Crystal structure of 4-methyl­sulfanyl-2-(2H-tetra­zol-2-yl)pyrimidine

The title compound, C₆H₆N₆S, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. The conformation of the two mol­ecules differs slightly. While the tetra­zole ring is inclined to the pyrim­idene ring by 5.48 (7) and 4.24 (7)° in mol­ecules A and B, respectively, the N—C—S—C torsion angles of the thio­methyl groups differ by ca 180°. In the crystal, the A and B mol­ecules are linked via a C—H⋯N hydrogen bond. They stack along the b-axis direction forming columns within which there are weak π–π inter­actions present [shortest inter-centroid distance = 3.6933 (13) Å].

1. Related literature

For applications of tetra­zolyl-substituted aromatic systems in metal–ligand research, see: Kim et al. (2008); Stoessel et al. (2010); in drug development, see: Pasternak et al. (2012); Biswas et al. (2015); in polymer synthesis, see: Yu et al. (2008); Sengupta et al. (2010). For the synthesis of 4-methyl­sulfanyl-2-(1H-tetra­zol-1-yl)pyrimidine and the title compound, see: Thomann et al. (2014).

2. Experimental

2.1. Crystal data

• C₆H₆N₆S

• M_r = 194.23

• Triclinic,

• a = 6.3001 (17) Å

• b = 7.393 (2) Å

• c = 18.159 (5) Å

• α = 91.407 (7)°

• β = 95.864 (7)°

• γ = 102.695 (8)°

• V = 819.9 (4) ų

• Z = 4

• Mo Kα radiation

• μ = 0.35 mm⁻¹

• T = 143 K

• 0.22 × 0.22 × 0.01 mm

2.2. Data collection

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2010) T_min = 0.716, T_max = 0.746

• 15501 measured reflections

• 4581 independent reflections

• 3596 reflections with I > 2σ(I)

• R_int = 0.028

2.3. Refinement

• R[F² > 2σ(F²)] = 0.034

• wR(F²) = 0.086

• S = 1.01

• 4581 reflections

• 283 parameters

• All H-atom parameters refined

• Δρ_max = 0.35 e Å⁻³

• Δρ_min = −0.30 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H1⋯N9^i	0.89 (2)	2.58 (2)	3.203 (2)	129 (2)
Symmetry code: (i) x-1, y, z.

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 and PLATON.

Supporting information

S1. Comment

4-tetra­zolyl­pyrimidines are well reported scaffolds in many bioactive entities. Besides synthetic chemistry, tetra­zolyl substituted aromatic systems are also of high inter­est for example, in metal-ligand research (Kim et al., 2008; Stoessel et al., 2010), drug development (Pasternak et al., 2012; Biswas et al., 2015) and polymer discovery (Yu et al., 2008; Sengupta et al., 2010). Thus, the knowledge of the three dimensional structure of these moieties is of crucial importance for the rational design in these fields of research. Recently, we have reported a novel method to synthesize such compounds (Thomann et al., 2014). We have reported the synthesis of 4-(methyl­thio)-2-(1H-tetra­zol-1-yl)pyrimidine (1). Inter­estingly, when scaling up the reaction, another product was found in small amounts. NMR analytical characterization revealed the compound to be the 2-tetra­zolyl regioisomer (2). To determine unequivocally proof of the structure of this compound, we determined its crystal structure.

The title compound (2), crystallized with two independent molecules (A and B) in the asymmetric unit (Fig. 1). Inter­estingly, the two molecules differ in their conformation. While the tetra­zole moieties are arranged similarly, with the tetra­zole ring is inclined to the pyrim­idene ring by 5.48 (7) and 4.24 (7) ° in molecules A and B, respectively, the thio­methyl groups have a difference of the torsion angle about the C_ar···S bond of ca. 180° [for example, torsion angle N5—C4—S1—C6 = 0.89 (12) °, compared to torsion angle N11—C10—S2—C12 = -176.78 (10) °] indicating higher rotational freedom than the tetra­zoles (Fig. 1). The latter finding is of importance for computational chemists in medicinal chemistry, as the polarized hydrogen at atom C5 of the tetra­zole ring is able to form non-classical hydrogen bonds. Therefore, the results from the crystal structure may favour this conformational isomer for in silico predictions.

In the crystal, the A and B molecules are linked via a C—H···N hydrogen bond (Table 1 and Fig. 2). They stack along the b axis direction forming columns within which there are weak π-π inter­actions present [shortest inter-centroid distance is Cg2···Cg4ⁱ = 3.6918 (5) Å; Cg2 and Cg4 are the centroids of rings N5/N6/C1—C4 and N11/N12/C7—C10, respectively; symmetry code: (i) x, y + 1, z].

S2. Synthesis and crystallization

The title compound (2), was synthesized following a previously reported procedure (Thomann et al., 2014). A mixture of 4-chloro-2-(methyl­thio)­pyrimidine, 1H-tetra­zole and tri­ethyl­amine, in the ratio 1:1:1, was stirred under microwave irradiation at 50 W, 353 K for 1 h. The crude product was purified by flash chromatography (hexane:ethyl acetate, 8:2, R_f = 0.25) to yield a white solid (9%). Crystals formed at 294 K after 16 h from a saturated solution of 2 in ethyl acetate.¹H NMR (CDCl₃, 300MHz) 8.80 (dd, J = 5.3, 0.6 Hz, 1 H), 8.77 (s, 1 H), 7.77 (dd, J = 5.3, 0.7 Hz, 1 H), 2.69 ppm (d, J = 0.7 Hz, 3 H).

S3. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were located in a difference Fourier map and freely refined.

Related literature

For applications of tetrazolyl-substituted aromatic systems in metal–ligand research, see: Kim et al. (2008); Stoessel et al. (2010); in drug development, see: Pasternak et al. (2012); Biswas et al. (2015); in polymer discovery, see: Yu et al. (2008); Sengupta et al. (2010). For the synthesis of 4-methylsulfanyl-2-(1H-tetrazol-1-yl)pyrimidine and the title compound, see: Thomann et al. (2014).

Structure description

4-tetra­zolyl­pyrimidines are well reported scaffolds in many bioactive entities. Besides synthetic chemistry, tetra­zolyl substituted aromatic systems are also of high inter­est for example, in metal-ligand research (Kim et al., 2008; Stoessel et al., 2010), drug development (Pasternak et al., 2012; Biswas et al., 2015) and polymer discovery (Yu et al., 2008; Sengupta et al., 2010). Thus, the knowledge of the three dimensional structure of these moieties is of crucial importance for the rational design in these fields of research. Recently, we have reported a novel method to synthesize such compounds (Thomann et al., 2014). We have reported the synthesis of 4-(methyl­thio)-2-(1H-tetra­zol-1-yl)pyrimidine (1). Inter­estingly, when scaling up the reaction, another product was found in small amounts. NMR analytical characterization revealed the compound to be the 2-tetra­zolyl regioisomer (2). To determine unequivocally proof of the structure of this compound, we determined its crystal structure.

The title compound (2), crystallized with two independent molecules (A and B) in the asymmetric unit (Fig. 1). Inter­estingly, the two molecules differ in their conformation. While the tetra­zole moieties are arranged similarly, with the tetra­zole ring is inclined to the pyrim­idene ring by 5.48 (7) and 4.24 (7) ° in molecules A and B, respectively, the thio­methyl groups have a difference of the torsion angle about the C_ar···S bond of ca. 180° [for example, torsion angle N5—C4—S1—C6 = 0.89 (12) °, compared to torsion angle N11—C10—S2—C12 = -176.78 (10) °] indicating higher rotational freedom than the tetra­zoles (Fig. 1). The latter finding is of importance for computational chemists in medicinal chemistry, as the polarized hydrogen at atom C5 of the tetra­zole ring is able to form non-classical hydrogen bonds. Therefore, the results from the crystal structure may favour this conformational isomer for in silico predictions.

In the crystal, the A and B molecules are linked via a C—H···N hydrogen bond (Table 1 and Fig. 2). They stack along the b axis direction forming columns within which there are weak π-π inter­actions present [shortest inter-centroid distance is Cg2···Cg4ⁱ = 3.6918 (5) Å; Cg2 and Cg4 are the centroids of rings N5/N6/C1—C4 and N11/N12/C7—C10, respectively; symmetry code: (i) x, y + 1, z].

For applications of tetrazolyl-substituted aromatic systems in metal–ligand research, see: Kim et al. (2008); Stoessel et al. (2010); in drug development, see: Pasternak et al. (2012); Biswas et al. (2015); in polymer discovery, see: Yu et al. (2008); Sengupta et al. (2010). For the synthesis of 4-methylsulfanyl-2-(1H-tetrazol-1-yl)pyrimidine and the title compound, see: Thomann et al. (2014).

Synthesis and crystallization

The title compound (2), was synthesized following a previously reported procedure (Thomann et al., 2014). A mixture of 4-chloro-2-(methyl­thio)­pyrimidine, 1H-tetra­zole and tri­ethyl­amine, in the ratio 1:1:1, was stirred under microwave irradiation at 50 W, 353 K for 1 h. The crude product was purified by flash chromatography (hexane:ethyl acetate, 8:2, R_f = 0.25) to yield a white solid (9%). Crystals formed at 294 K after 16 h from a saturated solution of 2 in ethyl acetate.¹H NMR (CDCl₃, 300MHz) 8.80 (dd, J = 5.3, 0.6 Hz, 1 H), 8.77 (s, 1 H), 7.77 (dd, J = 5.3, 0.7 Hz, 1 H), 2.69 ppm (d, J = 0.7 Hz, 3 H).

Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were located in a difference Fourier map and freely refined.

Computing details

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015) and PLATON (Spek, 2009).

Figures

	Fig. 1. The molecular structure of the two independent molecules (A and B) of the title compound (2), with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. The crystal packing of the two independent molecules (A black; B red) of the title compound (2), viewed along the a axis. Hydrogen bonds are shown as dashed lines (see Table 1).
	Fig. 3. Compounds (1) and (2).

4-Methylsulfanyl-2-(2H-tetrazol-2-yl)pyrimidine

Crystal data

C6H6N6S	Z = 4
Mr = 194.23	F(000) = 400
Triclinic, P1	Dx = 1.574 Mg m^−3
a = 6.3001 (17) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.393 (2) Å	Cell parameters from 728 reflections
c = 18.159 (5) Å	θ = 3.6–24.3°
α = 91.407 (7)°	µ = 0.35 mm^−1
β = 95.864 (7)°	T = 143 K
γ = 102.695 (8)°	Cuboid, colourless
V = 819.9 (4) Å^3	0.22 × 0.22 × 0.01 mm

Data collection

Bruker APEXII CCD diffractometer	3596 reflections with I > 2σ(I)
φ and ω scans	Rint = 0.028
Absorption correction: multi-scan (SADABS; Bruker, 2010)	θmax = 29.6°, θmin = 2.3°
Tmin = 0.716, Tmax = 0.746	h = −8→8
15501 measured reflections	k = −10→10
4581 independent reflections	l = −24→25

Refinement

Refinement on F^2	0 restraints
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.034	All H-atom parameters refined
wR(F^2) = 0.086	w = 1/[σ^2(Fo^2) + (0.0376P)^2 + 0.2718P] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max = 0.001
4581 reflections	Δρmax = 0.35 e Å^−3
283 parameters	Δρmin = −0.30 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.84117 (6)	0.83334 (5)	0.58281 (2)	0.01975 (9)
N1	1.04303 (18)	0.69484 (15)	0.84617 (6)	0.0152 (2)
N2	1.00906 (19)	0.60999 (17)	0.90974 (6)	0.0208 (3)
N3	1.24517 (19)	0.79683 (17)	0.84553 (7)	0.0209 (3)
N4	1.3498 (2)	0.77865 (18)	0.91059 (7)	0.0233 (3)
N5	0.93885 (18)	0.76012 (15)	0.72442 (6)	0.0159 (2)
N6	0.56784 (19)	0.65519 (16)	0.66803 (7)	0.0200 (3)
C1	0.8749 (2)	0.67900 (17)	0.78527 (7)	0.0148 (3)
C2	0.6647 (2)	0.58341 (19)	0.79335 (8)	0.0184 (3)
C3	0.5146 (2)	0.5770 (2)	0.73096 (8)	0.0203 (3)
C4	0.7801 (2)	0.74205 (18)	0.66783 (8)	0.0162 (3)
C5	1.2034 (2)	0.6651 (2)	0.94818 (8)	0.0209 (3)
C6	1.1309 (2)	0.9298 (2)	0.60068 (9)	0.0230 (3)
H1	0.629 (3)	0.532 (2)	0.8352 (10)	0.028 (5)*
H2	0.366 (3)	0.512 (2)	0.7313 (9)	0.023 (4)*
H3	1.235 (3)	0.634 (2)	0.9944 (11)	0.030 (5)*
H4	1.204 (3)	0.833 (2)	0.6178 (10)	0.032 (5)*
H5	1.160 (3)	1.037 (2)	0.6366 (10)	0.030 (5)*
H6	1.172 (3)	0.969 (3)	0.5531 (11)	0.040 (5)*
S2	0.91337 (6)	0.35407 (5)	0.59998 (2)	0.02003 (10)
N7	1.07557 (18)	0.19569 (15)	0.85809 (6)	0.0156 (2)
N8	1.0376 (2)	0.11547 (17)	0.92240 (7)	0.0219 (3)
N9	1.28032 (19)	0.29223 (17)	0.85739 (7)	0.0218 (3)
N10	1.3817 (2)	0.27602 (18)	0.92304 (7)	0.0241 (3)
N11	0.97742 (18)	0.26119 (15)	0.73636 (6)	0.0159 (2)
N12	0.60819 (19)	0.16413 (16)	0.67866 (7)	0.0192 (2)
C7	0.9101 (2)	0.18161 (17)	0.79690 (7)	0.0146 (3)
C8	0.6975 (2)	0.08981 (19)	0.80433 (8)	0.0181 (3)
C9	0.5511 (2)	0.0862 (2)	0.74162 (8)	0.0204 (3)
C10	0.8194 (2)	0.24779 (18)	0.67912 (8)	0.0162 (3)
C11	1.2311 (2)	0.1686 (2)	0.96118 (8)	0.0218 (3)
C12	0.6629 (3)	0.3216 (2)	0.53901 (9)	0.0256 (3)
H7	0.658 (3)	0.041 (2)	0.8462 (10)	0.028 (5)*
H8	0.400 (3)	0.022 (2)	0.7410 (10)	0.027 (4)*
H9	1.264 (3)	0.138 (3)	1.0104 (11)	0.035 (5)*
H10	0.564 (3)	0.385 (2)	0.5600 (10)	0.035 (5)*
H11	0.702 (3)	0.373 (3)	0.4949 (11)	0.037 (5)*
H12	0.600 (3)	0.192 (3)	0.5294 (10)	0.038 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.02103 (18)	0.02210 (18)	0.01490 (18)	0.00253 (13)	−0.00004 (13)	0.00614 (13)
N1	0.0152 (5)	0.0167 (5)	0.0130 (5)	0.0007 (4)	0.0036 (4)	0.0040 (4)
N2	0.0216 (6)	0.0250 (6)	0.0152 (6)	0.0020 (5)	0.0040 (5)	0.0078 (5)
N3	0.0155 (6)	0.0260 (6)	0.0190 (6)	−0.0011 (5)	0.0024 (5)	0.0049 (5)
N4	0.0203 (6)	0.0295 (7)	0.0186 (6)	0.0031 (5)	0.0005 (5)	0.0046 (5)
N5	0.0166 (5)	0.0159 (5)	0.0149 (6)	0.0028 (4)	0.0030 (4)	0.0019 (4)
N6	0.0182 (6)	0.0193 (6)	0.0212 (6)	0.0019 (4)	0.0009 (5)	0.0034 (5)
C1	0.0155 (6)	0.0138 (6)	0.0150 (6)	0.0030 (5)	0.0025 (5)	0.0011 (5)
C2	0.0186 (7)	0.0180 (7)	0.0181 (7)	0.0012 (5)	0.0057 (5)	0.0042 (5)
C3	0.0168 (7)	0.0200 (7)	0.0232 (8)	0.0008 (5)	0.0039 (6)	0.0026 (5)
C4	0.0181 (6)	0.0149 (6)	0.0157 (7)	0.0034 (5)	0.0026 (5)	0.0020 (5)
C5	0.0221 (7)	0.0251 (7)	0.0153 (7)	0.0044 (6)	0.0022 (6)	0.0045 (5)
C6	0.0203 (7)	0.0305 (8)	0.0190 (7)	0.0053 (6)	0.0042 (6)	0.0093 (6)
S2	0.02219 (18)	0.02074 (18)	0.01648 (18)	0.00230 (13)	0.00321 (14)	0.00600 (13)
N7	0.0134 (5)	0.0181 (5)	0.0149 (6)	0.0015 (4)	0.0037 (4)	0.0045 (4)
N8	0.0203 (6)	0.0281 (7)	0.0170 (6)	0.0028 (5)	0.0044 (5)	0.0090 (5)
N9	0.0152 (6)	0.0265 (6)	0.0213 (6)	−0.0005 (5)	0.0014 (5)	0.0057 (5)
N10	0.0182 (6)	0.0316 (7)	0.0203 (7)	0.0015 (5)	−0.0004 (5)	0.0048 (5)
N11	0.0159 (5)	0.0160 (5)	0.0155 (6)	0.0021 (4)	0.0029 (4)	0.0033 (4)
N12	0.0170 (6)	0.0214 (6)	0.0184 (6)	0.0020 (5)	0.0026 (5)	0.0016 (5)
C7	0.0139 (6)	0.0142 (6)	0.0160 (6)	0.0039 (5)	0.0019 (5)	0.0008 (5)
C8	0.0171 (7)	0.0200 (7)	0.0170 (7)	0.0018 (5)	0.0056 (5)	0.0036 (5)
C9	0.0164 (7)	0.0233 (7)	0.0206 (7)	0.0019 (5)	0.0034 (6)	0.0014 (5)
C10	0.0189 (7)	0.0139 (6)	0.0160 (7)	0.0039 (5)	0.0023 (5)	0.0008 (5)
C11	0.0188 (7)	0.0294 (8)	0.0168 (7)	0.0039 (6)	0.0023 (6)	0.0060 (6)
C12	0.0305 (8)	0.0281 (8)	0.0181 (8)	0.0075 (7)	−0.0006 (6)	0.0034 (6)

Geometric parameters (Å, º)

S1—C4	1.7453 (15)	S2—C10	1.7487 (15)
S1—C6	1.8004 (16)	S2—C12	1.7992 (16)
N1—N3	1.3311 (16)	N7—N9	1.3314 (16)
N1—N2	1.3412 (16)	N7—N8	1.3421 (16)
N1—C1	1.4347 (17)	N7—C7	1.4291 (17)
N2—C5	1.3207 (19)	N8—C11	1.3182 (19)
N3—N4	1.3176 (17)	N9—N10	1.3148 (17)
N4—C5	1.356 (2)	N10—C11	1.3566 (19)
N5—C1	1.3267 (17)	N11—C7	1.3237 (17)
N5—C4	1.3412 (17)	N11—C10	1.3496 (17)
N6—C3	1.3336 (19)	N12—C10	1.3377 (18)
N6—C4	1.3506 (18)	N12—C9	1.3393 (19)
C1—C2	1.3815 (19)	C7—C8	1.3837 (19)
C2—C3	1.393 (2)	C8—C9	1.386 (2)
C2—H1	0.885 (19)	C8—H7	0.886 (19)
C3—H2	0.951 (17)	C9—H8	0.965 (18)
C5—H3	0.891 (19)	C11—H9	0.940 (19)
C6—H4	0.974 (17)	C12—H10	0.955 (19)
C6—H5	0.988 (17)	C12—H11	0.93 (2)
C6—H6	0.96 (2)	C12—H12	0.957 (19)
C4—S1—C6	101.92 (7)	C10—S2—C12	101.37 (8)
N3—N1—N2	113.78 (11)	N9—N7—N8	113.63 (11)
N3—N1—C1	123.45 (11)	N9—N7—C7	123.40 (11)
N2—N1—C1	122.75 (11)	N8—N7—C7	122.96 (11)
C5—N2—N1	101.28 (11)	C11—N8—N7	101.34 (12)
N4—N3—N1	105.82 (12)	N10—N9—N7	105.89 (12)
N3—N4—C5	106.17 (12)	N9—N10—C11	106.19 (12)
C1—N5—C4	114.47 (12)	C7—N11—C10	114.67 (12)
C3—N6—C4	115.71 (12)	C10—N12—C9	115.82 (12)
N5—C1—C2	125.31 (12)	N11—C7—C8	125.20 (12)
N5—C1—N1	115.33 (12)	N11—C7—N7	115.25 (12)
C2—C1—N1	119.36 (12)	C8—C7—N7	119.55 (12)
C1—C2—C3	114.59 (13)	C7—C8—C9	114.40 (13)
C1—C2—H1	122.4 (11)	C7—C8—H7	122.5 (11)
C3—C2—H1	123.0 (12)	C9—C8—H7	123.1 (12)
N6—C3—C2	123.19 (13)	N12—C9—C8	123.46 (14)
N6—C3—H2	116.5 (10)	N12—C9—H8	116.1 (11)
C2—C3—H2	120.3 (10)	C8—C9—H8	120.5 (11)
N5—C4—N6	126.72 (13)	N12—C10—N11	126.44 (13)
N5—C4—S1	119.87 (10)	N12—C10—S2	119.96 (10)
N6—C4—S1	113.41 (10)	N11—C10—S2	113.60 (10)
N2—C5—N4	112.96 (13)	N8—C11—N10	112.94 (13)
N2—C5—H3	124.0 (12)	N8—C11—H9	124.6 (12)
N4—C5—H3	123.0 (12)	N10—C11—H9	122.5 (12)
S1—C6—H4	108.9 (11)	S2—C12—H10	109.7 (11)
S1—C6—H5	110.3 (10)	S2—C12—H11	105.7 (12)
H4—C6—H5	112.5 (14)	H10—C12—H11	110.6 (16)
S1—C6—H6	103.5 (11)	S2—C12—H12	110.3 (11)
H4—C6—H6	110.8 (15)	H10—C12—H12	111.9 (16)
H5—C6—H6	110.4 (15)	H11—C12—H12	108.4 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H1···N9^i	0.89 (2)	2.58 (2)	3.203 (2)	129 (2)

Symmetry code: (i) x−1, y, z.