(2S,3R,4R,5R)-3,4-Dihydr­oxy-5-(hydroxy­meth­yl)pyrrolidine-2-carboxylic acid [(2S,3R,4R,5R)-3,4-dihydr­oxy-5-(hydroxy­meth­yl)proline]

Best, D.; Jenkinson, S.F.; Thompson, A.L.; Watkin, D.J.; Wilson, F.X.; Nash, R.J.; Fleet, G.W.J.

doi:10.1107/S1600536809035636

organic compounds

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Volume 65| Part 10| October 2009| Pages o2418-o2419

doi:10.1107/S1600536809035636

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(2S,3R,4R,5R)-3,4-Dihydroxy-5-(hydroxymethyl)pyrrolidine-2-carboxylic acid [(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)proline]

Daniel Best,^a Sarah F. Jenkinson,^a ^* Amber L. Thompson,^b David J. Watkin,^b Francis X. Wilson,^c Robert J. Nash ^d and George W. J. Fleet ^a

^aDepartment of Organic Chemistry, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England, ^bDepartment of Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, England, ^cSummit PLC, 91 Milton Park, Abingdon, Oxon OX14 4RY, England, and ^dPhytoquest Limited, IBERS, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, Ceredigion, Wales
^*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 28 August 2009; accepted 3 September 2009; online 9 September 2009)

The crystal structure of the title compound, C₆H₁₁NO₅, establishes the relative configuration at the four stereogenic centres; the absolute configuration is determined by the use of D-glucuronolactone as the starting material for the synthesis. Molecules are linked by intermolecular O—H⋯O and N—H⋯O hydrogen bonds into a three-dimensional network, with each molecule acting as a donor and acceptor for five hydrogen bonds.

Related literature

For related literature on iminosugars, see: Asano et al. (2000 ); Watson et al. (2001 ). For related literature on pipecolic acids, see: Fleet et al. (1987 ); Booth et al. (2007 ); Bashyal, Chow, Fellows & Fleet (1987 ); Manning et al. (1985 ); di Bello et al. (1984 ); Yoshimura et al. (2008 ). For related literature on bulgecinine, see: Toumi et al. (2008 ); Bashyal et al. (1986 ); Bashyal, Chow & Fleet (1987 ); Shinagawa et al. (1984 , 1985 ). For related literature on alexines, see: Pereira et al. (1991 ); Donohoe et al. (2008 ); Kato et al. (2003 ); Wormald et al. (1998 ). For absolute configuration, see: Flack (1983 ); Flack & Bernardinelli (2000 ); Flack & Shmueli (2007 ); Hooft et al. (2008 ); Thompson et al. (2008 ); Watkin (1994 ). For the weighting scheme, see: Prince (1982 ); Thompson & Watkin (2009 ).

Experimental

Crystal data

C₆H₁₁NO₅
M_r = 177.16
Triclinic, P 1
a = 5.4160 (2) Å
b = 5.8236 (3) Å
c = 6.6006 (3) Å
α = 102.836 (2)°
β = 104.776 (2)°
γ = 102.8244 (19)°
V = 187.50 (2) Å³
Z = 1
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 150 K
0.25 × 0.17 × 0.06 mm

Data collection

Area diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.94, T_max = 0.99
2314 measured reflections
834 independent reflections
814 reflections with I > 2σ(I)
R_int = 0.025

Refinement

R[F² > 2σ(F²)] = 0.027
wR(F²) = 0.066
S = 1.00
834 reflections
109 parameters
3 restraints
H-atom parameters constrained
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O8—H81⋯O1ⁱ	0.83	1.85	2.679 (3)	175
N5—H51⋯O11ⁱⁱ	0.88	2.03	2.873 (3)	160
N5—H52⋯O3ⁱⁱⁱ	0.89	1.93	2.814 (3)	173
O11—H111⋯O1ⁱⁱⁱ	0.82	1.89	2.696 (3)	170
O12—H121⋯O8^iv	0.82	1.91	2.668 (3)	154
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z; (iii) x+1, y, z; (iv) x-1, y-1, z.

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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809035636/lh2896sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809035636/lh2896Isup2.hkl

checkCIF report

Comment top

This paper firmly establishes the structure of the trihydroxyproline 1 (Fig. 1), the amino acid corresponding to DMDP 2. There are over 100 iminosugars that have been isolated as natural products [such as DMDP 2 and DNJ 4] that are the equivalent of carbohydrates with the ring oxygen replaced by nitrogen (Asano et al., 2000; Watson et al., 2001). In contrast, the pipecolic acid BR1 3 [related to DNJ 4 in the same way as 1 to 2] (Fleet et al.,1987; Booth et al., 2007; Bashyal, Chow, Fellows & Fleet, 1987) is among the rare examples of naturally occurring amino acid sugar analogues. BR1 3 was isolated from the seeds of Baphia racemosa (Manning et al., 1985) and is an inhibitor of glucuronidase and iduronidase (di Bello et al., 1984; Yoshimura et al., 2008). Bulgecinine 5 (Toumi et al., 2008; Bashyal et al., 1986; Bashyal, Chow & Fleet, 1987), a deoxy analogue of 1, is a constituent of the bulgecin glycopeptide antibiotics (Shinagawa et al., 1984; Shinagawa et al., 1985). 7a-Epialexaflorine 6, isolated from the leaves of Alexa grandiflora (Pereira et al., 1991), is the only example of an amino acid analogue of the alexines (Donohoe et al., 2008; Kato et al., 2003; Wormald et al., 1998).

The title compound (Fig. 2) was seen to adopt an envelope conformation with C4 out of the plane. The absolute configuration was determined by the use of D-glucuronolactone as the starting material for the synthesis. The molecule exists as an extensively hydrogen bonded nextwork with each molecule acting as a donor and acceptor for 5 hydrogen bonds (Fig. 3, Fig. 4). Only classical hydrogen bonding has been considered.

Related literature top

For related literature on iminosugars, see: Asano et al. (2000); Watson et al. (2001). For related literature on pipecolic acids, see: Fleet et al. (1987); Booth et al. (2007); Bashyal, Chow, Fellows & Fleet (1987), Bashyal, Chow & Fleet (1987); Manning et al. (1985); di Bello et al. (1984); Yoshimura et al. (2008). For related literature on bulgecinine, see: Toumi et al. (2008); Bashyal et al. (1986); Bashyal, Chow, Fellows & Fleet (1987), Bashyal, Chow & Fleet (1987); Shinagawa et al. (1984, 1985). For related literature on alexines, see: Pereira et al. (1991); Donohoe et al. (2008); Kato et al. (2003); Wormald et al. (1998).

For related literature, see: Flack (1983); Flack & Bernardinelli (2000); Flack & Shmueli (2007); Hooft et al. (2008); Prince (1982); Shinagawa et al. (1984, 1985); Thompson & Watkin (2009); Thompson et al. (2008); Watkin (1994).

Experimental top

The title compound was recrystallized from a mixture of hot ethanol and water: m.p. 449 K - decomposed; [α]_D²⁵ +14.7 (c, 1.13 in H₂O).

Computing details top

Data collection: COLLECT (Nonius, 2001).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); 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 (Betteridge et al., 2003).

Figures top

	Fig. 1. Synthetic scheme.
	Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram for the title compound projected along the b-axis.
	Fig. 4. Packing diagram for the title compound. The compound exists as an extensively hydrogen bonded nextwork.

(2S,3R,4R,5R)-3,4-Dihydroxy-5- (hydroxymethyl)pyrrolidine-2-carboxylic acid top

Crystal data top

C₆H₁₁NO₅	Z = 1
M_r = 177.16	F(000) = 94
Triclinic, P1	D_x = 1.569 Mg m⁻³
Hall symbol: P 1	Melting point: not measured K
a = 5.4160 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 5.8236 (3) Å	Cell parameters from 696 reflections
c = 6.6006 (3) Å	θ = 5–27°
α = 102.836 (2)°	µ = 0.14 mm⁻¹
β = 104.776 (2)°	T = 150 K
γ = 102.8244 (19)°	Plate, clear_pale_colourless
V = 187.50 (2) Å³	0.25 × 0.17 × 0.06 mm

Data collection top

Area diffractometer	814 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.025
ω scans	θ_max = 27.5°, θ_min = 5.6°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −7→7
T_min = 0.94, T_max = 0.99	k = −6→7
2314 measured reflections	l = −8→7
834 independent reflections

Refinement top

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)] = 0.027	H-atom parameters constrained
wR(F²) = 0.066	Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A₀T₀(x) + A₁T₁(x) ··· + A_n-1]T_n-1(x)] where A_i are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] [1-(deltaF/6*sigmaF)²]² A_i are: 22.5 35.8 21.7 10.1 2.91
S = 1.00	(Δ/σ)_max = 0.0000793
834 reflections	Δρ_max = 0.24 e Å⁻³
109 parameters	Δρ_min = −0.17 e Å⁻³
3 restraints

Crystal data top

C₆H₁₁NO₅	γ = 102.8244 (19)°
M_r = 177.16	V = 187.50 (2) Å³
Triclinic, P1	Z = 1
a = 5.4160 (2) Å	Mo Kα radiation
b = 5.8236 (3) Å	µ = 0.14 mm⁻¹
c = 6.6006 (3) Å	T = 150 K
α = 102.836 (2)°	0.25 × 0.17 × 0.06 mm
β = 104.776 (2)°

Data collection top

Area diffractometer	834 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	814 reflections with I > 2σ(I)
T_min = 0.94, T_max = 0.99	R_int = 0.025
2314 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.027	3 restraints
wR(F²) = 0.066	H-atom parameters constrained
S = 1.00	Δρ_max = 0.24 e Å⁻³
834 reflections	Δρ_min = −0.17 e Å⁻³
109 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.1323 (3)	0.4021 (3)	0.0397 (3)	0.0170
C2	0.3330 (4)	0.5769 (4)	0.1694 (3)	0.0124
O3	0.3285 (3)	0.7782 (3)	0.2816 (3)	0.0161
C4	0.6067 (4)	0.5299 (3)	0.1892 (3)	0.0118
N5	0.8297 (3)	0.7483 (3)	0.3462 (3)	0.0120
C6	0.8425 (4)	0.7309 (4)	0.5744 (3)	0.0130
C7	1.1277 (4)	0.8313 (4)	0.7284 (3)	0.0167
O8	1.2417 (3)	1.0809 (3)	0.7415 (3)	0.0209
C9	0.7092 (4)	0.4584 (4)	0.5443 (3)	0.0150
C10	0.6269 (4)	0.3243 (4)	0.2968 (3)	0.0135
O11	0.8192 (3)	0.2063 (3)	0.2544 (3)	0.0229
O12	0.4844 (4)	0.4511 (3)	0.6175 (3)	0.0252
H41	0.6365	0.4960	0.0477	0.0144*
H61	0.7333	0.8262	0.6278	0.0169*
H72	1.1284	0.8203	0.8747	0.0191*
H71	1.2343	0.7354	0.6770	0.0194*
H91	0.8360	0.3904	0.6257	0.0183*
H101	0.4566	0.2013	0.2549	0.0154*
H81	1.2048	1.1744	0.8368	0.0313*
H51	0.7954	0.8869	0.3332	0.0177*
H52	0.9817	0.7443	0.3204	0.0178*
H111	0.8993	0.2734	0.1839	0.0347*
H121	0.4206	0.3112	0.6224	0.0383*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0115 (7)	0.0187 (7)	0.0178 (7)	0.0024 (5)	0.0034 (5)	0.0030 (6)
C2	0.0128 (9)	0.0137 (9)	0.0134 (9)	0.0052 (7)	0.0051 (7)	0.0074 (7)
O3	0.0153 (7)	0.0148 (7)	0.0210 (7)	0.0075 (6)	0.0074 (5)	0.0057 (6)
C4	0.0113 (9)	0.0115 (8)	0.0130 (9)	0.0032 (7)	0.0050 (7)	0.0032 (7)
N5	0.0123 (8)	0.0098 (7)	0.0150 (8)	0.0039 (6)	0.0052 (6)	0.0042 (6)
C6	0.0142 (9)	0.0115 (8)	0.0136 (9)	0.0030 (7)	0.0053 (7)	0.0041 (7)
C7	0.0154 (9)	0.0161 (9)	0.0152 (9)	0.0013 (8)	0.0023 (7)	0.0042 (8)
O8	0.0246 (8)	0.0151 (8)	0.0190 (7)	−0.0019 (6)	0.0100 (6)	0.0020 (6)
C9	0.0173 (10)	0.0130 (9)	0.0165 (10)	0.0042 (7)	0.0066 (8)	0.0067 (7)
C10	0.0121 (9)	0.0124 (9)	0.0176 (9)	0.0049 (7)	0.0058 (7)	0.0050 (7)
O11	0.0280 (8)	0.0223 (8)	0.0356 (9)	0.0180 (7)	0.0218 (7)	0.0179 (7)
O12	0.0325 (9)	0.0164 (7)	0.0304 (9)	0.0018 (7)	0.0222 (8)	0.0056 (7)

Geometric parameters (Å, º) top

O1—C2	1.264 (3)	C7—O8	1.421 (2)
C2—O3	1.249 (2)	C7—H72	0.981
C2—C4	1.545 (2)	C7—H71	0.959
C4—N5	1.498 (2)	O8—H81	0.832
C4—C10	1.532 (3)	C9—C10	1.545 (3)
C4—H41	0.972	C9—O12	1.415 (2)
N5—C6	1.517 (2)	C9—H91	0.972
N5—H51	0.885	C10—O11	1.420 (2)
N5—H52	0.886	C10—H101	0.963
C6—C7	1.515 (3)	O11—H111	0.816
C6—C9	1.535 (3)	O12—H121	0.823
C6—H61	0.973

O1—C2—O3	126.24 (18)	C6—C7—O8	111.22 (16)
O1—C2—C4	115.43 (17)	C6—C7—H72	108.8
O3—C2—C4	118.32 (17)	O8—C7—H72	109.4
C2—C4—N5	110.92 (15)	C6—C7—H71	109.8
C2—C4—C10	109.46 (14)	O8—C7—H71	108.5
N5—C4—C10	103.55 (15)	H72—C7—H71	109.1
C2—C4—H41	111.2	C7—O8—H81	110.0
N5—C4—H41	108.5	C6—C9—C10	106.41 (15)
C10—C4—H41	113.0	C6—C9—O12	106.33 (16)
C4—N5—C6	106.33 (14)	C10—C9—O12	111.81 (16)
C4—N5—H51	110.5	C6—C9—H91	110.0
C6—N5—H51	109.1	C10—C9—H91	109.3
C4—N5—H52	109.8	O12—C9—H91	112.7
C6—N5—H52	111.2	C9—C10—C4	103.65 (15)
H51—N5—H52	109.8	C9—C10—O11	109.89 (16)
N5—C6—C7	110.92 (15)	C4—C10—O11	113.98 (15)
N5—C6—C9	105.61 (15)	C9—C10—H101	108.3
C7—C6—C9	114.30 (16)	C4—C10—H101	111.8
N5—C6—H61	108.0	O11—C10—H101	109.0
C7—C6—H61	109.9	C10—O11—H111	110.0
C9—C6—H61	107.9	C9—O12—H121	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H71···O12ⁱ	0.96	2.39	3.328 (3)	166
C10—H101···O3ⁱⁱ	0.96	2.47	3.199 (3)	133
O8—H81···O1ⁱⁱⁱ	0.83	1.85	2.679 (3)	175
N5—H51···O11^iv	0.88	2.03	2.873 (3)	160
N5—H52···O3ⁱ	0.89	1.93	2.814 (3)	173
O11—H111···O1ⁱ	0.82	1.89	2.696 (3)	170
O12—H121···O8^v	0.82	1.91	2.668 (3)	154

Symmetry codes: (i) x+1, y, z; (ii) x, y−1, z; (iii) x+1, y+1, z+1; (iv) x, y+1, z; (v) x−1, y−1, z.

Experimental details

Crystal data
Chemical formula	C₆H₁₁NO₅
M_r	177.16
Crystal system, space group	Triclinic, P1
Temperature (K)	150
a, b, c (Å)	5.4160 (2), 5.8236 (3), 6.6006 (3)
α, β, γ (°)	102.836 (2), 104.776 (2), 102.8244 (19)
V (Å³)	187.50 (2)
Z	1
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.25 × 0.17 × 0.06

Data collection
Diffractometer	Area diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.94, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	2314, 834, 814
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.027, 0.066, 1.00
No. of reflections	834
No. of parameters	109
No. of restraints	3
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.17

Computer programs: COLLECT (Nonius, 2001)., DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O8—H81···O1ⁱ	0.83	1.85	2.679 (3)	175
N5—H51···O11ⁱⁱ	0.88	2.03	2.873 (3)	160
N5—H52···O3ⁱⁱⁱ	0.89	1.93	2.814 (3)	173
O11—H111···O1ⁱⁱⁱ	0.82	1.89	2.696 (3)	170
O12—H121···O8^iv	0.82	1.91	2.668 (3)	154

Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z; (iii) x+1, y, z; (iv) x−1, y−1, z.

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ISSN: 2056-9890

Volume 65| Part 10| October 2009| Pages o2418-o2419

doi:10.1107/S1600536809035636

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

(2S,3R,4R,5R)-3,4-Dihydr­­oxy-5-(hy­droxy­meth­yl)pyrrolidine-2-carboxylic acid [(2S,3R,4R,5R)-3,4-dihydr­­oxy-5-(hy­droxy­meth­yl)proline]

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Experimental

Crystal data

Data collection

Refinement

Supporting information

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organic compounds

(2S,3R,4R,5R)-3,4-Dihydroxy-5-(hydroxymethyl)pyrrolidine-2-carboxylic acid [(2S,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)proline]