Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680201406X/ob6161sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S160053680201406X/ob6161Isup2.hkl |
CCDC reference: 197466
Key indicators
- Single-crystal X-ray study
- T = 120 K
- Mean (C-C) = 0.002 Å
- R factor = 0.026
- wR factor = 0.061
- Data-to-parameter ratio = 9.4
checkCIF results
No syntax errors found ADDSYM reports no extra symmetry
Alert Level C:
STRVAL_01 From the CIF: _refine_ls_abs_structure_Flack -0.300 From the CIF: _refine_ls_abs_structure_Flack_su 1.100 Alert C Flack parameter is too small General Notes
REFLT_03 From the CIF: _diffrn_reflns_theta_max 27.43 From the CIF: _reflns_number_total 1174 Count of symmetry unique reflns 851 Completeness (_total/calc) 137.96% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 323 Fraction of Friedel pairs measured 0.380 Are heavy atom types Z>Si present no ALERT: MoKa measured Friedel data cannot be used to determine absolute structure in a light-atom study EXCEPT under VERY special conditions. It is preferred that Friedel data is merged in such cases.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check
Dehydrated and pulverized fruit skin was extracted with methanol following extraction with hexanes and chloroform. The resulting brown solutions were concentrated and stored at 277 K. The crystals which formed were collected and washed with cold ethanol. 1H and 13C NMR spectra were run on a Bruker Avance 360 and Bruker DRX 500, respectively (D2O). The chemical shifts and multiplicity corresponded well to the solid state structure. 13C data (p.p.m.): 173, C; 70.39, CH; 69.81, CH; 62.90, CH2; 43.47, CH3; 38.58, CH2 for C1 to C6, respectively. 1H data (p.p.m.): 4.5 (q, H); 4.08 (m, H); 3.85 (dd, H); 3.09 (dd, H); 2.94 (s,3H); 2.38 (q, H); 2.14 (m, H).
The methyl H atoms were positioned geometrically, and the other H atoms were refined isotropically. The C—H, N—-H and O–H bond lengths are 0.94 (2)—1.01 (2), 0.97 (2) and 0.87 (2) Å, respectively. The model structure is consistent with the known absolute configuration of the molecule although the Flack (1983) test results are meaningless.
Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO-SMN (Otwinoski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 1999).
Fig. 1. The molecular structure of (I), with ellipsoids at the 00% probability level.. | |
Fig. 2. Packing diagram of (I), showing the hydrogen bonding. |
C6H11NO3 | F(000) = 156 |
Mr = 145.16 | Dx = 1.431 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.6709 (6) Å | Cell parameters from 1174 reflections |
b = 5.7814 (5) Å | θ = 3.1–27.4° |
c = 8.8881 (6) Å | µ = 0.12 mm−1 |
β = 100.684 (5)° | T = 120 K |
V = 336.85 (5) Å3 | Block, colourless |
Z = 2 | 0.40 × 0.30 × 0.30 mm |
KappaCCD diffractometer | 1174 independent reflections |
Radiation source: fine-focus sealed tube | 1112 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.030 |
ϕ and ω scans | θmax = 27.4°, θmin = 3.1° |
Absorption correction: empirical (using intensity measurements) (Otwinowski & Minor, 1996) | h = −8→7 |
Tmin = 0.956, Tmax = 0.966 | k = −6→7 |
1732 measured reflections | l = −8→11 |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.027 | w = 1/[σ2(Fo2) + (0.0251P)2 + 0.0385P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.061 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.14 e Å−3 |
1174 reflections | Δρmin = −0.18 e Å−3 |
125 parameters | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.086 (12) |
Primary atom site location: structure-invariant direct methods | Absolute structure: (Flack, 1983), 323 Friedel pairs |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.3 (11) |
C6H11NO3 | V = 336.85 (5) Å3 |
Mr = 145.16 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 6.6709 (6) Å | µ = 0.12 mm−1 |
b = 5.7814 (5) Å | T = 120 K |
c = 8.8881 (6) Å | 0.40 × 0.30 × 0.30 mm |
β = 100.684 (5)° |
KappaCCD diffractometer | 1174 independent reflections |
Absorption correction: empirical (using intensity measurements) (Otwinowski & Minor, 1996) | 1112 reflections with I > 2σ(I) |
Tmin = 0.956, Tmax = 0.966 | Rint = 0.030 |
1732 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.061 | Δρmax = 0.14 e Å−3 |
S = 1.07 | Δρmin = −0.18 e Å−3 |
1174 reflections | Absolute structure: (Flack, 1983), 323 Friedel pairs |
125 parameters | Absolute structure parameter: −0.3 (11) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.65316 (15) | 0.4875 (2) | 0.77293 (10) | 0.0198 (3) | |
O2 | 0.60321 (14) | 0.69843 (19) | 0.97492 (10) | 0.0173 (3) | |
O3 | 0.12484 (16) | 0.9698 (2) | 0.45160 (11) | 0.0212 (3) | |
N1 | 0.23753 (19) | 0.8671 (2) | 0.82572 (13) | 0.0126 (3) | |
C1 | 0.5611 (2) | 0.6353 (3) | 0.83761 (15) | 0.0139 (3) | |
C2 | 0.3805 (2) | 0.7544 (3) | 0.73613 (15) | 0.0139 (3) | |
C3 | 0.4369 (2) | 0.9602 (3) | 0.64447 (16) | 0.0163 (3) | |
C4 | 0.2313 (2) | 1.0755 (3) | 0.58794 (16) | 0.0163 (4) | |
C5 | 0.1079 (2) | 1.0278 (3) | 0.71444 (16) | 0.0172 (4) | |
C6 | 0.1198 (2) | 0.7025 (3) | 0.90355 (16) | 0.0182 (4) | |
H6A | 0.2142 | 0.6019 | 0.9717 | 0.027* | |
H6B | 0.0317 | 0.6081 | 0.8268 | 0.027* | |
H6C | 0.0356 | 0.7889 | 0.9636 | 0.027* | |
H1 | 0.313 (3) | 0.967 (4) | 0.9043 (19) | 0.024 (4)* | |
H5A | −0.023 (3) | 0.943 (3) | 0.6735 (19) | 0.020 (4)* | |
H3 | 0.205 (3) | 0.971 (4) | 0.385 (2) | 0.041 (5)* | |
H3B | 0.522 (3) | 1.064 (3) | 0.7104 (18) | 0.021 (4)* | |
H2 | 0.304 (2) | 0.644 (3) | 0.6706 (15) | 0.008 (4)* | |
H5B | 0.084 (3) | 1.164 (4) | 0.7692 (19) | 0.028 (5)* | |
H4 | 0.243 (2) | 1.237 (4) | 0.5758 (17) | 0.016 (4)* | |
H3A | 0.499 (3) | 0.914 (3) | 0.5594 (18) | 0.023 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0196 (5) | 0.0205 (7) | 0.0204 (5) | 0.0055 (5) | 0.0068 (4) | 0.0023 (5) |
O2 | 0.0203 (6) | 0.0159 (6) | 0.0137 (5) | 0.0010 (5) | −0.0023 (4) | 0.0001 (4) |
O3 | 0.0197 (5) | 0.0311 (7) | 0.0120 (5) | −0.0011 (6) | 0.0009 (4) | −0.0004 (5) |
N1 | 0.0132 (6) | 0.0130 (7) | 0.0112 (6) | 0.0003 (5) | 0.0009 (5) | −0.0002 (5) |
C1 | 0.0131 (7) | 0.0123 (8) | 0.0166 (7) | −0.0027 (6) | 0.0036 (6) | 0.0031 (6) |
C2 | 0.0150 (8) | 0.0140 (8) | 0.0122 (6) | −0.0007 (7) | 0.0017 (6) | −0.0026 (6) |
C3 | 0.0186 (8) | 0.0170 (8) | 0.0132 (7) | 0.0000 (7) | 0.0027 (6) | 0.0020 (6) |
C4 | 0.0195 (8) | 0.0144 (9) | 0.0145 (7) | −0.0009 (7) | 0.0015 (6) | 0.0012 (6) |
C5 | 0.0174 (8) | 0.0198 (10) | 0.0139 (7) | 0.0053 (7) | 0.0014 (6) | 0.0012 (6) |
C6 | 0.0168 (8) | 0.0194 (9) | 0.0188 (7) | −0.0042 (8) | 0.0047 (6) | 0.0013 (7) |
O1—C1 | 1.2525 (18) | C3—C4 | 1.524 (2) |
O2—C1 | 1.2547 (16) | C3—H3B | 0.948 (18) |
O3—C4 | 1.4236 (18) | C3—H3A | 0.963 (17) |
N1—C6 | 1.4843 (18) | C4—C5 | 1.536 (2) |
N1—C2 | 1.4999 (17) | C4—H4 | 0.94 (2) |
N1—C5 | 1.508 (2) | C5—H5A | 1.01 (2) |
N1—H1 | 0.971 (19) | C5—H5B | 0.96 (2) |
C1—C2 | 1.528 (2) | C6—H6A | 0.9800 |
C2—C3 | 1.527 (2) | C6—H6B | 0.9800 |
C2—H2 | 0.948 (15) | C6—H6C | 0.9800 |
C4—O3—H3 | 107.7 (15) | C2—C3—H3A | 112.7 (11) |
C6—N1—C2 | 114.38 (12) | H3B—C3—H3A | 111.6 (14) |
C6—N1—C5 | 114.33 (12) | O3—C4—C3 | 111.67 (13) |
C2—N1—C5 | 105.27 (10) | O3—C4—C5 | 107.20 (13) |
C6—N1—H1 | 107.1 (10) | C3—C4—C5 | 104.59 (12) |
C2—N1—H1 | 110.2 (10) | O3—C4—H4 | 111.5 (10) |
C5—N1—H1 | 105.2 (12) | C3—C4—H4 | 112.3 (10) |
O1—C1—O2 | 127.19 (14) | C5—C4—H4 | 109.3 (9) |
O1—C1—C2 | 115.87 (12) | N1—C5—C4 | 105.69 (12) |
O2—C1—C2 | 116.93 (13) | N1—C5—H5A | 107.0 (10) |
N1—C2—C3 | 100.87 (12) | C4—C5—H5A | 111.6 (9) |
N1—C2—C1 | 113.05 (10) | N1—C5—H5B | 107.8 (11) |
C3—C2—C1 | 114.88 (12) | C4—C5—H5B | 112.8 (11) |
N1—C2—H2 | 107.3 (9) | H5A—C5—H5B | 111.6 (14) |
C3—C2—H2 | 110.9 (9) | N1—C6—H6A | 109.5 |
C1—C2—H2 | 109.4 (9) | N1—C6—H6B | 109.5 |
C4—C3—C2 | 102.77 (12) | H6A—C6—H6B | 109.5 |
C4—C3—H3B | 108.9 (10) | N1—C6—H6C | 109.5 |
C2—C3—H3B | 109.9 (10) | H6A—C6—H6C | 109.5 |
C4—C3—H3A | 110.6 (10) | H6B—C6—H6C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.971 (19) | 1.74 (2) | 2.6907 (16) | 164.7 (18) |
O3—H3···O1ii | 0.87 (2) | 1.84 (2) | 2.6985 (13) | 173 (2) |
Symmetry codes: (i) −x+1, y+1/2, −z+2; (ii) −x+1, y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H11NO3 |
Mr | 145.16 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 120 |
a, b, c (Å) | 6.6709 (6), 5.7814 (5), 8.8881 (6) |
β (°) | 100.684 (5) |
V (Å3) | 336.85 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.40 × 0.30 × 0.30 |
Data collection | |
Diffractometer | KappaCCD diffractometer |
Absorption correction | Empirical (using intensity measurements) (Otwinowski & Minor, 1996) |
Tmin, Tmax | 0.956, 0.966 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1732, 1174, 1112 |
Rint | 0.030 |
(sin θ/λ)max (Å−1) | 0.648 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.061, 1.07 |
No. of reflections | 1174 |
No. of parameters | 125 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.14, −0.18 |
Absolute structure | (Flack, 1983), 323 Friedel pairs |
Absolute structure parameter | −0.3 (11) |
Computer programs: COLLECT (Hooft, 1998), DENZO-SMN (Otwinoski & Minor, 1997), DENZO-SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), X-SEED (Barbour, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.971 (19) | 1.74 (2) | 2.6907 (16) | 164.7 (18) |
O3—H3···O1ii | 0.87 (2) | 1.84 (2) | 2.6985 (13) | 173 (2) |
Symmetry codes: (i) −x+1, y+1/2, −z+2; (ii) −x+1, y+1/2, −z+1. |
Subscribe to Acta Crystallographica Section E: Crystallographic Communications
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- If you have already subscribed, you may need to register
The leaves, fruit skin, seed and bark of Lansium domesticum, a fruit tree found in Malaysia, have been used to treat malaria by traditional healers. The title compound, (I), a cyclic hydroxyamino acid was isolated from methanol extracts of the fruit skin during studies into the antimalarial activity of the plant (Yapp & Yap, 2002). The free structure of (I) has not been previously described, although the hydrochloride salt of the compound has (Jones et al., 1988). We also report here for the first time, the 1H and 13C NMR spectra of (I) in solution.
Compound (I) adopts an envelope conformation typical of five-membered rings, with the carboxyl and hydroxyl groups trans to one another (Fig. 1). The structure of the free compound is essentially the same as the hydrochloride salt; no significant differences in bond lengths and angles between the two structures were found. In the free compound, however, two types of hydrogen bonds were found (Fig. 2 and Table 1).
Compound (I) was tested for antiplasmodial activity towards a strain of chloroquine resistant plasmodium falciparum, t9, but activity was only found at concentrations greater than 1 mg ml−1.