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

The optically active title morpholino­nitro­imidazole derivative, C₁₀H₁₅ClN₄O₄, was synthesized and the absolute configuration has been determined as S.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.044
• wR factor = 0.123
• Data-to-parameter ratio = 11.7

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT850_ALERT_2_C Check Flack Parameter Exact Value 0.00 and su ..       0.02

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           70.20
           From the CIF: _reflns_number_total               2229
           Count of symmetry unique reflns         1343
           Completeness (_total/calc)            165.97%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       886
           Fraction of Friedel pairs measured     0.660
           Are heavy atom types Z>Si present          yes

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 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
   1 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

---

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).

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

Crystal data

C10H15ClN4O4	F(000) = 304
Mr = 290.71	Dx = 1.534 Mg m^−3
Monoclinic, P21	Melting point = 423–427 K
Hall symbol: P 2yb	Cu Kα radiation, λ = 1.54178 Å
a = 9.677 (2) Å	Cell parameters from 42 reflections
b = 5.291 (1) Å	θ = 9.7–27.0°
c = 12.818 (3) Å	µ = 2.88 mm^−1
β = 106.45 (3)°	T = 293 K
V = 629.4 (2) Å^3	Needle, yellow
Z = 2	0.60 × 0.08 × 0.05 mm

Data collection

Kuma KM-4 diffractometer	1953 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.061
Graphite monochromator	θmax = 70.2°, θmin = 3.6°
ω/2θ scans	h = −11→11
Absorption correction: ψ scan (North et al., 1968)	k = −6→6
Tmin = 0.401, Tmax = 0.866	l = 0→15
2272 measured reflections	2 standard reflections every 100 reflections
2229 independent reflections	intensity decay: 2.6%

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)] = 0.044	w = 1/[σ^2(Fo^2) + (0.0961P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.123	(Δ/σ)max < 0.001
S = 1.09	Δρmax = 0.42 e Å^−3
2229 reflections	Δρmin = −0.46 e Å^−3
191 parameters	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.013 (2)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), mit 950 Friedel-Reflexpaare
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.00 (2)

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	0.7533 (2)	0.0894 (5)	0.94524 (18)	0.0359 (5)
C2	0.8597 (3)	0.2438 (6)	0.9965 (2)	0.0399 (6)
H2A	0.9017	0.3594	0.9601	0.052 (10)*
N3	0.9003 (2)	0.2187 (5)	1.10299 (19)	0.0389 (5)
C4	0.8117 (3)	0.0382 (6)	1.1254 (2)	0.0353 (6)
C5	0.7202 (3)	−0.0493 (6)	1.0268 (2)	0.0347 (5)
C6	0.6800 (3)	0.1020 (6)	0.8286 (2)	0.0378 (6)
H6A	0.6684	0.2774	0.8058	0.044 (9)*
H6B	0.5849	0.0275	0.8144	0.036 (8)*
C7	0.7648 (3)	−0.0369 (6)	0.7634 (2)	0.0376 (6)
H7A	0.7774	−0.2125	0.7886	0.038 (8)*
C8	0.6865 (4)	−0.0373 (7)	0.6433 (2)	0.0467 (7)
H8A	0.5952	−0.1243	0.6319	0.054 (11)*
H8B	0.7432	−0.1302	0.6048	0.066 (12)*
Cl9	0.65360 (9)	0.27363 (18)	0.58757 (7)	0.0593 (3)
O10	0.9007 (2)	0.0727 (4)	0.78200 (19)	0.0447 (5)
H10A	0.974 (5)	0.009 (10)	0.805 (4)	0.062 (13)*
N11	0.8219 (3)	−0.0351 (6)	1.22860 (19)	0.0408 (5)
C12	0.9519 (3)	0.0276 (6)	1.3145 (2)	0.0399 (6)
H12A	0.9451	0.1981	1.3404	0.039 (9)*
H12B	1.0353	0.0183	1.2869	0.031 (7)*
C13	0.9673 (3)	−0.1574 (6)	1.4057 (2)	0.0432 (7)
H13A	0.9827	−0.3250	1.3804	0.054 (11)*
H13B	1.0515	−0.1133	1.4647	0.042 (9)*
O14	0.8446 (3)	−0.1625 (5)	1.44572 (18)	0.0526 (6)
C15	0.7188 (3)	−0.2244 (8)	1.3603 (3)	0.0522 (8)
H15A	0.6357	−0.2233	1.3884	0.056 (10)*
H15B	0.7288	−0.3934	1.3341	0.057 (11)*
C16	0.6950 (3)	−0.0422 (7)	1.2684 (2)	0.0446 (6)
H16A	0.6116	−0.0932	1.2102	0.051 (10)*
H16B	0.6767	0.1249	1.2927	0.072 (14)*
N17	0.6425 (2)	−0.2745 (5)	1.0065 (2)	0.0390 (5)
O18	0.6184 (3)	−0.3875 (5)	1.0836 (2)	0.0549 (6)
O19	0.6031 (3)	−0.3540 (5)	0.9115 (2)	0.0534 (6)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0340 (11)	0.0419 (13)	0.0312 (11)	−0.0017 (9)	0.0083 (9)	0.0010 (9)
C2	0.0391 (13)	0.0404 (14)	0.0398 (14)	−0.0058 (12)	0.0107 (10)	0.0007 (12)
N3	0.0362 (11)	0.0414 (14)	0.0376 (11)	−0.0070 (10)	0.0078 (9)	−0.0015 (10)
C4	0.0313 (12)	0.0388 (14)	0.0351 (13)	−0.0017 (10)	0.0080 (10)	−0.0004 (10)
C5	0.0301 (12)	0.0413 (14)	0.0322 (12)	−0.0048 (10)	0.0081 (9)	−0.0017 (10)
C6	0.0324 (12)	0.0474 (16)	0.0320 (13)	0.0060 (11)	0.0063 (10)	0.0030 (12)
C7	0.0396 (14)	0.0404 (14)	0.0334 (12)	0.0041 (11)	0.0113 (10)	0.0014 (11)
C8	0.0504 (16)	0.0553 (18)	0.0352 (14)	0.0017 (14)	0.0133 (12)	−0.0035 (13)
Cl9	0.0556 (5)	0.0739 (6)	0.0461 (4)	0.0117 (4)	0.0105 (3)	0.0181 (4)
O10	0.0344 (11)	0.0515 (13)	0.0490 (12)	0.0066 (9)	0.0132 (9)	0.0098 (10)
N11	0.0364 (12)	0.0543 (14)	0.0307 (11)	−0.0045 (10)	0.0077 (9)	0.0016 (10)
C12	0.0416 (14)	0.0431 (15)	0.0330 (13)	−0.0031 (11)	0.0072 (11)	−0.0025 (11)
C13	0.0436 (15)	0.0524 (18)	0.0332 (13)	0.0035 (12)	0.0104 (11)	0.0026 (12)
O14	0.0517 (12)	0.0759 (17)	0.0337 (10)	0.0057 (11)	0.0174 (8)	0.0026 (10)
C15	0.0480 (16)	0.066 (2)	0.0469 (16)	−0.0055 (16)	0.0211 (13)	0.0068 (16)
C16	0.0375 (14)	0.0558 (17)	0.0417 (15)	0.0025 (13)	0.0131 (12)	−0.0003 (13)
N17	0.0333 (11)	0.0394 (13)	0.0439 (12)	−0.0042 (10)	0.0104 (9)	−0.0035 (10)
O18	0.0591 (13)	0.0505 (14)	0.0579 (14)	−0.0154 (11)	0.0211 (11)	0.0018 (10)
O19	0.0581 (13)	0.0486 (13)	0.0509 (13)	−0.0095 (11)	0.0110 (10)	−0.0158 (10)

Geometric parameters (Å, º)

N1—C2	1.333 (4)	O10—H10A	0.77 (5)
N1—C5	1.387 (4)	N11—C12	1.456 (4)
N1—C6	1.464 (3)	N11—C16	1.458 (4)
C2—N3	1.316 (4)	C12—C13	1.499 (4)
C2—H2A	0.9300	C12—H12A	0.9700
N3—C4	1.367 (4)	C12—H12B	0.9700
C4—N11	1.356 (4)	C13—O14	1.421 (4)
C4—C5	1.400 (4)	C13—H13A	0.9700
C5—N17	1.394 (4)	C13—H13B	0.9700
C6—C7	1.516 (4)	O14—C15	1.425 (4)
C6—H6A	0.9700	C15—C16	1.489 (5)
C6—H6B	0.9700	C15—H15A	0.9700
C7—O10	1.395 (4)	C15—H15B	0.9700
C7—C8	1.511 (4)	C16—H16A	0.9700
C7—H7A	0.9800	C16—H16B	0.9700
C8—Cl9	1.786 (4)	N17—O18	1.232 (3)
C8—H8A	0.9700	N17—O19	1.242 (3)
C8—H8B	0.9700
C2—N1—C5	105.3 (2)	C4—N11—C12	118.8 (2)
C2—N1—C6	124.0 (2)	C4—N11—C16	120.9 (2)
C5—N1—C6	130.2 (2)	C12—N11—C16	112.0 (2)
N3—C2—N1	114.3 (3)	N11—C12—C13	108.3 (3)
N3—C2—H2A	122.8	N11—C12—H12A	110.0
N1—C2—H2A	122.8	C13—C12—H12A	110.0
C2—N3—C4	105.5 (2)	N11—C12—H12B	110.0
N11—C4—N3	121.9 (3)	C13—C12—H12B	110.0
N11—C4—C5	129.7 (3)	H12A—C12—H12B	108.4
N3—C4—C5	108.4 (2)	O14—C13—C12	112.7 (3)
N1—C5—N17	122.6 (2)	O14—C13—H13A	109.1
N1—C5—C4	106.4 (2)	C12—C13—H13A	109.1
N17—C5—C4	128.4 (2)	O14—C13—H13B	109.1
N1—C6—C7	111.1 (2)	C12—C13—H13B	109.1
N1—C6—H6A	109.4	H13A—C13—H13B	107.8
C7—C6—H6A	109.4	C13—O14—C15	110.2 (2)
N1—C6—H6B	109.4	O14—C15—C16	111.5 (3)
C7—C6—H6B	109.4	O14—C15—H15A	109.3
H6A—C6—H6B	108.0	C16—C15—H15A	109.3
O10—C7—C8	110.5 (2)	O14—C15—H15B	109.3
O10—C7—C6	109.6 (2)	C16—C15—H15B	109.3
C8—C7—C6	111.6 (2)	H15A—C15—H15B	108.0
O10—C7—H7A	108.3	N11—C16—C15	109.7 (3)
C8—C7—H7A	108.3	N11—C16—H16A	109.7
C6—C7—H7A	108.3	C15—C16—H16A	109.7
C7—C8—Cl9	112.8 (2)	N11—C16—H16B	109.7
C7—C8—H8A	109.0	C15—C16—H16B	109.7
Cl9—C8—H8A	109.0	H16A—C16—H16B	108.2
C7—C8—H8B	109.0	O18—N17—O19	123.1 (3)
Cl9—C8—H8B	109.0	O18—N17—C5	118.6 (2)
H8A—C8—H8B	107.8	O19—N17—C5	118.2 (2)
C7—O10—H10A	128 (4)
C5—N1—C2—N3	0.6 (3)	C6—C7—C8—Cl9	59.7 (3)
C6—N1—C2—N3	173.0 (2)	N3—C4—N11—C12	−16.5 (4)
N1—C2—N3—C4	−1.7 (3)	C5—C4—N11—C12	161.7 (3)
C2—N3—C4—N11	−179.3 (3)	N3—C4—N11—C16	129.2 (3)
C2—N3—C4—C5	2.2 (3)	C5—C4—N11—C16	−52.6 (5)
C2—N1—C5—N17	−162.5 (3)	C4—N11—C12—C13	−156.0 (3)
C6—N1—C5—N17	25.7 (4)	C16—N11—C12—C13	55.4 (3)
C2—N1—C5—C4	0.8 (3)	N11—C12—C13—O14	−56.5 (3)
C6—N1—C5—C4	−171.0 (3)	C12—C13—O14—C15	58.1 (4)
N11—C4—C5—N1	179.8 (3)	C13—O14—C15—C16	−57.7 (4)
N3—C4—C5—N1	−1.9 (3)	C4—N11—C16—C15	155.8 (3)
N11—C4—C5—N17	−18.2 (5)	C12—N11—C16—C15	−56.3 (4)
N3—C4—C5—N17	160.1 (3)	O14—C15—C16—N11	56.7 (4)
C2—N1—C6—C7	82.9 (3)	N1—C5—N17—O18	179.5 (3)
C5—N1—C6—C7	−106.6 (3)	C4—C5—N17—O18	20.1 (4)
N1—C6—C7—O10	−60.2 (3)	N1—C5—N17—O19	0.8 (4)
N1—C6—C7—C8	177.0 (3)	C4—C5—N17—O19	−158.6 (3)
O10—C7—C8—Cl9	−62.5 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O10—H10A···N3^i	0.76 (5)	2.10 (5)	2.790 (3)	150 (5)
C6—H6A···Cl9	0.97	2.76	3.160 (3)	105
C6—H6B···O19	0.97	2.35	2.820 (4)	109
C6—H6A···O19^ii	0.97	2.55	3.227 (4)	127
C8—H8B···O14^iii	0.97	2.51	3.375 (4)	149
C16—H16A···O18	0.97	2.26	2.916 (4)	124
C16—H16A···O19^iv	0.97	2.55	3.296 (4)	134

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