Pyrazine-2-carbohydrazide: a three-dimensional hydrogen-bonded framework structure

Wardell, S.M.S.V.; de Souza, M.V.N.; Wardell, J.L.; Low, J.N.; Glidewell, C.

doi:10.1107/S1600536806029394

organic compounds

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Volume 62| Part 9| September 2006| Pages o3765-o3767

https://doi.org/10.1107/S1600536806029394

Pyrazine-2-carbohydrazide: a three-dimensional hydrogen-bonded framework structure

Solange M. S. V. Wardell,^a Marcus V. N. de Souza,^a James L. Wardell,^b John N. Low ^c and Christopher Glidewell ^d ^*

^aInstituto de Tecnologia em Fármacos, Far-Manguinhos, FIOCRUZ, 21041-250, Rio de Janeiro, RJ, Brazil, ^bInstituto de Química, Departamento de Química Inorgânica, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil, ^cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and ^dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
^*Correspondence e-mail: cg@st-andrews.ac.uk

(Received 27 July 2006; accepted 28 July 2006; online 9 August 2006)

Molecules of the title compound, C₅H₆N₄O, are linked into a three-dimensional framework structure by a combination of N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds.

Comment

As part of our general study of the supramolecular structures of amine and hydrazine derivatives, we report here the molecular and supramolecular structure of the title compound, (I). Within the hydrazino fragment, the coordination at C7 and N2 is planar within experimental uncertainty, while the coordination at N3 is markedly pyramidal (Fig. 1). Apart from the H atoms bonded to atom N3, the molecule is effectively planar, as shown by the key torsion angles (Table 1); the bond distances and angles show no unexpected features.

The molecules are linked by hydrogen bonds (Table 2) into a three-dimensional framework of some complexity, whose formation can, nonetheless, be readily analysed in terms of two simple substructures. In the first of these substructures, atom N3 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H31 and H32, respectively, to atoms O1 in the molecules at (1 − x, 1 − y, 1 − z) and (−x, 1 − y, 1 − z), so generating by inversion a chain of edge-fused R₂²(10) (Bernstein et al., 1995 ) rings running along (x, $[{1\over 2}]$ , $[{1\over 2}]$ ) (Fig. 2). The rings containing H31 are centred at (n + $[{1\over 2}]$ , $[{1\over 2}]$ , $[{1\over 2}]$ ), where n = zero or an integer) and those containing H32 are centred at (n, $[{1\over 2}]$ , $[{1\over 2}]$ ) (n = zero or integer).

In the second substructure, atom N2 in the molecule at (x, y, z), which lies in the chain of rings along (x, $[{1\over 2}]$ , $[{1\over 2}]$ ), acts as hydrogen-bond donor to atom N4 in the molecule at (1 − x, $[{1\over 2}]$ − y, $[{1\over 2}]$ + z), which lies in the chain along (x, 0, 1); at the same time, atom C3 at (1 − x, $[{1\over 2}]$ − y, $[{1\over 2}]$ + z) acts as donor to atom N1 in the molecule at (x, y, z), so forming an R₂²(8) motif (Fig. 3). Propagation of this motif by the symmetry operations of the space group then links the chain of rings along (x, $[{1\over 2}]$ , $[{1\over 2}]$ ) directly to the four chains along (x, 0, 0), (x, 0, 1), (x, 1, 0) and (x, 1, 1), thence linking all of the [100] chains into a single three-dimensional framework structure (Fig. 4).

Figure 1
The molecular structure of compound (I)

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

Figure 2
A stereoview of part of the crystal structure of compound (I)

, showing the formation of a chain of edge-fused rings along (x, $[{1\over 2}]$ , $[{1\over 2}]$ ). For the sake of clarity, H atoms not involved in the motifs shown have been omitted.

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

, showing the concerted action of the N—H⋯N and C—H⋯N hydrogen bonds. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (1 + x, $[{1\over 2}]$ − y, $[{1\over 2}]$ + z) and (−1 + x, $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z), respectively.

Figure 4
A projection down [100] of part of the crystal structure of compound (I)

, showing the linking of the chain of rings along (x, $[{1\over 2}]$ , $[{1\over 2}]$ ) to four adjacent chains. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.

Experimental

A solution of methyl pyrazinecarboxylate and a fivefold molar excess of hydrazine hydrate was held at 353 K for 12 h. The solvent was removed under reduced pressure and the residue was purified by washing successively with cold ethanol and with diethyl ether to give crystalline (I) (yield 87%, m.p. 431–432 K). NMR (DMSO-d₆): δ(H) 10.14 (1H, s, NH), 9.13 (1H, d, J = 1.2 Hz, H3), 8.84 (1H, d, J = 2.8 Hz, H6), 8.70 (1H, dd, J = 1.2 and 2.8 Hz, H5), 4.70 (2H, s, NH₂); δ(C) 161.4, 147.2, 144.8, 143.4, 143.1. IR (KBr disk, cm⁻¹) 3306–3238 (NH), 1648 (CO).

Crystal data

C₅H₆N₄O
M_r = 138.14
Monoclinic, P 2₁ /c
a = 3.7193 (5) Å
b = 16.978 (2) Å
c = 9.7858 (10) Å
β = 99.185 (8)°
V = 610.01 (13) Å³
Z = 4
D_x = 1.504 Mg m⁻³
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 120 (2) K
Plate, colourless
0.50 × 0.18 × 0.01 mm

Data collection

Bruker–Nonius KappaCCD diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.965, T_max = 0.999
6568 measured reflections
1395 independent reflections
1080 reflections with I > 2σ(I)
R_int = 0.057
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.059
wR(F²) = 0.138
S = 1.08
1395 reflections
91 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0462P)² + 0.4947P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Selected torsion angles (°)

N1—C2—C7—N2	−1.9 (3)
C2—C7—N2—N3	179.60 (18)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯N4ⁱ	0.96	2.06	2.976 (3)	160
N3—H31⋯O1ⁱⁱ	0.92	2.31	3.079 (3)	140
N3—H32⋯O1ⁱⁱⁱ	0.92	2.25	3.138 (2)	161
C3—H3⋯N1^iv	0.95	2.59	3.312 (3)	133
Symmetry codes: (i) $[x+1, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (ii) -x+1, -y+1, -z+1; (iii) -x, -y+1, -z+1; (iv) $[x-1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

All H atoms were located in difference maps, and then treated as riding atoms, with C—H = 0.95 Å and N—H = 0.92 (NH₂) or 0.96 Å (NH), with U_iso(H) = 1.2U_eq(C,N).

Data collection: COLLECT (Hooft, 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/S1600536806029394/wn2053sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806029394/wn2053Isup2.hkl

Computing details top

Data collection: COLLECT (Hooft, 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).

Pyrazine-2-carbohydrazide top

Crystal data top

C₅H₆N₄O	F(000) = 288
M_r = 138.14	D_x = 1.504 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1395 reflections
a = 3.7193 (5) Å	θ = 4.2–27.5°
b = 16.978 (2) Å	µ = 0.11 mm⁻¹
c = 9.7858 (10) Å	T = 120 K
β = 99.185 (8)°	Plate, colourless
V = 610.01 (13) Å³	0.50 × 0.18 × 0.01 mm
Z = 4

Data collection top

Bruker–Nonius KappaCCD diffractometer	1395 independent reflections
Radiation source: Bruker–Nonius FR591 rotating anode	1080 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.057
Detector resolution: 9.091 pixels mm^-1	θ_max = 27.5°, θ_min = 4.2°
φ and ω scans	h = −4→4
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −22→19
T_min = 0.965, T_max = 0.999	l = −12→12
6568 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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.138	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.0462P)² + 0.4947P] where P = (F_o² + 2F_c²)/3
1395 reflections	(Δ/σ)_max < 0.001
91 parameters	Δρ_max = 0.20 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

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

	x	y	z	U_iso*/U_eq
N1	0.2754 (5)	0.23490 (10)	0.66747 (17)	0.0223 (4)
C2	0.1216 (6)	0.27960 (12)	0.5616 (2)	0.0199 (5)
C3	−0.1032 (6)	0.24786 (13)	0.4486 (2)	0.0218 (5)
N4	−0.1773 (5)	0.17092 (11)	0.43778 (19)	0.0255 (4)
C5	−0.0225 (6)	0.12634 (13)	0.5431 (2)	0.0269 (5)
C6	0.1998 (6)	0.15799 (13)	0.6573 (2)	0.0255 (5)
C7	0.1993 (6)	0.36628 (12)	0.5634 (2)	0.0214 (5)
O1	0.0679 (4)	0.40779 (9)	0.46448 (15)	0.0273 (4)
N2	0.4142 (5)	0.39368 (10)	0.67541 (18)	0.0237 (4)
N3	0.5100 (6)	0.47441 (11)	0.6892 (2)	0.0305 (5)
H2	0.5180	0.3612	0.7520	0.028*
H3	−0.2086	0.2820	0.3763	0.026*
H5	−0.0659	0.0712	0.5400	0.032*
H6	0.3014	0.1239	0.7304	0.031*
H31	0.6722	0.4855	0.6300	0.037*
H32	0.3048	0.5034	0.6571	0.037*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0249 (10)	0.0235 (10)	0.0180 (8)	0.0030 (7)	0.0020 (7)	0.0022 (7)
C2	0.0195 (10)	0.0232 (11)	0.0173 (10)	0.0034 (8)	0.0036 (8)	0.0002 (8)
C3	0.0207 (10)	0.0253 (11)	0.0189 (10)	0.0014 (9)	0.0018 (8)	−0.0008 (8)
N4	0.0252 (10)	0.0275 (11)	0.0238 (9)	−0.0001 (8)	0.0038 (8)	−0.0027 (7)
C5	0.0317 (13)	0.0203 (11)	0.0291 (12)	−0.0021 (9)	0.0067 (10)	−0.0001 (9)
C6	0.0284 (12)	0.0242 (11)	0.0239 (11)	0.0042 (9)	0.0046 (9)	0.0031 (9)
C7	0.0211 (11)	0.0231 (11)	0.0200 (10)	0.0020 (9)	0.0028 (8)	0.0008 (8)
O1	0.0316 (9)	0.0237 (8)	0.0236 (8)	0.0014 (7)	−0.0048 (6)	0.0042 (6)
N2	0.0279 (10)	0.0201 (10)	0.0213 (9)	−0.0011 (7)	−0.0017 (7)	0.0006 (7)
N3	0.0340 (11)	0.0210 (10)	0.0333 (11)	−0.0015 (8)	−0.0039 (8)	0.0001 (8)

Geometric parameters (Å, º) top

N1—C6	1.336 (3)	N3—H31	0.92
N1—C2	1.337 (3)	N3—H32	0.92
C2—C3	1.385 (3)	C3—N4	1.336 (3)
C2—C7	1.499 (3)	C3—H3	0.95
C7—O1	1.234 (2)	N4—C5	1.333 (3)
C7—N2	1.333 (3)	C5—C6	1.388 (3)
N2—N3	1.417 (3)	C5—H5	0.95
N2—H2	0.96	C6—H6	0.95

C6—N1—C2	115.99 (18)	H31—N3—H32	105.5
N1—C2—C3	121.8 (2)	N4—C3—C2	122.32 (19)
N1—C2—C7	119.37 (18)	N4—C3—H3	118.8
C3—C2—C7	118.81 (18)	C2—C3—H3	118.8
O1—C7—N2	123.8 (2)	C5—N4—C3	115.82 (19)
O1—C7—C2	120.01 (18)	N4—C5—C6	122.1 (2)
N2—C7—C2	116.19 (17)	N4—C5—H5	119.0
C7—N2—N3	121.63 (18)	C6—C5—H5	119.0
C7—N2—H2	123.7	N1—C6—C5	122.0 (2)
N3—N2—H2	114.6	N1—C6—H6	119.0
N2—N3—H31	108.5	C5—C6—H6	119.0
N2—N3—H32	107.6

C6—N1—C2—C3	0.2 (3)	C2—C7—N2—N3	179.60 (18)
C6—N1—C2—C7	−178.60 (18)	N1—C2—C3—N4	−0.7 (3)
N1—C2—C7—O1	177.82 (19)	C7—C2—C3—N4	178.14 (19)
C3—C2—C7—O1	−1.0 (3)	C2—C3—N4—C5	0.4 (3)
N1—C2—C7—N2	−1.9 (3)	C3—N4—C5—C6	0.4 (3)
C3—C2—C7—N2	179.31 (18)	C2—N1—C6—C5	0.5 (3)
O1—C7—N2—N3	−0.1 (3)	N4—C5—C6—N1	−0.8 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N4ⁱ	0.96	2.06	2.976 (3)	160
N3—H31···O1ⁱⁱ	0.92	2.31	3.079 (3)	140
N3—H32···O1ⁱⁱⁱ	0.92	2.25	3.138 (2)	161
C3—H3···N1^iv	0.95	2.59	3.312 (3)	133

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

Acknowledgements

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

References

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada. Google Scholar
Hooft, R. W. W. (1999). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography Centre, Chemistry Department, NUI Galway, Ireland. 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
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar

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ISSN: 2056-9890

Volume 62| Part 9| September 2006| Pages o3765-o3767

https://doi.org/10.1107/S1600536806029394

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

Pyrazine-2-carbohydrazide: a three-dimensional hydrogen-bonded framework structure

Comment

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds