research communications
N-(2-Acetamido-2-deoxy-β-D-glucopyranosyl)-N-(3-azidopropyl)-O-methylhydroxylamine
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
The structure of the title compound, C12H23N5O6, solved using adequate data from a thin crystal plate, confirmed that this useful 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 was not unambiguously determined but was known from the synthetic chemistry, which used natural 2-acetamido-2-deoxy-D-glucose as the starting material.
Keywords: crystal structure; oxyamine glycoside; carbohydrate.
CCDC reference: 1451795
1. Chemical context
Oxyamine 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 to a substrate of choice, such as proteins, fluorophores and biotin. The analysis confirmed that the was obtained in the ring-closed β-pyranose configuration.
such as the title compound, can be utilised for the synthesis of a wide variety of complex glycoconjugates (Kwase2. Structural commentary
The title compound crystallizes with one independent molecule in the ) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The was not ambiguously determined but was known from the synthetic chemistry.
(Fig. 13. 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). 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.
4. Database survey
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).
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) 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 . 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).
details are summarized in Table 2Supporting information
CCDC reference: 1451795
10.1107/S2056989016002164/lh5798sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989016002164/lh5798Isup2.hkl
Oxyamine β-pyranose configuration.
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 to a substrate of choice, such as proteins, fluorophores and biotin. The analysis confirmed that the was obtained in the ring-closedThe title compound crystallizes with one independent molecule in the
(Fig. 1) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The 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).
\ 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).
Crystal data, data collection and structure
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).Oxyamine β-pyranose configuration.
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 to a substrate of choice, such as proteins, fluorophores and biotin. The analysis confirmed that the was obtained in the ring-closedThe title compound crystallizes with one independent molecule in the
(Fig. 1) in the C1(R), C2(R), C3(R), C4(S), C5(R) configuration. The 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)
\ 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).
detailsCrystal data, data collection and structure
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).Data collection: CrysAlis PRO (Agilent, 2014); cell
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).Fig. 1. View of the title molecule, drawn with 25% probability displacement ellipsoids. | |
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.] | |
Fig. 3. The O6—N1—C1—O1 and C9—O6—N1—C1 torsion angles of N-glycosyloxyamines. |
C12H23N5O6 | F(000) = 356 |
Mr = 333.35 | Dx = 1.382 Mg m−3 |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54184 Å |
a = 13.5605 (18) Å | Cell parameters from 2327 reflections |
b = 4.7386 (3) Å | θ = 3.7–75.3° |
c = 14.140 (2) Å | µ = 0.95 mm−1 |
β = 118.181 (19)° | T = 120 K |
V = 800.9 (2) Å3 | Needle, colourless |
Z = 2 | 0.57 × 0.14 × 0.02 mm |
Agilent SuperNova Dual Source diffractometer with an Atlas detector | 2355 independent reflections |
Radiation source: sealed X-ray tube, SuperNova (Cu) X-ray Source | 2073 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.053 |
Detector resolution: 10.6501 pixels mm-1 | θmax = 66.6°, θmin = 3.6° |
ω scans | h = −16→16 |
Absorption correction: gaussian (CrysAlis PRO; Agilent, 2014) | k = −5→5 |
Tmin = 0.792, Tmax = 0.985 | l = −17→16 |
6061 measured reflections |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H 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 = 1.03 | Δρmax = 0.39 e Å−3 |
2355 reflections | Δρmin = −0.31 e Å−3 |
221 parameters | Absolute structure: Flack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004) |
1 restraint | Absolute structure parameter: 0.2 (4) |
C12H23N5O6 | V = 800.9 (2) Å3 |
Mr = 333.35 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 13.5605 (18) Å | µ = 0.95 mm−1 |
b = 4.7386 (3) Å | T = 120 K |
c = 14.140 (2) Å | 0.57 × 0.14 × 0.02 mm |
β = 118.181 (19)° |
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 = 0.985 | Rint = 0.053 |
6061 measured reflections |
R[F2 > 2σ(F2)] = 0.059 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.165 | Δρmax = 0.39 e Å−3 |
S = 1.03 | Δρmin = −0.31 e Å−3 |
2355 reflections | Absolute structure: Flack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004) |
221 parameters | Absolute structure parameter: 0.2 (4) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.3682 (2) | 0.2828 (6) | 0.5792 (2) | 0.0314 (7) | |
O2 | 0.1361 (3) | 0.5357 (7) | 0.7397 (3) | 0.0378 (8) | |
O3 | 0.0442 (2) | 0.1637 (7) | 0.5080 (3) | 0.0368 (8) | |
H3O | 0.007 (4) | 0.017 (14) | 0.498 (6) | 0.055* | |
O4 | 0.1155 (3) | 0.0380 (8) | 0.3491 (3) | 0.0426 (8) | |
H4O | 0.050 (6) | 0.058 (17) | 0.328 (5) | 0.064* | |
O5 | 0.4546 (3) | 0.2456 (8) | 0.4382 (3) | 0.0401 (8) | |
H5O | 0.486 (6) | 0.385 (16) | 0.486 (6) | 0.060* | |
O6 | 0.4312 (3) | 0.5384 (7) | 0.7784 (3) | 0.0369 (7) | |
N1 | 0.4434 (3) | 0.2390 (8) | 0.7677 (3) | 0.0329 (8) | |
N2 | 0.2088 (3) | 0.1158 (8) | 0.7250 (3) | 0.0326 (8) | |
H2N | 0.205 (4) | −0.077 (14) | 0.732 (4) | 0.039* | |
N3 | 0.7789 (3) | −0.1042 (10) | 0.8833 (4) | 0.0480 (11) | |
N4 | 0.8722 (3) | −0.1684 (10) | 0.8948 (4) | 0.0451 (10) | |
N5 | 0.9545 (4) | −0.2571 (12) | 0.9039 (4) | 0.0566 (12) | |
C1 | 0.3557 (3) | 0.1498 (10) | 0.6645 (4) | 0.0308 (9) | |
H1 | 0.3616 | −0.0591 | 0.6585 | 0.037* | |
C2 | 0.2369 (3) | 0.2191 (9) | 0.6435 (3) | 0.0304 (9) | |
H2 | 0.2276 | 0.4289 | 0.6387 | 0.036* | |
C3 | 0.1552 (3) | 0.0914 (9) | 0.5340 (4) | 0.0318 (9) | |
H3 | 0.1626 | −0.1187 | 0.5392 | 0.038* | |
C4 | 0.1797 (3) | 0.1921 (9) | 0.4452 (4) | 0.0320 (9) | |
H4 | 0.1613 | 0.3974 | 0.4317 | 0.038* | |
C5 | 0.3030 (3) | 0.1481 (10) | 0.4789 (4) | 0.0338 (10) | |
H5 | 0.3197 | −0.0587 | 0.4869 | 0.041* | |
C6 | 0.3382 (4) | 0.2715 (11) | 0.4006 (4) | 0.0349 (9) | |
H6A | 0.2977 | 0.1734 | 0.3308 | 0.042* | |
H6B | 0.3172 | 0.4735 | 0.3890 | 0.042* | |
C7 | 0.1536 (3) | 0.2815 (10) | 0.7623 (4) | 0.0324 (9) | |
C8 | 0.1154 (4) | 0.1435 (11) | 0.8351 (4) | 0.0436 (11) | |
H8A | 0.1627 | 0.2070 | 0.9090 | 0.065* | |
H8B | 0.1212 | −0.0619 | 0.8313 | 0.065* | |
H8C | 0.0375 | 0.1955 | 0.8123 | 0.065* | |
C9 | 0.4282 (4) | 0.5914 (10) | 0.8765 (4) | 0.0395 (11) | |
H9A | 0.4977 | 0.5240 | 0.9370 | 0.059* | |
H9B | 0.3644 | 0.4919 | 0.8757 | 0.059* | |
H9C | 0.4203 | 0.7945 | 0.8842 | 0.059* | |
C10 | 0.5538 (3) | 0.1952 (11) | 0.7742 (4) | 0.0389 (11) | |
H10A | 0.5617 | 0.3227 | 0.7227 | 0.047* | |
H10B | 0.5589 | −0.0014 | 0.7532 | 0.047* | |
C11 | 0.6489 (4) | 0.2502 (12) | 0.8862 (4) | 0.0443 (11) | |
H11A | 0.6441 | 0.4474 | 0.9068 | 0.053* | |
H11B | 0.6405 | 0.1240 | 0.9378 | 0.053* | |
C12 | 0.7623 (4) | 0.2026 (12) | 0.8934 (4) | 0.0451 (12) | |
H12A | 0.7675 | 0.3074 | 0.8353 | 0.054* | |
H12B | 0.8216 | 0.2735 | 0.9630 | 0.054* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0257 (13) | 0.0269 (16) | 0.0409 (16) | −0.0022 (12) | 0.0150 (12) | 0.0014 (13) |
O2 | 0.0370 (16) | 0.0236 (16) | 0.056 (2) | 0.0021 (13) | 0.0245 (15) | 0.0010 (15) |
O3 | 0.0235 (13) | 0.0265 (16) | 0.060 (2) | −0.0025 (12) | 0.0190 (14) | −0.0003 (15) |
O4 | 0.0270 (15) | 0.047 (2) | 0.0476 (19) | −0.0046 (16) | 0.0129 (14) | −0.0117 (17) |
O5 | 0.0322 (15) | 0.0397 (19) | 0.0533 (19) | −0.0004 (14) | 0.0243 (14) | −0.0017 (17) |
O6 | 0.0412 (17) | 0.0222 (15) | 0.0421 (17) | −0.0018 (14) | 0.0152 (14) | 0.0019 (14) |
N1 | 0.0277 (17) | 0.0250 (19) | 0.042 (2) | 0.0011 (14) | 0.0130 (15) | 0.0004 (15) |
N2 | 0.0313 (17) | 0.0212 (18) | 0.049 (2) | 0.0013 (14) | 0.0223 (16) | 0.0030 (15) |
N3 | 0.033 (2) | 0.042 (2) | 0.066 (3) | −0.0007 (19) | 0.021 (2) | 0.001 (2) |
N4 | 0.038 (2) | 0.042 (2) | 0.051 (2) | −0.0025 (18) | 0.0174 (19) | 0.0016 (19) |
N5 | 0.036 (2) | 0.055 (3) | 0.079 (3) | 0.003 (2) | 0.027 (2) | −0.002 (3) |
C1 | 0.0266 (19) | 0.027 (2) | 0.037 (2) | 0.0008 (17) | 0.0136 (17) | 0.0035 (17) |
C2 | 0.0266 (19) | 0.022 (2) | 0.045 (2) | 0.0031 (16) | 0.0187 (18) | 0.0052 (18) |
C3 | 0.0256 (19) | 0.021 (2) | 0.047 (2) | 0.0000 (16) | 0.0160 (18) | 0.0006 (18) |
C4 | 0.027 (2) | 0.026 (2) | 0.041 (2) | 0.0014 (17) | 0.0143 (18) | 0.0008 (19) |
C5 | 0.0249 (19) | 0.033 (2) | 0.042 (2) | 0.0018 (18) | 0.0146 (17) | 0.0022 (19) |
C6 | 0.033 (2) | 0.034 (2) | 0.039 (2) | −0.002 (2) | 0.0172 (18) | 0.000 (2) |
C7 | 0.0297 (19) | 0.022 (2) | 0.045 (2) | −0.0016 (17) | 0.0173 (18) | −0.0012 (18) |
C8 | 0.056 (3) | 0.028 (2) | 0.061 (3) | 0.000 (2) | 0.039 (2) | 0.003 (2) |
C9 | 0.042 (2) | 0.030 (2) | 0.041 (2) | −0.0021 (19) | 0.016 (2) | −0.004 (2) |
C10 | 0.027 (2) | 0.040 (3) | 0.044 (3) | 0.0000 (19) | 0.0112 (19) | 0.001 (2) |
C11 | 0.034 (2) | 0.044 (3) | 0.046 (3) | 0.001 (2) | 0.012 (2) | −0.001 (2) |
C12 | 0.033 (2) | 0.040 (3) | 0.048 (3) | −0.002 (2) | 0.007 (2) | 0.000 (2) |
O1—C5 | 1.420 (6) | C3—C4 | 1.520 (6) |
O1—C1 | 1.441 (5) | C3—H3 | 1.0000 |
O2—C7 | 1.240 (6) | C4—C5 | 1.521 (5) |
O3—C3 | 1.413 (5) | C4—H4 | 1.0000 |
O3—H3O | 0.84 (8) | C5—C6 | 1.515 (6) |
O4—C4 | 1.421 (6) | C5—H5 | 1.0000 |
O4—H4O | 0.80 (7) | C6—H6A | 0.9900 |
O5—C6 | 1.413 (5) | C6—H6B | 0.9900 |
O5—H5O | 0.90 (8) | C7—C8 | 1.502 (6) |
O6—C9 | 1.430 (6) | C8—H8A | 0.9800 |
O6—N1 | 1.445 (5) | C8—H8B | 0.9800 |
N1—C1 | 1.443 (6) | C8—H8C | 0.9800 |
N1—C10 | 1.470 (5) | C9—H9A | 0.9800 |
N2—C7 | 1.352 (6) | C9—H9B | 0.9800 |
N2—C2 | 1.459 (5) | C9—H9C | 0.9800 |
N2—H2N | 0.93 (7) | C10—C11 | 1.520 (6) |
N3—N4 | 1.235 (6) | C10—H10A | 0.9900 |
N3—C12 | 1.488 (7) | C10—H10B | 0.9900 |
N4—N5 | 1.141 (6) | C11—C12 | 1.510 (7) |
C1—C2 | 1.529 (5) | C11—H11A | 0.9900 |
C1—H1 | 1.0000 | C11—H11B | 0.9900 |
C2—C3 | 1.539 (6) | C12—H12A | 0.9900 |
C2—H2 | 1.0000 | C12—H12B | 0.9900 |
C5—O1—C1 | 112.0 (3) | C6—C5—H5 | 109.1 |
C3—O3—H3O | 109.5 | C4—C5—H5 | 109.1 |
C4—O4—H4O | 112 (5) | O5—C6—C5 | 111.9 (3) |
C6—O5—H5O | 106 (5) | O5—C6—H6A | 109.2 |
C9—O6—N1 | 109.4 (3) | C5—C6—H6A | 109.2 |
C1—N1—O6 | 108.2 (3) | O5—C6—H6B | 109.2 |
C1—N1—C10 | 110.6 (3) | C5—C6—H6B | 109.2 |
O6—N1—C10 | 107.2 (3) | H6A—C6—H6B | 107.9 |
C7—N2—C2 | 120.9 (4) | O2—C7—N2 | 122.5 (4) |
C7—N2—H2N | 118 (3) | O2—C7—C8 | 120.9 (4) |
C2—N2—H2N | 118 (3) | N2—C7—C8 | 116.6 (4) |
N4—N3—C12 | 114.8 (4) | C7—C8—H8A | 109.5 |
N5—N4—N3 | 172.6 (6) | C7—C8—H8B | 109.5 |
O1—C1—N1 | 110.6 (3) | H8A—C8—H8B | 109.5 |
O1—C1—C2 | 105.9 (3) | C7—C8—H8C | 109.5 |
N1—C1—C2 | 115.1 (4) | H8A—C8—H8C | 109.5 |
O1—C1—H1 | 108.4 | H8B—C8—H8C | 109.5 |
N1—C1—H1 | 108.4 | O6—C9—H9A | 109.5 |
C2—C1—H1 | 108.4 | O6—C9—H9B | 109.5 |
N2—C2—C1 | 114.7 (3) | H9A—C9—H9B | 109.5 |
N2—C2—C3 | 109.3 (3) | O6—C9—H9C | 109.5 |
C1—C2—C3 | 107.6 (3) | H9A—C9—H9C | 109.5 |
N2—C2—H2 | 108.4 | H9B—C9—H9C | 109.5 |
C1—C2—H2 | 108.4 | N1—C10—C11 | 112.2 (4) |
C3—C2—H2 | 108.4 | N1—C10—H10A | 109.2 |
O3—C3—C4 | 109.3 (4) | C11—C10—H10A | 109.2 |
O3—C3—C2 | 109.8 (3) | N1—C10—H10B | 109.2 |
C4—C3—C2 | 111.9 (3) | C11—C10—H10B | 109.2 |
O3—C3—H3 | 108.6 | H10A—C10—H10B | 107.9 |
C4—C3—H3 | 108.6 | C12—C11—C10 | 112.3 (4) |
C2—C3—H3 | 108.6 | C12—C11—H11A | 109.1 |
O4—C4—C3 | 110.8 (4) | C10—C11—H11A | 109.1 |
O4—C4—C5 | 108.4 (3) | C12—C11—H11B | 109.1 |
C3—C4—C5 | 109.5 (3) | C10—C11—H11B | 109.1 |
O4—C4—H4 | 109.4 | H11A—C11—H11B | 107.9 |
C3—C4—H4 | 109.4 | N3—C12—C11 | 109.5 (4) |
C5—C4—H4 | 109.4 | N3—C12—H12A | 109.8 |
O1—C5—C6 | 107.1 (3) | C11—C12—H12A | 109.8 |
O1—C5—C4 | 109.0 (3) | N3—C12—H12B | 109.8 |
C6—C5—C4 | 113.4 (4) | C11—C12—H12B | 109.8 |
O1—C5—H5 | 109.1 | H12A—C12—H12B | 108.2 |
C9—O6—N1—C1 | 127.1 (3) | C2—C3—C4—O4 | 170.7 (3) |
C9—O6—N1—C10 | −113.6 (4) | O3—C3—C4—C5 | 173.0 (4) |
C5—O1—C1—N1 | 164.6 (3) | C2—C3—C4—C5 | 51.1 (5) |
C5—O1—C1—C2 | −70.2 (4) | C1—O1—C5—C6 | −170.3 (3) |
O6—N1—C1—O1 | 64.2 (4) | C1—O1—C5—C4 | 66.7 (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—C6 | 65.3 (5) |
C7—N2—C2—C1 | 136.0 (4) | C3—C4—C5—C6 | −173.7 (4) |
C7—N2—C2—C3 | −103.1 (4) | O1—C5—C6—O5 | 55.3 (5) |
O1—C1—C2—N2 | −176.8 (3) | C4—C5—C6—O5 | 175.6 (4) |
N1—C1—C2—N2 | −54.4 (5) | C2—N2—C7—O2 | −8.8 (7) |
O1—C1—C2—C3 | 61.4 (4) | C2—N2—C7—C8 | 172.2 (4) |
N1—C1—C2—C3 | −176.2 (3) | C1—N1—C10—C11 | −172.5 (4) |
N2—C2—C3—O3 | 58.2 (4) | O6—N1—C10—C11 | 69.7 (5) |
C1—C2—C3—O3 | −176.7 (3) | N1—C10—C11—C12 | 179.5 (4) |
N2—C2—C3—C4 | 179.7 (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) |
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−1/2, −z+1; (ii) −x+1, y+1/2, −z+1; (iii) x, y−1, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3O···O3i | 0.84 | 1.79 | 2.616 (5) | 167.1 |
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−1/2, −z+1; (ii) −x+1, y+1/2, −z+1; (iii) x, y−1, z. |
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) |
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, −0.31 |
Absolute structure | Flack x determined using 619 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004) |
Absolute structure parameter | 0.2 (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.
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