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The title compound, C11H11NO5, is almost planar. The mol­ecules pack as hydrogen-bonded dimers.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803018774/fl6056sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536803018774/fl6056Isup2.hkl
Contains datablock I

CCDC reference: 222918

Key indicators

  • Single-crystal X-ray study
  • T = 173 K
  • Mean [sigma](C-C) = 0.002 Å
  • R factor = 0.042
  • wR factor = 0.098
  • Data-to-parameter ratio = 19.3

checkCIF/PLATON results

No syntax errors found



Alert level A PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low ....... 0.93
Alert level C REFLT03_ALERT_3_C Reflection count < 95% complete From the CIF: _diffrn_reflns_theta_max 30.55 From the CIF: _diffrn_reflns_theta_full 0.00 From the CIF: _reflns_number_total 3064 TEST2: Reflns within _diffrn_reflns_theta_max Count of symmetry unique reflns 3309 Completeness (_total/calc) 92.60% PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C5 - C6 = 1.54 Ang.
1 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

N– and C-protected ethyl oxamates are excellent nitrogen nucleophiles in Gabriel reactions (Berrée et al., 1999). They are available by oxidation of protected serine or threonine (Stachulski, 1982). For our synthesis of methyl N-(benzyloxycarbonyl)oxamate, (I), we chose oxidation with RuO2/NaIO4 (Garner & Park, 1990), which leads to better yields.

The title compound is almost planar (r.m.s. deviation for all non-H atoms is 0.06 Å). All torsion angles excluding H atoms are close to either 0 or 180°. The biggest deviations from planarity are −2.75 (18)° for O2—C3—N4—C5 and 175.02 (10)° for C11—C1—O2—C3. An interesting feature of (I) is the rather long Csp3—Csp3 bond between atoms C5 and C6. The molecules pack as hydrogen-bonded dimers.

Only one similar compound, (II) (Wyss et al., 1984), has been found in the Cambridge Structural Database (CSD, Version 5.24 of April 2003; Allen, 2002) which differs from (I) by the terminal groups: the benzyl group in (I) is replaced by a tert-butyl group in (II) and the methyl group in (I) is replaced by a benzyl group in (II). Although this leads to a completely different conformation of (II), the latter also packs as hydrogen-bonded dimers. The rather long Csp3—Csp3 (1.533 Å) is also observed in (II).

Experimental top

N-Benzyloxycarbonyl-L-serine methyl ester (2 g) was dissolved in 200 ml of a 3:2 mixture of acetone and water. Under stirring, 10 equivalents of sodium periodate and 0.08 equivalents of ruthenium dioxide were added. The suspension was stirred for 24 h at room temperature. 10 ml of 2-propanol was added and the mixture stirred for a further 90 min to consume excess oxidant. The suspension was separated by centrifugation, yielding a clear yellow solution which was then concentrated in vacuo. HPLC purification yielded 1.44 g of pure N-benzyloxycarbonyl methyl oxamate (77%). The crystals were obtained directly from the HPLC fractions.

Refinement top

H atoms bonded to C atoms were refined with fixed individual displacement parameters [Uiso(H) = 1.2 Ueq(C) or 1.5 Ueq(Cmethyl)] using a riding model with C—H = 0.99 Å or methyl C—H = 0.98 Å. The H atom bonded to N was refined freely.

Computing details top

Cell refinement: SMART (Siemens, 1995); data reduction: SAINT (Siemens, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1990); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. Perspective view of the title compound with the atom numbering; displacement ellipsoids are drawn at the 50% probability level.
(I) top
Crystal data top
C11H11NO5F(000) = 496
Mr = 237.21Dx = 1.458 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 512 reflections
a = 8.0139 (8) Åθ = 3.2–20.7°
b = 5.4828 (5) ŵ = 0.12 mm1
c = 24.701 (3) ÅT = 173 K
β = 95.446 (2)°Plate, colourless
V = 1080.4 (2) Å30.52 × 0.28 × 0.12 mm
Z = 4
Data collection top
Siemens 1K CCD three-circle
diffractometer
2248 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.042
Graphite monochromatorθmax = 30.6°, θmin = 1.7°
ω scansh = 1111
17271 measured reflectionsk = 77
3064 independent reflectionsl = 3334
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.042H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.098 w = 1/[σ2(Fo2) + (0.0434P)2 + 0.2657P]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
3064 reflectionsΔρmax = 0.36 e Å3
159 parametersΔρmin = 0.20 e Å3
0 restraintsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0114 (17)
Crystal data top
C11H11NO5V = 1080.4 (2) Å3
Mr = 237.21Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.0139 (8) ŵ = 0.12 mm1
b = 5.4828 (5) ÅT = 173 K
c = 24.701 (3) Å0.52 × 0.28 × 0.12 mm
β = 95.446 (2)°
Data collection top
Siemens 1K CCD three-circle
diffractometer
2248 reflections with I > 2σ(I)
17271 measured reflectionsRint = 0.042
3064 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.098H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.36 e Å3
3064 reflectionsΔρmin = 0.20 e Å3
159 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > σ(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) top
xyzUiso*/Ueq
C10.14106 (17)0.0537 (2)0.34404 (5)0.0263 (3)
H1A0.01810.07690.33870.032*
H1B0.19310.21100.35590.032*
O20.18237 (11)0.13170 (16)0.38516 (3)0.0237 (2)
C30.12055 (15)0.0899 (2)0.43214 (5)0.0203 (3)
O310.03334 (11)0.08206 (17)0.44151 (4)0.0276 (2)
N40.16544 (13)0.2661 (2)0.47111 (4)0.0209 (2)
H40.1215 (19)0.243 (3)0.5013 (7)0.034 (4)*
C50.26733 (14)0.4662 (2)0.46824 (5)0.0190 (2)
O510.34199 (11)0.52955 (17)0.43049 (4)0.0258 (2)
C60.27838 (15)0.6067 (2)0.52258 (5)0.0201 (3)
O610.20617 (12)0.54188 (18)0.56038 (4)0.0294 (2)
O70.37597 (11)0.80055 (16)0.52109 (3)0.0229 (2)
C80.39785 (16)0.9384 (3)0.57169 (5)0.0265 (3)
H8A0.47141.07830.56720.040*
H8B0.44830.83320.60090.040*
H8C0.28860.99650.58100.040*
C110.20499 (15)0.0259 (2)0.29166 (5)0.0202 (3)
C120.16574 (16)0.1226 (3)0.24647 (5)0.0258 (3)
H120.10380.26850.25010.031*
C130.21605 (18)0.0597 (3)0.19636 (5)0.0311 (3)
H130.18770.16120.16570.037*
C140.30793 (18)0.1515 (3)0.19085 (5)0.0314 (3)
H140.34330.19440.15650.038*
C150.34800 (17)0.2995 (3)0.23544 (5)0.0287 (3)
H150.41110.44410.23160.034*
C160.29631 (15)0.2378 (2)0.28601 (5)0.0238 (3)
H160.32360.34070.31650.029*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0358 (7)0.0243 (7)0.0196 (6)0.0076 (6)0.0058 (5)0.0043 (5)
O20.0291 (5)0.0252 (5)0.0176 (4)0.0078 (4)0.0068 (3)0.0029 (4)
C30.0198 (5)0.0219 (6)0.0196 (6)0.0003 (5)0.0043 (4)0.0002 (5)
O310.0318 (5)0.0277 (5)0.0248 (5)0.0097 (4)0.0103 (4)0.0029 (4)
N40.0233 (5)0.0226 (6)0.0175 (5)0.0031 (4)0.0059 (4)0.0005 (4)
C50.0182 (5)0.0188 (6)0.0201 (6)0.0020 (5)0.0020 (4)0.0018 (5)
O510.0309 (5)0.0242 (5)0.0237 (5)0.0045 (4)0.0097 (4)0.0007 (4)
C60.0197 (5)0.0194 (6)0.0211 (6)0.0010 (5)0.0019 (4)0.0010 (5)
O610.0378 (5)0.0299 (5)0.0220 (5)0.0095 (4)0.0100 (4)0.0021 (4)
O70.0263 (4)0.0210 (5)0.0217 (4)0.0050 (4)0.0034 (3)0.0014 (4)
C80.0301 (7)0.0253 (7)0.0239 (6)0.0043 (5)0.0008 (5)0.0053 (5)
C110.0210 (6)0.0207 (6)0.0189 (6)0.0027 (5)0.0015 (4)0.0012 (5)
C120.0300 (7)0.0226 (7)0.0248 (6)0.0034 (5)0.0022 (5)0.0018 (5)
C130.0416 (8)0.0325 (8)0.0189 (6)0.0001 (6)0.0019 (5)0.0043 (6)
C140.0413 (8)0.0329 (8)0.0208 (6)0.0030 (6)0.0075 (5)0.0064 (6)
C150.0335 (7)0.0225 (7)0.0307 (7)0.0018 (5)0.0073 (5)0.0055 (6)
C160.0270 (6)0.0215 (7)0.0230 (6)0.0013 (5)0.0035 (5)0.0014 (5)
Geometric parameters (Å, º) top
C1—O21.4529 (15)C8—H8A0.9800
C1—C111.5010 (17)C8—H8B0.9800
C1—H1A0.9900C8—H8C0.9800
C1—H1B0.9900C11—C161.3872 (18)
O2—C31.3243 (14)C11—C121.3935 (17)
C3—O311.2088 (15)C12—C131.3813 (19)
C3—N41.3868 (16)C12—H120.9500
N4—C51.3737 (16)C13—C141.386 (2)
N4—H40.863 (17)C13—H130.9500
C5—O511.2057 (14)C14—C151.381 (2)
C5—C61.5430 (17)C14—H140.9500
C6—O611.1980 (14)C15—C161.3945 (18)
C6—O71.3221 (15)C15—H150.9500
O7—C81.4570 (15)C16—H160.9500
O2—C1—C11108.98 (10)H8A—C8—H8B109.5
O2—C1—H1A109.9O7—C8—H8C109.5
C11—C1—H1A109.9H8A—C8—H8C109.5
O2—C1—H1B109.9H8B—C8—H8C109.5
C11—C1—H1B109.9C16—C11—C12119.34 (11)
H1A—C1—H1B108.3C16—C11—C1123.84 (11)
C3—O2—C1114.33 (10)C12—C11—C1116.81 (11)
O31—C3—O2125.02 (11)C13—C12—C11120.60 (12)
O31—C3—N4121.80 (11)C13—C12—H12119.7
O2—C3—N4113.18 (10)C11—C12—H12119.7
C5—N4—C3129.57 (11)C12—C13—C14119.98 (13)
C5—N4—H4117.0 (11)C12—C13—H13120.0
C3—N4—H4113.4 (11)C14—C13—H13120.0
O51—C5—N4127.66 (12)C15—C14—C13119.88 (12)
O51—C5—C6122.49 (11)C15—C14—H14120.1
N4—C5—C6109.84 (10)C13—C14—H14120.1
O61—C6—O7126.23 (11)C14—C15—C16120.36 (13)
O61—C6—C5122.53 (11)C14—C15—H15119.8
O7—C6—C5111.24 (10)C16—C15—H15119.8
C6—O7—C8114.61 (10)C11—C16—C15119.85 (12)
O7—C8—H8A109.5C11—C16—H16120.1
O7—C8—H8B109.5C15—C16—H16120.1
C11—C1—O2—C3175.02 (10)C5—C6—O7—C8177.86 (9)
C1—O2—C3—O311.71 (18)O2—C1—C11—C163.18 (17)
C1—O2—C3—N4178.40 (10)O2—C1—C11—C12175.53 (11)
O31—C3—N4—C5177.35 (12)C16—C11—C12—C130.38 (19)
O2—C3—N4—C52.75 (18)C1—C11—C12—C13178.39 (12)
C3—N4—C5—O511.0 (2)C11—C12—C13—C140.7 (2)
C3—N4—C5—C6179.91 (11)C12—C13—C14—C150.4 (2)
O51—C5—C6—O61178.88 (12)C13—C14—C15—C160.1 (2)
N4—C5—C6—O610.12 (16)C12—C11—C16—C150.15 (19)
O51—C5—C6—O70.91 (16)C1—C11—C16—C15178.82 (12)
N4—C5—C6—O7179.92 (10)C14—C15—C16—C110.4 (2)
O61—C6—O7—C81.92 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O31i0.863 (17)2.156 (17)2.9778 (14)158.9 (14)
Symmetry code: (i) x, y, z+1.

Experimental details

Crystal data
Chemical formulaC11H11NO5
Mr237.21
Crystal system, space groupMonoclinic, P21/c
Temperature (K)173
a, b, c (Å)8.0139 (8), 5.4828 (5), 24.701 (3)
β (°) 95.446 (2)
V3)1080.4 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.52 × 0.28 × 0.12
Data collection
DiffractometerSiemens 1K CCD three-circle
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
17271, 3064, 2248
Rint0.042
(sin θ/λ)max1)0.715
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.098, 1.02
No. of reflections3064
No. of parameters159
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.36, 0.20

Computer programs: SMART (Siemens, 1995), SAINT (Siemens, 1995), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 1990), SHELXL97.

Selected bond lengths (Å) top
C1—O21.4529 (15)C5—O511.2057 (14)
O2—C31.3243 (14)C5—C61.5430 (17)
C3—O311.2088 (15)C6—O611.1980 (14)
C3—N41.3868 (16)C6—O71.3221 (15)
N4—C51.3737 (16)O7—C81.4570 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O31i0.863 (17)2.156 (17)2.9778 (14)158.9 (14)
Symmetry code: (i) x, y, z+1.
 

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