research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 72| Part 3| March 2016| Pages 340-342
doi:10.1107/S2056989016002164

N-(2-Acetamido-2-de­­oxy-β-D-gluco­pyranos­yl)-N-(3-azido­prop­yl)-O-methyl­hydroxyl­amine

CROSSMARK_Color_square_no_text.svg
Stefan Munneke,a Bridget L. Stocker,a Mattie S. M. Timmera* and Graeme J. Gainsfordb

aSchool of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand, and bCallaghan Innovation, PO Box 31-310, Lower Hutt 5040, New Zealand
*Correspondence e-mail: mattie.timmer@vuw.ac.nz

Edited by A. J. Lough, University of Toronto, Canada (Received 19 November 2015; accepted 3 February 2016; online 17 February 2016)

The structure of the title compound, C12H23N5O6, solved using adequate data from a thin crystal plate, confirmed that this useful glycoconjugate was obtained in the ring-closed β-pyran­ose configuration with 4C1 conformation. The mol­ecules are bound by O—H⋯O(OH) hydrogen bonds, notably in a zigzag C(2) chain along the short b (screw) axis, supplemented with an R22(12) O—H⋯O(carbon­yl) link along the a axis and other C(2) links. The absolute configuration was not unambiguously determined but was known from the synthetic chemistry, which used natural 2-acetamido-2-de­oxy-D-glucose as the starting material.

CCDC reference: 1451795

1. Chemical context

Oxyamine glycosides, such as the title compound, can be utilised for the synthesis of a wide variety of complex glycoconjugates (Kwase et al.,2014[Kwase, Y. A., Cochran, M. & Nitz, M. (2014). Modern Synthetic Methods in Carbohydrate Chemistry: From Monosaccharides to Complex Glycoconjugates, pp. 67-94, edited by D. B. Werz & S. Vidal. Wiley-VCH Verlag GmbH & Co. KGaA.]; Munneke et al., 2015[Munneke, S., Prevost, J. R. C., Painter, G. F., Stocker, B. L. & Timmer, M. S. M. (2015). Org. Lett. 17, 624-627.]; Wang et al., 2013[Wang, Z., Chinoy, Z. S., Ambre, S. G., Peng, W., McBride, R., de Vries, R. P., Glushka, J., Paulson, J. C. & Boons, G.-J. (2013). Science, 341, 379-383.]). In particular, the use of an oxyamine bifunctional linker allows for the conjugation of carbohydrates to a substrate of choice, such as proteins, fluoro­phores and biotin. The crystal structure analysis confirmed that the glycoconjugate was obtained in the ring-closed β-pyran­ose configuration.

[Scheme 1]

2. Structural commentary

The title compound crystallizes with one independent mol­ecule in the asymmetric unit (Fig. 1[link]) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The absolute configuration was not ambiguously determined but was known from the synthetic chemistry.

[Figure 1]
Figure 1
View of the title mol­ecule, drawn with 25% probability displacement ellipsoids.

3. Supra­molecular features

The mol­ecules are bound together with a comprehensive net of O—H⋯O(alcohol) hydrogen bonds, as well as one N—H⋯O(carbon­yl) and one O—H⋯O(carbon­yl) hydrogen bond (Table 1[link]). The basic inter­actions are chain C(2) and C(8) types which combine to form a larger chain and rings e.g. R22(12), as shown on the right of Fig. 2[link].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O3—H3O⋯O3i 0.84 1.79 2.616 (5) 167
O4—H4O⋯O2i 0.80 (7) 2.23 (7) 3.027 (4) 170 (8)
O5—H5O⋯O5ii 0.90 (8) 1.98 (8) 2.855 (4) 167 (7)
N2—H2N⋯O2iii 0.93 (7) 2.08 (6) 2.961 (5) 158 (5)
Symmetry codes: (i) [-x, y-{\script{1\over 2}}, -z+1]; (ii) [-x+1, y+{\script{1\over 2}}, -z+1]; (iii) x, y-1, z.
[Figure 2]
Figure 2
The unit-cell contents viewed along approximately the b axis. Some inter­molecular binding contacts are shown as blue dotted lines. [Symmetry codes: (i) −x, y + [{1\over 2}], 1 − z; (ii) 1 − x, y − [{1\over 2}], 1 − z; (iii) 1 − x, y + [{1\over 2}], 1 − z.]

4. Database survey

The Cambridge Structural Database (CSD, Version 5.36, update 3; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]) was searched for N-alkyl-N-(tetra­hydro-2H-pyran-2-yl)oxyamines, and two structures were found, both of which are N-β-glycosyl­oxyamines, viz. an N-β-gluco­pyran­osyloxyamine (Langenhan et al., 2005[Langenhan, J. M., Peters, N. R., Guzei, I. A., Hoffmann, F. M. & Thorson, J. S. (2005). Proc. Nat. Acad. Sci. USA, 102, 12305-12310.]) and an N-β-galacto­pyran­osyloxyamine (Renaudet & Dumy, 2002[Renaudet, O. & Dumy, P. (2002). Tetrahedron, 58, 2127-2135.]). Inter­estingly, all three structures have a similar conformation around the anomeric linkage, with O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of 62.9 (8) and 115.6 (2) for the glu­cosyl­oxyamine derivative, 50.8 (1) and 126.3 (8) for the galactosyl­oxyamine and 64.2 (4) and 127.1 (3) for the title compound (Fig. 3[link]). A configuration that allows both the meth­oxy group to adopt a pseudoaxial orientation, and positions the nitro­gen for optimal overlap between the nitro­gen lone pair and the C1—O1 σ* (n → σ* inter­action).

[Figure 3]
Figure 3
The O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of N-glycosyl­oxyamines: left – title compound; middle – N-β-gluco­pyran­osyl­oxy­amine (Langenhan et al., 2005[Langenhan, J. M., Peters, N. R., Guzei, I. A., Hoffmann, F. M. & Thorson, J. S. (2005). Proc. Nat. Acad. Sci. USA, 102, 12305-12310.]); right – N-β-galacto­pyran­osyl­oxy­amine (Renaudet & Dumy, 2002[Renaudet, O. & Dumy, P. (2002). Tetrahedron, 58, 2127-2135.]).

5. Synthesis and crystallization

N-(2-Acetamido-2-de­oxy-β-D-gluco­pyranos­yl)-N-(3-azidoprop­yl)-O-methyl­hydroxyl­amine was prepared as described in Munneke et al. (2015[Munneke, S., Prevost, J. R. C., Painter, G. F., Stocker, B. L. & Timmer, M. S. M. (2015). Org. Lett. 17, 624-627.]) from 3-azido-1-meth­oxy­amino­propane and commercially available N-acetyl­glucosa­mine. The title compound was recrystallized from freshly distilled MeOH–Et2O (1:8 v/v).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All methyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bond. All other O,C-bound H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 0.99 (methyl­ene) and 1.0 (tertiary) Å, O—H = 0.84 Å and with Uiso(H) = 1.2Ueq(C,O). The nitro­gen H atom was located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(N).

Table 2
Experimental details

Crystal data
Chemical formula C12H23N5O6
Mr 333.35
Crystal system, space group Monoclinic, P21
Temperature (K) 120
a, b, c (Å) 13.5605 (18), 4.7386 (3), 14.140 (2)
β (°) 118.181 (19)
V (Å3) 800.9 (2)
Z 2
Radiation type Cu Kα
μ (mm−1) 0.95
Crystal size (mm) 0.57 × 0.14 × 0.02
 
Data collection
Diffractometer Agilent SuperNova Dual Source diffractometer with an Atlas detector
Absorption correction Gaussian (CrysAlis PRO; Agilent, 2014[Agilent (2014). CryslAis PRO. Agilent Technologies Ltd, Yarnton, England.])
Tmin, Tmax 0.792, 0.985
No. of measured, independent and observed [I > 2σ(I)] reflections 6061, 2355, 2073
Rint 0.053
(sin θ/λ)max (Å−1) 0.595
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.059, 0.165, 1.03
No. of reflections 2355
No. of parameters 221
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.39, −0.32
Absolute structure Flack x determined using 619 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons & Flack, 2004[Parsons, S. & Flack, H. (2004). Acta Cryst. A60, s61.])
Absolute structure parameter 0.2 (4)
Computer programs: CrysAlis PRO (Agilent, 2014[Agilent (2014). CryslAis PRO. Agilent Technologies Ltd, Yarnton, England.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2012 and SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

CCDC reference: 1451795

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989016002164/lh5798sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989016002164/lh5798Isup2.hkl

checkCIF report


Chemical context top

Oxyamine glycosides, such as the title compound, can be utilized for the synthesis of a wide variety of complex glycoconjugates (Kwase et al.,2014; Munneke et al., 2015; Wang et al., 2013). In particular, the use of an oxyamine bifunctional linker allows for the conjugation of carbohydrates to a substrate of choice, such as proteins, fluoro­phores and biotin. The crystal structure analysis confirmed that the glycoconjugate was obtained in the ring-closed β-pyran­ose configuration.

Structural commentary top

The title compound crystallizes with one independent molecule in the asymmetric unit (Fig. 1) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The absolute configuration was not ambiguously determined but was known from the synthetic chemistry.

Supra­molecular features top

The molecules are bound together with a comprehensive net of O—H···O(alcohol) hydrogen bonds, as well as one N—H···O(carbonyl) and one O—H···O(carbonyl) hydrogen bond (Table 1). The basic inter­actions are chain C(2) and C(8) types which combine to form larger chain and rings e.g. R22(12), as shown on the right of Fig. 2.

Database survey top

The Cambridge Structural Database (CSD, Version 5.36, update 3; Groom & Allen, 2014) was searched for N-alkyl-N-(tetra­hydro-2H-pyran-2-yl)oxyamines, and two structures were found, both of which are N-β-glycosyl­oxyamines, viz. an N-β-gluco­pyran­osyloxyamine (Langenhan et al., 2005) and an N-β-galacto­pyran­osyloxyamine (Renaudet & Dumy, 2002). Inter­estingly, all three structures have a similar conformation around the anomeric linkage, with O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of 62.9 (8) and 115.6 (2) for the glu­cosyl­oxyamine derivative, 50.8 (1) and 126.3 (8) for the galactosyl­oxyamine and 64.2 (4) and 127.1 (3) for the title compound (Fig. 3). A configuration that allows both the meth­oxy group to adopt a pseudoaxial orientation, and positions the nitro­gen for optimal overlap between the nitro­gen lone pair and the C1—O1 σ* (n → σ* inter­action).

Synthesis and crystallization top

\ N-(2-Acetamido-2-de­oxy-β-D-gluco­pyran­osyl)-N-(3-\ azido­propyl) -O-methyl­hydroxyl­amine was prepared as described in Munneke et al. (2015) from 3-azido-1-meth­oxy­amino­propane and commercially available N-acetyl­glucosamine. The title compound was recrystallized from freshly distilled MeOH–Et2O (1:8 v/v).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. A l l me thyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bond. All other O,C-bound H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 0.99 (methyl­ene) and 1.0 (tertiary) Å, O—H = 0.84 Å and with Uiso(H) = 1.2Ueq(C,O). The nitro­gen H atom was located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(N).

Related literature top

For related structures, see N-β-glucopyranosyloxyamine (Langenhan et al., 2005) and N-β-galactopyranosyloxyamine (Renaudet & Dumy, 2002)

Structure description top

Oxyamine glycosides, such as the title compound, can be utilized for the synthesis of a wide variety of complex glycoconjugates (Kwase et al.,2014; Munneke et al., 2015; Wang et al., 2013). In particular, the use of an oxyamine bifunctional linker allows for the conjugation of carbohydrates to a substrate of choice, such as proteins, fluoro­phores and biotin. The crystal structure analysis confirmed that the glycoconjugate was obtained in the ring-closed β-pyran­ose configuration.

The title compound crystallizes with one independent molecule in the asymmetric unit (Fig. 1) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The absolute configuration was not ambiguously determined but was known from the synthetic chemistry.

The molecules are bound together with a comprehensive net of O—H···O(alcohol) hydrogen bonds, as well as one N—H···O(carbonyl) and one O—H···O(carbonyl) hydrogen bond (Table 1). The basic inter­actions are chain C(2) and C(8) types which combine to form larger chain and rings e.g. R22(12), as shown on the right of Fig. 2.

The Cambridge Structural Database (CSD, Version 5.36, update 3; Groom & Allen, 2014) was searched for N-alkyl-N-(tetra­hydro-2H-pyran-2-yl)oxyamines, and two structures were found, both of which are N-β-glycosyl­oxyamines, viz. an N-β-gluco­pyran­osyloxyamine (Langenhan et al., 2005) and an N-β-galacto­pyran­osyloxyamine (Renaudet & Dumy, 2002). Inter­estingly, all three structures have a similar conformation around the anomeric linkage, with O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of 62.9 (8) and 115.6 (2) for the glu­cosyl­oxyamine derivative, 50.8 (1) and 126.3 (8) for the galactosyl­oxyamine and 64.2 (4) and 127.1 (3) for the title compound (Fig. 3). A configuration that allows both the meth­oxy group to adopt a pseudoaxial orientation, and positions the nitro­gen for optimal overlap between the nitro­gen lone pair and the C1—O1 σ* (n → σ* inter­action).

For related structures, see N-β-glucopyranosyloxyamine (Langenhan et al., 2005) and N-β-galactopyranosyloxyamine (Renaudet & Dumy, 2002)

Synthesis and crystallization top

\ N-(2-Acetamido-2-de­oxy-β-D-gluco­pyran­osyl)-N-(3-\ azido­propyl) -O-methyl­hydroxyl­amine was prepared as described in Munneke et al. (2015) from 3-azido-1-meth­oxy­amino­propane and commercially available N-acetyl­glucosamine. The title compound was recrystallized from freshly distilled MeOH–Et2O (1:8 v/v).

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. A l l me thyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bond. All other O,C-bound H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 0.99 (methyl­ene) and 1.0 (tertiary) Å, O—H = 0.84 Å and with Uiso(H) = 1.2Ueq(C,O). The nitro­gen H atom was located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(N).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2012 (Sheldrick, 2015) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. View of the title molecule, drawn with 25% probability displacement ellipsoids.
[Figure 2] Fig. 2. The unit-cell contents viewed along approximately the b axis. Some intermolecular binding contacts are shown as blue dotted lines. [Symmetry codes: (i) −x, y + 1/2, 1 − z; (ii) 1 − x, y − 1/2, 1 − z; (iii) 1 − x, y + 1/2, 1 − z.]
[Figure 3] Fig. 3. The O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of N-glycosyloxyamines.
N-(2-Acetamido-2-deoxy-β-D-glucopyranosyl)-N-(3-azidopropyl)-O-methylhydroxylamine top
Crystal data top
C12H23N5O6F(000) = 356
Mr = 333.35Dx = 1.382 Mg m−3
Monoclinic, P21Cu Kα radiation, λ = 1.54184 Å
a = 13.5605 (18) ÅCell parameters from 2327 reflections
b = 4.7386 (3) Åθ = 3.7–75.3°
c = 14.140 (2) ŵ = 0.95 mm−1
β = 118.181 (19)°T = 120 K
V = 800.9 (2) Å3Needle, colourless
Z = 20.57 × 0.14 × 0.02 mm
Data collection top
Agilent SuperNova Dual Source
diffractometer with an Atlas detector		2355 independent reflections
Radiation source: sealed X-ray tube, SuperNova (Cu) X-ray Source2073 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.053
Detector resolution: 10.6501 pixels mm-1θmax = 66.6°, θmin = 3.6°
ω scansh = −16→16
Absorption correction: gaussian
(CrysAlis PRO; Agilent, 2014)		k = −5→5
Tmin = 0.792, Tmax = 0.985l = −17→16
6061 measured reflections
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.059 w = 1/[σ2(Fo2) + (0.1194P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.165(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.39 e Å−3
2355 reflectionsΔρmin = −0.31 e Å−3
221 parametersAbsolute structure: Flack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004)
1 restraintAbsolute structure parameter: 0.2 (4)
Crystal data top
C12H23N5O6V = 800.9 (2) Å3
Mr = 333.35Z = 2
Monoclinic, P21Cu Kα radiation
a = 13.5605 (18) ŵ = 0.95 mm−1
b = 4.7386 (3) ÅT = 120 K
c = 14.140 (2) Å0.57 × 0.14 × 0.02 mm
β = 118.181 (19)°
Data collection top
Agilent SuperNova Dual Source
diffractometer with an Atlas detector		2355 independent reflections
Absorption correction: gaussian
(CrysAlis PRO; Agilent, 2014)		2073 reflections with I > 2σ(I)
Tmin = 0.792, Tmax = 0.985Rint = 0.053
6061 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.059H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.165Δρmax = 0.39 e Å−3
S = 1.03Δρmin = −0.31 e Å−3
2355 reflectionsAbsolute structure: Flack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004)
221 parametersAbsolute structure parameter: 0.2 (4)
1 restraint
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.3682 (2)0.2828 (6)0.5792 (2)0.0314 (7)
O20.1361 (3)0.5357 (7)0.7397 (3)0.0378 (8)
O30.0442 (2)0.1637 (7)0.5080 (3)0.0368 (8)
H3O0.007 (4)0.017 (14)0.498 (6)0.055*
O40.1155 (3)0.0380 (8)0.3491 (3)0.0426 (8)
H4O0.050 (6)0.058 (17)0.328 (5)0.064*
O50.4546 (3)0.2456 (8)0.4382 (3)0.0401 (8)
H5O0.486 (6)0.385 (16)0.486 (6)0.060*
O60.4312 (3)0.5384 (7)0.7784 (3)0.0369 (7)
N10.4434 (3)0.2390 (8)0.7677 (3)0.0329 (8)
N20.2088 (3)0.1158 (8)0.7250 (3)0.0326 (8)
H2N0.205 (4)−0.077 (14)0.732 (4)0.039*
N30.7789 (3)−0.1042 (10)0.8833 (4)0.0480 (11)
N40.8722 (3)−0.1684 (10)0.8948 (4)0.0451 (10)
N50.9545 (4)−0.2571 (12)0.9039 (4)0.0566 (12)
C10.3557 (3)0.1498 (10)0.6645 (4)0.0308 (9)
H10.3616−0.05910.65850.037*
C20.2369 (3)0.2191 (9)0.6435 (3)0.0304 (9)
H20.22760.42890.63870.036*
C30.1552 (3)0.0914 (9)0.5340 (4)0.0318 (9)
H30.1626−0.11870.53920.038*
C40.1797 (3)0.1921 (9)0.4452 (4)0.0320 (9)
H40.16130.39740.43170.038*
C50.3030 (3)0.1481 (10)0.4789 (4)0.0338 (10)
H50.3197−0.05870.48690.041*
C60.3382 (4)0.2715 (11)0.4006 (4)0.0349 (9)
H6A0.29770.17340.33080.042*
H6B0.31720.47350.38900.042*
C70.1536 (3)0.2815 (10)0.7623 (4)0.0324 (9)
C80.1154 (4)0.1435 (11)0.8351 (4)0.0436 (11)
H8A0.16270.20700.90900.065*
H8B0.1212−0.06190.83130.065*
H8C0.03750.19550.81230.065*
C90.4282 (4)0.5914 (10)0.8765 (4)0.0395 (11)
H9A0.49770.52400.93700.059*
H9B0.36440.49190.87570.059*
H9C0.42030.79450.88420.059*
C100.5538 (3)0.1952 (11)0.7742 (4)0.0389 (11)
H10A0.56170.32270.72270.047*
H10B0.5589−0.00140.75320.047*
C110.6489 (4)0.2502 (12)0.8862 (4)0.0443 (11)
H11A0.64410.44740.90680.053*
H11B0.64050.12400.93780.053*
C120.7623 (4)0.2026 (12)0.8934 (4)0.0451 (12)
H12A0.76750.30740.83530.054*
H12B0.82160.27350.96300.054*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0257 (13)0.0269 (16)0.0409 (16)−0.0022 (12)0.0150 (12)0.0014 (13)
O20.0370 (16)0.0236 (16)0.056 (2)0.0021 (13)0.0245 (15)0.0010 (15)
O30.0235 (13)0.0265 (16)0.060 (2)−0.0025 (12)0.0190 (14)−0.0003 (15)
O40.0270 (15)0.047 (2)0.0476 (19)−0.0046 (16)0.0129 (14)−0.0117 (17)
O50.0322 (15)0.0397 (19)0.0533 (19)−0.0004 (14)0.0243 (14)−0.0017 (17)
O60.0412 (17)0.0222 (15)0.0421 (17)−0.0018 (14)0.0152 (14)0.0019 (14)
N10.0277 (17)0.0250 (19)0.042 (2)0.0011 (14)0.0130 (15)0.0004 (15)
N20.0313 (17)0.0212 (18)0.049 (2)0.0013 (14)0.0223 (16)0.0030 (15)
N30.033 (2)0.042 (2)0.066 (3)−0.0007 (19)0.021 (2)0.001 (2)
N40.038 (2)0.042 (2)0.051 (2)−0.0025 (18)0.0174 (19)0.0016 (19)
N50.036 (2)0.055 (3)0.079 (3)0.003 (2)0.027 (2)−0.002 (3)
C10.0266 (19)0.027 (2)0.037 (2)0.0008 (17)0.0136 (17)0.0035 (17)
C20.0266 (19)0.022 (2)0.045 (2)0.0031 (16)0.0187 (18)0.0052 (18)
C30.0256 (19)0.021 (2)0.047 (2)0.0000 (16)0.0160 (18)0.0006 (18)
C40.027 (2)0.026 (2)0.041 (2)0.0014 (17)0.0143 (18)0.0008 (19)
C50.0249 (19)0.033 (2)0.042 (2)0.0018 (18)0.0146 (17)0.0022 (19)
C60.033 (2)0.034 (2)0.039 (2)−0.002 (2)0.0172 (18)0.000 (2)
C70.0297 (19)0.022 (2)0.045 (2)−0.0016 (17)0.0173 (18)−0.0012 (18)
C80.056 (3)0.028 (2)0.061 (3)0.000 (2)0.039 (2)0.003 (2)
C90.042 (2)0.030 (2)0.041 (2)−0.0021 (19)0.016 (2)−0.004 (2)
C100.027 (2)0.040 (3)0.044 (3)0.0000 (19)0.0112 (19)0.001 (2)
C110.034 (2)0.044 (3)0.046 (3)0.001 (2)0.012 (2)−0.001 (2)
C120.033 (2)0.040 (3)0.048 (3)−0.002 (2)0.007 (2)0.000 (2)
Geometric parameters (Å, º) top
O1—C51.420 (6)C3—C41.520 (6)
O1—C11.441 (5)C3—H31.0000
O2—C71.240 (6)C4—C51.521 (5)
O3—C31.413 (5)C4—H41.0000
O3—H3O0.84 (8)C5—C61.515 (6)
O4—C41.421 (6)C5—H51.0000
O4—H4O0.80 (7)C6—H6A0.9900
O5—C61.413 (5)C6—H6B0.9900
O5—H5O0.90 (8)C7—C81.502 (6)
O6—C91.430 (6)C8—H8A0.9800
O6—N11.445 (5)C8—H8B0.9800
N1—C11.443 (6)C8—H8C0.9800
N1—C101.470 (5)C9—H9A0.9800
N2—C71.352 (6)C9—H9B0.9800
N2—C21.459 (5)C9—H9C0.9800
N2—H2N0.93 (7)C10—C111.520 (6)
N3—N41.235 (6)C10—H10A0.9900
N3—C121.488 (7)C10—H10B0.9900
N4—N51.141 (6)C11—C121.510 (7)
C1—C21.529 (5)C11—H11A0.9900
C1—H11.0000C11—H11B0.9900
C2—C31.539 (6)C12—H12A0.9900
C2—H21.0000C12—H12B0.9900
C5—O1—C1112.0 (3)C6—C5—H5109.1
C3—O3—H3O109.5C4—C5—H5109.1
C4—O4—H4O112 (5)O5—C6—C5111.9 (3)
C6—O5—H5O106 (5)O5—C6—H6A109.2
C9—O6—N1109.4 (3)C5—C6—H6A109.2
C1—N1—O6108.2 (3)O5—C6—H6B109.2
C1—N1—C10110.6 (3)C5—C6—H6B109.2
O6—N1—C10107.2 (3)H6A—C6—H6B107.9
C7—N2—C2120.9 (4)O2—C7—N2122.5 (4)
C7—N2—H2N118 (3)O2—C7—C8120.9 (4)
C2—N2—H2N118 (3)N2—C7—C8116.6 (4)
N4—N3—C12114.8 (4)C7—C8—H8A109.5
N5—N4—N3172.6 (6)C7—C8—H8B109.5
O1—C1—N1110.6 (3)H8A—C8—H8B109.5
O1—C1—C2105.9 (3)C7—C8—H8C109.5
N1—C1—C2115.1 (4)H8A—C8—H8C109.5
O1—C1—H1108.4H8B—C8—H8C109.5
N1—C1—H1108.4O6—C9—H9A109.5
C2—C1—H1108.4O6—C9—H9B109.5
N2—C2—C1114.7 (3)H9A—C9—H9B109.5
N2—C2—C3109.3 (3)O6—C9—H9C109.5
C1—C2—C3107.6 (3)H9A—C9—H9C109.5
N2—C2—H2108.4H9B—C9—H9C109.5
C1—C2—H2108.4N1—C10—C11112.2 (4)
C3—C2—H2108.4N1—C10—H10A109.2
O3—C3—C4109.3 (4)C11—C10—H10A109.2
O3—C3—C2109.8 (3)N1—C10—H10B109.2
C4—C3—C2111.9 (3)C11—C10—H10B109.2
O3—C3—H3108.6H10A—C10—H10B107.9
C4—C3—H3108.6C12—C11—C10112.3 (4)
C2—C3—H3108.6C12—C11—H11A109.1
O4—C4—C3110.8 (4)C10—C11—H11A109.1
O4—C4—C5108.4 (3)C12—C11—H11B109.1
C3—C4—C5109.5 (3)C10—C11—H11B109.1
O4—C4—H4109.4H11A—C11—H11B107.9
C3—C4—H4109.4N3—C12—C11109.5 (4)
C5—C4—H4109.4N3—C12—H12A109.8
O1—C5—C6107.1 (3)C11—C12—H12A109.8
O1—C5—C4109.0 (3)N3—C12—H12B109.8
C6—C5—C4113.4 (4)C11—C12—H12B109.8
O1—C5—H5109.1H12A—C12—H12B108.2
C9—O6—N1—C1127.1 (3)C2—C3—C4—O4170.7 (3)
C9—O6—N1—C10−113.6 (4)O3—C3—C4—C5173.0 (4)
C5—O1—C1—N1164.6 (3)C2—C3—C4—C551.1 (5)
C5—O1—C1—C2−70.2 (4)C1—O1—C5—C6−170.3 (3)
O6—N1—C1—O164.2 (4)C1—O1—C5—C466.7 (4)
C10—N1—C1—O1−52.9 (5)O4—C4—C5—O1−175.5 (3)
O6—N1—C1—C2−55.6 (4)C3—C4—C5—O1−54.5 (5)
C10—N1—C1—C2−172.8 (4)O4—C4—C5—C665.3 (5)
C7—N2—C2—C1136.0 (4)C3—C4—C5—C6−173.7 (4)
C7—N2—C2—C3−103.1 (4)O1—C5—C6—O555.3 (5)
O1—C1—C2—N2−176.8 (3)C4—C5—C6—O5175.6 (4)
N1—C1—C2—N2−54.4 (5)C2—N2—C7—O2−8.8 (7)
O1—C1—C2—C361.4 (4)C2—N2—C7—C8172.2 (4)
N1—C1—C2—C3−176.2 (3)C1—N1—C10—C11−172.5 (4)
N2—C2—C3—O358.2 (4)O6—N1—C10—C1169.7 (5)
C1—C2—C3—O3−176.7 (3)N1—C10—C11—C12179.5 (4)
N2—C2—C3—C4179.7 (3)N4—N3—C12—C11−175.7 (4)
C1—C2—C3—C4−55.1 (4)C10—C11—C12—N3−69.7 (6)
O3—C3—C4—O4−67.5 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3O···O3i0.841.792.616 (5)167
O4—H4O···O2i0.80 (7)2.23 (7)3.027 (4)170 (8)
O5—H5O···O5ii0.90 (8)1.98 (8)2.855 (4)167 (7)
N2—H2N···O2iii0.93 (7)2.08 (6)2.961 (5)158 (5)
Symmetry codes: (i) −x, y−1/2, −z+1; (ii) −x+1, y+1/2, −z+1; (iii) x, y−1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3O···O3i0.841.792.616 (5)167.1
O4—H4O···O2i0.80 (7)2.23 (7)3.027 (4)170 (8)
O5—H5O···O5ii0.90 (8)1.98 (8)2.855 (4)167 (7)
N2—H2N···O2iii0.93 (7)2.08 (6)2.961 (5)158 (5)
Symmetry codes: (i) −x, y−1/2, −z+1; (ii) −x+1, y+1/2, −z+1; (iii) x, y−1, z.

Experimental details

Crystal data
Chemical formulaC12H23N5O6
Mr333.35
Crystal system, space groupMonoclinic, P21
Temperature (K)120
a, b, c (Å)13.5605 (18), 4.7386 (3), 14.140 (2)
β (°) 118.181 (19)
V (Å3)800.9 (2)
Z2
Radiation typeCu Kα
µ (mm−1)0.95
Crystal size (mm)0.57 × 0.14 × 0.02
Data collection
DiffractometerAgilent SuperNova Dual Source
diffractometer with an Atlas detector
Absorption correctionGaussian
(CrysAlis PRO; Agilent, 2014)
Tmin, Tmax0.792, 0.985
No. of measured, independent and
observed [I > 2σ(I)] reflections		6061, 2355, 2073
Rint0.053
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.059, 0.165, 1.03
No. of reflections2355
No. of parameters221
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.39, −0.31
Absolute structureFlack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004)
Absolute structure parameter0.2 (4)

Computer programs: CrysAlis PRO (Agilent, 2014), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008), SHELXL2012 (Sheldrick, 2015) and PLATON (Spek, 2009).

 

Acknowledgements

We thank Dr M. Polson of the University of Canterbury, New Zealand, for the data collection.

References

First citationAgilent (2014). CryslAis PRO. Agilent Technologies Ltd, Yarnton, England.  Google Scholar
 First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationGroom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662–671.  Web of Science CSD CrossRef CAS Google Scholar
 First citationKwase, Y. A., Cochran, M. & Nitz, M. (2014). Modern Synthetic Methods in Carbohydrate Chemistry: From Monosaccharides to Complex Glycoconjugates, pp. 67–94, edited by D. B. Werz & S. Vidal. Wiley–VCH Verlag GmbH & Co. KGaA.  Google Scholar
 First citationLangenhan, J. M., Peters, N. R., Guzei, I. A., Hoffmann, F. M. & Thorson, J. S. (2005). Proc. Nat. Acad. Sci. USA, 102, 12305–12310.  CSD CrossRef PubMed CAS Google Scholar
 First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationMunneke, S., Prevost, J. R. C., Painter, G. F., Stocker, B. L. & Timmer, M. S. M. (2015). Org. Lett. 17, 624–627.  CrossRef CAS PubMed Google Scholar
 First citationParsons, S. & Flack, H. (2004). Acta Cryst. A60, s61.  CrossRef IUCr Journals Google Scholar
 First citationRenaudet, O. & Dumy, P. (2002). Tetrahedron, 58, 2127–2135.  CSD CrossRef CAS Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
 First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationWang, Z., Chinoy, Z. S., Ambre, S. G., Peng, W., McBride, R., de Vries, R. P., Glushka, J., Paulson, J. C. & Boons, G.-J. (2013). Science, 341, 379–383.  CrossRef CAS PubMed Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 72| Part 3| March 2016| Pages 340-342
doi:10.1107/S2056989016002164
Follow Acta Cryst. E
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS