5-Fluoro-1H-indole-2-carbohydrazide

Harrison, W.T.A.; Yathirajan, H.S.; Ashalatha, B.V.; Vijaya Raj, K.K.; Narayana, B.

doi:10.1107/S1600536806040943

organic compounds

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ISSN: 2056-9890

Volume 62| Part 11| November 2006| Pages o4986-o4988

https://doi.org/10.1107/S1600536806040943

5-Fluoro-1H-indole-2-carbohydrazide

William T. A. Harrison,^a ^* H. S. Yathirajan,^b B. V. Ashalatha,^c K. K. Vijaya Raj ^c and B. Narayana ^c

^aDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, ^bDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570 006, India, and ^cDepartment of Chemistry, Mangalore University, Mangalagangotri 574 199, India
^*Correspondence e-mail: w.harrison@abdn.ac.uk

(Received 4 October 2006; accepted 4 October 2006; online 13 October 2006)

The geometric parameters for the essentially planar molecule of the title compound, C₉H₈FN₃O, are normal. A network of N—H⋯O and N—H⋯N hydrogen bonds helps to establish the crystal packing.

Comment

As part of our ongoing research into indole carboxylic acid derivatives (Harrison et al., 2006 ), the synthesis and crystal structure of the title compound, (I) (Fig. 1), are now presented.

The geometric paramaters for (I) fall within their expected ranges (Allen et al., 1987 ). The indole ring system is essentially flat (r.m.s. deviation from the mean plane = 0.005 Å). The mean plane of atoms C9, O1, N2 and N3 of the carbohydrazide side chain is slightly twisted away from the indole mean plane [dihedral angle = 5.27 (9)°]. The bond angle sum about N2 is 359°, suggesting sp²-hybridization for this atom. Conversely, the average bond angle for N3 of 108° suggests sp³-hybridization.

The crystal packing in (I) is influenced by N—H⋯O and N—H⋯N hydrogen bonds (Table 1). Inversion-generated dimeric pairs of molecules are linked by a pair of N3—H3⋯O1ⁱⁱⁱ hydrogen bonds (Fig. 2). Adjacent molecules are then linked into ribbons by a combination of the N2—H2⋯O1ⁱⁱ and N1⋯H1—N3ⁱ bonds. In terms of graph theory (Bernstein et al., 1995 ) these two hydrogen-bonding motifs result in R₂²(10) and R₂²(8) loops, respectively. Combining the two results in (001) sheets of molecules. Atom H4, attached to N3, does not participate in hydrogen bonds. A PLATON (Spek, 2003 ) analysis of (I) indicated a short C—H⋯F contact that may also help to consolidate the crystal packing. In the packing of (I), a zigzag stacking of molecules with respect to the c direction is seen (Fig. 3). Any π–π stacking interactions in (I) must be very weak, the shortest intermolecular ring-centroid separation being 4.08 Å.

Figure 1
View of the molecular structure of (I)

, showing 50% probability displacement ellipsoids and arbitrary spheres for the H atoms.

Figure 2
Fragment of the crystal structure of (I)

, showing the hydrogen-bonding (dashed lines) scheme, with C-bound H atoms omitted for clarity. Symmetry codes as in Table 1

Figure 3
The packing for (I)

, with all H atoms omitted for clarity.

Experimental

Methyl-5-fluoroindole-2-carboxylate (2.34 g, 0.01 mol) (Harrison et al., 2006) in 25 ml of absolute ethanol was refluxed with 1.0 ml of hydrazine hydrate for 2 h, with the reaction progress monitored by thin-layer chromatography. Upon completion, the mixture was cooled to room temperature. The separated solid was filtered off and washed with cold ethanol; cubes of (I) were recrystallized from ethanol (m.p. 505–507 K). Analysis found (calculated) for C₉H₈FN₃O: C 55.70 (55.96), H 4.12 (4.17), N 21.65 (21.75)%.

Crystal data

C₉H₈FN₃O
M_r = 193.18
Orthorhombic, P b c a
a = 10.0451 (3) Å
b = 9.4978 (2) Å
c = 18.5293 (6) Å
V = 1767.81 (9) Å³
Z = 8
D_x = 1.452 Mg m⁻³
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 120 (2) K
Cube, colourless
0.20 × 0.20 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Bruker, 2003 ) T_min = 0.978, T_max = 0.978
11208 measured reflections
1733 independent reflections
1497 reflections with I > 2σ(I)
R_int = 0.029
θ_max = 26.1°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.089
S = 1.06
1733 reflections
140 parameters
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ²(F_o²) + (0.0434P)² + 0.7328P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.19 e Å⁻³
Extinction correction: SHELXL97
Extinction coefficient: 0.015 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N3ⁱ	0.898 (16)	2.096 (16)	2.9864 (15)	171.3 (13)
N2—H2⋯O1ⁱⁱ	0.870 (16)	2.073 (16)	2.9193 (14)	163.9 (14)
N3—H3⋯O1ⁱⁱⁱ	0.920 (16)	2.124 (16)	3.0241 (15)	165.8 (13)
C3—H3A⋯F1^iv	0.95	2.55	3.2082 (15)	127
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iii) -x+1, -y+2, -z+1; (iv) $[x-{\script{1\over 2}}, y, -z+{\script{3\over 2}}]$ .

The N-bound H atoms were located in difference maps and their positions were freely refined with U_iso(H) set equal to 1.2U_eq(N). The C-bound H atoms were placed in idealized locations (C—H = 0.95 Å) and refined as riding with U_iso(H) = 1.2U_eq(C).

Data collection: COLLECT (Nonius, 1998 ); cell refinement: HKL SCALEPACK (Otwinowski & Minor 1997 ); data reduction: HKL DENZO and SCALEPACK (Otwinowski & Minor 1997), and SORTAV (Blessing, 1995 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536806040943/bt2203sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806040943/bt2203Isup2.hkl

Computing details top

Data collection: Collect (Nonius, 1998); cell refinement: HKL SCALEPACK (Otwinowski & Minor 1997); data reduction: HKL DENZO and SCALEPACK (Otwinowski & Minor 1997), and SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

5-Fluoro-1H-indole-2-carbohydrazide top

Crystal data top

C₉H₈FN₃O	F(000) = 800
M_r = 193.18	D_x = 1.452 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1996 reflections
a = 10.0451 (3) Å	θ = 1.0–26.0°
b = 9.4978 (2) Å	µ = 0.11 mm⁻¹
c = 18.5293 (6) Å	T = 120 K
V = 1767.81 (9) Å³	Cube, colourless
Z = 8	0.20 × 0.20 × 0.20 mm

Data collection top

Nonius KappaCCD diffractometer	1733 independent reflections
Radiation source: fine-focus sealed tube	1497 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
φ and ω scans	θ_max = 26.1°, θ_min = 3.7°
Absorption correction: multi-scan (SADABS; Bruker, 2003)	h = −12→12
T_min = 0.978, T_max = 0.978	k = −11→10
11208 measured reflections	l = −22→18

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difmap (N-H) and geom (others)
R[F² > 2σ(F²)] = 0.032	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.089	w = 1/[σ²(F_o²) + (0.0434P)² + 0.7328P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.001
1733 reflections	Δρ_max = 0.25 e Å⁻³
140 parameters	Δρ_min = −0.19 e Å⁻³
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.015 (2)

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.48589 (12)	0.44387 (13)	0.63425 (6)	0.0181 (3)
C2	0.41098 (13)	0.34193 (14)	0.67046 (7)	0.0217 (3)
H2A	0.3166	0.3410	0.6676	0.026*
C3	0.47908 (13)	0.24262 (14)	0.71057 (7)	0.0228 (3)
H3A	0.4319	0.1713	0.7358	0.027*
C4	0.61805 (13)	0.24800 (13)	0.71369 (7)	0.0216 (3)
C5	0.69439 (13)	0.34626 (13)	0.67917 (7)	0.0211 (3)
H5	0.7887	0.3462	0.6829	0.025*
C6	0.62640 (12)	0.44730 (13)	0.63784 (6)	0.0179 (3)
C7	0.66864 (12)	0.56243 (13)	0.59462 (7)	0.0192 (3)
H7	0.7578	0.5914	0.5863	0.023*
C8	0.55545 (12)	0.62391 (13)	0.56713 (7)	0.0179 (3)
C9	0.54006 (11)	0.74680 (14)	0.51939 (7)	0.0175 (3)
N1	0.44498 (10)	0.55295 (11)	0.59124 (6)	0.0186 (3)
H1	0.3600 (16)	0.5719 (15)	0.5798 (8)	0.022*
N2	0.65387 (10)	0.80349 (11)	0.49559 (6)	0.0208 (3)
H2	0.7311 (16)	0.7653 (16)	0.5037 (8)	0.025*
N3	0.65712 (11)	0.91675 (12)	0.44592 (6)	0.0209 (3)
H3	0.6249 (15)	0.9963 (17)	0.4682 (8)	0.025*
H4	0.6008 (16)	0.8927 (16)	0.4082 (9)	0.025*
O1	0.42915 (8)	0.79502 (10)	0.50288 (5)	0.0217 (2)
F1	0.67988 (8)	0.14679 (8)	0.75401 (4)	0.0297 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0176 (6)	0.0185 (6)	0.0182 (6)	0.0013 (5)	0.0000 (5)	−0.0022 (5)
C2	0.0170 (6)	0.0236 (7)	0.0244 (7)	−0.0007 (5)	0.0022 (5)	−0.0002 (5)
C3	0.0228 (7)	0.0216 (7)	0.0240 (7)	−0.0022 (5)	0.0043 (5)	0.0014 (5)
C4	0.0234 (7)	0.0199 (6)	0.0216 (6)	0.0042 (5)	−0.0017 (5)	0.0022 (5)
C5	0.0168 (6)	0.0237 (7)	0.0229 (6)	0.0013 (5)	−0.0006 (5)	−0.0007 (5)
C6	0.0172 (6)	0.0182 (6)	0.0185 (6)	0.0007 (5)	0.0000 (5)	−0.0029 (5)
C7	0.0154 (6)	0.0205 (6)	0.0216 (6)	−0.0009 (5)	0.0004 (5)	−0.0014 (5)
C8	0.0161 (6)	0.0181 (6)	0.0196 (6)	−0.0007 (5)	0.0008 (5)	−0.0024 (5)
C9	0.0154 (6)	0.0171 (6)	0.0200 (6)	0.0000 (5)	−0.0007 (5)	−0.0035 (5)
N1	0.0139 (5)	0.0197 (6)	0.0223 (6)	0.0003 (4)	0.0001 (4)	0.0013 (4)
N2	0.0139 (5)	0.0206 (6)	0.0280 (6)	0.0011 (4)	−0.0002 (4)	0.0060 (5)
N3	0.0191 (6)	0.0178 (6)	0.0258 (6)	−0.0006 (4)	−0.0007 (4)	0.0039 (5)
O1	0.0140 (4)	0.0213 (5)	0.0297 (5)	0.0008 (3)	−0.0009 (4)	0.0023 (4)
F1	0.0259 (4)	0.0281 (5)	0.0352 (5)	0.0030 (3)	−0.0019 (3)	0.0124 (4)

Geometric parameters (Å, º) top

C1—N1	1.3702 (17)	C7—C8	1.3759 (17)
C1—C2	1.3978 (18)	C7—H7	0.9500
C1—C6	1.4133 (18)	C8—N1	1.3730 (16)
C2—C3	1.3820 (19)	C8—C9	1.4727 (18)
C2—H2A	0.9500	C9—O1	1.2428 (14)
C3—C4	1.3981 (19)	C9—N2	1.3384 (16)
C3—H3A	0.9500	N1—H1	0.898 (16)
C4—F1	1.3667 (14)	N2—N3	1.4161 (15)
C4—C5	1.3667 (18)	N2—H2	0.870 (16)
C5—C6	1.4050 (17)	N3—H3	0.920 (16)
C5—H5	0.9500	N3—H4	0.927 (17)
C6—C7	1.4203 (17)

N1—C1—C2	129.90 (12)	C8—C7—C6	106.77 (11)
N1—C1—C6	108.02 (11)	C8—C7—H7	126.6
C2—C1—C6	122.08 (11)	C6—C7—H7	126.6
C3—C2—C1	117.67 (12)	N1—C8—C7	109.83 (11)
C3—C2—H2A	121.2	N1—C8—C9	119.98 (11)
C1—C2—H2A	121.2	C7—C8—C9	130.19 (11)
C2—C3—C4	119.44 (12)	O1—C9—N2	122.44 (12)
C2—C3—H3A	120.3	O1—C9—C8	122.27 (11)
C4—C3—H3A	120.3	N2—C9—C8	115.28 (10)
F1—C4—C5	118.76 (11)	C1—N1—C8	108.54 (10)
F1—C4—C3	116.78 (11)	C1—N1—H1	125.0 (9)
C5—C4—C3	124.46 (12)	C8—N1—H1	126.4 (9)
C4—C5—C6	116.66 (12)	C9—N2—N3	122.64 (10)
C4—C5—H5	121.7	C9—N2—H2	122.5 (10)
C6—C5—H5	121.7	N3—N2—H2	114.1 (10)
C5—C6—C1	119.69 (11)	N2—N3—H3	108.9 (9)
C5—C6—C7	133.47 (12)	N2—N3—H4	106.8 (10)
C1—C6—C7	106.84 (11)	H3—N3—H4	109.0 (14)

N1—C1—C2—C3	179.90 (12)	C1—C6—C7—C8	0.22 (13)
C6—C1—C2—C3	−0.06 (18)	C6—C7—C8—N1	0.14 (14)
C1—C2—C3—C4	0.29 (19)	C6—C7—C8—C9	179.73 (12)
C2—C3—C4—F1	−179.81 (11)	N1—C8—C9—O1	4.26 (19)
C2—C3—C4—C5	−0.1 (2)	C7—C8—C9—O1	−175.31 (13)
F1—C4—C5—C6	179.40 (11)	N1—C8—C9—N2	−176.29 (11)
C3—C4—C5—C6	−0.27 (19)	C7—C8—C9—N2	4.1 (2)
C4—C5—C6—C1	0.49 (17)	C2—C1—N1—C8	−179.38 (12)
C4—C5—C6—C7	−179.26 (13)	C6—C1—N1—C8	0.58 (14)
N1—C1—C6—C5	179.69 (11)	C7—C8—N1—C1	−0.45 (15)
C2—C1—C6—C5	−0.35 (18)	C9—C8—N1—C1	179.90 (11)
N1—C1—C6—C7	−0.49 (13)	O1—C9—N2—N3	−4.4 (2)
C2—C1—C6—C7	179.47 (11)	C8—C9—N2—N3	176.16 (11)
C5—C6—C7—C8	180.00 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3ⁱ	0.898 (16)	2.096 (16)	2.9864 (15)	171.3 (13)
N2—H2···O1ⁱⁱ	0.870 (16)	2.073 (16)	2.9193 (14)	163.9 (14)
N3—H3···O1ⁱⁱⁱ	0.920 (16)	2.124 (16)	3.0241 (15)	165.8 (13)
C3—H3A···F1^iv	0.95	2.55	3.2082 (15)	127

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

Acknowledgements

The authors thank the EPSRC National Crystallographic Service (University of Southampton) for data collection. ABV thanks Mangalore University for provision of research facilities.

References

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CSD CrossRef Web of Science Google Scholar
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Blessing, R. H. (1995). Acta Cryst. A51, 33–38. CrossRef CAS Web of Science IUCr Journals Google Scholar
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Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
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Nonius (1998). COLLECT. Nonius, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
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https://doi.org/10.1107/S1600536806040943

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

5-Fluoro-1H-indole-2-carbohydrazide

Comment

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds