1-(Hex-5-en-1-yl)-4-{[3-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidene]methyl}quinolin-1-ium iodide monohydrate

The structure of 4-hexenyl thiazole orange is presented.


Structure description
Intercalating dyes are a standard means to detect duplex DNA or RNA in vitro and in vivo. The cyanine dye thiazole orange has been used extensively as a on/off fluorescent probe in a host of biological applications (Suss et al., 2021). The bis-intercalating dye based on thiazole orange has been shown to have an increased affinity towards duplexed oligomers and retains its fluorogenic characteristic (Rye et al., 1992). In an effort to enhance the binding affinity further, and essentially create a non-covalent interaction that is effectively permanent, we synthesized a thiazole orange dye bearing an alkene substituent that is capable of participating in polymerization reactions. Access to polymeric thiazole orange dye and other cyanine dyes will afford extremely bright, highly organized, and versatile fluorescent probes that can be attached to molecules of interest and mitigate the equilibrium the dye would establish with endogenous duplexes.
Herein we report the crystal structure of 4-hexenyl thiazole orange iodide monohydrate, C 24 H 25 N 2 S + ÁI À ÁH 2 O, which crystallizes in the triclinic space group P1. In the cation (Fig. 1), the benzothiazole ring is titled by 3.32 (13) with respect to the quinoline ring system: as a result the molecule is close to planar (excluding the hex-1-ene group) data reports with an r.m.s. deviation of 0.048 Å for the non-hydrogen atoms; including the hex-1-ene group increases the r.m.s.d to 0.416 Å for the non-hydrogen atoms. The crystal structure contains a water molecule of crystallization bound to the cation via a weak O1-H1AÁ Á ÁN1 hydrogen bond [OÁ Á ÁN = 3.014 (10) Å ] and the anion via an O1-H1BÁ Á ÁI1 link [O1Á Á ÁI1 = 3.546 (10) Å ] (Table 1). There is also a weak C2-H2Á Á ÁS1 intramolecular interaction with CÁ Á ÁS = 3.128 (7) that helps to maintain the coplanarity of the two ring systems.
In the extended structure ( Fig. 2), aromaticstacking is observed with Cg1Á Á ÁCg2 i = 3.559 (6) Å [symmetry code: (i) 2 À x, 2 À y, 1 À z] and Cg1Á Á ÁCg3 i = 3.492 (5) Å , where Cg1 is the centroid of the phenyl ring of the benzothiazole group containing atoms C18-C23, Cg2 is the centroid of the phenyl ring of the quinoline group containing atoms C4-C9, and Cg3 is the centroid of the pyridyl ring of the quinoline groups containing atoms N1/C1-C4/C9. These -stacking interactions run along the [100] direction with neighboring layers held together with van der Waals interactions.

Synthesis and crystallization
All materials were purchased from Fisher Scientific or Sigma Aldrich and used as received. All flash chromatography was performed with 230 Â 400 mesh silica gel. Pure samples were analyzed with a Joel 300 MHz NMR and HRMS of the title compound was acquired on a Shimadzu LCMS 9030 QTof operating in positive mode. The reaction scheme is shown in Fig. 3.

Figure 2
Crystal packing diagram of the title compound viewed down the b-axis direction with H atoms omitted for clarity. Table 1 Hydrogen-bond geometry (Å , ).

D-HÁ
Into a conical reaction vial with a magnetic stir bar was added 106 mg (0.3 mmol, 1 eqv) of 2 that was dissolved in 2 ml of DMF. A total of 97 mg (0.3 mmol, 1 eqv) of 3 was added followed by the addition of 42 mg (0.3 mmol, 1 equiv.) of triethylamine. The solution immediately turned dark red and was allowed to stir for 48 h.
The solution was then added to ether, and the orange solid was collected.
The title compound was then purified using a gradient (2-5%) of methanol in DCM. Yield 45 mg (30% Crystal formation: the title compound was taken up in methanol and then allowed to crystallize as dark-red prisms by slow evaporation of the solvent.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2.

quinolin-1-ium iodide monohydrate
Nathaniel Shank, Andrea L. Stadler, Sean P. Barrett and Clifford W. Padgett  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. Refinement. All H atoms were placed in idealized locations (C-H = 0.93-0.97, O-H = 0.85 Å) and refined as riding atoms.