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

Mokhtaruddin, N.S.M.; Ravoof, T.B.S.A.; Tahir, M.I.M.; Tiekink, E.R.T.

doi:10.1107/S2056989015005034

organic compounds

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

doi:10.1107/S2056989015005034

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

Nur Shuhada Mohd Mokhtaruddin,^a Thahira Begum S. A. Ravoof,^a ^* Mohamed Ibrahim Mohamed Tahir ^a and Edward R. T. Tiekink ^b

^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.

Keywords: crystal structure; hydrogen bonding; thiosemicarbazone.

CCDC reference: 1053448

1. Related literature

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 pyridine N atom is anti to the imine N atom, see: West et al. (1996 ). For the synthesis of the title compound, see: Ali et al. (1997 ).

2. Experimental

2.1. Crystal data

C₉H₁₂N₄S·H₂O
M_r = 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 ) T_min = 0.860, T_max = 1.000
14591 measured reflections
2160 independent reflections
2044 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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 ).

Supporting information

CCDC reference: 1053448

Crystal structure: contains datablocks 1, I. DOI: 10.1107/S2056989015005034/hb7381sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015005034/hb7381Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015005034/hb7381Isup3.cml

checkCIF report

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%.

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

	Fig. 1. The molecular structure of the title compound showing the atom-labelling scheme and displacement ellipsoids at the 70% probability level.
	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.
	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·H₂O	F(000) = 480
M_r = 226.30	D_x = 1.342 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.5418 Å
a = 10.4493 (3) Å	Cell parameters from 7855 reflections
b = 13.6989 (3) Å	θ = 3.2–71.2°
c = 8.0235 (3) Å	µ = 2.42 mm⁻¹
β = 102.816 (3)°	T = 100 K
V = 1119.90 (6) Å³	Prism, pale-brown
Z = 4	0.30 × 0.20 × 0.10 mm

Data collection top

Oxford Diffraction Xcaliber Eos Gemini diffractometer	2160 independent reflections
Radiation source: fine-focus sealed tube	2044 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.022
Detector resolution: 16.1952 pixels mm^-1	θ_max = 71.4°, θ_min = 4.3°
ω scans	h = −12→12
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	k = −16→16
T_min = 0.860, T_max = 1.000	l = −9→9
14591 measured reflections

Refinement top

Refinement on F²	5 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.034	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.097	w = 1/[σ²(F_o²) + (0.0657P)² + 0.3425P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
2160 reflections	Δρ_max = 0.31 e Å⁻³
150 parameters	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₉H₁₂N₄S·H₂O	V = 1119.90 (6) Å³
M_r = 226.30	Z = 4
Monoclinic, P2₁/c	Cu Kα radiation
a = 10.4493 (3) Å	µ = 2.42 mm⁻¹
b = 13.6989 (3) Å	T = 100 K
c = 8.0235 (3) Å	0.30 × 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)
T_min = 0.860, T_max = 1.000	R_int = 0.022
14591 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.034	5 restraints
wR(F²) = 0.097	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	Δρ_max = 0.31 e Å⁻³
2160 reflections	Δρ_min = −0.25 e Å⁻³
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

	x	y	z	U_iso*/U_eq
S1	0.73687 (3)	0.84153 (2)	0.49693 (4)	0.01984 (14)
N1	0.52525 (11)	0.80894 (8)	0.61677 (14)	0.0178 (3)
H1N	0.5225 (16)	0.8721 (7)	0.636 (2)	0.021*
N2	0.43392 (11)	0.74878 (8)	0.66067 (14)	0.0178 (3)
N3	0.25907 (11)	0.63228 (8)	0.77276 (14)	0.0199 (3)
N4	0.62430 (11)	0.67137 (8)	0.54238 (14)	0.0187 (3)
H4N	0.5662 (14)	0.6409 (12)	0.588 (2)	0.022*
C1	0.62415 (13)	0.76805 (9)	0.55465 (16)	0.0168 (3)
C2	0.34637 (13)	0.78964 (9)	0.72608 (16)	0.0177 (3)
H2	0.3482	0.8582	0.7437	0.021*
C3	0.24297 (13)	0.73011 (10)	0.77382 (16)	0.0168 (3)
C4	0.16527 (14)	0.57657 (10)	0.81199 (18)	0.0228 (3)
H4	0.1760	0.5077	0.8116	0.027*
C5	0.05263 (14)	0.61413 (10)	0.85338 (18)	0.0224 (3)
H5	−0.0125	0.5719	0.8792	0.027*
C6	0.03765 (13)	0.71450 (10)	0.85609 (17)	0.0211 (3)
H6	−0.0381	0.7420	0.8848	0.025*
C7	0.13356 (13)	0.77500 (9)	0.81675 (16)	0.0177 (3)
C7'	0.11857 (15)	0.88417 (10)	0.8229 (2)	0.0270 (3)
H7'1	0.0318	0.9001	0.8432	0.040*
H7'2	0.1274	0.9125	0.7139	0.040*
H7'3	0.1867	0.9109	0.9158	0.040*
C8	0.72818 (13)	0.61612 (11)	0.49226 (17)	0.0225 (3)
H8A	0.7460	0.6438	0.3871	0.034*
H8B	0.7008	0.5479	0.4724	0.034*
H8C	0.8079	0.6194	0.5834	0.034*
O1W	0.49697 (10)	0.51694 (7)	0.77859 (13)	0.0232 (2)
H1W	0.4330 (14)	0.5544 (12)	0.774 (2)	0.035*
H2W	0.5595 (14)	0.5483 (13)	0.841 (2)	0.035*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0178 (2)	0.0182 (2)	0.0254 (2)	−0.00111 (11)	0.00872 (14)	−0.00060 (11)
N1	0.0179 (6)	0.0137 (5)	0.0231 (6)	−0.0011 (4)	0.0075 (5)	−0.0007 (4)
N2	0.0173 (6)	0.0177 (5)	0.0179 (6)	−0.0021 (4)	0.0030 (4)	0.0011 (4)
N3	0.0194 (6)	0.0163 (5)	0.0238 (6)	0.0013 (4)	0.0045 (5)	0.0013 (4)
N4	0.0197 (6)	0.0163 (6)	0.0210 (6)	0.0006 (4)	0.0060 (5)	0.0001 (4)
C1	0.0163 (6)	0.0182 (6)	0.0152 (6)	0.0009 (5)	0.0017 (5)	0.0002 (5)
C2	0.0181 (6)	0.0146 (6)	0.0197 (6)	−0.0005 (5)	0.0029 (5)	0.0006 (5)
C3	0.0164 (6)	0.0175 (6)	0.0154 (6)	0.0000 (5)	0.0015 (5)	0.0005 (5)
C4	0.0244 (7)	0.0159 (6)	0.0282 (7)	−0.0005 (5)	0.0061 (6)	0.0023 (5)
C5	0.0208 (7)	0.0205 (7)	0.0266 (7)	−0.0044 (5)	0.0066 (5)	0.0025 (5)
C6	0.0174 (6)	0.0238 (7)	0.0226 (7)	0.0010 (5)	0.0055 (5)	−0.0003 (5)
C7	0.0184 (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)
C8	0.0217 (7)	0.0187 (7)	0.0261 (7)	0.0051 (5)	0.0036 (6)	−0.0024 (5)
O1W	0.0207 (5)	0.0180 (5)	0.0309 (5)	0.0003 (4)	0.0055 (4)	−0.0032 (4)

Geometric parameters (Å, º) top

S1—C1	1.6903 (13)	C4—H4	0.9500
N1—C1	1.3633 (17)	C5—C6	1.385 (2)
N1—N2	1.3649 (15)	C5—H5	0.9500
N1—H1N	0.881 (9)	C6—C7	1.3896 (19)
N2—C2	1.2801 (18)	C6—H6	0.9500
N3—C4	1.3338 (18)	C7—C7'	1.5057 (18)
N3—C3	1.3510 (17)	C7'—H7'1	0.9800
N4—C1	1.3281 (17)	C7'—H7'2	0.9800
N4—C8	1.4513 (17)	C7'—H7'3	0.9800
N4—H4N	0.879 (9)	C8—H8A	0.9800
C2—C3	1.4706 (18)	C8—H8B	0.9800
C2—H2	0.9500	C8—H8C	0.9800
C3—C7	1.4066 (18)	O1W—H1W	0.836 (9)
C4—C5	1.391 (2)	O1W—H2W	0.848 (9)

C1—N1—N2	118.45 (11)	C6—C5—H5	120.8
C1—N1—H1N	121.7 (11)	C4—C5—H5	120.8
N2—N1—H1N	119.6 (11)	C5—C6—C7	119.93 (13)
C2—N2—N1	116.49 (11)	C5—C6—H6	120.0
C4—N3—C3	117.84 (12)	C7—C6—H6	120.0
C1—N4—C8	123.63 (12)	C6—C7—C3	117.47 (12)
C1—N4—H4N	115.5 (12)	C6—C7—C7'	119.96 (12)
C8—N4—H4N	119.7 (11)	C3—C7—C7'	122.58 (12)
N4—C1—N1	116.76 (12)	C7—C7'—H7'1	109.5
N4—C1—S1	124.14 (10)	C7—C7'—H7'2	109.5
N1—C1—S1	119.10 (10)	H7'1—C7'—H7'2	109.5
N2—C2—C3	119.83 (12)	C7—C7'—H7'3	109.5
N2—C2—H2	120.1	H7'1—C7'—H7'3	109.5
C3—C2—H2	120.1	H7'2—C7'—H7'3	109.5
N3—C3—C7	122.98 (12)	N4—C8—H8A	109.5
N3—C3—C2	116.66 (12)	N4—C8—H8B	109.5
C7—C3—C2	120.36 (12)	H8A—C8—H8B	109.5
N3—C4—C5	123.36 (13)	N4—C8—H8C	109.5
N3—C4—H4	118.3	H8A—C8—H8C	109.5
C5—C4—H4	118.3	H8B—C8—H8C	109.5
C6—C5—C4	118.41 (12)	H1W—O1W—H2W	102.7 (18)

C1—N1—N2—C2	176.76 (11)	C3—N3—C4—C5	0.1 (2)
C8—N4—C1—N1	−174.76 (11)	N3—C4—C5—C6	−0.8 (2)
C8—N4—C1—S1	5.79 (18)	C4—C5—C6—C7	0.5 (2)
N2—N1—C1—N4	−0.36 (17)	C5—C6—C7—C3	0.53 (19)
N2—N1—C1—S1	179.12 (9)	C5—C6—C7—C7'	−178.83 (12)
N1—N2—C2—C3	178.85 (11)	N3—C3—C7—C6	−1.32 (19)
C4—N3—C3—C7	1.02 (19)	C2—C3—C7—C6	178.27 (12)
C4—N3—C3—C2	−178.58 (11)	N3—C3—C7—C7'	178.02 (12)
N2—C2—C3—N3	11.03 (18)	C2—C3—C7—C7'	−2.39 (19)
N2—C2—C3—C7	−168.58 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, −z+3/2; (ii) x, −y+3/2, z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4N···N2	0.881 (15)	2.189 (16)	2.6116 (16)	109.0 (13)
N1—H1N···O1Wⁱ	0.881 (10)	2.124 (11)	2.9940 (15)	169.7 (15)
N4—H4N···O1W	0.881 (15)	2.497 (16)	3.3100 (15)	153.8 (14)
O1W—H1W···N3	0.837 (16)	2.106 (15)	2.9371 (16)	172.3 (15)
O1W—H2W···S1ⁱⁱ	0.847 (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

Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England. Google Scholar
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Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
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Volume 71| Part 4| April 2015| Pages o253-o254

doi:10.1107/S2056989015005034

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

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

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