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Logo of actae2this articlesearchopen accesssubmitActa Crystallographica Section E: Crystallographic CommunicationsActa Crystallographica Section E: Crystallographic Communications
 
Acta Crystallogr E Crystallogr Commun. 2017 July 1; 73(Pt 8): 1180–1183.
Published online 2017 July 17. doi:  10.1107/S2056989017010271
PMCID: PMC5598844

Crystal structure and DFT study of 2-(pyren-1-yl)-1H-benzimidazole

Abstract

In the title compound, C23H14N2, (I), the dihedral angle between the mean planes of the pyrene and benzimidazole ring systems is 42.08 (5)°, with a bridging C—C bond length of 1.463 (3) Å. In the crystal, mol­ecules are linked by N—H(...)N hydrogen bonds, forming columns propagating along the b-axis direction. The columns are linked via C—H(...)π inter­actions, forming slabs parallel to the ab plane. There are no significant π–π inter­actions present in the crystal structure. The density functional theory (DFT) optimized structure, at the B3LYP/ 6-311G(d,p) level, is compared with the experimentally determined solid-state structure of the title compound.

Keywords: crystal structure, pyrene-1-carbaldehyde, o-phenyl­enedi­amine, benzimidazole, N—H(...)N hydrogen bonding, C—H(...)π inter­actions, DFT

Chemical context  

Benzimidazoles, which are analogues of imidazole contained in histidine, are an important class of biologically active compounds (Collman et al., 1973  ). In addition, they are excellent organic ligands of many metal ions (Sundberg & Martin, 1974  ). The pyrene unit is one of the most commonly used fluoro­phores due to its strong luminescence and chemical stability (Aoki et al., 1991  ; Nishizawa et al., 1999  ; van der Veen et al., 2000  ). Another inter­esting feature of the pyrene unit is the inter­action between the pyrene aromatic rings in the crystal packing, which can permit the formation of highly ordered mol­ecular aggregates in the solid state by architecturally controlled self-assembly (Desiraju & Gavezzotti, 1989  ; Munakata et al., 1994  ). Pyrene is a commonly used fluoro­phore due to its unusual fluorescence properties, viz. intense fluorescence signals and vibronic band dependence with the media (Karpovich & Blanchard, 1995  ), and has been used in fluorescence sensors (Bell & Hext, 2004  ) and excimer formation (Lodeiro et al., 2006  ). As a result of these particular properties and because of its chemical stability, it is also employed as a probe for solid-state studies and polymer association (Seixas de Melo et al., 2003  ).

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The title compound was prepared from an equimolar mixuture of 1:1 o-phenyl­enedi­amine and pyrene-1-carbaldehyde. Synthesis and characterization of many benzimidazole-ring-containing compounds have been reported (Yan et al., 2009  ; Hallett et al., 2012  ; Xia et al., 2014  ; Dhanalakshmi et al., 2014  ; Guo et al., 2015  ; Song et al., 2010  ), but very few compounds have been structurally characterized. Previously, Zhao et al. (2016  ) reported on the synthesis of 2-(pyren-1-yl)benzimidazole, used as a fluorescent probe for the detection of iron(III) ions in aqueous solution, but gave no structural details of the compound. The present work is part of an ongoing structural study of pyrene-ring-system derivatives (Faizi & Prisyazhnaya, 2015  ). The results of the calculations by density functional theory (DFT) on (I), carried out at the B3LYP/6-311G(d,p) level, are compared with the experimentally determined mol­ecular structure in the solid state.

Structural commentary  

The mol­ecular structure of the title compound, (I), is illustrated in Fig. 1  . The compound is nonplanar, the rotation around the bond connecting the two aromatic moieties, which is predominantly σ in character [C16—C17 = 1.463 (3) Å], being described by the torsion angle N1—C17—C16—C1 of −39.49 (10)°. The mean planes of the pyrene (atoms C1–C16; r.m.s. deviation = 0.038 Å) and benzimidazole (N1/N2/C17–C23) ring systems are inclined to one another by 42.08 (5)°, reflecting the significant deviation from overall mol­ecular planarity.

Figure 1
The mol­ecular structure of compound (I), with the atom labelling. Displacement ellipsoids are drawn at the 40% probability level.

Supra­molecular features  

In the crystal of (I), mol­ecules are assembled via N2—H(...)N1i hydrogen bonds (Table 1  ) into columns propagating along the b-axis direction (Fig. 2  ). The columns are linked by C—H(...)π inter­actions (Table 1  ), forming slabs parallel to the ab plane (Fig. 3  ).

Figure 2
A view of the N—H(...)N hydrogen-bonded column (dashed lines; Table 1  ) in the crystal of compound (I), propagating along the b-axis direction.
Figure 3
A view along the b axis of the crystal packing of compound (I). The C—H(...)π inter­actions are illustrated by dashed lines (Table 1  ).
Table 1
Hydrogen-bond geometry (Å, °)

Database survey  

A search of the Cambridge Structural Database (CSD, Version 5.38, last update May 2017; Groom et al., 2016  ) gave a number of hits for similar compounds, viz. phenyl-2-benzimidazole derivatives (II) (CSD refcode FOBZUS; Li et al., 2005  ) and (III) (LIYTIW; Bei et al., 2000  ), and phenanthro­imidazole derivatives (IV) (ERODOE; Bu et al., 2003  ) and (V) (SUZHIE; Krebs et al., 2001  ). All four organic compounds are nonplanar and have a similar C—C bond length between the aromatic ring systems. In (I), this bond (C16—C17) is 1.463 (3) Å, and the two ring systems are inclined to one another by 42.08 (5)°. These values are close to those reported for compounds (II) (1.474 Å and 40.17°), (III) (1.467 Å and 31.12°) and (V) (1.436 and 30.12°), but the anthracene–phenanthro­imidazole compound (IV) has a larger deviation from planarity, with the two aromatic ring systems being almost perpendicular to one another (1.488 Å and 76.54°) due to significant steric hindrance of the anthracene moiety. Two other compounds are worth mentioning, viz. 9-(1H-benzimidazol-2-yl)-2,3,6,7-tetra­hydro-1H,5H-pyrido[3,2,1-ij]quinoline (VI) (TAQHUR; Gonzalez & Unnamatla, 2017  ) and 2-(pyren-1-yl)-1H-phenanthro[9,10-d]imidazole unknown solvate (VII) (KUFLOO; Subeesh et al., 2015  ). In (VI), the mean plane of the pyrido­quinoline moiety is inclined to the benzimidole ring system by 37.94 (10)° and the bridging C—C bond is 1.467 (3) Å, similar to the situation in (I). In (VII), the mean plane of the pyrene ring system is inclined to the phenanthro­imidazole mean plane by 63.37 (6)° and the bridging C—C bond is 1.463 (5) Å. As in (IV), this large dihedral angle is due to steric hinderance.

DFT study  

The DFT quantum-chemical calculations were performed at the B3LYP/6-311G(d,p) level (Becke, 1993  ), as implemented in GAUSSIAN09 (Frisch et al., 2009  ). DFT structure optimization of (I) was performed starting from the X-ray geometry and the values compared with experimental values (see Table 2  ). From these results we can conclude that basis set 6-311G(d,p) is well suited in its approach to the experimental data.

Table 2
Comparison of selected geometric data for (I) (Å, °) from X-ray and calculated (DFT) data

The DFT study of (I) shows that the HOMO and LUMO are localized in the plane extending from the whole pyrene ring to the benzimidazole ring. The electron distribution of the HOMO-1, HOMO, LUMO and the LUMO+1 energy levels are shown in Fig. 4  . The mol­ecular orbital of HOMO contains both σ and π character, whereas HOMO-1 is dominated by orbital density. The LUMO is mainly composed of density, while LUMO+1 has both σ and π character and electronic density. The HOMO–LUMO gap was found to be 0.273 a.u. and the frontier mol­ecular orbital energies, E HOMO and E LUMO, were −0.20083 and −0.07230 a.u., respectively.

Figure 4
Electron distribution of the HOMO-1, HOMO, LUMO and LUMO+1 energy levels for compound (I).

Synthesis and crystallization  

Pyrene-1-carbaldehyde (0.2306 g, 1.0 mmol) was added to a 50 ml round-bottomed flask containing 10 ml of CH2Cl2. Then a 10 ml CH2Cl2 solution containing 0.1080 g (1.0 mmol) o-phenyl­enedi­amine was added dropwise over a period of 30 min with stirring. The mixture was stirred at room temperature for 48 h. The solvent was then evaporated and the residue purified by aluminium oxide gel-column chromatography using CH2Cl2 as the eluent to obtain a pale-yellow powder of (I) (yield 0.2311 g, 72.6%). Colourless prismatic crystals were obtained by slow evaporation of a solution of (I) from methanol.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 3  . The N-bound H atoms were located in a difference Fourier map and refined with U iso(H) = 1.2U eq(N). The C-bound H atoms were included in calculated positions and refined as riding, with C—H = 0.93–0.96 Å and U iso(H) = 1.2U eq(C).

Table 3
Experimental details

Supplementary Material

Crystal structure: contains datablock(s) I, Global. DOI: 10.1107/S2056989017010271/su5378sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017010271/su5378Isup2.hkl

CCDC reference: 1547858

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors are grateful to the Ondokuz Mayıs University, Arts and Sciences Faculty, Department of Physics, Samsun, Turkey, for X-ray data collection and the Department of Chemistry, National Taras Shevchenko University of Kiev, Kyiv, Ukraine.

supplementary crystallographic information

Crystal data

C23H14N2Dx = 1.386 Mg m3
Mr = 318.36Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 1528 reflections
a = 8.7344 (8) Åθ = 2.4–16.1°
b = 9.5967 (9) ŵ = 0.08 mm1
c = 36.410 (3) ÅT = 273 K
V = 3052.0 (5) Å3Prism, colorless
Z = 80.65 × 0.43 × 0.32 mm
F(000) = 1328

Data collection

Bruker APEXII CCD area detector diffractometer1951 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.103
Graphite monochromatorθmax = 26.0°, θmin = 2.6°
phi and ω scansh = −10→10
36046 measured reflectionsk = −11→11
2986 independent reflectionsl = −44→44

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0467P)2 + 1.2809P] where P = (Fo2 + 2Fc2)/3
2986 reflections(Δ/σ)max < 0.001
230 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = −0.26 e Å3

Special details

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)

xyzUiso*/Ueq
N10.15929 (18)0.66443 (16)0.32741 (4)0.0190 (4)
N20.21591 (19)0.89171 (17)0.32393 (5)0.0195 (4)
C230.0470 (2)0.73209 (19)0.30713 (5)0.0176 (5)
C170.2581 (2)0.7637 (2)0.33673 (5)0.0190 (5)
C160.4042 (2)0.74213 (19)0.35556 (5)0.0195 (5)
C180.0808 (2)0.8748 (2)0.30499 (5)0.0179 (4)
C10.4229 (2)0.6448 (2)0.38432 (5)0.0193 (5)
C120.5724 (2)0.6212 (2)0.39850 (5)0.0199 (5)
C110.6999 (2)0.6952 (2)0.38411 (5)0.0210 (5)
C19−0.0099 (2)0.9680 (2)0.28557 (5)0.0214 (5)
H190.0121571.0628110.2849370.026*
C20−0.1341 (2)0.9132 (2)0.26728 (5)0.0235 (5)
H20−0.1954760.9718870.2532750.028*
C130.5956 (2)0.5241 (2)0.42759 (5)0.0220 (5)
C20.2978 (2)0.5706 (2)0.40072 (6)0.0235 (5)
H20.1989430.5858750.3921520.028*
C80.7452 (2)0.4990 (2)0.44151 (5)0.0252 (5)
C140.6749 (2)0.7950 (2)0.35696 (6)0.0239 (5)
H140.7567690.8472630.3481920.029*
C40.4691 (2)0.4519 (2)0.44303 (6)0.0253 (5)
C150.5309 (2)0.8170 (2)0.34299 (6)0.0231 (5)
H150.5173650.8835320.3247010.028*
C22−0.0814 (2)0.6796 (2)0.28931 (5)0.0224 (5)
H22−0.1066570.5856270.2908630.027*
C21−0.1703 (2)0.7709 (2)0.26926 (5)0.0247 (5)
H21−0.2557420.7375910.2568260.030*
C100.8497 (2)0.6653 (2)0.39798 (6)0.0273 (5)
H100.9338990.7112580.3881200.033*
C90.8707 (2)0.5716 (2)0.42512 (6)0.0292 (5)
H90.9694830.5536700.4333850.035*
C30.3207 (2)0.4788 (2)0.42841 (6)0.0271 (5)
H30.2369390.4318240.4381850.033*
C70.7635 (3)0.4060 (2)0.47055 (6)0.0311 (6)
H70.8609610.3891930.4797950.037*
C50.4941 (3)0.3609 (2)0.47218 (6)0.0318 (6)
H50.4115500.3143830.4826430.038*
C60.6397 (3)0.3386 (2)0.48582 (6)0.0357 (6)
H60.6541090.2777460.5054010.043*
H1A0.271 (2)0.975 (2)0.3280 (6)0.033 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0191 (9)0.0153 (9)0.0225 (9)0.0003 (7)−0.0016 (8)0.0003 (8)
N20.0203 (10)0.0129 (9)0.0253 (9)−0.0010 (8)−0.0014 (8)0.0010 (7)
C230.0207 (11)0.0152 (10)0.0170 (10)0.0012 (8)0.0014 (9)0.0013 (8)
C170.0198 (11)0.0168 (11)0.0205 (10)0.0007 (9)0.0039 (10)0.0006 (8)
C160.0200 (11)0.0158 (10)0.0227 (11)0.0009 (9)0.0000 (10)−0.0016 (8)
C180.0177 (11)0.0180 (10)0.0181 (10)0.0013 (8)0.0016 (9)−0.0006 (8)
C10.0201 (11)0.0167 (11)0.0210 (11)0.0009 (9)0.0014 (9)−0.0029 (9)
C120.0208 (11)0.0187 (11)0.0202 (10)0.0009 (9)0.0008 (9)−0.0029 (9)
C110.0201 (11)0.0205 (11)0.0224 (11)0.0009 (9)0.0002 (9)−0.0035 (9)
C190.0258 (12)0.0151 (10)0.0234 (11)0.0019 (9)0.0021 (10)0.0015 (9)
C200.0254 (12)0.0232 (12)0.0221 (11)0.0076 (9)−0.0011 (10)0.0011 (9)
C130.0228 (12)0.0220 (11)0.0213 (11)0.0038 (9)−0.0002 (10)−0.0012 (9)
C20.0200 (12)0.0235 (11)0.0270 (12)0.0024 (9)−0.0002 (10)0.0027 (10)
C80.0246 (12)0.0265 (12)0.0246 (11)0.0052 (9)−0.0009 (10)0.0005 (9)
C140.0212 (12)0.0218 (11)0.0288 (12)−0.0035 (9)0.0036 (10)0.0010 (9)
C40.0260 (12)0.0237 (12)0.0263 (12)0.0027 (10)0.0006 (10)0.0027 (9)
C150.0260 (12)0.0174 (11)0.0259 (11)0.0005 (9)−0.0005 (10)0.0036 (9)
C220.0253 (12)0.0154 (11)0.0267 (11)−0.0014 (9)−0.0005 (10)−0.0022 (9)
C210.0240 (12)0.0246 (12)0.0256 (12)0.0009 (9)−0.0043 (10)−0.0032 (9)
C100.0208 (12)0.0316 (13)0.0296 (12)−0.0013 (10)0.0027 (10)0.0018 (10)
C90.0183 (12)0.0361 (14)0.0333 (13)0.0056 (10)−0.0041 (10)−0.0008 (11)
C30.0209 (12)0.0287 (12)0.0317 (12)−0.0023 (10)0.0046 (10)0.0075 (10)
C70.0259 (13)0.0351 (13)0.0325 (12)0.0066 (10)−0.0054 (11)0.0050 (10)
C50.0289 (13)0.0341 (14)0.0326 (13)0.0015 (11)0.0033 (11)0.0102 (10)
C60.0367 (14)0.0382 (14)0.0322 (13)0.0097 (11)−0.0022 (12)0.0143 (11)

Geometric parameters (Å, º)

N1—C171.330 (2)C13—C81.423 (3)
N1—C231.389 (2)C2—C31.354 (3)
N2—C171.364 (2)C2—H20.9300
N2—C181.376 (2)C8—C71.392 (3)
N2—H1A0.94 (2)C8—C91.429 (3)
C23—C221.390 (3)C14—C151.373 (3)
C23—C181.403 (3)C14—H140.9300
C17—C161.463 (3)C4—C51.391 (3)
C16—C151.397 (3)C4—C31.425 (3)
C16—C11.412 (3)C15—H150.9300
C18—C191.389 (3)C22—C211.380 (3)
C1—C121.422 (3)C22—H220.9300
C1—C21.434 (3)C21—H210.9300
C12—C111.421 (3)C10—C91.349 (3)
C12—C131.426 (3)C10—H100.9300
C11—C141.393 (3)C9—H90.9300
C11—C101.431 (3)C3—H30.9300
C19—C201.377 (3)C7—C61.378 (3)
C19—H190.9300C7—H70.9300
C20—C211.403 (3)C5—C61.381 (3)
C20—H200.9300C5—H50.9300
C13—C41.420 (3)C6—H60.9300
C17—N1—C23105.01 (16)C7—C8—C13118.9 (2)
C17—N2—C18107.25 (16)C7—C8—C9122.8 (2)
C17—N2—H1A124.7 (13)C13—C8—C9118.26 (18)
C18—N2—H1A128.1 (13)C15—C14—C11120.81 (19)
N1—C23—C22130.42 (18)C15—C14—H14119.6
N1—C23—C18109.72 (17)C11—C14—H14119.6
C22—C23—C18119.84 (18)C5—C4—C13119.1 (2)
N1—C17—N2112.48 (17)C5—C4—C3122.8 (2)
N1—C17—C16125.73 (17)C13—C4—C3118.12 (18)
N2—C17—C16121.57 (17)C14—C15—C16121.67 (19)
C15—C16—C1119.46 (18)C14—C15—H15119.2
C15—C16—C17117.66 (17)C16—C15—H15119.2
C1—C16—C17122.80 (18)C21—C22—C23118.06 (19)
N2—C18—C19131.90 (18)C21—C22—H22121.0
N2—C18—C23105.54 (16)C23—C22—H22121.0
C19—C18—C23122.51 (18)C22—C21—C20121.24 (19)
C16—C1—C12118.71 (18)C22—C21—H21119.4
C16—C1—C2123.31 (19)C20—C21—H21119.4
C12—C1—C2117.96 (18)C9—C10—C11121.1 (2)
C11—C12—C1120.40 (18)C9—C10—H10119.4
C11—C12—C13119.29 (18)C11—C10—H10119.4
C1—C12—C13120.30 (18)C10—C9—C8121.8 (2)
C14—C11—C12118.83 (18)C10—C9—H9119.1
C14—C11—C10122.10 (19)C8—C9—H9119.1
C12—C11—C10119.07 (18)C2—C3—C4122.0 (2)
C20—C19—C18116.68 (19)C2—C3—H3119.0
C20—C19—H19121.7C4—C3—H3119.0
C18—C19—H19121.7C6—C7—C8121.2 (2)
C19—C20—C21121.62 (19)C6—C7—H7119.4
C19—C20—H20119.2C8—C7—H7119.4
C21—C20—H20119.2C6—C5—C4121.1 (2)
C4—C13—C8119.43 (18)C6—C5—H5119.5
C4—C13—C12120.17 (18)C4—C5—H5119.5
C8—C13—C12120.40 (19)C7—C6—C5120.3 (2)
C3—C2—C1121.41 (19)C7—C6—H6119.9
C3—C2—H2119.3C5—C6—H6119.9
C1—C2—H2119.3

Hydrogen-bond geometry (Å, º)

Cg1, Cg6 and Cg7 are the centroids of rings N1/N2/C17/C18/C23, C18-C23 and N1/N2/C17-C23.

D—H···AD—HH···AD···AD—H···A
N2—H1A···N1i0.94 (2)1.92 (2)2.838 (2)164 (2)
C14—H14···Cg6ii0.932.833.537 (2)134
C21—H21···Cg1iii0.932.953.605 (2)129
C21—H21···Cg7iii0.932.843.618 (2)142

Symmetry codes: (i) −x+1/2, y+1/2, z; (ii) x+1, y, z; (iii) x−1/2, y, −z+1/2.

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