5-Amino-1-(2-chloro­nicotino­yl)-3-trifluoro­methyl-1H-1,2,4-triazole: hydrogen-bonded sheets of alternating R22(8) and R66(36) rings

Wardell, J.L.; Low, J.N.; Glidewell, C.

doi:10.1107/S1600536806044990

organic compounds

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Volume 62| Part 12| December 2006| Pages o5383-o5385

https://doi.org/10.1107/S1600536806044990

5-Amino-1-(2-chloronicotinoyl)-3-trifluoromethyl-1H-1,2,4-triazole: hydrogen-bonded sheets of alternating R₂²(8) and R₆⁶(36) rings

James L. Wardell,^a John N. Low ^b and Christopher Glidewell ^c ^*

^aInstituto de Química, Departamento de Química Inorgânica, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil, ^bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and ^cSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
^*Correspondence e-mail: cg@st-andrews.ac.uk

(Received 27 October 2006; accepted 27 October 2006; online 3 November 2006)

The molecules of the title compound, C₉H₅ClF₃N₅O, are linked by two independent N—H⋯N hydrogen bonds into sheets containing alternating R₂²(8) and R₆⁶(36) rings.

Comment

We have recently reported the molecular and supramolecular structures of a number of N-aryl-2-chloronicotinamides obtained from the reactions between 2-chloronicotinoyl chloride and substituted anilines (de Souza et al., 2005 ; Cuffini et al., 2006 ). In a continuation of this study, we now report the structure of the title compound, (I), obtained from the reaction between 2-chloronicotinoyl chloride and 5-amino-3-trifluoromethyl-1H-1,2,4-triazole. The formation of (I) was unexpected, as reaction at the exocyclic amino group was expected to yield the isomeric compound, (II) (see scheme).

The carbonyl group of (I) is almost coplanar with the triazole ring (Fig. 1, Table 1) and this is possibly controlled by the intramolecular N—H⋯O hydrogen bond (Table 2). On the other hand, the pyridyl ring is rotated significantly out of this plane. The bond distances in the triazole ring provide evidence for strong bond fixation within this ring.

The molecules of compound (I) are linked by two independent N—H⋯N hydrogen bonds (Table 2) into sheets, whose formation can readily be analysed in terms of two simple substructures, each utilizing just one hydrogen bond. One substructure is finite and zero-dimensional, while the other is one-dimensional.

The finite substructure is formed from paired hydrogen bonds. Amino atom N5 in the molecule at (x, y, z) acts as hydrogen-bond donor, via atom H5B, to the triazole ring atom N4 in the molecule at (1 − x, 1 − y, 1 − z), so forming by inversion an R₂²(8) (Bernstein et al., 1995 ) dimer centred at ( $[{1 \over 2}]$ , $[{1 \over 2}]$ , $[{1 \over 2}]$ ) (Fig. 2). This dimer can conveniently be regarded as the basic building block in the sheet structure.

In the second substructure, amino atom N5 acts as hydrogen-bond donor, via atom H5A, to pyridyl ring atom N21 in the molecule at ( $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z), so forming a C(8) chain running parallel to the [10 $[\overline{1}]$ ] direction and generated by the c-glide plane at y = $[{3 \over 4}]$ (Fig. 3). This chain motif directly links the R₂²(8) dimer unit centred at ( $[{1 \over 2}]$ , $[{1 \over 2}]$ , $[{1 \over 2}]$ ) to the four dimers centred at (0, 0, 1), (0, 1, 1), (1, 0, 0) and (1, 1, 0), thereby generating a sheet of alternating R₂²(8) and R₆⁶(36) rings parallel to (101) (Fig. 4).

There are no direction-specific interactions between adjacent sheets. In particular, C—H⋯π hydrogen bonds and π–π stacking interactions are absent.

Figure 1
The molecular structure of compound (I)

, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.

Figure 2
Part of the crystal structure of compound (I)

, showing the formation of the hydrogen-bonded R₂²(8) dimer centred at ( $[{1 \over 2}]$ , $[{1 \over 2}]$ , $[{1 \over 2}]$ ). For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) are at the symmetry position (1 − x, 1 − y, 1 − z).

Figure 3
Part of the crystal structure of compound (I)

, showing the formation of a hydrogen-bonded C(8) chain along [10 $[\overline{1}]$ ]. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions ( $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z) and (− $[{1\over 2}]$ + x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z) respectively.

Figure 4
A stereoscopic view of part of the crystal structure of compound (I)

, showing the formation of a sheet of alternating R₂²(8) and R₆⁶(36) rings parallel to (101). For the sake of clarity, H atoms bonded to C atoms have been omitted.

Experimental

A mixture of 2-chloronicotinoyl chloride (0.88 g, 5 mmol) and 5-amino-3-trifluoromethyl-1H-1,2,4-triazole (0.76 g, 5 mmol) (Lopyrev & Rakhmatulina, 1983 ) in 1,2-dichloroethane (15 ml) was heated under reflux for 1 h. The mixture was then cooled and the solvent removed under reduced pressure. The resulting solid product, (I), was recrystallized from ethyl acetate to give crystals suitable for single-crystal X-ray diffraction.

Crystal data

C₉H₅ClF₃N₅O
M_r = 291.63
Monoclinic, P 2₁ /n
a = 4.64770 (10) Å
b = 19.7414 (10) Å
c = 12.3721 (5) Å
β = 91.147 (3)°
V = 1134.94 (8) Å³
Z = 4
D_x = 1.707 Mg m⁻³
Mo Kα radiation
μ = 0.38 mm⁻¹
T = 120 (2) K
Needle, colourless
0.26 × 0.06 × 0.05 mm

Data collection

Bruker Nonius KappaCCD area-detector diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.927, T_max = 0.981
14659 measured reflections
2588 independent reflections
1923 reflections with I > 2σ(I)
R_int = 0.049
θ_max = 27.6°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.094
S = 1.04
2588 reflections
172 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0386P)² + 0.619P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.33 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

N1—N2	1.391 (2)
N2—C3	1.305 (2)
C3—N4	1.364 (2)
N4—C5	1.328 (2)
C5—N1	1.392 (2)
N1—C27	1.401 (2)
C27—O27	1.209 (2)
C3—C31	1.488 (3)
C5—N5	1.324 (2)

N2—N1—C27—O27	−178.39 (17)
N2—N1—C27—C23	0.1 (3)
N1—C27—C23—C22	70.4 (2)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H5A⋯O27	0.88	2.25	2.836 (2)	124
N5—H5A⋯N21ⁱ	0.88	2.40	3.053 (2)	131
N5—H5B⋯N4ⁱⁱ	0.88	2.13	2.985 (2)	163
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (ii) -x+1, -y+1, -z+1.

All H atoms were located in difference maps and then treated as riding atoms, with C—H = 0.95 Å and N—H = 0.88 Å, and with U_iso(H) = 1.2U_eq(C,N).

Data collection: COLLECT (Nonius, 1999 ); cell refinement: DENZO (Otwinowski & Minor, 1997 ) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003 ) and SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536806044990/lh2228sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806044990/lh2228Isup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1999); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

5-Amino-1-(2-chloronicotinoyl)-3-trifluoromethyl-1H-1,2,4-triazole top

Crystal data top

C₉H₅ClF₃N₅O	F(000) = 584
M_r = 291.63	D_x = 1.707 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2588 reflections
a = 4.6477 (1) Å	θ = 3.9–27.6°
b = 19.7414 (10) Å	µ = 0.38 mm⁻¹
c = 12.3721 (5) Å	T = 120 K
β = 91.147 (3)°	Needle, colourless
V = 1134.94 (8) Å³	0.26 × 0.06 × 0.05 mm
Z = 4

Data collection top

Bruker Nonius KappaCCD area-detector diffractometer	2588 independent reflections
Radiation source: Bruker Nonius FR591 rotating anode	1923 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.049
Detector resolution: 9.091 pixels mm^-1	θ_max = 27.6°, θ_min = 3.9°
φ and ω scans	h = −5→6
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −24→25
T_min = 0.927, T_max = 0.981	l = −16→16
14659 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.094	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0386P)² + 0.619P] where P = (F_o² + 2F_c²)/3
2588 reflections	(Δ/σ)_max = 0.001
172 parameters	Δρ_max = 0.25 e Å⁻³
0 restraints	Δρ_min = −0.33 e Å⁻³

Special details top

Experimental. IR (KBr disk, ν, cm^-1): 3368, 3304, 3213, 3156, 1655, 1581, 1567, 1446, 1408, 1383, 1332, 1202, 1139, 1080, 985, 812, 759, 730, 657, 556, 503.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.3230 (3)	0.66804 (8)	0.53946 (13)	0.0196 (4)
N2	0.1330 (3)	0.66249 (8)	0.62443 (13)	0.0204 (4)
C3	0.1366 (4)	0.59720 (10)	0.64084 (15)	0.0188 (4)
C31	−0.0261 (4)	0.56599 (10)	0.73046 (17)	0.0229 (5)
F31	−0.2485 (3)	0.60360 (6)	0.76044 (10)	0.0316 (3)
F32	−0.1271 (3)	0.50499 (6)	0.70283 (11)	0.0346 (3)
F33	0.1419 (3)	0.55681 (7)	0.81869 (10)	0.0391 (4)
N4	0.3061 (3)	0.55840 (8)	0.57685 (13)	0.0198 (4)
C5	0.4244 (4)	0.60400 (10)	0.51248 (15)	0.0183 (4)
N5	0.6132 (4)	0.59136 (9)	0.43635 (13)	0.0229 (4)
C27	0.4050 (4)	0.73123 (10)	0.49861 (15)	0.0189 (4)
O27	0.5656 (3)	0.73437 (7)	0.42315 (11)	0.0236 (3)
N21	0.2498 (3)	0.86511 (9)	0.70620 (13)	0.0227 (4)
C22	0.3523 (4)	0.81141 (10)	0.65678 (15)	0.0184 (4)
Cl22	0.61338 (10)	0.76614 (3)	0.72787 (4)	0.02480 (15)
C23	0.2760 (4)	0.79157 (10)	0.55210 (15)	0.0177 (4)
C24	0.0833 (4)	0.83207 (10)	0.49519 (17)	0.0222 (4)
C25	−0.0272 (4)	0.88902 (11)	0.54533 (17)	0.0265 (5)
C26	0.0579 (4)	0.90288 (11)	0.65022 (18)	0.0262 (5)
H5A	0.6809	0.6248	0.3972	0.027*
H5B	0.6709	0.5496	0.4249	0.027*
H24	0.0276	0.8211	0.4230	0.027*
H25	−0.1591	0.9179	0.5080	0.032*
H26	−0.0232	0.9411	0.6848	0.031*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0229 (9)	0.0167 (9)	0.0194 (9)	0.0009 (7)	0.0067 (7)	0.0003 (7)
N2	0.0220 (8)	0.0207 (9)	0.0188 (9)	0.0003 (7)	0.0074 (7)	−0.0007 (7)
C3	0.0205 (10)	0.0172 (10)	0.0186 (10)	0.0004 (8)	0.0010 (8)	−0.0012 (8)
C31	0.0215 (10)	0.0225 (11)	0.0249 (11)	0.0006 (8)	0.0024 (8)	0.0004 (9)
F31	0.0292 (7)	0.0296 (7)	0.0365 (7)	0.0042 (5)	0.0157 (5)	0.0004 (6)
F32	0.0414 (8)	0.0215 (7)	0.0415 (8)	−0.0087 (6)	0.0152 (6)	0.0003 (6)
F33	0.0351 (7)	0.0578 (10)	0.0243 (7)	−0.0024 (6)	0.0001 (5)	0.0129 (6)
N4	0.0228 (9)	0.0172 (9)	0.0195 (8)	0.0004 (7)	0.0046 (7)	0.0001 (7)
C5	0.0207 (10)	0.0168 (10)	0.0173 (10)	0.0002 (8)	−0.0006 (8)	−0.0029 (8)
N5	0.0307 (9)	0.0159 (9)	0.0224 (9)	0.0025 (7)	0.0096 (7)	−0.0003 (7)
C27	0.0192 (9)	0.0197 (10)	0.0177 (10)	−0.0008 (8)	−0.0005 (8)	−0.0009 (8)
O27	0.0277 (8)	0.0211 (8)	0.0222 (7)	−0.0017 (6)	0.0076 (6)	−0.0015 (6)
N21	0.0258 (9)	0.0199 (9)	0.0225 (9)	−0.0001 (7)	0.0048 (7)	−0.0027 (7)
C22	0.0190 (9)	0.0165 (10)	0.0197 (10)	−0.0015 (8)	0.0030 (8)	0.0026 (8)
Cl22	0.0241 (3)	0.0272 (3)	0.0230 (3)	0.0032 (2)	−0.00125 (19)	0.0024 (2)
C23	0.0188 (9)	0.0148 (10)	0.0196 (10)	−0.0023 (8)	0.0044 (8)	0.0007 (8)
C24	0.0250 (10)	0.0221 (11)	0.0196 (10)	−0.0009 (8)	0.0008 (8)	0.0007 (8)
C25	0.0293 (11)	0.0211 (11)	0.0290 (12)	0.0066 (9)	0.0018 (9)	0.0048 (9)
C26	0.0291 (11)	0.0200 (11)	0.0298 (12)	0.0053 (9)	0.0059 (9)	−0.0033 (9)

Geometric parameters (Å, º) top

N1—N2	1.391 (2)	N5—H5B	0.88
N2—C3	1.305 (2)	C27—C23	1.494 (3)
C3—N4	1.364 (2)	N21—C22	1.318 (3)
N4—C5	1.328 (2)	N21—C26	1.344 (3)
C5—N1	1.392 (2)	C22—C23	1.392 (3)
N1—C27	1.401 (2)	C22—Cl22	1.7328 (19)
C27—O27	1.209 (2)	C23—C24	1.383 (3)
C3—C31	1.488 (3)	C24—C25	1.388 (3)
C31—F31	1.331 (2)	C24—H24	0.95
C31—F32	1.334 (2)	C25—C26	1.377 (3)
C31—F33	1.342 (2)	C25—H25	0.95
C5—N5	1.324 (2)	C26—H26	0.95
N5—H5A	0.88

N2—N1—C5	109.43 (15)	O27—C27—N1	120.05 (18)
N2—N1—C27	121.60 (15)	O27—C27—C23	124.11 (18)
C5—N1—C27	128.76 (16)	N1—C27—C23	115.82 (16)
C3—N2—N1	100.91 (15)	C22—N21—C26	116.71 (17)
N2—C3—N4	118.04 (17)	N21—C22—C23	124.78 (18)
N2—C3—C31	121.34 (17)	N21—C22—Cl22	115.82 (15)
N4—C3—C31	120.54 (18)	C23—C22—Cl22	119.32 (15)
F31—C31—F32	107.68 (16)	C24—C23—C22	117.46 (18)
F31—C31—F33	106.92 (16)	C24—C23—C27	119.80 (17)
F32—C31—F33	106.41 (17)	C22—C23—C27	122.66 (17)
F31—C31—C3	112.67 (17)	C23—C24—C25	118.87 (19)
F32—C31—C3	111.36 (17)	C23—C24—H24	120.6
F33—C31—C3	111.47 (16)	C25—C24—H24	120.6
C5—N4—C3	102.61 (16)	C26—C25—C24	118.71 (19)
N5—C5—N4	125.95 (18)	C26—C25—H25	120.6
N5—C5—N1	125.04 (18)	C24—C25—H25	120.6
N4—C5—N1	109.00 (16)	N21—C26—C25	123.43 (19)
C5—N5—H5A	120.0	N21—C26—H26	118.3
C5—N5—H5B	120.0	C25—C26—H26	118.3
H5A—N5—H5B	120.0

C5—N1—N2—C3	0.0 (2)	C5—N1—C27—O27	7.3 (3)
C27—N1—N2—C3	−175.24 (17)	N2—N1—C27—C23	0.1 (3)
N1—N2—C3—N4	−0.1 (2)	C5—N1—C27—C23	−174.18 (18)
N1—N2—C3—C31	176.58 (17)	C26—N21—C22—C23	0.0 (3)
N2—C3—C31—F31	24.8 (3)	C26—N21—C22—Cl22	176.68 (14)
N4—C3—C31—F31	−158.62 (17)	N21—C22—C23—C24	1.5 (3)
N2—C3—C31—F32	145.91 (18)	Cl22—C22—C23—C24	−175.11 (14)
N4—C3—C31—F32	−37.5 (2)	N21—C22—C23—C27	178.22 (18)
N2—C3—C31—F33	−95.4 (2)	Cl22—C22—C23—C27	1.6 (3)
N4—C3—C31—F33	81.2 (2)	O27—C27—C23—C24	65.5 (3)
N2—C3—N4—C5	0.1 (2)	N1—C27—C23—C24	−112.9 (2)
C31—C3—N4—C5	−176.59 (17)	O27—C27—C23—C22	−111.2 (2)
C3—N4—C5—N5	178.57 (19)	N1—C27—C23—C22	70.4 (2)
C3—N4—C5—N1	−0.1 (2)	C22—C23—C24—C25	−1.2 (3)
N2—N1—C5—N5	−178.62 (17)	C27—C23—C24—C25	−178.06 (18)
C27—N1—C5—N5	−3.8 (3)	C23—C24—C25—C26	−0.4 (3)
N2—N1—C5—N4	0.0 (2)	C22—N21—C26—C25	−1.8 (3)
C27—N1—C5—N4	174.86 (18)	C24—C25—C26—N21	2.0 (3)
N2—N1—C27—O27	−178.39 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5A···O27	0.88	2.25	2.836 (2)	124
N5—H5A···N21ⁱ	0.88	2.40	3.053 (2)	131
N5—H5B···N4ⁱⁱ	0.88	2.13	2.985 (2)	163

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

Acknowledgements

The X-ray data were collected at the EPSRC X-Ray Crystallographic Service, University of Southampton, UK; the authors thank the staff of the Service for all their help and advice. JLW thanks CNPq and FAPERJ for financial support.

References

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