Literature DB >> 21837231

Benzyl N-(1-{N'-[(E)-2-chloro-benzyl-idene]hydrazinecarbon-yl}-2-hy-droxy-eth-yl)carbamate.

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

Abstract

The mol-ecule of the title compound, C(18)H(18)ClN(3)O(4), is twisted about the chiral C atom with the dihedral angle between the two amide residues being 87.8 (5)°, but, overall, it can be described as curved, with the benzene rings lying on the same side of the mol-ecule [dihedral angle = 62.8 (4)°]. The conformation about the imine bond [1.294 (7) Å] is E. In the crystal, a two-dimensional array in the ab plane is mediated by O-H⋯O and N-H⋯O hydrogen bonds as well as C-H⋯Cl inter-actions. The layers stack along the c-axis direction, being connected by C-H⋯.π contacts.

Entities:  

Year:  2011        PMID: 21837231      PMCID: PMC3151956          DOI: 10.1107/S1600536811024895

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For background to the use of l-serine derivatives in anti-tumour therapy, see: Jiao et al. (2009 ▶); Yakura et al. (2007 ▶). For background to N-acyl­hydrazone derivatives from l-serine for anti-tumour testing, see: Pinheiro et al. (2010 ▶, 2011a ▶,b ▶); de Souza et al. (2010 ▶); Howie et al. (2011 ▶).

Experimental

Crystal data

C18H18ClN3O4 M = 375.80 Triclinic, a = 4.6804 (4) Å b = 5.6037 (7) Å c = 16.946 (2) Å α = 95.669 (6)° β = 95.886 (7)° γ = 94.467 (6)° V = 438.20 (8) Å3 Z = 1 Mo Kα radiation μ = 0.25 mm−1 T = 120 K 0.12 × 0.03 × 0.02 mm

Data collection

Bruker–Nonius Roper CCD camera on κ-goniostat diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2007 ▶) T min = 0.682, T max = 1.000 6351 measured reflections 3438 independent reflections 2520 reflections with I > 2σ(I) R int = 0.062

Refinement

R[F 2 > 2σ(F 2)] = 0.070 wR(F 2) = 0.196 S = 1.10 3438 reflections 244 parameters 6 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.38 e Å−3 Δρmin = −0.39 e Å−3 Absolute structure: Flack (1983 ▶), 1476 Friedel pairs Flack parameter: 0.15 (12) Data collection: COLLECT (Hooft, 1998 ▶); cell refinement: 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 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811024895/hb5927sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811024895/hb5927Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811024895/hb5927Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C18H18ClN3O4Z = 1
Mr = 375.80F(000) = 196
Triclinic, P1Dx = 1.424 Mg m3
Hall symbol: P 1Mo Kα radiation, λ = 0.71073 Å
a = 4.6804 (4) ÅCell parameters from 13950 reflections
b = 5.6037 (7) Åθ = 2.9–27.5°
c = 16.946 (2) ŵ = 0.25 mm1
α = 95.669 (6)°T = 120 K
β = 95.886 (7)°Needle, yellow
γ = 94.467 (6)°0.12 × 0.03 × 0.02 mm
V = 438.20 (8) Å3
Bruker–Nonius Roper CCD camera on κ-goniostat diffractometer3438 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode2520 reflections with I > 2σ(I)
graphiteRint = 0.062
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 3.7°
φ and ω scansh = −6→6
Absorption correction: multi-scan (SADABS; Sheldrick, 2007)k = −7→7
Tmin = 0.682, Tmax = 1.000l = −21→21
6351 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.070H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.196w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
3438 reflectionsΔρmax = 0.38 e Å3
244 parametersΔρmin = −0.39 e Å3
6 restraintsAbsolute structure: Flack (1983), 1476 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.15 (12)
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.
xyzUiso*/Ueq
Cl1.3824 (2)1.3694 (2)0.28152 (10)0.0301 (4)
O10.5726 (7)0.6300 (8)0.4667 (3)0.0298 (10)
O21.2666 (8)0.1671 (7)0.5712 (3)0.0270 (10)
H2O1.181 (14)0.079 (11)0.600 (4)0.041*
O30.9314 (8)0.8947 (7)0.6569 (2)0.0273 (10)
O40.5835 (8)0.6630 (7)0.7041 (2)0.0265 (9)
N10.8863 (9)0.7934 (8)0.3539 (3)0.0198 (10)
N21.0058 (10)0.6984 (9)0.4208 (3)0.0221 (10)
H2N1.195 (3)0.713 (11)0.429 (4)0.026*
N30.8117 (10)0.4981 (8)0.6072 (3)0.0230 (11)
H3N0.683 (10)0.377 (7)0.610 (4)0.028*
C10.9669 (12)0.9974 (11)0.2410 (4)0.0233 (13)
C21.1001 (11)1.2101 (10)0.2184 (4)0.0248 (13)
C30.9976 (13)1.3025 (11)0.1494 (4)0.0287 (14)
H31.08441.44980.13590.034*
C40.7682 (13)1.1799 (12)0.1000 (4)0.0315 (15)
H40.69961.24190.05210.038*
C50.6399 (13)0.9705 (12)0.1198 (4)0.0308 (15)
H50.48420.88660.08510.037*
C60.7337 (12)0.8786 (11)0.1900 (3)0.0228 (12)
H60.63940.73440.20350.027*
C71.0712 (12)0.9037 (10)0.3152 (3)0.0223 (12)
H71.27040.92330.33450.027*
C80.8341 (11)0.6206 (10)0.4736 (3)0.0212 (12)
C90.9896 (11)0.5108 (10)0.5429 (3)0.0207 (12)
H91.17100.61480.56290.025*
C101.0689 (11)0.2567 (11)0.5148 (3)0.0218 (12)
H10A0.89100.14540.50480.026*
H10B1.15400.26130.46380.026*
C110.7900 (11)0.7019 (10)0.6551 (3)0.0190 (11)
C120.5549 (12)0.8631 (11)0.7614 (3)0.0236 (13)
H12A0.47890.99620.73370.028*
H12B0.74650.92170.79000.028*
C130.3567 (11)0.7911 (11)0.8197 (4)0.0244 (13)
C140.2025 (12)0.5668 (11)0.8127 (4)0.0286 (14)
H140.22190.45100.76910.034*
C150.0196 (14)0.5110 (13)0.8693 (5)0.0373 (16)
H15−0.08300.35630.86480.045*
C16−0.0126 (13)0.6770 (13)0.9310 (4)0.0363 (16)
H16−0.14060.63830.96880.044*
C170.1389 (13)0.9020 (13)0.9394 (4)0.0336 (15)
H170.11621.01660.98300.040*
C180.3217 (12)0.9584 (11)0.8845 (4)0.0275 (13)
H180.42611.11270.89030.033*
U11U22U33U12U13U23
Cl0.0278 (7)0.0258 (8)0.0367 (9)0.0003 (6)0.0059 (6)0.0024 (6)
O10.017 (2)0.048 (3)0.029 (2)0.0077 (19)0.0078 (17)0.016 (2)
O20.025 (2)0.025 (2)0.034 (3)0.0034 (18)0.0036 (18)0.0113 (19)
O30.025 (2)0.028 (2)0.028 (2)−0.0022 (18)0.0054 (17)−0.0004 (18)
O40.024 (2)0.031 (2)0.023 (2)−0.0005 (18)0.0069 (17)−0.0022 (17)
N10.020 (2)0.020 (2)0.018 (2)0.0046 (19)−0.0017 (18)0.001 (2)
N20.017 (2)0.027 (3)0.022 (3)0.0034 (19)0.0024 (19)0.005 (2)
N30.019 (2)0.023 (3)0.028 (3)−0.0027 (19)0.008 (2)0.004 (2)
C10.022 (3)0.029 (3)0.022 (3)0.008 (2)0.009 (2)0.002 (3)
C20.022 (3)0.028 (3)0.025 (3)0.008 (2)0.008 (2)−0.007 (3)
C30.034 (3)0.027 (3)0.031 (3)0.007 (3)0.016 (3)0.012 (3)
C40.036 (3)0.044 (4)0.017 (3)0.009 (3)0.006 (3)0.010 (3)
C50.028 (3)0.040 (4)0.025 (3)0.005 (3)0.004 (3)0.004 (3)
C60.022 (3)0.025 (3)0.023 (3)0.007 (2)0.001 (2)0.009 (2)
C70.020 (3)0.020 (3)0.025 (3)0.001 (2)0.002 (2)0.001 (2)
C80.012 (2)0.023 (3)0.027 (3)−0.001 (2)0.004 (2)0.000 (2)
C90.015 (2)0.026 (3)0.020 (3)−0.001 (2)0.001 (2)0.002 (2)
C100.019 (3)0.028 (3)0.018 (3)0.002 (2)0.002 (2)0.000 (2)
C110.012 (2)0.027 (3)0.019 (3)0.003 (2)0.004 (2)0.004 (2)
C120.021 (3)0.029 (3)0.022 (3)0.005 (2)0.005 (2)0.001 (2)
C130.014 (3)0.035 (3)0.025 (3)0.012 (2)0.003 (2)0.001 (3)
C140.024 (3)0.035 (4)0.030 (3)0.012 (3)0.008 (3)0.000 (3)
C150.027 (3)0.035 (4)0.053 (4)0.003 (3)0.013 (3)0.014 (3)
C160.031 (3)0.053 (4)0.032 (4)0.019 (3)0.014 (3)0.015 (3)
C170.027 (3)0.047 (4)0.026 (3)0.011 (3)0.003 (3)−0.003 (3)
C180.021 (3)0.032 (3)0.028 (3)0.001 (3)0.003 (2)0.000 (3)
Cl—C21.739 (6)C5—H50.9500
O1—C81.223 (6)C6—H60.9500
O2—C101.417 (7)C7—H70.9500
O2—H2O0.842 (10)C8—C91.525 (8)
O3—C111.218 (7)C9—C101.541 (8)
O4—C111.357 (6)C9—H91.0000
O4—C121.433 (6)C10—H10A0.9900
N1—C71.294 (7)C10—H10B0.9900
N1—N21.385 (6)C12—C131.485 (8)
N2—C81.343 (7)C12—H12A0.9900
N2—H2N0.877 (10)C12—H12B0.9900
N3—C111.351 (7)C13—C141.388 (9)
N3—C91.441 (7)C13—C181.403 (8)
N3—H3N0.878 (10)C14—C151.391 (9)
C1—C61.400 (8)C14—H140.9500
C1—C21.407 (8)C15—C161.357 (10)
C1—C71.462 (8)C15—H150.9500
C2—C31.381 (8)C16—C171.385 (10)
C3—C41.383 (9)C16—H160.9500
C3—H30.9500C17—C181.371 (8)
C4—C51.364 (9)C17—H170.9500
C4—H40.9500C18—H180.9500
C5—C61.386 (9)
C10—O2—H2O111 (5)N3—C9—H9108.7
C11—O4—C12114.7 (4)C8—C9—H9108.7
C7—N1—N2114.6 (4)C10—C9—H9108.7
C8—N2—N1119.6 (4)O2—C10—C9112.6 (4)
C8—N2—H2N124 (4)O2—C10—H10A109.1
N1—N2—H2N115 (4)C9—C10—H10A109.1
C11—N3—C9118.3 (5)O2—C10—H10B109.1
C11—N3—H3N117 (4)C9—C10—H10B109.1
C9—N3—H3N123 (4)H10A—C10—H10B107.8
C6—C1—C2117.8 (5)O3—C11—N3127.3 (5)
C6—C1—C7121.4 (5)O3—C11—O4122.9 (5)
C2—C1—C7120.7 (5)N3—C11—O4109.8 (5)
C3—C2—C1120.9 (5)O4—C12—C13110.4 (5)
C3—C2—Cl119.5 (5)O4—C12—H12A109.6
C1—C2—Cl119.4 (5)C13—C12—H12A109.6
C2—C3—C4119.8 (6)O4—C12—H12B109.6
C2—C3—H3120.1C13—C12—H12B109.6
C4—C3—H3120.1H12A—C12—H12B108.1
C5—C4—C3120.3 (6)C14—C13—C18118.4 (5)
C5—C4—H4119.9C14—C13—C12123.1 (5)
C3—C4—H4119.9C18—C13—C12118.5 (5)
C4—C5—C6120.8 (6)C13—C14—C15120.2 (6)
C4—C5—H5119.6C13—C14—H14119.9
C6—C5—H5119.6C15—C14—H14119.9
C5—C6—C1120.3 (6)C16—C15—C14120.2 (7)
C5—C6—H6119.9C16—C15—H15119.9
C1—C6—H6119.9C14—C15—H15119.9
N1—C7—C1118.5 (5)C15—C16—C17120.8 (6)
N1—C7—H7120.7C15—C16—H16119.6
C1—C7—H7120.7C17—C16—H16119.6
O1—C8—N2123.7 (5)C18—C17—C16119.6 (6)
O1—C8—C9121.7 (5)C18—C17—H17120.2
N2—C8—C9114.6 (4)C16—C17—H17120.2
N3—C9—C8110.6 (4)C17—C18—C13120.8 (6)
N3—C9—C10109.7 (5)C17—C18—H18119.6
C8—C9—C10110.2 (5)C13—C18—H18119.6
C7—N1—N2—C8167.6 (5)N2—C8—C9—N3163.1 (5)
C6—C1—C2—C32.1 (8)O1—C8—C9—C10102.9 (6)
C7—C1—C2—C3−178.3 (5)N2—C8—C9—C10−75.4 (6)
C6—C1—C2—Cl177.8 (4)N3—C9—C10—O2−70.8 (5)
C7—C1—C2—Cl−2.6 (7)C8—C9—C10—O2167.1 (4)
C1—C2—C3—C4−2.6 (8)C9—N3—C11—O3−9.6 (8)
Cl—C2—C3—C4−178.3 (5)C9—N3—C11—O4171.2 (5)
C2—C3—C4—C51.1 (9)C12—O4—C11—O3−3.2 (7)
C3—C4—C5—C60.9 (10)C12—O4—C11—N3176.0 (4)
C4—C5—C6—C1−1.4 (9)C11—O4—C12—C13−171.5 (5)
C2—C1—C6—C5−0.1 (8)O4—C12—C13—C14−6.0 (7)
C7—C1—C6—C5−179.7 (5)O4—C12—C13—C18174.6 (5)
N2—N1—C7—C1176.4 (5)C18—C13—C14—C15−0.4 (8)
C6—C1—C7—N1−33.8 (8)C12—C13—C14—C15−179.8 (6)
C2—C1—C7—N1146.7 (5)C13—C14—C15—C161.0 (10)
N1—N2—C8—O1−0.6 (8)C14—C15—C16—C17−1.1 (10)
N1—N2—C8—C9177.6 (5)C15—C16—C17—C180.5 (10)
C11—N3—C9—C8−77.4 (6)C16—C17—C18—C130.2 (9)
C11—N3—C9—C10160.8 (5)C14—C13—C18—C17−0.2 (8)
O1—C8—C9—N3−18.6 (7)C12—C13—C18—C17179.3 (5)
Cg1 is the centroid of the C13–C18 benzene ring.
D—H···AD—HH···AD···AD—H···A
O2—H2o···O3i0.84 (8)1.89 (9)2.728 (7)171 (9)
N3—H3n···O2ii0.88 (6)2.20 (6)3.006 (8)153 (7)
N2—H2n···O1iii0.88 (3)1.93 (4)2.758 (8)158 (7)
C6—H6···Cliv0.952.813.734 (8)166
C12—H12b···Cg1iii0.992.693.474 (8)137
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C13–C18 benzene ring.

D—H⋯AD—HH⋯ADAD—H⋯A
O2—H2o⋯O3i0.84 (8)1.89 (9)2.728 (7)171 (9)
N3—H3n⋯O2ii0.88 (6)2.20 (6)3.006 (8)153 (7)
N2—H2n⋯O1iii0.88 (3)1.93 (4)2.758 (8)158 (7)
C6—H6⋯Cliv0.952.813.734 (8)166
C12—H12b⋯Cg1iii0.992.693.474 (8)137

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

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1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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3.  Benzyl N-((S)-2-hydr-oxy-1-{N'-[(E)-2-methoxy-benzyl-idene]hydrazinecarbon-yl}eth-yl)carbamate from synchrotron data.

Authors:  Alessandra C Pinheiro; Marcus V N de Souza; Edward R T Tiekink; James L Wardell; Solange M S V Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-03-31

4.  tert-Butyl N-{(1S)-1-[(2,4-dihy-droxy-benzyl-idene)hydrazinecarbon-yl]-2-hy-droxy-eth-yl}carbamate ethanol monosolvate.

Authors:  Alessandra C Pinheiro; Marcus V N de Souza; Edward R T Tiekink; Solange M S V Wardell; James L Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-02-09

5.  Benzyl N-[(S)-2-hy-droxy-1-({[(E)-2-hy-droxy-4-meth-oxy-benzyl-idene]hydrazin-yl}carbon-yl)eth-yl]carbamate.

Authors:  Marcus V N de Souza; Alessandra C Pinheiro; Edward R T Tiekink; Solange M S V Wardell; James L Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-11-20

6.  tert-Butyl N-((1S)-2-hy-droxy-1-{N'-[(1E)-4-meth-oxy-benzyl-idene]hydrazinecarbon-yl}eth-yl)carbamate.

Authors:  Alessandra C Pinheiro; Marcus V N de Souza; Edward R T Tiekink; Solange M S V Wardell; James L Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-06-25
  6 in total
  3 in total

1.  Benzyl N-(2-hy-droxy-1-{N'-[(1E)-2-hy-droxy-benzyl-idene]hydrazinecarbon-yl}eth-yl)carbamate.

Authors:  Edward R T Tiekink; Marcus V N de Souza; Alessandra C Pinheiro; Solange M S V Wardell; James L Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-06-30

2.  Benzyl N-(1-{N'-[(E)-2,3-dihy-droxy-benzyl-idene]hydrazinecarbon-yl}-2-hy-droxy-eth-yl)carbamate dihydrate.

Authors:  Solange M S V Wardell; Edward R T Tiekink; Marcus V N de Souza; Alessandra C Pinheiro; James L Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-07-30

3.  tert-Butyl N-((1S)-2-hy-droxy-1-{N'-[(E)-2-hy-droxy-4-meth-oxy-benzyl-idene]hydrazinecarbon-yl}eth-yl)carbamate.

Authors:  James L Wardell; Marcus V N de Souza; Alessandra C Pinheiro; Edward R T Tiekink; Solange M S V Wardell
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-07-02
  3 in total

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