Methyl 4,6-O-benzyl­idene-2,3-dide­oxy-3-hydroxyimino-α-D-erythro-pyran­oside methanol solvate

The title compound, C₁₄H₁₇NO₅·CH₃OH, is a methyl- and benzyl­idene-protected precursor for the synthesis of the amino sugar daunosamine (3-amino-2,3,6-tride­oxy-L-lyxo-hexose). The configuration is determined by the stereochemistry of the starting material. The bond lengths and angles are normal and the mol­ecule has the preferred ⁴C₁ conformation (cf. the standard carbohydrate atomic numbering). One methanol mol­ecule per asymmetric unit acts both as a hydrogen-bond acceptor and donor for the oxime group. This pattern is enlarged by the twofold axis of the space group to a homodromic cycle supported by σ-cooperativity via the oxime N—O bond.

Key indicators

• Single-crystal X-ray study
• T = 200 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.048
• wR factor = 0.128
• Data-to-parameter ratio = 9.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT245_ALERT_2_C U(iso) H13     Smaller than U(eq) C13     by ...       0.01 AngSq

Author Response: C13's environment appears as less rigid. Cf. next point.

PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          5

Author Response: Outside of the hydrogen-bonded part, no typical weak interactions of some directionality have been found. For example, C--H/pi stacking or weak hydrogen bonds towards O acceptors are badly defined. The molecules thus appear as badly fixed in the structure.

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           27.63
           From the CIF: _reflns_number_total               2006
           Count of symmetry unique reflns         2028
           Completeness (_total/calc)             98.92%
           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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     ...          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     ...          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C8     ...          R
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

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

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

S1. Comment

The title compound, (I), was prepared in the course of the synthesis of the aminosugar daunosamine (3-amino-2,3,6-trideoxy-L-lyxo-hexose).

The molecular structure shows the pyranoside in its preferred ⁴C₁ chair conformation (Fig. 1). In the crystal structure, two pyranoside and two methanol molecules form a hydrogen-bond-connected cluster, the methanol molecules acting both as a hydrogen-bond donor and acceptor, whereas the nitrogen atom of the oxime group is a hydrogen-bond acceptor und the oxime's hydroxyl group is a donor. The central hydrogen-bonded motif thus is a 10-membered ring of donor and acceptor atoms with the shape of a pseudo-hexagon (Fig. 2).

Related literature

The title compound was prepared according to the procedure described by Horton & Weckerle (1975).

S2. Experimental

The title compound was prepared upon the reaction of hydroxylamine and methyl 2-deoxy-D-erythro-hex-3-ulose-4O,6O-benzylidene- α-pyranoside in methanol. Colourless crystals were obtained by cooling the solution to 277 K [m.p. 478–479 K (decomp.)].

S3. Refinement

All H atoms were located initially in a difference map, then their positions were optimized geometrically and refined as riding on their parent atoms with one common refined isotropic displacement parameter for the methyl H atoms and one parameter for the remaining H atoms. The methyl and hydroxy H atoms were allowed to rotate about the axes of their respective groups.

Computing details

Data collection: COLLECT (Nonius 2004); cell refinement: SCALEPACK (Otwinowski & Minor 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. The molecular structure of (I), with atom labels and anisotropic displacement ellipsoids (drawn at the 50% probability level) for non-H atoms. The hydrogen bond to the methanol molecule is drawn as a yellow bar.
	Fig. 2. The packing of (I), viewed along [0 1 0]. The hydrogen bonds are drawn as yellow bars.

Methyl 4,6-O-benzylidene-2,3-dideoxy-3-hydroxyimino-α-D-erythro-πyranoside methanol solvate

Crystal data

C14H17NO5·CH4O	F(000) = 664
Mr = 311.33	Dx = 1.326 Mg m^−3
Monoclinic, C2	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2y	Cell parameters from 8876 reflections
a = 21.8696 (12) Å	θ = 3.1–27.5°
b = 4.7001 (2) Å	µ = 0.10 mm^−1
c = 16.0494 (8) Å	T = 200 K
β = 109.009 (3)°	Needle, colourless
V = 1559.74 (13) Å^3	0.40 × 0.05 × 0.05 mm
Z = 4

Data collection

Nonius KappaCCD diffractometer	1238 reflections with I > 2σ(I)
Radiation source: rotating anode	Rint = 0.073
MONTEL, graded multilayered X-ray optics monochromator	θmax = 27.6°, θmin = 3.7°
CCD; rotation images; thick slices scans	h = −28→28
6634 measured reflections	k = −6→6
2006 independent reflections	l = −20→20

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)] = 0.048	Hydrogen site location: difference Fourier map
wR(F^2) = 0.128	H-atom parameters constrained
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0692P)^2] where P = (Fo^2 + 2Fc^2)/3
2006 reflections	(Δ/σ)max < 0.001
205 parameters	Δρmax = 0.18 e Å^−3
1 restraint	Δρmin = −0.24 e Å^−3

Special details

Refinement. Due to the absence of significant anomalous scattering the absolute structure factor is meaningless. Thus, Friedel opposites were merged. The absolute structure is determined by the stereochemistry of the starting material.

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

	x	y	z	Uiso*/Ueq
O1	0.82189 (10)	0.8533 (6)	0.73526 (14)	0.0475 (6)
O4	0.98051 (9)	0.5771 (5)	0.74614 (12)	0.0403 (6)
O6	0.97148 (11)	0.5728 (7)	0.88686 (14)	0.0604 (8)
O7	0.76006 (10)	0.5196 (6)	0.63550 (15)	0.0513 (6)
O8	0.87819 (10)	0.5175 (7)	0.48398 (13)	0.0506 (7)
H88	0.9010	0.4539	0.4550	0.057 (3)*
N1	0.91647 (11)	0.5482 (7)	0.57293 (15)	0.0395 (7)
C1	0.78439 (16)	0.7958 (8)	0.6454 (2)	0.0448 (9)
H1	0.7472	0.9315	0.6274	0.057 (3)*
C2	0.82390 (14)	0.8336 (9)	0.5833 (2)	0.0472 (8)
H21	0.7993	0.7539	0.5248	0.057 (3)*
H22	0.8302	1.0392	0.5755	0.057 (3)*
C3	0.88860 (14)	0.6914 (7)	0.6164 (2)	0.0374 (7)
C4	0.92304 (13)	0.7422 (8)	0.7127 (2)	0.0387 (8)
H4	0.9350	0.9480	0.7211	0.057 (3)*
C5	0.87757 (14)	0.6750 (8)	0.7645 (2)	0.0443 (8)
H5	0.8643	0.4706	0.7562	0.057 (3)*
C6	0.91267 (17)	0.7332 (11)	0.8605 (2)	0.0607 (11)
H61	0.9224	0.9388	0.8696	0.057 (3)*
H62	0.8853	0.6770	0.8963	0.057 (3)*
C7	0.71604 (17)	0.4730 (10)	0.6834 (3)	0.0647 (12)
H71	0.6869	0.6366	0.6755	0.110 (7)*
H72	0.7404	0.4498	0.7461	0.110 (7)*
H73	0.6907	0.3008	0.6614	0.110 (7)*
C8	1.01113 (16)	0.6450 (8)	0.8370 (2)	0.0475 (9)
H8	1.0199	0.8542	0.8426	0.057 (3)*
C9	1.07425 (15)	0.4886 (8)	0.8695 (2)	0.0456 (8)
C10	1.11891 (16)	0.5232 (11)	0.8264 (2)	0.0598 (10)
H10	1.1085	0.6407	0.7756	0.057 (3)*
C11	1.17843 (17)	0.3908 (10)	0.8557 (2)	0.0600 (11)
H11	1.2088	0.4198	0.8257	0.057 (3)*
C12	1.19364 (18)	0.2166 (10)	0.9285 (2)	0.0601 (11)
H12	1.2341	0.1209	0.9483	0.057 (3)*
C13	1.14973 (19)	0.1827 (11)	0.9724 (3)	0.0706 (13)
H13	1.1603	0.0653	1.0233	0.057 (3)*
C14	1.09005 (16)	0.3177 (10)	0.9433 (2)	0.0556 (10)
H14	1.0601	0.2924	0.9743	0.057 (3)*
O9	0.95366 (10)	0.3482 (5)	0.39429 (15)	0.0450 (6)
H89	0.9861	0.4391	0.3918	0.110 (7)*
C15	0.9600 (2)	0.0630 (10)	0.3752 (4)	0.0866 (16)
H151	0.9493	0.0391	0.3114	0.110 (7)*
H152	0.9305	−0.0522	0.3960	0.110 (7)*
H153	1.0046	0.0013	0.4048	0.110 (7)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0450 (11)	0.0520 (14)	0.0465 (12)	0.0088 (12)	0.0165 (10)	−0.0091 (12)
O4	0.0380 (10)	0.0493 (14)	0.0300 (10)	0.0059 (11)	0.0063 (8)	−0.0017 (10)
O6	0.0576 (14)	0.090 (2)	0.0361 (12)	0.0198 (16)	0.0187 (11)	0.0043 (15)
O7	0.0430 (12)	0.0505 (17)	0.0638 (15)	0.0044 (13)	0.0223 (11)	−0.0119 (14)
O8	0.0441 (11)	0.0719 (18)	0.0323 (11)	0.0110 (14)	0.0078 (9)	−0.0057 (13)
N1	0.0359 (12)	0.0500 (18)	0.0298 (13)	0.0004 (14)	0.0067 (11)	−0.0022 (14)
C1	0.0428 (17)	0.047 (2)	0.0451 (19)	0.0067 (17)	0.0147 (15)	−0.0061 (17)
C2	0.0454 (17)	0.050 (2)	0.0454 (18)	0.0123 (19)	0.0133 (15)	0.0045 (18)
C3	0.0349 (15)	0.0388 (18)	0.0399 (18)	0.0002 (15)	0.0141 (14)	0.0006 (16)
C4	0.0357 (15)	0.0407 (19)	0.0392 (18)	0.0024 (15)	0.0117 (14)	−0.0027 (15)
C5	0.0453 (18)	0.049 (2)	0.0401 (18)	0.0090 (17)	0.0162 (15)	−0.0016 (17)
C6	0.058 (2)	0.083 (3)	0.045 (2)	0.018 (2)	0.0227 (17)	−0.004 (2)
C7	0.053 (2)	0.062 (3)	0.090 (3)	−0.003 (2)	0.038 (2)	−0.015 (2)
C8	0.0493 (19)	0.054 (2)	0.0320 (17)	0.0026 (17)	0.0034 (15)	−0.0049 (16)
C9	0.0452 (17)	0.050 (2)	0.0336 (16)	0.0003 (18)	0.0016 (14)	−0.0079 (17)
C10	0.058 (2)	0.078 (3)	0.0384 (18)	0.017 (2)	0.0083 (16)	0.008 (2)
C11	0.051 (2)	0.074 (3)	0.049 (2)	0.013 (2)	0.0084 (17)	−0.004 (2)
C12	0.051 (2)	0.055 (2)	0.061 (2)	0.002 (2)	−0.0012 (19)	0.001 (2)
C13	0.056 (2)	0.074 (3)	0.068 (3)	−0.004 (2)	0.000 (2)	0.027 (2)
C14	0.0479 (19)	0.062 (3)	0.049 (2)	−0.006 (2)	0.0046 (16)	0.009 (2)
O9	0.0444 (12)	0.0445 (14)	0.0494 (13)	−0.0022 (12)	0.0196 (10)	−0.0060 (12)
C15	0.065 (3)	0.046 (3)	0.159 (5)	−0.004 (2)	0.050 (3)	−0.024 (3)

Geometric parameters (Å, º)

O1—C5	1.426 (4)	C6—H62	0.9900
O1—C1	1.433 (4)	C7—H71	0.9800
O4—C4	1.425 (4)	C7—H72	0.9800
O4—C8	1.429 (3)	C7—H73	0.9800
O6—C8	1.400 (4)	C8—C9	1.500 (5)
O6—C6	1.431 (4)	C8—H8	1.0000
O7—C1	1.392 (5)	C9—C10	1.378 (5)
O7—C7	1.431 (4)	C9—C14	1.378 (5)
O8—N1	1.407 (3)	C10—C11	1.380 (5)
O8—H88	0.8400	C10—H10	0.9500
N1—C3	1.260 (4)	C11—C12	1.376 (6)
C1—C2	1.528 (4)	C11—H11	0.9500
C1—H1	1.0000	C12—C13	1.372 (6)
C2—C3	1.497 (4)	C12—H12	0.9500
C2—H21	0.9900	C13—C14	1.388 (5)
C2—H22	0.9900	C13—H13	0.9500
C3—C4	1.501 (4)	C14—H14	0.9500
C4—C5	1.523 (4)	O9—C15	1.392 (5)
C4—H4	1.0000	O9—H89	0.8400
C5—C6	1.506 (4)	C15—H151	0.9800
C5—H5	1.0000	C15—H152	0.9800
C6—H61	0.9900	C15—H153	0.9800
C5—O1—C1	111.6 (2)	H61—C6—H62	108.4
C4—O4—C8	109.0 (2)	O7—C7—H71	109.5
C8—O6—C6	111.6 (3)	O7—C7—H72	109.5
C1—O7—C7	112.3 (3)	H71—C7—H72	109.5
N1—O8—H88	109.5	O7—C7—H73	109.5
C3—N1—O8	112.4 (2)	H71—C7—H73	109.5
O7—C1—O1	111.3 (3)	H72—C7—H73	109.5
O7—C1—C2	108.0 (3)	O6—C8—O4	111.0 (3)
O1—C1—C2	112.0 (3)	O6—C8—C9	110.7 (3)
O7—C1—H1	108.5	O4—C8—C9	108.5 (3)
O1—C1—H1	108.5	O6—C8—H8	108.9
C2—C1—H1	108.5	O4—C8—H8	108.9
C3—C2—C1	112.7 (3)	C9—C8—H8	108.9
C3—C2—H21	109.0	C10—C9—C14	118.7 (3)
C1—C2—H21	109.0	C10—C9—C8	119.4 (3)
C3—C2—H22	109.0	C14—C9—C8	122.0 (3)
C1—C2—H22	109.0	C9—C10—C11	121.3 (4)
H21—C2—H22	107.8	C9—C10—H10	119.3
N1—C3—C2	127.9 (3)	C11—C10—H10	119.3
N1—C3—C4	118.9 (3)	C12—C11—C10	119.8 (4)
C2—C3—C4	113.2 (3)	C12—C11—H11	120.1
O4—C4—C3	112.7 (3)	C10—C11—H11	120.1
O4—C4—C5	109.5 (3)	C13—C12—C11	119.3 (4)
C3—C4—C5	109.4 (2)	C13—C12—H12	120.4
O4—C4—H4	108.4	C11—C12—H12	120.4
C3—C4—H4	108.4	C12—C13—C14	120.8 (4)
C5—C4—H4	108.4	C12—C13—H13	119.6
O1—C5—C6	109.0 (3)	C14—C13—H13	119.6
O1—C5—C4	109.8 (3)	C9—C14—C13	120.0 (4)
C6—C5—C4	108.4 (3)	C9—C14—H14	120.0
O1—C5—H5	109.9	C13—C14—H14	120.0
C6—C5—H5	109.9	C15—O9—H89	109.5
C4—C5—H5	109.9	O9—C15—H151	109.5
O6—C6—C5	108.4 (3)	O9—C15—H152	109.5
O6—C6—H61	110.0	H151—C15—H152	109.5
C5—C6—H61	110.0	O9—C15—H153	109.5
O6—C6—H62	110.0	H151—C15—H153	109.5
C5—C6—H62	110.0	H152—C15—H153	109.5
C7—O7—C1—O1	63.5 (3)	C3—C4—C5—C6	−178.9 (3)
C7—O7—C1—C2	−173.1 (3)	C8—O6—C6—C5	59.1 (4)
C5—O1—C1—O7	63.2 (3)	O1—C5—C6—O6	−174.7 (3)
C5—O1—C1—C2	−57.8 (4)	C4—C5—C6—O6	−55.3 (4)
O7—C1—C2—C3	−75.9 (4)	C6—O6—C8—O4	−63.1 (4)
O1—C1—C2—C3	47.0 (4)	C6—O6—C8—C9	176.3 (3)
O8—N1—C3—C2	−2.8 (5)	C4—O4—C8—O6	62.8 (3)
O8—N1—C3—C4	179.7 (3)	C4—O4—C8—C9	−175.3 (3)
C1—C2—C3—N1	137.9 (4)	O6—C8—C9—C10	177.5 (3)
C1—C2—C3—C4	−44.5 (4)	O4—C8—C9—C10	55.5 (5)
C8—O4—C4—C3	178.2 (3)	O6—C8—C9—C14	−4.8 (5)
C8—O4—C4—C5	−59.8 (3)	O4—C8—C9—C14	−126.8 (4)
N1—C3—C4—O4	−9.8 (4)	C14—C9—C10—C11	0.1 (6)
C2—C3—C4—O4	172.4 (3)	C8—C9—C10—C11	177.9 (4)
N1—C3—C4—C5	−131.8 (3)	C9—C10—C11—C12	1.0 (7)
C2—C3—C4—C5	50.3 (4)	C10—C11—C12—C13	−1.6 (7)
C1—O1—C5—C6	−176.7 (3)	C11—C12—C13—C14	1.1 (7)
C1—O1—C5—C4	64.8 (3)	C10—C9—C14—C13	−0.6 (6)
O4—C4—C5—O1	176.1 (3)	C8—C9—C14—C13	−178.3 (4)
C3—C4—C5—O1	−59.9 (4)	C12—C13—C14—C9	0.0 (7)
O4—C4—C5—C6	57.2 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O8—H88···O9	0.84	1.80	2.641 (3)	175
O9—H89···N1^i	0.84	2.08	2.873 (4)	157

Symmetry code: (i) −x+2, y, −z+1.