Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807039281/wn2187sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807039281/wn2187Isup2.hkl |
CCDC reference: 660271
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.003 Å
- R factor = 0.038
- wR factor = 0.097
- Data-to-parameter ratio = 9.6
checkCIF/PLATON results
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Alert level B PLAT417_ALERT_2_B Short Inter D-H..H-D H8 .. H14 .. 1.37 Ang.
Alert level C ABSTM02_ALERT_3_C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90 Tmin and Tmax reported: 0.700 0.990 Tmin(prime) and Tmax expected: 0.917 0.993 RR(prime) = 0.766 Please check that your absorption correction is appropriate. PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.98 PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large ............. 0.76 PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT352_ALERT_3_C Short N-H Bond (0.87A) N6 - H2 ... 0.76 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 27.45 From the CIF: _reflns_number_total 1232 Count of symmetry unique reflns 1246 Completeness (_total/calc) 98.88% 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 PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4 = . S
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 5 ALERT level G = General alerts; check 4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 4 ALERT type 3 Indicator that the structure quality may be low 2 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: Booth, Kathrine V. - crystallographer; Jenkinson, Sarah F. - Post Doc chemist and crystallographer; Watkin, David J. - senior crystallographer; Sharp, Hazel - collaborator on project; Wyn Jones, Paul - collaborator on project; Nash, Robert J. - Industrial collaborator on project; 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
1 g of BR1 was isolated from the 50% aqueous ethanol extract of 2 kg of seeds of Baphia confusum (Leguminosae). The compound was isolated by binding it to Amberlite IR-120 (H+ form, 2L) and after washing with copious water it was displaced with 2M NH4OH. The bound material was concentrated by rotary evaporation and BR1 bound to Amberlite CG400 (OH- form), washed well with water and displaced with 2M AcOH. After further concentration the oil was applied to an Amberlite CG-50 column (3.6 x 48 cm, NH4+ form) and eluted with distilled water. Analysis of fractions using GC—MS of the pretrimethylsilyl-derivative (Nash et al., 1986) allowed fractions containing BR1 to be combined and these were then freeze-dried. Scanning the mass range 100–500 daltons on the GC—MS shows characteristic ions for BR1 at 217 (100%), 258 (50%), 348 (30%) and 375 (10%). BR1 was readily crystallized from 95% aq. EtOH by layering with acetone. m. p. 230–232 °C (dec), [α]D18 +14.5 (c, 0.13 in water) [lit. (Fleet et al., 1987): m.p. 228–232 °C, [α]D20 +14.1 (0.3 in H2O)]
The relatively large ratio of minimum to maximum corrections applied in the multi-scan process (1:1.41) reflect changes in the illuminated volume of the crystal, which were kept to a minimum, and were taken into account (Görbitz, 1999) by the multi-scan inter-frame scaling (DENZO/SCALEPACK, Otwinowski & Minor, 1997).
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, N—H to 0.86, 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.
BR1 [(2S,3R,4R,5S)-3,4,5-trihydroxypipecolic acid] (1) previously obtained from seeds of Baphia racemosa (Manning et al., 1985) and Baphia parvaflora, (Kite, 2003) has been isolated for the first time from seeds of the African medicinal tree Baphia confusum. BR1 (1) is the only trihydroxypipecolic acid that has been found in nature. Although there are over 100 naturally occurring pyrrolidines and piperidines, such as DNJ (2), (Asano et al., 2000) which may be viewed as sugars mimics (Watson et al., 2001), polyhydroxylated amino acids are relatively uncommon (Pereira et al., 1991) though several other trihydroxypipecolic acids have been synthesized (Bruce et al., 1992; Shilvock et al., 1996; Shilvock et al., 1998). This paper reports the determination by X-ray crystallographic analysis of the conformation and relative configuration of BR1. The absolute configuration is determined by comparison with the specific rotation of synthetic samples from D-glucuronolactone (Fleet et al., 1986; Fleet et al., 1987) and from D-glucose (Bernotas & Ganem, 1985).
The title compound (Fig. 2) crystallizes as its dihydrate. The crystal structure consists of hydrogen-bonded sheets lying approximately perpendicular to the c axis. O13 is embedded in the sheet and hydrogen bonded to adjacent molecules. O14 lies between the sheets and links them, acting as both a donor and an acceptor (Fig. 3).
For related literature see: Manning et al. (1985); Kite (2003); Asano et al. (2000); Watson et al. (2001); Pereira et al. (1991); Bruce et al. (1992); Shilvock et al. (1996, 1998); Fleet et al. (1986, 1987); Bernotas & Ganem (1985); Nash et al. (1986); Görbitz (1999).
Data collection: COLLECT (Nonius, 2001).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; 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.
C6H11NO5·2H2O | Dx = 1.553 Mg m−3 |
Mr = 213.19 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 1088 reflections |
a = 6.4536 (2) Å | θ = 5–27° |
b = 6.7954 (2) Å | µ = 0.14 mm−1 |
c = 20.7965 (8) Å | T = 150 K |
V = 912.03 (5) Å3 | Lath, colourless |
Z = 4 | 0.60 × 0.20 × 0.05 mm |
F(000) = 456 |
Nonius KappaCCD diffractometer | 1130 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.028 |
ω scans | θmax = 27.5°, θmin = 5.3° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −8→8 |
Tmin = 0.70, Tmax = 0.99 | k = −8→8 |
4710 measured reflections | l = −26→26 |
1232 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.038 | H-atom parameters constrained |
wR(F2) = 0.097 | Method = Modified Sheldrick
w = 1/[σ2(F2) + (0.04P)2 + 0.79P], where P = [max(Fo2,0) + 2Fc2]/3 |
S = 0.97 | (Δ/σ)max = 0.000133 |
1216 reflections | Δρmax = 0.51 e Å−3 |
127 parameters | Δρmin = −0.49 e Å−3 |
0 restraints |
C6H11NO5·2H2O | V = 912.03 (5) Å3 |
Mr = 213.19 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 6.4536 (2) Å | µ = 0.14 mm−1 |
b = 6.7954 (2) Å | T = 150 K |
c = 20.7965 (8) Å | 0.60 × 0.20 × 0.05 mm |
Nonius KappaCCD diffractometer | 1232 independent reflections |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | 1130 reflections with I > 2σ(I) |
Tmin = 0.70, Tmax = 0.99 | Rint = 0.028 |
4710 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 0.97 | Δρmax = 0.51 e Å−3 |
1216 reflections | Δρmin = −0.49 e Å−3 |
127 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.2706 (4) | 0.4469 (3) | 0.09371 (10) | 0.0125 | |
C2 | 0.4597 (4) | 0.5852 (3) | 0.09037 (11) | 0.0135 | |
C3 | 0.5846 (4) | 0.5616 (3) | 0.15241 (10) | 0.0140 | |
C4 | 0.6474 (4) | 0.3472 (3) | 0.16360 (10) | 0.0145 | |
C5 | 0.4652 (4) | 0.2059 (4) | 0.15918 (10) | 0.0162 | |
N6 | 0.3496 (3) | 0.2409 (3) | 0.09815 (9) | 0.0138 | |
O7 | 0.7297 (3) | 0.3209 (3) | 0.22635 (8) | 0.0201 | |
O8 | 0.7650 (3) | 0.6819 (3) | 0.15172 (8) | 0.0203 | |
O9 | 0.3908 (3) | 0.7817 (2) | 0.08402 (8) | 0.0188 | |
C10 | 0.1319 (4) | 0.4703 (3) | 0.03465 (11) | 0.0145 | |
O11 | 0.1734 (3) | 0.3657 (2) | −0.01336 (8) | 0.0182 | |
O12 | −0.0094 (3) | 0.5953 (3) | 0.03846 (8) | 0.0197 | |
O13 | 0.5093 (3) | 0.4875 (3) | −0.09049 (9) | 0.0245 | |
O14 | 0.1139 (3) | 0.4431 (3) | 0.25178 (8) | 0.0219 | |
H53 | 0.1888 | 0.4763 | 0.1325 | 0.0144* | |
H21 | 0.5494 | 0.5483 | 0.0542 | 0.0152* | |
H31 | 0.4980 | 0.6064 | 0.1881 | 0.0164* | |
H41 | 0.7446 | 0.3060 | 0.1304 | 0.0185* | |
H51 | 0.3738 | 0.2288 | 0.1943 | 0.0194* | |
H52 | 0.5136 | 0.0728 | 0.1598 | 0.0200* | |
H8 | 0.4482 | 0.7978 | 0.0488 | 0.0298* | |
H9 | 0.8379 | 0.3808 | 0.2289 | 0.0308* | |
H11 | 0.8225 | 0.6618 | 0.1179 | 0.0318* | |
H12 | 0.4020 | 0.4671 | −0.0716 | 0.0382* | |
H13 | 0.5566 | 0.5959 | −0.0797 | 0.0377* | |
H54 | 0.1524 | 0.3750 | 0.2828 | 0.0338* | |
H15 | 0.1530 | 0.5584 | 0.2601 | 0.0337* | |
H2 | 0.3560 | 0.1726 | 0.0693 | 0.0227* | |
H14 | −0.0891 | 0.6336 | 0.0122 | 0.0341* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0129 (11) | 0.0128 (10) | 0.0117 (9) | 0.0014 (9) | −0.0002 (9) | −0.0008 (9) |
C2 | 0.0157 (11) | 0.0108 (10) | 0.0139 (9) | 0.0004 (9) | 0.0010 (9) | 0.0003 (9) |
C3 | 0.0150 (11) | 0.0135 (10) | 0.0137 (9) | −0.0042 (9) | −0.0011 (9) | −0.0019 (9) |
C4 | 0.0147 (11) | 0.0157 (10) | 0.0131 (10) | −0.0001 (10) | −0.0022 (8) | −0.0015 (8) |
C5 | 0.0186 (11) | 0.0153 (11) | 0.0148 (10) | −0.0016 (10) | −0.0031 (9) | 0.0008 (8) |
N6 | 0.0176 (9) | 0.0122 (9) | 0.0115 (8) | 0.0011 (8) | −0.0013 (8) | −0.0020 (7) |
O7 | 0.0190 (9) | 0.0225 (9) | 0.0189 (8) | −0.0048 (8) | −0.0075 (7) | 0.0031 (7) |
O8 | 0.0191 (9) | 0.0206 (9) | 0.0210 (8) | −0.0092 (8) | 0.0005 (7) | −0.0019 (7) |
O9 | 0.0272 (10) | 0.0112 (7) | 0.0179 (7) | 0.0014 (8) | 0.0001 (8) | 0.0014 (6) |
C10 | 0.0133 (11) | 0.0153 (10) | 0.0150 (10) | −0.0031 (10) | 0.0005 (9) | 0.0012 (8) |
O11 | 0.0183 (8) | 0.0215 (8) | 0.0147 (7) | 0.0005 (8) | −0.0015 (6) | −0.0036 (7) |
O12 | 0.0195 (9) | 0.0240 (9) | 0.0157 (7) | 0.0072 (8) | −0.0020 (7) | 0.0011 (7) |
O13 | 0.0186 (9) | 0.0196 (8) | 0.0353 (10) | 0.0016 (8) | 0.0032 (8) | −0.0010 (8) |
O14 | 0.0265 (10) | 0.0202 (8) | 0.0189 (8) | −0.0019 (9) | −0.0046 (7) | 0.0010 (7) |
C1—C2 | 1.542 (3) | C5—H51 | 0.952 |
C1—N6 | 1.493 (3) | C5—H52 | 0.957 |
C1—C10 | 1.528 (3) | N6—H2 | 0.760 |
C1—H53 | 0.985 | O7—H9 | 0.810 |
C2—C3 | 1.530 (3) | O8—H11 | 0.807 |
C2—O9 | 1.414 (3) | O9—H8 | 0.828 |
C2—H21 | 0.982 | C10—O11 | 1.255 (3) |
C3—C4 | 1.530 (3) | C10—O12 | 1.248 (3) |
C3—O8 | 1.423 (3) | O12—H14 | 0.794 |
C3—H31 | 0.978 | O13—H12 | 0.807 |
C4—C5 | 1.521 (3) | O13—H13 | 0.829 |
C4—O7 | 1.420 (3) | O14—H54 | 0.832 |
C4—H41 | 0.974 | O14—H15 | 0.841 |
C5—N6 | 1.491 (3) | ||
C2—C1—N6 | 107.68 (18) | C3—C4—H41 | 109.7 |
C2—C1—C10 | 111.34 (18) | C5—C4—H41 | 105.9 |
N6—C1—C10 | 110.34 (18) | O7—C4—H41 | 112.0 |
C2—C1—H53 | 109.7 | C4—C5—N6 | 109.73 (18) |
N6—C1—H53 | 108.8 | C4—C5—H51 | 109.3 |
C10—C1—H53 | 108.9 | N6—C5—H51 | 108.5 |
C1—C2—C3 | 108.35 (18) | C4—C5—H52 | 110.0 |
C1—C2—O9 | 109.31 (19) | N6—C5—H52 | 109.0 |
C3—C2—O9 | 110.11 (18) | H51—C5—H52 | 110.2 |
C1—C2—H21 | 110.2 | C1—N6—C5 | 111.90 (17) |
C3—C2—H21 | 108.0 | C1—N6—H2 | 122.8 |
O9—C2—H21 | 110.8 | C5—N6—H2 | 123.2 |
C2—C3—C4 | 111.59 (18) | C4—O7—H9 | 108.6 |
C2—C3—O8 | 111.22 (18) | C3—O8—H11 | 106.7 |
C4—C3—O8 | 109.39 (19) | C2—O9—H8 | 93.8 |
C2—C3—H31 | 107.9 | C1—C10—O11 | 117.1 (2) |
C4—C3—H31 | 109.4 | C1—C10—O12 | 116.59 (19) |
O8—C3—H31 | 107.2 | O11—C10—O12 | 126.3 (2) |
C3—C4—C5 | 112.76 (19) | C10—O12—H14 | 130.8 |
C3—C4—O7 | 111.00 (18) | H12—O13—H13 | 109.7 |
C5—C4—O7 | 105.40 (18) | H54—O14—H15 | 105.6 |
D—H···A | D—H | H···A | D···A | D—H···A |
O9—H8···O12i | 0.83 | 1.97 | 2.757 (2) | 157 |
O7—H9···O14ii | 0.81 | 1.89 | 2.667 (2) | 160 |
O8—H11···O12ii | 0.81 | 2.03 | 2.831 (2) | 174 |
O13—H12···O11 | 0.81 | 2.03 | 2.821 (2) | 166 |
O14—H54···O8iii | 0.83 | 1.96 | 2.791 (2) | 172 |
O14—H15···O7iv | 0.84 | 1.96 | 2.796 (2) | 174 |
O12—H14···O9v | 0.79 | 2.09 | 2.757 (2) | 142 |
Symmetry codes: (i) x+1/2, −y+3/2, −z; (ii) x+1, y, z; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+1, y+1/2, −z+1/2; (v) x−1/2, −y+3/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C6H11NO5·2H2O |
Mr | 213.19 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 150 |
a, b, c (Å) | 6.4536 (2), 6.7954 (2), 20.7965 (8) |
V (Å3) | 912.03 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.60 × 0.20 × 0.05 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.70, 0.99 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4710, 1232, 1130 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.097, 0.97 |
No. of reflections | 1216 |
No. of parameters | 127 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.51, −0.49 |
Computer programs: COLLECT (Nonius, 2001)., DENZO/SCALEPACK (Otwinowski & Minor, 1997), DENZO/SCALEPACK, 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 |
O9—H8···O12i | 0.83 | 1.97 | 2.757 (2) | 157 |
O7—H9···O14ii | 0.81 | 1.89 | 2.667 (2) | 160 |
O8—H11···O12ii | 0.81 | 2.03 | 2.831 (2) | 174 |
O13—H12···O11 | 0.81 | 2.03 | 2.821 (2) | 166 |
O14—H54···O8iii | 0.83 | 1.96 | 2.791 (2) | 172 |
O14—H15···O7iv | 0.84 | 1.96 | 2.796 (2) | 174 |
O12—H14···O9v | 0.79 | 2.09 | 2.757 (2) | 142 |
Symmetry codes: (i) x+1/2, −y+3/2, −z; (ii) x+1, y, z; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+1, y+1/2, −z+1/2; (v) x−1/2, −y+3/2, −z. |
BR1 [(2S,3R,4R,5S)-3,4,5-trihydroxypipecolic acid] (1) previously obtained from seeds of Baphia racemosa (Manning et al., 1985) and Baphia parvaflora, (Kite, 2003) has been isolated for the first time from seeds of the African medicinal tree Baphia confusum. BR1 (1) is the only trihydroxypipecolic acid that has been found in nature. Although there are over 100 naturally occurring pyrrolidines and piperidines, such as DNJ (2), (Asano et al., 2000) which may be viewed as sugars mimics (Watson et al., 2001), polyhydroxylated amino acids are relatively uncommon (Pereira et al., 1991) though several other trihydroxypipecolic acids have been synthesized (Bruce et al., 1992; Shilvock et al., 1996; Shilvock et al., 1998). This paper reports the determination by X-ray crystallographic analysis of the conformation and relative configuration of BR1. The absolute configuration is determined by comparison with the specific rotation of synthetic samples from D-glucuronolactone (Fleet et al., 1986; Fleet et al., 1987) and from D-glucose (Bernotas & Ganem, 1985).
The title compound (Fig. 2) crystallizes as its dihydrate. The crystal structure consists of hydrogen-bonded sheets lying approximately perpendicular to the c axis. O13 is embedded in the sheet and hydrogen bonded to adjacent molecules. O14 lies between the sheets and links them, acting as both a donor and an acceptor (Fig. 3).