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The structure determination of an oxyamine glycoside confirmed that it was obtained in the ring-closed β-pyran­ose configuration with a 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 R_{2}^{2}(12) OH...O(carbon­yl) link along the a axis and other C(2) links.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989016002164/lh5798sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2056989016002164/lh5798Isup2.hkl
Contains datablock I

CCDC reference: 1451795

Key indicators

  • Single-crystal X-ray study
  • T = 120 K
  • Mean [sigma](C-C) = 0.007 Å
  • R factor = 0.059
  • wR factor = 0.165
  • Data-to-parameter ratio = 10.7

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.964 Note PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........ 7.15 Note PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds ............... 0.00712 Ang. PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.595 19 Report PLAT915_ALERT_3_C Low Friedel Pair Coverage ....(No Flack x Check) 63 %
Alert level G PLAT032_ALERT_4_G Std. Uncertainty on Flack Parameter Value High . 0.400 Report PLAT072_ALERT_2_G SHELXL First Parameter in WGHT Unusually Large 0.12 Report PLAT484_ALERT_4_G Round D-H..A Angle Rep for O3 .. O3 to 167 Degree PLAT791_ALERT_4_G The Model has Chirality at C1 (Chiral SPGR) R Verify PLAT791_ALERT_4_G The Model has Chirality at C2 (Chiral SPGR) R Verify PLAT791_ALERT_4_G The Model has Chirality at C3 (Chiral SPGR) R Verify PLAT791_ALERT_4_G The Model has Chirality at C4 (Chiral SPGR) S Verify PLAT791_ALERT_4_G The Model has Chirality at C5 (Chiral SPGR) R Verify PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) Still 77 % PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Th(Min) ... 3 Report PLAT955_ALERT_1_G Reported (CIF) and Actual (FCF) Lmax Differ by . 1 Units PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density 1 Note
0 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 5 ALERT level C = Check. Ensure it is not caused by an omission or oversight 12 ALERT level G = General information/check it is not something unexpected 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 7 ALERT type 3 Indicator that the structure quality may be low 7 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

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 NH···O(carbonyl) and one OH···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 NH···O(carbonyl) and one OH···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 m3
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 mm1
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 = 1616
Absorption correction: gaussian
(CrysAlis PRO; Agilent, 2014)
k = 55
Tmin = 0.792, Tmax = 0.985l = 1716
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 Å3
2355 reflectionsΔρmin = 0.31 e Å3
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 mm1
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 Å3
S = 1.03Δρmin = 0.31 e Å3
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)
H10.36160.05910.65850.037*
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)
H30.16260.11870.53920.038*
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)
H50.31970.05870.48690.041*
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*
H8B0.12120.06190.83130.065*
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*
H10B0.55890.00140.75320.047*
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—C10113.6 (4)O3—C3—C4—C5173.0 (4)
C5—O1—C1—N1164.6 (3)C2—C3—C4—C551.1 (5)
C5—O1—C1—C270.2 (4)C1—O1—C5—C6170.3 (3)
O6—N1—C1—O164.2 (4)C1—O1—C5—C466.7 (4)
C10—N1—C1—O152.9 (5)O4—C4—C5—O1175.5 (3)
O6—N1—C1—C255.6 (4)C3—C4—C5—O154.5 (5)
C10—N1—C1—C2172.8 (4)O4—C4—C5—C665.3 (5)
C7—N2—C2—C1136.0 (4)C3—C4—C5—C6173.7 (4)
C7—N2—C2—C3103.1 (4)O1—C5—C6—O555.3 (5)
O1—C1—C2—N2176.8 (3)C4—C5—C6—O5175.6 (4)
N1—C1—C2—N254.4 (5)C2—N2—C7—O28.8 (7)
O1—C1—C2—C361.4 (4)C2—N2—C7—C8172.2 (4)
N1—C1—C2—C3176.2 (3)C1—N1—C10—C11172.5 (4)
N2—C2—C3—O358.2 (4)O6—N1—C10—C1169.7 (5)
C1—C2—C3—O3176.7 (3)N1—C10—C11—C12179.5 (4)
N2—C2—C3—C4179.7 (3)N4—N3—C12—C11175.7 (4)
C1—C2—C3—C455.1 (4)C10—C11—C12—N369.7 (6)
O3—C3—C4—O467.5 (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, y1/2, z+1; (ii) x+1, y+1/2, z+1; (iii) x, y1, 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, y1/2, z+1; (ii) x+1, y+1/2, z+1; (iii) x, y1, 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)
V3)800.9 (2)
Z2
Radiation typeCu Kα
µ (mm1)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)max1)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 Å3)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).

 

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