4-Iodo-1H-pyrrole-2-carbaldehyde

The title compound, C₅H₄INO, was synthesized during research aimed at producing suitable halogenated pyrrole building blocks for Suzuki–Miyaura coupling reactions. In the crystal structure, the mol­ecules are planar and exhibit N—H...O bonding to form centrosymmetric dimers.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.026
• wR factor = 0.068
• Data-to-parameter ratio = 20.3

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:      0.250     0.533
            Tmin and Tmax expected:      0.167     0.487
            RR =      1.368
            Please check that your absorption correction is appropriate.
PLAT060_ALERT_3_C Ratio Tmax/Tmin (Exp-to-Rep) (too) Large .......       1.35
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.91

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      0.914
            Tmax scaled      0.487 Tmin scaled      0.229

   0 ALERT level A = In general: serious problem
   0 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
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   1 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) was synthesized during research aimed at producing suitable halogenated pyrrole building blocks for Suzuki–Miyaura coupling reactions (Miyaura & Suzuki, 1995; Davis et al., 2002). Although compound (I) has been previously synthesized using a variety of methods (Mitsui et al., 2003; Monti & Sleiter 1990; Sonnet, 1972) this is the first report of the X-ray crystal structure for 4-iodo-1H-pyrrole-2-carbaldehyde. As observed for related structures (Smith et al., 1985), the molecules are planar and exhibit N—H···O bonding to form centrosymmetric dimers (Fig. 2).

Related literature

For related literature, see: Davis et al. (2002); Mitsui et al. (2003); Miyaura & Suzuki (1995); Monti & Sleiter (1990); Smith et al. (1985); Sonnet (1972).

S2. Experimental

The commercial reagent pyrrole-2-carbaldehyde (475 mg, 5 mmol) was added to an argon charged two-necked flask (50 ml) to which dry THF (20 ml) was added and the mixture stirred for 10 min before being cooled to 195 K. N-iodosuccinimide (1.12 g, 5 mmol) was added portionwise over 15 min then the mixture was stirred at 195 K for 1 h before being transferred to a 258 K refrigerator for 16 h. The solvent was removed under vacuum and the material was partitioned between H₂O (50 ml) and DCM (2 x 50 ml). The organic phase was dried (MgSO₄), then the DCM was evaporated under reduced pressure. The resulting residue was dissolved in DMSO (10 ml) then chromatographed over a C₁₈ flash column (40 mm x 80 mm) using 10% stepwise elutions from 20% MeOH/80% H₂O to 100% MeOH. The 70% MeOH/30% H₂O elution contained a 9:1 mixture of 4-iodo-1H-pyrrole-2-carbaldehyde and 5-iodo-1H-pyrrole-2-carbaldehyde (165 mg), which proved to be inseparable by reversed-phase HPLC. Fractional crystallization using DCM/hexanes produced pure 4-iodo-1H-pyrrole-2-carbaldehyde (72 mg, 6.5% yield). Low yielding di-iodinated and tri-iodinated pyrrole derivatives were also detected during the purification work however no crystalline material was obtained for these compounds. NMR assignments for compound (I) were determined following analysis of the one-dimensional and two-dimensional NMR (1H, 13 C, gCOSY, gHSQC, gHMBC) data.

4-iodo-1H-pyrrole-2-carbaldehyde (I): clear needles, m.p. 390–391 K. ¹H NMR (DMSO-d₆, 600 MHz) δ 7.12 (1H, s, H-3), 7.33 (1H, s, H-5), 9.43 (1H, s, 2-CHO), 12.37 (1H, br s, 1-NH). ¹³C NMR (DMSO-d₆, 150 MHz) δ 62.7 (C-4), 126.0 (C-3), 131.3 (C-5), 134.4 (C-2), 178.7 (2-CHO). (-)-LRESIMS (rel. int.) m/z 220 (100%) [M—H, C₅H₃INO]^-.

S3. Refinement

The carbon-bound H atoms were constrained as riding atoms with C—H = 0.95–0.96 Å. The pyrrole proton was located in a difference Fourier synthesis and constrained with N—H = 0.88 Å. U_iso(H) values were set at 1.2U_eq of the parent atom.

Computing details

Data collection: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); cell refinement: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); data reduction: TEXSAN (Molecular Structure Corporation, 2001); program(s) used to solve structure: TEXSAN (Molecular Structure Corporation, 2001); program(s) used to refine structure: TEXSAN (Molecular Structure Corporation, 2001) and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: TEXSAN (Molecular Structure Corporation, 2001) and PLATON (Spek, 2003).

Figures

	Fig. 1. View of (I) with the atom numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 30% probability level.
	Fig. 2. View of the centrosymmetric dimers of (I).

4-iodo-1H-pyrrole-2-carbaldehyde

Crystal data

C5H4INO	F(000) = 408
Mr = 220.99	Dx = 2.243 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 10.245 (3) Å	θ = 12.5–16.3°
b = 4.726 (2) Å	µ = 4.79 mm^−1
c = 13.531 (4) Å	T = 295 K
β = 92.73 (2)°	Plate, colourless
V = 654.4 (4) Å^3	0.40 × 0.40 × 0.15 mm
Z = 4

Data collection

Rigaku AFC-7R diffractometer	1281 reflections with I > 2σ(I)
Radiation source: Rigaku rotating anode	Rint = 0.018
Graphite monochromator	θmax = 27.5°, θmin = 3.0°
ω/2θ scans	h = −13→13
Absorption correction: ψ scan (North et al., 1968)	k = −2→6
Tmin = 0.250, Tmax = 0.533	l = −7→17
1793 measured reflections	3 standard reflections every 150 reflections
1505 independent reflections	intensity decay: 1.8%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.026	H-atom parameters constrained
wR(F^2) = 0.068	w = 1/[σ^2(Fo^2) + (0.0254P)^2 + 0.8517P] where P = (Fo^2 + 2Fc^2)/3
S = 1.11	(Δ/σ)max < 0.001
1505 reflections	Δρmax = 0.56 e Å^−3
74 parameters	Δρmin = −0.69 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001Fc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0057 (6)

Special details

Experimental. The scan width was (1.79 + 0.30tanθ)° with an ω scan speed of 16° per minute (up to 5 scans to achieve I/σ(I) > 10). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodness of fit values S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs 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
I1	0.10101 (3)	0.11438 (6)	0.17038 (2)	0.0593 (1)
O2	0.4065 (3)	0.9850 (9)	−0.1241 (2)	0.0696 (10)
N1	0.3783 (3)	0.6731 (8)	0.0582 (2)	0.0536 (10)
C2	0.2945 (4)	0.6628 (9)	−0.0239 (3)	0.0521 (13)
C3	0.1952 (4)	0.4801 (10)	−0.0045 (3)	0.0531 (11)
C4	0.2196 (4)	0.3788 (8)	0.0908 (3)	0.0490 (11)
C5	0.3333 (4)	0.5006 (10)	0.1282 (3)	0.0547 (13)
C21	0.3154 (4)	0.8263 (11)	−0.1112 (3)	0.0601 (14)
H1	0.45070	0.77370	0.06420	0.0630*
H2	0.25140	0.80760	−0.16460	0.0710*
H3	0.12300	0.42850	−0.04790	0.0630*
H5	0.37100	0.46580	0.19280	0.0640*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
I1	0.0656 (2)	0.0567 (2)	0.0560 (2)	0.0093 (1)	0.0078 (1)	0.0053 (1)
O2	0.0663 (18)	0.096 (2)	0.0456 (15)	−0.0168 (18)	−0.0061 (13)	0.0071 (17)
N1	0.0476 (16)	0.071 (2)	0.0417 (16)	0.0030 (16)	−0.0029 (13)	−0.0036 (16)
C2	0.053 (2)	0.065 (3)	0.0376 (17)	0.0046 (19)	−0.0053 (15)	−0.0039 (17)
C3	0.053 (2)	0.062 (2)	0.0435 (19)	−0.0021 (19)	−0.0067 (16)	−0.0025 (19)
C4	0.0533 (19)	0.052 (2)	0.0418 (18)	0.0109 (17)	0.0035 (15)	−0.0023 (17)
C5	0.056 (2)	0.069 (3)	0.0387 (18)	0.013 (2)	−0.0017 (16)	−0.0012 (19)
C21	0.058 (2)	0.081 (3)	0.0404 (19)	−0.008 (2)	−0.0070 (16)	0.002 (2)

Geometric parameters (Å, º)

I1—C4	2.079 (4)	C2—C21	1.436 (6)
O2—C21	1.216 (6)	C3—C4	1.387 (6)
N1—C2	1.372 (5)	C4—C5	1.374 (6)
N1—C5	1.348 (5)	C3—H3	0.9500
N1—H1	0.8800	C5—H5	0.9500
C2—C3	1.369 (6)	C21—H2	0.9600
I1···C4^i	3.853 (4)	C4···I1^vii	3.853 (4)
I1···C5^i	3.812 (5)	C5···I1^vii	3.812 (5)
I1···I1^ii	3.8646 (17)	C5···O2^viii	3.400 (5)
I1···I1^iii	3.8646 (17)	C21···H1^vi	3.0900
I1···H2^iv	3.3200	C21···H5^v	2.9100
O2···N1	2.900 (5)	H1···O2	2.7500
O2···C5^v	3.400 (5)	H1···O2^vi	2.0000
O2···N1^vi	2.843 (5)	H1···C21^vi	3.0900
O2···H1^vi	2.0000	H2···I1^ix	3.3200
O2···H1	2.7500	H2···H5^v	2.5700
O2···H5^v	2.5000	H5···O2^viii	2.5000
N1···O2	2.900 (5)	H5···C21^viii	2.9100
N1···O2^vi	2.843 (5)	H5···H2^viii	2.5700
C2—N1—C5	109.0 (3)	C3—C4—C5	108.1 (4)
C5—N1—H1	125.00	N1—C5—C4	107.9 (3)
C2—N1—H1	126.00	O2—C21—C2	126.5 (4)
N1—C2—C21	122.3 (4)	C2—C3—H3	127.00
N1—C2—C3	108.0 (4)	C4—C3—H3	126.00
C3—C2—C21	129.7 (4)	N1—C5—H5	128.00
C2—C3—C4	107.1 (4)	C4—C5—H5	124.00
I1—C4—C5	124.6 (3)	O2—C21—H2	117.00
I1—C4—C3	127.2 (3)	C2—C21—H2	117.00
C5—N1—C2—C3	0.0 (5)	C3—C2—C21—O2	−179.7 (5)
C5—N1—C2—C21	179.5 (4)	C2—C3—C4—I1	175.5 (3)
C2—N1—C5—C4	−0.1 (5)	C2—C3—C4—C5	0.0 (5)
N1—C2—C3—C4	0.0 (5)	I1—C4—C5—N1	−175.6 (3)
C21—C2—C3—C4	−179.4 (4)	C3—C4—C5—N1	0.1 (5)
N1—C2—C21—O2	1.1 (7)

Symmetry codes: (i) x, y−1, z; (ii) −x, y−1/2, −z+1/2; (iii) −x, y+1/2, −z+1/2; (iv) x, −y+1/2, z+1/2; (v) x, −y+3/2, z−1/2; (vi) −x+1, −y+2, −z; (vii) x, y+1, z; (viii) x, −y+3/2, z+1/2; (ix) x, −y+1/2, z−1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^vi	0.88	2.00	2.843 (5)	161
C5—H5···O2^viii	0.95	2.50	3.400 (5)	158

Symmetry codes: (vi) −x+1, −y+2, −z; (viii) x, −y+3/2, z+1/2.