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The relative configuration of the title compound, C6H11NO5·2H2O, was determined by X-ray crystallography; the absolute configuration was determined by the comparison of physical data with the literature [Fleet, Bashyal & Chow (1986). Tetra­hedron Lett. 27, 3205-3207; Fleet, Bashyal, Chow & Fellows (1987). Tetra­hedron, 43, 415-422; Bernotas & Ganem (1985). Tetra­hedron Lett. 26, 4981-4982]. The structure exists as an extensively hydrogen-bonded lattice, with each mol­ecule acting as a donor and acceptor for seven hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807039281/wn2187sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807039281/wn2187Isup2.hkl
Contains datablock I

CCDC reference: 660271

Key indicators

  • Single-crystal X-ray study
  • T = 150 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.038
  • wR factor = 0.097
  • Data-to-parameter ratio = 9.6

checkCIF/PLATON results

No syntax errors found



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
checkCIF publication errors
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

Comment top

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).

Related literature top

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).

Experimental top

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)]

Refinement top

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.

Structure description top

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).

Computing details top

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.

Figures top
[Figure 1] Fig. 1. The title compound (1) and related compound DNJ (2).
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
[Figure 3] Fig. 3. Packing diagram viewed perpendicular to the plane of the hydrogen bonded (dashed lines) sheets. O13, coloured red, is embedded within the sheet. O14, coloured yellow, links the sheets together. O13 and O14 are drawn with a radius of 0.5 Å.
(2S,3R,4R,5S)-3,4,5-Trihydroxypiperidine-2-carboxylic acid dihydrate top
Crystal data top
C6H11NO5·2H2ODx = 1.553 Mg m3
Mr = 213.19Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 1088 reflections
a = 6.4536 (2) Åθ = 5–27°
b = 6.7954 (2) ŵ = 0.14 mm1
c = 20.7965 (8) ÅT = 150 K
V = 912.03 (5) Å3Lath, colourless
Z = 40.60 × 0.20 × 0.05 mm
F(000) = 456
Data collection top
Nonius KappaCCD
diffractometer
1130 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.028
ω scansθmax = 27.5°, θmin = 5.3°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 88
Tmin = 0.70, Tmax = 0.99k = 88
4710 measured reflectionsl = 2626
1232 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H-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 reflectionsΔρmax = 0.51 e Å3
127 parametersΔρmin = 0.49 e Å3
0 restraints
Crystal data top
C6H11NO5·2H2OV = 912.03 (5) Å3
Mr = 213.19Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.4536 (2) ŵ = 0.14 mm1
b = 6.7954 (2) ÅT = 150 K
c = 20.7965 (8) Å0.60 × 0.20 × 0.05 mm
Data collection top
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 = 0.99Rint = 0.028
4710 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.097H-atom parameters constrained
S = 0.97Δρmax = 0.51 e Å3
1216 reflectionsΔρmin = 0.49 e Å3
127 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2706 (4)0.4469 (3)0.09371 (10)0.0125
C20.4597 (4)0.5852 (3)0.09037 (11)0.0135
C30.5846 (4)0.5616 (3)0.15241 (10)0.0140
C40.6474 (4)0.3472 (3)0.16360 (10)0.0145
C50.4652 (4)0.2059 (4)0.15918 (10)0.0162
N60.3496 (3)0.2409 (3)0.09815 (9)0.0138
O70.7297 (3)0.3209 (3)0.22635 (8)0.0201
O80.7650 (3)0.6819 (3)0.15172 (8)0.0203
O90.3908 (3)0.7817 (2)0.08402 (8)0.0188
C100.1319 (4)0.4703 (3)0.03465 (11)0.0145
O110.1734 (3)0.3657 (2)0.01336 (8)0.0182
O120.0094 (3)0.5953 (3)0.03846 (8)0.0197
O130.5093 (3)0.4875 (3)0.09049 (9)0.0245
O140.1139 (3)0.4431 (3)0.25178 (8)0.0219
H530.18880.47630.13250.0144*
H210.54940.54830.05420.0152*
H310.49800.60640.18810.0164*
H410.74460.30600.13040.0185*
H510.37380.22880.19430.0194*
H520.51360.07280.15980.0200*
H80.44820.79780.04880.0298*
H90.83790.38080.22890.0308*
H110.82250.66180.11790.0318*
H120.40200.46710.07160.0382*
H130.55660.59590.07970.0377*
H540.15240.37500.28280.0338*
H150.15300.55840.26010.0337*
H20.35600.17260.06930.0227*
H140.08910.63360.01220.0341*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0129 (11)0.0128 (10)0.0117 (9)0.0014 (9)0.0002 (9)0.0008 (9)
C20.0157 (11)0.0108 (10)0.0139 (9)0.0004 (9)0.0010 (9)0.0003 (9)
C30.0150 (11)0.0135 (10)0.0137 (9)0.0042 (9)0.0011 (9)0.0019 (9)
C40.0147 (11)0.0157 (10)0.0131 (10)0.0001 (10)0.0022 (8)0.0015 (8)
C50.0186 (11)0.0153 (11)0.0148 (10)0.0016 (10)0.0031 (9)0.0008 (8)
N60.0176 (9)0.0122 (9)0.0115 (8)0.0011 (8)0.0013 (8)0.0020 (7)
O70.0190 (9)0.0225 (9)0.0189 (8)0.0048 (8)0.0075 (7)0.0031 (7)
O80.0191 (9)0.0206 (9)0.0210 (8)0.0092 (8)0.0005 (7)0.0019 (7)
O90.0272 (10)0.0112 (7)0.0179 (7)0.0014 (8)0.0001 (8)0.0014 (6)
C100.0133 (11)0.0153 (10)0.0150 (10)0.0031 (10)0.0005 (9)0.0012 (8)
O110.0183 (8)0.0215 (8)0.0147 (7)0.0005 (8)0.0015 (6)0.0036 (7)
O120.0195 (9)0.0240 (9)0.0157 (7)0.0072 (8)0.0020 (7)0.0011 (7)
O130.0186 (9)0.0196 (8)0.0353 (10)0.0016 (8)0.0032 (8)0.0010 (8)
O140.0265 (10)0.0202 (8)0.0189 (8)0.0019 (9)0.0046 (7)0.0010 (7)
Geometric parameters (Å, º) top
C1—C21.542 (3)C5—H510.952
C1—N61.493 (3)C5—H520.957
C1—C101.528 (3)N6—H20.760
C1—H530.985O7—H90.810
C2—C31.530 (3)O8—H110.807
C2—O91.414 (3)O9—H80.828
C2—H210.982C10—O111.255 (3)
C3—C41.530 (3)C10—O121.248 (3)
C3—O81.423 (3)O12—H140.794
C3—H310.978O13—H120.807
C4—C51.521 (3)O13—H130.829
C4—O71.420 (3)O14—H540.832
C4—H410.974O14—H150.841
C5—N61.491 (3)
C2—C1—N6107.68 (18)C3—C4—H41109.7
C2—C1—C10111.34 (18)C5—C4—H41105.9
N6—C1—C10110.34 (18)O7—C4—H41112.0
C2—C1—H53109.7C4—C5—N6109.73 (18)
N6—C1—H53108.8C4—C5—H51109.3
C10—C1—H53108.9N6—C5—H51108.5
C1—C2—C3108.35 (18)C4—C5—H52110.0
C1—C2—O9109.31 (19)N6—C5—H52109.0
C3—C2—O9110.11 (18)H51—C5—H52110.2
C1—C2—H21110.2C1—N6—C5111.90 (17)
C3—C2—H21108.0C1—N6—H2122.8
O9—C2—H21110.8C5—N6—H2123.2
C2—C3—C4111.59 (18)C4—O7—H9108.6
C2—C3—O8111.22 (18)C3—O8—H11106.7
C4—C3—O8109.39 (19)C2—O9—H893.8
C2—C3—H31107.9C1—C10—O11117.1 (2)
C4—C3—H31109.4C1—C10—O12116.59 (19)
O8—C3—H31107.2O11—C10—O12126.3 (2)
C3—C4—C5112.76 (19)C10—O12—H14130.8
C3—C4—O7111.00 (18)H12—O13—H13109.7
C5—C4—O7105.40 (18)H54—O14—H15105.6
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O9—H8···O12i0.831.972.757 (2)157
O7—H9···O14ii0.811.892.667 (2)160
O8—H11···O12ii0.812.032.831 (2)174
O13—H12···O110.812.032.821 (2)166
O14—H54···O8iii0.831.962.791 (2)172
O14—H15···O7iv0.841.962.796 (2)174
O12—H14···O9v0.792.092.757 (2)142
Symmetry codes: (i) x+1/2, y+3/2, z; (ii) x+1, y, z; (iii) x+1, y1/2, z+1/2; (iv) x+1, y+1/2, z+1/2; (v) x1/2, y+3/2, z.

Experimental details

Crystal data
Chemical formulaC6H11NO5·2H2O
Mr213.19
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)6.4536 (2), 6.7954 (2), 20.7965 (8)
V3)912.03 (5)
Z4
Radiation typeMo Kα
µ (mm1)0.14
Crystal size (mm)0.60 × 0.20 × 0.05
Data collection
DiffractometerNonius KappaCCD
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.70, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
4710, 1232, 1130
Rint0.028
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.097, 0.97
No. of reflections1216
No. of parameters127
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O9—H8···O12i0.831.972.757 (2)157
O7—H9···O14ii0.811.892.667 (2)160
O8—H11···O12ii0.812.032.831 (2)174
O13—H12···O110.812.032.821 (2)166
O14—H54···O8iii0.831.962.791 (2)172
O14—H15···O7iv0.841.962.796 (2)174
O12—H14···O9v0.792.092.757 (2)142
Symmetry codes: (i) x+1/2, y+3/2, z; (ii) x+1, y, z; (iii) x+1, y1/2, z+1/2; (iv) x+1, y+1/2, z+1/2; (v) x1/2, y+3/2, z.
 

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