The title compound, C11H11NO5, is almost planar. The molecules pack as hydrogen-bonded dimers.
Supporting information
CCDC reference: 222918
Key indicators
- Single-crystal X-ray study
- T = 173 K
- Mean (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
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.
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.
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.
Crystal data top
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) Å3 | 0.52 × 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 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 top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.042 | H 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 reflections | Δρmax = 0.36 e Å−3 |
159 parameters | Δρmin = −0.20 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0114 (17) |
Crystal data top
C11H11NO5 | V = 1080.4 (2) Å3 |
Mr = 237.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.0139 (8) Å | µ = 0.12 mm−1 |
b = 5.4828 (5) Å | T = 173 K |
c = 24.701 (3) Å | 0.52 × 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 reflections | Rint = 0.042 |
3064 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.36 e Å−3 |
3064 reflections | Δρmin = −0.20 e Å−3 |
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 | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O31i | 0.863 (17) | 2.156 (17) | 2.9778 (14) | 158.9 (14) |
Symmetry code: (i) −x, −y, −z+1. |
Experimental details
Crystal data |
Chemical formula | C11H11NO5 |
Mr | 237.21 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 173 |
a, b, c (Å) | 8.0139 (8), 5.4828 (5), 24.701 (3) |
β (°) | 95.446 (2) |
V (Å3) | 1080.4 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.52 × 0.28 × 0.12 |
|
Data collection |
Diffractometer | Siemens 1K CCD three-circle diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 17271, 3064, 2248 |
Rint | 0.042 |
(sin θ/λ)max (Å−1) | 0.715 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.098, 1.02 |
No. of reflections | 3064 |
No. of parameters | 159 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.36, −0.20 |
Selected bond lengths (Å) topC1—O2 | 1.4529 (15) | C5—O51 | 1.2057 (14) |
O2—C3 | 1.3243 (14) | C5—C6 | 1.5430 (17) |
C3—O31 | 1.2088 (15) | C6—O61 | 1.1980 (14) |
C3—N4 | 1.3868 (16) | C6—O7 | 1.3221 (15) |
N4—C5 | 1.3737 (16) | O7—C8 | 1.4570 (15) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O31i | 0.863 (17) | 2.156 (17) | 2.9778 (14) | 158.9 (14) |
Symmetry code: (i) −x, −y, −z+1. |
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).