2-(2-Methyl-5-nitro-1H-imidazol-1-yl)­ethaneselenol

In the title compound, C₆H₉N₃O₂Se, which is a selenol substituent derivative of metronidazole, all bond lengths and angles are normal. The imidazole ring and nitro group make a dihedral angle of 6.6 (1)°, while the N-C-C-Se torsion angle is 59.5 (8)°.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.011 Å
• R factor = 0.065
• wR factor = 0.177
• Data-to-parameter ratio = 14.7

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSTM02_ALERT_3_C  The ratio of expected to reported Tmax/Tmin(RR) is > 1.10
            Tmin and Tmax reported:      0.272     0.352
            Tmin and Tmax expected:      0.220     0.333
            RR =      1.169
            Please check that your absorption correction is appropriate.
PLAT060_ALERT_3_C Ratio Tmax/Tmin (Exp-to-Rep) (too) Large .......       1.15
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.95
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT341_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...         11
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety         C3
PLAT420_ALERT_2_C D-H Without Acceptor       Se     -   H1     ...          ?

Alert level G
ABSTM02_ALERT_3_G  When printed, the submitted absorption T values will be
            replaced by the scaled T values. Since the ratio of scaled T's
            is identical to the ratio of reported T values, the scaling
            does not imply a change to the absorption corrections used in
            the study.
            Ratio of Tmax expected/reported      0.946
            Tmax scaled      0.333 Tmin scaled      0.258
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
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
   7 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

   2 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
   5 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

The title compound, (I) (Fig. 1), is a selenol substituent derivative of metronidazole, which is extensively used in the treatment of anaerobic infections and is under continuing investigation. Earlier, the crystal structures of chloro- and iodometronidazole were reported by Pi et al. (2005) and Yang et al. (2005), respectively.

In (I), the imidazole ring and nitro group make a dihedral angle of 6.6 (1)°, while the torsion angle N2—C2—C1—Se is 59.5 (8)°.

Related literature

The crystal structures of chloro- and iodometronidazole were reported by Pi et al. (2005) and Yang et al. (2005), respectively.

S2. Experimental

Metronidazole (96%) and HSe aqua-solution (50%) wee purchased from Nanjing Chemical Company, Nanjing, P. R. China. TLC was run on the silica gel coated aluminium sheets (silica gel 60 GF254, E. Merk, Germany) and visualized in UV light (254 nm).

Metronidazole was dissolved in anhydrous DMF and the solution was stirred at 100 °C for 15 min. Then HSe in anhydrous DMF (20 ml) was carefully added, the mixed solution was stirred at 100 °C for 4 h. The mixture was cooled to the room temperature, and the solvent was removed under reduced pressure. The residue was suspended in EtOH and filtered, the solvent was removed under reduced pressure, and the residue was chromatographed. Elution with EtOAc gave an oil, which was recrystallized from EtOAc/petroleum ether (3/1) to give the title compound. Mp: 88.5–89.5 °C; Yield: 73%; 1H NMR (DMSO-d6): 2.50 (s, 3H, –CH3-); 3.51 (t, J = 8.68 Hz, 2H, N—CH2-); 4.61 (t, J = 8.51 Hz, 2H, –CH2-); 8.05 (s, 1H).

S3. Refinement

H atoms attached to C atoms were refined in the riding model approximation, with C–H = 0.93 Å and U_iso(H) = 1.2U_eq(C). The H atom attached to Se atom was located from a difference Fourier map and refined with bond restraint Se–H = 0.97 (1) Å, and with U_iso(H) = 1.2U_iso(Se).

Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997a); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997a); molecular graphics: SHELXTL (Sheldrick, 1997b); software used to prepare material for publication: SHELXTL (Sheldrick, 1997b).

Figures

Fig. 1. The molecular structure of (I), showing 30% probability displacement ellipsoids and the atom-numbering scheme.

2-(2-Methyl-5-nitro-1H-imidazol-1-yl)ethaneselenol

Crystal data

C6H9N3O2Se	F(000) = 464
Mr = 234.12	Dx = 1.836 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
a = 12.079 (2) Å	Cell parameters from 1542 reflections
b = 11.089 (2) Å	θ = 3.9–26.4°
c = 6.3800 (13) Å	µ = 4.40 mm^−1
β = 97.57 (3)°	T = 293 K
V = 847.1 (3) Å^3	Prism, yellow
Z = 4	0.36 × 0.32 × 0.25 mm

Data collection

Bruker APEX area-detector diffractometer	1647 independent reflections
Radiation source: fine-focus sealed tube	960 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.046
φ and ω scans	θmax = 26.0°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −14→14
Tmin = 0.272, Tmax = 0.352	k = −13→0
1804 measured reflections	l = 0→7

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.065	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.178	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ^2(Fo^2) + (0.0611P)^2 + 4.5156P] where P = (Fo^2 + 2Fc^2)/3
1647 reflections	(Δ/σ)max < 0.001
112 parameters	Δρmax = 0.48 e Å^−3
1 restraint	Δρmin = −0.63 e Å^−3

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
Se	0.27158 (9)	0.08541 (10)	1.19615 (16)	0.0625 (4)
O1	0.0341 (5)	−0.1194 (5)	0.6752 (10)	0.0483 (15)
O2	0.1029 (5)	−0.2980 (6)	0.6766 (10)	0.0546 (17)
N1	0.4065 (6)	−0.1286 (7)	0.7038 (10)	0.0402 (17)
N2	0.2522 (5)	−0.0209 (5)	0.7252 (8)	0.0263 (14)
N3	0.1135 (6)	−0.1880 (7)	0.6843 (9)	0.0364 (16)
C1	0.1470 (6)	0.0813 (8)	0.9825 (13)	0.0408 (19)
H1B	0.1035	0.0093	0.9999	0.049*
H1C	0.0999	0.1507	0.9979	0.049*
C2	0.1822 (6)	0.0817 (7)	0.7604 (12)	0.0331 (17)
H2A	0.1159	0.0805	0.6564	0.040*
H2B	0.2225	0.1556	0.7407	0.040*
C3	0.4326 (7)	0.0927 (8)	0.7434 (14)	0.051 (2)
H3A	0.5097	0.0723	0.7408	0.076*
H3B	0.4246	0.1328	0.8740	0.076*
H3C	0.4079	0.1452	0.6270	0.076*
C4	0.3641 (6)	−0.0192 (8)	0.7257 (11)	0.0343 (19)
C5	0.3193 (7)	−0.2051 (8)	0.6905 (12)	0.040 (2)
H5A	0.3237	−0.2883	0.6758	0.048*
C6	0.2233 (6)	−0.1415 (7)	0.7020 (11)	0.0275 (16)
H1	0.3517 (14)	0.079 (7)	1.193 (12)	0.072*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Se	0.0718 (8)	0.0693 (7)	0.0437 (6)	0.0085 (6)	−0.0024 (5)	−0.0086 (5)
O1	0.029 (3)	0.064 (4)	0.050 (4)	−0.005 (3)	−0.002 (3)	−0.009 (3)
O2	0.052 (4)	0.043 (4)	0.067 (4)	−0.014 (3)	0.005 (3)	−0.012 (3)
N1	0.031 (4)	0.059 (5)	0.032 (4)	0.005 (3)	0.007 (3)	−0.002 (3)
N2	0.027 (4)	0.037 (4)	0.015 (3)	0.001 (3)	0.003 (2)	0.002 (3)
N3	0.040 (4)	0.050 (5)	0.020 (3)	−0.007 (4)	0.004 (3)	−0.010 (3)
C1	0.028 (4)	0.046 (5)	0.048 (5)	0.010 (4)	0.003 (4)	−0.004 (4)
C2	0.025 (4)	0.037 (4)	0.036 (4)	0.002 (4)	−0.002 (3)	0.004 (4)
C3	0.039 (5)	0.062 (6)	0.051 (5)	−0.014 (5)	0.007 (4)	0.004 (5)
C4	0.036 (5)	0.051 (5)	0.016 (4)	−0.005 (4)	0.007 (3)	0.001 (3)
C5	0.050 (5)	0.041 (5)	0.029 (4)	0.013 (4)	0.008 (4)	−0.006 (4)
C6	0.030 (4)	0.035 (4)	0.016 (4)	−0.002 (4)	0.001 (3)	−0.002 (3)

Geometric parameters (Å, º)

Se—C1	1.893 (8)	C1—H1B	0.9700
Se—H1	0.974 (10)	C1—H1C	0.9700
O1—N3	1.220 (8)	C2—H2A	0.9700
O2—N3	1.226 (8)	C2—H2B	0.9700
N1—C4	1.331 (10)	C3—C4	1.489 (11)
N1—C5	1.346 (10)	C3—H3A	0.9600
N2—C4	1.350 (9)	C3—H3B	0.9600
N2—C6	1.385 (9)	C3—H3C	0.9600
N2—C2	1.454 (9)	C5—C6	1.367 (10)
N3—C6	1.413 (10)	C5—H5A	0.9300
C1—C2	1.532 (11)
C1—Se—H1	133 (5)	C1—C2—H2B	109.2
C4—N1—C5	105.8 (7)	H2A—C2—H2B	107.9
C4—N2—C6	104.6 (6)	C4—C3—H3A	109.5
C4—N2—C2	126.3 (6)	C4—C3—H3B	109.5
C6—N2—C2	128.9 (6)	H3A—C3—H3B	109.5
O1—N3—O2	122.7 (7)	C4—C3—H3C	109.5
O1—N3—C6	120.0 (7)	H3A—C3—H3C	109.5
O2—N3—C6	117.3 (7)	H3B—C3—H3C	109.5
C2—C1—Se	112.0 (5)	N1—C4—N2	112.7 (7)
C2—C1—H1B	109.2	N1—C4—C3	123.4 (7)
Se—C1—H1B	109.2	N2—C4—C3	123.9 (8)
C2—C1—H1C	109.2	N1—C5—C6	109.5 (7)
Se—C1—H1C	109.2	N1—C5—H5A	125.3
H1B—C1—H1C	107.9	C6—C5—H5A	125.3
N2—C2—C1	112.2 (6)	C5—C6—N2	107.4 (7)
N2—C2—H2A	109.2	C5—C6—N3	126.9 (7)
C1—C2—H2A	109.2	N2—C6—N3	125.6 (7)
N2—C2—H2B	109.2
C4—N2—C2—C1	−103.4 (8)	N1—C5—C6—N2	−0.5 (8)
C6—N2—C2—C1	70.6 (9)	N1—C5—C6—N3	176.9 (7)
Se—C1—C2—N2	59.5 (8)	C4—N2—C6—C5	0.1 (8)
C5—N1—C4—N2	−0.6 (8)	C2—N2—C6—C5	−174.9 (6)
C5—N1—C4—C3	−179.2 (7)	C4—N2—C6—N3	−177.3 (6)
C6—N2—C4—N1	0.3 (8)	C2—N2—C6—N3	7.7 (11)
C2—N2—C4—N1	175.5 (6)	O1—N3—C6—C5	−172.2 (7)
C6—N2—C4—C3	178.9 (7)	O2—N3—C6—C5	7.1 (11)
C2—N2—C4—C3	−5.9 (11)	O1—N3—C6—N2	4.7 (11)
C4—N1—C5—C6	0.7 (8)	O2—N3—C6—N2	−176.0 (7)