organic compounds
N-(2-Carboxyethyl)-2,5-dideoxy-2,5-imino-D-mannonic acid [(3R,4R,5R)-1-(2-carboxyethyl)-3,4-dihydroxy-5-hydroxymethyl-L-proline]
aDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, bDepartment of Organic Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, and cPhytoquest Limited, IBERS, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, Wales
*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk
The absolute stereochemistry of the title compound, C9H15NO7, was determined from the use of D-glucuronolactone as the starting material. The compound crystallizes as the zwitterion. The five-membered ring adopts an with the –CH2OH-substituted C atom forming the flap. An intramolecular N—H⋯O hydrogen-bond occurs. In the crystal, the compound exists as a three-dimensional O—H⋯O intermolecular hydrogen-bonded network with each molecule acting as a donor and acceptor for four hydrogen bonds.
Related literature
For related literature on naturally occurring iminosugars, see: Asano et al. (2000); Watson et al. (2001); Nash et al. (1991); Welter et al. (1976); Manning et al. (1985); Pereira et al. (1991). For the synthesis of the diacid, see: Best et al. (2010); Martínez et al. (2012). For the extinction correction, see: Larson (1970). For hydrogen-atom see: Cooper et al. (2010). For the temperature controller, see: Cosier & Glazer (1986). For the Chebychev polynomial used in the weighting scheme, see: Prince (1982); Watkin (1994).
Experimental
Crystal data
|
Refinement
|
Data collection: COLLECT (Nonius, 2001); cell DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: Superflip (Palatinus & Chapuis, 2007); 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.
Supporting information
https://doi.org/10.1107/S1600536812037488/lh5524sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812037488/lh5524Isup2.hkl
The synthetic procedure is described in the comment section and illustrated in Fig. 1. The title compound was recrystallized from water: [α]D25 -6.7 (c 0.75 in H2O); m.p. 523 K (decomposed).
In the absence of significant
Friedel pairs were merged and the was assigned from the starting material.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 Uĩso~(H) (in the range 1.2–1.5 times U~eq~ of the parent atom), after which the positions were refined with riding constraints (Cooper et al., 2010).
More than 250 iminosugars, sugar mimics in which the ring oxygen in a pyranose or furanose is replaced by nitrogen to form polyhydroxylated piperidines and pyrrolidines, have been isolated from plants (Asano et al., 2000; Watson et al., 2001). DMDP 1 (Fig. 1), originally isolated from Derris eliptica (Welter et al., 1976), but the most widely occurring iminosugar, is even found in potatoes (Nash et al., 1991). In contrast, BR1 2 from Baphia racemosa (Manning et al., 1985) and 7a-epialexaflorine 3 from Alexa grandiflora (Pereira et al., 1991) are among the very few corresponding sugar amino acids (SAA) found in nature. From examination of crude extracts of plants, it is clear that other SAA are natural products. As part of a program to make authentic samples of such SAA to identify them in crude plant extracts, the SAA corresponding to DMDP 4 (Best et al., 2010) was converted to the diacid 5 by initial reaction with tert-butyl acrylate in methanol in the presence of triethylamine followed by treatment with aqueous trifluoroacetic acid (Martínez, 2012). The structure of 5 was unequivocally determined by X-ray crystallographic analysis; the
was determined by the use of d-glucuronolactone as the starting material for the synthesis.The five ring adopts an
with C5 out of the plane (Fig. 2). The compound exisits as a three-dimensional O—H···O intermolecular hydrogen-bonded network with each molecule acting as a donor and acceptor for four hydrogen bonds (Fig. 3).For related literature on naturally occurring iminosugars, see: Asano et al. (2000); Watson et al. (2001); Nash et al. (1991); Welter et al. (1976); Manning et al. (1985); Pereira et al. (1991). For the synthesis of the diacid, see: Best et al. (2010); Martínez et al. (2012). For the extinction correction, see: Larson (1970). For hydrogen-atom
see: Cooper et al. (2010). For the temperature controller, see: Cosier & Glazer (1986). For the Chebychev polynomial used in the weighting scheme, see: Prince (1982); Watkin (1994).Data collection: COLLECT (Nonius, 2001); cell
DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: Superflip (Palatinus & Chapuis, 2007); 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 (Betteridge et al., 2003).C9H15NO7 | F(000) = 528 |
Mr = 249.22 | Dx = 1.578 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1401 reflections |
a = 8.5242 (1) Å | θ = 5–27° |
b = 8.5707 (1) Å | µ = 0.14 mm−1 |
c = 14.3585 (3) Å | T = 190 K |
V = 1049.01 (3) Å3 | Plate, colourless |
Z = 4 | 0.32 × 0.30 × 0.11 mm |
Nonius KappaCCD diffractometer | 1321 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.009 |
ω scans | θmax = 27.5°, θmin = 5.3° |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | h = −11→11 |
Tmin = 0.93, Tmax = 0.99 | k = −11→11 |
18435 measured reflections | l = −18→18 |
1385 independent reflections |
Refinement on F2 | Hydrogen site location: difference Fourier map |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.024 | Method, part 1, Chebychev polynomial, (Watkin, 1994; Prince, 1982) [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: 24.6 39.9 23.9 10.2 2.48 |
wR(F2) = 0.062 | (Δ/σ)max = 0.0004353 |
S = 0.93 | Δρmax = 0.21 e Å−3 |
1385 reflections | Δρmin = −0.14 e Å−3 |
155 parameters | Extinction correction: Larson (1970), Equation 22 |
0 restraints | Extinction coefficient: 190 (20) |
Primary atom site location: Other |
C9H15NO7 | V = 1049.01 (3) Å3 |
Mr = 249.22 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.5242 (1) Å | µ = 0.14 mm−1 |
b = 8.5707 (1) Å | T = 190 K |
c = 14.3585 (3) Å | 0.32 × 0.30 × 0.11 mm |
Nonius KappaCCD diffractometer | 1385 independent reflections |
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) | 1321 reflections with I > 2σ(I) |
Tmin = 0.93, Tmax = 0.99 | Rint = 0.009 |
18435 measured reflections |
R[F2 > 2σ(F2)] = 0.024 | 0 restraints |
wR(F2) = 0.062 | H-atom parameters constrained |
S = 0.93 | Δρmax = 0.21 e Å−3 |
1385 reflections | Δρmin = −0.14 e Å−3 |
155 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier & Glazer, 1986) with a nominal stability of 0.1 K. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.25779 (14) | 0.79237 (13) | 0.78008 (7) | 0.0203 | |
C2 | 0.21884 (17) | 0.76687 (17) | 0.68515 (10) | 0.0156 | |
C3 | 0.34616 (17) | 0.82784 (16) | 0.61866 (10) | 0.0153 | |
O4 | 0.27181 (12) | 0.86546 (13) | 0.53261 (7) | 0.0199 | |
C5 | 0.45582 (16) | 0.68918 (15) | 0.60409 (9) | 0.0148 | |
N6 | 0.33646 (14) | 0.56002 (13) | 0.59290 (8) | 0.0141 | |
C7 | 0.21204 (16) | 0.58889 (17) | 0.66539 (10) | 0.0144 | |
C8 | 0.05081 (18) | 0.54093 (16) | 0.62872 (10) | 0.0155 | |
O9 | 0.03760 (13) | 0.51412 (12) | 0.54371 (7) | 0.0196 | |
O10 | −0.05866 (13) | 0.53953 (13) | 0.68791 (7) | 0.0205 | |
C11 | 0.39382 (17) | 0.39407 (16) | 0.59147 (11) | 0.0168 | |
C12 | 0.51896 (18) | 0.36273 (17) | 0.51838 (9) | 0.0177 | |
C13 | 0.48212 (17) | 0.41891 (17) | 0.42111 (10) | 0.0178 | |
O14 | 0.57147 (14) | 0.35134 (13) | 0.35801 (7) | 0.0218 | |
O15 | 0.38504 (14) | 0.51908 (13) | 0.40387 (7) | 0.0241 | |
C16 | 0.56756 (17) | 0.66168 (17) | 0.68540 (11) | 0.0191 | |
O17 | 0.66018 (13) | 0.79709 (15) | 0.69892 (8) | 0.0252 | |
H21 | 0.1206 | 0.8129 | 0.6680 | 0.0190* | |
H31 | 0.3983 | 0.9179 | 0.6450 | 0.0177* | |
H51 | 0.5150 | 0.6992 | 0.5452 | 0.0178* | |
H71 | 0.2358 | 0.5326 | 0.7211 | 0.0155* | |
H111 | 0.3007 | 0.3304 | 0.5802 | 0.0199* | |
H112 | 0.4377 | 0.3698 | 0.6517 | 0.0210* | |
H121 | 0.5390 | 0.2510 | 0.5152 | 0.0211* | |
H122 | 0.6181 | 0.4132 | 0.5352 | 0.0221* | |
H162 | 0.6327 | 0.5676 | 0.6725 | 0.0238* | |
H161 | 0.5065 | 0.6450 | 0.7429 | 0.0230* | |
H171 | 0.7288 | 0.8063 | 0.6573 | 0.0384* | |
H141 | 0.5503 | 0.3854 | 0.3035 | 0.0342* | |
H11 | 0.1995 | 0.8611 | 0.8000 | 0.0308* | |
H41 | 0.3391 | 0.9087 | 0.5016 | 0.0308* | |
H61 | 0.2882 | 0.5748 | 0.5379 | 0.0220* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0242 (5) | 0.0209 (5) | 0.0158 (5) | 0.0028 (5) | 0.0009 (4) | −0.0050 (4) |
C2 | 0.0150 (6) | 0.0164 (6) | 0.0153 (6) | 0.0016 (5) | 0.0004 (5) | −0.0010 (5) |
C3 | 0.0158 (6) | 0.0143 (6) | 0.0158 (6) | 0.0003 (5) | −0.0004 (5) | 0.0005 (5) |
O4 | 0.0173 (5) | 0.0230 (5) | 0.0195 (5) | 0.0015 (4) | 0.0003 (4) | 0.0065 (4) |
C5 | 0.0133 (6) | 0.0146 (6) | 0.0166 (6) | −0.0001 (5) | 0.0012 (5) | −0.0005 (5) |
N6 | 0.0134 (5) | 0.0142 (5) | 0.0148 (5) | 0.0008 (4) | 0.0011 (5) | −0.0004 (4) |
C7 | 0.0144 (6) | 0.0148 (6) | 0.0140 (6) | 0.0014 (5) | 0.0020 (5) | 0.0002 (5) |
C8 | 0.0161 (6) | 0.0137 (6) | 0.0167 (6) | −0.0004 (5) | −0.0008 (5) | 0.0016 (5) |
O9 | 0.0196 (5) | 0.0233 (5) | 0.0160 (5) | 0.0003 (5) | −0.0016 (4) | −0.0015 (4) |
O10 | 0.0154 (5) | 0.0266 (5) | 0.0196 (5) | −0.0028 (4) | 0.0036 (4) | −0.0011 (4) |
C11 | 0.0202 (7) | 0.0124 (6) | 0.0179 (6) | 0.0024 (5) | 0.0038 (6) | 0.0012 (5) |
C12 | 0.0198 (7) | 0.0157 (6) | 0.0176 (6) | 0.0034 (6) | 0.0020 (6) | −0.0005 (5) |
C13 | 0.0184 (6) | 0.0176 (6) | 0.0174 (6) | −0.0005 (6) | 0.0013 (6) | −0.0020 (5) |
O14 | 0.0257 (6) | 0.0246 (5) | 0.0151 (5) | 0.0056 (5) | 0.0016 (4) | −0.0016 (4) |
O15 | 0.0254 (5) | 0.0277 (6) | 0.0191 (5) | 0.0085 (5) | −0.0010 (5) | 0.0005 (4) |
C16 | 0.0168 (6) | 0.0195 (7) | 0.0209 (7) | 0.0018 (6) | −0.0022 (6) | −0.0029 (6) |
O17 | 0.0189 (5) | 0.0334 (6) | 0.0232 (5) | −0.0089 (5) | 0.0013 (5) | −0.0051 (5) |
O1—C2 | 1.4198 (17) | C7—H71 | 0.956 |
O1—H11 | 0.822 | C8—O9 | 1.2471 (17) |
C2—C3 | 1.537 (2) | C8—O10 | 1.2622 (18) |
C2—C7 | 1.553 (2) | C11—C12 | 1.5204 (19) |
C2—H21 | 0.958 | C11—H111 | 0.976 |
C3—O4 | 1.4257 (16) | C11—H112 | 0.965 |
C3—C5 | 1.5263 (19) | C12—C13 | 1.5103 (19) |
C3—H31 | 0.968 | C12—H121 | 0.974 |
O4—H41 | 0.815 | C12—H122 | 0.980 |
C5—N6 | 1.5121 (17) | C13—O14 | 1.3177 (18) |
C5—C16 | 1.525 (2) | C13—O15 | 1.2178 (19) |
C5—H51 | 0.989 | O14—H141 | 0.855 |
N6—C7 | 1.5064 (17) | C16—O17 | 1.4171 (18) |
N6—C11 | 1.5041 (17) | C16—H162 | 0.997 |
N6—H61 | 0.900 | C16—H161 | 0.987 |
C7—C8 | 1.528 (2) | O17—H171 | 0.840 |
C2—O1—H11 | 107.6 | C2—C7—H71 | 109.5 |
O1—C2—C3 | 112.26 (12) | N6—C7—H71 | 110.3 |
O1—C2—C7 | 109.60 (12) | C8—C7—H71 | 110.1 |
C3—C2—C7 | 104.29 (11) | C7—C8—O9 | 117.91 (13) |
O1—C2—H21 | 112.8 | C7—C8—O10 | 115.82 (12) |
C3—C2—H21 | 108.5 | O9—C8—O10 | 126.19 (15) |
C7—C2—H21 | 109.0 | N6—C11—C12 | 113.87 (12) |
C2—C3—O4 | 107.53 (11) | N6—C11—H111 | 105.5 |
C2—C3—C5 | 104.65 (11) | C12—C11—H111 | 110.9 |
O4—C3—C5 | 109.24 (11) | N6—C11—H112 | 108.5 |
C2—C3—H31 | 110.6 | C12—C11—H112 | 108.0 |
O4—C3—H31 | 111.2 | H111—C11—H112 | 110.1 |
C5—C3—H31 | 113.2 | C11—C12—C13 | 115.85 (12) |
C3—O4—H41 | 105.3 | C11—C12—H121 | 109.2 |
C3—C5—N6 | 99.93 (10) | C13—C12—H121 | 107.9 |
C3—C5—C16 | 113.45 (11) | C11—C12—H122 | 111.0 |
N6—C5—C16 | 112.86 (11) | C13—C12—H122 | 105.4 |
C3—C5—H51 | 111.2 | H121—C12—H122 | 107.1 |
N6—C5—H51 | 108.4 | C12—C13—O14 | 112.05 (12) |
C16—C5—H51 | 110.5 | C12—C13—O15 | 123.65 (13) |
C5—N6—C7 | 106.26 (10) | O14—C13—O15 | 124.25 (14) |
C5—N6—C11 | 118.36 (11) | C13—O14—H141 | 111.0 |
C7—N6—C11 | 113.18 (11) | C5—C16—O17 | 109.05 (12) |
C5—N6—H61 | 107.3 | C5—C16—H162 | 109.3 |
C7—N6—H61 | 105.2 | O17—C16—H162 | 112.2 |
C11—N6—H61 | 105.7 | C5—C16—H161 | 109.5 |
C2—C7—N6 | 105.15 (11) | O17—C16—H161 | 107.4 |
C2—C7—C8 | 111.15 (12) | H162—C16—H161 | 109.4 |
N6—C7—C8 | 110.54 (11) | C16—O17—H171 | 111.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
C5—H51···O4i | 0.99 | 2.52 | 3.366 (2) | 143 (1) |
C7—H71···O17ii | 0.96 | 2.49 | 3.352 (2) | 151 (1) |
C11—H112···O17ii | 0.97 | 2.38 | 3.156 (2) | 137 (1) |
C12—H121···O9iii | 0.97 | 2.43 | 3.354 (2) | 160 (1) |
C12—H122···O4i | 0.98 | 2.50 | 3.257 (2) | 134 (1) |
C16—H161···O1 | 0.99 | 2.53 | 3.174 (2) | 123 |
O17—H171···O15i | 0.84 | 2.19 | 2.887 (2) | 141 (1) |
O14—H141···O10iv | 0.86 | 1.78 | 2.618 (2) | 166 (1) |
O1—H11···O10v | 0.82 | 1.95 | 2.753 (2) | 165 (1) |
O4—H41···O9i | 0.82 | 1.93 | 2.720 (2) | 163 (1) |
N6—H61···O15 | 0.90 | 2.15 | 2.768 (2) | 125 |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+1, y−1/2, −z+3/2; (iii) x+1/2, −y+1/2, −z+1; (iv) −x+1/2, −y+1, z−1/2; (v) −x, y+1/2, −z+3/2. |
Experimental details
Crystal data | |
Chemical formula | C9H15NO7 |
Mr | 249.22 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 190 |
a, b, c (Å) | 8.5242 (1), 8.5707 (1), 14.3585 (3) |
V (Å3) | 1049.01 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.32 × 0.30 × 0.11 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.93, 0.99 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 18435, 1385, 1321 |
Rint | 0.009 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.024, 0.062, 0.93 |
No. of reflections | 1385 |
No. of parameters | 155 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.21, −0.14 |
Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), Superflip (Palatinus & Chapuis, 2007), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).
D—H···A | D—H | H···A | D···A | D—H···A |
O17—H171···O15i | 0.840 | 2.188 | 2.887 (2) | 140.69 (4) |
O14—H141···O10ii | 0.855 | 1.781 | 2.618 (2) | 165.53 (5) |
O1—H11···O10iii | 0.822 | 1.952 | 2.753 (2) | 164.63 (4) |
O4—H41···O9i | 0.815 | 1.930 | 2.720 (2) | 163.14 (4) |
N6—H61···O15 | 0.900 | 2.147 | 2.768 (2) | 125.42 |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+1/2, −y+1, z−1/2; (iii) −x, y+1/2, −z+3/2. |
Acknowledgements
This work was supported by the Fundación Ramón Areces (RFM).
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More than 250 iminosugars, sugar mimics in which the ring oxygen in a pyranose or furanose is replaced by nitrogen to form polyhydroxylated piperidines and pyrrolidines, have been isolated from plants (Asano et al., 2000; Watson et al., 2001). DMDP 1 (Fig. 1), originally isolated from Derris eliptica (Welter et al., 1976), but the most widely occurring iminosugar, is even found in potatoes (Nash et al., 1991). In contrast, BR1 2 from Baphia racemosa (Manning et al., 1985) and 7a-epialexaflorine 3 from Alexa grandiflora (Pereira et al., 1991) are among the very few corresponding sugar amino acids (SAA) found in nature. From examination of crude extracts of plants, it is clear that other SAA are natural products. As part of a program to make authentic samples of such SAA to identify them in crude plant extracts, the SAA corresponding to DMDP 4 (Best et al., 2010) was converted to the diacid 5 by initial reaction with tert-butyl acrylate in methanol in the presence of triethylamine followed by treatment with aqueous trifluoroacetic acid (Martínez, 2012). The structure of 5 was unequivocally determined by X-ray crystallographic analysis; the absolute configuration was determined by the use of d-glucuronolactone as the starting material for the synthesis.
The five ring adopts an envelope conformation with C5 out of the plane (Fig. 2). The compound exisits as a three-dimensional O—H···O intermolecular hydrogen-bonded network with each molecule acting as a donor and acceptor for four hydrogen bonds (Fig. 3).