3,5-Di-p-toluoyl-1,2-dide­oxy-β-1-(imidazol-1-yl)-D-ribofuranose

The title compound, C₂₄H₂₄N₂O₅, was obtained as a reaction inter­mediate in the synthesis of the artificial imidazole nucleoside, which is a highly useful synthetic nucleoside for the formation of metal-ion-mediated base pairs. Compared to the free nucleoside, both OH groups of the sugar moiety are protected by p-toluoyl groups. The sugar is in its C3′-endo conformation.

Key indicators

• Single-crystal X-ray study
• T = 103 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.060
• wR factor = 0.137
• Data-to-parameter ratio = 9.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          6
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety         C6
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C11

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               2647
           Count of symmetry unique reflns         2659
           Completeness (_total/calc)             99.55%
           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 C7     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C13    = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C21    = .          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
   3 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
   0 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
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

In the course of our studies regarding the use of artificial azole nucleosides (azole = imidazole, 1,2,4-triazole, tetrazole) in metal-ion mediated base pairs (Böhme et al., 2007; Müller et al., 2007; Polonius & Müller, 2007; Müller et al., 2005) we have isolated the title compound (Figure 1) as a reaction intermediate in the synthesis of imidazole nucleoside. It crystallizes in the same space group and with very similar unit-cell dimensions as the related triazole nucleoside (Müller et al., 2005). All bond lengths and angles are within the normal range (Allen et al., 1987). The artificial nucleobase is connected to the sugar moiety via an N-glycosidic bond. It is oriented anti with respect to the sugar. The deoxyribose adopts a C3'-endo conformation (phase angle of pseudorotation = 7.7 (5)°). The title compound forms long columns along the crystallographic b axis (Fig. 2). However, there is no π stacking between neighboring toluoyl rings that are related by the symmetry operator (x, y + 1, z). Instead, neighboring rings that are related by the symmetry operator (1 - x, y + 1/2, 3 - z) are oriented at an angle of 62.7 (2)° with respect to each other.

Related literature

The structures of the analogous 1,2,4-triazole and tetrazole nucleosides have been reported recently (Müller et al., 2005). These nucleosides have been used in metal-ion-mediated base pairs (Böhme et al., 2007). For related literature, see: Polonius & Müller (2007); Müller et al. (2007); Allen et al. (1987); Farrugia (1997, 1999); Flack (1983).

S2. Experimental

The title compound was prepared as reported previously (Müller et al., 2005). Single crystals suitable for X-ray measurement were obtained by crystallization from dichloromethane and cyclohexane with triethylamine at room temperature. A satisfactory elemental analysis was obtained: Calcd. for C₂₄H₂₄N₂O₅: C 68.6, H 5.8, N 6.7; found: C 68.2, H 6.2, N 6.6.

S3. Refinement

In the absence of significant anomalous dispersion effects, a total of 1277 Friedel pairs have been merged during the final refinement.

Hydrogen atoms were included in the refinement at calculated positions with C—H = 0.95–1.00 Å and U_iso(H) = 1.2U_eq(C) or 1.5U_eq(C) for methyl groups.

Computing details

Data collection: KappaCCD (Nonius, 2000); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (Sheldrick, 1990); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures

	Fig. 1. View of the title compound showing displacement ellipsoids at the 50% probability level.
	Fig. 2. Packing of the title compound with a view along the b axis.

3,5-Di-p-toluoyl-1,2-dideoxy-β-1-(imidazol-1-yl)-D-ribofuranose

Crystal data

C24H24N2O5	Z = 2
Mr = 420.45	F(000) = 444
Monoclinic, P21	Dx = 1.33 Mg m^−3
Hall symbol: P 2yb	Mo Kα radiation, λ = 0.71073 Å
a = 14.436 (3) Å	θ = 3–27.5°
b = 5.3850 (11) Å	µ = 0.09 mm^−1
c = 15.061 (3) Å	T = 103 K
β = 116.25 (3)°	Cubes, colorless
V = 1050.1 (5) Å^3	0.1 × 0.1 × 0.1 mm

Data collection

Bruker–Nonius Kappa CCD diffractometer	Rint = 0.097
profile fitled scans	θmax = 27.5°, θmin = 3.0°
12891 measured reflections	h = −18→18
2647 independent reflections	k = −7→5
1726 reflections with I > 2σ(I)	l = −19→19

Refinement

Refinement on F^2	1 restraint
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.060	w = 1/[σ^2(Fo^2) + (0.0694P)^2 + 0.2112P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.137	(Δ/σ)max < 0.001
S = 1.01	Δρmax = 0.28 e Å^−3
2647 reflections	Δρmin = −0.34 e Å^−3
280 parameters

Special details

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.

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

	x	y	z	Uiso*/Ueq
O30	0.3603 (2)	0.8395 (6)	0.96544 (19)	0.0222 (7)
N29	0.1239 (2)	1.0452 (6)	0.9936 (2)	0.0200 (8)
O28	0.44002 (19)	0.7940 (6)	1.24729 (19)	0.0221 (7)
O27	0.4201 (2)	0.9804 (6)	0.8587 (2)	0.0259 (7)
C26	0.5335 (3)	0.5234 (8)	1.3793 (3)	0.0200 (9)
C25	0.0239 (3)	0.8334 (9)	0.8628 (3)	0.0268 (10)
H25A	−0.0014	0.7064	0.8141	0.032*
C24	0.6206 (3)	0.6745 (9)	1.4091 (3)	0.0267 (11)
H24A	0.6179	0.822	1.3734	0.032*
N23	−0.0292 (3)	1.0479 (8)	0.8608 (3)	0.0303 (9)
C22	0.1929 (3)	0.5296 (8)	0.6379 (3)	0.0242 (10)
H22A	0.1737	0.5516	0.5694	0.029*
C21	0.2101 (3)	1.1388 (8)	1.0832 (3)	0.0205 (10)
H21A	0.1866	1.2855	1.1085	0.025*
C20	0.2901 (3)	0.6638 (8)	0.8066 (3)	0.0196 (9)
C19	0.0339 (3)	1.1715 (9)	0.9398 (3)	0.0249 (10)
H19A	0.0187	1.3304	0.9575	0.03*
O18	0.3571 (2)	0.4591 (6)	1.2656 (2)	0.0262 (7)
C17	0.1172 (3)	0.8278 (9)	0.9437 (3)	0.0256 (10)
H17A	0.1675	0.6995	0.962	0.031*
C16	0.7183 (3)	0.3957 (9)	1.5446 (3)	0.0283 (12)
C15	0.2466 (3)	0.4697 (8)	0.8370 (3)	0.0214 (9)
H15A	0.2654	0.4478	0.9054	0.026*
C14	0.5391 (3)	0.3097 (9)	1.4337 (3)	0.0257 (10)
H14A	0.48	0.2064	1.4147	0.031*
C13	0.3831 (3)	1.0697 (8)	1.1102 (3)	0.0194 (9)
H13A	0.4338	1.1726	1.1657	0.023*
C12	0.4342 (3)	0.5834 (8)	1.2935 (3)	0.0209 (10)
C11	0.8179 (3)	0.3260 (12)	1.6335 (3)	0.0429 (14)
H11A	0.8709	0.4508	1.6431	0.064*
H11B	0.8412	0.1632	1.6223	0.064*
H11C	0.8059	0.3188	1.6927	0.064*
C10	0.1487 (3)	0.3368 (9)	0.6677 (3)	0.0245 (10)
C9	0.1769 (3)	0.3097 (9)	0.7689 (3)	0.0261 (10)
H9A	0.1477	0.1794	0.7907	0.031*
C8	0.3638 (3)	0.8416 (9)	0.8767 (3)	0.0220 (9)
C7	0.3513 (3)	0.8494 (8)	1.1542 (3)	0.0180 (9)
H7A	0.3321	0.7032	1.1087	0.022*
C6	0.0724 (3)	0.1619 (9)	0.5931 (3)	0.0337 (12)
H6A	0.0619	0.2086	0.5265	0.051*
H6B	0.0064	0.1713	0.5969	0.051*
H6C	0.0991	−0.0082	0.6075	0.051*
C5	0.6310 (3)	0.2462 (9)	1.5159 (3)	0.0299 (11)
H5A	0.634	0.1001	1.5524	0.036*
C4	0.2640 (3)	0.6893 (9)	0.7056 (3)	0.0266 (10)
H4A	0.295	0.8159	0.6838	0.032*
C3	0.4296 (3)	1.0075 (9)	1.0408 (3)	0.0234 (10)
H3A	0.4392	1.1609	1.0096	0.028*
H3B	0.4979	0.9279	1.0779	0.028*
C2	0.7116 (3)	0.6093 (10)	1.4912 (3)	0.0315 (12)
H2A	0.7703	0.714	1.511	0.038*
C1	0.2577 (3)	0.9476 (9)	1.1657 (3)	0.0199 (9)
H1A	0.2082	0.8122	1.1576	0.024*
H1B	0.2792	1.0256	1.2314	0.024*
O31	0.2904 (2)	1.2143 (5)	1.05768 (19)	0.0208 (7)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O30	0.0189 (14)	0.0291 (16)	0.0216 (15)	−0.0078 (14)	0.0116 (12)	−0.0057 (14)
N29	0.0149 (17)	0.0197 (19)	0.0251 (18)	−0.0006 (16)	0.0087 (15)	−0.0016 (16)
O28	0.0160 (14)	0.0252 (16)	0.0221 (15)	0.0017 (13)	0.0057 (12)	0.0027 (13)
O27	0.0230 (15)	0.0327 (19)	0.0266 (16)	−0.0017 (15)	0.0153 (13)	−0.0005 (15)
C26	0.022 (2)	0.022 (2)	0.020 (2)	0.0020 (19)	0.0131 (18)	−0.0048 (18)
C25	0.023 (2)	0.027 (2)	0.029 (2)	−0.003 (2)	0.010 (2)	−0.001 (2)
C24	0.021 (2)	0.032 (3)	0.029 (2)	0.001 (2)	0.014 (2)	−0.001 (2)
N23	0.0244 (19)	0.033 (2)	0.027 (2)	−0.0011 (19)	0.0055 (17)	0.0014 (19)
C22	0.026 (2)	0.025 (3)	0.022 (2)	0.005 (2)	0.0110 (19)	−0.001 (2)
C21	0.014 (2)	0.023 (2)	0.027 (2)	−0.0015 (19)	0.0100 (18)	0.001 (2)
C20	0.016 (2)	0.023 (2)	0.022 (2)	0.006 (2)	0.0095 (18)	0.000 (2)
C19	0.017 (2)	0.026 (2)	0.033 (2)	0.007 (2)	0.012 (2)	0.006 (2)
O18	0.0247 (16)	0.0233 (16)	0.0275 (16)	−0.0036 (15)	0.0087 (13)	0.0007 (15)
C17	0.020 (2)	0.028 (2)	0.027 (2)	0.001 (2)	0.009 (2)	−0.001 (2)
C16	0.025 (2)	0.043 (3)	0.019 (2)	0.011 (2)	0.010 (2)	0.001 (2)
C15	0.022 (2)	0.026 (2)	0.018 (2)	0.004 (2)	0.0107 (18)	0.005 (2)
C14	0.026 (2)	0.026 (2)	0.026 (2)	0.004 (2)	0.012 (2)	0.001 (2)
C13	0.016 (2)	0.021 (2)	0.021 (2)	0.0005 (18)	0.0076 (17)	−0.0008 (19)
C12	0.025 (2)	0.018 (2)	0.021 (2)	0.006 (2)	0.0122 (19)	0.002 (2)
C11	0.026 (2)	0.066 (4)	0.034 (3)	0.019 (3)	0.012 (2)	0.010 (3)
C10	0.017 (2)	0.025 (2)	0.028 (2)	0.007 (2)	0.0070 (19)	0.001 (2)
C9	0.021 (2)	0.026 (2)	0.035 (2)	0.005 (2)	0.016 (2)	0.000 (2)
C8	0.018 (2)	0.028 (2)	0.024 (2)	0.006 (2)	0.0132 (19)	0.002 (2)
C7	0.0150 (19)	0.023 (2)	0.017 (2)	−0.0027 (19)	0.0075 (17)	0.0003 (19)
C6	0.024 (2)	0.033 (3)	0.036 (3)	0.001 (2)	0.006 (2)	−0.003 (2)
C5	0.034 (3)	0.035 (3)	0.025 (2)	0.009 (2)	0.017 (2)	0.010 (2)
C4	0.024 (2)	0.033 (3)	0.028 (2)	0.003 (2)	0.016 (2)	0.002 (2)
C3	0.018 (2)	0.029 (3)	0.025 (2)	−0.004 (2)	0.0101 (18)	−0.001 (2)
C2	0.024 (2)	0.044 (3)	0.025 (2)	−0.002 (2)	0.010 (2)	0.000 (2)
C1	0.0130 (19)	0.026 (2)	0.023 (2)	−0.0015 (19)	0.0096 (17)	0.000 (2)
O31	0.0145 (14)	0.0247 (16)	0.0266 (15)	0.0009 (13)	0.0123 (12)	0.0029 (13)

Geometric parameters (Å, º)

O30—C8	1.360 (5)	C16—C2	1.382 (6)
O30—C3	1.450 (5)	C16—C5	1.393 (7)
N29—C19	1.370 (5)	C16—C11	1.516 (6)
N29—C17	1.371 (6)	C15—C9	1.377 (6)
N29—C21	1.462 (5)	C15—H15A	0.95
O28—C12	1.352 (5)	C14—C5	1.400 (6)
O28—C7	1.451 (4)	C14—H14A	0.95
O27—C8	1.220 (5)	C13—O31	1.445 (5)
C26—C14	1.394 (6)	C13—C3	1.509 (5)
C26—C24	1.395 (6)	C13—C7	1.525 (6)
C26—C12	1.480 (5)	C13—H13A	1
C25—C17	1.360 (6)	C11—H11A	0.98
C25—N23	1.379 (6)	C11—H11B	0.98
C25—H25A	0.95	C11—H11C	0.98
C24—C2	1.393 (6)	C10—C9	1.400 (6)
C24—H24A	0.95	C10—C6	1.506 (6)
N23—C19	1.315 (6)	C9—H9A	0.95
C22—C4	1.381 (6)	C7—C1	1.530 (6)
C22—C10	1.393 (6)	C7—H7A	1
C22—H22A	0.95	C6—H6A	0.98
C21—O31	1.432 (5)	C6—H6B	0.98
C21—C1	1.523 (6)	C6—H6C	0.98
C21—H21A	1	C5—H5A	0.95
C20—C15	1.396 (6)	C4—H4A	0.95
C20—C4	1.404 (5)	C3—H3A	0.99
C20—C8	1.473 (6)	C3—H3B	0.99
C19—H19A	0.95	C2—H2A	0.95
O18—C12	1.205 (5)	C1—H1A	0.99
C17—H17A	0.95	C1—H1B	0.99
C8—O30—C3	116.8 (3)	O28—C12—C26	112.1 (4)
C19—N29—C17	106.3 (3)	C16—C11—H11A	109.5
C19—N29—C21	124.9 (4)	C16—C11—H11B	109.5
C17—N29—C21	128.7 (3)	H11A—C11—H11B	109.5
C12—O28—C7	116.1 (3)	C16—C11—H11C	109.5
C14—C26—C24	118.9 (4)	H11A—C11—H11C	109.5
C14—C26—C12	118.3 (4)	H11B—C11—H11C	109.5
C24—C26—C12	122.7 (4)	C22—C10—C9	118.3 (4)
C17—C25—N23	111.0 (4)	C22—C10—C6	121.0 (4)
C17—C25—H25A	124.5	C9—C10—C6	120.7 (4)
N23—C25—H25A	124.5	C15—C9—C10	120.7 (4)
C2—C24—C26	120.0 (4)	C15—C9—H9A	119.6
C2—C24—H24A	120	C10—C9—H9A	119.6
C26—C24—H24A	120	O27—C8—O30	122.8 (4)
C19—N23—C25	104.4 (4)	O27—C8—C20	125.5 (4)
C4—C22—C10	121.5 (4)	O30—C8—C20	111.7 (4)
C4—C22—H22A	119.2	O28—C7—C13	105.9 (3)
C10—C22—H22A	119.2	O28—C7—C1	114.1 (3)
O31—C21—N29	108.0 (3)	C13—C7—C1	103.3 (3)
O31—C21—C1	106.5 (3)	O28—C7—H7A	111
N29—C21—C1	114.4 (4)	C13—C7—H7A	111
O31—C21—H21A	109.3	C1—C7—H7A	111
N29—C21—H21A	109.3	C10—C6—H6A	109.5
C1—C21—H21A	109.3	C10—C6—H6B	109.5
C15—C20—C4	119.0 (4)	H6A—C6—H6B	109.5
C15—C20—C8	122.6 (4)	C10—C6—H6C	109.5
C4—C20—C8	118.4 (4)	H6A—C6—H6C	109.5
N23—C19—N29	112.3 (4)	H6B—C6—H6C	109.5
N23—C19—H19A	123.8	C16—C5—C14	120.5 (4)
N29—C19—H19A	123.8	C16—C5—H5A	119.8
C25—C17—N29	105.9 (4)	C14—C5—H5A	119.8
C25—C17—H17A	127.1	C22—C4—C20	119.7 (4)
N29—C17—H17A	127.1	C22—C4—H4A	120.2
C2—C16—C5	118.6 (4)	C20—C4—H4A	120.2
C2—C16—C11	121.0 (5)	O30—C3—C13	108.4 (3)
C5—C16—C11	120.3 (4)	O30—C3—H3A	110
C9—C15—C20	120.7 (4)	C13—C3—H3A	110
C9—C15—H15A	119.6	O30—C3—H3B	110
C20—C15—H15A	119.6	C13—C3—H3B	110
C26—C14—C5	120.4 (4)	H3A—C3—H3B	108.4
C26—C14—H14A	119.8	C16—C2—C24	121.5 (5)
C5—C14—H14A	119.8	C16—C2—H2A	119.2
O31—C13—C3	109.2 (3)	C24—C2—H2A	119.2
O31—C13—C7	105.8 (3)	C21—C1—C7	104.1 (3)
C3—C13—C7	116.1 (4)	C21—C1—H1A	110.9
O31—C13—H13A	108.5	C7—C1—H1A	110.9
C3—C13—H13A	108.5	C21—C1—H1B	110.9
C7—C13—H13A	108.5	C7—C1—H1B	110.9
O18—C12—O28	123.0 (4)	H1A—C1—H1B	109
O18—C12—C26	124.9 (4)	C21—O31—C13	111.3 (3)
C12—O28—C7—C1	75.4 (5)	C22—C4—C20—C8	−178.2 (4)
C12—O28—C7—C13	−171.7 (3)	C22—C4—C20—C15	2.7 (7)
C7—O28—C12—O18	−7.0 (6)	C20—C4—C22—C10	−2.3 (7)
C7—O28—C12—C26	171.5 (3)	C14—C5—C16—C2	1.0 (7)
C8—O30—C3—C13	153.6 (4)	C14—C5—C16—C11	−179.8 (4)
C3—O30—C8—O27	−1.7 (6)	C16—C5—C14—C26	0.0 (7)
C3—O30—C8—C20	180.0 (4)	O28—C7—C13—O31	−146.7 (3)
C21—O31—C13—C3	139.0 (4)	O28—C7—C13—C3	92.0 (4)
C21—O31—C13—C7	13.4 (4)	C1—C7—C13—O31	−26.5 (4)
C13—O31—C21—N29	−117.7 (3)	C1—C7—C13—C3	−147.8 (4)
C13—O31—C21—C1	5.6 (4)	O30—C8—C20—C15	−17.9 (6)
C19—N23—C25—C17	1.3 (5)	O27—C8—C20—C15	163.9 (5)
C25—N23—C19—N29	−1.3 (5)	O30—C8—C20—C4	163.0 (4)
C19—N29—C17—C25	0.0 (5)	O27—C8—C20—C4	−15.2 (7)
C19—N29—C21—O31	−104.2 (4)	C15—C9—C10—C6	−180.0 (4)
C19—N29—C21—C1	137.4 (4)	C10—C9—C15—C20	0.5 (7)
C21—N29—C19—N23	177.9 (4)	C15—C9—C10—C22	0.0 (7)
C21—N29—C17—C25	−176.9 (4)	C6—C10—C22—C4	−179.1 (4)
C17—N29—C19—N23	0.9 (5)	C9—C10—C22—C4	1.0 (7)
C17—N29—C21—O31	72.1 (5)	O18—C12—C26—C24	−179.6 (4)
C17—N29—C21—C1	−46.3 (6)	O28—C12—C26—C14	−179.6 (4)
C21—C1—C7—C13	29.4 (4)	O18—C12—C26—C14	−1.1 (7)
C7—C1—C21—O31	−22.1 (4)	O28—C12—C26—C24	1.9 (6)
C21—C1—C7—O28	143.8 (4)	C5—C14—C26—C12	−179.5 (4)
C7—C1—C21—N29	97.1 (4)	C5—C14—C26—C24	−0.9 (7)
C16—C2—C24—C26	0.2 (7)	C9—C15—C20—C8	179.1 (4)
C24—C2—C16—C11	179.7 (4)	C9—C15—C20—C4	−1.8 (7)
C24—C2—C16—C5	−1.1 (7)	N29—C17—C25—N23	−0.8 (5)
O30—C3—C13—O31	−67.2 (4)	C2—C24—C26—C14	0.8 (7)
O30—C3—C13—C7	52.4 (5)	C2—C24—C26—C12	179.3 (4)