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The title compound, C6H11NO3, was isolated from methano­lic extracts of Lansium domesticum, a plant with reported antimalarial activity. The structure is a cyclic hydroxy-amino acid with the carboxyl and hydroxyl groups trans to one another.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680201406X/ob6161sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S160053680201406X/ob6161Isup2.hkl
Contains datablock I

CCDC reference: 197466

Key indicators

  • Single-crystal X-ray study
  • T = 120 K
  • Mean [sigma](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


Yellow Alert 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

Comment top

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.

Experimental top

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).

Refinement top

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.

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), with ellipsoids at the 00% probability level..
[Figure 2] Fig. 2. Packing diagram of (I), showing the hydrogen bonding.
n-Methyl-4-hydroxyproline top
Crystal data top
C6H11NO3F(000) = 156
Mr = 145.16Dx = 1.431 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 6.6709 (6) ÅCell parameters from 1174 reflections
b = 5.7814 (5) Åθ = 3.1–27.4°
c = 8.8881 (6) ŵ = 0.12 mm1
β = 100.684 (5)°T = 120 K
V = 336.85 (5) Å3Block, colourless
Z = 20.40 × 0.30 × 0.30 mm
Data collection top
KappaCCD
diffractometer
1174 independent reflections
Radiation source: fine-focus sealed tube1112 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ϕ and ω scansθmax = 27.4°, θmin = 3.1°
Absorption correction: empirical (using intensity measurements)
(Otwinowski & Minor, 1996)
h = 87
Tmin = 0.956, Tmax = 0.966k = 67
1732 measured reflectionsl = 811
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH 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 = 1.07Δρmax = 0.14 e Å3
1174 reflectionsΔρmin = 0.18 e Å3
125 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.086 (12)
Primary atom site location: structure-invariant direct methodsAbsolute structure: (Flack, 1983), 323 Friedel pairs
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.3 (11)
Crystal data top
C6H11NO3V = 336.85 (5) Å3
Mr = 145.16Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.6709 (6) ŵ = 0.12 mm1
b = 5.7814 (5) ÅT = 120 K
c = 8.8881 (6) Å0.40 × 0.30 × 0.30 mm
β = 100.684 (5)°
Data collection top
KappaCCD
diffractometer
1174 independent reflections
Absorption correction: empirical (using intensity measurements)
(Otwinowski & Minor, 1996)
1112 reflections with I > 2σ(I)
Tmin = 0.956, Tmax = 0.966Rint = 0.030
1732 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.027H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.061Δρmax = 0.14 e Å3
S = 1.07Δρmin = 0.18 e Å3
1174 reflectionsAbsolute structure: (Flack, 1983), 323 Friedel pairs
125 parametersAbsolute structure parameter: 0.3 (11)
1 restraint
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
xyzUiso*/Ueq
O10.65316 (15)0.4875 (2)0.77293 (10)0.0198 (3)
O20.60321 (14)0.69843 (19)0.97492 (10)0.0173 (3)
O30.12484 (16)0.9698 (2)0.45160 (11)0.0212 (3)
N10.23753 (19)0.8671 (2)0.82572 (13)0.0126 (3)
C10.5611 (2)0.6353 (3)0.83761 (15)0.0139 (3)
C20.3805 (2)0.7544 (3)0.73613 (15)0.0139 (3)
C30.4369 (2)0.9602 (3)0.64447 (16)0.0163 (3)
C40.2313 (2)1.0755 (3)0.58794 (16)0.0163 (4)
C50.1079 (2)1.0278 (3)0.71444 (16)0.0172 (4)
C60.1198 (2)0.7025 (3)0.90355 (16)0.0182 (4)
H6A0.21420.60190.97170.027*
H6B0.03170.60810.82680.027*
H6C0.03560.78890.96360.027*
H10.313 (3)0.967 (4)0.9043 (19)0.024 (4)*
H5A0.023 (3)0.943 (3)0.6735 (19)0.020 (4)*
H30.205 (3)0.971 (4)0.385 (2)0.041 (5)*
H3B0.522 (3)1.064 (3)0.7104 (18)0.021 (4)*
H20.304 (2)0.644 (3)0.6706 (15)0.008 (4)*
H5B0.084 (3)1.164 (4)0.7692 (19)0.028 (5)*
H40.243 (2)1.237 (4)0.5758 (17)0.016 (4)*
H3A0.499 (3)0.914 (3)0.5594 (18)0.023 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0196 (5)0.0205 (7)0.0204 (5)0.0055 (5)0.0068 (4)0.0023 (5)
O20.0203 (6)0.0159 (6)0.0137 (5)0.0010 (5)0.0023 (4)0.0001 (4)
O30.0197 (5)0.0311 (7)0.0120 (5)0.0011 (6)0.0009 (4)0.0004 (5)
N10.0132 (6)0.0130 (7)0.0112 (6)0.0003 (5)0.0009 (5)0.0002 (5)
C10.0131 (7)0.0123 (8)0.0166 (7)0.0027 (6)0.0036 (6)0.0031 (6)
C20.0150 (8)0.0140 (8)0.0122 (6)0.0007 (7)0.0017 (6)0.0026 (6)
C30.0186 (8)0.0170 (8)0.0132 (7)0.0000 (7)0.0027 (6)0.0020 (6)
C40.0195 (8)0.0144 (9)0.0145 (7)0.0009 (7)0.0015 (6)0.0012 (6)
C50.0174 (8)0.0198 (10)0.0139 (7)0.0053 (7)0.0014 (6)0.0012 (6)
C60.0168 (8)0.0194 (9)0.0188 (7)0.0042 (8)0.0047 (6)0.0013 (7)
Geometric parameters (Å, º) top
O1—C11.2525 (18)C3—C41.524 (2)
O2—C11.2547 (16)C3—H3B0.948 (18)
O3—C41.4236 (18)C3—H3A0.963 (17)
N1—C61.4843 (18)C4—C51.536 (2)
N1—C21.4999 (17)C4—H40.94 (2)
N1—C51.508 (2)C5—H5A1.01 (2)
N1—H10.971 (19)C5—H5B0.96 (2)
C1—C21.528 (2)C6—H6A0.9800
C2—C31.527 (2)C6—H6B0.9800
C2—H20.948 (15)C6—H6C0.9800
C4—O3—H3107.7 (15)C2—C3—H3A112.7 (11)
C6—N1—C2114.38 (12)H3B—C3—H3A111.6 (14)
C6—N1—C5114.33 (12)O3—C4—C3111.67 (13)
C2—N1—C5105.27 (10)O3—C4—C5107.20 (13)
C6—N1—H1107.1 (10)C3—C4—C5104.59 (12)
C2—N1—H1110.2 (10)O3—C4—H4111.5 (10)
C5—N1—H1105.2 (12)C3—C4—H4112.3 (10)
O1—C1—O2127.19 (14)C5—C4—H4109.3 (9)
O1—C1—C2115.87 (12)N1—C5—C4105.69 (12)
O2—C1—C2116.93 (13)N1—C5—H5A107.0 (10)
N1—C2—C3100.87 (12)C4—C5—H5A111.6 (9)
N1—C2—C1113.05 (10)N1—C5—H5B107.8 (11)
C3—C2—C1114.88 (12)C4—C5—H5B112.8 (11)
N1—C2—H2107.3 (9)H5A—C5—H5B111.6 (14)
C3—C2—H2110.9 (9)N1—C6—H6A109.5
C1—C2—H2109.4 (9)N1—C6—H6B109.5
C4—C3—C2102.77 (12)H6A—C6—H6B109.5
C4—C3—H3B108.9 (10)N1—C6—H6C109.5
C2—C3—H3B109.9 (10)H6A—C6—H6C109.5
C4—C3—H3A110.6 (10)H6B—C6—H6C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.971 (19)1.74 (2)2.6907 (16)164.7 (18)
O3—H3···O1ii0.87 (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 formulaC6H11NO3
Mr145.16
Crystal system, space groupMonoclinic, P21
Temperature (K)120
a, b, c (Å)6.6709 (6), 5.7814 (5), 8.8881 (6)
β (°) 100.684 (5)
V3)336.85 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.40 × 0.30 × 0.30
Data collection
DiffractometerKappaCCD
diffractometer
Absorption correctionEmpirical (using intensity measurements)
(Otwinowski & Minor, 1996)
Tmin, Tmax0.956, 0.966
No. of measured, independent and
observed [I > 2σ(I)] reflections
1732, 1174, 1112
Rint0.030
(sin θ/λ)max1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.061, 1.07
No. of reflections1174
No. of parameters125
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.14, 0.18
Absolute structure(Flack, 1983), 323 Friedel pairs
Absolute structure parameter0.3 (11)

Computer programs: COLLECT (Hooft, 1998), DENZO-SMN (Otwinoski & Minor, 1997), DENZO-SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), X-SEED (Barbour, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.971 (19)1.74 (2)2.6907 (16)164.7 (18)
O3—H3···O1ii0.87 (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.
 

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