| Literature DB >> 29850067 |
Siti Aminah Omar1, Chee Keong Chah1, Thahira B S A Ravoof1, Mukesh M Jotani2, Edward R T Tiekink3.
Abstract
In the title di-thio-carbazate ester, C16H17N3S2 (systematic name: (Z)-{[(benzyl-sulfan-yl)methane-thio-yl]amino}[1-(6-methyl-pyridin-2-yl)ethyl-idene]amine), the central methyl-idenehydrazinecarbodi-thio-ate (C2N2S2) core is almost planar (r.m.s. deviation = 0.0111 Å) and forms dihedral angles of 71.67 (3)° with the approximately orthogonally inclined thio-ester phenyl ring, and 7.16 (7)° with the approximately coplanar substituted pyridyl ring. The latter arrangement and the Z configuration about the imine-C=N bond allows for the formation of an intra-molecular hydrazine-N-H⋯N(pyrid-yl) hydrogen bond that closes an S(6) loop. In the crystal, phenyl-C-H⋯S(thione), methyl-ene-C-H⋯π(pyrid-yl), methyl-ene- and phenyl-C-H⋯π(phen-yl) contacts connect mol-ecules into supra-molecular layers propagating in the bc plane; the layers stack along the a axis with no directional inter-actions between them. The analysis of the Hirshfeld surface indicates the relative importance of an intra-layer phenyl-H⋯H(pyrid-yl) contact upon the mol-ecular packing.Entities:
Keywords: Hirshfeld surface analysis; crystal structure; dithiocarbazate ester; hydrogen bonding
Year: 2018 PMID: 29850067 PMCID: PMC5956350 DOI: 10.1107/S2056989018001330
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of (I), showing the atom-labelling scheme and displacement ellipsoids at the 70% probability level.
Hydrogen-bond geometry (Å, °)
Cg1 and Cg2 are the centroids of the (N3,C11–C15) and (C3—C8) rings, respectively.
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N1—H1 | 0.87 (1) | 1.91 (2) | 2.6123 (16) | 138 (1) |
| C8—H8⋯S2i | 0.95 | 2.90 | 3.6184 (16) | 154 |
| C2—H2 | 0.99 | 2.76 | 3.5325 (15) | 135 |
| C7—H7⋯ | 0.95 | 2.89 | 3.5760 (16) | 130 |
| C10—H10 | 0.98 | 2.68 | 3.5842 (15) | 153 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .
Figure 2Molecular packing in (I), showing (a) a view of the supramolecular layer sustained by C—H⋯S and C—H⋯π interactions and (b) a view of the unit-cell contents shown in projection down the b axis, highlighting the stacking of layers. The C—H⋯S and C—H⋯π interactions are shown as orange and purple dashed lines, respectively.
Summary of short surface contacts (Å) in (I)
| Contact | Distance | Symmetry operation |
|---|---|---|
| H4⋯H15 | 1.98 |
|
| H7⋯C8 | 2.74 | - |
| H2 | 2.85 |
|
| H10 | 2.86 |
|
| H16 | 3.05 | - |
Figure 3Views of Hirshfeld surface mapped over d norm for (I): (a) in the range −0.120 to +1.541 au highlighting short interatomic H⋯H contacts with yellow dashed lines and label ‘1’ and (b) in the range −0.050 to +1.541 au highlighting short interatomic C⋯H/H⋯C contacts with black dashed lines and label ‘3’. Weak intermolecular C—H⋯S/S⋯H—C contacts are indicated by sky-blue dashed lines and label ‘2’ in both (a) and (b).
Figure 4Two views of the Hirshfeld surface mapped over the electrostatic potential for (I) in the range ±0.055 au. The red and blue regions represent negative and positive electrostatic potentials, respectively.
Figure 5Two views of Hirshfeld surface mapped with shape-index properties for (I) highlighting (a) C—H⋯π contacts and (b) their reciprocal i.e. π⋯H—C contacts, with red and blue dotted lines, respectively, and labels ‘1’–‘3’.
Figure 6(a) The full two-dimensional fingerprint plot for (I) and fingerprint plots delineated into (b) H⋯H, (c) C⋯H/H⋯C, (d) S⋯H/H⋯S and (e) S⋯H/H⋯S contacts.
Relative percentage contributions of close contacts to the Hirshfeld surface of (I)
| H⋯H | 45.1 |
| C⋯H/H⋯C | 25.6 |
| S⋯H/H⋯S | 16.8 |
| N⋯H/H⋯N | 8.8 |
| C⋯S/S⋯C | 2.1 |
| S⋯N/N⋯S | 0.9 |
| C⋯C | 0.7 |
Experimental details
| Crystal data | |
| Chemical formula | C16H17N3S2 |
|
| 315.44 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 100 |
|
| 17.0395 (3), 5.5354 (1), 16.4292 (2) |
| β (°) | 91.355 (1) |
|
| 1549.18 (4) |
|
| 4 |
| Radiation type | Cu |
| μ (mm−1) | 3.08 |
| Crystal size (mm) | 0.28 × 0.18 × 0.08 |
| Data collection | |
| Diffractometer | Rigaku Oxford Diffraction Gemini E |
| Absorption correction | Multi-scan ( |
|
| 0.561, 1.000 |
| No. of measured, independent and observed [ | 29598, 3000, 2888 |
|
| 0.034 |
| Refinement | |
|
| 0.032, 0.092, 1.04 |
| No. of reflections | 3000 |
| No. of parameters | 195 |
| No. of restraints | 1 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.40, −0.26 |
Computer programs: CrysAlis PRO (Agilent, 2011 ▸), SHELXS97 (Sheldrick, 2008 ▸), SHELXL2014 (Sheldrick, 2015 ▸), ORTEP-3 for Windows (Farrugia, 2012 ▸), DIAMOND (Brandenburg, 2006 ▸) and publCIF (Westrip, 2010 ▸).
| C16H17N3S2 | |
| Monoclinic, | Cu |
| Cell parameters from 16086 reflections | |
| θ = 3.7–71.4° | |
| µ = 3.08 mm−1 | |
| β = 91.355 (1)° | |
| Prism, yellow | |
| 0.28 × 0.18 × 0.08 mm |
| Rigaku Oxford Diffraction Gemini E diffractometer | 3000 independent reflections |
| Radiation source: Enhance X-ray source | 2888 reflections with |
| Mirror monochromator | |
| Detector resolution: 16.1952 pixels mm-1 | θmax = 71.5°, θmin = 5.2° |
| ω scan | |
| Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011) | |
| 29598 measured reflections |
| Refinement on | 1 restraint |
| Least-squares matrix: full | Hydrogen site location: mixed |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 3000 reflections | Δρmax = 0.40 e Å−3 |
| 195 parameters | Δρmin = −0.26 e Å−3 |
| 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. |
| S1 | 0.36900 (2) | 0.02321 (6) | 0.35206 (2) | 0.01816 (12) | |
| S2 | 0.20666 (2) | 0.21559 (6) | 0.30590 (2) | 0.01465 (12) | |
| N1 | 0.29576 (7) | 0.3795 (2) | 0.42370 (7) | 0.0161 (3) | |
| H1N | 0.3346 (8) | 0.396 (3) | 0.4582 (9) | 0.019* | |
| N2 | 0.23272 (7) | 0.5327 (2) | 0.43063 (7) | 0.0156 (3) | |
| N3 | 0.35999 (7) | 0.5890 (2) | 0.55123 (7) | 0.0151 (2) | |
| C1 | 0.29438 (8) | 0.2120 (2) | 0.36453 (8) | 0.0144 (3) | |
| C2 | 0.21915 (8) | −0.0396 (3) | 0.23758 (8) | 0.0168 (3) | |
| H2A | 0.2609 | −0.0060 | 0.1982 | 0.020* | |
| H2B | 0.2333 | −0.1872 | 0.2686 | 0.020* | |
| C3 | 0.14062 (8) | −0.0702 (3) | 0.19410 (8) | 0.0141 (3) | |
| C4 | 0.11330 (8) | 0.1021 (3) | 0.13811 (8) | 0.0166 (3) | |
| H4 | 0.1456 | 0.2360 | 0.1253 | 0.020* | |
| C5 | 0.03983 (8) | 0.0805 (3) | 0.10104 (8) | 0.0182 (3) | |
| H5 | 0.0221 | 0.1992 | 0.0631 | 0.022* | |
| C6 | −0.00811 (8) | −0.1147 (3) | 0.11931 (8) | 0.0178 (3) | |
| H6 | −0.0586 | −0.1298 | 0.0940 | 0.021* | |
| C7 | 0.01836 (9) | −0.2871 (3) | 0.17477 (9) | 0.0187 (3) | |
| H7 | −0.0140 | −0.4211 | 0.1873 | 0.022* | |
| C8 | 0.09226 (9) | −0.2646 (3) | 0.21221 (9) | 0.0166 (3) | |
| H8 | 0.1097 | −0.3829 | 0.2504 | 0.020* | |
| C9 | 0.23507 (8) | 0.6991 (2) | 0.48580 (8) | 0.0147 (3) | |
| C10 | 0.16295 (8) | 0.8567 (3) | 0.48703 (8) | 0.0175 (3) | |
| H10A | 0.1261 | 0.8058 | 0.4437 | 0.026* | |
| H10B | 0.1780 | 1.0254 | 0.4783 | 0.026* | |
| H10C | 0.1379 | 0.8411 | 0.5399 | 0.026* | |
| C11 | 0.29926 (8) | 0.7469 (3) | 0.54680 (8) | 0.0146 (3) | |
| C12 | 0.41782 (8) | 0.6242 (3) | 0.60655 (8) | 0.0167 (3) | |
| C13 | 0.41666 (9) | 0.8185 (3) | 0.66067 (9) | 0.0203 (3) | |
| H13 | 0.4580 | 0.8395 | 0.6999 | 0.024* | |
| C14 | 0.35505 (9) | 0.9797 (3) | 0.65674 (9) | 0.0215 (3) | |
| H14 | 0.3533 | 1.1126 | 0.6932 | 0.026* | |
| C15 | 0.29548 (8) | 0.9452 (3) | 0.59868 (9) | 0.0192 (3) | |
| H15 | 0.2528 | 1.0553 | 0.5945 | 0.023* | |
| C16 | 0.48418 (9) | 0.4453 (3) | 0.60873 (10) | 0.0222 (3) | |
| H16A | 0.4773 | 0.3303 | 0.5638 | 0.033* | |
| H16B | 0.4844 | 0.3579 | 0.6606 | 0.033* | |
| H16C | 0.5341 | 0.5309 | 0.6032 | 0.033* |
| S1 | 0.0127 (2) | 0.0190 (2) | 0.0227 (2) | 0.00341 (12) | −0.00205 (14) | −0.00368 (13) |
| S2 | 0.01277 (19) | 0.0172 (2) | 0.01385 (19) | 0.00289 (12) | −0.00273 (13) | −0.00297 (12) |
| N1 | 0.0123 (6) | 0.0196 (6) | 0.0162 (6) | 0.0017 (5) | −0.0029 (4) | −0.0036 (5) |
| N2 | 0.0133 (6) | 0.0174 (6) | 0.0160 (6) | 0.0005 (5) | 0.0007 (4) | 0.0005 (4) |
| N3 | 0.0150 (6) | 0.0160 (6) | 0.0141 (5) | −0.0020 (5) | −0.0001 (4) | 0.0015 (4) |
| C1 | 0.0127 (7) | 0.0164 (7) | 0.0141 (6) | −0.0014 (5) | 0.0004 (5) | 0.0019 (5) |
| C2 | 0.0162 (7) | 0.0172 (7) | 0.0168 (6) | 0.0032 (5) | −0.0014 (5) | −0.0054 (5) |
| C3 | 0.0140 (6) | 0.0156 (6) | 0.0125 (6) | 0.0017 (5) | 0.0005 (5) | −0.0042 (5) |
| C4 | 0.0175 (7) | 0.0159 (7) | 0.0165 (6) | −0.0040 (5) | 0.0016 (5) | 0.0003 (5) |
| C5 | 0.0197 (7) | 0.0201 (7) | 0.0146 (6) | 0.0014 (6) | −0.0022 (5) | 0.0012 (5) |
| C6 | 0.0140 (7) | 0.0225 (7) | 0.0168 (6) | −0.0006 (5) | −0.0001 (5) | −0.0053 (6) |
| C7 | 0.0184 (7) | 0.0173 (7) | 0.0206 (7) | −0.0036 (5) | 0.0050 (6) | −0.0025 (5) |
| C8 | 0.0194 (7) | 0.0150 (7) | 0.0155 (6) | 0.0025 (5) | 0.0025 (5) | 0.0004 (5) |
| C9 | 0.0140 (7) | 0.0163 (7) | 0.0137 (6) | −0.0017 (5) | 0.0018 (5) | 0.0020 (5) |
| C10 | 0.0161 (7) | 0.0183 (7) | 0.0181 (6) | 0.0019 (6) | 0.0009 (5) | 0.0006 (5) |
| C11 | 0.0138 (7) | 0.0170 (7) | 0.0133 (6) | −0.0027 (5) | 0.0031 (5) | 0.0011 (5) |
| C12 | 0.0157 (7) | 0.0199 (7) | 0.0144 (6) | −0.0046 (5) | 0.0000 (5) | 0.0036 (5) |
| C13 | 0.0185 (7) | 0.0269 (8) | 0.0155 (7) | −0.0069 (6) | −0.0005 (5) | −0.0009 (6) |
| C14 | 0.0209 (8) | 0.0251 (8) | 0.0188 (7) | −0.0051 (6) | 0.0039 (6) | −0.0074 (6) |
| C15 | 0.0160 (7) | 0.0214 (7) | 0.0203 (7) | −0.0004 (6) | 0.0036 (5) | −0.0036 (6) |
| C16 | 0.0189 (7) | 0.0225 (8) | 0.0250 (7) | −0.0004 (6) | −0.0064 (6) | 0.0010 (6) |
| S1—C1 | 1.6624 (14) | C7—C8 | 1.394 (2) |
| S2—C1 | 1.7591 (14) | C7—H7 | 0.9500 |
| S2—C2 | 1.8199 (14) | C8—H8 | 0.9500 |
| N1—C1 | 1.3432 (18) | C9—C11 | 1.4895 (19) |
| N1—N2 | 1.3754 (16) | C9—C10 | 1.5074 (19) |
| N1—H1N | 0.865 (9) | C10—H10A | 0.9800 |
| N2—C9 | 1.2924 (18) | C10—H10B | 0.9800 |
| N3—C12 | 1.3390 (18) | C10—H10C | 0.9800 |
| N3—C11 | 1.3554 (18) | C11—C15 | 1.392 (2) |
| C2—C3 | 1.5113 (19) | C12—C13 | 1.396 (2) |
| C2—H2A | 0.9900 | C12—C16 | 1.503 (2) |
| C2—H2B | 0.9900 | C13—C14 | 1.378 (2) |
| C3—C8 | 1.392 (2) | C13—H13 | 0.9500 |
| C3—C4 | 1.397 (2) | C14—C15 | 1.389 (2) |
| C4—C5 | 1.384 (2) | C14—H14 | 0.9500 |
| C4—H4 | 0.9500 | C15—H15 | 0.9500 |
| C5—C6 | 1.392 (2) | C16—H16A | 0.9800 |
| C5—H5 | 0.9500 | C16—H16B | 0.9800 |
| C6—C7 | 1.387 (2) | C16—H16C | 0.9800 |
| C6—H6 | 0.9500 | ||
| C1—S2—C2 | 102.63 (7) | C7—C8—H8 | 119.7 |
| C1—N1—N2 | 119.01 (11) | N2—C9—C11 | 127.48 (13) |
| C1—N1—H1N | 123.2 (12) | N2—C9—C10 | 114.20 (12) |
| N2—N1—H1N | 117.8 (12) | C11—C9—C10 | 118.31 (12) |
| C9—N2—N1 | 119.09 (12) | C9—C10—H10A | 109.5 |
| C12—N3—C11 | 119.42 (12) | C9—C10—H10B | 109.5 |
| N1—C1—S1 | 121.52 (10) | H10A—C10—H10B | 109.5 |
| N1—C1—S2 | 112.88 (10) | C9—C10—H10C | 109.5 |
| S1—C1—S2 | 125.60 (8) | H10A—C10—H10C | 109.5 |
| C3—C2—S2 | 105.26 (9) | H10B—C10—H10C | 109.5 |
| C3—C2—H2A | 110.7 | N3—C11—C15 | 121.47 (13) |
| S2—C2—H2A | 110.7 | N3—C11—C9 | 117.98 (12) |
| C3—C2—H2B | 110.7 | C15—C11—C9 | 120.54 (13) |
| S2—C2—H2B | 110.7 | N3—C12—C13 | 121.55 (14) |
| H2A—C2—H2B | 108.8 | N3—C12—C16 | 117.48 (13) |
| C8—C3—C4 | 118.60 (13) | C13—C12—C16 | 120.97 (13) |
| C8—C3—C2 | 120.51 (13) | C14—C13—C12 | 119.43 (13) |
| C4—C3—C2 | 120.81 (12) | C14—C13—H13 | 120.3 |
| C5—C4—C3 | 120.98 (13) | C12—C13—H13 | 120.3 |
| C5—C4—H4 | 119.5 | C13—C14—C15 | 119.11 (14) |
| C3—C4—H4 | 119.5 | C13—C14—H14 | 120.4 |
| C4—C5—C6 | 120.09 (13) | C15—C14—H14 | 120.4 |
| C4—C5—H5 | 120.0 | C14—C15—C11 | 119.02 (14) |
| C6—C5—H5 | 120.0 | C14—C15—H15 | 120.5 |
| C7—C6—C5 | 119.49 (13) | C11—C15—H15 | 120.5 |
| C7—C6—H6 | 120.3 | C12—C16—H16A | 109.5 |
| C5—C6—H6 | 120.3 | C12—C16—H16B | 109.5 |
| C6—C7—C8 | 120.32 (13) | H16A—C16—H16B | 109.5 |
| C6—C7—H7 | 119.8 | C12—C16—H16C | 109.5 |
| C8—C7—H7 | 119.8 | H16A—C16—H16C | 109.5 |
| C3—C8—C7 | 120.53 (13) | H16B—C16—H16C | 109.5 |
| C3—C8—H8 | 119.7 | ||
| C1—N1—N2—C9 | −177.73 (12) | N1—N2—C9—C11 | −1.3 (2) |
| N2—N1—C1—S1 | 179.30 (10) | N1—N2—C9—C10 | 179.55 (11) |
| N2—N1—C1—S2 | −1.64 (16) | C12—N3—C11—C15 | −0.14 (19) |
| C2—S2—C1—N1 | −175.99 (10) | C12—N3—C11—C9 | −178.65 (12) |
| C2—S2—C1—S1 | 3.02 (11) | N2—C9—C11—N3 | −6.2 (2) |
| C1—S2—C2—C3 | 171.62 (9) | C10—C9—C11—N3 | 172.96 (12) |
| S2—C2—C3—C8 | −107.95 (12) | N2—C9—C11—C15 | 175.28 (14) |
| S2—C2—C3—C4 | 68.72 (14) | C10—C9—C11—C15 | −5.57 (19) |
| C8—C3—C4—C5 | −0.2 (2) | C11—N3—C12—C13 | 0.81 (19) |
| C2—C3—C4—C5 | −176.92 (12) | C11—N3—C12—C16 | −179.56 (12) |
| C3—C4—C5—C6 | 0.0 (2) | N3—C12—C13—C14 | −0.7 (2) |
| C4—C5—C6—C7 | −0.1 (2) | C16—C12—C13—C14 | 179.73 (13) |
| C5—C6—C7—C8 | 0.3 (2) | C12—C13—C14—C15 | −0.2 (2) |
| C4—C3—C8—C7 | 0.4 (2) | C13—C14—C15—C11 | 0.8 (2) |
| C2—C3—C8—C7 | 177.14 (12) | N3—C11—C15—C14 | −0.7 (2) |
| C6—C7—C8—C3 | −0.4 (2) | C9—C11—C15—C14 | 177.80 (13) |
| H··· | ||||
| N1—H1 | 0.87 (1) | 1.91 (2) | 2.6123 (16) | 138 (1) |
| C8—H8···S2i | 0.95 | 2.90 | 3.6184 (16) | 154 |
| C2—H2 | 0.99 | 2.76 | 3.5325 (15) | 135 |
| C7—H7··· | 0.95 | 2.89 | 3.5760 (16) | 130 |
| C10—H10 | 0.98 | 2.68 | 3.5842 (15) | 153 |