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

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Crystal structure of (Z)-4-methylbenzyl 3-[1-(5-methylpyridin-2-yl)ethyl­idene]di­thiocarbazate1

aDepartment of Chemistry, Universiti Putra Malaysia, 43400 Serdang, Malaysia, and bCentre for Crystalline Materials, Faculty of Science and Technology, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
*Correspondence e-mail: edwardt@sunway.edu.my

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 2 December 2015; accepted 15 December 2015; online 19 December 2015)

In the title di­thio­carbazate compound, C17H19N3S2, the central CN2S2 residue is essentially planar (r.m.s. deviation = 0.0288 Å) and forms dihedral angles of 9.77 (8) and 77.47 (7)° with the substituted-pyridyl and p-tolyl rings, respectively, indicating a highly twisted mol­ecule; the dihedral angle between the rings is 85.56 (8)°. The configuration about the C=N bond is Z, which allows for the formation of an intra­molecular N—H⋯N(pyrid­yl) hydrogen bond. The packing features tolyl-methyl-C—H⋯N(imine), pyridyl-C—H⋯π(tol­yl) and ππ inter­actions [between pyridyl rings with a distance = 3.7946 (13) Å], which generates jagged supra­molecular layers that stack along the b axis with no directional inter­actions between them.

1. Related literature

For the structure of the 4-methyl­pyridin-2-yl derivative, with an E configuration for the C=N bond, allowing for the formation of centrosymmetric {⋯HNCS}2 synthons in the crystal, see: Omar et al. (2014[Omar, S. A., Ravoof, T. B. S. A., Tahir, M. I. M. & Crouse, K. A. (2014). Transition Met. Chem. 39, 119-126.]). For the synthesis, see: Ravoof et al. (2010[Ravoof, T. B. S. A., Crouse, K. A., Tahir, M. I. M., How, F. N. F., Rosli, R. & Watkins, D. J. (2010). Transition Met. Chem. 35, 871-876.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C17H19N3S2

  • Mr = 329.47

  • Monoclinic, P c

  • a = 9.0073 (2) Å

  • b = 12.3856 (2) Å

  • c = 7.5553 (1) Å

  • β = 98.620 (2)°

  • V = 833.35 (3) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 2.88 mm−1

  • T = 100 K

  • 0.31 × 0.22 × 0.18 mm

2.2. Data collection

  • Agilent Xcalibur, Eos, Gemini diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, England.]) Tmin = 0.43, Tmax = 0.60

  • 16118 measured reflections

  • 3195 independent reflections

  • 3191 reflections with I > 2σ(I)

  • Rint = 0.021

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.030

  • wR(F2) = 0.081

  • S = 1.05

  • 3195 reflections

  • 205 parameters

  • 3 restraints

  • H-atom parameters constrained

  • Δρmax = 0.28 e Å−3

  • Δρmin = −0.30 e Å−3

  • Absolute structure: Flack x determined using 1558 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]).

  • Absolute structure parameter: −0.011 (13)

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C3–C8 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N⋯N3 0.88 (2) 1.98 (3) 2.624 (3) 130 (3)
C12′—H12C⋯N2i 0.98 2.58 3.483 (3) 154
C13—H13⋯Cg1ii 0.95 2.76 3.582 (3) 145
Symmetry codes: (i) x+1, y, z; (ii) [x+1, -y+2, z-{\script{1\over 2}}].

Data collection: CrysAlis PRO (Agilent, 2011[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL2014/7 (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 the structure of the 4-methylpyridin-2-yl derivative, with an E configuration for the CN bond, allowing for the formation of centrosymmetric {···HNCS}2 synthons in the crystal, see: Omar et al. (2014). For the synthesis, see: Ravoof et al. (2010).

Experimental top

The precursor molecule, S-4-methylbenzyldithiocarbazate, was prepared by adapting the literature procedure of Ravoof et al. (2010). Thus, KOH (11.2 g, 0.2 mol) was dissolved in absolute ethanol (70 ml) and to this solution was added hydrazine hydrate (10 g, 0.2 mol) followed by cooling in an ice-salt bath. Drop wise addition of carbon disulphide (15.2 g, 0.2 mol) with constant stirring over 1 h followed. The two layers that subsequently formed were separated. The light-brown lower layer was dissolved in 40% ethanol (60 ml) below 268 K. The mixture was kept in an ice-bath and 4-methylbenzyl chloride (26.5 ml, 0.2 mol) was added drop wise with vigorous stirring. The major product, which was white and sticky was filtered and left overnight to dry over anhydrous silica gel in a desiccator. Recrystallization to yield analytically pure S-4-methylbenzyldithiocarbazate was achieved from hot acetonitrile. Yield: 82%; M.pt: 160–161 °C.

S-4-Methylbenzyldithiocarbazate (2.12 g, 0.01 mol) was dissolved in hot acetonitrile (100 ml) and added to an equimolar solution of 5-methyl-pyridine-2-aldehyde (1.21 g, 0.01 mol) in ethanol (25 ml). The mixture was then heated on a water bath until the volume has been reduced by half. A yellow precipitate formed after standing at room temperature for 1 h and this was washed with ethanol. Yellow prisms were deposited from its acetonitrile solution within a week. Yield: 78%. M.pt: 112–113 °C. Anal. Found (calc'd for C17H19N3S2): C, 62.32 (61.97); H, 5.59 (5.81); N 12.80 (12.75).

Refinement top

Carbon-bound H-atoms were placed in calculated positions (C—H = 0.95 to 0.99 Å) and were included in the refinement in the riding model approximation with Uiso(H) = 1.2–1.5Ueq(C). The N—H atom was refined with N—H = 0.88±0.01 Å, and with Uiso(H) = 1.2Ueq(N).

Structure description top

For the structure of the 4-methylpyridin-2-yl derivative, with an E configuration for the CN bond, allowing for the formation of centrosymmetric {···HNCS}2 synthons in the crystal, see: Omar et al. (2014). For the synthesis, see: Ravoof et al. (2010).

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, 2008); program(s) used to refine structure: SHELXL2014/7 (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 unit-cell contents in projection down the a axis. The tolyl-methyl-C—H···N(imine), pyridyl-C—H···π(tolyl) and ππ interactions are shown as orange, pink and orange dashed lines, respectively.
(Z)-4-Methylbenzyl 3-[1-(5-methylpyridin-2-yl)ethylidene]dithiocarbazate top
Crystal data top
C17H19N3S2F(000) = 348
Mr = 329.47Dx = 1.313 Mg m3
Monoclinic, PcCu Kα radiation, λ = 1.5418 Å
a = 9.0073 (2) ÅCell parameters from 12240 reflections
b = 12.3856 (2) Åθ = 4–71°
c = 7.5553 (1) ŵ = 2.88 mm1
β = 98.620 (2)°T = 100 K
V = 833.35 (3) Å3Prism, yellow
Z = 20.31 × 0.22 × 0.18 mm
Data collection top
Agilent Xcalibur, Eos, Gemini
diffractometer
3195 independent reflections
Radiation source: Enhance (Cu) X-ray Source3191 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
Detector resolution: 16.1952 pixels mm-1θmax = 71.5°, θmin = 3.6°
ω scansh = 1111
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
k = 1515
Tmin = 0.43, Tmax = 0.60l = 99
16118 measured reflections
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.030 w = 1/[σ2(Fo2) + (0.0663P)2 + 0.1105P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.081(Δ/σ)max = 0.001
S = 1.05Δρmax = 0.28 e Å3
3195 reflectionsΔρmin = 0.30 e Å3
205 parametersAbsolute structure: Flack x determined using 1558 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
3 restraintsAbsolute structure parameter: 0.011 (13)
Crystal data top
C17H19N3S2V = 833.35 (3) Å3
Mr = 329.47Z = 2
Monoclinic, PcCu Kα radiation
a = 9.0073 (2) ŵ = 2.88 mm1
b = 12.3856 (2) ÅT = 100 K
c = 7.5553 (1) Å0.31 × 0.22 × 0.18 mm
β = 98.620 (2)°
Data collection top
Agilent Xcalibur, Eos, Gemini
diffractometer
3195 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
3191 reflections with I > 2σ(I)
Tmin = 0.43, Tmax = 0.60Rint = 0.021
16118 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.081Δρmax = 0.28 e Å3
S = 1.05Δρmin = 0.30 e Å3
3195 reflectionsAbsolute structure: Flack x determined using 1558 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
205 parametersAbsolute structure parameter: 0.011 (13)
3 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.01004 (7)0.74703 (4)0.22309 (8)0.01770 (17)
S20.20197 (7)0.59121 (5)0.07598 (9)0.02369 (18)
N10.2382 (2)0.80053 (17)0.1071 (3)0.0165 (4)
H1N0.324 (2)0.788 (3)0.069 (4)0.020*
N20.1881 (2)0.90223 (17)0.1402 (3)0.0151 (4)
N30.4835 (2)0.88995 (18)0.0262 (3)0.0171 (4)
C10.1524 (3)0.7141 (2)0.1305 (3)0.0164 (5)
C20.0843 (3)0.6138 (2)0.2616 (4)0.0227 (6)
H2A0.13170.58170.14690.027*
H2B0.00250.56550.31600.027*
C30.1993 (3)0.6274 (2)0.3865 (4)0.0187 (5)
C40.1541 (3)0.6423 (2)0.5698 (4)0.0211 (5)
H40.05020.64810.61530.025*
C50.2590 (3)0.6487 (2)0.6864 (4)0.0232 (5)
H50.22590.65870.81070.028*
C60.4129 (3)0.6409 (2)0.6239 (4)0.0224 (6)
C6'0.5270 (4)0.6430 (2)0.7516 (4)0.0309 (7)
H6'10.54770.71800.78120.046*
H6'20.48720.60380.86120.046*
H6'30.62000.60850.69500.046*
C70.4574 (3)0.6281 (2)0.4406 (4)0.0239 (6)
H70.56130.62380.39460.029*
C80.3525 (3)0.6216 (2)0.3238 (4)0.0221 (5)
H80.38570.61300.19920.027*
C9'0.1975 (3)1.0925 (2)0.1434 (4)0.0174 (5)
H9'10.10471.08010.19370.026*
H9'20.17431.13220.03050.026*
H9'30.26751.13480.22820.026*
C90.2679 (3)0.9857 (2)0.1097 (3)0.0149 (5)
C100.4164 (3)0.9860 (2)0.0464 (3)0.0148 (5)
C110.6190 (3)0.8899 (2)0.0256 (3)0.0174 (5)
H110.66570.82210.03780.021*
C12'0.8495 (3)0.9734 (2)0.1194 (3)0.0198 (5)
H12A0.87761.04260.16790.030*
H12B0.84700.91740.21150.030*
H12C0.92330.95380.01560.030*
C120.6969 (3)0.9832 (2)0.0632 (3)0.0164 (5)
C130.6260 (3)1.0811 (2)0.0445 (3)0.0174 (5)
H130.67341.14680.06920.021*
C140.4852 (3)1.0830 (2)0.0107 (3)0.0166 (5)
H140.43631.14980.02390.020*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0175 (3)0.0118 (3)0.0255 (3)0.0019 (2)0.0087 (2)0.0006 (2)
S20.0239 (3)0.0140 (3)0.0359 (4)0.0007 (3)0.0131 (3)0.0039 (3)
N10.0152 (10)0.0128 (10)0.0220 (10)0.0006 (7)0.0043 (8)0.0006 (8)
N20.0138 (10)0.0142 (11)0.0165 (9)0.0007 (7)0.0001 (8)0.0002 (7)
N30.0147 (9)0.0160 (10)0.0198 (10)0.0023 (8)0.0008 (8)0.0003 (8)
C10.0144 (11)0.0196 (13)0.0154 (11)0.0002 (10)0.0029 (9)0.0003 (10)
C20.0276 (14)0.0112 (12)0.0326 (15)0.0066 (10)0.0151 (11)0.0013 (10)
C30.0215 (12)0.0098 (11)0.0266 (13)0.0010 (10)0.0096 (10)0.0011 (9)
C40.0215 (12)0.0131 (12)0.0285 (13)0.0016 (10)0.0031 (10)0.0021 (10)
C50.0324 (14)0.0160 (13)0.0219 (12)0.0013 (10)0.0061 (10)0.0016 (10)
C60.0276 (14)0.0090 (12)0.0342 (14)0.0017 (10)0.0162 (11)0.0007 (10)
C6'0.0382 (16)0.0168 (13)0.0434 (17)0.0032 (12)0.0246 (13)0.0037 (12)
C70.0196 (13)0.0149 (13)0.0376 (15)0.0032 (10)0.0057 (11)0.0035 (11)
C80.0252 (13)0.0157 (13)0.0256 (13)0.0042 (10)0.0043 (10)0.0033 (10)
C9'0.0166 (12)0.0156 (13)0.0196 (11)0.0005 (8)0.0012 (9)0.0007 (9)
C90.0147 (11)0.0175 (12)0.0115 (10)0.0010 (9)0.0019 (8)0.0000 (8)
C100.0150 (11)0.0167 (12)0.0115 (10)0.0015 (9)0.0021 (8)0.0002 (9)
C110.0148 (11)0.0171 (12)0.0200 (12)0.0009 (9)0.0018 (9)0.0001 (9)
C12'0.0145 (11)0.0229 (13)0.0218 (12)0.0027 (9)0.0023 (10)0.0025 (10)
C120.0138 (12)0.0217 (13)0.0125 (10)0.0031 (9)0.0022 (9)0.0002 (9)
C130.0171 (11)0.0176 (12)0.0166 (11)0.0040 (9)0.0005 (9)0.0022 (9)
C140.0172 (11)0.0155 (12)0.0160 (12)0.0002 (9)0.0008 (9)0.0001 (9)
Geometric parameters (Å, º) top
S1—C11.762 (3)C6'—H6'20.9800
S1—C21.820 (3)C6'—H6'30.9800
S2—C11.655 (3)C7—C81.389 (4)
N1—C11.348 (3)C7—H70.9500
N1—N21.374 (3)C8—H80.9500
N1—H1N0.872 (14)C9'—C91.505 (3)
N2—C91.299 (3)C9'—H9'10.9800
N3—C111.336 (3)C9'—H9'20.9800
N3—C101.353 (3)C9'—H9'30.9800
C2—C31.512 (4)C9—C101.486 (3)
C2—H2A0.9900C10—C141.397 (4)
C2—H2B0.9900C11—C121.403 (4)
C3—C81.391 (4)C11—H110.9500
C3—C41.396 (4)C12'—C121.503 (3)
C4—C51.387 (4)C12'—H12A0.9800
C4—H40.9500C12'—H12B0.9800
C5—C61.399 (4)C12'—H12C0.9800
C5—H50.9500C12—C131.388 (4)
C6—C71.392 (4)C13—C141.394 (4)
C6—C6'1.511 (3)C13—H130.9500
C6'—H6'10.9800C14—H140.9500
C1—S1—C2101.58 (12)C6—C7—H7119.4
C1—N1—N2119.6 (2)C7—C8—C3121.0 (3)
C1—N1—H1N117 (3)C7—C8—H8119.5
N2—N1—H1N123 (3)C3—C8—H8119.5
C9—N2—N1119.5 (2)C9—C9'—H9'1109.5
C11—N3—C10118.5 (2)C9—C9'—H9'2109.5
N1—C1—S2121.07 (18)H9'1—C9'—H9'2109.5
N1—C1—S1113.26 (19)C9—C9'—H9'3109.5
S2—C1—S1125.66 (16)H9'1—C9'—H9'3109.5
C3—C2—S1107.59 (18)H9'2—C9'—H9'3109.5
C3—C2—H2A110.2N2—C9—C10127.3 (2)
S1—C2—H2A110.2N2—C9—C9'114.3 (2)
C3—C2—H2B110.2C10—C9—C9'118.4 (2)
S1—C2—H2B110.2N3—C10—C14121.0 (2)
H2A—C2—H2B108.5N3—C10—C9118.3 (2)
C8—C3—C4118.2 (2)C14—C10—C9120.7 (2)
C8—C3—C2121.2 (2)N3—C11—C12124.5 (2)
C4—C3—C2120.6 (2)N3—C11—H11117.8
C5—C4—C3120.8 (2)C12—C11—H11117.8
C5—C4—H4119.6C12—C12'—H12A109.5
C3—C4—H4119.6C12—C12'—H12B109.5
C4—C5—C6121.1 (2)H12A—C12'—H12B109.5
C4—C5—H5119.4C12—C12'—H12C109.5
C6—C5—H5119.4H12A—C12'—H12C109.5
C7—C6—C5117.8 (2)H12B—C12'—H12C109.5
C7—C6—C6'121.0 (3)C13—C12—C11116.6 (2)
C5—C6—C6'121.2 (3)C13—C12—C12'123.6 (2)
C6—C6'—H6'1109.5C11—C12—C12'119.8 (2)
C6—C6'—H6'2109.5C12—C13—C14119.9 (2)
H6'1—C6'—H6'2109.5C12—C13—H13120.1
C6—C6'—H6'3109.5C14—C13—H13120.1
H6'1—C6'—H6'3109.5C13—C14—C10119.6 (2)
H6'2—C6'—H6'3109.5C13—C14—H14120.2
C8—C7—C6121.1 (2)C10—C14—H14120.2
C8—C7—H7119.4
C1—N1—N2—C9176.9 (2)C2—C3—C8—C7176.4 (3)
N2—N1—C1—S2174.81 (17)N1—N2—C9—C102.4 (4)
N2—N1—C1—S15.6 (3)N1—N2—C9—C9'177.39 (19)
C2—S1—C1—N1173.23 (18)C11—N3—C10—C141.3 (3)
C2—S1—C1—S26.4 (2)C11—N3—C10—C9178.1 (2)
C1—S1—C2—C3164.66 (18)N2—C9—C10—N34.0 (4)
S1—C2—C3—C8104.6 (2)C9'—C9—C10—N3176.2 (2)
S1—C2—C3—C477.7 (3)N2—C9—C10—C14176.6 (2)
C8—C3—C4—C51.4 (4)C9'—C9—C10—C143.1 (3)
C2—C3—C4—C5176.4 (2)C10—N3—C11—C120.9 (4)
C3—C4—C5—C60.2 (4)N3—C11—C12—C130.1 (4)
C4—C5—C6—C71.0 (4)N3—C11—C12—C12'179.6 (2)
C4—C5—C6—C6'177.3 (3)C11—C12—C13—C140.5 (3)
C5—C6—C7—C81.1 (4)C12'—C12—C13—C14179.1 (2)
C6'—C6—C7—C8177.3 (3)C12—C13—C14—C100.1 (3)
C6—C7—C8—C30.1 (4)N3—C10—C14—C130.9 (3)
C4—C3—C8—C71.3 (4)C9—C10—C14—C13178.5 (2)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C3–C8 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1N···N30.88 (2)1.98 (3)2.624 (3)130 (3)
C12—H12C···N2i0.982.583.483 (3)154
C13—H13···Cg1ii0.952.763.582 (3)145
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+2, z1/2.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C3–C8 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1N···N30.88 (2)1.98 (3)2.624 (3)130 (3)
C12'—H12C···N2i0.982.583.483 (3)154
C13—H13···Cg1ii0.952.763.582 (3)145
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+2, z1/2.
 

Footnotes

1Additional correspondence author: thahira@upm.edu.my

Acknowledgements

This research was funded by Universiti Putra Malaysia (UPM) under Research University Grant Schemes (RUGS No. 9419400), the Fundamental Research Grant Scheme (FRGS No. 5524425) and the Science Fund (Science Fund No: 06–01-04-SF810). SAO wishes to thank the UPM for the award of a Graduate Research Fellowship.

References

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