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ISSN: 2414-3146

Crystal structure of 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium bromide

CROSSMARK_Color_square_no_text.svg

aInstitute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
*Correspondence e-mail: eigner@fzu.cz

Edited by J. Simpson, University of Otago, New Zealand (Received 11 November 2020; accepted 13 November 2020; online 17 November 2020)

Herein we report the crystal structure of 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium bromide, C12H13N2S+·Br, which crystallizes in the monoclinic P21/c centrosymmetric space group. The asymmetric unit contains one 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium cation and one bromide anion. The methyl­ene carbon lies in plane of the naphthalene core. In comparison with reference structures, elongation of C—S bonds as well as tilting of the iso­thio­uronium group is observed. Given the ionic nature of the compound, the structure is held by charge-assisted N—H⋯Br hydrogen bonds, with a noteworthy contribution of dipole–dipole inter­actions, which form bilayers in the structure. The bilayers are held by the weak London forces.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Iso­thio­uronium salts have been investigated because of their ability to bind anions by charge-assisted hydrogen bonds (Yeo & Hong, 1998[Yeo, W. S. & Hong, J. I. (1998). Tetrahedron Lett. 39, 8137-8140.]; Seong et al., 2004[Seong, H. R., Kim, D. S., Kim, S. G., Choi, H. J. & Ahn, K. H. (2004). Tetrahedron Lett. 45, 723-727.]). Despite their potential in crystal engineering, only 23 crystal structures of 2-(aryl­meth­yl)iso­thio­uronium salts are present in the CSD (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]). In our studies of iso­thio­uronia, we have managed to synthesize and crystallize naphthalene-2-ylmethyl-bearing iso­thio­uronium bromide, and we report here its structure and a comparison with similar crystal structures.

The title compound crystallizes in the monoclinic P21/c centrosymmetric space group with one 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium cation and one bromide anion in the asymmetric unit, see Fig. 1[link]. The naphthalene core is almost perfectly planar, with a maximum deviation of 0.026 (3) Å for atom C6. The C11 atom can be considered to be in the plane of naphthalene core, with a deviation of 0.039 (3) Å from the mean plane. The single bonds around carbon C11 and S1 allow for the free rotation of the iso­thio­uronium group.

[Figure 1]
Figure 1
The title compound showing the numbering scheme with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.

There are no 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronia structures in the the CSD; therefore, we decided to compare the title compound with 2-benzyl­iso­thio­uronia structures. The published structures of 2-benzyl­iso­thio­uronia can be divided according to the Car—Cme—S—Cth torsion angle into linear and non-linear groups. Since the relevant torsion angle of the title compound is −68.1 (3)°, only the non-linear 2-benzyl­iso­thio­uronia, will be used as a reference group [CCDC codes EBIFOK (Ishii et al., 2000[Ishii, Y., Matsunaka, K. & Sakaguchi, S. (2000). J. Am. Chem. Soc. 122, 7390-7391.]), IGECIG (Raptopoulou et al., 2002[Raptopoulou, C. P., Terzis, A., Mousdis, G. A. & Papavassiliou, G. C. (2002). Z. Naturforsch. 57, 645-650.]), JALSOE (Mikolajczyk et al., 1989[Mikolajczyk, M., Lyzwa, P., Drabowicz, J., Wieczorek, M. & Bujacz, G. (1989). Angew. Chem. Int. Ed. Engl. 28, 97-98.]), SEFRUQ (Barker & Powell, 1998[Barker, J. & Powell, H. R. (1998). Acta Cryst. C54, 2019-2021.]), TAWVAP (Stergiou et al., 2005[Stergiou, D. V., Skoulika, S., Evmiridis, N. P. & Veltsistas, P. G. (2005). Chem. Mater. 17, 1307-1312.]), TOBNEE (Gayathri et al., 2008[Gayathri, D., Velmurugan, D., Hemalatha, P., Veeravazhuthi, V. & Ravikumar, K. (2008). Acta Cryst. E64, m848-m849.]) and YOCRUE (Fun et al., 2008[Fun, H.-K., Jebas, S. R., Razak, I. A., Deepak D'Silva, E., Patil, P. S. & Dharmaprakash, S. M. (2008). Acta Cryst. E64, o1195-o1196.])]. The C2—C11 bond length of 1.495 (5) Å in the title compound is within the usually observed values among the reference group, while the C11—S1 and S1—C12 bond lengths of 1.855 (3) Å and 1.771 (3) Å respectively are larger than usually observed, with average values of 1.819 Å and 1.739 Å. The C2—C11—S1 and C11—S1—C12 angles of 111.7 (2) and 96.98 (15)°, respectively, are less obtuse than the average values among the reference group, 115.21 and 103.91°. This deviation is most likely caused by the difference of electronic behaviour between the benzyl group and the 2-naphthyl­methyl unit.

The C11—S1 bond is almost perpendicular to the naphthalene core, with C1—C2—C11—S1 and C3—C2—C11—S1 torsion angle values of 91.8 (3) and −88.0 (3)°, respectively. Among the reference group, such a conformation is unusual, with average values being 61.45 and 120.53°. The iso­thio­uronium group is significantly tilted, with C11—S1—C12—N1 and C11—S1—C12—N2 torsion angles of −68.5 (3) and 110.7 (3)°, respectively. Such a tilt is not observed among the reference group, where the average values are 20.46 and 160.94°. The tilting of the group can be explained by the steric demands of the 2-naphthyl­methyl unit on the packing.

The N—H⋯Br charge-assisted hydrogen bonds (Table 1[link]) have the most significant impact on crystal structure of 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium bromide, with every iso­thio­uronium cation forming three hydrogen bonds, one of them bifurcated, with bromide anions. This is a major difference from the structure of 2-benzyl­iso­thio­uronium chloride (Barker & Powell, 1998[Barker, J. & Powell, H. R. (1998). Acta Cryst. C54, 2019-2021.]), the only structure of 2-aryl­methyl­iso­thio­uronium with simple halide anion, where the iso­thio­uronium group forms four charge-assisted hydrogen bonds with four different chloride anions. The charge-assisted hydrogen bonds form layers in the structure through five chains, N1—H1n1⋯Br1⋯H2n1iii—N1iii, and N2—H1n2⋯Br1ii⋯H2n2ii—N2ii classified as C12(4) and N1—H1n1⋯Br1⋯H1n2iv—N2iv—C12iv—N1iv, N1—H2n1⋯Br1i⋯H1n2v—N2v—C12v—N1v, and N1—H2n1⋯Br1i⋯H2n2i—N2i—C12i—N1i classified as C12(6) [symmetry codes: (i) x, y − 1, z; (ii) x, −y + [{3\over 2}], z − [{1\over 2}]; (iii) x, y + 1, z; (iv) x, −y + [{3\over 2}], z + [{1\over 2}]; (v) x, −y + [{1\over 2}], z + [{1\over 2}]], see Fig. 2[link]. The layers are connected by dipole–dipole inter­actions between C12 and Br1vi [symmetry code: (vi) −x, y − [{1\over 2}], −z + [{1\over 2}]] with a distance of 3.535 (4) Å into bilayers along the (100) plane, see Fig. 3[link]. The bilayers are held by weak London forces only.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1n1⋯Br1 0.86 (3) 2.54 (3) 3.332 (3) 153 (3)
N1—H2n1⋯Br1i 0.86 (2) 2.49 (2) 3.350 (3) 180 (3)
N2—H1n2⋯Br1ii 0.860 (19) 2.55 (3) 3.381 (3) 164 (4)
N2—H2n2⋯Br1 0.86 (3) 2.68 (3) 3.434 (3) 147 (3)
Symmetry codes: (i) [x, y-1, z]; (ii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].
[Figure 2]
Figure 2
The charge-assisted hydrogen bonds in the title compound. Hydrogen atoms not involved in hydrogen bonding are omitted for clarity. Symmetry codes: (i) x, y − 1, z; (ii) x, −y + [{3\over 2}], z − [{1\over 2}]; (iii) x, y + 1, z; (iv) x, −y + [{3\over 2}], z + [{1\over 2}]; (v) x, −y + [{1\over 2}], z + [{1\over 2}].
[Figure 3]
Figure 3
The bilayers formed in the title compound by charge-assisted hydrogen bonds, depicted in red, and dipole–dipole inter­actions, depicted in green. Hydrogen atoms not involved in hydrogen bonding are omitted for clarity.

Synthesis and crystallization

Thio­urea (0.23 g, 3 mmol) was dissolved in 25 ml of anhydrous aceto­nitrile. The solution was then treated with 2-(bromo­meth­yl)naphthalene (0.55 g, 2.5 mmol). The reaction mixture was stirred for 4 h at room temperature. The resulting white precipitate was filtered and washed with diethyl ether and left to dry at room temperature, resulting in yield 0.72 g (97%) of 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium bromide.

The 2-[(naphthalen-2-yl)meth­yl]iso­thio­uronium bromide (20 mg) was dissolved in 10 ml of methanol and left to slowly evaporate at room temperature. After 5 d, colorless platelets were collected.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C12H13N2S+·Br
Mr 297.2
Crystal system, space group Monoclinic, P21/c
Temperature (K) 120
a, b, c (Å) 16.2976 (8), 6.1294 (2), 12.2221 (6)
β (°) 99.070 (4)
V3) 1205.65 (9)
Z 4
Radiation type Cu Kα
μ (mm−1) 6.04
Crystal size (mm) 0.21 × 0.08 × 0.01
 
Data collection
Diffractometer Rigaku Oxford Diffraction Gemini ultra, AtlasS2
Absorption correction Analytical CrysAlis PRO (Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.])
Tmin, Tmax 0.522, 0.917
No. of measured, independent and observed [I > 3σ(I)] reflections 12512, 2162, 1699
Rint 0.057
(sin θ/λ)max−1) 0.598
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.081, 1.18
No. of reflections 2162
No. of parameters 157
No. of restraints 4
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.48, −0.36
Computer programs: CrysAlis PRO (Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]), SUPERFLIP (Palatinus & Chapuis, 2007[Palatinus, L. & Chapuis, G. (2007). J. Appl. Cryst. 40, 786-790.]), MCE (Rohlíček & Hušák, 2007[Rohlíček, J. & Hušák, M. (2007). J. Appl. Cryst. 40, 600-601.]), DIAMOND (Brandenburg & Putz, 1999[Brandenburg, K. & Putz, H. (1999). DIAMOND. Crystal Impact GbR, Bonn, Germany.]), JANA2006 (Petricek et al., 2014[Petricek, V., Dusek, M. & Palatinus, L. (2014). Z. Kristallogr. 229(5), 345-352.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2015); cell refinement: CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015); program(s) used to solve structure: Superflip (Palatinus & Chapuis, 2007), MCE (Rohlíček & Hušák, 2007); program(s) used to refine structure: Jana2006 (Petricek et al., 2014); molecular graphics: DIAMOND (Brandenburg & Putz, 1999); software used to prepare material for publication: Jana2006 (Petricek et al., 2014) and publCIF (Westrip, 2010).

2-[(Naphthalen-2-yl)methyl]isothiouronium bromide top
Crystal data top
C12H13N2S+·BrF(000) = 600
Mr = 297.2Dx = 1.637 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ycbCell parameters from 3162 reflections
a = 16.2976 (8) Åθ = 7.4–67.1°
b = 6.1294 (2) ŵ = 6.04 mm1
c = 12.2221 (6) ÅT = 120 K
β = 99.070 (4)°Platelet, colourless
V = 1205.65 (9) Å30.21 × 0.08 × 0.01 mm
Z = 4
Data collection top
Rigaku Oxford Diffraction Gemini ultra, AtlasS2
diffractometer
2162 independent reflections
Radiation source: X-ray tube1699 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.057
Detector resolution: 5.1783 pixels mm-1θmax = 67.2°, θmin = 5.5°
ω scansh = 1918
Absorption correction: analytical
CrysAlisPro (Rigaku OD, 2015)
k = 76
Tmin = 0.522, Tmax = 0.917l = 1413
12512 measured reflections
Refinement top
Refinement on F240 constraints
R[F2 > 2σ(F2)] = 0.030H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.081Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
S = 1.18(Δ/σ)max = 0.017
2162 reflectionsΔρmax = 0.48 e Å3
157 parametersΔρmin = 0.36 e Å3
4 restraints
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.12634 (2)0.79627 (6)0.40347 (3)0.02124 (12)
S10.09471 (5)0.11747 (14)0.09911 (6)0.0181 (2)
N10.09225 (19)0.2979 (5)0.2973 (2)0.0222 (9)
N20.08363 (19)0.5365 (5)0.1520 (2)0.0221 (9)
C10.2898 (2)0.3770 (6)0.1961 (3)0.0188 (10)
C20.2633 (2)0.2128 (6)0.1229 (3)0.0193 (10)
C30.2926 (2)0.2072 (6)0.0196 (3)0.0211 (10)
C40.3465 (2)0.3612 (6)0.0066 (3)0.0224 (11)
C50.4332 (2)0.6914 (6)0.0454 (3)0.0222 (10)
C60.4595 (2)0.8519 (6)0.1203 (3)0.0252 (11)
C70.4283 (2)0.8638 (6)0.2208 (3)0.0245 (11)
C80.3725 (2)0.7122 (6)0.2466 (3)0.0222 (10)
C90.3453 (2)0.5398 (6)0.1715 (3)0.0192 (10)
C100.3751 (2)0.5322 (6)0.0686 (3)0.0198 (10)
C110.2043 (2)0.0410 (6)0.1493 (3)0.0208 (10)
C120.0894 (2)0.3369 (5)0.1920 (3)0.0177 (10)
H1c10.2700010.381330.2660450.0226*
H1c30.274260.0933620.0324660.0253*
H1c40.3655630.3543850.0769390.0269*
H1c50.454250.6863120.0236280.0266*
H1c60.4996140.9570740.1041510.0302*
H1c70.446160.9794550.2720540.0294*
H1c80.3516460.7222930.3157010.0267*
H1c110.2118920.0181250.2279290.0249*
H2c110.2166230.094480.1159860.0249*
H1n10.096 (3)0.403 (5)0.344 (3)0.0267*
H2n10.101 (3)0.169 (3)0.324 (3)0.0267*
H1n20.091 (3)0.552 (7)0.0843 (11)0.0266*
H2n20.086 (3)0.646 (4)0.196 (3)0.0266*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0348 (2)0.01257 (19)0.01671 (19)0.00035 (15)0.00505 (13)0.00032 (13)
S10.0234 (4)0.0138 (4)0.0174 (4)0.0010 (3)0.0041 (3)0.0024 (3)
N10.0367 (16)0.0108 (14)0.0198 (15)0.0000 (13)0.0066 (12)0.0011 (12)
N20.0337 (16)0.0142 (15)0.0193 (14)0.0026 (12)0.0068 (12)0.0022 (11)
C10.0220 (16)0.0188 (17)0.0164 (16)0.0038 (14)0.0056 (12)0.0012 (13)
C20.0202 (16)0.0183 (17)0.0191 (16)0.0011 (14)0.0023 (12)0.0005 (14)
C30.0262 (17)0.0185 (17)0.0184 (16)0.0016 (14)0.0026 (13)0.0028 (14)
C40.0249 (17)0.025 (2)0.0180 (16)0.0020 (14)0.0058 (13)0.0025 (13)
C50.0228 (17)0.0234 (19)0.0205 (17)0.0008 (15)0.0040 (13)0.0018 (14)
C60.0248 (17)0.023 (2)0.0274 (18)0.0030 (14)0.0024 (14)0.0036 (14)
C70.0276 (18)0.0184 (18)0.0262 (18)0.0023 (14)0.0001 (14)0.0011 (14)
C80.0227 (17)0.0231 (19)0.0207 (17)0.0005 (14)0.0029 (13)0.0045 (14)
C90.0176 (16)0.0199 (18)0.0192 (16)0.0035 (13)0.0001 (12)0.0013 (13)
C100.0216 (16)0.0179 (18)0.0195 (16)0.0006 (14)0.0017 (13)0.0019 (13)
C110.0270 (18)0.0173 (18)0.0183 (16)0.0041 (14)0.0043 (13)0.0026 (13)
C120.0190 (16)0.0127 (18)0.0228 (16)0.0014 (12)0.0077 (12)0.0003 (12)
Geometric parameters (Å, º) top
S1—C111.855 (3)C4—C101.423 (5)
S1—C121.771 (3)C4—H1c40.96
N1—C121.302 (4)C5—C61.366 (5)
N1—H1n10.86 (3)C5—C101.419 (5)
N1—H2n10.86 (2)C5—H1c50.96
N2—C121.316 (4)C6—C71.404 (5)
N2—H1n20.860 (19)C6—H1c60.96
N2—H2n20.86 (3)C7—C81.372 (5)
C1—C21.370 (5)C7—H1c70.96
C1—C91.411 (5)C8—C91.424 (5)
C1—H1c10.96C8—H1c80.96
C2—C31.419 (5)C9—C101.419 (5)
C2—C111.495 (5)C11—H1c110.96
C3—C41.361 (5)C11—H2c110.96
C3—H1c30.96
C11—S1—C1296.98 (15)C5—C6—H1c6119.84
C12—N1—H1n1121 (2)C7—C6—H1c6119.84
C12—N1—H2n1122 (3)C6—C7—C8120.7 (3)
H1n1—N1—H2n1117 (3)C6—C7—H1c7119.63
C12—N2—H1n2117 (3)C8—C7—H1c7119.63
C12—N2—H2n2120 (2)C7—C8—C9120.3 (3)
H1n2—N2—H2n2121 (4)C7—C8—H1c8119.84
C2—C1—C9121.8 (3)C9—C8—H1c8119.84
C2—C1—H1c1119.12C1—C9—C8122.1 (3)
C9—C1—H1c1119.12C1—C9—C10119.1 (3)
C1—C2—C3118.9 (3)C8—C9—C10118.7 (3)
C1—C2—C11121.5 (3)C4—C10—C5122.6 (3)
C3—C2—C11119.5 (3)C4—C10—C9118.3 (3)
C2—C3—C4120.8 (3)C5—C10—C9119.2 (3)
C2—C3—H1c3119.59S1—C11—C2111.7 (2)
C4—C3—H1c3119.58S1—C11—H1c11109.47
C3—C4—C10121.1 (3)S1—C11—H2c11109.47
C3—C4—H1c4119.45C2—C11—H1c11109.47
C10—C4—H1c4119.45C2—C11—H2c11109.47
C6—C5—C10120.7 (3)H1c11—C11—H2c11107.17
C6—C5—H1c5119.66S1—C12—N1119.8 (3)
C10—C5—H1c5119.66S1—C12—N2118.4 (3)
C5—C6—C7120.3 (3)N1—C12—N2121.8 (3)
C9—C1—C2—C30.0 (2)C7—C8—C9—C101.8 (5)
C9—C1—C2—C11179.8 (3)C8—C9—C1—C2179.4 (3)
C1—C2—C3—C40.3 (5)C10—C9—C1—C20.6 (5)
C11—C2—C3—C4179.9 (3)C4—C10—C9—C11.0 (5)
C2—C3—C4—C100.0 (3)C4—C10—C9—C8179.0 (3)
C3—C4—C10—C5178.0 (3)C5—C10—C9—C1177.8 (3)
C3—C4—C10—C90.7 (5)C5—C10—C9—C82.2 (5)
C4—C10—C5—C6179.5 (3)C1—C2—C11—S191.8 (3)
C9—C10—C5—C60.8 (5)C3—C2—C11—S188.0 (3)
C10—C5—C6—C71.1 (5)C2—C11—S1—C1268.1 (3)
C5—C6—C7—C81.5 (5)C11—S1—C12—N168.5 (3)
C6—C7—C8—C90.0 (3)C11—S1—C12—N2110.7 (3)
C7—C8—C9—C1178.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1n1···Br10.86 (3)2.54 (3)3.332 (3)153 (3)
N1—H2n1···Br1i0.86 (2)2.49 (2)3.350 (3)180 (3)
N2—H1n2···Br1ii0.860 (19)2.55 (3)3.381 (3)164 (4)
N2—H2n2···Br10.86 (3)2.68 (3)3.434 (3)147 (3)
Symmetry codes: (i) x, y1, z; (ii) x, y+3/2, z1/2.
 

Funding information

This research was supported by project LO1603 under the Ministry of Education, Youth and Sports National Sustainability Programme I of the Czech Republic..

References

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