Iso­propyl 6-amino-2,5-an­hydro-3,6-di­deoxy-6-N-(2,5-an­hydro-6-azido-3,6-di­deoxy-L-arabino-hexonyl)-L-arabino-hexonate

The title compound, C₁₅H₂₄N₄O₇, crystallizes with great difficulty as fine hair-like crystals. It is a significant material, because it displays a weak internal hydrogen bond which may help with the interpretation of the secondary structure preferences of this class of compounds.

Key indicators

• Single-crystal X-ray study
• T = 190 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.054
• wR factor = 0.106
• Data-to-parameter ratio = 9.0

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT063_ALERT_3_A Crystal Probably too Large for Beam Size .......      12.30 mm

Author Response: Attempts at cutting the only other crystal resulted in its destruction. See text

PLAT220_ALERT_2_A Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       4.83 Ratio

Author Response: The isopropyl group is almost certainly librating. A disordered model refined no better than large adps. Note also the very large proportion of weak reflections (20% with I< 2( \s I). See text

Alert level B
CRYSS02_ALERT_3_B  The value of _exptl_crystal_size_max is > 1.0
   Maximum crystal size given =  12.300
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.99
PLAT222_ALERT_3_B Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       4.36 Ratio
PLAT242_ALERT_2_B Check Low    U(eq) as Compared to Neighbors ....        C16
PLAT411_ALERT_2_B Short Inter H...H Contact  H101   ..  H211     =       2.06 Ang.
PLAT432_ALERT_2_B Short Inter X...Y Contact  O19    ..  C25      =       2.89 Ang.

Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5
PLAT360_ALERT_2_C Short  C(sp3)-C(sp3) Bond  C16    -   C17      =       1.42 Ang.

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           27.47
           From the CIF: _reflns_number_total               2204
           Count of symmetry unique reflns         2262
           Completeness (_total/calc)             97.44%
           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
   6 ALERT level B = Potentially serious problem
   3 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
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion

---

Computing details

Data collection: COLLECT (Nonius, 1997); cell refinement: DENZO/SCALEPACK; data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Watkin et al., 2001); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

isopropyl 6-amino-2,5-anhydro-3,6-dideoxy-6-N-(2,5-anhydro-6- azido-3,6-dideoxy-L-arabino-hexonyl)-L-arabino-hexonate

Crystal data

C15H24N4O7	F(000) = 396.000
Mr = 372.38	Dx = 1.388 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
a = 9.7238 (3) Å	Cell parameters from 1985 reflections
b = 5.6312 (2) Å	θ = 5–27°
c = 16.2836 (5) Å	µ = 0.11 mm^−1
β = 92.0137 (14)°	T = 190 K
V = 891.08 (5) Å^3	Plate, colourless
Z = 2	12.30 × 0.02 × 0.01 mm

Data collection

Nonius KappaCCD diffractometer	2204 reflections with I > −10σ(I)
Graphite monochromator	Rint = 0.02
ω scans	θmax = 27.5°, θmin = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −12→12
Tmin = 0.5, Tmax = 0.99	k = −7→7
3754 measured reflections	l = −21→21
2204 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.054	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.106	w = 1/[σ^2(F^2) + (0.0472P)^2 + 0.453P], where P = (2max(Fo^2,0) + Fc^2)/3
S = 0.95	(Δ/σ)max = 0.001
2204 reflections	Δρmax = 0.51 e Å^−3
244 parameters	Δρmin = −0.41 e Å^−3
1 restraint

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

	x	y	z	Uiso*/Ueq
N1	0.7869 (4)	0.6875 (7)	1.4509 (2)	0.0648
N2	0.8679 (3)	0.5564 (6)	1.43180 (14)	0.0437
N3	0.9659 (3)	0.4331 (6)	1.41502 (16)	0.0488
C4	0.9289 (3)	0.2011 (7)	1.37722 (18)	0.0396
C5	0.9001 (3)	0.2205 (6)	1.28524 (16)	0.0313
O6	0.7937 (2)	0.3929 (4)	1.26945 (11)	0.0335
C7	0.6763 (3)	0.2819 (6)	1.22909 (16)	0.0294
C8	0.6629 (3)	0.3389 (5)	1.13810 (16)	0.0272
N9	0.7566 (2)	0.4861 (5)	1.10799 (13)	0.0292
C10	0.7451 (3)	0.5813 (6)	1.02492 (15)	0.0304
C11	0.8231 (3)	0.4371 (5)	0.96212 (15)	0.0263
O12	0.80336 (19)	0.5540 (4)	0.8828 (1)	0.0283
C13	0.6931 (3)	0.4391 (6)	0.83712 (15)	0.0281
C14	0.7458 (3)	0.3541 (6)	0.75626 (16)	0.0295
O15	0.64492 (19)	0.2535 (6)	0.71156 (12)	0.0482
C16	0.6840 (4)	0.1374 (8)	0.6346 (2)	0.0494
C17	0.6905 (7)	−0.112 (1)	0.6489 (3)	0.1037
C18	0.5769 (8)	0.2126 (13)	0.5716 (3)	0.1270
O19	0.8610 (2)	0.3760 (5)	0.73379 (12)	0.0434
C20	0.6441 (3)	0.2354 (6)	0.89128 (16)	0.0336
C21	0.7685 (3)	0.1897 (5)	0.94767 (16)	0.0294
O22	0.8731 (2)	0.0606 (4)	0.90686 (14)	0.0388
O23	0.56542 (19)	0.2547 (5)	1.09749 (12)	0.0372
C24	0.6935 (3)	0.0168 (6)	1.24604 (17)	0.0314
C25	0.8494 (3)	−0.0147 (6)	1.24915 (16)	0.0289
O26	0.8910 (2)	−0.0483 (5)	1.16649 (11)	0.0347
H41	1.0059	0.0859	1.38742	0.0389*
H42	0.8438	0.1412	1.40331	0.0389*
H51	0.9881	0.2663	1.25914	0.0348*
H71	0.5885	0.3444	1.25121	0.0329*
H91	0.820 (4)	0.543 (8)	1.141 (2)	0.0500*
H101	0.7828	0.7465	1.02549	0.0331*
H102	0.6454	0.5850	1.00757	0.0331*
H111	0.9202	0.4271	0.98419	0.0300*
H131	0.6139	0.5475	0.82376	0.0317*
H161	0.7748	0.1877	0.6131	0.0564*
H171	0.7162	−0.198	0.5980	0.1082*
H172	0.7627	−0.140	0.6929	0.1082*
H173	0.5997	−0.172	0.6675	0.1082*
H181	0.5990	0.1369	0.5182	0.1274*
H182	0.5753	0.3891	0.5650	0.1274*
H183	0.4846	0.1566	0.5891	0.1274*
H201	0.5627	0.2852	0.92323	0.0352*
H202	0.6197	0.0916	0.85799	0.0352*
H211	0.7448	0.0972	0.99755	0.0292*
H221	0.846 (4)	−0.066 (9)	0.894 (2)	0.0500*
H241	0.6513	−0.0293	1.29882	0.0327*
H242	0.6510	−0.0790	1.20025	0.0327*
H251	0.8849	−0.1511	1.28287	0.0326*
H261	0.978 (4)	−0.056 (8)	1.170 (2)	0.0500*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.079 (2)	0.055 (2)	0.0609 (19)	0.005 (2)	0.0149 (17)	−0.0162 (19)
N2	0.0605 (17)	0.0453 (18)	0.0254 (11)	−0.0068 (16)	0.0017 (11)	−0.0054 (14)
N3	0.0494 (15)	0.055 (2)	0.0413 (14)	0.0020 (16)	−0.0054 (12)	−0.0161 (16)
C4	0.0454 (16)	0.041 (2)	0.0322 (14)	0.0037 (15)	−0.0065 (13)	−0.0049 (15)
C5	0.0341 (14)	0.0315 (17)	0.0285 (13)	−0.0002 (13)	0.0033 (11)	−0.0038 (13)
O6	0.0438 (11)	0.0263 (11)	0.0302 (9)	0.0016 (9)	−0.0022 (8)	−0.0033 (9)
C7	0.0286 (13)	0.0311 (16)	0.0289 (13)	0.0014 (13)	0.005 (1)	−0.0013 (13)
C8	0.0274 (12)	0.0231 (15)	0.0311 (13)	0.0040 (12)	0.002 (1)	−0.0013 (12)
N9	0.0364 (12)	0.0257 (13)	0.025 (1)	−0.0044 (11)	−0.0012 (9)	0.0006 (11)
C10	0.0448 (15)	0.0203 (14)	0.0262 (12)	0.0017 (13)	0.0026 (11)	0.0019 (12)
C11	0.0344 (13)	0.0211 (14)	0.0231 (12)	0.0013 (12)	−0.002 (1)	0.0048 (12)
O12	0.036 (1)	0.023 (1)	0.0248 (8)	−0.0057 (9)	−0.0018 (7)	0.0026 (9)
C13	0.0256 (12)	0.0293 (16)	0.0293 (12)	−0.0011 (12)	−0.002 (1)	0.0002 (13)
C14	0.0281 (13)	0.0324 (16)	0.0278 (12)	0.0011 (13)	−0.003 (1)	0.0032 (13)
O15	0.029 (1)	0.084 (2)	0.031 (1)	−0.0055 (13)	−0.0025 (8)	−0.0187 (13)
C16	0.0447 (18)	0.075 (3)	0.0286 (15)	−0.0109 (19)	0.0036 (13)	−0.0156 (17)
C17	0.176 (6)	0.068 (4)	0.072 (3)	0.043 (4)	0.056 (3)	−0.003 (3)
C18	0.216 (7)	0.107 (5)	0.054 (3)	0.069 (6)	−0.054 (3)	−0.031 (3)
O19	0.034 (1)	0.0583 (16)	0.039 (1)	−0.0136 (11)	0.0081 (8)	−0.0092 (12)
C20	0.0341 (14)	0.0351 (17)	0.0319 (13)	−0.0096 (14)	0.0030 (11)	−0.0046 (14)
C21	0.0394 (15)	0.0207 (14)	0.0287 (13)	0.0032 (12)	0.0080 (11)	0.0017 (12)
O22	0.0518 (13)	0.0227 (11)	0.0426 (11)	0.0034 (11)	0.013 (1)	−0.0035 (11)
O23	0.030 (1)	0.0418 (14)	0.039 (1)	−0.004 (1)	−0.0040 (8)	0.0028 (11)
C24	0.0319 (14)	0.0300 (17)	0.0324 (13)	−0.0029 (13)	0.0044 (11)	0.0049 (13)
C25	0.0305 (13)	0.0268 (15)	0.0295 (13)	0.0027 (12)	0.001 (1)	−0.0027 (13)
O26	0.0310 (9)	0.0449 (14)	0.0281 (9)	0.003 (1)	0.0012 (7)	−0.008 (1)

Geometric parameters (Å, º)

N1—N2	1.131 (4)	C13—C14	1.508 (4)
N2—N3	1.218 (4)	C14—O19	1.197 (3)
N3—C4	1.483 (5)	C14—O15	1.328 (3)
C4—H42	1.002	O15—C16	1.475 (4)
C4—H41	1.000	C16—H161	1.002
C4—C5	1.518 (4)	C16—C18	1.497 (6)
C5—H51	1.002	C16—C17	1.424 (7)
C5—C25	1.524 (4)	C17—H173	1.002
C5—O6	1.436 (4)	C17—H172	0.998
O6—C7	1.440 (3)	C17—H171	0.999
C7—H71	1.002	C18—H183	1.002
C7—C24	1.527 (5)	C18—H182	0.999
C7—C8	1.517 (4)	C18—H181	0.999
C8—O23	1.232 (3)	C20—H202	0.999
C8—N9	1.337 (4)	C20—H201	1.002
N9—H91	0.86 (4)	C20—C21	1.515 (4)
N9—C10	1.456 (3)	C21—H211	0.999
C10—H102	1.001	C21—O22	1.433 (4)
C10—H101	1.000	O22—H221	0.78 (5)
C10—C11	1.528 (4)	C24—H242	0.998
C11—H111	1.000	C24—H241	1.000
C11—C21	1.506 (4)	C24—C25	1.526 (4)
C11—O12	1.456 (3)	C25—H251	0.999
O12—C13	1.437 (3)	C25—O26	1.431 (3)
C13—H131	1.000	O26—H261	0.85 (4)
C13—C20	1.533 (4)
N3—N2—N1	172.6 (4)	O19—C14—C13	125.8 (3)
C4—N3—N2	114.5 (3)	O15—C14—C13	110.3 (2)
H42—C4—H41	109.6	C16—O15—C14	116.6 (2)
H42—C4—C5	108.4	H161—C16—C18	106.3
H41—C4—C5	108.7	H161—C16—C17	107.5
H42—C4—N3	108.2	C18—C16—C17	114.6 (5)
H41—C4—N3	109.5	H161—C16—O15	115.3
C5—C4—N3	112.3 (3)	C18—C16—O15	105.2 (3)
H51—C5—C25	109.2	C17—C16—O15	108.0 (4)
H51—C5—O6	111.8	H173—C17—H172	109.6
C25—C5—O6	107.3 (2)	H173—C17—H171	109.6
H51—C5—C4	107.8	H172—C17—H171	109.2
C25—C5—C4	111.3 (3)	H173—C17—C16	110.2
O6—C5—C4	109.4 (2)	H172—C17—C16	107.4
C7—O6—C5	110.1 (2)	H171—C17—C16	110.7
H71—C7—C24	111.6	H183—C18—H182	109.4
H71—C7—C8	103.4	H183—C18—H181	109.6
C24—C7—C8	112.9 (2)	H182—C18—H181	109.5
H71—C7—O6	110.8	H183—C18—C16	108.9
C24—C7—O6	105.2 (2)	H182—C18—C16	111.3
C8—C7—O6	113.1 (2)	H181—C18—C16	108.1
O23—C8—N9	124.3 (2)	H202—C20—H201	109.4
O23—C8—C7	118.7 (2)	H202—C20—C21	111.1
N9—C8—C7	117.0 (2)	H201—C20—C21	111.2
H91—N9—C10	118 (3)	H202—C20—C13	111.6
H91—N9—C8	119 (3)	H201—C20—C13	110.9
C10—N9—C8	122.6 (2)	C21—C20—C13	102.6 (2)
H102—C10—H101	109.5	H211—C21—O22	107.5
H102—C10—C11	108.7	H211—C21—C11	116.5
H101—C10—C11	108.1	O22—C21—C11	106.9 (2)
H102—C10—N9	108.1	H211—C21—C20	112.3
H101—C10—N9	108.5	O22—C21—C20	111.7 (2)
C11—C10—N9	113.8 (2)	C11—C21—C20	102.0 (2)
H111—C11—C21	109.1	H221—O22—C21	110 (3)
H111—C11—O12	116.0	H242—C24—H241	109.3
C21—C11—O12	104.2 (2)	H242—C24—C25	110.3
H111—C11—C10	105.9	H241—C24—C25	112.3
C21—C11—C10	114.6 (2)	H242—C24—C7	110.7
O12—C11—C10	107.5 (2)	H241—C24—C7	111.3
C13—O12—C11	109.2 (2)	C25—C24—C7	102.8 (2)
H131—C13—C20	109.2	H251—C25—O26	108.2
H131—C13—C14	106.7	H251—C25—C5	110.8
C20—C13—C14	112.8 (3)	O26—C25—C5	112.3 (2)
H131—C13—O12	113.1	H251—C25—C24	115.6
C20—C13—O12	106.3 (2)	O26—C25—C24	107.3 (2)
C14—C13—O12	108.9 (2)	C5—C25—C24	102.7 (2)
O19—C14—O15	123.9 (3)	H261—O26—C25	105 (2)