Benzyl 2-amino-4,6-O-benzyl­idene-2-de­oxy-α-D-glucopyran­oside

The title compound, C₂₀H₂₃NO₅, crystallizes exclusively as the α-anomer. All substituents are in equatorial positions except the benzyl substituent which occupies an axial position. Owing to its two vicinal donor atoms and its enanti­omeric purity, the title compound is a suitable N,O-bidentate ligand for complexation of transition metals.

Key indicators

• Single-crystal X-ray study
• T = 183 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.045
• wR factor = 0.104
• Data-to-parameter ratio = 9.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       2.70 Ratio
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           27.48
           From the CIF: _reflns_number_total               2278
           Count of symmetry unique reflns         2289
           Completeness (_total/calc)             99.52%
           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 C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R
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 C14    = .          R

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

   6 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
   1 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

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Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP (Siemens, 1990); software used to prepare material for publication: XP.

Benzyl 2-amino-4,6-O-benzylidene-2-deoxy-α-D-glucopyranoside

Crystal data

C20H23NO5	F(000) = 380
Mr = 357.39	Dx = 1.331 Mg m^−3
Monoclinic, P21	Melting point: 178 K
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 13.089 (3) Å	Cell parameters from 3728 reflections
b = 4.9156 (10) Å	θ = 1.7–27.5°
c = 15.196 (3) Å	µ = 0.10 mm^−1
β = 114.15 (3)°	T = 183 K
V = 892.1 (4) Å^3	Prism, colourless
Z = 2	0.5 × 0.5 × 0.5 mm

Data collection

Nonius KappaCCD diffractometer	1607 reflections with I > 2σ(I)
Radiation source: Fine-focus sealed tube	Rint = 0.054
Graphite monochromator	θmax = 27.5°, θmin = 1.7°
φ and ω scans	h = −16→16
6072 measured reflections	k = −5→6
2278 independent reflections	l = −19→15

Refinement

Refinement on F^2	Secondary atom site location: Difmap
Least-squares matrix: Full	Hydrogen site location: Geom
R[F^2 > 2σ(F^2)] = 0.045	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.104	w = 1/[σ^2(Fo^2) + (0.0394P)^2 + 0.1892P] where P = (Fo^2 + 2Fc^2)/3
S = 1.05	(Δ/σ)max < 0.001
2278 reflections	Δρmax = 0.18 e Å^−3
244 parameters	Δρmin = −0.24 e Å^−3
1 restraint	Absolute structure: Determined by NMR
Primary atom site location: Direct

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

	x	y	z	Uiso*/Ueq
N	0.2240 (3)	0.7418 (6)	0.6883 (2)	0.0333 (7)
H1A	0.259 (3)	0.605 (10)	0.731 (3)	0.055 (13)*
H1B	0.151 (3)	0.753 (8)	0.677 (2)	0.039 (10)*
O1	0.37743 (16)	0.5854 (4)	0.53584 (14)	0.0251 (5)
O2	0.39668 (15)	0.4152 (4)	0.68639 (15)	0.0255 (5)
O3	0.05014 (15)	0.5119 (4)	0.51590 (16)	0.0268 (5)
H3A	0.0119	0.3685	0.5024	0.040*
O4	0.12537 (16)	0.1981 (4)	0.39236 (14)	0.0224 (5)
O5	0.26052 (16)	0.1148 (4)	0.33234 (15)	0.0284 (5)
C1	0.3597 (2)	0.6343 (6)	0.6210 (2)	0.0221 (7)
H1	0.4026	0.8007	0.6534	0.027*
C2	0.2363 (2)	0.6812 (6)	0.5988 (2)	0.0231 (7)
H2	0.2125	0.8476	0.5575	0.028*
C3	0.1650 (2)	0.4468 (6)	0.5401 (2)	0.0195 (6)
H3	0.1854	0.2756	0.5791	0.023*
C4	0.1890 (2)	0.4160 (6)	0.4524 (2)	0.0191 (6)
H4	0.1689	0.5892	0.4146	0.023*
C5	0.3127 (2)	0.3587 (6)	0.4815 (2)	0.0225 (7)
H5	0.3348	0.1895	0.5214	0.027*
C6	0.3342 (2)	0.3238 (7)	0.3908 (2)	0.0285 (7)
H6A	0.3198	0.4971	0.3545	0.034*
H6B	0.4132	0.2713	0.4085	0.034*
C7	0.5152 (2)	0.3844 (7)	0.7280 (2)	0.0300 (8)
H7A	0.5510	0.5608	0.7547	0.036*
H7B	0.5406	0.3273	0.6778	0.036*
C8	0.5496 (2)	0.1749 (7)	0.8071 (2)	0.0275 (7)
C9	0.4759 (3)	0.0576 (8)	0.8398 (2)	0.0323 (8)
H9	0.3988	0.1054	0.8111	0.039*
C10	0.5140 (3)	−0.1298 (8)	0.9145 (3)	0.0410 (9)
H10	0.4625	−0.2116	0.9360	0.049*
C11	0.6258 (3)	−0.1990 (9)	0.9579 (3)	0.0473 (10)
H11	0.6518	−0.3238	1.0102	0.057*
C12	0.6995 (3)	−0.0853 (9)	0.9246 (3)	0.0513 (11)
H12	0.7765	−0.1335	0.9536	0.062*
C13	0.6619 (3)	0.0993 (8)	0.8490 (3)	0.0407 (9)
H13	0.7130	0.1744	0.8256	0.049*
C14	0.1463 (2)	0.1827 (7)	0.3084 (2)	0.0235 (7)
H14	0.1293	0.3626	0.2748	0.028*
C15	0.0722 (2)	−0.0317 (6)	0.2420 (2)	0.0224 (7)
C16	−0.0125 (2)	−0.1563 (6)	0.2600 (2)	0.0262 (7)
H16	−0.0236	−0.1104	0.3162	0.031*
C17	−0.0815 (3)	−0.3493 (7)	0.1954 (2)	0.0317 (8)
H17	−0.1403	−0.4322	0.2072	0.038*
C18	−0.0645 (3)	−0.4196 (7)	0.1145 (2)	0.0316 (8)
H18	−0.1107	−0.5533	0.0713	0.038*
C19	0.0197 (3)	−0.2957 (7)	0.0962 (2)	0.0329 (8)
H19	0.0316	−0.3450	0.0407	0.039*
C20	0.0869 (3)	−0.0994 (7)	0.1589 (2)	0.0292 (7)
H20	0.1432	−0.0108	0.1451	0.035*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N	0.0309 (16)	0.0388 (18)	0.0349 (17)	−0.0047 (15)	0.0182 (14)	−0.0143 (15)
O1	0.0235 (10)	0.0246 (11)	0.0282 (12)	−0.0046 (10)	0.0116 (9)	−0.0016 (9)
O2	0.0190 (10)	0.0278 (12)	0.0275 (12)	−0.0004 (9)	0.0073 (9)	0.0036 (10)
O3	0.0209 (10)	0.0200 (11)	0.0409 (13)	−0.0003 (9)	0.0143 (10)	−0.0039 (10)
O4	0.0240 (10)	0.0233 (11)	0.0217 (11)	−0.0013 (9)	0.0112 (9)	−0.0024 (10)
O5	0.0224 (10)	0.0346 (13)	0.0293 (12)	0.0022 (10)	0.0117 (9)	−0.0035 (10)
C1	0.0240 (15)	0.0193 (16)	0.0231 (16)	0.0015 (13)	0.0097 (13)	0.0017 (13)
C2	0.0248 (15)	0.0192 (15)	0.0265 (17)	0.0016 (13)	0.0118 (13)	−0.0023 (14)
C3	0.0190 (14)	0.0159 (14)	0.0255 (16)	0.0028 (12)	0.0112 (12)	0.0014 (12)
C4	0.0179 (13)	0.0156 (14)	0.0236 (16)	−0.0008 (12)	0.0083 (12)	0.0002 (12)
C5	0.0182 (14)	0.0251 (17)	0.0239 (16)	0.0000 (14)	0.0084 (12)	0.0015 (14)
C6	0.0229 (15)	0.0366 (19)	0.0287 (17)	−0.0026 (15)	0.0133 (13)	−0.0049 (15)
C7	0.0222 (15)	0.0332 (19)	0.0320 (18)	0.0000 (15)	0.0084 (14)	0.0007 (15)
C8	0.0252 (16)	0.0257 (16)	0.0261 (17)	−0.0010 (14)	0.0050 (13)	−0.0033 (14)
C9	0.0298 (16)	0.0349 (18)	0.0319 (19)	0.0042 (16)	0.0123 (15)	0.0031 (16)
C10	0.047 (2)	0.037 (2)	0.040 (2)	0.0039 (19)	0.0193 (17)	0.0055 (17)
C11	0.055 (2)	0.044 (2)	0.035 (2)	0.008 (2)	0.0110 (19)	0.0093 (18)
C12	0.0350 (19)	0.051 (2)	0.054 (3)	0.0087 (19)	0.0032 (18)	0.014 (2)
C13	0.0255 (16)	0.042 (2)	0.048 (2)	0.0012 (17)	0.0080 (16)	0.0075 (18)
C14	0.0227 (15)	0.0263 (16)	0.0235 (16)	0.0032 (14)	0.0116 (13)	0.0024 (14)
C15	0.0257 (15)	0.0185 (15)	0.0197 (15)	0.0043 (13)	0.0061 (13)	0.0028 (12)
C16	0.0253 (15)	0.0278 (17)	0.0237 (16)	0.0035 (14)	0.0082 (13)	0.0013 (14)
C17	0.0294 (16)	0.0318 (19)	0.0311 (19)	−0.0003 (15)	0.0096 (14)	0.0011 (15)
C18	0.0332 (17)	0.0249 (17)	0.0280 (18)	−0.0008 (16)	0.0036 (14)	−0.0012 (14)
C19	0.0431 (19)	0.0319 (18)	0.0210 (17)	0.0041 (17)	0.0104 (15)	0.0009 (15)
C20	0.0317 (16)	0.0296 (17)	0.0265 (17)	0.0010 (15)	0.0121 (14)	0.0031 (15)

Geometric parameters (Å, º)

N—C2	1.465 (4)	C7—H7A	0.9900
N—H1A	0.92 (4)	C7—H7B	0.9900
N—H1B	0.89 (4)	C8—C9	1.380 (5)
O1—C1	1.426 (4)	C8—C13	1.392 (4)
O1—C5	1.438 (4)	C9—C10	1.387 (5)
O2—C1	1.410 (4)	C9—H9	0.9500
O2—C7	1.424 (3)	C10—C11	1.380 (5)
O3—C3	1.430 (3)	C10—H10	0.9500
O3—H3A	0.8400	C11—C12	1.378 (5)
O4—C14	1.412 (3)	C11—H11	0.9500
O4—C4	1.432 (3)	C12—C13	1.387 (5)
O5—C14	1.426 (3)	C12—H12	0.9500
O5—C6	1.440 (4)	C13—H13	0.9500
C1—C2	1.526 (4)	C14—C15	1.506 (4)
C1—H1	1.0000	C14—H14	1.0000
C2—C3	1.521 (4)	C15—C16	1.388 (4)
C2—H2	1.0000	C15—C20	1.393 (4)
C3—C4	1.497 (4)	C16—C17	1.398 (4)
C3—H3	1.0000	C16—H16	0.9500
C4—C5	1.521 (4)	C17—C18	1.379 (5)
C4—H4	1.0000	C17—H17	0.9500
C5—C6	1.524 (4)	C18—C19	1.384 (5)
C5—H5	1.0000	C18—H18	0.9500
C6—H6A	0.9900	C19—C20	1.388 (5)
C6—H6B	0.9900	C19—H19	0.9500
C7—C8	1.505 (5)	C20—H20	0.9500
C2—N—H1A	107 (3)	C8—C7—H7A	109.6
C2—N—H1B	110 (2)	O2—C7—H7B	109.6
H1A—N—H1B	111 (4)	C8—C7—H7B	109.6
C1—O1—C5	112.1 (2)	H7A—C7—H7B	108.2
C1—O2—C7	113.1 (2)	C9—C8—C13	119.2 (3)
C3—O3—H3A	109.5	C9—C8—C7	123.3 (3)
C14—O4—C4	109.8 (2)	C13—C8—C7	117.6 (3)
C14—O5—C6	111.0 (2)	C8—C9—C10	120.1 (3)
O2—C1—O1	112.0 (2)	C8—C9—H9	119.9
O2—C1—C2	107.4 (2)	C10—C9—H9	119.9
O1—C1—C2	112.0 (2)	C11—C10—C9	120.8 (4)
O2—C1—H1	108.4	C11—C10—H10	119.6
O1—C1—H1	108.4	C9—C10—H10	119.6
C2—C1—H1	108.4	C12—C11—C10	119.3 (4)
N—C2—C3	115.1 (3)	C12—C11—H11	120.4
N—C2—C1	109.5 (3)	C10—C11—H11	120.4
C3—C2—C1	110.8 (2)	C11—C12—C13	120.4 (3)
N—C2—H2	107.0	C11—C12—H12	119.8
C3—C2—H2	107.0	C13—C12—H12	119.8
C1—C2—H2	107.0	C12—C13—C8	120.2 (4)
O3—C3—C4	112.0 (2)	C12—C13—H13	119.9
O3—C3—C2	108.0 (2)	C8—C13—H13	119.9
C4—C3—C2	107.3 (2)	O4—C14—O5	110.7 (2)
O3—C3—H3	109.8	O4—C14—C15	109.4 (2)
C4—C3—H3	109.8	O5—C14—C15	109.1 (2)
C2—C3—H3	109.8	O4—C14—H14	109.2
O4—C4—C3	111.3 (2)	O5—C14—H14	109.2
O4—C4—C5	108.6 (2)	C15—C14—H14	109.2
C3—C4—C5	110.2 (2)	C16—C15—C20	119.4 (3)
O4—C4—H4	108.9	C16—C15—C14	121.6 (3)
C3—C4—H4	108.9	C20—C15—C14	118.9 (3)
C5—C4—H4	108.9	C15—C16—C17	120.0 (3)
O1—C5—C4	109.3 (2)	C15—C16—H16	120.0
O1—C5—C6	108.9 (2)	C17—C16—H16	120.0
C4—C5—C6	109.1 (2)	C18—C17—C16	120.2 (3)
O1—C5—H5	109.9	C18—C17—H17	119.9
C4—C5—H5	109.9	C16—C17—H17	119.9
C6—C5—H5	109.9	C17—C18—C19	120.0 (3)
O5—C6—C5	108.3 (2)	C17—C18—H18	120.0
O5—C6—H6A	110.0	C19—C18—H18	120.0
C5—C6—H6A	110.0	C18—C19—C20	120.1 (3)
O5—C6—H6B	110.0	C18—C19—H19	120.0
C5—C6—H6B	110.0	C20—C19—H19	120.0
H6A—C6—H6B	108.4	C19—C20—C15	120.3 (3)
O2—C7—C8	110.1 (3)	C19—C20—H20	119.9
O2—C7—H7A	109.6	C15—C20—H20	119.9

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3A···O3^i	0.84	1.90	2.735 (5)	170

Symmetry code: (i) −x, y−1/2, −z+1.