organic compounds
Nicotinohydrazide
aDepto. de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
*Correspondence e-mail: adajb@qmc.ufsc.br
The title molecule (alternative name: pyridine-3-carbohydrazide; C6H7N3O) was obtained from the reaction of ethyl nicotinate with hydrazine hydrate in methanol. In the amide group, the C—N bond is relatively short, suggesting some degree of electronic delocalization in the molecule. The stabilized conformation may be compared with those of isomeric compounds picolinohydrazide (pyridine-2-carbohydrazide) and isonicotinohydrazide (pyridine-4-carbohydrazide). In the title isomer, the pyridine ring forms an angle of 33.79 (9)° with the plane of the non-H atoms of the hydrazide group. This lack of coplanarity between the hydrazide functionality and the pyridine ring is considerably greater than that observed in isonicotinohydrazide (dihedral angle = 17.14°), while picolinohydrazide is almost fully planar. The title isomer forms intermolecular N—H⋯O and N—H⋯N hydrogen bonds, which stabilize the crystal structure.
Related literature
The structure of the same compound has been determined independently and is reported in the following paper (Portalone & Colapietro, 2008). The structures of picolinohydrazide (Zareef et al., 2006) and isonicotinohydrazide (Jensen, 1954; Bhat et al., 1974) have been published. For related literature on the biological activity of these molecules, see: Ouelleta et al. (2004); Zhao et al. (2007). For related literature, see: Bhat et al. (1974); Zareef et al. (2006).
Experimental
Crystal data
|
Data collection
|
Refinement
|
|
Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell CAD-4 EXPRESS; data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S160053680706655X/bh2145sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053680706655X/bh2145Isup2.hkl
Nicotinic acid hydrazine was synthesized by the reaction of ethyl nicotinate (43.9 mmol) and hydrazine hydrate 99% (27.5 mmol) in methanol. The reaction mixture was refluxed for 24 h., yielding a yellow solution. Upon cooling to 298 K, the product precipitated and it was washed with methanol and filtered. Colorless needle shaped crystals of (I) suitable for X-ray analysis were grown by recrystallization from a chloroform-methanol (9:1) solution by slow evaporation at room temperature.
All non-H atoms were refined with anisotropic displacement parameters. H atoms attached to C atoms were added at their calculated positions, with C—H = 0.93 Å and Uiso(H) = 1.2Ueq(carrier C). H atoms of the hydrazide group were found in a difference map and treated with a riding model and with Uiso(H) = 1.2Ueq(carrier N). In the absence of significant
effects, no Friedel pairs were collected.The importance of aromatic
is closely related to their biological activity and to the fact that they can be used for the syntheses of several other biologically active compounds. Nicotinohydrazide, (I), for example, is an efficient peroxidase-activated inhibitor of the POX activity of PGHS-2 (Ouelleta et al., 2004). On the other hand, the isomer isonicotinohydrazide, (III, scheme 2), is not a potent inhibitor, with an IC50 of 129 mM against 15 mM for (I).Structure also plays a major role in the activity of the anti-tuberculosis drug isonicotinohydrazide, which requires Mycobacterium tuberculosis catalase-peroxidase (KatG) activation to produce an acyl-NAD adduct (Zhao et al., 2007). This adduct is of extreme importance since it is an inhibitor of the enoyl reductase (Mtb InhA), essential for the biosynthesis of acids present in mycobacterial cell walls. Picolinohydrazide, (II), and isonicotinohydrazide, (III), generate the hydrazide-NAD adduct in this system, while nicotinohydrazide, (I), does not. However, the yield of the (II)-NAD adduct is around 35% of that of the (III)-NAD adduct. As a result, (III) is a potent antituberculosis drug, while (I) and (II) are not.
In this context, studies of structural analogues of these biologically active compounds become fundamental and will be useful in elucidating the mechanism of action, which strongly depends on substrate selection and binding stoichiometry to the (III) binding site in KatG, which still has not been completely elucidated.
The crystal structures of picolinohydrazide, (II) (Zareef et al., 2006), and isonicotinohydrazide, (III) (Jensen, 1954; Bhat et al., 1974), have been previously reported and the structure of nicotinohydrazide (I) is here described. The three isomeric
are distinguished by just the position of the N atom in the pyridine ring with respect to hydrazide group (scheme 2). A selection of their structural parameters is shown in Table 2.When the structural parameters of isomeric
are compared, some interesting aspects can be observed, which depend on the structural relation between the N atom in the ring and the hydrazide group. Indeed, while (II) crystallizes in the monoclinic system, isomers (I) and (III) crystallize in the orthorhombic system. The C6?O1 bond length in (I) and also in (II) and (III) are smaller than those usually observed in (1.365 Å, Zareef et al., 2006). Similarly, the C6—N2 bond distance observed in (I) is consistent with those reported for (II) and (III) suggesting a significant partial double-bond character; the bond lengths are consistent with resonance hybrids between a polar and a neutral form (Bhat et al., 1974). Similar to the results reported (Bhat et al., 1974) for isonicotinohydrazide, the N2—N3 and C2—C6 bonds of (II) have distances similar to their corresponding single bonds. In (I), the pyridine ring bond lengths are very similar to those obtained in related compounds and the ring lies in a plane which forms an angle of 33.79 (9)° with that of the non-H atoms in the hydrazide group. This lack of coplanarity between the hydrazide functionality and the pyridine ring is considerably greater than that observed in isonicotinohydrazide (-17.14°), while picolinohydrazide is almost fully planar, probably because in (II) N2 is in the same side and therefore closer to N1, favoring intramolecular N2—H···N1 hydrogen bond. Conversely, in the of (I) N2 and N1 are on opposite sides of the molecule, and in this case only intermolecular hydrogen bonding takes place. The intermolecular hydrogen bonds N3—H···O1 and N2—H···N1 (Table 1), which form a three-dimensional polymeric structure (Fig. 2) are fundamental for the stability of the of (I).The structure of the same compound has been determined independently and is reported in the following paper (Portalone & Colapietro, 2008). The structures of picolinohydrazide (Zareef et al., 2006) and isonicotinohydrazide (Jensen, 1954; Bhat et al., 1974) have been published. For related literature about biological activity of these molecules, see: Ouelleta et al. (2004); Zhao et al. (2007). For related literature, see: Bhat et al. (1974); Zareef et al. (2006).
Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell
CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: HELENA (Spek, 1996); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).C6H7N3O | F(000) = 288 |
Mr = 137.15 | Dx = 1.401 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 25 reflections |
a = 3.8855 (7) Å | θ = 5.5–18.7° |
b = 10.5191 (5) Å | µ = 0.10 mm−1 |
c = 15.9058 (9) Å | T = 293 K |
V = 650.10 (13) Å3 | Prismatic, colourless |
Z = 4 | 0.46 × 0.30 × 0.20 mm |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.015 |
Radiation source: fine-focus sealed tube | θmax = 29.0°, θmin = 2.3° |
Graphite monochromator | h = −5→2 |
ω–2θ scans | k = −14→0 |
1534 measured reflections | l = −21→0 |
1051 independent reflections | 3 standard reflections every 200 reflections |
866 reflections with I > 2σ(I) | intensity decay: <1% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.031 | H-atom parameters constrained |
wR(F2) = 0.087 | w = 1/[σ2(Fo2) + (0.0344P)2 + 0.1144P] where P = (Fo2 + 2Fc2)/3 |
S = 1.09 | (Δ/σ)max < 0.001 |
1051 reflections | Δρmax = 0.18 e Å−3 |
92 parameters | Δρmin = −0.15 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.040 (6) |
C6H7N3O | V = 650.10 (13) Å3 |
Mr = 137.15 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 3.8855 (7) Å | µ = 0.10 mm−1 |
b = 10.5191 (5) Å | T = 293 K |
c = 15.9058 (9) Å | 0.46 × 0.30 × 0.20 mm |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.015 |
1534 measured reflections | 3 standard reflections every 200 reflections |
1051 independent reflections | intensity decay: <1% |
866 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.031 | 0 restraints |
wR(F2) = 0.087 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.18 e Å−3 |
1051 reflections | Δρmin = −0.15 e Å−3 |
92 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.3825 (5) | 0.84759 (16) | 0.25136 (11) | 0.0373 (4) | |
H1 | 0.4007 | 0.9092 | 0.2930 | 0.045* | |
C2 | 0.2298 (5) | 0.73203 (14) | 0.27215 (10) | 0.0319 (4) | |
C3 | 0.2025 (5) | 0.64013 (16) | 0.20969 (10) | 0.0382 (4) | |
H3 | 0.1029 | 0.5617 | 0.2212 | 0.046* | |
C4 | 0.3262 (6) | 0.66735 (19) | 0.12995 (11) | 0.0455 (5) | |
H4 | 0.3114 | 0.6076 | 0.0870 | 0.055* | |
C5 | 0.4720 (7) | 0.78517 (19) | 0.11576 (11) | 0.0472 (5) | |
H5 | 0.5524 | 0.8032 | 0.0620 | 0.057* | |
C6 | 0.0965 (5) | 0.71648 (17) | 0.36028 (10) | 0.0344 (4) | |
N1 | 0.5043 (5) | 0.87491 (14) | 0.17489 (10) | 0.0440 (4) | |
N2 | 0.1167 (5) | 0.59906 (15) | 0.39179 (9) | 0.0405 (4) | |
H2N | 0.2155 | 0.5365 | 0.3637 | 0.049* | |
N3 | −0.0001 (5) | 0.56759 (16) | 0.47365 (9) | 0.0472 (4) | |
H3NA | 0.0877 | 0.6189 | 0.5112 | 0.057* | |
H3NB | −0.2101 | 0.5876 | 0.4784 | 0.057* | |
O1 | −0.0227 (5) | 0.80795 (12) | 0.39876 (8) | 0.0487 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0405 (9) | 0.0307 (7) | 0.0405 (9) | 0.0021 (8) | −0.0023 (8) | −0.0007 (6) |
C2 | 0.0312 (8) | 0.0314 (7) | 0.0330 (7) | 0.0041 (8) | −0.0025 (7) | −0.0001 (6) |
C3 | 0.0445 (11) | 0.0316 (8) | 0.0384 (8) | 0.0007 (8) | −0.0049 (8) | −0.0009 (7) |
C4 | 0.0594 (14) | 0.0442 (9) | 0.0328 (8) | 0.0060 (11) | −0.0039 (9) | −0.0057 (7) |
C5 | 0.0550 (13) | 0.0522 (10) | 0.0345 (8) | 0.0062 (11) | 0.0050 (9) | 0.0069 (8) |
C6 | 0.0324 (9) | 0.0367 (8) | 0.0339 (7) | 0.0012 (8) | −0.0035 (7) | −0.0040 (7) |
N1 | 0.0481 (10) | 0.0388 (7) | 0.0451 (8) | 0.0002 (8) | 0.0019 (8) | 0.0078 (6) |
N2 | 0.0505 (10) | 0.0373 (7) | 0.0337 (7) | 0.0027 (7) | 0.0057 (7) | 0.0007 (6) |
N3 | 0.0557 (11) | 0.0519 (9) | 0.0338 (7) | −0.0021 (10) | 0.0028 (8) | 0.0045 (6) |
O1 | 0.0604 (10) | 0.0447 (7) | 0.0409 (6) | 0.0120 (7) | 0.0060 (7) | −0.0060 (5) |
C1—N1 | 1.336 (2) | C5—N1 | 1.338 (2) |
C1—C2 | 1.392 (2) | C5—H5 | 0.9300 |
C1—H1 | 0.9300 | C6—O1 | 1.231 (2) |
C2—C3 | 1.390 (2) | C6—N2 | 1.335 (2) |
C2—C6 | 1.503 (2) | N2—N3 | 1.418 (2) |
C3—C4 | 1.386 (2) | N2—H2N | 0.8830 |
C3—H3 | 0.9300 | N3—H3NA | 0.8746 |
C4—C5 | 1.381 (3) | N3—H3NB | 0.8461 |
C4—H4 | 0.9300 | ||
N1—C1—C2 | 123.70 (16) | N1—C5—H5 | 118.1 |
N1—C1—H1 | 118.2 | C4—C5—H5 | 118.1 |
C2—C1—H1 | 118.2 | O1—C6—N2 | 123.96 (16) |
C3—C2—C1 | 118.02 (16) | O1—C6—C2 | 120.55 (16) |
C3—C2—C6 | 124.35 (16) | N2—C6—C2 | 115.49 (15) |
C1—C2—C6 | 117.60 (15) | C1—N1—C5 | 117.04 (16) |
C4—C3—C2 | 118.93 (17) | C6—N2—N3 | 122.80 (15) |
C4—C3—H3 | 120.5 | C6—N2—H2N | 121.7 |
C2—C3—H3 | 120.5 | N3—N2—H2N | 115.4 |
C5—C4—C3 | 118.49 (17) | N2—N3—H3NA | 111.0 |
C5—C4—H4 | 120.8 | N2—N3—H3NB | 109.4 |
C3—C4—H4 | 120.8 | H3NA—N3—H3NB | 99.3 |
N1—C5—C4 | 123.81 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···N1i | 0.88 | 2.11 | 2.975 (2) | 166 |
N3—H3NA···O1ii | 0.87 | 2.22 | 3.045 (2) | 157 |
N3—H3NB···O1iii | 0.85 | 2.55 | 3.155 (2) | 130 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x+1/2, −y+3/2, −z+1; (iii) x−1/2, −y+3/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H7N3O |
Mr | 137.15 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 293 |
a, b, c (Å) | 3.8855 (7), 10.5191 (5), 15.9058 (9) |
V (Å3) | 650.10 (13) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.46 × 0.30 × 0.20 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1534, 1051, 866 |
Rint | 0.015 |
(sin θ/λ)max (Å−1) | 0.681 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.031, 0.087, 1.09 |
No. of reflections | 1051 |
No. of parameters | 92 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.18, −0.15 |
Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), HELENA (Spek, 1996), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003) and Mercury (Macrae et al., 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···N1i | 0.88 | 2.11 | 2.975 (2) | 166.4 |
N3—H3NA···O1ii | 0.87 | 2.22 | 3.045 (2) | 157.0 |
N3—H3NB···O1iii | 0.85 | 2.55 | 3.155 (2) | 129.5 |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x+1/2, −y+3/2, −z+1; (iii) x−1/2, −y+3/2, −z+1. |
(I) | (II) | (III) | |
N2—N3 | 1.418 (2) | 1.422 | 1.429 |
C6—N2 | 1.335 (2) | 1.334 | 1.346 |
C6—O1 | 1.231 (2) | 1.235 | 1.235 |
C6—C2 | 1.503 (2) | 1.507 | 1.513 |
N3—N2—C6 | 122.80 (15) | 121.45 | 121.06 |
N2—C6—O1 | 123.96 (16) | 123.04 | 122.07 |
N2—C6—C2 | 115.49 (15) | 116.08 | 115.90 |
O1—C6—C2 | 120.55 (16) | 120.87 | 122.00 |
N3—N2—C6—O1 | 0.17 (32) | 177.39 | 175.13 |
C2—N2—C6—N3 | 179.56 (19) | 177.72 | 173.03 |
N2—C6—C2—C3 | 34.62 (27) | 177.06 | 162.86 |
Acknowledgements
The authors thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Apoio à Pesquisa Científica e Tecnológica do Estado de Santa Catarina (FAPESC), Financiadora de Estudos e Projetos (FINEP) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).
References
Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119. Web of Science CrossRef CAS IUCr Journals Google Scholar
Bhat, T. N., Singh, T. P. & Vijayan, M. (1974). Acta Cryst. B30, 2921–2922. CSD CrossRef CAS IUCr Journals Google Scholar
Enraf–Nonius (1994). CAD-4 EXPRESS. Version 5.1/1.2. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Jensen, L. H. (1954). J. Am. Chem. Soc. 76, 4663–4667. CSD CrossRef CAS Web of Science Google Scholar
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Ouelleta, M., Aitkenb, S. M., Englishc, A. M. & Percivala, M. D. (2004). Arch. Biochem. Biophys. 431, 107–118. Web of Science PubMed Google Scholar
Portalone, G. & Colapietro, M. (2008). Acta Cryst. E64, o304. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany. Google Scholar
Spek, A. L. (1996). HELENA. University of Utrecht, The Netherlands. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zareef, M., Iqbla, R., Zaidi, J. H., Qadeer, G., Wong, W. Y. & Akhtar, H. (2006). Z. Kristallogr. New Cryst. Struct. 221, 307–308. CAS Google Scholar
Zhao, X., Yu, S. & Magliozzo, R. S. (2007). Biochemistry, 46, 3161–3170. Web of Science CrossRef PubMed CAS Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
The importance of aromatic hydrazides is closely related to their biological activity and to the fact that they can be used for the syntheses of several other biologically active compounds. Nicotinohydrazide, (I), for example, is an efficient peroxidase-activated inhibitor of the POX activity of PGHS-2 (Ouelleta et al., 2004). On the other hand, the isomer isonicotinohydrazide, (III, scheme 2), is not a potent inhibitor, with an IC50 of 129 mM against 15 mM for (I).
Structure also plays a major role in the activity of the anti-tuberculosis drug isonicotinohydrazide, which requires Mycobacterium tuberculosis catalase-peroxidase (KatG) activation to produce an acyl-NAD adduct (Zhao et al., 2007). This adduct is of extreme importance since it is an inhibitor of the enoyl reductase (Mtb InhA), essential for the biosynthesis of acids present in mycobacterial cell walls. Picolinohydrazide, (II), and isonicotinohydrazide, (III), generate the hydrazide-NAD adduct in this system, while nicotinohydrazide, (I), does not. However, the yield of the (II)-NAD adduct is around 35% of that of the (III)-NAD adduct. As a result, (III) is a potent antituberculosis drug, while (I) and (II) are not.
In this context, studies of structural analogues of these biologically active compounds become fundamental and will be useful in elucidating the mechanism of action, which strongly depends on substrate selection and binding stoichiometry to the (III) binding site in KatG, which still has not been completely elucidated.
The crystal structures of picolinohydrazide, (II) (Zareef et al., 2006), and isonicotinohydrazide, (III) (Jensen, 1954; Bhat et al., 1974), have been previously reported and the structure of nicotinohydrazide (I) is here described. The three isomeric hydrazides are distinguished by just the position of the N atom in the pyridine ring with respect to hydrazide group (scheme 2). A selection of their structural parameters is shown in Table 2.
When the structural parameters of isomeric hydrazides are compared, some interesting aspects can be observed, which depend on the structural relation between the N atom in the ring and the hydrazide group. Indeed, while (II) crystallizes in the monoclinic system, isomers (I) and (III) crystallize in the orthorhombic system. The C6?O1 bond length in (I) and also in (II) and (III) are smaller than those usually observed in carboxylic acids (1.365 Å, Zareef et al., 2006). Similarly, the C6—N2 bond distance observed in (I) is consistent with those reported for (II) and (III) hydrazides, suggesting a significant partial double-bond character; the bond lengths are consistent with resonance hybrids between a polar and a neutral form (Bhat et al., 1974). Similar to the results reported (Bhat et al., 1974) for isonicotinohydrazide, the N2—N3 and C2—C6 bonds of (II) have distances similar to their corresponding single bonds. In (I), the pyridine ring bond lengths are very similar to those obtained in related compounds and the ring lies in a plane which forms an angle of 33.79 (9)° with that of the non-H atoms in the hydrazide group. This lack of coplanarity between the hydrazide functionality and the pyridine ring is considerably greater than that observed in isonicotinohydrazide (-17.14°), while picolinohydrazide is almost fully planar, probably because in (II) N2 is in the same side and therefore closer to N1, favoring intramolecular N2—H···N1 hydrogen bond. Conversely, in the crystal structure of (I) N2 and N1 are on opposite sides of the molecule, and in this case only intermolecular hydrogen bonding takes place. The intermolecular hydrogen bonds N3—H···O1 and N2—H···N1 (Table 1), which form a three-dimensional polymeric structure (Fig. 2) are fundamental for the stability of the crystal structure of (I).