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

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4-Hydrazino-2-(methyl­sulfan­yl)­pyrimidine

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[Ghorab, M. M., Ismail, Z. H., Abdel-Gawad, S. M. & Aziem, A. A. (2004). Heteroat. Chem. 15, 57-62.]); Anderson et al. (1990[Anderson, J. D., Cottam, H. B., Larson, S. B., Nord, L. D., Revankar, G. R. & Robins, R. K. (1990). J. Heterocycl. Chem. 27, 439-453.]); Géza et al. (2001[Géza, S., Kaaztreiner, E., Mátyus, P. & Czakó, K. (1981). Synth. Commun. 11, 835-847.]); Gante (1989[Gante, J. (1989). Synthesis, pp. 405-413.]); Powers et al. (1998[Powers, D. R., Papadakos, P. J. & Wallin, J. D. (1998). J. Emerg. Med. 16, 191-196.]); Vidrio et al. (2003[Vidrio, H., Fernandez, G., Medina, M., Alvarez, E. & Orallo, F. (2003). Vascul. Pharmacol. 40, 13-21.]). For details of hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C5H8N4S

  • Mr = 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[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.821, Tmax = 0.938

  • 16377 measured reflections

  • 3160 independent reflections

  • 2760 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.55 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: SAINT (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information


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.

Refinement top

All H atoms were positioned geometrically and refined with a riding model approximation with C—H = 0.93–0.96 Å, and with Uiso(H) = 1.2–1.5Ueq(C). The rotating model group was employed for the methyl group. In the case of N3 and N4 atoms, the H atoms were located from a difference Fourier map and refined isotropically, see Table 1 for bond distances.

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
[Figure 1] Fig. 1. The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] 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
C5H8N4SF(000) = 656
Mr = 156.21Dx = 1.446 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 6385 reflections
a = 12.7906 (2) Åθ = 3.2–38.6°
b = 7.7731 (1) ŵ = 0.38 mm1
c = 14.4354 (3) ÅT = 100 K
V = 1435.21 (4) Å3Block, colourless
Z = 80.55 × 0.37 × 0.17 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
3160 independent reflections
Radiation source: fine-focus sealed tube2760 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
ϕ and ω scansθmax = 35.0°, θmin = 2.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
h = 2019
Tmin = 0.821, Tmax = 0.938k = 1210
16377 measured reflectionsl = 1523
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.087H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0429P)2 + 0.4069P]
where P = (Fo2 + 2Fc2)/3
3160 reflections(Δ/σ)max < 0.001
104 parametersΔρmax = 0.55 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C5H8N4SV = 1435.21 (4) Å3
Mr = 156.21Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 12.7906 (2) ŵ = 0.38 mm1
b = 7.7731 (1) ÅT = 100 K
c = 14.4354 (3) Å0.55 × 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)
Tmin = 0.821, Tmax = 0.938Rint = 0.029
16377 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.087H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.55 e Å3
3160 reflectionsΔρmin = 0.23 e Å3
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
xyzUiso*/Ueq
S10.009609 (17)0.58095 (3)0.239703 (15)0.01516 (6)
N10.07742 (5)0.47877 (10)0.39095 (5)0.01315 (13)
N20.17805 (6)0.42798 (10)0.25325 (5)0.01321 (13)
N30.13619 (6)0.40510 (11)0.53498 (5)0.01709 (15)
N40.21443 (6)0.34229 (11)0.59510 (5)0.01670 (14)
C10.15419 (6)0.40931 (10)0.44356 (6)0.01236 (14)
C20.24631 (6)0.34361 (11)0.40217 (6)0.01379 (14)
H2A0.29940.29430.43730.017*
C30.25315 (6)0.35641 (11)0.30784 (6)0.01370 (14)
H3A0.31280.31350.27920.016*
C40.09458 (6)0.48345 (10)0.29943 (5)0.01199 (13)
C50.01837 (8)0.53439 (15)0.12034 (7)0.02202 (19)
H5A0.03650.57970.08200.033*
H5B0.08360.58650.10330.033*
H5C0.02290.41210.11190.033*
H1N30.0801 (12)0.4477 (18)0.5550 (10)0.027 (4)*
H1N40.2343 (11)0.420 (2)0.6293 (10)0.025 (4)*
H2N40.1890 (10)0.2573 (19)0.6296 (10)0.024 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.01382 (10)0.01761 (11)0.01405 (10)0.00356 (7)0.00068 (6)0.00078 (7)
N10.0126 (3)0.0153 (3)0.0115 (3)0.0011 (2)0.0007 (2)0.0003 (2)
N20.0126 (3)0.0147 (3)0.0123 (3)0.0004 (2)0.0012 (2)0.0003 (2)
N30.0135 (3)0.0266 (4)0.0111 (3)0.0045 (3)0.0009 (2)0.0012 (3)
N40.0149 (3)0.0223 (4)0.0129 (3)0.0009 (3)0.0026 (2)0.0012 (3)
C10.0119 (3)0.0134 (3)0.0117 (3)0.0008 (2)0.0004 (2)0.0003 (3)
C20.0119 (3)0.0155 (3)0.0140 (3)0.0016 (3)0.0004 (2)0.0001 (3)
C30.0118 (3)0.0150 (3)0.0143 (3)0.0007 (3)0.0017 (2)0.0008 (3)
C40.0119 (3)0.0117 (3)0.0123 (3)0.0006 (2)0.0001 (2)0.0003 (2)
C50.0187 (4)0.0334 (5)0.0139 (4)0.0036 (4)0.0017 (3)0.0008 (3)
Geometric parameters (Å, º) top
S1—C41.7589 (8)N4—H1N40.822 (15)
S1—C51.7967 (10)N4—H2N40.889 (15)
N1—C41.3397 (10)C1—C21.4164 (11)
N1—C11.3537 (11)C2—C31.3681 (12)
N2—C41.3305 (11)C2—H2A0.9300
N2—C31.3613 (11)C3—H3A0.9300
N3—C11.3399 (11)C5—H5A0.9600
N3—N41.4118 (11)C5—H5B0.9600
N3—H1N30.841 (15)C5—H5C0.9600
C4—S1—C5103.44 (4)C1—C2—H2A121.7
C4—N1—C1116.44 (7)N2—C3—C2124.11 (8)
C4—N2—C3114.11 (7)N2—C3—H3A117.9
C1—N3—N4119.48 (7)C2—C3—H3A117.9
C1—N3—H1N3118.4 (10)N2—C4—N1128.08 (8)
N4—N3—H1N3121.9 (10)N2—C4—S1120.13 (6)
N3—N4—H1N4109.5 (10)N1—C4—S1111.77 (6)
N3—N4—H2N4110.0 (9)S1—C5—H5A109.5
H1N4—N4—H2N4109.0 (13)S1—C5—H5B109.5
N3—C1—N1115.96 (7)H5A—C5—H5B109.5
N3—C1—C2123.34 (8)S1—C5—H5C109.5
N1—C1—C2120.70 (7)H5A—C5—H5C109.5
C3—C2—C1116.54 (8)H5B—C5—H5C109.5
C3—C2—H2A121.7
N4—N3—C1—N1176.97 (8)C1—C2—C3—N20.32 (13)
N4—N3—C1—C24.05 (13)C3—N2—C4—N10.91 (12)
C4—N1—C1—N3179.94 (8)C3—N2—C4—S1179.53 (6)
C4—N1—C1—C20.92 (12)C1—N1—C4—N20.07 (13)
N3—C1—C2—C3179.68 (8)C1—N1—C4—S1178.65 (6)
N1—C1—C2—C30.74 (12)C5—S1—C4—N212.16 (8)
C4—N2—C3—C21.08 (12)C5—S1—C4—N1169.01 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H1N3···N1i0.84 (2)2.24 (2)3.070 (1)172 (1)
N4—H1N4···N2ii0.82 (2)2.42 (2)3.208 (1)161 (1)
N4—H2N4···N2iii0.89 (1)2.30 (2)3.137 (1)157 (1)
Symmetry codes: (i) x, y+1, z+1; (ii) x1/2, y+1, z+1/2; (iii) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H8N4S
Mr156.21
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)100
a, b, c (Å)12.7906 (2), 7.7731 (1), 14.4354 (3)
V3)1435.21 (4)
Z8
Radiation typeMo Kα
µ (mm1)0.38
Crystal size (mm)0.55 × 0.37 × 0.17
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.821, 0.938
No. of measured, independent and
observed [I > 2σ(I)] reflections
16377, 3160, 2760
Rint0.029
(sin θ/λ)max1)0.807
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.087, 1.05
No. of reflections3160
No. of parameters104
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N3—H1N3···N1i0.84 (2)2.24 (2)3.070 (1)172 (1)
N4—H1N4···N2ii0.82 (2)2.42 (2)3.208 (1)161 (1)
N4—H2N4···N2iii0.89 (1)2.30 (2)3.137 (1)157 (1)
Symmetry codes: (i) x, y+1, z+1; (ii) x1/2, 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).

References

First citationAnderson, J. D., Cottam, H. B., Larson, S. B., Nord, L. D., Revankar, G. R. & Robins, R. K. (1990). J. Heterocycl. Chem. 27, 439–453.  CrossRef CAS Google Scholar
First citationBernstein, 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
First citationBruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationGante, J. (1989). Synthesis, pp. 405–413.  CrossRef Google Scholar
First citationGéza, S., Kaaztreiner, E., Mátyus, P. & Czakó, K. (1981). Synth. Commun. 11, 835–847.  Google Scholar
First citationGhorab, M. M., Ismail, Z. H., Abdel-Gawad, S. M. & Aziem, A. A. (2004). Heteroat. Chem. 15, 57–62.  Web of Science CrossRef CAS Google Scholar
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First citationSpek, A. L. (2003). J. Appl. Cryst. 36, 7–13.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationVidrio, H., Fernandez, G., Medina, M., Alvarez, E. & Orallo, F. (2003). Vascul. Pharmacol. 40, 13–21.  Web of Science CrossRef PubMed CAS Google Scholar

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