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The title mol­ecule, C18H15N3S2, is a transcis conformer. The thione S atom is in a trans configuration with respect to the pyridine ring but adopts a cis configuration with respect to the napthylmethyl substituent. In the crystal structure, mol­ecules are linked by inter­molecular N—H...N hydrogen bonds viaα-N donor atoms and pyridyl N acceptor atoms into one-dimensional chains along the a axis. In addition, pairs of inversion-related dithio­carbazate groups and the attached pyridine groups are arranged with an inter­planar distance 3.30 Å, leading to π–π stacking inter­actions. The crystal used for the structure determination was twinned.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807025676/lh2397sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807025676/lh2397Isup2.hkl
Contains datablock I

CCDC reference: 654898

Key indicators

  • Single-crystal X-ray study
  • T = 150 K
  • Mean [sigma](C-C) = 0.005 Å
  • R factor = 0.056
  • wR factor = 0.198
  • Data-to-parameter ratio = 21.2

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT128_ALERT_4_C Non-standard setting of Space group P21/c .... P21/a PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 5
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

It is well established that Schiff bases derived from substituted dithiocarbazic acids and their metal complexes are biologically active [Ali et al., 2005 & Crouse et al., 2004]. As part of our continuing efforts to prepare new dithiocarbazate derivatives, we have introduced a new substituted dithiocarbazate ligand, S-napthalen-2-ylmethyldithiocarbazate. The title compound (the molecular structure is shown in Fig. 1) is one of the new Schiff base compounds synthesized, which was derived from S-napthalen-2-ylmethyldithiocarbazate.

The C5—N6 bond [1.352 (4) Å] is comparable with Schiff bases derived from S-benzyl- and -quinolin-2-ylmethyldithiocarbazate. [1.342 (2) Å; Chan et al., 2003] and [1.352 (2) Å; How et al., 2007b].

The C5—S15 bond [1.659 (4) Å] displays double bond character. It is comparable with Schiff bases derived from S-benzyl- and -quinolin-2-ylmethyl-dithiocarbazate. [1.6503 (17) Å; Chan et al., 2003 and 1.6593 (17) Å; How et al., 2007b].

The N7—N6—C5 bond angle [116.9 (3)°] is comparable with schiff base derived from S-quinolin-2-yldithiocarbazate [117.61 (13)°; How et al., 2007b] but slightly shorter than schiff bases derived from S-benzyldithiocarbazate [119.20 (14)°; Chan et al., 2003].

The bond angle S15—C5—S4 [125.7 (2)°] is comparable with literature values [125.60 (10)°; Chan et al., 2003 and 125.7 (3)°; Ali et al., 2005].

The dihedral angle between the C1/C2/C3/C16/C17/C18/C19/C20/C21/C22/C23 fragment and the S4/C5/N6/N7/C8/C9/C10/N11/C12/C13/C14/S15 fragment is 79.4 (1)°. Molecules in the crystal structure are packed in diagonal layers of napthalene residues lying parallel to bc plane. The dithiocarbazate moiety together with the pyridine fragments are arranged above and below this plane [Fig. 2].

In the crystal structure, molecules display π-π interaction forming pairs of overlapping S4/C5/N6/N7/C8/C9/C10/N11/C12/C13/C14/S15 fragments related by inversion symmetry with a mean distance of 3.43 Å. Similarly pairs of inversion related N6/N7/C8/C9/C10/N11/C12/C13/C14 fragments with a mean separation of 3.30 Å [Fig. 4]. The pyridine fragment C8/C9/C10/N11/C12/C13/C14 undergoes substantial libration with mean square displacement of 16.8 Å2.

There is an intermolecular N—H—N hydrogen bond formed via the pyridyl N atom and the α-nitrogen atom linking molecules together [Fig. 3] and this is also present in the Schiff base derived from 4-acetylpyridine [2.839 (2)°; How et al., 2007a].

Related literature top

S-Napthalen-2-ylmethyldithiocarbazate was used as a starting material (How et al., 2007a). Interatomic parameters for the crystal structure are comparable to those reported by Chan et al. (2003), Ali et al. (2005) and How et al. (2007a,b).

For related literature, see: Crouse et al. (2004); Parsons & Gould (2001); Shanmuga Sundara Raj, Yamin, Yussof, Tarafder, Fun & Grouse (2000).

Experimental top

S-Napthalen-2-ylmethyldithiocarbazate (SNMDTC) was used as a starting ligand for the synthesis of Schiff base. S-napthalen-2-ylmethyldithiocarbazate (SNMDTC) was prepared as reported for S-substituted dithiocarbazates (How et al., 2007a) except the addition of benzyl chloride being replaced with 1-(chloromethyl) naphthalene (29.9 ml, 0.2 mol).

SNMDTC (0.02 mol) was dissolved in hot acetonitrile (30 ml) with dropwise addition of equimolar amount of pyridine-3-carboxyaldehyde. The mixture was left heated with stirring to reduce half the volume. The mixture was allowed to stand for 1 day. Precipitates formed were filtered and recrystallized from ethanol. The recrystallized product was then dried over silica gel. (yield: 65.8%) Yellow needle like crystals were formed upon slow evaporation in a ethanol solution.

Refinement top

The H atoms were all located in a difference map, but were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98, N—H in the range 0.86–0.89 Å) and Uiso(H) (in the range 1.2–1.5 times Ueq of the parent atom), after which the positions were refined with riding constraints.

The unusual scattering of reflection in the Fo versus Fc plot with a high R-factor (9.9%) were indicators of potential twinning. Twining was confirmed using ROTAX (Parsons & Gould, 2001) to analyze the structure factor residuals. Refinement were done using twinning matrix [1 0 0, 0 - 1 0, -0.622 0 - 1], which gave a twin ratio of 0.837:0.163 (2).

Structure description top

It is well established that Schiff bases derived from substituted dithiocarbazic acids and their metal complexes are biologically active [Ali et al., 2005 & Crouse et al., 2004]. As part of our continuing efforts to prepare new dithiocarbazate derivatives, we have introduced a new substituted dithiocarbazate ligand, S-napthalen-2-ylmethyldithiocarbazate. The title compound (the molecular structure is shown in Fig. 1) is one of the new Schiff base compounds synthesized, which was derived from S-napthalen-2-ylmethyldithiocarbazate.

The C5—N6 bond [1.352 (4) Å] is comparable with Schiff bases derived from S-benzyl- and -quinolin-2-ylmethyldithiocarbazate. [1.342 (2) Å; Chan et al., 2003] and [1.352 (2) Å; How et al., 2007b].

The C5—S15 bond [1.659 (4) Å] displays double bond character. It is comparable with Schiff bases derived from S-benzyl- and -quinolin-2-ylmethyl-dithiocarbazate. [1.6503 (17) Å; Chan et al., 2003 and 1.6593 (17) Å; How et al., 2007b].

The N7—N6—C5 bond angle [116.9 (3)°] is comparable with schiff base derived from S-quinolin-2-yldithiocarbazate [117.61 (13)°; How et al., 2007b] but slightly shorter than schiff bases derived from S-benzyldithiocarbazate [119.20 (14)°; Chan et al., 2003].

The bond angle S15—C5—S4 [125.7 (2)°] is comparable with literature values [125.60 (10)°; Chan et al., 2003 and 125.7 (3)°; Ali et al., 2005].

The dihedral angle between the C1/C2/C3/C16/C17/C18/C19/C20/C21/C22/C23 fragment and the S4/C5/N6/N7/C8/C9/C10/N11/C12/C13/C14/S15 fragment is 79.4 (1)°. Molecules in the crystal structure are packed in diagonal layers of napthalene residues lying parallel to bc plane. The dithiocarbazate moiety together with the pyridine fragments are arranged above and below this plane [Fig. 2].

In the crystal structure, molecules display π-π interaction forming pairs of overlapping S4/C5/N6/N7/C8/C9/C10/N11/C12/C13/C14/S15 fragments related by inversion symmetry with a mean distance of 3.43 Å. Similarly pairs of inversion related N6/N7/C8/C9/C10/N11/C12/C13/C14 fragments with a mean separation of 3.30 Å [Fig. 4]. The pyridine fragment C8/C9/C10/N11/C12/C13/C14 undergoes substantial libration with mean square displacement of 16.8 Å2.

There is an intermolecular N—H—N hydrogen bond formed via the pyridyl N atom and the α-nitrogen atom linking molecules together [Fig. 3] and this is also present in the Schiff base derived from 4-acetylpyridine [2.839 (2)°; How et al., 2007a].

S-Napthalen-2-ylmethyldithiocarbazate was used as a starting material (How et al., 2007a). Interatomic parameters for the crystal structure are comparable to those reported by Chan et al. (2003), Ali et al. (2005) and How et al. (2007a,b).

For related literature, see: Crouse et al. (2004); Parsons & Gould (2001); Shanmuga Sundara Raj, Yamin, Yussof, Tarafder, Fun & Grouse (2000).

Computing details top

Data collection: COLLECT (Nonius, 2001).; cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS.

Figures top
[Figure 1] Fig. 1. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
[Figure 2] Fig. 2. The packing of the molecule viewed along the b axis.
[Figure 3] Fig. 3. The molecules are stabilized by intermolecular N—H—N hydrogen bond. Dotted line denotes the N—H—N hydrogen bond.
[Figure 4] Fig. 4. View of the π···π stacking of N6/N7/C8/C9/C10/N11/C12/C13/C14 fragments realted by inversion symmetry.
2-Naphthylmethyl N-(3-pyridylmethylene)hydrazinecarbodithioate top
Crystal data top
C18H15N3S2F(000) = 704
Mr = 337.47Dx = 1.377 Mg m3
Monoclinic, P21/aMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yabCell parameters from 4600 reflections
a = 13.0527 (3) Åθ = 5–30°
b = 7.8222 (2) ŵ = 0.33 mm1
c = 16.4471 (4) ÅT = 150 K
β = 104.2903 (12)°Plate, yellow
V = 1627.30 (7) Å30.48 × 0.28 × 0.14 mm
Z = 4
Data collection top
Bruker–Nonius KappaCCD
diffractometer
3138 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.000
ω scansθmax = 29.5°, θmin = 5.1°
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
h = 1718
Tmin = 0.91, Tmax = 0.95k = 1010
8557 measured reflectionsl = 2222
4436 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.057H-atom parameters constrained
wR(F2) = 0.198 Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.12P)2 + 5.11P] ,
where P = (max(Fo2,0) + 2Fc2)/3
S = 0.82(Δ/σ)max = 0.000125
4435 reflectionsΔρmax = 0.63 e Å3
209 parametersΔρmin = 0.62 e Å3
0 restraints
Crystal data top
C18H15N3S2V = 1627.30 (7) Å3
Mr = 337.47Z = 4
Monoclinic, P21/aMo Kα radiation
a = 13.0527 (3) ŵ = 0.33 mm1
b = 7.8222 (2) ÅT = 150 K
c = 16.4471 (4) Å0.48 × 0.28 × 0.14 mm
β = 104.2903 (12)°
Data collection top
Bruker–Nonius KappaCCD
diffractometer
4436 independent reflections
Absorption correction: multi-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
3138 reflections with I > 2σ(I)
Tmin = 0.91, Tmax = 0.95Rint = 0.000
8557 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0570 restraints
wR(F2) = 0.198H-atom parameters constrained
S = 0.82Δρmax = 0.63 e Å3
4435 reflectionsΔρmin = 0.62 e Å3
209 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2346 (3)0.8628 (5)0.3705 (2)0.0263
C20.1883 (3)1.0170 (5)0.3308 (2)0.0255
C30.0720 (3)1.0276 (5)0.2894 (2)0.0273
S40.05644 (6)0.92864 (11)0.18668 (5)0.0247
C50.0791 (2)0.9565 (4)0.1406 (2)0.0226
N60.1078 (2)0.8992 (4)0.06063 (18)0.0243
N70.0311 (2)0.8166 (4)0.03065 (17)0.0238
C80.0624 (2)0.7433 (4)0.0410 (2)0.0230
C90.0152 (2)0.6506 (4)0.0743 (2)0.0225
C100.1205 (3)0.6408 (5)0.0295 (2)0.0266
N110.1951 (2)0.5563 (4)0.05595 (19)0.0277
C120.1665 (3)0.4786 (5)0.1315 (2)0.0278
C130.0639 (3)0.4804 (5)0.1802 (2)0.0265
C140.0133 (3)0.5658 (4)0.1511 (2)0.0257
S150.16657 (7)1.03963 (13)0.18748 (6)0.0317
C160.2517 (3)1.1548 (5)0.3274 (2)0.0315
C170.3622 (3)1.1501 (5)0.3616 (2)0.0354
C180.4075 (3)1.0046 (6)0.3989 (2)0.0336
C190.3472 (3)0.8590 (5)0.4056 (2)0.0289
C200.3926 (3)0.7082 (6)0.4469 (2)0.0384
C210.3316 (4)0.5685 (5)0.4530 (3)0.0414
C220.2230 (4)0.5725 (5)0.4182 (3)0.0388
C230.1755 (3)0.7142 (5)0.3777 (2)0.0310
H310.05051.14680.28220.0361*
H320.02910.96840.32230.0361*
H810.13400.74750.07110.0298*
H1010.14040.69770.02230.0338*
H1210.21880.42340.15160.0370*
H1310.04660.42370.22980.0323*
H1410.08350.56580.18120.0320*
H1610.22151.25610.30220.0392*
H1710.40341.24690.35770.0460*
H1810.47930.99870.42180.0430*
H2010.46540.70530.46980.0481*
H2110.36370.47010.48070.0471*
H2210.18250.47570.42230.0500*
H2310.10280.71480.35540.0411*
H610.17200.91240.02960.0316*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0286 (17)0.0293 (17)0.0205 (14)0.0020 (14)0.0052 (12)0.0015 (13)
C20.0247 (15)0.0304 (17)0.0213 (14)0.0017 (13)0.0057 (12)0.0002 (13)
C30.0241 (16)0.0308 (18)0.0263 (15)0.0057 (13)0.0051 (12)0.0010 (13)
S40.0185 (4)0.0297 (4)0.0249 (4)0.0029 (3)0.0033 (3)0.0009 (3)
C50.0173 (14)0.0227 (16)0.0272 (15)0.0009 (12)0.0039 (12)0.0027 (12)
N60.0162 (12)0.0277 (14)0.0290 (14)0.0013 (11)0.0055 (10)0.0005 (11)
N70.0199 (12)0.0242 (13)0.0273 (13)0.0026 (11)0.0059 (11)0.0029 (11)
C80.0193 (14)0.0228 (15)0.0259 (15)0.0002 (12)0.0038 (12)0.0023 (12)
C90.0193 (14)0.0227 (16)0.0255 (15)0.0026 (12)0.0055 (12)0.0017 (12)
C100.0192 (14)0.0306 (18)0.0283 (16)0.0008 (13)0.0027 (12)0.0004 (14)
N110.0217 (13)0.0289 (15)0.0328 (15)0.0001 (11)0.0073 (11)0.0010 (12)
C120.0248 (16)0.0282 (17)0.0327 (17)0.0010 (13)0.0118 (13)0.0003 (14)
C130.0276 (16)0.0312 (17)0.0212 (14)0.0053 (13)0.0068 (13)0.0015 (13)
C140.0246 (15)0.0277 (17)0.0226 (15)0.0027 (13)0.0016 (12)0.0022 (13)
S150.0218 (4)0.0409 (5)0.0335 (4)0.0047 (3)0.0087 (3)0.0037 (4)
C160.0347 (18)0.0294 (19)0.0276 (16)0.0033 (15)0.0026 (14)0.0003 (14)
C170.0344 (19)0.040 (2)0.0311 (18)0.0106 (16)0.0062 (15)0.0034 (16)
C180.0243 (16)0.052 (2)0.0226 (16)0.0042 (16)0.0025 (13)0.0059 (16)
C190.0279 (16)0.037 (2)0.0215 (15)0.0076 (15)0.0057 (13)0.0004 (14)
C200.0335 (19)0.053 (3)0.0270 (17)0.0150 (18)0.0045 (15)0.0035 (17)
C210.051 (2)0.037 (2)0.038 (2)0.0177 (19)0.0148 (19)0.0105 (17)
C220.047 (2)0.032 (2)0.040 (2)0.0056 (17)0.0156 (18)0.0044 (16)
C230.0320 (18)0.0329 (19)0.0287 (16)0.0020 (15)0.0085 (14)0.0007 (14)
Geometric parameters (Å, º) top
C1—C21.433 (5)N11—C121.350 (5)
C1—C191.441 (5)C12—C131.380 (5)
C1—C231.416 (5)C12—H1210.935
C2—C31.504 (5)C13—C141.390 (5)
C2—C161.368 (5)C13—H1310.905
C3—S41.824 (4)C14—H1410.928
C3—H310.973C16—C171.414 (5)
C3—H320.985C16—H1610.935
S4—C51.758 (3)C17—C181.357 (6)
C5—N61.352 (4)C17—H1710.940
C5—S151.659 (3)C18—C191.404 (6)
N6—N71.381 (4)C18—H1810.921
N6—H610.873C19—C201.416 (5)
N7—C81.283 (4)C20—C211.369 (6)
C8—C91.458 (5)C20—H2010.933
C8—H810.944C21—C221.393 (7)
C9—C101.392 (4)C21—H2110.939
C9—C141.393 (5)C22—C231.362 (6)
C10—N111.336 (4)C22—H2210.935
C10—H1010.939C23—H2310.929
C2—C1—C19118.3 (3)C13—C12—H121119.1
C2—C1—C23123.5 (3)C12—C13—C14119.1 (3)
C19—C1—C23118.2 (3)C12—C13—H131120.6
C1—C2—C3121.1 (3)C14—C13—H131120.3
C1—C2—C16119.4 (3)C9—C14—C13119.2 (3)
C3—C2—C16119.4 (3)C9—C14—H141119.4
C2—C3—S4105.3 (2)C13—C14—H141121.4
C2—C3—H31109.7C2—C16—C17122.1 (4)
S4—C3—H31109.2C2—C16—H161119.5
C2—C3—H32111.9C17—C16—H161118.4
S4—C3—H32111.2C16—C17—C18119.4 (4)
H31—C3—H32109.4C16—C17—H171119.7
C3—S4—C5102.53 (16)C18—C17—H171120.9
S4—C5—N6112.7 (2)C17—C18—C19121.7 (3)
S4—C5—S15125.7 (2)C17—C18—H181120.9
N6—C5—S15121.7 (2)C19—C18—H181117.4
C5—N6—N7116.9 (3)C1—C19—C18119.2 (3)
C5—N6—H61121.7C1—C19—C20118.3 (4)
N7—N6—H61121.4C18—C19—C20122.5 (3)
N6—N7—C8116.2 (3)C19—C20—C21121.2 (4)
N7—C8—C9118.3 (3)C19—C20—H201118.5
N7—C8—H81121.0C21—C20—H201120.3
C9—C8—H81120.7C20—C21—C22120.2 (4)
C8—C9—C10121.0 (3)C20—C21—H211119.5
C8—C9—C14121.5 (3)C22—C21—H211120.3
C10—C9—C14117.5 (3)C21—C22—C23120.9 (4)
C9—C10—N11123.9 (3)C21—C22—H221119.3
C9—C10—H101118.1C23—C22—H221119.8
N11—C10—H101118.0C1—C23—C22121.2 (4)
C10—N11—C12117.7 (3)C1—C23—H231119.2
N11—C12—C13122.6 (3)C22—C23—H231119.7
N11—C12—H121118.3
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H61···N11i0.871.962.825 (2)170
Symmetry code: (i) x1/2, y+3/2, z.

Experimental details

Crystal data
Chemical formulaC18H15N3S2
Mr337.47
Crystal system, space groupMonoclinic, P21/a
Temperature (K)150
a, b, c (Å)13.0527 (3), 7.8222 (2), 16.4471 (4)
β (°) 104.2903 (12)
V3)1627.30 (7)
Z4
Radiation typeMo Kα
µ (mm1)0.33
Crystal size (mm)0.48 × 0.28 × 0.14
Data collection
DiffractometerBruker–Nonius KappaCCD
Absorption correctionMulti-scan
(DENZO/SCALEPACK; Otwinowski & Minor, 1997)
Tmin, Tmax0.91, 0.95
No. of measured, independent and
observed [I > 2σ(I)] reflections
8557, 4436, 3138
Rint0.000
(sin θ/λ)max1)0.693
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.057, 0.198, 0.82
No. of reflections4435
No. of parameters209
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.63, 0.62

Computer programs: COLLECT (Nonius, 2001)., DENZO/SCALEPACK (Otwinowski & Minor, 1997), DENZO/SCALEPACK, SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996), CRYSTALS.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H61···N11i0.871.962.825 (2)170
Symmetry code: (i) x1/2, y+3/2, z.
 

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