Methyl N-(benzyl­oxy­carbonyl)­oxamate

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

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

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S1. Comment

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).

S2. Experimental

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.

S3. Refinement

H atoms bonded to C atoms were refined with fixed individual displacement parameters [U_iso(H) = 1.2 U_eq(C) or 1.5 U_eq(C_methyl)] 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

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

Fig. 1. Perspective view of the title compound with the atom numbering; displacement ellipsoids are drawn at the 50% probability level.

(I)

Crystal data

C11H11NO5	F(000) = 496
Mr = 237.21	Dx = 1.458 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 512 reflections
a = 8.0139 (8) Å	θ = 3.2–20.7°
b = 5.4828 (5) Å	µ = 0.12 mm^−1
c = 24.701 (3) Å	T = 173 K
β = 95.446 (2)°	Plate, colourless
V = 1080.4 (2) Å^3	0.52 × 0.28 × 0.12 mm
Z = 4

Data collection

Siemens 1K CCD three-circle diffractometer	2248 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.042
Graphite monochromator	θmax = 30.6°, θmin = 1.7°
ω scans	h = −11→11
17271 measured reflections	k = −7→7
3064 independent reflections	l = −33→34

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.042	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.098	w = 1/[σ^2(Fo^2) + (0.0434P)^2 + 0.2657P] where P = (Fo^2 + 2Fc^2)/3
S = 1.02	(Δ/σ)max < 0.001
3064 reflections	Δρmax = 0.36 e Å^−3
159 parameters	Δρmin = −0.20 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0114 (17)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.14106 (17)	−0.0537 (2)	0.34404 (5)	0.0263 (3)
H1A	0.0181	−0.0769	0.3387	0.032*
H1B	0.1931	−0.2110	0.3559	0.032*
O2	0.18237 (11)	0.13170 (16)	0.38516 (3)	0.0237 (2)
C3	0.12055 (15)	0.0899 (2)	0.43214 (5)	0.0203 (3)
O31	0.03334 (11)	−0.08206 (17)	0.44151 (4)	0.0276 (2)
N4	0.16544 (13)	0.2661 (2)	0.47111 (4)	0.0209 (2)
H4	0.1215 (19)	0.243 (3)	0.5013 (7)	0.034 (4)*
C5	0.26733 (14)	0.4662 (2)	0.46824 (5)	0.0190 (2)
O51	0.34199 (11)	0.52955 (17)	0.43049 (4)	0.0258 (2)
C6	0.27838 (15)	0.6067 (2)	0.52258 (5)	0.0201 (3)
O61	0.20617 (12)	0.54188 (18)	0.56038 (4)	0.0294 (2)
O7	0.37597 (11)	0.80055 (16)	0.52109 (3)	0.0229 (2)
C8	0.39785 (16)	0.9384 (3)	0.57169 (5)	0.0265 (3)
H8A	0.4714	1.0783	0.5672	0.040*
H8B	0.4483	0.8332	0.6009	0.040*
H8C	0.2886	0.9965	0.5810	0.040*
C11	0.20499 (15)	0.0259 (2)	0.29166 (5)	0.0202 (3)
C12	0.16574 (16)	−0.1226 (3)	0.24647 (5)	0.0258 (3)
H12	0.1038	−0.2685	0.2501	0.031*
C13	0.21605 (18)	−0.0597 (3)	0.19636 (5)	0.0311 (3)
H13	0.1877	−0.1612	0.1657	0.037*
C14	0.30793 (18)	0.1515 (3)	0.19085 (5)	0.0314 (3)
H14	0.3433	0.1944	0.1565	0.038*
C15	0.34800 (17)	0.2995 (3)	0.23544 (5)	0.0287 (3)
H15	0.4111	0.4441	0.2316	0.034*
C16	0.29631 (15)	0.2378 (2)	0.28601 (5)	0.0238 (3)
H16	0.3236	0.3407	0.3165	0.029*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0358 (7)	0.0243 (7)	0.0196 (6)	−0.0076 (6)	0.0058 (5)	−0.0043 (5)
O2	0.0291 (5)	0.0252 (5)	0.0176 (4)	−0.0078 (4)	0.0068 (3)	−0.0029 (4)
C3	0.0198 (5)	0.0219 (6)	0.0196 (6)	−0.0003 (5)	0.0043 (4)	0.0002 (5)
O31	0.0318 (5)	0.0277 (5)	0.0248 (5)	−0.0097 (4)	0.0103 (4)	−0.0029 (4)
N4	0.0233 (5)	0.0226 (6)	0.0175 (5)	−0.0031 (4)	0.0059 (4)	−0.0005 (4)
C5	0.0182 (5)	0.0188 (6)	0.0201 (6)	0.0020 (5)	0.0020 (4)	0.0018 (5)
O51	0.0309 (5)	0.0242 (5)	0.0237 (5)	−0.0045 (4)	0.0097 (4)	0.0007 (4)
C6	0.0197 (5)	0.0194 (6)	0.0211 (6)	0.0010 (5)	0.0019 (4)	0.0010 (5)
O61	0.0378 (5)	0.0299 (5)	0.0220 (5)	−0.0095 (4)	0.0100 (4)	−0.0021 (4)
O7	0.0263 (4)	0.0210 (5)	0.0217 (4)	−0.0050 (4)	0.0034 (3)	−0.0014 (4)
C8	0.0301 (7)	0.0253 (7)	0.0239 (6)	−0.0043 (5)	0.0008 (5)	−0.0053 (5)
C11	0.0210 (6)	0.0207 (6)	0.0189 (6)	0.0027 (5)	0.0015 (4)	0.0012 (5)
C12	0.0300 (7)	0.0226 (7)	0.0248 (6)	−0.0034 (5)	0.0022 (5)	−0.0018 (5)
C13	0.0416 (8)	0.0325 (8)	0.0189 (6)	−0.0001 (6)	0.0019 (5)	−0.0043 (6)
C14	0.0413 (8)	0.0329 (8)	0.0208 (6)	0.0030 (6)	0.0075 (5)	0.0064 (6)
C15	0.0335 (7)	0.0225 (7)	0.0307 (7)	−0.0018 (5)	0.0073 (5)	0.0055 (6)
C16	0.0270 (6)	0.0215 (7)	0.0230 (6)	−0.0013 (5)	0.0035 (5)	−0.0014 (5)

Geometric parameters (Å, º)

C1—O2	1.4529 (15)	C8—H8A	0.9800
C1—C11	1.5010 (17)	C8—H8B	0.9800
C1—H1A	0.9900	C8—H8C	0.9800
C1—H1B	0.9900	C11—C16	1.3872 (18)
O2—C3	1.3243 (14)	C11—C12	1.3935 (17)
C3—O31	1.2088 (15)	C12—C13	1.3813 (19)
C3—N4	1.3868 (16)	C12—H12	0.9500
N4—C5	1.3737 (16)	C13—C14	1.386 (2)
N4—H4	0.863 (17)	C13—H13	0.9500
C5—O51	1.2057 (14)	C14—C15	1.381 (2)
C5—C6	1.5430 (17)	C14—H14	0.9500
C6—O61	1.1980 (14)	C15—C16	1.3945 (18)
C6—O7	1.3221 (15)	C15—H15	0.9500
O7—C8	1.4570 (15)	C16—H16	0.9500
O2—C1—C11	108.98 (10)	H8A—C8—H8B	109.5
O2—C1—H1A	109.9	O7—C8—H8C	109.5
C11—C1—H1A	109.9	H8A—C8—H8C	109.5
O2—C1—H1B	109.9	H8B—C8—H8C	109.5
C11—C1—H1B	109.9	C16—C11—C12	119.34 (11)
H1A—C1—H1B	108.3	C16—C11—C1	123.84 (11)
C3—O2—C1	114.33 (10)	C12—C11—C1	116.81 (11)
O31—C3—O2	125.02 (11)	C13—C12—C11	120.60 (12)
O31—C3—N4	121.80 (11)	C13—C12—H12	119.7
O2—C3—N4	113.18 (10)	C11—C12—H12	119.7
C5—N4—C3	129.57 (11)	C12—C13—C14	119.98 (13)
C5—N4—H4	117.0 (11)	C12—C13—H13	120.0
C3—N4—H4	113.4 (11)	C14—C13—H13	120.0
O51—C5—N4	127.66 (12)	C15—C14—C13	119.88 (12)
O51—C5—C6	122.49 (11)	C15—C14—H14	120.1
N4—C5—C6	109.84 (10)	C13—C14—H14	120.1
O61—C6—O7	126.23 (11)	C14—C15—C16	120.36 (13)
O61—C6—C5	122.53 (11)	C14—C15—H15	119.8
O7—C6—C5	111.24 (10)	C16—C15—H15	119.8
C6—O7—C8	114.61 (10)	C11—C16—C15	119.85 (12)
O7—C8—H8A	109.5	C11—C16—H16	120.1
O7—C8—H8B	109.5	C15—C16—H16	120.1
C11—C1—O2—C3	175.02 (10)	C5—C6—O7—C8	−177.86 (9)
C1—O2—C3—O31	−1.71 (18)	O2—C1—C11—C16	3.18 (17)
C1—O2—C3—N4	178.40 (10)	O2—C1—C11—C12	−175.53 (11)
O31—C3—N4—C5	177.35 (12)	C16—C11—C12—C13	−0.38 (19)
O2—C3—N4—C5	−2.75 (18)	C1—C11—C12—C13	178.39 (12)
C3—N4—C5—O51	−1.0 (2)	C11—C12—C13—C14	0.7 (2)
C3—N4—C5—C6	−179.91 (11)	C12—C13—C14—C15	−0.4 (2)
O51—C5—C6—O61	−178.88 (12)	C13—C14—C15—C16	−0.1 (2)
N4—C5—C6—O61	0.12 (16)	C12—C11—C16—C15	−0.15 (19)
O51—C5—C6—O7	0.91 (16)	C1—C11—C16—C15	−178.82 (12)
N4—C5—C6—O7	179.92 (10)	C14—C15—C16—C11	0.4 (2)
O61—C6—O7—C8	1.92 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···O31^i	0.863 (17)	2.156 (17)	2.9778 (14)	158.9 (14)

Symmetry code: (i) −x, −y, −z+1.