The title compound, C
11H
19NO
4, is a precursor for the preparation of (1
S,2
R,4
R)-4-amino-2-(hydroxymethyl)cyclopentanol, which is an important carbocyclic analogue of β-2-deoxyribosylamine. The crystal packing of the title compound is stabilized by intermolecular O—H
O hydrogen bonds.
Supporting information
CCDC reference: 262429
Key indicators
- Single-crystal X-ray study
- T = 193 K
- Mean (C-C) = 0.003 Å
- R factor = 0.032
- wR factor = 0.087
- Data-to-parameter ratio = 9.1
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ?
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C8
Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 26.24
From the CIF: _reflns_number_total 1428
Count of symmetry unique reflns 1434
Completeness (_total/calc) 99.58%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 0
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
2 ALERT level C = Check and explain
1 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
0 ALERT type 3 Indicator that the structure quality may be low
2 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: X-AREA (Stoe & Cie, 2003); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Diamond (Brandenburg, 2001); software used to prepare material for publication: WinGX (Farrugia, 1999).
(1
S,2
R,4
R,5
R)-
tert-Butyl
N-(4-hydroxymethyl-6-oxabicyclo[3.1.0]hex-2-yl)carbamate
top
Crystal data top
C11H19NO4 | Dx = 1.245 Mg m−3 |
Mr = 229.27 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 15158 reflections |
a = 9.4088 (6) Å | θ = 2–26° |
b = 10.2617 (8) Å | µ = 0.09 mm−1 |
c = 12.6689 (8) Å | T = 193 K |
V = 1223.19 (15) Å3 | Prism, colourless |
Z = 4 | 0.35 × 0.3 × 0.28 mm |
F(000) = 496 | |
Data collection top
Stoe IPDS-II diffractometer | 1256 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.056 |
Graphite monochromator | θmax = 26.2°, θmin = 2.6° |
area detector, ω scans | h = −11→11 |
17917 measured reflections | k = −12→12 |
1428 independent reflections | l = −15→15 |
Refinement top
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
Least-squares matrix: full | w = 1/[σ2(Fo2) + (0.0613P)2 + 0.0043P] where P = (Fo2 + 2Fc2)/3 |
R[F2 > 2σ(F2)] = 0.032 | (Δ/σ)max < 0.001 |
wR(F2) = 0.087 | Δρmax = 0.17 e Å−3 |
S = 1.06 | Δρmin = −0.14 e Å−3 |
1428 reflections | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
157 parameters | Extinction coefficient: 0.051 (8) |
0 restraints | |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.70776 (17) | 1.02960 (17) | 0.37727 (12) | 0.0445 (4) | |
O1 | 0.50575 (18) | 1.30213 (14) | 0.49559 (11) | 0.0606 (4) | |
C1 | 0.6226 (2) | 1.2350 (2) | 0.44583 (15) | 0.0482 (5) | |
H1 | 0.7149 | 1.2695 | 0.4564 | 0.058* | |
O2 | 0.58230 (16) | 1.14434 (16) | 0.19918 (11) | 0.0539 (4) | |
C2 | 0.60267 (18) | 1.09014 (19) | 0.44512 (13) | 0.0400 (4) | |
H2 | 0.6158 | 1.0489 | 0.5173 | 0.048* | |
O3 | 0.82637 (15) | 0.91699 (16) | 0.50292 (10) | 0.0525 (4) | |
C3 | 0.45105 (19) | 1.07299 (19) | 0.40280 (15) | 0.0435 (4) | |
H32 | 0.3821 | 1.0698 | 0.4615 | 0.052* | |
H31 | 0.4461 | 0.9891 | 0.3605 | 0.052* | |
O4 | 0.89085 (14) | 0.91190 (15) | 0.32971 (10) | 0.0497 (4) | |
C4 | 0.4165 (2) | 1.1949 (2) | 0.33648 (15) | 0.0473 (5) | |
H4 | 0.3134 | 1.2196 | 0.3453 | 0.057* | |
C5 | 0.5128 (3) | 1.2961 (2) | 0.38177 (15) | 0.0540 (5) | |
H5 | 0.531 | 1.378 | 0.3455 | 0.065* | |
C6 | 0.4390 (2) | 1.1787 (2) | 0.21842 (15) | 0.0512 (5) | |
H62 | 0.3725 | 1.1005 | 0.1886 | 0.061* | |
H61 | 0.4144 | 1.262 | 0.1797 | 0.061* | |
C7 | 0.81084 (18) | 0.95041 (17) | 0.41163 (13) | 0.0378 (4) | |
C8 | 1.0166 (2) | 0.82927 (19) | 0.34463 (15) | 0.0442 (4) | |
C9 | 1.1217 (2) | 0.8950 (3) | 0.4152 (2) | 0.0681 (7) | |
H93 | 1.0805 | 0.9055 | 0.4857 | 0.102* | |
H92 | 1.1457 | 0.9807 | 0.3862 | 0.102* | |
H91 | 1.2079 | 0.8417 | 0.4199 | 0.102* | |
C10 | 0.9740 (3) | 0.6976 (2) | 0.3869 (3) | 0.0817 (9) | |
H103 | 0.9343 | 0.7076 | 0.4579 | 0.123* | |
H102 | 1.0577 | 0.6408 | 0.3898 | 0.123* | |
H101 | 0.9024 | 0.6588 | 0.3403 | 0.123* | |
C11 | 1.0738 (3) | 0.8180 (4) | 0.2343 (2) | 0.0912 (11) | |
H113 | 1.16 | 0.7644 | 0.2349 | 0.137* | |
H112 | 1.0965 | 0.905 | 0.2073 | 0.137* | |
H111 | 1.0022 | 0.7772 | 0.1889 | 0.137* | |
H10 | 0.703 (3) | 1.043 (2) | 0.311 (2) | 0.058 (7)* | |
H20 | 0.598 (3) | 1.133 (3) | 0.136 (2) | 0.072 (8)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0427 (8) | 0.0580 (9) | 0.0326 (7) | 0.0137 (7) | 0.0028 (6) | 0.0049 (7) |
O1 | 0.0857 (11) | 0.0529 (8) | 0.0431 (7) | 0.0100 (8) | 0.0097 (7) | −0.0121 (7) |
C1 | 0.0530 (11) | 0.0510 (11) | 0.0407 (9) | −0.0088 (9) | 0.0041 (8) | −0.0090 (8) |
O2 | 0.0478 (8) | 0.0800 (10) | 0.0340 (7) | 0.0136 (7) | −0.0007 (6) | −0.0009 (7) |
C2 | 0.0396 (9) | 0.0456 (9) | 0.0348 (8) | 0.0038 (8) | 0.0053 (7) | 0.0015 (7) |
O3 | 0.0483 (8) | 0.0711 (9) | 0.0380 (6) | 0.0099 (7) | 0.0021 (6) | 0.0137 (7) |
C3 | 0.0377 (9) | 0.0452 (10) | 0.0478 (10) | −0.0025 (8) | 0.0076 (7) | −0.0004 (8) |
O4 | 0.0503 (8) | 0.0609 (8) | 0.0381 (6) | 0.0229 (7) | 0.0009 (6) | 0.0021 (6) |
C4 | 0.0431 (10) | 0.0544 (11) | 0.0445 (10) | 0.0130 (9) | 0.0033 (8) | −0.0014 (8) |
C5 | 0.0818 (15) | 0.0393 (9) | 0.0410 (10) | 0.0057 (10) | 0.0086 (10) | −0.0016 (7) |
C6 | 0.0487 (11) | 0.0622 (12) | 0.0427 (10) | 0.0140 (9) | −0.0031 (8) | −0.0008 (9) |
C7 | 0.0361 (9) | 0.0413 (9) | 0.0362 (8) | 0.0006 (7) | 0.0011 (7) | 0.0039 (7) |
C8 | 0.0404 (10) | 0.0449 (10) | 0.0474 (10) | 0.0104 (8) | −0.0017 (8) | 0.0016 (8) |
C9 | 0.0381 (10) | 0.0783 (16) | 0.0879 (17) | 0.0037 (11) | −0.0014 (11) | −0.0193 (14) |
C10 | 0.0599 (14) | 0.0440 (12) | 0.141 (3) | 0.0050 (11) | −0.0007 (15) | 0.0090 (15) |
C11 | 0.098 (2) | 0.121 (2) | 0.0542 (13) | 0.067 (2) | 0.0142 (13) | 0.0002 (15) |
Geometric parameters (Å, º) top
N1—C7 | 1.338 (2) | C4—C5 | 1.493 (3) |
N1—C2 | 1.450 (2) | C4—C6 | 1.520 (3) |
N1—H10 | 0.85 (2) | C4—H4 | 1.0083 |
O1—C1 | 1.443 (2) | C5—H5 | 0.9725 |
O1—C5 | 1.445 (2) | C6—H62 | 1.0853 |
C1—C5 | 1.456 (3) | C6—H61 | 1.0123 |
C1—C2 | 1.498 (3) | C8—C9 | 1.494 (3) |
C1—H1 | 0.9468 | C8—C11 | 1.502 (3) |
O2—C6 | 1.415 (2) | C8—C10 | 1.507 (3) |
O2—H20 | 0.83 (3) | C9—H93 | 0.98 |
C2—C3 | 1.534 (3) | C9—H92 | 0.98 |
C2—H2 | 1.0157 | C9—H91 | 0.98 |
O3—C7 | 1.215 (2) | C10—H103 | 0.98 |
C3—C4 | 1.542 (3) | C10—H102 | 0.98 |
C3—H32 | 0.9875 | C10—H101 | 0.98 |
C3—H31 | 1.0154 | C11—H113 | 0.98 |
O4—C7 | 1.342 (2) | C11—H112 | 0.98 |
O4—C8 | 1.467 (2) | C11—H111 | 0.98 |
| | | |
C7—N1—C2 | 124.17 (15) | C4—C5—H5 | 121.8 |
C7—N1—H10 | 117.1 (17) | O2—C6—C4 | 109.26 (16) |
C2—N1—H10 | 118.7 (17) | O2—C6—H62 | 107.8 |
C1—O1—C5 | 60.57 (14) | C4—C6—H62 | 110 |
O1—C1—C5 | 59.78 (13) | O2—C6—H61 | 110.2 |
O1—C1—C2 | 112.39 (17) | C4—C6—H61 | 110.7 |
C5—C1—C2 | 109.57 (17) | H62—C6—H61 | 108.9 |
O1—C1—H1 | 117.3 | O3—C7—N1 | 124.62 (17) |
C5—C1—H1 | 124.6 | O3—C7—O4 | 125.85 (17) |
C2—C1—H1 | 119.1 | N1—C7—O4 | 109.51 (15) |
C6—O2—H20 | 112.2 (19) | O4—C8—C9 | 110.50 (16) |
N1—C2—C1 | 110.06 (16) | O4—C8—C11 | 102.34 (16) |
N1—C2—C3 | 112.20 (15) | C9—C8—C11 | 110.7 (2) |
C1—C2—C3 | 103.44 (16) | O4—C8—C10 | 110.46 (17) |
N1—C2—H2 | 105.8 | C9—C8—C10 | 111.6 (2) |
C1—C2—H2 | 113.1 | C11—C8—C10 | 110.9 (2) |
C3—C2—H2 | 112.4 | C8—C9—H93 | 109.5 |
C2—C3—C4 | 107.07 (15) | C8—C9—H92 | 109.5 |
C2—C3—H32 | 110.6 | H93—C9—H92 | 109.5 |
C4—C3—H32 | 107.4 | C8—C9—H91 | 109.5 |
C2—C3—H31 | 109 | H93—C9—H91 | 109.5 |
C4—C3—H31 | 113 | H92—C9—H91 | 109.5 |
H32—C3—H31 | 109.8 | C8—C10—H103 | 109.5 |
C7—O4—C8 | 121.52 (14) | C8—C10—H102 | 109.5 |
C5—C4—C6 | 111.69 (18) | H103—C10—H102 | 109.5 |
C5—C4—C3 | 103.12 (15) | C8—C10—H101 | 109.5 |
C6—C4—C3 | 114.72 (16) | H103—C10—H101 | 109.5 |
C5—C4—H4 | 111.5 | H102—C10—H101 | 109.5 |
C6—C4—H4 | 105.7 | C8—C11—H113 | 109.5 |
C3—C4—H4 | 110.2 | C8—C11—H112 | 109.5 |
O1—C5—C1 | 59.64 (13) | H113—C11—H112 | 109.5 |
O1—C5—C4 | 112.69 (18) | C8—C11—H111 | 109.5 |
C1—C5—C4 | 110.20 (17) | H113—C11—H111 | 109.5 |
O1—C5—H5 | 116.3 | H112—C11—H111 | 109.5 |
C1—C5—H5 | 120.7 | | |
| | | |
C5—O1—C1—C2 | −100.33 (19) | C2—C1—C5—C4 | 0.0 (2) |
C7—N1—C2—C1 | 114.1 (2) | C6—C4—C5—O1 | −172.90 (17) |
C7—N1—C2—C3 | −131.33 (18) | C3—C4—C5—O1 | −49.2 (2) |
O1—C1—C2—N1 | 169.07 (15) | C6—C4—C5—C1 | −108.36 (18) |
C5—C1—C2—N1 | 104.62 (18) | C3—C4—C5—C1 | 15.3 (2) |
O1—C1—C2—C3 | 49.02 (19) | C5—C4—C6—O2 | 58.3 (2) |
C5—C1—C2—C3 | −15.44 (19) | C3—C4—C6—O2 | −58.5 (2) |
N1—C2—C3—C4 | −93.73 (18) | C2—N1—C7—O3 | 2.1 (3) |
C1—C2—C3—C4 | 24.85 (18) | C2—N1—C7—O4 | −179.40 (17) |
C2—C3—C4—C5 | −24.80 (18) | C8—O4—C7—O3 | −4.6 (3) |
C2—C3—C4—C6 | 96.9 (2) | C8—O4—C7—N1 | 176.95 (16) |
C1—O1—C5—C4 | 100.89 (19) | C7—O4—C8—C9 | −59.4 (2) |
C2—C1—C5—O1 | 105.11 (17) | C7—O4—C8—C11 | −177.3 (2) |
O1—C1—C5—C4 | −105.11 (19) | C7—O4—C8—C10 | 64.6 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H10···O2 | 0.85 (2) | 2.10 (2) | 2.805 (2) | 141 (2) |
O2—H20···O3i | 0.83 (3) | 1.90 (3) | 2.7050 (18) | 166 (3) |
Symmetry code: (i) −x+3/2, −y+2, z−1/2. |