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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 64| Part 8| August 2008| Pages o1568-o1569
doi:10.1107/S1600536808022563

6-Azido-6-de­­oxy-α-L-galactose (6-azido-L-fucose) monohydrate

K. Victoria Booth,a* Sarah F. Jenkinson,a Devendar Rao,b Tsuyosi Simonisi,b George W. J. Fleet,a Ken Izumorib and David J. Watkinc

aDepartment of Organic Chemistry, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, bRare Sugar Research Centre, Kagawa University, 2393 Miki-cho, Kita-gun, Kagawa 761-0795, Japan, and cDepartment of Chemical Crystallography, Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, England
*Correspondence e-mail: victoria.booth@chem.ox.ac.uk

(Received 25 June 2008; accepted 18 July 2008; online 23 July 2008)

Although 6-azido-6-de­oxy-L-galactose in aqueous solution is in equilibrium between the open-chain, furan­ose and pyran­ose forms, it crystallizes solely as 6-azido-6-de­oxy-α-L-galactopyran­ose monohydrate, C6H11N3O5·H2O, with the six-membered ring adopting a chair conformation. The structure exists as hydrogen-bonded chains, with each mol­ecule acting as a donor and acceptor of five hydrogen bonds. There are no unusual crystal packing features and the absolute configuration was determined from the use of 1-azido-1-de­oxy-D-galactitol as the starting material.

Related literature

For related literature see: Beadle et al. (1992[Beadle, J. R., Saunders, J. P. & Wajda, T. J. (1992). US Patent 5 078 796.]); Izumori (2002[Izumori, K. (2002). Naturwissenschaften, 89, 120-124.], 2006[Izumori, K. (2006). J. Biotechnol. 124, 717-722.]); Granstrom et al. (2004[Granstrom, T. B., Takata, G., Tokuda, M. & Izumori, K. (2004). J. Biosci. Bioeng. 97, 89-94.]); Sun et al. (2007[Sun, Y. X., Hayakawa, S., Ogawa, M. & Izumori, K. (2007). Food. Contr. 18, 220-227.]); Levin (2002[Levin, G. V. (2002). J. Med. Food, 5, 23-36.]); Skytte (2002[Skytte, U. P. (2002). Cereal Foods World, 47, 224-224.]); Nakajima et al. (2004[Nakajima, Y., Gotanda, T., Uchimiya, H., Furukawa, T., Haraguchi, M., Ikeda, R., Sumizawa, T., Yoshida, H. & Akiyama, S. (2004). Cancer Res. 64, 1794-1801.]); Sui et al. (2005[Sui, L., Dong, Y. Y., Watanabe, Y., Yamaguchi, F., Hatano, N., Tsukamoto, I., Izumori, K. & Tokuda, M. (2005). Int. J. Oncol. 27, 907-912.]); Hossain et al. (2006[Hossain, M. A., Wakabayashi, H., Izuishi, K., Okano, K., Yachida, S., Tokuda, M., Izumori, K. & Maeta, H. (2006). J. Biosci. Bioeng. 101, 369-371.]); Kolb & Sharpless (2003[Kolb, H. C. & Sharpless, K. B. (2003). Drug Discovery Today, 8, 1128-???.]); Chesterton et al. (2006[Chesterton, A. K. S., Jenkinson, S. F., Jones, N. A., Fleet, G. W. J. & Watkin, D. J. (2006). Acta Cryst. E62, o2983-o2985.]); Görbitz (1999[Görbitz, C. H. (1999). Acta Cryst. B55, 1090-1098.]); Larson (1970[Larson, A. C. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, pp. 291-294. Copenhagen: Munksgaard.]); Prince (1982[Prince, E. (1982). Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.]); Watkin (1994[Watkin, D. (1994). Acta Cryst. A50, 411-437.]); Yoshihara et al. (2008[Yoshihara, A., Haraguchi, S., Gullapalli, P., Rao, D., Morimoto, K., Takata, G., Jones, N., Jenkinson, S. F., Wormald, M. R., Dwek, R. A., Fleet, G. W. J. & Izumori, K. (2008). Tetrahedron Asymmetry, 19, 739-745.]).

[Scheme 1]

Experimental

Crystal data

  • C6H11N3O5·H2O

  • Mr = 223.19

  • Orthorhombic, P 21 21 21

  • a = 5.9687 (3) Å

  • b = 7.7395 (4) Å

  • c = 20.9768 (11) Å

  • V = 969.02 (9) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.14 mm−1

  • T = 150 K

  • 0.50 × 0.05 × 0.05 mm
Data collection

  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan DENZO/SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]) Tmin = 0.86, Tmax = 0.99

  • 7317 measured reflections

  • 1296 independent reflections

  • 792 reflections with I > 2σ(I)

  • Rint = 0.053
Refinement

  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.073

  • S = 0.80

  • 1095 reflections

  • 136 parameters

  • H-atom parameters constrained

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.36 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H11⋯O4i 0.81 1.96 2.760 (4) 169
O4—H41⋯O6i 0.83 1.83 2.648 (4) 171
O15—H151⋯O4ii 0.83 2.19 2.989 (4) 163
O8—H81⋯O15iii 0.83 1.90 2.732 (4) 177
O6—H62⋯O1iv 0.81 1.98 2.755 (4) 162
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [-x+{\script{3\over 2}}, -y+1, z-{\script{1\over 2}}]; (iii) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]; (iv) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: COLLECT (Nonius, 2001[Nonius (2001). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: CAMERON (Watkin et al., 1996[Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON. Chemical Crystallography Laboratory, Oxford, UK.]); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808022563/lh2654sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808022563/lh2654Isup2.hkl

checkCIF report


Comment top

The range of rare sugars that are now readily available has increased in recent years due to both chemical (Beadle et al., 1992) and biotechnological (Izumori, 2002,2006; Granstrom et al., 2004) advances. Interest in rare sugars has been prompted by the search for low calorie alternative food stuffs (Sun et al., 2007; Levin, 2002; Skytte, 2002) and also a potential range of other beneficial therapeutic properties (Nakajima et al., 2004; Sui et al., 2005; Hossain et al., 2006).

The methodology developed by Izumori (2002,2006) for the interconversion of tetroses, pentoses and hexoses by enzymatic oxidation, inversion at C3 with a single epimerase, and reduction to the aldose has been seen to be generally applicable for the 1-deoxy ketohexoses (Yoshihara et al., 2008). The viability of the methodology for the corresponding azido substituted systems was investigated with the synthesis 6-azido-6-deoxy-L-galactose 3 by microbial oxidation of 1-azido-1-deoxy-D-galactitol 1 with K.Pneumoniae 40bR followed by isomerization to the aldose 3 using D-arabinose isomerase (Fig. 1).

6-Azido-6-deoxy sugars have been little investigated and may have similar interesting properties. They are also of interest as Click Chemistry substrates, allowing a wide range of novel sugar substituted triazoles to be synthesized quickly, utilizing a few easy and reliable reactions. A click reaction should be wide in scope and easy to perform, use only readily available reagents, and be insensitive to oxygen and water. Reaction work-up and purification uses benign solvents and avoids chromatography. In many cases the reaction can be performed in, or on top of water; (Kolb and Sharpless, 2003) presenting an obvious environmental benefit to many existing precedures.

6-Azido-6-deoxy-L-galactose monohydrate crystallized solely in the α-pyranose form with the 6-membered ring adopting a chair conformation (Fig. 2). Each molecule acts as a donor and acceptor for 5 hydrogen bonds. A non standard hydrogen bond to the terminal azide nitrogen has been removed from the packing diagrams. The structure exists as discrete chains of molecules run ning parallel to the a-axis and exhibits no unusual crystal packing features. As is common with these materials, the azide group is non linear [N12—N13—N14 171.91° (6)] (Chesterton et al. 2006).

Related literature top

For related literature see: Beadle et al. (1992); Izumori (2002, 2006); Granstrom et al. (2004); Sun et al. (2007); Levin (2002); Skytte (2002); Nakajima et al. (2004); Sui et al. (2005); Hossain et al. (2006); Kolb & Sharpless (2003).

For related literature, see: Chesterton et al. (2006); Görbitz (1999); Larson (1970); Prince (1982); Watkin (1994); Yoshihara et al. (2008).

Experimental top

The title compound was crystallized from water: m.p. 345 - 348K; [α]D21-52.3 (c, 1.05 in H2O).

Refinement top

In the absence of significant anomalous scattering, Friedel pairs were merged. The relatively large ratio of minimum to maximum corrections applied in the multiscan process (1:1.15) reflect changes in the illuminated volume of the crystal. Changes in illuminated volume 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, 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.

A few very weak reflections were ignored in the refinement, and was therefore carried out on only 1095 reflections, not the full 1296 originally collected.

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
[Figure 1] Fig. 1. Synthetic scheme.
[Figure 2] Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 3] Fig. 3. The packing diagram for the title compound projected along the b-axis.
6-Azido-6-deoxy-α-L-galactose monohydrate top
Crystal data top
C6H11N3O5·H2OF(000) = 472
Mr = 223.19Dx = 1.530 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2018 reflections
a = 5.9687 (3) Åθ = 5–27°
b = 7.7395 (4) ŵ = 0.14 mm−1
c = 20.9768 (11) ÅT = 150 K
V = 969.02 (9) Å3Plate, colourless
Z = 40.50 × 0.05 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer		792 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
ω scansθmax = 27.4°, θmin = 5.2°
Absorption correction: multi-scan
DENZO/SCALEPACK (Otwinowski & Minor, 1997)		h = −7→7
Tmin = 0.86, Tmax = 0.99k = −9→10
7317 measured reflectionsl = −26→27
1296 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)] = 0.033H-atom parameters constrained
wR(F2) = 0.073 w = 1/[σ2(F2)]
S = 0.80(Δ/σ)max = 0.000272
1095 reflectionsΔρmax = 0.37 e Å−3
136 parametersΔρmin = −0.36 e Å−3
0 restraints
Crystal data top
C6H11N3O5·H2OV = 969.02 (9) Å3
Mr = 223.19Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.9687 (3) ŵ = 0.14 mm−1
b = 7.7395 (4) ÅT = 150 K
c = 20.9768 (11) Å0.50 × 0.05 × 0.05 mm
Data collection top
Nonius KappaCCD
diffractometer		1296 independent reflections
Absorption correction: multi-scan
DENZO/SCALEPACK (Otwinowski & Minor, 1997)		792 reflections with I > 2σ(I)
Tmin = 0.86, Tmax = 0.99Rint = 0.053
7317 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0330 restraints
wR(F2) = 0.073H-atom parameters constrained
S = 0.80Δρmax = 0.37 e Å−3
1095 reflectionsΔρmin = −0.36 e Å−3
136 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.7366 (3)0.6574 (2)0.68646 (7)0.0240
C20.8440 (4)0.5120 (3)0.65721 (11)0.0207
C30.8824 (4)0.3657 (4)0.70492 (11)0.0198
O41.0088 (3)0.4176 (3)0.76006 (7)0.0239
C50.6592 (4)0.2991 (4)0.72879 (11)0.0185
O60.7020 (3)0.1614 (2)0.77263 (7)0.0218
C70.5141 (4)0.2396 (3)0.67315 (11)0.0203
O80.6145 (3)0.0996 (3)0.64297 (8)0.0276
O90.4833 (3)0.3840 (2)0.63098 (7)0.0228
C100.6911 (4)0.4467 (4)0.60441 (11)0.0223
C110.6234 (5)0.5891 (4)0.55904 (11)0.0286
N120.5055 (4)0.5214 (3)0.50147 (10)0.0336
N130.3088 (4)0.4780 (4)0.51035 (10)0.0347
N140.1278 (4)0.4350 (5)0.51097 (11)0.0585
O150.7358 (3)0.5841 (3)0.38440 (7)0.0372
H210.98660.54680.63850.0251*
H310.96060.26840.68300.0246*
H510.57930.39280.75110.0236*
H710.36160.20560.68780.0253*
H1010.76430.35120.58170.0281*
H1110.75960.64320.54320.0344*
H1120.53290.67740.58030.0343*
H1520.65320.53770.41050.0561*
H110.82390.73120.69830.0373*
H411.11030.48660.75140.0381*
H1510.65820.60440.35270.0563*
H810.50110.04230.63350.0441*
H620.58440.14680.79090.0334*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0231 (9)0.0184 (10)0.0306 (9)0.0001 (9)0.0005 (9)−0.0023 (9)
C20.0192 (13)0.0202 (16)0.0226 (12)0.0007 (13)0.0055 (12)−0.0010 (13)
C30.0164 (12)0.0236 (18)0.0193 (12)0.0008 (13)−0.0022 (11)−0.0033 (13)
O40.0215 (9)0.0256 (11)0.0247 (9)−0.0089 (9)−0.0044 (8)0.0023 (9)
C50.0192 (13)0.0169 (16)0.0193 (12)−0.0005 (12)0.0002 (11)0.0020 (13)
O60.0193 (9)0.0225 (11)0.0236 (8)0.0003 (9)0.0017 (8)0.0046 (10)
C70.0217 (13)0.0184 (14)0.0207 (13)0.0012 (14)−0.0002 (13)−0.0003 (13)
O80.0269 (10)0.0248 (11)0.0310 (9)−0.0028 (10)−0.0001 (9)−0.0065 (10)
O90.0194 (9)0.0267 (11)0.0223 (9)−0.0011 (9)0.0005 (8)0.0043 (9)
C100.0218 (14)0.0238 (16)0.0213 (12)0.0001 (13)0.0043 (12)0.0004 (13)
C110.0293 (15)0.0334 (17)0.0232 (13)−0.0028 (16)−0.0001 (12)0.0066 (15)
N120.0253 (12)0.0542 (19)0.0213 (11)−0.0009 (13)0.0003 (11)0.0049 (13)
N130.0364 (15)0.0501 (19)0.0174 (13)0.0037 (14)0.0003 (11)0.0006 (13)
N140.0350 (16)0.107 (3)0.0336 (15)−0.0156 (19)0.0022 (14)−0.0111 (19)
O150.0357 (10)0.0476 (13)0.0283 (9)0.0078 (12)0.0071 (9)0.0092 (11)
Geometric parameters (Å, º) top
O1—C21.433 (3)C7—O91.437 (3)
O1—H110.812C7—H710.997
C2—C31.529 (3)O8—H810.834
C2—C101.522 (3)O9—C101.444 (3)
C2—H210.975C10—C111.511 (4)
C3—O41.438 (3)C10—H1010.982
C3—C51.514 (3)C11—N121.493 (3)
C3—H310.999C11—H1110.973
O4—H410.828C11—H1120.978
C5—O61.431 (3)N12—N131.235 (3)
C5—C71.524 (3)N13—N141.130 (3)
C5—H510.986O15—H1520.820
O6—H620.807O15—H1510.825
C7—O81.391 (3)
C2—O1—H11113.3C5—C7—O9108.0 (2)
O1—C2—C3111.62 (19)O8—C7—O9112.39 (18)
O1—C2—C10107.7 (2)C5—C7—H71111.2
C3—C2—C10108.7 (2)O8—C7—H71109.2
O1—C2—H21110.3O9—C7—H71106.2
C3—C2—H21109.7C7—O8—H81100.0
C10—C2—H21108.8C7—O9—C10112.87 (18)
C2—C3—O4113.5 (2)C2—C10—O9110.25 (19)
C2—C3—C5109.7 (2)C2—C10—C11112.1 (2)
O4—C3—C5106.90 (18)O9—C10—C11104.97 (19)
C2—C3—H31109.1C2—C10—H101109.6
O4—C3—H31109.6O9—C10—H101108.5
C5—C3—H31107.9C11—C10—H101111.2
C3—O4—H41112.7C10—C11—N12112.3 (3)
C3—C5—O6108.02 (19)C10—C11—H111107.7
C3—C5—C7110.46 (18)N12—C11—H111105.6
O6—C5—C7111.6 (2)C10—C11—H112111.8
C3—C5—H51109.4N12—C11—H112110.7
O6—C5—H51109.2H111—C11—H112108.4
C7—C5—H51108.1C11—N12—N13114.9 (2)
C5—O6—H62104.7N12—N13—N14171.9 (3)
C5—C7—O8109.8 (2)H152—O15—H151106.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O15—H152···N120.822.112.856 (4)152
O1—H11···O4i0.811.962.760 (4)169
O4—H41···O6i0.831.832.648 (4)171
O15—H151···O4ii0.832.192.989 (4)163
O8—H81···O15iii0.831.902.732 (4)177
O6—H62···O1iv0.811.982.755 (4)162
Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+3/2, −y+1, z−1/2; (iii) x−1/2, −y+1/2, −z+1; (iv) −x+1, y−1/2, −z+3/2.

Experimental details

Crystal data
Chemical formulaC6H11N3O5·H2O
Mr223.19
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)5.9687 (3), 7.7395 (4), 20.9768 (11)
V (Å3)969.02 (9)
Z4
Radiation typeMo Kα
µ (mm−1)0.14
Crystal size (mm)0.50 × 0.05 × 0.05
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
DENZO/SCALEPACK (Otwinowski & Minor, 1997)
Tmin, Tmax0.86, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections		7317, 1296, 792
Rint0.053
(sin θ/λ)max (Å−1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.073, 0.80
No. of reflections1095
No. of parameters136
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.37, −0.36

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···AD—HH···AD···AD—H···A
O1—H11···O4i0.811.962.760 (4)169
O4—H41···O6i0.831.832.648 (4)171
O15—H151···O4ii0.832.192.989 (4)163
O8—H81···O15iii0.831.902.732 (4)177
O6—H62···O1iv0.811.982.755 (4)162
Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+3/2, −y+1, z−1/2; (iii) x−1/2, −y+1/2, −z+1; (iv) −x+1, y−1/2, −z+3/2.
 

Acknowledgements

This work was supported in part by the Programme for the Promotion of Basic Research Activities for Innovative Bio­sciences (PROBRAIN). The authors also thank the Oxford University Chemical Crystallography Service for use of the instruments.

References

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ISSN: 2056-9890
Volume 64| Part 8| August 2008| Pages o1568-o1569
doi:10.1107/S1600536808022563
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