research communications
N,N′-bis[3-(methylsulfanyl)propyl]-1,8:4,5-naphthalenetetracarboxylic diimide
ofaDepartment of Chemistry (BK21 plus) and Research Institute of Natural Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
*Correspondence e-mail: mychoi@gnu.ac.kr, thkim@gnu.ac.kr
The title compound, C22H22N2O4S2, was synthesized by the reaction of 1,4,5,8-naphthalenetetracarboxylic dianhydride with 3-(methylsulfanyl)propylamine. The whole molecule is generated by an inversion operation of the This molecule has an anti form with the terminal methylthiopropyl groups above and below the aromatic diimide plane, where four intramolecular C—H⋯O and C—H⋯S hydrogen bonds are present and the O⋯H⋯S angle is 100.8°. DFT calculations revealed slight differences between the solid state and gas phase structures. In the crystal, C—H⋯O and C—H⋯S hydrogen bonds link the molecules into chains along the [2 direction. adjacent chains are interconnected by π–π interactions, forming a two-dimensional network parallel to the (001) plane. Each two-dimensional layer is further packed in an ABAB sequence along the c-axis direction. Hirshfeld surface analysis shows that van der Waals interactions make important contributions to the intermolecular contacts. The most important contacts found in the Hirshfeld surface analysis are H⋯H (44.2%), H⋯O/O⋯H (18.2%), H⋯C/C⋯H (14.4%), and H⋯S/S⋯H (10.2%).
Keywords: crystal structure; naphthalenetetracarboxylic diimide; crystal packing; hydrogen bonding; DFT calculations; Hirshfeld surface analysis..
CCDC reference: 1919395
1. Chemical context
Naphthalene diimide, which has an expanded π-electron-deficient plane has attracted considerable interest as an excellent organic linker material for the production of photochromic coordination polymers as a result of their from neutral organic moieties to stable anionic radicals (Liu et al., 2018). Aromatic are highly fluorescent residues that are used in the signal generation of sensors or on–off molecular switches. They have also been used in the design of receptors (Claudio-Catalán et al., 2016) and sensors to recognize charged species and other guests (Landey-Álvarez et al., 2016). In addition, naphthalene diimides are ideal for studying anionic⋯π interactions because the quadrupole moments are highly positive (Fang et al., 2015). We have extended our work on naphthalene diimides to produce the title compound by the reaction of naphthalenecarboxylic dianhydride with methylthiopyrimidine and report its here.
2. Structural commentary
The title compound comprises a central naphthalene diimide with terminal thiopropyl chains (Fig. 1). The molecule lies on a crystallographic inversion center located at the centroid of the naphthalene ring system and the is composed of one half of the molecule. As expected, the naphthalene diimide plane (N1/C5/O1/C6/C10/C7/C8/C11/C9/O2) is roughly planar with an r.m.s. deviation of 0.024 Å. The total distance between the terminal carbon atoms is 18.621 Å. Furthermore, this molecule has an anti form as a result of the intramolecular C4—H4A⋯O1 and C4—H4A⋯S1 hydrogen bonds (Table 1). The terminal methylthiopropylamine group is fixed at an O1⋯H4A⋯S1 angle of 100.8° by the aforementioned intramolecular hydrogen bonds. The C3/C2/S1/C1 section of the methylthiopropyl substituent is almost parallel to the naphthalene diimide unit with the C3/C2/S1/C1 mean plane inclined to the naphthalene diimide plane at a dihedral angle of 13.1 (2)°.
3. Theoretical calculations
DFT calculations were performed using the GAUSSIAN09 software package (Frisch et al., 2009) and the calculated distances and angles were compared with experimental values from the X-ray diffraction studies. The overall structural calculation was performed using the B3LYP level theory with a 6–311++G** basis set. The parameters optimized for bond lengths and bond angles are in close agreement with experimental crystallographic data (Table 2). The terminal methylthiopropyl group is fixed by internal hydrogen bonding in the crystal, whereas its internal hydrogen bonds are broken in the gas-phase structural calculation. This can be confirmed by the fact that the O1⋯H4A⋯S1 angle of the methylthiopropyl group has changed from 100.8 to 122.0° (Fig. 2). However, even in the gas phase the molecule has an anti form similar to that found in the solid state.
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4. Supramolecular features
In the crystal, C—H⋯O and C—H⋯S hydrogen bonds (Table 1) link the molecules, forming R22(11) and R22(10) rings (Fig. 3) and resulting in chains along the [20] direction. Adjacent chains are linked by intermolecular π–π interactions between naphthalene diimide rings [Cg1⋯Cg2 = 3.5756 (12) Å; Cg1 and Cg2 are the centroids of the C6/C7/C7iii/C8iii/C10/C11iii and C6iv/C7iv/C7v/C8v/C10iv/C11v rings, respectively; symmetry codes: (iii) −x + 2, −y + 1, −z; (iv) −x + 2, −y, −z; (v) x, y − 1, z]. These π–π interactions lead to a two-dimensional network structure parallel to the (001) plane (Fig. 4). The network structures are stacked in an alternating ABAB sequence along the c-axis direction (Fig. 5).
5. Hirshfeld surface analysis
Hirshfeld surface analysis was performed using CrystalExplorer (Turner et al., 2017) to quantify the various intermolecular interactions in the molecular packing of the title compound. The bright red dots in Fig. 6 showing the Hirshfeld surface mapped to the normalized contact distance (dnorm) indicate the R22(11) and R22(10) loops, and the contact points of the intermolecular C—H⋯O and C—H⋯S hydrogen bonds. The lighter red dot on the surface represents the π–π interaction with adjacent molecules. The white and blue colours that make up the majority of the surface indicate contact distances that are equal to or greater than the van der Waals radii.
The C—H⋯O and C—H⋯S hydrogen bonds and π–π stacking interactions are identified in the two-dimensional fingerprint plots (Fig. 7a–e), which show the H⋯H, H⋯C/C⋯H, H⋯O/ O⋯H, H⋯N/N⋯H, and H⋯S/S⋯H contacts. The relative contributions of the atomic contacts to the Hirshfeld surface are summarized in Table 3. These show that the dominant interaction, accounting for 44.2% of the surface, is the H⋯H van der Waals interaction. Substantial contributions are also made by H⋯O/O⋯H (18.3%), H⋯C/C⋯H (14.4%), and H⋯S/S⋯H (10.2%) contacts, which are indicated by two sharp peaks in each fingerprint plot. Lesser contributions from C⋯O/O⋯C, C⋯C, H⋯N/N⋯H, O⋯O, N⋯O/O⋯N, and C⋯S/S⋯C contacts are included in Table 3 for completeness.
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6. Synthesis and crystallization
A mixture of 1,4,5,8-naphthalenetetracarboxylic dianhydride (6.70 g, 25.0 mmol) and 3-(methylsulfanyl)propylamine (5.6 mL, 50.0 mmol) in toluene (5 mL) and quinoline (15 mL) was heated at 453 K with stirring for 1h. Upon cooling to room temperature, a golden yellow crude solid was filtered off and washed with diethyl ether. A golden yellow powder was obtained. Crystals suitable for X-ray
were obtained by slow evaporation of a dichloromethane solution of the title compound.1H NMR (300 MHz, CDCl3): δ 8.77 (s, 2H, Ar), 4.33 (t, 2H, CH2N), 2.64 (t, 2H, CH2), 2.14 (s, 3H, CH3), 2.07 (t, 2H, CH2S). 13C NMR (75.4 MHz, CDCl3): δ 162.81, 130.99, 126.69, 126.57, 40.01, 31.61, 27.16 and 15.31. IR (ν, cm−1): 3344 (m); 3071 (m); 2916 (s); 2848 (s); 1999 (s); 1693 (s).
7. Database survey
A search of the Cambridge Structural Database (CSD, Version 5.40, updated February 2019; Groom et al., 2016) for naphthalene diimide derivatives gave 31 hits for structures that include a terminal propyl group. The title compound was not found. Related compounds include a series of cycloalkyl-substituted naphthalene tetracarboxylic diimides (Kakinuma et al., 2013). Other terminal n-alkyl groups are known with 2,7-dibutylbenzo[lmn][3,8]phenanthroline-1,3,6,8-tetraone (Alvey et al., 2010), bis-N,N′-dipentylnaphthalene-1,4,5,8-tetracarboxylic diimide (Andric et al., 2004), N,N′-di-n-hexyl-1,4;5,8-naphthalenetetracarboxylic diimide (Ofir et al., 2006), and N,N′-di(n-dodecyl)naphthalene-4,5,8,9-tetracarboxylic acid diimide (Kozycz et al., 2015).
8. Refinement
Crystal data, data collection and structure . All H atoms were positioned geometrically and refined using a riding model with d(C—H) = 0.95 Å, Uiso = 1.2Ueq(C) for aromatic, d(C—H) = 0.99 Å, Uiso = 1.2Ueq(C) for methylene, and d(C—H) = 0.98 Å, Uiso = 1.5Ueq(C) for the methyl H atoms.
details are summarized in Table 4Supporting information
CCDC reference: 1919395
https://doi.org/10.1107/S2056989019007771/sj5571sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989019007771/sj5571Isup2.hkl
Data collection: APEX2 (Bruker, 2014); cell
SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2010); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).C22H22N2O4S2 | F(000) = 464 |
Mr = 442.53 | Dx = 1.485 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 8.0500 (2) Å | Cell parameters from 1676 reflections |
b = 4.9407 (1) Å | θ = 3.1–26.1° |
c = 24.9626 (7) Å | µ = 0.30 mm−1 |
β = 94.333 (2)° | T = 173 K |
V = 989.99 (4) Å3 | Rod, yellow |
Z = 2 | 0.23 × 0.05 × 0.04 mm |
Bruker APEXII CCD diffractometer | 1360 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.046 |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | θmax = 25.0°, θmin = 1.6° |
Tmin = 0.676, Tmax = 0.746 | h = −9→9 |
5641 measured reflections | k = −5→5 |
1732 independent reflections | l = −29→25 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.042 | H-atom parameters constrained |
wR(F2) = 0.101 | w = 1/[σ2(Fo2) + (0.0403P)2 + 0.3426P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max < 0.001 |
1732 reflections | Δρmax = 0.25 e Å−3 |
137 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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.25895 (9) | 0.32924 (13) | 0.17605 (3) | 0.0356 (2) | |
O1 | 0.5336 (2) | 0.2804 (3) | 0.04996 (7) | 0.0310 (4) | |
O2 | 0.8407 (2) | 0.9669 (3) | 0.12693 (6) | 0.0326 (5) | |
N1 | 0.6852 (2) | 0.6297 (4) | 0.08708 (8) | 0.0243 (5) | |
C1 | 0.0764 (4) | 0.4611 (6) | 0.20299 (12) | 0.0458 (8) | |
H1A | 0.0888 | 0.4506 | 0.2423 | 0.069* | |
H1B | −0.0207 | 0.3548 | 0.1895 | 0.069* | |
H1C | 0.0609 | 0.6503 | 0.1919 | 0.069* | |
C2 | 0.4130 (3) | 0.5621 (5) | 0.20506 (10) | 0.0273 (6) | |
H2A | 0.3685 | 0.7488 | 0.2024 | 0.033* | |
H2B | 0.4374 | 0.5191 | 0.2436 | 0.033* | |
C3 | 0.5728 (3) | 0.5448 (5) | 0.17623 (9) | 0.0276 (6) | |
H3A | 0.6650 | 0.6315 | 0.1985 | 0.033* | |
H3B | 0.6023 | 0.3526 | 0.1710 | 0.033* | |
C4 | 0.5500 (3) | 0.6857 (5) | 0.12200 (10) | 0.0274 (6) | |
H4A | 0.4431 | 0.6269 | 0.1035 | 0.033* | |
H4B | 0.5434 | 0.8834 | 0.1279 | 0.033* | |
C5 | 0.6592 (3) | 0.4151 (4) | 0.05056 (9) | 0.0243 (6) | |
C6 | 0.7912 (3) | 0.3668 (4) | 0.01356 (9) | 0.0214 (5) | |
C7 | 0.9374 (3) | 0.5241 (4) | 0.01778 (8) | 0.0200 (5) | |
C8 | 0.9613 (3) | 0.7304 (4) | 0.05690 (9) | 0.0228 (5) | |
C9 | 0.8287 (3) | 0.7878 (4) | 0.09317 (9) | 0.0249 (6) | |
C10 | 0.7698 (3) | 0.1661 (4) | −0.02484 (9) | 0.0234 (5) | |
H10 | 0.6712 | 0.0598 | −0.0273 | 0.028* | |
C11 | 1.1054 (3) | 0.8802 (4) | 0.06017 (9) | 0.0242 (6) | |
H11 | 1.1210 | 1.0173 | 0.0868 | 0.029* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0366 (5) | 0.0304 (4) | 0.0400 (4) | −0.0049 (3) | 0.0038 (3) | −0.0064 (3) |
O1 | 0.0268 (11) | 0.0293 (9) | 0.0371 (10) | −0.0088 (8) | 0.0036 (8) | −0.0010 (8) |
O2 | 0.0372 (11) | 0.0284 (9) | 0.0322 (10) | −0.0041 (8) | 0.0025 (8) | −0.0113 (8) |
N1 | 0.0252 (12) | 0.0200 (10) | 0.0273 (11) | −0.0021 (9) | 0.0009 (9) | −0.0004 (8) |
C1 | 0.0360 (19) | 0.0483 (17) | 0.0541 (19) | −0.0024 (14) | 0.0104 (14) | 0.0018 (15) |
C2 | 0.0320 (16) | 0.0220 (12) | 0.0276 (13) | −0.0002 (11) | −0.0003 (11) | −0.0003 (10) |
C3 | 0.0292 (15) | 0.0272 (13) | 0.0260 (13) | 0.0017 (11) | −0.0011 (11) | −0.0019 (10) |
C4 | 0.0254 (15) | 0.0255 (13) | 0.0314 (14) | 0.0034 (11) | 0.0038 (11) | 0.0005 (11) |
C5 | 0.0275 (15) | 0.0199 (12) | 0.0247 (13) | −0.0006 (11) | −0.0034 (10) | 0.0039 (10) |
C6 | 0.0237 (14) | 0.0150 (11) | 0.0248 (13) | 0.0001 (10) | −0.0031 (10) | 0.0028 (9) |
C7 | 0.0226 (14) | 0.0152 (11) | 0.0214 (12) | −0.0006 (10) | −0.0037 (9) | 0.0028 (9) |
C8 | 0.0253 (14) | 0.0178 (11) | 0.0246 (13) | −0.0015 (10) | −0.0026 (10) | 0.0028 (9) |
C9 | 0.0284 (15) | 0.0211 (12) | 0.0246 (13) | 0.0008 (10) | −0.0021 (10) | 0.0034 (10) |
C10 | 0.0220 (14) | 0.0198 (12) | 0.0273 (13) | −0.0028 (10) | −0.0065 (10) | 0.0044 (10) |
C11 | 0.0302 (15) | 0.0177 (11) | 0.0236 (13) | −0.0019 (10) | −0.0045 (10) | −0.0018 (9) |
S1—C1 | 1.785 (3) | C3—H3B | 0.9900 |
S1—C2 | 1.803 (2) | C4—H4A | 0.9900 |
O1—C5 | 1.210 (3) | C4—H4B | 0.9900 |
O2—C9 | 1.221 (3) | C5—C6 | 1.479 (3) |
N1—C9 | 1.394 (3) | C6—C10 | 1.381 (3) |
N1—C5 | 1.404 (3) | C6—C7 | 1.408 (3) |
N1—C4 | 1.471 (3) | C7—C7i | 1.413 (4) |
C1—H1A | 0.9800 | C7—C8 | 1.415 (3) |
C1—H1B | 0.9800 | C8—C11 | 1.373 (3) |
C1—H1C | 0.9800 | C8—C9 | 1.478 (3) |
C2—C3 | 1.523 (3) | C10—C11i | 1.404 (3) |
C2—H2A | 0.9900 | C10—H10 | 0.9500 |
C2—H2B | 0.9900 | C11—C10i | 1.404 (3) |
C3—C4 | 1.521 (3) | C11—H11 | 0.9500 |
C3—H3A | 0.9900 | ||
C1—S1—C2 | 100.17 (12) | N1—C4—H4B | 108.9 |
C9—N1—C5 | 125.2 (2) | C3—C4—H4B | 108.9 |
C9—N1—C4 | 118.31 (19) | H4A—C4—H4B | 107.7 |
C5—N1—C4 | 116.52 (19) | O1—C5—N1 | 120.4 (2) |
S1—C1—H1A | 109.5 | O1—C5—C6 | 122.9 (2) |
S1—C1—H1B | 109.5 | N1—C5—C6 | 116.7 (2) |
H1A—C1—H1B | 109.5 | C10—C6—C7 | 120.5 (2) |
S1—C1—H1C | 109.5 | C10—C6—C5 | 119.5 (2) |
H1A—C1—H1C | 109.5 | C7—C6—C5 | 120.0 (2) |
H1B—C1—H1C | 109.5 | C6—C7—C7i | 119.5 (2) |
C3—C2—S1 | 110.75 (16) | C6—C7—C8 | 121.3 (2) |
C3—C2—H2A | 109.5 | C7i—C7—C8 | 119.3 (3) |
S1—C2—H2A | 109.5 | C11—C8—C7 | 120.0 (2) |
C3—C2—H2B | 109.5 | C11—C8—C9 | 120.4 (2) |
S1—C2—H2B | 109.5 | C7—C8—C9 | 119.6 (2) |
H2A—C2—H2B | 108.1 | O2—C9—N1 | 120.2 (2) |
C4—C3—C2 | 110.2 (2) | O2—C9—C8 | 122.6 (2) |
C4—C3—H3A | 109.6 | N1—C9—C8 | 117.2 (2) |
C2—C3—H3A | 109.6 | C6—C10—C11i | 119.7 (2) |
C4—C3—H3B | 109.6 | C6—C10—H10 | 120.1 |
C2—C3—H3B | 109.6 | C11i—C10—H10 | 120.1 |
H3A—C3—H3B | 108.1 | C8—C11—C10i | 121.1 (2) |
N1—C4—C3 | 113.37 (19) | C8—C11—H11 | 119.5 |
N1—C4—H4A | 108.9 | C10i—C11—H11 | 119.5 |
C3—C4—H4A | 108.9 | ||
C1—S1—C2—C3 | −163.99 (17) | C6—C7—C8—C11 | 179.8 (2) |
S1—C2—C3—C4 | 75.4 (2) | C7i—C7—C8—C11 | −0.3 (4) |
C9—N1—C4—C3 | −84.9 (2) | C6—C7—C8—C9 | −1.7 (3) |
C5—N1—C4—C3 | 94.0 (2) | C7i—C7—C8—C9 | 178.1 (2) |
C2—C3—C4—N1 | −167.95 (19) | C5—N1—C9—O2 | −178.5 (2) |
C9—N1—C5—O1 | 176.4 (2) | C4—N1—C9—O2 | 0.3 (3) |
C4—N1—C5—O1 | −2.5 (3) | C5—N1—C9—C8 | 2.2 (3) |
C9—N1—C5—C6 | −4.1 (3) | C4—N1—C9—C8 | −178.94 (19) |
C4—N1—C5—C6 | 177.07 (18) | C11—C8—C9—O2 | 0.0 (3) |
O1—C5—C6—C10 | 2.3 (3) | C7—C8—C9—O2 | −178.4 (2) |
N1—C5—C6—C10 | −177.28 (19) | C11—C8—C9—N1 | 179.24 (19) |
O1—C5—C6—C7 | −177.5 (2) | C7—C8—C9—N1 | 0.8 (3) |
N1—C5—C6—C7 | 3.0 (3) | C7—C6—C10—C11i | −0.4 (3) |
C10—C6—C7—C7i | 0.2 (4) | C5—C6—C10—C11i | 179.8 (2) |
C5—C6—C7—C7i | 179.9 (2) | C7—C8—C11—C10i | 0.5 (3) |
C10—C6—C7—C8 | −179.9 (2) | C9—C8—C11—C10i | −177.9 (2) |
C5—C6—C7—C8 | −0.2 (3) |
Symmetry code: (i) −x+2, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4A···S1 | 0.99 | 2.84 | 3.300 (2) | 109 |
C4—H4A···O1 | 0.99 | 2.32 | 2.688 (3) | 101 |
C10—H10···O1ii | 0.95 | 2.39 | 3.316 (3) | 164 |
C11—H11···S1iii | 0.95 | 2.86 | 3.779 (2) | 162 |
Symmetry codes: (ii) −x+1, −y, −z; (iii) x+1, y+1, z. |
Bond | X-ray | B3LYP (6-311++G**) |
O1—C5 | 1.210 (3) | 1.2158 |
O2—C9 | 1.221 (3) | 1.2173 |
N1—C4 | 1.471 (3) | 1.4779 |
N1—C5 | 1.404 (3) | 1.4047 |
N1—C9 | 1.394 (3) | 1.4029 |
S1—C1 | 1.785 (3) | 1.8244 |
S1—C2 | 1.803 (2) | 1.8399 |
C2—C3 | 1.523 (3) | 1.5301 |
C3—C4 | 1.521 (3) | 1.5341 |
C5—C6 | 1.479 (3) | 1.4880 |
C6—C7 | 1.408 (3) | 1.4135 |
C7—C8 | 1.415 (3) | 1.4136 |
C8—C9 | 1.478 (3) | 1.4877 |
C6—C10 | 1.381 (3) | 1.3835 |
C8—C11 | 1.373 (3) | 1.3835 |
Contact | Percentage contribution |
H···H | 44.2 |
H···O/O···H | 18.3 |
H···C/C···H | 14.4 |
H···S/S···H | 10.2 |
C···O/O···C | 5.6 |
C···C | 4.5 |
H···N/N···H | 1.4 |
O···O | 0.5 |
N···O/O···N | 0.4 |
C···S/S···C | 0.4 |
Acknowledgements
The authors thank Dr J.-E. Lee of the Central Research Facilities for her assistance with the NMR and XRD experiments.
Funding information
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (grant Nos. 2017M2B2A9A020049940 and 2018R1D1A3B07042615).
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