4-Hydrazino-2-(methyl­sulfan­yl)­pyrimidine

Fun, H.-K.; Razak, I.A.; Adhikari, A.; Kalluraya, B.

doi:10.1107/S1600536809003286

organic compounds

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ISSN: 2056-9890

Volume 65| Part 2| February 2009| Page o422

doi:10.1107/S1600536809003286

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4-Hydrazino-2-(methylsulfanyl)pyrimidine

Hoong-Kun Fun,^a ^* Ibrahim Abdul Razak,^a ‡ Adithya Adhikari ^b and Balakrishna Kalluraya ^b

^aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and ^bDepartment of Studies in Chemistry, Mangalore University, Mangalagangothri 574 199, Karnataka, India
^*Correspondence e-mail: hkfun@usm.my

(Received 23 January 2009; accepted 27 January 2009; online 31 January 2009)

In the crystal of the title compound, C₅H₈N₄, centrosymmetric dimers are linked by pairs of N—H⋯N hydrogen bonds. Further N—H⋯N links result in a two-dimensional array whereby wave-like supramolecular chains are interconnected by R₂²(8) ring motifs.

Related literature

For general background, see: Ghorab et al. (2004 ); Anderson et al. (1990 ); Géza et al. (2001 ); Gante (1989 ); Powers et al. (1998 ); Vidrio et al. (2003 ). For details of hydrogen-bond motifs, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₅H₈N₄S
M_r = 156.21
Orthorhombic, P b c a
a = 12.7906 (2) Å
b = 7.7731 (1) Å
c = 14.4354 (3) Å
V = 1435.21 (4) Å³
Z = 8
Mo Kα radiation
μ = 0.38 mm⁻¹
T = 100.0 (1) K
0.55 × 0.37 × 0.17 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ) T_min = 0.821, T_max = 0.938
16377 measured reflections
3160 independent reflections
2760 reflections with I > 2σ(I)
R_int = 0.029

Refinement

R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.087
S = 1.05
3160 reflections
104 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.55 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H1N3⋯N1ⁱ	0.84 (2)	2.24 (2)	3.070 (1)	172 (1)
N4—H1N4⋯N2ⁱⁱ	0.82 (2)	2.42 (2)	3.208 (1)	161 (1)
N4—H2N4⋯N2ⁱⁱⁱ	0.89 (1)	2.30 (2)	3.137 (1)	157 (1)
Symmetry codes: (i) -x, -y+1, -z+1; (ii) $[-x-{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (iii) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2; data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809003286/tk2360sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809003286/tk2360Isup2.hkl

checkCIF report

Comment top

Pyrimidines and their derivatives possess biological and pharmacological activities such as antibacterial, antimicrobial, anti-inflammatory, analgesic, anticonvulsant and anti-aggressive activities (Ghorab et al., 2004; Anderson et al., 1990). This prompted us to synthesize compounds bearing the pyrimidine moiety. Hydrazine derivatives are interesting building blocks of heterocyclic compounds containing N—N bonds (Geza et al., 1981; Gante, 1989). Some hydrazine derivatives such as phthalazin-1-yl-hydrazine are widely used as general antihypertensive and vasodilator agents, and are considered as a first-line drug in the management of pregnancy-induced hypertension (Powers et al., 1998; Vidrio et al., 2003). In addition, these compounds are known to decompose easily in the presence of radicals into hydrazine derivatives which are commonly used as rocket fuels. The structure of the title compound, (I), was determined in this context. The molecule of (I), Fig. 1, is essentially planar, with the maximum deviation from the least-squares plane being 0.297 (1) Å for the C5 atom.

The primary interactions in the crystal structure are of the type N—H···N, Table 1 and Fig. 2. Here, molecules form wave-like supramolecular chains along the b axis with successive molecules connected on either side via R₂²(8) motifs (Bernstein et al., 1995) to form a 2-D array.

Related literature top

For general background, see: Ghorab et al. (2004); Anderson et al. (1990); Géza et al. (2004); Gante (1989); Powers et al. (1998); Vidrio et al. (2003). For details of hydrogen-bond motifs, see: Bernstein et al. (1995). For related literature, see: Géza et al. (1981); Ghza (2004).

Experimental top

4-Chloro-2-(methylsulfanyl)pyrimidine (0.01 mol) was dissolved in methanol and 99% hydrazine hydrate (0.015 mol) was added dropwise with external cooling. The mixture was stirred at room temperature for 5 h. The precipitate was filtered, dried and recrystallized from ethyl acetate. Crystals suitable for X-ray studies are obtained from ethyl acetate by slow evaporation. Yield 65%, m.p. 413 K.

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2 (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures top

	Fig. 1. The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. A view of the crystal packing in (I), viewed down the c axis, showing wave-like chains along the b axis. H atoms involved in hydrogen bonds are shown as dotted lines. Other H atoms have been omitted for clarity.

4-Hydrazino-2-(methylsulfanyl)pyrimidine top

Crystal data top

C₅H₈N₄S	F(000) = 656
M_r = 156.21	D_x = 1.446 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 6385 reflections
a = 12.7906 (2) Å	θ = 3.2–38.6°
b = 7.7731 (1) Å	µ = 0.38 mm⁻¹
c = 14.4354 (3) Å	T = 100 K
V = 1435.21 (4) Å³	Block, colourless
Z = 8	0.55 × 0.37 × 0.17 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	3160 independent reflections
Radiation source: fine-focus sealed tube	2760 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
ϕ and ω scans	θ_max = 35.0°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −20→19
T_min = 0.821, T_max = 0.938	k = −12→10
16377 measured reflections	l = −15→23

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)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.087	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0429P)² + 0.4069P] where P = (F_o² + 2F_c²)/3
3160 reflections	(Δ/σ)_max < 0.001
104 parameters	Δρ_max = 0.55 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₅H₈N₄S	V = 1435.21 (4) Å³
M_r = 156.21	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 12.7906 (2) Å	µ = 0.38 mm⁻¹
b = 7.7731 (1) Å	T = 100 K
c = 14.4354 (3) Å	0.55 × 0.37 × 0.17 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	3160 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2005)	2760 reflections with I > 2σ(I)
T_min = 0.821, T_max = 0.938	R_int = 0.029
16377 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.087	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.55 e Å⁻³
3160 reflections	Δρ_min = −0.23 e Å⁻³
104 parameters

Special details top

Experimental. The data was collected with the Oxford Cryosystem Cobra low-temperature attachment

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
S1	0.009609 (17)	0.58095 (3)	0.239703 (15)	0.01516 (6)
N1	−0.07742 (5)	0.47877 (10)	0.39095 (5)	0.01315 (13)
N2	−0.17805 (6)	0.42798 (10)	0.25325 (5)	0.01321 (13)
N3	−0.13619 (6)	0.40510 (11)	0.53498 (5)	0.01709 (15)
N4	−0.21443 (6)	0.34229 (11)	0.59510 (5)	0.01670 (14)
C1	−0.15419 (6)	0.40931 (10)	0.44356 (6)	0.01236 (14)
C2	−0.24631 (6)	0.34361 (11)	0.40217 (6)	0.01379 (14)
H2A	−0.2994	0.2943	0.4373	0.017*
C3	−0.25315 (6)	0.35641 (11)	0.30784 (6)	0.01370 (14)
H3A	−0.3128	0.3135	0.2792	0.016*
C4	−0.09458 (6)	0.48345 (10)	0.29943 (5)	0.01199 (13)
C5	−0.01837 (8)	0.53439 (15)	0.12034 (7)	0.02202 (19)
H5A	0.0365	0.5797	0.0820	0.033*
H5B	−0.0836	0.5865	0.1033	0.033*
H5C	−0.0229	0.4121	0.1119	0.033*
H1N3	−0.0801 (12)	0.4477 (18)	0.5550 (10)	0.027 (4)*
H1N4	−0.2343 (11)	0.420 (2)	0.6293 (10)	0.025 (4)*
H2N4	−0.1890 (10)	0.2573 (19)	0.6296 (10)	0.024 (3)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01382 (10)	0.01761 (11)	0.01405 (10)	−0.00356 (7)	0.00068 (6)	0.00078 (7)
N1	0.0126 (3)	0.0153 (3)	0.0115 (3)	−0.0011 (2)	−0.0007 (2)	−0.0003 (2)
N2	0.0126 (3)	0.0147 (3)	0.0123 (3)	−0.0004 (2)	−0.0012 (2)	−0.0003 (2)
N3	0.0135 (3)	0.0266 (4)	0.0111 (3)	−0.0045 (3)	−0.0009 (2)	0.0012 (3)
N4	0.0149 (3)	0.0223 (4)	0.0129 (3)	−0.0009 (3)	0.0026 (2)	0.0012 (3)
C1	0.0119 (3)	0.0134 (3)	0.0117 (3)	0.0008 (2)	−0.0004 (2)	−0.0003 (3)
C2	0.0119 (3)	0.0155 (3)	0.0140 (3)	−0.0016 (3)	−0.0004 (2)	−0.0001 (3)
C3	0.0118 (3)	0.0150 (3)	0.0143 (3)	−0.0007 (3)	−0.0017 (2)	−0.0008 (3)
C4	0.0119 (3)	0.0117 (3)	0.0123 (3)	0.0006 (2)	0.0001 (2)	−0.0003 (2)
C5	0.0187 (4)	0.0334 (5)	0.0139 (4)	−0.0036 (4)	0.0017 (3)	0.0008 (3)

Geometric parameters (Å, º) top

S1—C4	1.7589 (8)	N4—H1N4	0.822 (15)
S1—C5	1.7967 (10)	N4—H2N4	0.889 (15)
N1—C4	1.3397 (10)	C1—C2	1.4164 (11)
N1—C1	1.3537 (11)	C2—C3	1.3681 (12)
N2—C4	1.3305 (11)	C2—H2A	0.9300
N2—C3	1.3613 (11)	C3—H3A	0.9300
N3—C1	1.3399 (11)	C5—H5A	0.9600
N3—N4	1.4118 (11)	C5—H5B	0.9600
N3—H1N3	0.841 (15)	C5—H5C	0.9600

C4—S1—C5	103.44 (4)	C1—C2—H2A	121.7
C4—N1—C1	116.44 (7)	N2—C3—C2	124.11 (8)
C4—N2—C3	114.11 (7)	N2—C3—H3A	117.9
C1—N3—N4	119.48 (7)	C2—C3—H3A	117.9
C1—N3—H1N3	118.4 (10)	N2—C4—N1	128.08 (8)
N4—N3—H1N3	121.9 (10)	N2—C4—S1	120.13 (6)
N3—N4—H1N4	109.5 (10)	N1—C4—S1	111.77 (6)
N3—N4—H2N4	110.0 (9)	S1—C5—H5A	109.5
H1N4—N4—H2N4	109.0 (13)	S1—C5—H5B	109.5
N3—C1—N1	115.96 (7)	H5A—C5—H5B	109.5
N3—C1—C2	123.34 (8)	S1—C5—H5C	109.5
N1—C1—C2	120.70 (7)	H5A—C5—H5C	109.5
C3—C2—C1	116.54 (8)	H5B—C5—H5C	109.5
C3—C2—H2A	121.7

N4—N3—C1—N1	176.97 (8)	C1—C2—C3—N2	−0.32 (13)
N4—N3—C1—C2	−4.05 (13)	C3—N2—C4—N1	−0.91 (12)
C4—N1—C1—N3	179.94 (8)	C3—N2—C4—S1	−179.53 (6)
C4—N1—C1—C2	0.92 (12)	C1—N1—C4—N2	−0.07 (13)
N3—C1—C2—C3	−179.68 (8)	C1—N1—C4—S1	178.65 (6)
N1—C1—C2—C3	−0.74 (12)	C5—S1—C4—N2	−12.16 (8)
C4—N2—C3—C2	1.08 (12)	C5—S1—C4—N1	169.01 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1N3···N1ⁱ	0.84 (2)	2.24 (2)	3.070 (1)	172 (1)
N4—H1N4···N2ⁱⁱ	0.82 (2)	2.42 (2)	3.208 (1)	161 (1)
N4—H2N4···N2ⁱⁱⁱ	0.89 (1)	2.30 (2)	3.137 (1)	157 (1)

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

Experimental details

Crystal data
Chemical formula	C₅H₈N₄S
M_r	156.21
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	100
a, b, c (Å)	12.7906 (2), 7.7731 (1), 14.4354 (3)
V (Å³)	1435.21 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.38
Crystal size (mm)	0.55 × 0.37 × 0.17

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.821, 0.938
No. of measured, independent and observed [I > 2σ(I)] reflections	16377, 3160, 2760
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.807

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.087, 1.05
No. of reflections	3160
No. of parameters	104
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.55, −0.23

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1N3···N1ⁱ	0.84 (2)	2.24 (2)	3.070 (1)	172 (1)
N4—H1N4···N2ⁱⁱ	0.82 (2)	2.42 (2)	3.208 (1)	161 (1)
N4—H2N4···N2ⁱⁱⁱ	0.89 (1)	2.30 (2)	3.137 (1)	157 (1)

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

Footnotes

‡On sabbatical leave at the Universiti Sains Malaysia.

Acknowledgements

HKF thanks the Malaysian Government and Universiti Sains Malaysia for a Science Fund Grant (No. 305/PFIZIK/613312).

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