(5-Methoxy­carbonyl)­pentyl α-d-manno­pyran­oside

Gainsford, G.J.; Luboradzki, R.; Pakulski, Z.

doi:10.1107/S1600536804005987

(5-Methoxycarbonyl)pentyl α-D-mannopyranoside

G. J. Gainsford, R. Luboradzki and Z. Pakulski

In the crystalline state, the title compound, C₁₃H₂₄O₈, forms hydrogen-bonded carbohydrate bilayers with interdigitated hydrophobically interacting alkyl chains.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536804005987/fl6092sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536804005987/fl6092Isup2.hkl Contains datablock I

CCDC reference: 238820

checkCIF report

Key indicators

Single-crystal X-ray study
T = 293 K
Mean (C-C) = 0.005 Å
R factor = 0.044
wR factor = 0.084
Data-to-parameter ratio = 6.5

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT027_ALERT_3_A _diffrn_reflns_theta_full (too) Low ............      23.79 Deg.

Author Response: : Data collected from a weakly diffracting crystal which showed no intensity data beyond 24 degrees; experimental limitations prevented collecting for longer measurement time.

 This limited the data/parameter ratio and resolution reflected
 in a few rather distorted thermal ellipsoids.

PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low .......       0.92

Author Response: ... See vrf_PLAT027. This is related to the same data collection problem.


Alert level B
THETM01_ALERT_3_B  The value of sine(theta_max)/wavelength is less than 0.575
            Calculated sin(theta_max)/wavelength =    0.5676
PLAT023_ALERT_3_B Resolution (too) Low [sin(th)/Lambda < 0.6].....      23.79 Deg.
PLAT063_ALERT_3_B Crystal Probably too Large for Beam Size .......       1.00 mm
PLAT213_ALERT_2_B Atom O2      has ADP max/min Ratio .............       4.10 prolat

Alert level C
REFLT03_ALERT_1_C  Reflection count < 95% complete
           From the CIF: _diffrn_reflns_theta_max           23.79
           From the CIF: _diffrn_reflns_theta_full           0.00
           From the CIF: _reflns_number_total               1283
           TEST2: Reflns within _diffrn_reflns_theta_max
           Count of symmetry unique reflns         1389
           Completeness (_total/calc)             92.37%
REFNR01_ALERT_3_C  Ratio of reflections to parameters is < 8 for a
            non-centrosymmetric structure, where ZMAX < 18
            sine(theta)/lambda                0.5676
            Proportion of unique data used    1.0000
            Ratio reflections to parameters   6.5459
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ....       0.92
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) .....       6.55
PLAT213_ALERT_2_C Atom C1      has ADP max/min Ratio .............       3.30 prolat
PLAT213_ALERT_2_C Atom C3      has ADP max/min Ratio .............       3.10 prolat
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.56 Ratio
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       3.28
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           23.79
           From the CIF: _reflns_number_total               1283
           Count of symmetry unique reflns         1389
           Completeness (_total/calc)             92.37%
           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

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

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

Computing details top

Data collection: KappaCCD; cell refinement: DENZO and SCALEPAK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPAK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003).

(5-methoxycarbonyl)pentyl α-D-mannopyranoside top

Crystal data top

C₁₃H₂₄O₈	F(000) = 664
M_r = 308.32	D_x = 1.360 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 969 reflections
a = 6.1389 (2) Å	θ = 1.0–23.8°
b = 7.2316 (2) Å	µ = 0.11 mm⁻¹
c = 33.9218 (14) Å	T = 293 K
V = 1505.93 (9) Å³	Poor quality, needle, colourless
Z = 4	1.0 × 0.2 × 0.1 mm

Data collection top

Nonius KappaCCD diffractometer	1112 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.032
Graphite monochromator	θ_max = 23.8°, θ_min = 3.1°
φ and ω scans	h = −6→6
2049 measured reflections	k = −8→8
1283 independent reflections	l = −37→38

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.084	H-atom parameters constrained
S = 1.12	w = 1/[σ²(F_o²) + (0.0321P)² + 0.3006P] where P = (F_o² + 2F_c²)/3
1283 reflections	(Δ/σ)_max < 0.001
196 parameters	Δρ_max = 0.15 e Å⁻³
0 restraints	Δρ_min = −0.16 e Å⁻³

Special details top

Experimental. Weakly diffracting crystal showed no intensity data beyond 24 degrees; experimental limitations prevented collecting for longer measurement time.

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.

Refinement. Refinement on F² for ALL reflections except for 1 with very negative F² or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating _R_factor_obs 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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.5505 (3)	0.7920 (3)	0.89028 (7)	0.0234 (6)
O2	0.4891 (5)	0.8553 (3)	0.99513 (8)	0.0430 (8)
H2O	0.5203	0.7539	1.0043	0.064*
O3	0.0933 (4)	0.9911 (3)	0.97456 (7)	0.0311 (6)
H3O	−0.0190	1.0298	0.9644	0.047*
O4	0.2529 (4)	1.3223 (3)	0.93026 (8)	0.0380 (7)
H4O	0.1462	1.3375	0.9444	0.057*
O5	0.7204 (4)	1.0172 (3)	0.92888 (7)	0.0307 (6)
O6	0.8357 (4)	1.3599 (3)	0.95382 (8)	0.0344 (7)
H6O	0.7624	1.4181	0.9698	0.052*
O7	0.2195 (4)	0.7309 (3)	0.68609 (7)	0.0280 (6)
O8	−0.1069 (4)	0.8327 (3)	0.70585 (8)	0.0278 (6)
C1	0.6179 (6)	0.8404 (4)	0.92840 (11)	0.0292 (9)
H1	0.7232	0.7480	0.9375	0.035*
C2	0.4203 (7)	0.8340 (4)	0.95530 (11)	0.0330 (10)
H2	0.3441	0.7158	0.9521	0.040*
C3	0.2667 (6)	0.9933 (5)	0.94586 (11)	0.0310 (9)
H3	0.2038	0.9725	0.9197	0.037*
C4	0.3834 (6)	1.1777 (4)	0.94572 (12)	0.0313 (9)
H4	0.4317	1.2089	0.9724	0.018 (9)*
C5	0.5785 (6)	1.1672 (4)	0.91807 (11)	0.0301 (9)
H5	0.5251	1.1452	0.8912	0.036*
C6	0.7158 (6)	1.3395 (4)	0.91784 (11)	0.0332 (10)
H6A	0.8167	1.3345	0.8959	0.040*
H6B	0.6226	1.4465	0.9142	0.040*
C7	0.7250 (5)	0.7876 (4)	0.86223 (11)	0.0241 (8)
H7A	0.8434	0.7119	0.8721	0.029*
H7B	0.7798	0.9116	0.8578	0.029*
C8	0.6385 (5)	0.7077 (4)	0.82430 (10)	0.0217 (8)
H8A	0.5924	0.5813	0.8290	0.026*
H8B	0.7552	0.7046	0.8050	0.026*
C9	0.4475 (5)	0.8163 (5)	0.80722 (10)	0.0244 (9)
H9A	0.3246	0.8065	0.8251	0.029*
H9B	0.4877	0.9458	0.8056	0.029*
C10	0.3774 (5)	0.7508 (4)	0.76666 (11)	0.0223 (8)
H10A	0.4956	0.7710	0.7482	0.027*
H10B	0.3488	0.6190	0.7677	0.027*
C11	0.1756 (5)	0.8496 (5)	0.75192 (10)	0.0235 (9)
H11A	0.0567	0.8246	0.7700	0.028*
H11B	0.2027	0.9818	0.7524	0.028*
C12	0.1057 (5)	0.7967 (4)	0.71127 (11)	0.0198 (8)
C13	−0.1923 (5)	0.7959 (5)	0.66689 (11)	0.0325 (10)
H13A	−0.1470	0.8921	0.6492	0.049*
H13B	−0.3485	0.7922	0.6679	0.049*
H13C	−0.1382	0.6791	0.6577	0.049*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0418 (14)	0.0163 (12)	0.0119 (15)	0.0010 (11)	0.0010 (11)	−0.0028 (10)
O2	0.106 (2)	0.0135 (12)	0.0097 (17)	0.0153 (15)	−0.0038 (15)	0.0031 (11)
O3	0.0597 (17)	0.0182 (12)	0.0154 (16)	0.0040 (13)	0.0077 (14)	0.0042 (11)
O4	0.0696 (19)	0.0150 (13)	0.0294 (19)	0.0097 (13)	0.0128 (14)	0.0107 (12)
O5	0.0645 (16)	0.0099 (11)	0.0178 (15)	−0.0025 (11)	−0.0072 (13)	0.0020 (10)
O6	0.0640 (17)	0.0200 (13)	0.0194 (19)	−0.0081 (12)	0.0068 (13)	−0.0080 (11)
O7	0.0279 (13)	0.0366 (15)	0.0194 (16)	0.0007 (12)	0.0032 (11)	−0.0085 (11)
O8	0.0243 (13)	0.0378 (14)	0.0212 (17)	0.0054 (12)	−0.0007 (11)	−0.0073 (12)
C1	0.066 (3)	0.0082 (16)	0.014 (2)	0.0000 (17)	−0.0072 (19)	−0.0036 (16)
C2	0.077 (3)	0.0110 (17)	0.011 (2)	0.0020 (19)	0.005 (2)	0.0010 (16)
C3	0.068 (3)	0.0149 (17)	0.010 (2)	0.0006 (18)	0.001 (2)	0.0047 (16)
C4	0.071 (3)	0.0107 (17)	0.013 (2)	0.0028 (18)	0.002 (2)	0.0021 (16)
C5	0.067 (3)	0.0117 (17)	0.011 (2)	0.0030 (19)	−0.0025 (19)	0.0020 (16)
C6	0.074 (3)	0.0125 (17)	0.013 (2)	0.0036 (19)	0.006 (2)	0.0012 (15)
C7	0.039 (2)	0.0191 (18)	0.014 (2)	−0.0024 (17)	0.0025 (16)	0.0012 (15)
C8	0.0331 (19)	0.0210 (17)	0.011 (2)	−0.0026 (16)	0.0048 (15)	−0.0036 (16)
C9	0.038 (2)	0.0184 (18)	0.017 (2)	−0.0027 (17)	0.0032 (15)	−0.0036 (15)
C10	0.0272 (18)	0.0190 (18)	0.021 (2)	−0.0041 (16)	0.0004 (15)	−0.0024 (16)
C11	0.0270 (19)	0.0244 (18)	0.019 (2)	−0.0062 (15)	0.0078 (16)	−0.0042 (16)
C12	0.0246 (19)	0.0140 (16)	0.021 (2)	−0.0027 (15)	0.0051 (16)	0.0000 (16)
C13	0.027 (2)	0.043 (2)	0.027 (3)	0.0042 (18)	−0.0019 (17)	−0.0081 (19)

Geometric parameters (Å, º) top

O1—C1	1.402 (4)	C5—C6	1.505 (5)
O1—C7	1.433 (4)	C5—H5	0.9800
O2—C2	1.424 (4)	C6—H6A	0.9700
O2—H2O	0.8200	C6—H6B	0.9700
O3—C3	1.443 (4)	C7—C8	1.507 (5)
O3—H3O	0.8200	C7—H7A	0.9700
O4—C4	1.418 (4)	C7—H7B	0.9700
O4—H4O	0.8200	C8—C9	1.525 (5)
O5—C1	1.425 (4)	C8—H8A	0.9700
O5—C5	1.439 (4)	C8—H8B	0.9700
O6—C6	1.433 (4)	C9—C10	1.517 (5)
O6—H6O	0.8200	C9—H9A	0.9700
O7—C12	1.202 (4)	C9—H9B	0.9700
O8—C12	1.344 (4)	C10—C11	1.515 (4)
O8—C13	1.446 (4)	C10—H10A	0.9700
C1—C2	1.519 (5)	C10—H10B	0.9700
C1—H1	0.9800	C11—C12	1.494 (5)
C2—C3	1.523 (5)	C11—H11A	0.9700
C2—H2	0.9800	C11—H11B	0.9700
C3—C4	1.514 (5)	C13—H13A	0.9600
C3—H3	0.9800	C13—H13B	0.9600
C4—C5	1.523 (5)	C13—H13C	0.9600
C4—H4	0.9800

C1—O1—C7	113.4 (3)	C5—C6—H6B	109.3
C2—O2—H2O	109.5	H6A—C6—H6B	108.0
C3—O3—H3O	109.5	O1—C7—C8	108.2 (3)
C4—O4—H4O	109.5	O1—C7—H7A	110.1
C1—O5—C5	114.0 (3)	C8—C7—H7A	110.1
C6—O6—H6O	109.5	O1—C7—H7B	110.1
C12—O8—C13	116.2 (3)	C8—C7—H7B	110.1
O1—C1—O5	111.4 (3)	H7A—C7—H7B	108.4
O1—C1—C2	108.1 (3)	C7—C8—C9	113.4 (3)
O5—C1—C2	111.9 (3)	C7—C8—H8A	108.9
O1—C1—H1	108.4	C9—C8—H8A	108.9
O5—C1—H1	108.4	C7—C8—H8B	108.9
C2—C1—H1	108.4	C9—C8—H8B	108.9
O2—C2—C1	109.3 (3)	H8A—C8—H8B	107.7
O2—C2—C3	107.5 (3)	C10—C9—C8	113.7 (3)
C1—C2—C3	110.2 (3)	C10—C9—H9A	108.8
O2—C2—H2	109.9	C8—C9—H9A	108.8
C1—C2—H2	109.9	C10—C9—H9B	108.8
C3—C2—H2	109.9	C8—C9—H9B	108.8
O3—C3—C4	111.2 (3)	H9A—C9—H9B	107.7
O3—C3—C2	107.9 (3)	C11—C10—C9	112.6 (3)
C4—C3—C2	112.0 (3)	C11—C10—H10A	109.1
O3—C3—H3	108.6	C9—C10—H10A	109.1
C4—C3—H3	108.6	C11—C10—H10B	109.1
C2—C3—H3	108.6	C9—C10—H10B	109.1
O4—C4—C3	112.6 (3)	H10A—C10—H10B	107.8
O4—C4—C5	104.7 (3)	C12—C11—C10	114.7 (3)
C3—C4—C5	109.3 (3)	C12—C11—H11A	108.6
O4—C4—H4	110.1	C10—C11—H11A	108.6
C3—C4—H4	110.1	C12—C11—H11B	108.6
C5—C4—H4	110.1	C10—C11—H11B	108.6
O5—C5—C6	106.7 (3)	H11A—C11—H11B	107.6
O5—C5—C4	110.9 (3)	O7—C12—O8	123.0 (3)
C6—C5—C4	113.7 (3)	O7—C12—C11	126.2 (3)
O5—C5—H5	108.5	O8—C12—C11	110.8 (3)
C6—C5—H5	108.5	O8—C13—H13A	109.5
C4—C5—H5	108.5	O8—C13—H13B	109.5
O6—C6—C5	111.6 (3)	H13A—C13—H13B	109.5
O6—C6—H6A	109.3	O8—C13—H13C	109.5
C5—C6—H6A	109.3	H13A—C13—H13C	109.5
O6—C6—H6B	109.3	H13B—C13—H13C	109.5

C7—O1—C1—O5	58.4 (4)	C1—O5—C5—C4	58.9 (4)
C7—O1—C1—C2	−178.2 (2)	O4—C4—C5—O5	−176.5 (3)
C5—O5—C1—O1	63.9 (4)	C3—C4—C5—O5	−55.7 (4)
C5—O5—C1—C2	−57.2 (4)	O4—C4—C5—C6	63.3 (4)
O1—C1—C2—O2	171.4 (2)	C3—C4—C5—C6	−175.9 (3)
O5—C1—C2—O2	−65.6 (3)	O5—C5—C6—O6	−51.4 (4)
O1—C1—C2—C3	−70.7 (3)	C4—C5—C6—O6	71.2 (4)
O5—C1—C2—C3	52.4 (4)	C1—O1—C7—C8	171.9 (2)
O2—C2—C3—O3	−55.6 (4)	O1—C7—C8—C9	58.3 (4)
C1—C2—C3—O3	−174.6 (3)	C7—C8—C9—C10	173.0 (3)
O2—C2—C3—C4	67.0 (4)	C8—C9—C10—C11	175.0 (3)
C1—C2—C3—C4	−52.0 (4)	C9—C10—C11—C12	177.2 (3)
O3—C3—C4—O4	−69.8 (4)	C13—O8—C12—O7	−2.8 (5)
C2—C3—C4—O4	169.5 (3)	C13—O8—C12—C11	177.0 (3)
O3—C3—C4—C5	174.4 (3)	C10—C11—C12—O7	−23.0 (5)
C2—C3—C4—C5	53.7 (4)	C10—C11—C12—O8	157.1 (3)
C1—O5—C5—C6	−176.7 (3)

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(5-Methoxy­carbonyl)­pentyl α-D-manno­pyran­oside

Supporting information

Key indicators

checkCIF/PLATON results

(5-Methoxycarbonyl)pentyl α-D-mannopyranoside