, 65.6, 65.4, 61.4, 61.1, 56.5, 54.4. IR (cm-1; KBr): 3392 (O—H), 1694 (COCH), 1672 (COO), 1555 and 1342 (NO2). EM/ESI: [M—H]: 385.3.

Refinement

The C-bound H atoms were geometrically placed (C–H = 0.95–1.00 Å) and refined as riding with Uiso(H) = 1.2Ueq(C). The O– and N-bound H atoms were located from a difference map and refined with the distance restraints O–H = 0.84±0.01 and N–H = 0.88±0.01 Å, and with Uiso(H) = 1.2Ueq(N) or 1.5Ueq(O). In the absence of significant anomalous scattering effects, 1489 Friedel pairs were averaged in the final refinement. However, the absolute configuration was assigned on the basis of the chiralty of the L-serine starting material.

Figures

Fig. 1.
The molecular structure of (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Fig. 2.
A view of the two-dimensional supramolecular array in the ab plane in (I) with the O–H···O and N–H···O hydrogen bonding shown as orange and blue dashed lines, respectively.
Fig. 3.
A view in projection down the a axis of (I) showing the stacking of the two-dimensional arrays along the c axis.

Crystal data

C18H18N4O6Z = 1
Mr = 386.36F(000) = 202
Triclinic, P1Dx = 1.462 Mg m3
Hall symbol: P 1Melting point = 428–429 K
a = 4.6675 (7) ÅMo Kα radiation, λ = 0.71073 Å
b = 5.7001 (7) ÅCell parameters from 18416 reflections
c = 16.645 (3) Åθ = 2.9–27.5°
α = 90.457 (9)°µ = 0.11 mm1
β = 92.087 (7)°T = 120 K
γ = 97.319 (9)°Plate, colourless
V = 438.90 (11) Å30.20 × 0.07 × 0.01 mm

Data collection

Nonius KappaCCD area-detector diffractometer1791 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode1243 reflections with I > 2σ(I)
10 cm confocal mirrorsRint = 0.093
Detector resolution: 9.091 pixels mm-1θmax = 26.5°, θmin = 3.6°
[var phi] and ω scansh = −5→5
Absorption correction: multi-scan (SADABS; Sheldrick, 2007)k = −6→7
Tmin = 0.624, Tmax = 1.000l = −20→20
7083 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.089Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.190H atoms treated by a mixture of independent and constrained refinement
S = 1.14w = 1/[σ2(Fo2) + (0.037P)2 + 1.2849P] where P = (Fo2 + 2Fc2)/3
1791 reflections(Δ/σ)max < 0.001
262 parametersΔρmax = 0.39 e Å3
6 restraintsΔρmin = −0.32 e Å3

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
O10.2947 (12)0.8892 (10)0.3007 (4)0.0270 (14)
O2−0.0905 (13)0.6386 (10)0.2534 (4)0.0294 (15)
O3−0.4518 (12)1.3215 (11)0.1633 (4)0.0297 (15)
H3O−0.350 (19)1.374 (18)0.204 (4)0.045*
O40.1745 (14)0.8327 (12)0.0625 (4)0.0395 (17)
O5−0.6765 (15)0.6119 (12)−0.2286 (4)0.0427 (19)
O6−0.6271 (16)0.4575 (13)−0.3452 (4)0.0450 (19)
N10.0112 (16)1.0119 (13)0.2030 (5)0.0267 (17)
H1N0.156 (13)1.122 (12)0.195 (6)0.032*
N2−0.2884 (15)0.7320 (14)0.0165 (5)0.0285 (18)
H2N−0.469 (7)0.718 (17)0.031 (5)0.034*
N3−0.1965 (16)0.5952 (12)−0.0441 (5)0.0272 (18)
N4−0.5754 (16)0.4722 (12)−0.2727 (5)0.0291 (18)
C10.0588 (17)0.8301 (16)0.2530 (5)0.024 (2)
C2−0.2011 (19)0.9716 (15)0.1386 (5)0.025 (2)
H2−0.37850.87600.15850.030*
C3−0.278 (2)1.2117 (16)0.1085 (5)0.029 (2)
H3A−0.09781.31880.10040.035*
H3B−0.38421.18770.05590.035*
C4−0.0811 (19)0.8361 (14)0.0693 (5)0.0221 (19)
C5−0.398 (2)0.4987 (15)−0.0938 (5)0.026 (2)
H5−0.59280.5308−0.09210.031*
C6−0.3011 (19)0.3339 (14)−0.1536 (6)0.026 (2)
C7−0.3789 (19)0.3147 (14)−0.2349 (6)0.026 (2)
C8−0.2776 (19)0.1553 (16)−0.2870 (6)0.029 (2)
H8−0.33470.1492−0.34240.035*
C9−0.092 (2)0.0061 (16)−0.2560 (6)0.032 (2)
H9−0.0215−0.1062−0.29020.039*
C10−0.006 (2)0.0190 (16)−0.1754 (6)0.031 (2)
H100.1263−0.0809−0.15480.038*
C11−0.1140 (18)0.1766 (14)−0.1252 (5)0.026 (2)
H11−0.06000.1790−0.06960.031*
C120.347 (2)0.7141 (16)0.3589 (6)0.030 (2)
H12A0.40090.57240.33130.036*
H12B0.16910.66620.38840.036*
C130.5886 (19)0.8140 (16)0.4173 (6)0.026 (2)
C140.737 (2)1.0378 (16)0.4112 (6)0.030 (2)
H140.68571.13800.36910.035*
C150.958 (2)1.1178 (18)0.4651 (6)0.038 (2)
H151.06091.27140.45960.045*
C161.031 (2)0.9758 (18)0.5270 (6)0.038 (3)
H161.18471.03110.56420.045*
C170.881 (2)0.7527 (18)0.5351 (6)0.037 (3)
H170.92940.65460.57810.045*
C180.659 (2)0.6729 (16)0.4798 (6)0.031 (2)
H180.55430.51990.48530.037*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.024 (3)0.030 (3)0.027 (4)0.003 (3)0.002 (3)0.012 (3)
O20.021 (3)0.029 (3)0.036 (4)−0.002 (3)−0.002 (3)0.000 (3)
O30.023 (4)0.035 (4)0.032 (4)0.003 (3)0.003 (3)−0.006 (3)
O40.022 (4)0.049 (4)0.047 (4)0.003 (3)−0.001 (3)−0.015 (3)
O50.048 (5)0.043 (4)0.041 (4)0.024 (4)−0.002 (4)−0.006 (3)
O60.053 (5)0.057 (5)0.027 (4)0.018 (4)−0.008 (3)−0.001 (3)
N10.022 (4)0.032 (5)0.025 (4)0.001 (3)−0.002 (3)−0.006 (3)
N20.016 (4)0.038 (4)0.032 (4)0.003 (3)0.003 (3)−0.013 (4)
N30.026 (4)0.024 (4)0.033 (4)0.003 (3)0.003 (4)0.000 (3)
N40.030 (5)0.022 (4)0.035 (5)0.004 (3)−0.004 (4)0.005 (3)
C10.010 (4)0.037 (5)0.023 (5)0.000 (4)−0.005 (4)−0.008 (4)
C20.018 (5)0.028 (5)0.028 (5)−0.003 (4)0.003 (4)−0.001 (4)
C30.039 (6)0.026 (5)0.022 (5)0.003 (4)−0.005 (4)−0.004 (4)
C40.026 (5)0.020 (4)0.021 (5)0.002 (3)0.013 (4)0.005 (3)
C50.028 (5)0.028 (5)0.022 (5)0.005 (4)0.004 (4)−0.006 (4)
C60.026 (5)0.016 (4)0.037 (6)0.000 (4)−0.004 (4)−0.007 (4)
C70.020 (5)0.016 (4)0.041 (6)−0.004 (3)0.005 (4)−0.001 (4)
C80.032 (5)0.034 (5)0.019 (5)0.000 (4)0.000 (4)−0.011 (4)
C90.037 (6)0.027 (5)0.036 (6)0.012 (4)0.006 (5)−0.013 (4)
C100.032 (5)0.028 (5)0.034 (6)0.000 (4)0.007 (5)−0.010 (4)
C110.028 (5)0.023 (5)0.023 (5)−0.005 (4)−0.001 (4)0.003 (4)
C120.031 (5)0.025 (5)0.033 (6)0.005 (4)−0.005 (4)0.002 (4)
C130.023 (5)0.030 (5)0.025 (5)0.005 (4)0.011 (4)0.000 (4)
C140.030 (5)0.030 (5)0.028 (5)0.003 (4)−0.005 (4)−0.002 (4)
C150.039 (6)0.036 (6)0.036 (6)−0.001 (5)−0.010 (5)0.000 (5)
C160.026 (5)0.046 (6)0.040 (6)0.004 (5)−0.007 (5)−0.021 (5)
C170.036 (6)0.043 (6)0.034 (6)0.010 (5)−0.009 (5)−0.004 (5)
C180.034 (6)0.026 (5)0.031 (6)0.000 (4)−0.001 (4)0.000 (4)

Geometric parameters (Å, °)

O1—C11.340 (10)C6—C111.402 (12)
O1—C121.433 (10)C7—C81.388 (12)
O2—C11.218 (11)C8—C91.381 (13)
O3—C31.433 (11)C8—H80.9500
O3—H3O0.84 (8)C9—C101.384 (13)
O4—C41.205 (10)C9—H90.9500
O5—N41.228 (10)C10—C111.375 (12)
O6—N41.223 (10)C10—H100.9500
N1—C11.369 (12)C11—H110.9500
N1—C21.430 (11)C12—C131.513 (13)
N1—H1N0.88 (7)C12—H12A0.9900
N2—C41.358 (11)C12—H12B0.9900
N2—N31.383 (10)C13—C141.379 (12)
N2—H2N0.88 (4)C13—C181.376 (13)
N3—C51.295 (11)C14—C151.372 (13)
N4—C71.490 (11)C14—H140.9500
C2—C41.544 (12)C15—C161.376 (15)
C2—C31.541 (12)C15—H150.9500
C2—H21.0000C16—C171.381 (14)
C3—H3A0.9900C16—H160.9500
C3—H3B0.9900C17—C181.391 (13)
C5—C61.485 (12)C17—H170.9500
C5—H50.9500C18—H180.9500
C6—C71.387 (13)
C1—O1—C12114.3 (7)C8—C7—N4115.2 (8)
C3—O3—H3O110 (7)C9—C8—C7118.1 (8)
C1—N1—C2119.6 (7)C9—C8—H8120.9
C1—N1—H1N118 (6)C7—C8—H8120.9
C2—N1—H1N116 (6)C10—C9—C8120.5 (8)
C4—N2—N3116.5 (7)C10—C9—H9119.8
C4—N2—H2N118 (6)C8—C9—H9119.8
N3—N2—H2N123 (6)C9—C10—C11119.9 (9)
C5—N3—N2115.3 (7)C9—C10—H10120.1
O6—N4—O5123.4 (8)C11—C10—H10120.1
O6—N4—C7119.1 (7)C10—C11—C6122.0 (8)
O5—N4—C7117.5 (7)C10—C11—H11119.0
O2—C1—O1124.3 (8)C6—C11—H11119.0
O2—C1—N1124.7 (8)O1—C12—C13109.6 (7)
O1—C1—N1111.0 (7)O1—C12—H12A109.7
N1—C2—C4109.8 (7)C13—C12—H12A109.7
N1—C2—C3109.1 (7)O1—C12—H12B109.7
C4—C2—C3109.9 (7)C13—C12—H12B109.7
N1—C2—H2109.3H12A—C12—H12B108.2
C4—C2—H2109.3C14—C13—C18119.1 (8)
C3—C2—H2109.3C14—C13—C12123.3 (8)
O3—C3—C2112.7 (7)C18—C13—C12117.5 (8)
O3—C3—H3A109.1C13—C14—C15120.9 (9)
C2—C3—H3A109.1C13—C14—H14119.6
O3—C3—H3B109.1C15—C14—H14119.6
C2—C3—H3B109.1C16—C15—C14120.1 (10)
H3A—C3—H3B107.8C16—C15—H15120.0
O4—C4—N2124.3 (8)C14—C15—H15120.0
O4—C4—C2121.9 (8)C15—C16—C17120.0 (9)
N2—C4—C2113.7 (7)C15—C16—H16120.0
N3—C5—C6114.6 (8)C17—C16—H16120.0
N3—C5—H5122.7C16—C17—C18119.4 (10)
C6—C5—H5122.7C16—C17—H17120.3
C7—C6—C11115.8 (8)C18—C17—H17120.3
C7—C6—C5127.2 (8)C13—C18—C17120.5 (9)
C11—C6—C5117.0 (8)C13—C18—H18119.7
C6—C7—C8123.6 (8)C17—C18—H18119.7
C6—C7—N4121.2 (7)
C4—N2—N3—C5−179.8 (9)O6—N4—C7—C6176.4 (9)
C12—O1—C1—O2−5.2 (12)O5—N4—C7—C6−3.3 (12)
C12—O1—C1—N1175.7 (7)O6—N4—C7—C8−2.2 (11)
C2—N1—C1—O2−9.2 (13)O5—N4—C7—C8178.1 (8)
C2—N1—C1—O1169.9 (7)C6—C7—C8—C90.7 (13)
C1—N1—C2—C4−76.5 (9)N4—C7—C8—C9179.2 (8)
C1—N1—C2—C3163.0 (8)C7—C8—C9—C10−1.0 (14)
N1—C2—C3—O3−73.3 (9)C8—C9—C10—C111.9 (14)
C4—C2—C3—O3166.2 (7)C9—C10—C11—C6−2.6 (14)
N3—N2—C4—O46.5 (13)C7—C6—C11—C102.2 (12)
N3—N2—C4—C2−176.0 (7)C5—C6—C11—C10−178.9 (8)
N1—C2—C4—O4−20.2 (11)C1—O1—C12—C13−171.3 (8)
C3—C2—C4—O499.8 (10)O1—C12—C13—C14−2.3 (12)
N1—C2—C4—N2162.3 (8)O1—C12—C13—C18177.0 (8)
C3—C2—C4—N2−77.7 (9)C18—C13—C14—C152.0 (14)
N2—N3—C5—C6−174.3 (7)C12—C13—C14—C15−178.8 (9)
N3—C5—C6—C7−137.9 (9)C13—C14—C15—C16−1.1 (15)
N3—C5—C6—C1143.3 (12)C14—C15—C16—C17−0.2 (15)
C11—C6—C7—C8−1.3 (12)C15—C16—C17—C180.6 (15)
C5—C6—C7—C8179.9 (9)C14—C13—C18—C17−1.6 (14)
C11—C6—C7—N4−179.7 (8)C12—C13—C18—C17179.2 (9)
C5—C6—C7—N41.5 (13)C16—C17—C18—C130.3 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H3o···O2i0.84 (8)1.97 (9)2.712 (9)147 (8)
N1—H1n···O3ii0.88 (7)2.12 (7)2.974 (10)167 (8)
N2—H2n···O4iii0.88 (4)1.95 (5)2.775 (10)155 (9)

Symmetry codes: (i) x, y+1, z; (ii) x+1, y, z; (iii) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZS2049).

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