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

Eigner, V.

doi:10.1107/S2414314620015114

organic compounds

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ISSN: 2414-3146

Volume 5| Part 11| November 2020| x201511

https://doi.org/10.1107/S2414314620015114

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

Václav Eigner ^a ^*

^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.

Keywords: crystal structure; isothiouronium salt; hydrogen bonds; dipole–dipole interactions.

CCDC reference: 2044275

Structure description

Isothiouronium salts have been investigated because of their ability to bind anions by charge-assisted hydrogen bonds (Yeo & Hong, 1998 ; Seong et al., 2004 ). Despite their potential in crystal engineering, only 23 crystal structures of 2-(arylmethyl)isothiouronium salts are present in the CSD (Groom et al., 2016 ). 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. 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
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 C_ar—C_me—S—C_th 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 ), IGECIG (Raptopoulou et al., 2002 ), JALSOE (Mikolajczyk et al., 1989 ), SEFRUQ (Barker & Powell, 1998 ), TAWVAP (Stergiou et al., 2005 ), TOBNEE (Gayathri et al., 2008 ) and YOCRUE (Fun et al., 2008 )]. 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) 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), 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⋯H1n2^iv—N2^iv—C12^iv—N1^iv, N1—H2n1⋯Br1ⁱ⋯H1n2^v—N2^v—C12^v—N1^v, 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. The layers are connected by dipole–dipole interactions between C12 and Br1^vi [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. The bilayers are held by weak London forces only.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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) ; (ii) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

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
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.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₃N₂S⁺·Br⁻
M_r	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)
V (Å³)	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 $[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffraction Ltd, Yarnton, Oxfordshire, England.]$ )
T_min, T_max	0.522, 0.917
No. of measured, independent and observed [I > 3σ(I)] reflections	12512, 2162, 1699
R_int	0.057
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (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 ), MCE (Rohlíček & Hušák, 2007 ), DIAMOND (Brandenburg & Putz, 1999 ), JANA2006 (Petricek et al., 2014 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 2044275

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314620015114/sj4217sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620015114/sj4217Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314620015114/sj4217Isup3.mol

checkCIF report

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⁺·Br⁻	F(000) = 600
M_r = 297.2	D_x = 1.637 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ycb	Cell parameters from 3162 reflections
a = 16.2976 (8) Å	θ = 7.4–67.1°
b = 6.1294 (2) Å	µ = 6.04 mm⁻¹
c = 12.2221 (6) Å	T = 120 K
β = 99.070 (4)°	Platelet, colourless
V = 1205.65 (9) Å³	0.21 × 0.08 × 0.01 mm
Z = 4

Data collection top

Rigaku Oxford Diffraction Gemini ultra, AtlasS2 diffractometer	2162 independent reflections
Radiation source: X-ray tube	1699 reflections with I > 3σ(I)
Mirror monochromator	R_int = 0.057
Detector resolution: 5.1783 pixels mm^-1	θ_max = 67.2°, θ_min = 5.5°
ω scans	h = −19→18
Absorption correction: analytical CrysAlisPro (Rigaku OD, 2015)	k = −7→6
T_min = 0.522, T_max = 0.917	l = −14→13
12512 measured reflections

Refinement top

Refinement on F²	40 constraints
R[F² > 2σ(F²)] = 0.030	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.081	Weighting scheme based on measured s.u.'s w = 1/(σ²(I) + 0.0016I²)
S = 1.18	(Δ/σ)_max = 0.017
2162 reflections	Δρ_max = 0.48 e Å⁻³
157 parameters	Δρ_min = −0.36 e Å⁻³
4 restraints

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Br1	0.12634 (2)	0.79627 (6)	0.40347 (3)	0.02124 (12)
S1	0.09471 (5)	0.11747 (14)	0.09911 (6)	0.0181 (2)
N1	0.09225 (19)	0.2979 (5)	0.2973 (2)	0.0222 (9)
N2	0.08363 (19)	0.5365 (5)	0.1520 (2)	0.0221 (9)
C1	0.2898 (2)	0.3770 (6)	0.1961 (3)	0.0188 (10)
C2	0.2633 (2)	0.2128 (6)	0.1229 (3)	0.0193 (10)
C3	0.2926 (2)	0.2072 (6)	0.0196 (3)	0.0211 (10)
C4	0.3465 (2)	0.3612 (6)	−0.0066 (3)	0.0224 (11)
C5	0.4332 (2)	0.6914 (6)	0.0454 (3)	0.0222 (10)
C6	0.4595 (2)	0.8519 (6)	0.1203 (3)	0.0252 (11)
C7	0.4283 (2)	0.8638 (6)	0.2208 (3)	0.0245 (11)
C8	0.3725 (2)	0.7122 (6)	0.2466 (3)	0.0222 (10)
C9	0.3453 (2)	0.5398 (6)	0.1715 (3)	0.0192 (10)
C10	0.3751 (2)	0.5322 (6)	0.0686 (3)	0.0198 (10)
C11	0.2043 (2)	0.0410 (6)	0.1493 (3)	0.0208 (10)
C12	0.0894 (2)	0.3369 (5)	0.1920 (3)	0.0177 (10)
H1c1	0.270001	0.38133	0.266045	0.0226*
H1c3	0.27426	0.093362	−0.032466	0.0253*
H1c4	0.365563	0.354385	−0.076939	0.0269*
H1c5	0.45425	0.686312	−0.023628	0.0266*
H1c6	0.499614	0.957074	0.104151	0.0302*
H1c7	0.44616	0.979455	0.272054	0.0294*
H1c8	0.351646	0.722293	0.315701	0.0267*
H1c11	0.211892	0.018125	0.227929	0.0249*
H2c11	0.216623	−0.09448	0.115986	0.0249*
H1n1	0.096 (3)	0.403 (5)	0.344 (3)	0.0267*
H2n1	0.101 (3)	0.169 (3)	0.324 (3)	0.0267*
H1n2	0.091 (3)	0.552 (7)	0.0843 (11)	0.0266*
H2n2	0.086 (3)	0.646 (4)	0.196 (3)	0.0266*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0348 (2)	0.01257 (19)	0.01671 (19)	0.00035 (15)	0.00505 (13)	0.00032 (13)
S1	0.0234 (4)	0.0138 (4)	0.0174 (4)	−0.0010 (3)	0.0041 (3)	−0.0024 (3)
N1	0.0367 (16)	0.0108 (14)	0.0198 (15)	0.0000 (13)	0.0066 (12)	0.0011 (12)
N2	0.0337 (16)	0.0142 (15)	0.0193 (14)	−0.0026 (12)	0.0068 (12)	−0.0022 (11)
C1	0.0220 (16)	0.0188 (17)	0.0164 (16)	0.0038 (14)	0.0056 (12)	0.0012 (13)
C2	0.0202 (16)	0.0183 (17)	0.0191 (16)	0.0011 (14)	0.0023 (12)	0.0005 (14)
C3	0.0262 (17)	0.0185 (17)	0.0184 (16)	0.0016 (14)	0.0026 (13)	−0.0028 (14)
C4	0.0249 (17)	0.025 (2)	0.0180 (16)	−0.0020 (14)	0.0058 (13)	−0.0025 (13)
C5	0.0228 (17)	0.0234 (19)	0.0205 (17)	−0.0008 (15)	0.0040 (13)	0.0018 (14)
C6	0.0248 (17)	0.023 (2)	0.0274 (18)	−0.0030 (14)	0.0024 (14)	0.0036 (14)
C7	0.0276 (18)	0.0184 (18)	0.0262 (18)	−0.0023 (14)	0.0001 (14)	−0.0011 (14)
C8	0.0227 (17)	0.0231 (19)	0.0207 (17)	0.0005 (14)	0.0029 (13)	−0.0045 (14)
C9	0.0176 (16)	0.0199 (18)	0.0192 (16)	0.0035 (13)	0.0001 (12)	0.0013 (13)
C10	0.0216 (16)	0.0179 (18)	0.0195 (16)	0.0006 (14)	0.0017 (13)	0.0019 (13)
C11	0.0270 (18)	0.0173 (18)	0.0183 (16)	0.0041 (14)	0.0043 (13)	0.0026 (13)
C12	0.0190 (16)	0.0127 (18)	0.0228 (16)	−0.0014 (12)	0.0077 (12)	−0.0003 (12)

Geometric parameters (Å, º) top

S1—C11	1.855 (3)	C4—C10	1.423 (5)
S1—C12	1.771 (3)	C4—H1c4	0.96
N1—C12	1.302 (4)	C5—C6	1.366 (5)
N1—H1n1	0.86 (3)	C5—C10	1.419 (5)
N1—H2n1	0.86 (2)	C5—H1c5	0.96
N2—C12	1.316 (4)	C6—C7	1.404 (5)
N2—H1n2	0.860 (19)	C6—H1c6	0.96
N2—H2n2	0.86 (3)	C7—C8	1.372 (5)
C1—C2	1.370 (5)	C7—H1c7	0.96
C1—C9	1.411 (5)	C8—C9	1.424 (5)
C1—H1c1	0.96	C8—H1c8	0.96
C2—C3	1.419 (5)	C9—C10	1.419 (5)
C2—C11	1.495 (5)	C11—H1c11	0.96
C3—C4	1.361 (5)	C11—H2c11	0.96
C3—H1c3	0.96

C11—S1—C12	96.98 (15)	C5—C6—H1c6	119.84
C12—N1—H1n1	121 (2)	C7—C6—H1c6	119.84
C12—N1—H2n1	122 (3)	C6—C7—C8	120.7 (3)
H1n1—N1—H2n1	117 (3)	C6—C7—H1c7	119.63
C12—N2—H1n2	117 (3)	C8—C7—H1c7	119.63
C12—N2—H2n2	120 (2)	C7—C8—C9	120.3 (3)
H1n2—N2—H2n2	121 (4)	C7—C8—H1c8	119.84
C2—C1—C9	121.8 (3)	C9—C8—H1c8	119.84
C2—C1—H1c1	119.12	C1—C9—C8	122.1 (3)
C9—C1—H1c1	119.12	C1—C9—C10	119.1 (3)
C1—C2—C3	118.9 (3)	C8—C9—C10	118.7 (3)
C1—C2—C11	121.5 (3)	C4—C10—C5	122.6 (3)
C3—C2—C11	119.5 (3)	C4—C10—C9	118.3 (3)
C2—C3—C4	120.8 (3)	C5—C10—C9	119.2 (3)
C2—C3—H1c3	119.59	S1—C11—C2	111.7 (2)
C4—C3—H1c3	119.58	S1—C11—H1c11	109.47
C3—C4—C10	121.1 (3)	S1—C11—H2c11	109.47
C3—C4—H1c4	119.45	C2—C11—H1c11	109.47
C10—C4—H1c4	119.45	C2—C11—H2c11	109.47
C6—C5—C10	120.7 (3)	H1c11—C11—H2c11	107.17
C6—C5—H1c5	119.66	S1—C12—N1	119.8 (3)
C10—C5—H1c5	119.66	S1—C12—N2	118.4 (3)
C5—C6—C7	120.3 (3)	N1—C12—N2	121.8 (3)

C9—C1—C2—C3	0.0 (2)	C7—C8—C9—C10	−1.8 (5)
C9—C1—C2—C11	−179.8 (3)	C8—C9—C1—C2	179.4 (3)
C1—C2—C3—C4	0.3 (5)	C10—C9—C1—C2	−0.6 (5)
C11—C2—C3—C4	−179.9 (3)	C4—C10—C9—C1	1.0 (5)
C2—C3—C4—C10	0.0 (3)	C4—C10—C9—C8	−179.0 (3)
C3—C4—C10—C5	178.0 (3)	C5—C10—C9—C1	−177.8 (3)
C3—C4—C10—C9	−0.7 (5)	C5—C10—C9—C8	2.2 (5)
C4—C10—C5—C6	−179.5 (3)	C1—C2—C11—S1	91.8 (3)
C9—C10—C5—C6	−0.8 (5)	C3—C2—C11—S1	−88.0 (3)
C10—C5—C6—C7	−1.1 (5)	C2—C11—S1—C12	−68.1 (3)
C5—C6—C7—C8	1.5 (5)	C11—S1—C12—N1	−68.5 (3)
C6—C7—C8—C9	0.0 (3)	C11—S1—C12—N2	110.7 (3)
C7—C8—C9—C1	178.2 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+3/2, z−1/2.

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..

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