supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers buy article online

Acta Cryst. (2007). E63, o3717    [ doi:10.1107/S1600536807038123 ]

(2R,3S)-3-Hydroxy-N,N-dimethylproline monohydrate

S. F. Jenkinson, A. Cowley, A. Kato, N. Kato, J. Hollinshead, R. J. Nash, K. V. Booth and G. W. J. Fleet

Abstract top

The absolute stereochemistry of the title compound, C7H13NO3·H2O, was firmly established by X-ray crystallography. The crystal structure exists as O-H...O hydrogen-bonded layers of molecules lying perpendicular to the a axis.

Comment top

L-N,N-Dimethylproline (L-stachydrine) and the L-2R,3S-3-hydroxy compound have been reported from the plant family Capparidaceae. Cornforth & Henry (1952) first reported the L-2R,3S compound from Capparis tomentosa and then Delaveau et al. (1973) conducted a taxonomic survey suggesting these compounds were ubiquitous in this plant family. The structure of the L-2R,3S form was confirmed by synthesis by Sakiyama et al. (1964). This is the first report of the L-2R,3S form in the genus Baphia (Leguminosae).

Refinement of the Flack enantiopole parameter gave a value of 0.08 (18), which for an enantio-pure material unambiguously shows the crystal to consist of the 2R enantiomer (i.e a derivative of a D amino acid).

The crystal structure of the title compound (Fig. 1) exists as hydrogen bonded layers of molecules lying perpendicular to the a axis (Fig. 2). One of the hydrogen bonds (involving atom O2) is bifurcated.

Related literature top

For related literature, see: Cornforth & Henry (1952); Delaveau et al. (1973); Sakiyama et al. (1964); Nash et al. (1986).

Experimental top

2.9 g of 2R, 3S 3-hydroxy-N, N-dimethylproline was obtained from the 50% EtOH extract of 2 kg of leaves of the African medicinal tree Baphia confusum (Fabaceae). The compound was isolated by binding it to Amberlite IR-120 (H+ form, 2L) and eluting with 2M NH4OH. The eluate was concentrated to give a brown oil (30.8 g). This oil was applied to an Amberlite CG-50 column (3.6 x 48 cm, NH4+ form) and eluted with distilled water. The concentrated eluate was chromatographed over a Dowex 1-X8 column (2.2 x 42 cm, OH−, form) with water. The eluate was concentrated to give a colorless oil (3.64 g). This oil was further chromatographed on a Amberlite CG-50 column (3.6 x 48 cm, NH4+ form) with water as an eluant to give 2R, 3S 3-hydroxy-N,N-dimethylproline·The compound was crystallized from 95% aq. EtOH by layering with acetone. The purification was followed using GC—MS of the trimethylsilyl-derivative (Nash et al., 1986) scanning from 100–400 daltons which gave distinctive fragmentation with major ions at 196 (20%), 226 (100%), 270 (20%) and 285 (80%) amu. m.p. crystals decomposed above 495 K, without melting; [α]D18 +17.2 (c, 0.21 in water).

Refinement top

The use of Cu—Kα radiation enabled the absolute configuration to be determined from the anomalous differences of the Friedel Pairs.

The H atoms were all located in a difference map, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98,O—H = 0.82 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2005)'; cell refinement: CrysAlis CCD (Oxford Diffraction, 2005); data reduction: CrysAlis RED (Oxford Diffraction, 2005); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

Figures top
[Figure 1] Fig. 1. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 2] Fig. 2. Packing diagram showing the hydrogen bonded (dashed lines) layers lying perpendicular to the a-axis and the hydrogen bonds between each molecule and a molecule of water.
(2R,3S)-3-Hydroxy-N,N-dimethylproline monohydrate top
Crystal data top
C7H13N1O3·H2OF000 = 192
Mr = 177.20Dx = 1.404 Mg m−3
Monoclinic, P21Cu Kα radiation
λ = 1.5418 Å
Hall symbol: P 2ybCell parameters from 2601 reflections
a = 6.0647 (2) Åθ = 5–70º
b = 7.1798 (2) ŵ = 0.97 mm−1
c = 10.1956 (2) ÅT = 150 K
β = 109.195 (2)ºFragment, colourless
V = 419.27 (2) Å30.30 × 0.30 × 0.24 mm
Z = 2
Data collection top
Oxford Diffraction Gemini area-detector
diffractometer		1407 reflections with I > 3σ(I)
Monochromator: graphiteRint = 0.010
T = 150 Kθmax = 71.8º
ω scansθmin = 4.6º
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2005)		h = −7→7
Tmin = 0.75, Tmax = 0.79k = −8→8
3114 measured reflectionsl = −12→12
1452 independent reflections
Refinement top
Refinement on FHydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of
independent and constrained refinement
R[F2 > 2σ(F2)] = 0.033  Method, part 1, Chebychev polynomial [Prince (1982). Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag; Watkin (1994). Acta Cryst. A50, 411–437] [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 13.0 -4.75 9.02
wR(F2) = 0.039(Δ/σ)max = 0.004
S = 1.08Δρmax = 0.35 e Å−3
1407 reflectionsΔρmin = −0.29 e Å−3
122 parametersExtinction correction: None
1 restraintAbsolute structure: Flack (1983), 571 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.08 (18)
Crystal data top
C7H13N1O3·H2OV = 419.27 (2) Å3
Mr = 177.20Z = 2
Monoclinic, P21Cu Kα
a = 6.0647 (2) ŵ = 0.97 mm−1
b = 7.1798 (2) ÅT = 150 K
c = 10.1956 (2) Å0.30 × 0.30 × 0.24 mm
β = 109.195 (2)º
Data collection top
Oxford Diffraction Gemini area-detector
diffractometer		1452 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2005)		1407 reflections with I > 3σ(I)
Tmin = 0.75, Tmax = 0.79Rint = 0.010
3114 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of
independent and constrained refinement
wR(F2) = 0.039Δρmax = 0.35 e Å−3
S = 1.08Δρmin = −0.29 e Å−3
1407 reflectionsAbsolute structure: Flack (1983), 571 Friedel pairs
122 parametersFlack parameter: 0.08 (18)
1 restraint
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.1524 (3)0.2948 (2)0.27919 (14)0.0152
C20.3289 (2)0.3724 (2)0.21421 (13)0.0140
C30.2330 (2)0.4103 (2)0.05749 (15)0.0152
C40.4060 (3)0.5546 (2)0.03266 (15)0.0187
C50.5849 (3)0.5926 (2)0.17550 (16)0.0188
N10.4544 (2)0.5514 (2)0.27595 (12)0.0151
O10.11267 (19)0.38049 (18)0.37433 (11)0.0209
O20.0669 (2)0.14086 (17)0.22910 (11)0.0212
O30.00020 (18)0.47790 (18)0.02103 (11)0.0184
C60.2944 (3)0.7127 (2)0.27524 (16)0.0188
C70.6228 (3)0.5226 (2)0.41945 (15)0.0203
O40.2618 (2)0.5178 (2)0.65461 (14)0.0289
H1−0.040 (4)0.524 (3)−0.056 (2)0.019 (5)*
H20.197 (5)0.497 (4)0.574 (3)0.043 (7)*
H30.153 (5)0.553 (4)0.682 (2)0.030 (5)*
H210.43980.26480.23670.0168*
H310.22300.2974−0.00160.0187*
H410.32200.6718−0.00780.0229*
H420.48450.5024−0.03150.0229*
H510.63750.72530.18340.0235*
H520.72330.50870.19310.0235*
H610.38980.82450.31730.0228*
H620.19110.67920.33050.0228*
H630.19630.74140.17750.0228*
H710.70120.64330.45610.0233*
H720.53660.47660.48150.0233*
H730.74290.42870.41660.0233*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0156 (6)0.0168 (6)0.0121 (6)0.0012 (5)0.0031 (5)0.0039 (5)
C20.0141 (6)0.0141 (6)0.0140 (7)0.0000 (5)0.0048 (5)−0.0012 (5)
C30.0168 (6)0.0163 (6)0.0137 (6)−0.0002 (5)0.0068 (5)0.0000 (5)
C40.0210 (7)0.0204 (7)0.0159 (7)−0.0030 (6)0.0076 (6)0.0010 (5)
C50.0169 (6)0.0231 (8)0.0188 (7)−0.0026 (5)0.0093 (6)0.0020 (6)
N10.0151 (5)0.0169 (6)0.0133 (6)−0.0006 (4)0.0047 (5)0.0006 (4)
O10.0249 (5)0.0226 (5)0.0189 (5)−0.0012 (4)0.0124 (4)−0.0024 (4)
O20.0270 (6)0.0215 (5)0.0170 (5)−0.0080 (5)0.0096 (4)−0.0020 (4)
O30.0164 (5)0.0239 (5)0.0134 (5)0.0015 (4)0.0029 (4)0.0037 (4)
C60.0219 (7)0.0149 (6)0.0202 (7)0.0007 (6)0.0075 (6)−0.0018 (5)
C70.0174 (7)0.0266 (8)0.0142 (7)−0.0034 (6)0.0015 (6)−0.0007 (6)
O40.0226 (5)0.0382 (8)0.0255 (7)0.0088 (5)0.0074 (5)−0.0059 (5)
Geometric parameters (Å, °) top
C1—C21.5366 (18)C5—H511.000
C1—O11.237 (2)C5—H521.000
C1—O21.256 (2)N1—C61.5098 (19)
C2—C31.5346 (19)N1—C71.4979 (18)
C2—N11.5207 (19)O3—H10.82 (2)
C2—H211.000C6—H611.000
C3—C41.553 (2)C6—H621.000
C3—O31.4217 (18)C6—H631.000
C3—H311.000C7—H711.000
C4—C51.528 (2)C7—H721.000
C4—H411.000C7—H731.000
C4—H421.000O4—H20.80 (3)
C5—N11.5152 (18)O4—H30.83 (3)
C2—C1—O1120.05 (13)C4—C5—H52110.8
C2—C1—O2113.37 (12)N1—C5—H52110.8
O1—C1—O2126.54 (14)H51—C5—H52109.5
C1—C2—C3115.71 (11)C2—N1—C5100.76 (11)
C1—C2—N1116.91 (11)C2—N1—C6114.40 (11)
C3—C2—N1104.34 (11)C5—N1—C6108.96 (12)
C1—C2—H2197.6C2—N1—C7112.05 (11)
C3—C2—H21111.9C5—N1—C7110.32 (11)
N1—C2—H21110.5C6—N1—C7109.94 (12)
C2—C3—C4104.06 (12)C3—O3—H1110.3 (14)
C2—C3—O3109.69 (11)N1—C6—H61109.5
C4—C3—O3113.31 (12)N1—C6—H62109.5
C2—C3—H31114.2H61—C6—H62109.5
C4—C3—H31110.7N1—C6—H63109.5
O3—C3—H31105.1H61—C6—H63109.5
C3—C4—C5105.65 (12)H62—C6—H63109.5
C3—C4—H41110.4N1—C7—H71109.5
C5—C4—H41110.4N1—C7—H72109.5
C3—C4—H42110.4H71—C7—H72109.5
C5—C4—H42110.4N1—C7—H73109.5
H41—C4—H42109.5H71—C7—H73109.5
C4—C5—N1104.15 (11)H72—C7—H73109.5
C4—C5—H51110.8H2—O4—H3103 (3)
N1—C5—H51110.8
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H1···O2i0.82 (2)1.91 (3)2.712 (2)168 (3)
O4—H3···O2ii0.83 (3)1.95 (3)2.777 (2)172 (3)
O4—H2···O10.80 (3)2.10 (3)2.873 (2)162 (3)
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x, y+1/2, −z+1.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O3—H1···O2i0.82 (2)1.91 (3)2.712 (2)168 (3)
O4—H3···O2ii0.83 (3)1.95 (3)2.777 (2)172 (3)
O4—H2···O10.80 (3)2.10 (3)2.873 (2)162 (3)
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x, y+1/2, −z+1.
Acknowledgements top

(type here to add acknowledgements)

references
References top

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435–?.

Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487–?.

Cornforth, J. W. & Henry, A. J. (1952). J. Chem. Soc. pp. 597–600.

Delaveau, P., Koudogbo, B. & Bousset, J.-L. (1973). Phytochemistry, 12, 2893–2895.

Flack, H. D. (1983). Acta Cryst. A39, 876–881.

Nash, R. J., Goldstein, W. S., Evans, S. V. & Fellows, L. E. (1986). J. Chromatogr. 366, 431–434.

Oxford Diffraction (2005). CrysAlis CCD and CrysAlis RED. Oxford Diffraction, Abingdon, Oxfordshire, England. Please check added reference.

Sakiyama, F., Irreverre, F., Friess, S. L. & Witkop, B. (1964). J. Am. Chem. Soc. 86, 1842–1844.

Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, England.