Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807038123/lh2473sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807038123/lh2473Isup2.hkl |
CCDC reference: 660217
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.002 Å
- R factor = 0.033
- wR factor = 0.038
- Data-to-parameter ratio = 11.5
checkCIF/PLATON results
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Alert level C PLAT153_ALERT_1_C The su's on the Cell Axes are Equal (x 100000) 20 Ang.
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 71.75 From the CIF: _reflns_number_total 1452 Count of symmetry unique reflns 899 Completeness (_total/calc) 161.51% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 553 Fraction of Friedel pairs measured 0.615 Are heavy atom types Z>Si present no PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . S PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 4 ALERT level G = General alerts; check 3 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 1 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
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Alert level A PUBL024_ALERT_1_A The number of authors is greater than 5. Please specify the role of each of the co-authors for your paper.
Author Response: |
Jenkinson, Sarah F. - Post Doc chemist and crystallographer Cowley,Andrew - Crystallographer Kato, Atsushi - collaborator on project Kato, Noriko - collaborator on project Hollinshead, Jackie - Industrial collaborator on project Nash, Robert J. - Industrial collaborator on project Booth, Kathrine V. - trainee crystallographer Fleet, George W. J. - Preparative Group Leader
1 ALERT level A = Data missing that is essential or data in wrong format 0 ALERT level G = General alerts. Data that may be required is missing
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).
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.
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.
For related literature, see: Cornforth & Henry (1952); Delaveau et al. (1973); Sakiyama et al. (1964); Nash et al. (1986).
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.
C7H13NO3·H2O | F(000) = 192 |
Mr = 177.20 | Dx = 1.404 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.5418 Å |
Hall symbol: P 2yb | Cell parameters from 2601 reflections |
a = 6.0647 (2) Å | θ = 5–70° |
b = 7.1798 (2) Å | µ = 0.97 mm−1 |
c = 10.1956 (2) Å | T = 150 K |
β = 109.195 (2)° | Fragment, colourless |
V = 419.27 (2) Å3 | 0.30 × 0.30 × 0.24 mm |
Z = 2 |
Oxford Diffraction Gemini area-detector diffractometer | 1407 reflections with I > 3σ(I) |
Graphite monochromator | Rint = 0.010 |
ω scans | θmax = 71.8°, θmin = 4.6° |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2005) | h = −7→7 |
Tmin = 0.75, Tmax = 0.79 | k = −8→8 |
3114 measured reflections | l = −12→12 |
1452 independent reflections |
Refinement on F | 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)] = 0.033 | 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 = 1.08 | Δρmax = 0.35 e Å−3 |
1407 reflections | Δρmin = −0.29 e Å−3 |
122 parameters | Absolute structure: Flack (1983), 571 Friedel pairs |
1 restraint | Absolute structure parameter: 0.08 (18) |
Primary atom site location: structure-invariant direct methods |
C7H13NO3·H2O | V = 419.27 (2) Å3 |
Mr = 177.20 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 6.0647 (2) Å | µ = 0.97 mm−1 |
b = 7.1798 (2) Å | T = 150 K |
c = 10.1956 (2) Å | 0.30 × 0.30 × 0.24 mm |
β = 109.195 (2)° |
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 = 0.79 | Rint = 0.010 |
3114 measured reflections |
R[F2 > 2σ(F2)] = 0.033 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.039 | Δρmax = 0.35 e Å−3 |
S = 1.08 | Δρmin = −0.29 e Å−3 |
1407 reflections | Absolute structure: Flack (1983), 571 Friedel pairs |
122 parameters | Absolute structure parameter: 0.08 (18) |
1 restraint |
x | y | z | Uiso*/Ueq | ||
C1 | 0.1524 (3) | 0.2948 (2) | 0.27919 (14) | 0.0152 | |
C2 | 0.3289 (2) | 0.3724 (2) | 0.21421 (13) | 0.0140 | |
C3 | 0.2330 (2) | 0.4103 (2) | 0.05749 (15) | 0.0152 | |
C4 | 0.4060 (3) | 0.5546 (2) | 0.03266 (15) | 0.0187 | |
C5 | 0.5849 (3) | 0.5926 (2) | 0.17550 (16) | 0.0188 | |
N1 | 0.4544 (2) | 0.5514 (2) | 0.27595 (12) | 0.0151 | |
O1 | 0.11267 (19) | 0.38049 (18) | 0.37433 (11) | 0.0209 | |
O2 | 0.0669 (2) | 0.14086 (17) | 0.22910 (11) | 0.0212 | |
O3 | 0.00020 (18) | 0.47790 (18) | 0.02103 (11) | 0.0184 | |
C6 | 0.2944 (3) | 0.7127 (2) | 0.27524 (16) | 0.0188 | |
C7 | 0.6228 (3) | 0.5226 (2) | 0.41945 (15) | 0.0203 | |
O4 | 0.2618 (2) | 0.5178 (2) | 0.65461 (14) | 0.0289 | |
H1 | −0.040 (4) | 0.524 (3) | −0.056 (2) | 0.019 (5)* | |
H2 | 0.197 (5) | 0.497 (4) | 0.574 (3) | 0.043 (7)* | |
H3 | 0.153 (5) | 0.553 (4) | 0.682 (2) | 0.030 (5)* | |
H21 | 0.4398 | 0.2648 | 0.2367 | 0.0168* | |
H31 | 0.2230 | 0.2974 | −0.0016 | 0.0187* | |
H41 | 0.3220 | 0.6718 | −0.0078 | 0.0229* | |
H42 | 0.4845 | 0.5024 | −0.0315 | 0.0229* | |
H51 | 0.6375 | 0.7253 | 0.1834 | 0.0235* | |
H52 | 0.7233 | 0.5087 | 0.1931 | 0.0235* | |
H61 | 0.3898 | 0.8245 | 0.3173 | 0.0228* | |
H62 | 0.1911 | 0.6792 | 0.3305 | 0.0228* | |
H63 | 0.1963 | 0.7414 | 0.1775 | 0.0228* | |
H71 | 0.7012 | 0.6433 | 0.4561 | 0.0233* | |
H72 | 0.5366 | 0.4766 | 0.4815 | 0.0233* | |
H73 | 0.7429 | 0.4287 | 0.4166 | 0.0233* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0156 (6) | 0.0168 (6) | 0.0121 (6) | 0.0012 (5) | 0.0031 (5) | 0.0039 (5) |
C2 | 0.0141 (6) | 0.0141 (6) | 0.0140 (7) | 0.0000 (5) | 0.0048 (5) | −0.0012 (5) |
C3 | 0.0168 (6) | 0.0163 (6) | 0.0137 (6) | −0.0002 (5) | 0.0068 (5) | 0.0000 (5) |
C4 | 0.0210 (7) | 0.0204 (7) | 0.0159 (7) | −0.0030 (6) | 0.0076 (6) | 0.0010 (5) |
C5 | 0.0169 (6) | 0.0231 (8) | 0.0188 (7) | −0.0026 (5) | 0.0093 (6) | 0.0020 (6) |
N1 | 0.0151 (5) | 0.0169 (6) | 0.0133 (6) | −0.0006 (4) | 0.0047 (5) | 0.0006 (4) |
O1 | 0.0249 (5) | 0.0226 (5) | 0.0189 (5) | −0.0012 (4) | 0.0124 (4) | −0.0024 (4) |
O2 | 0.0270 (6) | 0.0215 (5) | 0.0170 (5) | −0.0080 (5) | 0.0096 (4) | −0.0020 (4) |
O3 | 0.0164 (5) | 0.0239 (5) | 0.0134 (5) | 0.0015 (4) | 0.0029 (4) | 0.0037 (4) |
C6 | 0.0219 (7) | 0.0149 (6) | 0.0202 (7) | 0.0007 (6) | 0.0075 (6) | −0.0018 (5) |
C7 | 0.0174 (7) | 0.0266 (8) | 0.0142 (7) | −0.0034 (6) | 0.0015 (6) | −0.0007 (6) |
O4 | 0.0226 (5) | 0.0382 (8) | 0.0255 (7) | 0.0088 (5) | 0.0074 (5) | −0.0059 (5) |
C1—C2 | 1.5366 (18) | C5—H51 | 1.000 |
C1—O1 | 1.237 (2) | C5—H52 | 1.000 |
C1—O2 | 1.256 (2) | N1—C6 | 1.5098 (19) |
C2—C3 | 1.5346 (19) | N1—C7 | 1.4979 (18) |
C2—N1 | 1.5207 (19) | O3—H1 | 0.82 (2) |
C2—H21 | 1.000 | C6—H61 | 1.000 |
C3—C4 | 1.553 (2) | C6—H62 | 1.000 |
C3—O3 | 1.4217 (18) | C6—H63 | 1.000 |
C3—H31 | 1.000 | C7—H71 | 1.000 |
C4—C5 | 1.528 (2) | C7—H72 | 1.000 |
C4—H41 | 1.000 | C7—H73 | 1.000 |
C4—H42 | 1.000 | O4—H2 | 0.80 (3) |
C5—N1 | 1.5152 (18) | O4—H3 | 0.83 (3) |
C2—C1—O1 | 120.05 (13) | C4—C5—H52 | 110.8 |
C2—C1—O2 | 113.37 (12) | N1—C5—H52 | 110.8 |
O1—C1—O2 | 126.54 (14) | H51—C5—H52 | 109.5 |
C1—C2—C3 | 115.71 (11) | C2—N1—C5 | 100.76 (11) |
C1—C2—N1 | 116.91 (11) | C2—N1—C6 | 114.40 (11) |
C3—C2—N1 | 104.34 (11) | C5—N1—C6 | 108.96 (12) |
C1—C2—H21 | 97.6 | C2—N1—C7 | 112.05 (11) |
C3—C2—H21 | 111.9 | C5—N1—C7 | 110.32 (11) |
N1—C2—H21 | 110.5 | C6—N1—C7 | 109.94 (12) |
C2—C3—C4 | 104.06 (12) | C3—O3—H1 | 110.3 (14) |
C2—C3—O3 | 109.69 (11) | N1—C6—H61 | 109.5 |
C4—C3—O3 | 113.31 (12) | N1—C6—H62 | 109.5 |
C2—C3—H31 | 114.2 | H61—C6—H62 | 109.5 |
C4—C3—H31 | 110.7 | N1—C6—H63 | 109.5 |
O3—C3—H31 | 105.1 | H61—C6—H63 | 109.5 |
C3—C4—C5 | 105.65 (12) | H62—C6—H63 | 109.5 |
C3—C4—H41 | 110.4 | N1—C7—H71 | 109.5 |
C5—C4—H41 | 110.4 | N1—C7—H72 | 109.5 |
C3—C4—H42 | 110.4 | H71—C7—H72 | 109.5 |
C5—C4—H42 | 110.4 | N1—C7—H73 | 109.5 |
H41—C4—H42 | 109.5 | H71—C7—H73 | 109.5 |
C4—C5—N1 | 104.15 (11) | H72—C7—H73 | 109.5 |
C4—C5—H51 | 110.8 | H2—O4—H3 | 103 (3) |
N1—C5—H51 | 110.8 |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1···O2i | 0.82 (2) | 1.91 (3) | 2.712 (2) | 168 (3) |
O4—H3···O2ii | 0.83 (3) | 1.95 (3) | 2.777 (2) | 172 (3) |
O4—H2···O1 | 0.80 (3) | 2.10 (3) | 2.873 (2) | 162 (3) |
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x, y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C7H13NO3·H2O |
Mr | 177.20 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 150 |
a, b, c (Å) | 6.0647 (2), 7.1798 (2), 10.1956 (2) |
β (°) | 109.195 (2) |
V (Å3) | 419.27 (2) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 0.97 |
Crystal size (mm) | 0.30 × 0.30 × 0.24 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini area-detector |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2005) |
Tmin, Tmax | 0.75, 0.79 |
No. of measured, independent and observed [I > 3σ(I)] reflections | 3114, 1452, 1407 |
Rint | 0.010 |
(sin θ/λ)max (Å−1) | 0.616 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.033, 0.039, 1.08 |
No. of reflections | 1407 |
No. of parameters | 122 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.35, −0.29 |
Absolute structure | Flack (1983), 571 Friedel pairs |
Absolute structure parameter | 0.08 (18) |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2005)', CrysAlis CCD (Oxford Diffraction, 2005), CrysAlis RED (Oxford Diffraction, 2005), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996), CRYSTALS.
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H1···O2i | 0.82 (2) | 1.91 (3) | 2.712 (2) | 168 (3) |
O4—H3···O2ii | 0.83 (3) | 1.95 (3) | 2.777 (2) | 172 (3) |
O4—H2···O1 | 0.80 (3) | 2.10 (3) | 2.873 (2) | 162 (3) |
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x, y+1/2, −z+1. |
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.