Methyl 2,3,4-tri-O-acetyl-1-azido-1-deoxy-β-D-gluco­pyran­uronate at room temperature

The structure of the title compound, C₁₃H₁₇N₃O₉, has been determined as part of our continuing investigation into the development of modified sugar amino acid (SAA) scaffolds for dyamic combinatorial libraries of cyclic oligomers. The title compound serves as a viable synthetic precursor and a building block for the synthesis of reversible β-glucosidase inhibitors utilizing target-accelerated in situ click methodologies. The overall structure is stabilized by a number of C—H...O interactions.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.041
• wR factor = 0.124
• Data-to-parameter ratio = 9.9

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        N12
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C6
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C31
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           27.49
           From the CIF: _reflns_number_total               2227
           Count of symmetry unique reflns         2228
           Completeness (_total/calc)             99.96%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present           no

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

---

Computing details

Data collection: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); cell refinement: MSC/AFC7 Diffractometer Control Software; data reduction: TEXSAN for Windows (Molecular Structure Corporation, 2001); program(s) used to solve structure: TEXSAN for Windows; program(s) used to refine structure: TEXSAN for Windows and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: TEXSAN for Windows and PLATON (Spek, 2003).

Methyl 2,3,4-tetra-O-acetyl-1-azido-1-deoxy-β-D-glucopyranuronate

Crystal data

C13H17N3O9	F(000) = 752
Mr = 359.30	Dx = 1.413 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ac 2ab	Cell parameters from 20 reflections
a = 14.059 (3) Å	θ = 12.6–16.3°
b = 16.336 (2) Å	µ = 0.12 mm^−1
c = 7.356 (3) Å	T = 295 K
V = 1689.4 (8) Å^3	Prismatic, colourless
Z = 4	0.30 × 0.20 × 0.15 mm

Data collection

Rigaku AFC-7R diffractometer	Rint = 0.036
Radiation source: Rigaku rotating anode	θmax = 27.5°, θmin = 2.9°
Graphite monochromator	h = −8→18
ω–2θ scans	k = 0→21
2779 measured reflections	l = −4→9
2227 independent reflections	3 standard reflections every 150 reflections
1346 reflections with I > 2σ(I)	intensity decay: 3.2%

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.124	H-atom parameters constrained
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0489P)^2 + 0.1669P] where P = (Fo^2 + 2Fc^2)/3
2227 reflections	(Δ/σ)max < 0.001
226 parameters	Δρmax = 0.16 e Å^−3
0 restraints	Δρmin = −0.22 e Å^−3

Special details

Experimental. The scan width was (1.63 + 0.30tanθ)° with an ω scan speed of 16° per minute (up to 4 scans to achieve I/σ(I) > 10). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > 2σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.44966 (14)	0.07905 (13)	−0.1272 (3)	0.0385 (7)
O21	0.66354 (16)	0.20090 (14)	−0.0677 (4)	0.0456 (8)
O22	0.6253 (2)	0.31098 (19)	0.1017 (6)	0.0853 (14)
O31	0.64665 (15)	0.12035 (15)	0.2736 (3)	0.0427 (7)
O32	0.7704 (2)	0.03384 (19)	0.2821 (4)	0.0692 (11)
O41	0.55682 (16)	−0.04397 (14)	0.2295 (3)	0.0398 (7)
O42	0.5070 (3)	0.00184 (19)	0.4997 (4)	0.0768 (13)
O61	0.32954 (17)	−0.01908 (16)	0.0659 (4)	0.0608 (10)
O62	0.3998 (2)	−0.11951 (19)	−0.0852 (5)	0.0853 (13)
N11	0.4869 (2)	0.2030 (2)	−0.2617 (4)	0.0524 (10)
N12	0.4705 (2)	0.1977 (2)	−0.4272 (5)	0.0512 (11)
N13	0.4516 (3)	0.2025 (3)	−0.5731 (5)	0.0883 (18)
C1	0.5275 (2)	0.1301 (2)	−0.1781 (5)	0.0402 (10)
C2	0.5798 (2)	0.1579 (2)	−0.0084 (5)	0.0373 (10)
C3	0.6106 (2)	0.0859 (2)	0.1071 (5)	0.0368 (10)
C4	0.5265 (2)	0.0303 (2)	0.1426 (4)	0.0357 (9)
C5	0.4832 (2)	0.00622 (19)	−0.0416 (5)	0.0371 (10)
C6	0.4004 (3)	−0.0520 (2)	−0.0244 (5)	0.0443 (11)
C21	0.6772 (3)	0.2793 (2)	−0.0034 (7)	0.0543 (12)
C22	0.7641 (3)	0.3152 (3)	−0.0843 (8)	0.0760 (18)
C31	0.7290 (2)	0.0919 (2)	0.3418 (5)	0.0444 (11)
C32	0.7607 (3)	0.1422 (3)	0.4979 (7)	0.0683 (16)
C41	0.5432 (3)	−0.0506 (2)	0.4123 (5)	0.0474 (11)
C42	0.5836 (3)	−0.1285 (3)	0.4779 (6)	0.0640 (16)
C61	0.2441 (3)	−0.0680 (3)	0.0885 (8)	0.082 (2)
H1	0.56900	0.10270	−0.25980	0.0480*
H2	0.54050	0.19350	0.06050	0.0450*
H3	0.65950	0.05630	0.04700	0.0440*
H4	0.48060	0.05760	0.21530	0.0430*
H5	0.53080	−0.01800	−0.11580	0.0450*
H22A	0.76360	0.30640	−0.21200	0.0930*
H22B	0.76600	0.37220	−0.06000	0.0930*
H22C	0.81870	0.28960	−0.03310	0.0930*
H32A	0.72940	0.19370	0.49490	0.0820*
H32B	0.82770	0.15050	0.49020	0.0820*
H32C	0.74610	0.11490	0.60810	0.0820*
H42A	0.65090	−0.12280	0.49200	0.0780*
H42B	0.55630	−0.14230	0.59170	0.0780*
H42C	0.57110	−0.17070	0.39240	0.0780*
H61A	0.26110	−0.12260	0.11660	0.1000*
H61B	0.20700	−0.04580	0.18480	0.1000*
H61C	0.20820	−0.06680	−0.02080	0.1000*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0322 (11)	0.0423 (13)	0.0411 (13)	0.0006 (10)	−0.0026 (11)	−0.0014 (10)
O21	0.0398 (12)	0.0440 (13)	0.0530 (15)	−0.0096 (11)	0.0049 (12)	−0.0033 (12)
O22	0.071 (2)	0.0650 (19)	0.120 (3)	−0.0125 (16)	0.015 (2)	−0.043 (2)
O31	0.0379 (12)	0.0494 (13)	0.0407 (13)	0.0037 (11)	−0.0094 (11)	−0.0084 (12)
O32	0.0587 (17)	0.080 (2)	0.069 (2)	0.0241 (16)	−0.0193 (16)	−0.0071 (18)
O41	0.0438 (13)	0.0392 (12)	0.0365 (12)	0.0039 (11)	0.0011 (11)	0.0007 (10)
O42	0.121 (3)	0.0698 (19)	0.0396 (15)	0.012 (2)	0.0122 (19)	−0.0063 (15)
O61	0.0398 (13)	0.0606 (16)	0.082 (2)	−0.0099 (12)	0.0164 (15)	−0.0092 (16)
O62	0.083 (2)	0.0578 (18)	0.115 (3)	−0.0228 (17)	0.021 (2)	−0.031 (2)
N11	0.069 (2)	0.0466 (16)	0.0416 (16)	0.0075 (17)	−0.0095 (16)	0.0012 (15)
N12	0.0503 (18)	0.0572 (19)	0.0460 (19)	0.0070 (16)	−0.0046 (16)	0.0037 (17)
N13	0.115 (4)	0.102 (3)	0.048 (2)	0.044 (3)	−0.021 (3)	0.005 (2)
C1	0.0402 (18)	0.0406 (17)	0.0397 (19)	−0.0005 (16)	−0.0030 (16)	0.0024 (16)
C2	0.0358 (16)	0.0380 (16)	0.0381 (18)	−0.0021 (14)	0.0012 (16)	−0.0021 (16)
C3	0.0376 (16)	0.0401 (17)	0.0327 (18)	−0.0002 (15)	−0.0007 (16)	−0.0062 (14)
C4	0.0349 (15)	0.0385 (16)	0.0338 (17)	0.0046 (14)	0.0016 (15)	0.0004 (14)
C5	0.0353 (16)	0.0417 (18)	0.0344 (18)	0.0038 (15)	0.0003 (15)	−0.0012 (15)
C6	0.0449 (19)	0.047 (2)	0.041 (2)	−0.0024 (18)	0.0009 (17)	−0.0043 (17)
C21	0.054 (2)	0.045 (2)	0.064 (2)	−0.0081 (19)	−0.014 (2)	−0.003 (2)
C22	0.070 (3)	0.056 (2)	0.102 (4)	−0.020 (2)	−0.011 (3)	0.013 (3)
C31	0.0391 (18)	0.053 (2)	0.041 (2)	−0.0048 (17)	−0.0085 (17)	0.0062 (18)
C32	0.066 (3)	0.080 (3)	0.059 (2)	−0.006 (2)	−0.023 (2)	−0.004 (3)
C41	0.050 (2)	0.053 (2)	0.0391 (19)	−0.0092 (19)	−0.0056 (18)	0.0017 (19)
C42	0.079 (3)	0.057 (2)	0.056 (3)	−0.009 (2)	−0.017 (2)	0.016 (2)
C61	0.052 (2)	0.101 (4)	0.094 (4)	−0.027 (3)	0.018 (3)	0.009 (3)

Geometric parameters (Å, º)

O1—C1	1.426 (4)	C5—C6	1.509 (5)
O1—C5	1.426 (4)	C21—C22	1.480 (6)
O21—C2	1.439 (4)	C31—C32	1.481 (6)
O21—C21	1.379 (4)	C41—C42	1.475 (6)
O22—C21	1.182 (6)	C1—H1	0.9500
O31—C3	1.440 (4)	C2—H2	0.9500
O31—C31	1.345 (4)	C3—H3	0.9500
O32—C31	1.196 (4)	C4—H4	0.9500
O41—C4	1.436 (4)	C5—H5	0.9500
O41—C41	1.363 (4)	C22—H22A	0.9500
O42—C41	1.186 (5)	C22—H22B	0.9500
O61—C6	1.313 (5)	C22—H22C	0.9500
O61—C61	1.452 (5)	C32—H32A	0.9500
O62—C6	1.190 (5)	C32—H32B	0.9500
N11—N12	1.242 (5)	C32—H32C	0.9500
N11—C1	1.457 (5)	C42—H42A	0.9600
N12—N13	1.108 (5)	C42—H42B	0.9500
C1—C2	1.518 (5)	C42—H42C	0.9500
C2—C3	1.514 (5)	C61—H61A	0.9500
C3—C4	1.514 (4)	C61—H61B	0.9500
C4—C5	1.537 (5)	C61—H61C	0.9500
O1···O42^i	3.126 (4)	N13···H4^i	2.8600
O1···O61	2.728 (4)	C1···O42^i	3.177 (5)
O1···N12	2.952 (4)	C5···O42^i	3.392 (5)
O21···O31	2.845 (4)	C21···O31	3.329 (5)
O21···N11	2.864 (4)	C31···C41	3.537 (5)
O22···C41^ii	3.277 (5)	C31···O41	3.387 (4)
O22···C42^ii	3.154 (5)	C41···C31	3.537 (5)
O31···O42	3.220 (4)	C41···O22^viii	3.277 (5)
O31···C41	3.310 (4)	C41···O31	3.310 (4)
O31···O41	2.984 (4)	C42···O32^vi	3.408 (6)
O31···O21	2.845 (4)	C42···O22^viii	3.154 (5)
O31···C21	3.329 (5)	C2···H5	3.0600
O31···N13^iii	3.255 (5)	C6···H61B^v	3.0700
O32···C42^iv	3.408 (6)	C42···H22C^vi	2.9700
O41···C31	3.387 (4)	H1···O42^i	2.5700
O41···O31	2.984 (4)	H1···H5	2.3000
O42···O1^iii	3.126 (4)	H2···O22	2.2800
O42···C1^iii	3.177 (5)	H3···O32	2.3600
O42···C5^iii	3.392 (5)	H3···H5	2.4900
O42···O31	3.220 (4)	H3···O32^iv	2.6300
O61···O1	2.728 (4)	H4···O42	2.3100
O1···H61B^v	2.6600	H4···O61	2.7000
O22···H61A^ii	2.8300	H4···N13^iii	2.8600
O22···H2	2.2800	H5···O42^i	2.8700
O22···H42C^ii	2.7800	H5···C2	3.0600
O32···H42A^iv	2.8100	H5···H1	2.3000
O32···H3^vi	2.6300	H5···H3	2.4900
O32···H5^vi	2.9100	H5···O32^iv	2.9100
O32···H32C^iv	2.7600	H22B···O61^ix	2.5600
O32···H3	2.3600	H22C···C42^iv	2.9700
O42···H4	2.3100	H22C···H42C^iv	2.5400
O42···H5^iii	2.8700	H32C···O32^vi	2.7600
O42···H1^iii	2.5700	H42A···O32^vi	2.8100
O61···H4	2.7000	H42B···N11^viii	2.8800
O61···H22B^vii	2.5600	H42C···H22C^vi	2.5400
O62···H61A	2.4500	H42C···O22^viii	2.7800
O62···H61C	2.8700	H61A···O62	2.4500
N11···O21	2.864 (4)	H61A···O22^viii	2.8300
N12···O1	2.952 (4)	H61B···O1^x	2.6600
N13···O31^i	3.255 (5)	H61B···C6^x	3.0700
N11···H42B^ii	2.8800	H61C···O62	2.8700
C1—O1—C5	110.5 (2)	O21—C2—H2	110.00
C2—O21—C21	117.6 (3)	C1—C2—H2	110.00
C3—O31—C31	119.0 (3)	C3—C2—H2	110.00
C4—O41—C41	117.7 (2)	O31—C3—H3	110.00
C6—O61—C61	117.4 (3)	C2—C3—H3	110.00
N12—N11—C1	115.4 (3)	C4—C3—H3	110.00
N11—N12—N13	171.3 (4)	O41—C4—H4	110.00
O1—C1—N11	106.8 (2)	C3—C4—H4	110.00
O1—C1—C2	109.3 (3)	C5—C4—H4	110.00
N11—C1—C2	107.0 (3)	O1—C5—H5	109.00
O21—C2—C1	107.0 (3)	C4—C5—H5	110.00
O21—C2—C3	108.4 (2)	C6—C5—H5	109.00
C1—C2—C3	111.6 (3)	C21—C22—H22A	109.00
O31—C3—C2	105.9 (3)	C21—C22—H22B	110.00
O31—C3—C4	111.3 (3)	C21—C22—H22C	109.00
C2—C3—C4	109.9 (2)	H22A—C22—H22B	110.00
O41—C4—C3	110.6 (2)	H22A—C22—H22C	109.00
O41—C4—C5	107.1 (2)	H22B—C22—H22C	110.00
C3—C4—C5	108.1 (3)	C31—C32—H32A	110.00
O1—C5—C4	107.9 (2)	C31—C32—H32B	109.00
O1—C5—C6	107.9 (2)	C31—C32—H32C	110.00
C4—C5—C6	113.2 (3)	H32A—C32—H32B	109.00
O61—C6—O62	124.4 (4)	H32A—C32—H32C	110.00
O61—C6—C5	111.7 (3)	H32B—C32—H32C	109.00
O62—C6—C5	123.9 (4)	C41—C42—H42A	109.00
O21—C21—O22	123.0 (4)	C41—C42—H42B	110.00
O21—C21—C22	110.2 (4)	C41—C42—H42C	110.00
O22—C21—C22	126.8 (4)	H42A—C42—H42B	109.00
O31—C31—O32	123.8 (3)	H42A—C42—H42C	109.00
O31—C31—C32	110.9 (3)	H42B—C42—H42C	110.00
O32—C31—C32	125.3 (3)	O61—C61—H61A	110.00
O41—C41—O42	122.5 (3)	O61—C61—H61B	109.00
O41—C41—C42	109.7 (3)	O61—C61—H61C	109.00
O42—C41—C42	127.7 (4)	H61A—C61—H61B	110.00
O1—C1—H1	111.00	H61A—C61—H61C	110.00
N11—C1—H1	111.00	H61B—C61—H61C	109.00
C2—C1—H1	111.00
C5—O1—C1—N11	−179.3 (3)	O1—C1—C2—C3	55.0 (3)
C5—O1—C1—C2	−63.9 (3)	O1—C1—C2—O21	173.4 (2)
C1—O1—C5—C4	68.3 (3)	N11—C1—C2—O21	−71.4 (3)
C1—O1—C5—C6	−169.1 (3)	N11—C1—C2—C3	170.2 (2)
C21—O21—C2—C1	125.5 (3)	O21—C2—C3—O31	70.3 (3)
C21—O21—C2—C3	−114.1 (3)	C1—C2—C3—O31	−172.1 (2)
C2—O21—C21—O22	2.6 (6)	C1—C2—C3—C4	−51.8 (3)
C2—O21—C21—C22	−177.6 (3)	O21—C2—C3—C4	−169.4 (3)
C31—O31—C3—C2	−134.7 (3)	O31—C3—C4—O41	−71.2 (3)
C31—O31—C3—C4	106.0 (3)	C2—C3—C4—O41	171.8 (3)
C3—O31—C31—O32	−7.5 (5)	C2—C3—C4—C5	54.8 (3)
C3—O31—C31—C32	172.2 (3)	O31—C3—C4—C5	171.8 (2)
C41—O41—C4—C3	101.4 (3)	C3—C4—C5—O1	−62.8 (3)
C41—O41—C4—C5	−141.0 (3)	C3—C4—C5—C6	177.9 (3)
C4—O41—C41—O42	0.7 (5)	O41—C4—C5—O1	178.0 (2)
C4—O41—C41—C42	−176.8 (3)	O41—C4—C5—C6	58.7 (3)
C61—O61—C6—O62	−1.6 (6)	O1—C5—C6—O61	−56.9 (4)
C61—O61—C6—C5	178.5 (3)	C4—C5—C6—O62	−117.5 (4)
N12—N11—C1—C2	156.4 (3)	O1—C5—C6—O62	123.3 (4)
N12—N11—C1—O1	−86.7 (3)	C4—C5—C6—O61	62.4 (4)

Symmetry codes: (i) x, y, z−1; (ii) −x+1, y+1/2, −z+1/2; (iii) x, y, z+1; (iv) −x+3/2, −y, z−1/2; (v) −x+1/2, −y, z−1/2; (vi) −x+3/2, −y, z+1/2; (vii) x−1/2, −y+1/2, −z; (viii) −x+1, y−1/2, −z+1/2; (ix) x+1/2, −y+1/2, −z; (x) −x+1/2, −y, z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O42^i	0.95	2.57	3.177 (5)	122
C2—H2···O22	0.95	2.28	2.705 (5)	106
C3—H3···O32	0.95	2.36	2.725 (4)	103
C4—H4···O42	0.95	2.31	2.682 (4)	102
C22—H22B···O61^ix	0.95	2.56	3.458 (6)	158

Symmetry codes: (i) x, y, z−1; (ix) x+1/2, −y+1/2, −z.