The tricyclic title compound, C11H15NO4, is an intermediate in the synthesis of (1S,2R,4R)-4-amino-2-(hydroxymethyl)cyclopentanol, which is an important carbocyclic analogue of β-2-deoxyribosylamine. All bond lengths and angles in the `exo epoxide' are in normal ranges.
Supporting information
CCDC reference: 259865
Key indicators
- Single-crystal X-ray study
- T = 193 K
- Mean (C-C) = 0.003 Å
- R factor = 0.031
- wR factor = 0.074
- Data-to-parameter ratio = 8.1
checkCIF/PLATON results
No syntax errors found
Alert level C
REFLT03_ALERT_1_C Reflection count < 95% complete
From the CIF: _diffrn_reflns_theta_max 25.73
From the CIF: _diffrn_reflns_theta_full 0.00
From the CIF: _reflns_number_total 1170
TEST2: Reflns within _diffrn_reflns_theta_max
Count of symmetry unique reflns 1252
Completeness (_total/calc) 93.45%
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low .... 0.94
PLAT028_ALERT_3_C _diffrn_measured_fraction_theta_max Low ....... 0.93
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 25.73
From the CIF: _reflns_number_total 1170
Count of symmetry unique reflns 1252
Completeness (_total/calc) 93.45%
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
3 ALERT level C = Check and explain
1 ALERT level G = General alerts; check
1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
0 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
1 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).
Crystal data top
C11H15NO4 | F(000) = 480 |
Mr = 225.24 | Dx = 1.362 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 7535 reflections |
a = 5.8200 (3) Å | θ = 2.5–25.7° |
b = 8.0891 (5) Å | µ = 0.10 mm−1 |
c = 23.3254 (18) Å | T = 193 K |
V = 1098.13 (12) Å3 | Prism, colourless |
Z = 4 | 0.3 × 0.26 × 0.2 mm |
Data collection top
Stoe IPDS-II diffractometer | 992 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.064 |
Graphite monochromator | θmax = 25.7°, θmin = 2.7° |
ω scans | h = −6→7 |
5125 measured reflections | k = −9→9 |
1170 independent reflections | l = −28→28 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.031 | Riding |
wR(F2) = 0.074 | w = 1/[σ2(Fo2) + (0.0462P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.01 | (Δ/σ)max < 0.001 |
1170 reflections | Δρmax = 0.13 e Å−3 |
145 parameters | Δρmin = −0.15 e Å−3 |
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 | |
O1 | 0.3162 (2) | 0.26513 (18) | 0.15470 (5) | 0.0302 (4) | |
C1 | 0.6002 (3) | −0.1489 (3) | 0.06950 (8) | 0.0287 (5) | |
H1 | 0.5601 | −0.2629 | 0.0728 | 0.034* | |
O2 | 0.5339 (3) | 0.4038 (2) | 0.08969 (6) | 0.0374 (4) | |
C2 | 0.8474 (3) | −0.1043 (3) | 0.08741 (8) | 0.0306 (5) | |
H2 | 0.9125 | −0.1429 | 0.1215 | 0.037* | |
O3 | 1.0041 (2) | −0.0779 (2) | 0.04031 (6) | 0.0373 (4) | |
O4 | 0.3452 (2) | −0.07119 (19) | 0.14996 (5) | 0.0321 (4) | |
C4 | 0.8873 (3) | 0.0604 (3) | 0.06552 (8) | 0.0284 (5) | |
H4 | 0.9724 | 0.1412 | 0.0828 | 0.034* | |
C5 | 0.6594 (3) | 0.1063 (3) | 0.03654 (7) | 0.0277 (5) | |
H5 | 0.6566 | 0.2039 | 0.0124 | 0.033* | |
N6 | 0.4983 (3) | 0.1243 (2) | 0.08592 (6) | 0.0243 (4) | |
C7 | 0.4589 (3) | −0.0354 (3) | 0.10834 (8) | 0.0240 (5) | |
C8 | 0.5789 (3) | −0.0581 (3) | 0.01254 (8) | 0.0318 (6) | |
H82 | 0.6908 | −0.0959 | −0.0164 | 0.038* | |
H81 | 0.4186 | −0.0519 | −0.0015 | 0.038* | |
C9 | 0.4554 (3) | 0.2785 (3) | 0.10960 (8) | 0.0232 (4) | |
C10 | 0.2380 (3) | 0.4133 (3) | 0.18683 (8) | 0.0272 (5) | |
C11 | 0.4430 (4) | 0.5033 (4) | 0.21226 (10) | 0.0460 (7) | |
H113 | 0.5324 | 0.4193 | 0.2345 | 0.069* | |
H112 | 0.5333 | 0.5535 | 0.1818 | 0.069* | |
H111 | 0.397 | 0.5869 | 0.237 | 0.069* | |
C12 | 0.0968 (4) | 0.5220 (3) | 0.14804 (9) | 0.0361 (6) | |
H123 | 0.1913 | 0.5667 | 0.1185 | 0.054* | |
H122 | 0.0237 | 0.6091 | 0.1718 | 0.054* | |
H121 | −0.0235 | 0.4624 | 0.1285 | 0.054* | |
C13 | 0.0908 (4) | 0.3347 (3) | 0.23313 (10) | 0.0478 (7) | |
H133 | 0.024 | 0.4304 | 0.2568 | 0.072* | |
H132 | 0.1835 | 0.2525 | 0.2576 | 0.072* | |
H131 | −0.0379 | 0.2794 | 0.2154 | 0.072* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0318 (7) | 0.0242 (10) | 0.0346 (7) | 0.0027 (6) | 0.0115 (6) | −0.0015 (7) |
C1 | 0.0300 (10) | 0.0225 (13) | 0.0337 (10) | −0.0030 (8) | 0.0032 (8) | −0.0065 (10) |
O2 | 0.0407 (8) | 0.0269 (10) | 0.0448 (8) | −0.0014 (7) | 0.0130 (7) | 0.0046 (8) |
C2 | 0.0264 (9) | 0.0356 (15) | 0.0297 (9) | 0.0059 (9) | 0.0027 (8) | −0.0013 (11) |
O3 | 0.0250 (7) | 0.0445 (11) | 0.0423 (8) | 0.0087 (7) | 0.0089 (6) | −0.0045 (8) |
O4 | 0.0349 (7) | 0.0313 (10) | 0.0302 (6) | −0.0059 (6) | 0.0085 (6) | 0.0019 (7) |
C4 | 0.0242 (9) | 0.0277 (14) | 0.0333 (9) | −0.0002 (8) | 0.0025 (8) | −0.0074 (10) |
C5 | 0.0246 (9) | 0.0352 (14) | 0.0233 (8) | 0.0038 (10) | 0.0065 (8) | 0.0042 (10) |
N6 | 0.0217 (8) | 0.0253 (11) | 0.0260 (7) | 0.0027 (7) | 0.0075 (6) | 0.0013 (8) |
C7 | 0.0214 (9) | 0.0252 (13) | 0.0253 (9) | −0.0015 (8) | −0.0024 (8) | −0.0022 (9) |
C8 | 0.0248 (9) | 0.0445 (17) | 0.0261 (9) | 0.0019 (9) | 0.0004 (7) | −0.0077 (10) |
C9 | 0.0179 (8) | 0.0248 (13) | 0.0268 (9) | 0.0018 (8) | 0.0006 (8) | 0.0030 (9) |
C10 | 0.0277 (9) | 0.0240 (13) | 0.0299 (9) | 0.0053 (8) | 0.0033 (7) | −0.0052 (10) |
C11 | 0.0417 (13) | 0.0521 (19) | 0.0440 (12) | 0.0031 (12) | −0.0057 (10) | −0.0136 (13) |
C12 | 0.0359 (11) | 0.0374 (15) | 0.0350 (10) | 0.0122 (10) | 0.0014 (9) | −0.0004 (11) |
C13 | 0.0544 (14) | 0.0437 (18) | 0.0452 (12) | 0.0142 (12) | 0.0215 (11) | 0.0081 (12) |
Geometric parameters (Å, º) top
O1—C9 | 1.332 (2) | N6—C9 | 1.386 (3) |
O1—C10 | 1.485 (3) | N6—C7 | 1.413 (3) |
C1—C8 | 1.523 (3) | C8—H82 | 0.9865 |
C1—C7 | 1.530 (3) | C8—H81 | 0.9902 |
C1—C2 | 1.541 (3) | C10—C12 | 1.506 (3) |
C1—H1 | 0.954 | C10—C13 | 1.518 (3) |
O2—C9 | 1.205 (2) | C10—C11 | 1.518 (3) |
C2—O3 | 1.444 (2) | C11—H113 | 1.0007 |
C2—C4 | 1.446 (3) | C11—H112 | 0.973 |
C2—H2 | 0.9345 | C11—H111 | 0.9287 |
O3—C4 | 1.435 (2) | C12—H123 | 0.9535 |
O4—C7 | 1.210 (2) | C12—H122 | 0.9929 |
C4—C5 | 1.534 (3) | C12—H121 | 0.9643 |
C4—H4 | 0.9134 | C13—H133 | 1.0279 |
C5—N6 | 1.493 (2) | C13—H132 | 1.0287 |
C5—C8 | 1.517 (3) | C13—H131 | 0.9657 |
C5—H5 | 0.9708 | | |
| | | |
C9—O1—C10 | 121.31 (16) | C5—C8—H82 | 108.7 |
C8—C1—C7 | 100.58 (16) | C1—C8—H82 | 113.2 |
C8—C1—C2 | 101.51 (15) | C5—C8—H81 | 111.6 |
C7—C1—C2 | 101.59 (16) | C1—C8—H81 | 113 |
C8—C1—H1 | 121.1 | H82—C8—H81 | 114.3 |
C7—C1—H1 | 113.7 | O2—C9—O1 | 127.08 (19) |
C2—C1—H1 | 115.6 | O2—C9—N6 | 122.34 (16) |
O3—C2—C4 | 59.57 (13) | O1—C9—N6 | 110.56 (17) |
O3—C2—C1 | 114.72 (15) | O1—C10—C12 | 109.58 (15) |
C4—C2—C1 | 105.64 (17) | O1—C10—C13 | 101.19 (18) |
O3—C2—H2 | 116.2 | C12—C10—C13 | 111.35 (16) |
C4—C2—H2 | 122.9 | O1—C10—C11 | 110.09 (16) |
C1—C2—H2 | 122.1 | C12—C10—C11 | 112.57 (19) |
C4—O3—C2 | 60.29 (13) | C13—C10—C11 | 111.48 (18) |
O3—C4—C2 | 60.14 (13) | C10—C11—H113 | 106.6 |
O3—C4—C5 | 114.69 (16) | C10—C11—H112 | 109.8 |
C2—C4—C5 | 103.89 (17) | H113—C11—H112 | 112.4 |
O3—C4—H4 | 118.8 | C10—C11—H111 | 111.5 |
C2—C4—H4 | 126.2 | H113—C11—H111 | 108.8 |
C5—C4—H4 | 119.3 | H112—C11—H111 | 107.8 |
N6—C5—C8 | 100.15 (15) | C10—C12—H123 | 110 |
N6—C5—C4 | 103.11 (13) | C10—C12—H122 | 108.2 |
C8—C5—C4 | 102.57 (18) | H123—C12—H122 | 112.4 |
N6—C5—H5 | 111 | C10—C12—H121 | 112.9 |
C8—C5—H5 | 119.6 | H123—C12—H121 | 105.4 |
C4—C5—H5 | 117.9 | H122—C12—H121 | 107.9 |
C9—N6—C7 | 130.24 (14) | C10—C13—H133 | 106.3 |
C9—N6—C5 | 120.55 (16) | C10—C13—H132 | 111.7 |
C7—N6—C5 | 107.36 (15) | H133—C13—H132 | 112.8 |
O4—C7—N6 | 127.19 (18) | C10—C13—H131 | 109.1 |
O4—C7—C1 | 128.7 (2) | H133—C13—H131 | 106.6 |
N6—C7—C1 | 104.04 (15) | H132—C13—H131 | 110.2 |
C5—C8—C1 | 94.34 (14) | | |
| | | |
C8—C1—C2—O3 | −30.5 (2) | C9—N6—C7—C1 | −165.16 (18) |
C7—C1—C2—O3 | −133.92 (18) | C5—N6—C7—C1 | −0.97 (17) |
C8—C1—C2—C4 | 32.80 (19) | C8—C1—C7—O4 | 148.77 (18) |
C7—C1—C2—C4 | −70.68 (18) | C2—C1—C7—O4 | −107.0 (2) |
C1—C2—O3—C4 | 94.2 (2) | C8—C1—C7—N6 | −33.49 (17) |
C2—O3—C4—C5 | −92.33 (18) | C2—C1—C7—N6 | 70.72 (17) |
C1—C2—C4—O3 | −109.83 (15) | N6—C5—C8—C1 | −53.17 (15) |
O3—C2—C4—C5 | 110.74 (15) | C4—C5—C8—C1 | 52.85 (15) |
C1—C2—C4—C5 | 0.91 (19) | C7—C1—C8—C5 | 52.80 (16) |
O3—C4—C5—N6 | 132.28 (17) | C2—C1—C8—C5 | −51.47 (17) |
C2—C4—C5—N6 | 69.07 (19) | C10—O1—C9—O2 | 0.3 (3) |
O3—C4—C5—C8 | 28.6 (2) | C10—O1—C9—N6 | −178.21 (14) |
C2—C4—C5—C8 | −34.65 (18) | C7—N6—C9—O2 | 166.88 (18) |
C8—C5—N6—C9 | −158.78 (16) | C5—N6—C9—O2 | 4.5 (3) |
C4—C5—N6—C9 | 95.6 (2) | C7—N6—C9—O1 | −14.5 (3) |
C8—C5—N6—C7 | 35.19 (17) | C5—N6—C9—O1 | −176.94 (14) |
C4—C5—N6—C7 | −70.39 (19) | C9—O1—C10—C12 | 63.1 (2) |
C9—N6—C7—O4 | 12.6 (3) | C9—O1—C10—C13 | −179.23 (16) |
C5—N6—C7—O4 | 176.82 (16) | C9—O1—C10—C11 | −61.2 (2) |