(R)-(+)-3-Chlor-1-(4-morpholino-5-nitro-1H-imidazol-1-yl)propan-2-ol

The absolute configuration of the optically active title compound, (+)-3-chloro-1-(4-morpholino-5-nitro­imidazol-1-yl)­propan-2-ol, C₁₀H₁₅ClN₄O₄, has been confirmed as 2R by structure refinement using Friedel-pair reflections. The nitro group takes part in the conjugation system of the imidazole ring. In consequence, the exocyclic C—N bond is significantly shorter than the normal single Csp²—NO₂ bond. In the crystal structure, the mol­ecules are linked by O—H...N and C—H...O intermolecular hydrogen bonds into an infinite three-dimensional network.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.027
• wR factor = 0.076
• Data-to-parameter ratio = 12.6

checkCIF/PLATON results

No syntax errors found



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           70.11
           From the CIF: _reflns_number_total               2238
           Count of symmetry unique reflns         1343
           Completeness (_total/calc)            166.64%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       895
           Fraction of Friedel pairs measured     0.666
           Are heavy atom types Z>Si present          yes

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 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
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: KM-4 Software (Kuma, 1996); cell refinement: KM-4 Software; data reduction: KM-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

(R)-(+)-3-Chloro-1-(4-morpholino-5-nitro-1H-imidazol-1-yl)propan-2-ol

Crystal data

C10H15ClN4O4	F(000) = 304
Mr = 290.71	Dx = 1.532 Mg m^−3
Monoclinic, P21	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2yb	Cell parameters from 52 reflections
a = 9.6835 (16) Å	θ = 13.8–30.0°
b = 5.2925 (13) Å	µ = 2.87 mm^−1
c = 12.823 (2) Å	T = 293 K
β = 106.470 (15)°	Needle, yellow
V = 630.2 (2) Å^3	0.58 × 0.12 × 0.05 mm
Z = 2

Data collection

Kuma KM-4 diffractometer	2148 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.027
Graphite monochromator	θmax = 70.1°, θmin = 3.6°
ω/2θ scans	h = −11→11
Absorption correction: ψ scan (North et al., 1968)	k = −6→6
Tmin = 0.657, Tmax = 0.866	l = 0→15
2279 measured reflections	2 standard reflections every 100 reflections
2238 independent reflections	intensity decay: 2.1%

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.027	w = 1/[σ^2(Fo^2) + (0.0512P)^2 + 0.0863P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.076	(Δ/σ)max = 0.011
S = 1.03	Δρmax = 0.18 e Å^−3
2238 reflections	Δρmin = −0.27 e Å^−3
177 parameters	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0165 (14)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983)
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.006 (13)

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.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) 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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.25347 (14)	0.6353 (3)	0.44538 (11)	0.0329 (3)
C2	0.35942 (18)	0.4813 (4)	0.49594 (13)	0.0375 (4)
H2	0.4013	0.3660	0.4593	0.045*
N3	0.40024 (15)	0.5061 (3)	0.60283 (11)	0.0365 (3)
C4	0.31178 (17)	0.6857 (3)	0.62572 (13)	0.0326 (3)
C5	0.22011 (16)	0.7738 (4)	0.52702 (13)	0.0322 (3)
C6	0.17950 (17)	0.6224 (4)	0.32831 (13)	0.0350 (4)
H6A	0.0844	0.6964	0.3142	0.042*
H6B	0.1682	0.4470	0.3055	0.042*
C7	0.26447 (17)	0.7626 (4)	0.26322 (13)	0.0347 (4)
H7	0.2773	0.9379	0.2887	0.042*
C8	0.1862 (2)	0.7632 (4)	0.14289 (14)	0.0447 (4)
H8A	0.2430	0.8560	0.1044	0.054*
H8B	0.0949	0.8502	0.1314	0.054*
Cl9	0.15351 (5)	0.45081 (11)	0.08742 (4)	0.05672 (17)
O10	0.40089 (13)	0.6511 (3)	0.28189 (11)	0.0424 (3)
H10	0.465 (3)	0.732 (5)	0.308 (2)	0.048 (7)*
N11	0.32240 (14)	0.7606 (3)	0.72854 (11)	0.0374 (3)
C12	0.45182 (18)	0.6964 (4)	0.81478 (13)	0.0371 (4)
H12A	0.5354	0.7037	0.7874	0.045*
H12B	0.4440	0.5264	0.8408	0.045*
C13	0.46782 (19)	0.8826 (4)	0.90579 (14)	0.0409 (4)
H13A	0.5520	0.8388	0.9648	0.049*
H13B	0.4830	1.0499	0.8802	0.049*
O14	0.34469 (14)	0.8872 (3)	0.94570 (11)	0.0499 (4)
C15	0.2197 (2)	0.9512 (5)	0.86034 (16)	0.0497 (5)
H15A	0.2310	1.1194	0.8339	0.060*
H15B	0.1366	0.9530	0.8884	0.060*
C16	0.19447 (18)	0.7664 (4)	0.76813 (15)	0.0429 (4)
H16A	0.1765	0.5996	0.7928	0.051*
H16B	0.1110	0.8170	0.7099	0.051*
N17	0.14228 (14)	0.9982 (3)	0.50652 (11)	0.0365 (3)
O18	0.11854 (16)	1.1126 (3)	0.58347 (12)	0.0520 (4)
O19	0.10323 (16)	1.0791 (3)	0.41182 (12)	0.0502 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0321 (6)	0.0377 (8)	0.0273 (7)	0.0003 (6)	0.0057 (5)	−0.0012 (6)
C2	0.0373 (8)	0.0384 (9)	0.0362 (8)	0.0052 (8)	0.0094 (6)	−0.0020 (7)
N3	0.0354 (7)	0.0383 (9)	0.0336 (7)	0.0079 (6)	0.0060 (5)	0.0018 (6)
C4	0.0297 (7)	0.0351 (9)	0.0313 (8)	0.0013 (6)	0.0061 (6)	0.0007 (6)
C5	0.0280 (7)	0.0374 (9)	0.0301 (7)	0.0034 (6)	0.0065 (5)	0.0009 (7)
C6	0.0317 (7)	0.0445 (10)	0.0268 (8)	−0.0071 (7)	0.0048 (6)	−0.0016 (7)
C7	0.0367 (8)	0.0363 (9)	0.0316 (8)	−0.0062 (7)	0.0104 (6)	−0.0018 (7)
C8	0.0497 (10)	0.0520 (11)	0.0323 (8)	−0.0018 (9)	0.0115 (7)	0.0039 (8)
Cl9	0.0521 (3)	0.0720 (4)	0.0429 (2)	−0.0125 (2)	0.00846 (18)	−0.0191 (2)
O10	0.0315 (6)	0.0494 (8)	0.0461 (7)	−0.0075 (6)	0.0108 (5)	−0.0111 (6)
N11	0.0303 (6)	0.0522 (9)	0.0283 (6)	0.0055 (6)	0.0062 (5)	−0.0007 (6)
C12	0.0359 (8)	0.0424 (10)	0.0302 (8)	0.0058 (7)	0.0049 (6)	0.0022 (7)
C13	0.0403 (9)	0.0508 (11)	0.0311 (8)	−0.0032 (8)	0.0096 (6)	−0.0021 (7)
O14	0.0474 (7)	0.0738 (11)	0.0317 (6)	−0.0046 (7)	0.0166 (5)	−0.0033 (6)
C15	0.0432 (9)	0.0654 (13)	0.0447 (9)	0.0065 (10)	0.0191 (8)	−0.0039 (10)
C16	0.0335 (8)	0.0581 (12)	0.0379 (9)	−0.0009 (8)	0.0117 (7)	0.0015 (8)
N17	0.0316 (6)	0.0364 (8)	0.0405 (7)	0.0028 (6)	0.0087 (5)	0.0044 (6)
O18	0.0542 (7)	0.0492 (9)	0.0552 (9)	0.0164 (7)	0.0196 (6)	−0.0030 (7)
O19	0.0533 (7)	0.0476 (8)	0.0469 (8)	0.0108 (6)	0.0097 (6)	0.0170 (6)

Geometric parameters (Å, º)

N1—C2	1.327 (2)	O10—H10	0.75 (3)
N1—C5	1.389 (2)	N11—C12	1.457 (2)
N1—C6	1.470 (2)	N11—C16	1.466 (2)
C2—N3	1.321 (2)	C12—C13	1.501 (3)
C2—H2	0.9300	C12—H12A	0.9700
N3—C4	1.366 (2)	C12—H12B	0.9700
C4—N11	1.352 (2)	C13—O14	1.425 (2)
C4—C5	1.404 (2)	C13—H13A	0.9700
C5—N17	1.391 (2)	C13—H13B	0.9700
C6—C7	1.521 (2)	O14—C15	1.424 (2)
C6—H6A	0.9700	C15—C16	1.500 (3)
C6—H6B	0.9700	C15—H15A	0.9700
C7—O10	1.404 (2)	C15—H15B	0.9700
C7—C8	1.514 (2)	C16—H16A	0.9700
C7—H7	0.9800	C16—H16B	0.9700
C8—Cl9	1.792 (2)	N17—O18	1.233 (2)
C8—H8A	0.9700	N17—O19	1.241 (2)
C8—H8B	0.9700
C2—N1—C5	105.59 (13)	C4—N11—C12	118.87 (14)
C2—N1—C6	123.78 (15)	C4—N11—C16	120.36 (14)
C5—N1—C6	130.08 (14)	C12—N11—C16	111.81 (13)
N3—C2—N1	114.11 (15)	N11—C12—C13	108.30 (15)
N3—C2—H2	122.9	N11—C12—H12A	110.0
N1—C2—H2	122.9	C13—C12—H12A	110.0
C2—N3—C4	105.71 (14)	N11—C12—H12B	110.0
N11—C4—N3	122.31 (15)	C13—C12—H12B	110.0
N11—C4—C5	129.45 (16)	H12A—C12—H12B	108.4
N3—C4—C5	108.20 (14)	O14—C13—C12	112.22 (15)
N1—C5—N17	122.52 (14)	O14—C13—H13A	109.2
N1—C5—C4	106.34 (14)	C12—C13—H13A	109.2
N17—C5—C4	128.63 (15)	O14—C13—H13B	109.2
N1—C6—C7	110.79 (13)	C12—C13—H13B	109.2
N1—C6—H6A	109.5	H13A—C13—H13B	107.9
C7—C6—H6A	109.5	C15—O14—C13	110.10 (13)
N1—C6—H6B	109.5	O14—C15—C16	111.34 (18)
C7—C6—H6B	109.5	O14—C15—H15A	109.4
H6A—C6—H6B	108.1	C16—C15—H15A	109.4
O10—C7—C8	110.47 (14)	O14—C15—H15B	109.4
O10—C7—C6	109.31 (15)	C16—C15—H15B	109.4
C8—C7—C6	111.59 (14)	H15A—C15—H15B	108.0
O10—C7—H7	108.5	N11—C16—C15	108.78 (15)
C8—C7—H7	108.5	N11—C16—H16A	109.9
C6—C7—H7	108.5	C15—C16—H16A	109.9
C7—C8—Cl9	112.54 (14)	N11—C16—H16B	109.9
C7—C8—H8A	109.1	C15—C16—H16B	109.9
Cl9—C8—H8A	109.1	H16A—C16—H16B	108.3
C7—C8—H8B	109.1	O18—N17—O19	122.62 (17)
Cl9—C8—H8B	109.1	O18—N17—C5	118.80 (14)
H8A—C8—H8B	107.8	O19—N17—C5	118.54 (15)
C7—O10—H10	117 (2)
C5—N1—C2—N3	−0.6 (2)	C6—C7—C8—Cl9	−59.53 (18)
C6—N1—C2—N3	−172.85 (15)	N3—C4—N11—C12	15.3 (3)
N1—C2—N3—C4	1.9 (2)	C5—C4—N11—C12	−161.95 (18)
C2—N3—C4—N11	179.95 (17)	N3—C4—N11—C16	−129.28 (19)
C2—N3—C4—C5	−2.3 (2)	C5—C4—N11—C16	53.5 (3)
C2—N1—C5—N17	162.54 (16)	C4—N11—C12—C13	156.27 (16)
C6—N1—C5—N17	−25.9 (3)	C16—N11—C12—C13	−56.3 (2)
C2—N1—C5—C4	−0.89 (18)	N11—C12—C13—O14	57.1 (2)
C6—N1—C5—C4	170.69 (16)	C12—C13—O14—C15	−58.9 (2)
N11—C4—C5—N1	179.53 (17)	C13—O14—C15—C16	58.8 (2)
N3—C4—C5—N1	2.01 (18)	C4—N11—C16—C15	−156.16 (19)
N11—C4—C5—N17	17.5 (3)	C12—N11—C16—C15	57.0 (2)
N3—C4—C5—N17	−160.06 (16)	O14—C15—C16—N11	−57.5 (2)
C2—N1—C6—C7	−83.1 (2)	N1—C5—N17—O18	−179.01 (16)
C5—N1—C6—C7	106.64 (19)	C4—C5—N17—O18	−19.5 (3)
N1—C6—C7—O10	60.51 (19)	N1—C5—N17—O19	−1.1 (2)
N1—C6—C7—C8	−177.00 (16)	C4—C5—N17—O19	158.36 (18)
O10—C7—C8—Cl9	62.29 (18)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O10—H10···N3^i	0.75 (3)	2.07 (3)	2.795 (2)	164 (3)
C6—H6B···Cl9	0.97	2.76	3.1605 (19)	106
C6—H6A···O19	0.97	2.36	2.825 (3)	109
C6—H6B···O19^ii	0.97	2.56	3.226 (3)	126
C8—H8A···O14^iii	0.97	2.50	3.373 (2)	149
C16—H16B···O18	0.97	2.27	2.918 (3)	124
C16—H16B···O19^iv	0.97	2.55	3.293 (3)	134

Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) x, y−1, z; (iii) x, y, z−1; (iv) −x, y−1/2, −z+1.