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

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ISSN: 2056-9890
Volume 71| Part 4| April 2015| Pages o253-o254

Crystal structure of 3-methyl­pyridine-2-carbaldehyde 4-methyl­thio­semi­carba­zone monohydrate

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aDepartment of Chemistry, Universiti Putra Malaysia, 43400 Serdang, Malaysia, and bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: thahira@upm.edu.my

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 9 March 2015; accepted 12 March 2015; online 25 March 2015)

In the title hydrate, C9H12N4S·H2O (systematic name: 3-methyl-1-{(E)-[(3-methyl­pyridin-2-yl)methyl­idene]amino}­thio­urea monohydrate), a small twist is noted between the pyridine ring and the rest of the organic mol­ecule [dihedral angle = 6.96 (5)°]. The imine and pyridine N atoms are syn, and the amine H atoms are anti. The latter arrangement allows for the formation of an intra­molecular N—H⋯N(imine) hydrogen bond. Both the N-bonded H atoms form hydrogen bonds to symmetry-related water mol­ecules, and the latter forms O—H hydrogen bonds with the pyridine N and thione S atoms. These inter­actions lead to supra­molecular layers that stack along the a-axis direction with no specific inter­actions between them.

1. Related literature

For background to the coordination chemistry of thio­semicarbazones, see: Beraldo et al. (2001[Beraldo, H., Lima, R., Teixeira, L. R., Moura, A. A. & West, D. X. (2001). J. Mol. Struct. 559, 99-106.]); Sreekanth et al. (2004[Sreekanth, A., Kala, U. L., Nayar, C. R. & Kurup, M. P. (2004). Polyhedron, 23, 41-47.]). For the structure of the parent compound, in which the pyridine N atom is anti to the imine N atom, see: West et al. (1996[West, D. X., Bain, G. A., Butcher, R. J., Jasinski, J. P., Li, Y., Pozdniakiv, R. Y., Valdés-Martínez, J. V., Toscano, R. A. & Hernández-Ortega, S. (1996). Polyhedron, 15, 665-674.]). For the synthesis of the title compound, see: Ali et al. (1997[Ali, M. A., Majumder, S. M. M., Butcher, R. J., Jasinski, J. P. & Jasinski, J. M. (1997). Polyhedron, 16, 2749-2754.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C9H12N4S·H2O

  • Mr = 226.30

  • Monoclinic, P 21 /c

  • a = 10.4493 (3) Å

  • b = 13.6989 (3) Å

  • c = 8.0235 (3) Å

  • β = 102.816 (3)°

  • V = 1119.90 (6) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 2.42 mm−1

  • T = 100 K

  • 0.30 × 0.20 × 0.10 mm

2.2. Data collection

  • Oxford Diffraction Xcaliber Eos Gemini diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]) Tmin = 0.860, Tmax = 1.000

  • 14591 measured reflections

  • 2160 independent reflections

  • 2044 reflections with I > 2σ(I)

  • Rint = 0.022

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.034

  • wR(F2) = 0.097

  • S = 1.05

  • 2160 reflections

  • 150 parameters

  • 5 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.31 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N4—H4N⋯N2 0.88 (2) 2.19 (2) 2.6116 (16) 109 (1)
N1—H1N⋯O1Wi 0.88 (1) 2.12 (1) 2.9940 (15) 170 (2)
N4—H4N⋯O1W 0.88 (2) 2.50 (2) 3.3100 (15) 154 (1)
O1W—H1W⋯N3 0.84 (2) 2.11 (2) 2.9371 (16) 172 (2)
O1W—H2W⋯S1ii 0.85 (2) 2.50 (2) 3.3412 (11) 173 (2)
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

Data collection: CrysAlis PRO (Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Refinement top

Related literature top

For background to the coordination chemistry of thiosemicarbazones, see: Beraldo et al. (2001); Sreekanth et al. (2004). For the structure of the parent compound, in which the pyridyl N atom is anti to the imine N atom, see: West et al. (1996). For the synthesis, see: Ali et al. (1997).

Experimental top

The Schiff base ligand was prepared according to Ali et al. (1997). 4-Methyl-3-thiosemicarbazide (0.01 mol) was dissolved in hot 95% ethanol (50 ml), and an equimolar amount of 3-methylpyridine-2-carbaldehyde in the same solvent (20 ml) was added. The mixture was heated with occasional stirring until the volume reduced to 20 ml. It was allowed to stand overnight and a yellow precipitate formed, which was filtered off and washed with cold ethanol. Crystals suitable for X-ray diffraction analysis were obtained by recrystallization from ethanol. Yields were high, ca. 92%.

Refinement top

Carbon-bound H-atoms were placed in calculated positions (C—H = 0.95 to 0.98 Å) and were included in the refinement in the riding model approximation with Uiso(H) = 1.2–1.5Ueq(C). The O—H atoms were refined with O—H = 0.84±0.01 Å, and with Uiso(H) = 1.5Ueq(O). The N—H H atoms were treated similarly with N—H = 0.88±0.01 Å and Uiso(H) = 1.2Ueq(N).

Structure description top

For background to the coordination chemistry of thiosemicarbazones, see: Beraldo et al. (2001); Sreekanth et al. (2004). For the structure of the parent compound, in which the pyridyl N atom is anti to the imine N atom, see: West et al. (1996). For the synthesis, see: Ali et al. (1997).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2015); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing the atom-labelling scheme and displacement ellipsoids at the 70% probability level.
[Figure 2] Fig. 2. A view of the supramolecular layer in parallel to (1 0 0) sustained by N—H···O (blue dashed lines), O—H···N (pink) and O—H···S (orange) hydrogen bonding.
[Figure 3] Fig. 3. A view of the unit-cell contents in projection down the c axis. The N—H···O (blue), O—H···N (pink) and O—H···S (orange) hydrogen bonds are shown as dashed lines.
3-Methyl-1-{(E)-[(3-methylpyridin-2-yl)methylidene]amino}thiourea monohydrate top
Crystal data top
C9H12N4S·H2OF(000) = 480
Mr = 226.30Dx = 1.342 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.5418 Å
a = 10.4493 (3) ÅCell parameters from 7855 reflections
b = 13.6989 (3) Åθ = 3.2–71.2°
c = 8.0235 (3) ŵ = 2.42 mm1
β = 102.816 (3)°T = 100 K
V = 1119.90 (6) Å3Prism, pale-brown
Z = 40.30 × 0.20 × 0.10 mm
Data collection top
Oxford Diffraction Xcaliber Eos Gemini
diffractometer
2160 independent reflections
Radiation source: fine-focus sealed tube2044 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
Detector resolution: 16.1952 pixels mm-1θmax = 71.4°, θmin = 4.3°
ω scansh = 1212
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
k = 1616
Tmin = 0.860, Tmax = 1.000l = 99
14591 measured reflections
Refinement top
Refinement on F25 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.034H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.097 w = 1/[σ2(Fo2) + (0.0657P)2 + 0.3425P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2160 reflectionsΔρmax = 0.31 e Å3
150 parametersΔρmin = 0.25 e Å3
Crystal data top
C9H12N4S·H2OV = 1119.90 (6) Å3
Mr = 226.30Z = 4
Monoclinic, P21/cCu Kα radiation
a = 10.4493 (3) ŵ = 2.42 mm1
b = 13.6989 (3) ÅT = 100 K
c = 8.0235 (3) Å0.30 × 0.20 × 0.10 mm
β = 102.816 (3)°
Data collection top
Oxford Diffraction Xcaliber Eos Gemini
diffractometer
2160 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
2044 reflections with I > 2σ(I)
Tmin = 0.860, Tmax = 1.000Rint = 0.022
14591 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0345 restraints
wR(F2) = 0.097H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.31 e Å3
2160 reflectionsΔρmin = 0.25 e Å3
150 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.73687 (3)0.84153 (2)0.49693 (4)0.01984 (14)
N10.52525 (11)0.80894 (8)0.61677 (14)0.0178 (3)
H1N0.5225 (16)0.8721 (7)0.636 (2)0.021*
N20.43392 (11)0.74878 (8)0.66067 (14)0.0178 (3)
N30.25907 (11)0.63228 (8)0.77276 (14)0.0199 (3)
N40.62430 (11)0.67137 (8)0.54238 (14)0.0187 (3)
H4N0.5662 (14)0.6409 (12)0.588 (2)0.022*
C10.62415 (13)0.76805 (9)0.55465 (16)0.0168 (3)
C20.34637 (13)0.78964 (9)0.72608 (16)0.0177 (3)
H20.34820.85820.74370.021*
C30.24297 (13)0.73011 (10)0.77382 (16)0.0168 (3)
C40.16527 (14)0.57657 (10)0.81199 (18)0.0228 (3)
H40.17600.50770.81160.027*
C50.05263 (14)0.61413 (10)0.85338 (18)0.0224 (3)
H50.01250.57190.87920.027*
C60.03765 (13)0.71450 (10)0.85609 (17)0.0211 (3)
H60.03810.74200.88480.025*
C70.13356 (13)0.77500 (9)0.81675 (16)0.0177 (3)
C7'0.11857 (15)0.88417 (10)0.8229 (2)0.0270 (3)
H7'10.03180.90010.84320.040*
H7'20.12740.91250.71390.040*
H7'30.18670.91090.91580.040*
C80.72818 (13)0.61612 (11)0.49226 (17)0.0225 (3)
H8A0.74600.64380.38710.034*
H8B0.70080.54790.47240.034*
H8C0.80790.61940.58340.034*
O1W0.49697 (10)0.51694 (7)0.77859 (13)0.0232 (2)
H1W0.4330 (14)0.5544 (12)0.774 (2)0.035*
H2W0.5595 (14)0.5483 (13)0.841 (2)0.035*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0178 (2)0.0182 (2)0.0254 (2)0.00111 (11)0.00872 (14)0.00060 (11)
N10.0179 (6)0.0137 (5)0.0231 (6)0.0011 (4)0.0075 (5)0.0007 (4)
N20.0173 (6)0.0177 (5)0.0179 (6)0.0021 (4)0.0030 (4)0.0011 (4)
N30.0194 (6)0.0163 (5)0.0238 (6)0.0013 (4)0.0045 (5)0.0013 (4)
N40.0197 (6)0.0163 (6)0.0210 (6)0.0006 (4)0.0060 (5)0.0001 (4)
C10.0163 (6)0.0182 (6)0.0152 (6)0.0009 (5)0.0017 (5)0.0002 (5)
C20.0181 (6)0.0146 (6)0.0197 (6)0.0005 (5)0.0029 (5)0.0006 (5)
C30.0164 (6)0.0175 (6)0.0154 (6)0.0000 (5)0.0015 (5)0.0005 (5)
C40.0244 (7)0.0159 (6)0.0282 (7)0.0005 (5)0.0061 (6)0.0023 (5)
C50.0208 (7)0.0205 (7)0.0266 (7)0.0044 (5)0.0066 (5)0.0025 (5)
C60.0174 (6)0.0238 (7)0.0226 (7)0.0010 (5)0.0055 (5)0.0003 (5)
C70.0184 (6)0.0168 (7)0.0172 (6)0.0002 (5)0.0024 (5)0.0002 (5)
C7'0.0292 (8)0.0172 (7)0.0385 (8)0.0030 (6)0.0161 (6)0.0008 (6)
C80.0217 (7)0.0187 (7)0.0261 (7)0.0051 (5)0.0036 (6)0.0024 (5)
O1W0.0207 (5)0.0180 (5)0.0309 (5)0.0003 (4)0.0055 (4)0.0032 (4)
Geometric parameters (Å, º) top
S1—C11.6903 (13)C4—H40.9500
N1—C11.3633 (17)C5—C61.385 (2)
N1—N21.3649 (15)C5—H50.9500
N1—H1N0.881 (9)C6—C71.3896 (19)
N2—C21.2801 (18)C6—H60.9500
N3—C41.3338 (18)C7—C7'1.5057 (18)
N3—C31.3510 (17)C7'—H7'10.9800
N4—C11.3281 (17)C7'—H7'20.9800
N4—C81.4513 (17)C7'—H7'30.9800
N4—H4N0.879 (9)C8—H8A0.9800
C2—C31.4706 (18)C8—H8B0.9800
C2—H20.9500C8—H8C0.9800
C3—C71.4066 (18)O1W—H1W0.836 (9)
C4—C51.391 (2)O1W—H2W0.848 (9)
C1—N1—N2118.45 (11)C6—C5—H5120.8
C1—N1—H1N121.7 (11)C4—C5—H5120.8
N2—N1—H1N119.6 (11)C5—C6—C7119.93 (13)
C2—N2—N1116.49 (11)C5—C6—H6120.0
C4—N3—C3117.84 (12)C7—C6—H6120.0
C1—N4—C8123.63 (12)C6—C7—C3117.47 (12)
C1—N4—H4N115.5 (12)C6—C7—C7'119.96 (12)
C8—N4—H4N119.7 (11)C3—C7—C7'122.58 (12)
N4—C1—N1116.76 (12)C7—C7'—H7'1109.5
N4—C1—S1124.14 (10)C7—C7'—H7'2109.5
N1—C1—S1119.10 (10)H7'1—C7'—H7'2109.5
N2—C2—C3119.83 (12)C7—C7'—H7'3109.5
N2—C2—H2120.1H7'1—C7'—H7'3109.5
C3—C2—H2120.1H7'2—C7'—H7'3109.5
N3—C3—C7122.98 (12)N4—C8—H8A109.5
N3—C3—C2116.66 (12)N4—C8—H8B109.5
C7—C3—C2120.36 (12)H8A—C8—H8B109.5
N3—C4—C5123.36 (13)N4—C8—H8C109.5
N3—C4—H4118.3H8A—C8—H8C109.5
C5—C4—H4118.3H8B—C8—H8C109.5
C6—C5—C4118.41 (12)H1W—O1W—H2W102.7 (18)
C1—N1—N2—C2176.76 (11)C3—N3—C4—C50.1 (2)
C8—N4—C1—N1174.76 (11)N3—C4—C5—C60.8 (2)
C8—N4—C1—S15.79 (18)C4—C5—C6—C70.5 (2)
N2—N1—C1—N40.36 (17)C5—C6—C7—C30.53 (19)
N2—N1—C1—S1179.12 (9)C5—C6—C7—C7'178.83 (12)
N1—N2—C2—C3178.85 (11)N3—C3—C7—C61.32 (19)
C4—N3—C3—C71.02 (19)C2—C3—C7—C6178.27 (12)
C4—N3—C3—C2178.58 (11)N3—C3—C7—C7'178.02 (12)
N2—C2—C3—N311.03 (18)C2—C3—C7—C7'2.39 (19)
N2—C2—C3—C7168.58 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4N···N20.88 (2)2.19 (2)2.6116 (16)109 (1)
N1—H1N···O1Wi0.88 (1)2.12 (1)2.9940 (15)170 (2)
N4—H4N···O1W0.88 (2)2.50 (2)3.3100 (15)154 (1)
O1W—H1W···N30.84 (2)2.11 (2)2.9371 (16)172 (2)
O1W—H2W···S1ii0.85 (2)2.50 (2)3.3412 (11)173 (2)
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x, y+3/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4N···N20.881 (15)2.189 (16)2.6116 (16)109.0 (13)
N1—H1N···O1Wi0.881 (10)2.124 (11)2.9940 (15)169.7 (15)
N4—H4N···O1W0.881 (15)2.497 (16)3.3100 (15)153.8 (14)
O1W—H1W···N30.837 (16)2.106 (15)2.9371 (16)172.3 (15)
O1W—H2W···S1ii0.847 (16)2.500 (16)3.3412 (11)172.5 (15)
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x, y+3/2, z+1/2.
 

Acknowledgements

The research was funded by Universiti Putra Malaysia (UPM) under research University Grant Schemes (RUGS No. GP-IBT/2013/9419400), the Malaysian Fundamental Research Grant Scheme (FRGS No. 01-02-13-1344FR) and the Science Fund (Science Fund No. 06–01-04-SF810). NSMM wishes to thank UPM for the award of a Graduate Research Fellowship.

References

First citationAgilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.  Google Scholar
First citationAli, M. A., Majumder, S. M. M., Butcher, R. J., Jasinski, J. P. & Jasinski, J. M. (1997). Polyhedron, 16, 2749–2754.  CSD CrossRef CAS Web of Science Google Scholar
First citationBeraldo, H., Lima, R., Teixeira, L. R., Moura, A. A. & West, D. X. (2001). J. Mol. Struct. 559, 99–106.  Web of Science CSD CrossRef CAS Google Scholar
First citationBrandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSreekanth, A., Kala, U. L., Nayar, C. R. & Kurup, M. P. (2004). Polyhedron, 23, 41–47.  CSD CrossRef CAS Google Scholar
First citationWest, D. X., Bain, G. A., Butcher, R. J., Jasinski, J. P., Li, Y., Pozdniakiv, R. Y., Valdés-Martínez, J. V., Toscano, R. A. & Hernández-Ortega, S. (1996). Polyhedron, 15, 665–674.  CSD CrossRef CAS Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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Volume 71| Part 4| April 2015| Pages o253-o254
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