Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-di­methyl­benz­yl)sulfan­yl]pyrimidine-4,6-di­amine

Salieva, G.; Kholikov, T.; Okmanov, R.Y.; Matchanov, A.; Khodjaniyazov, K.U.; Kadirova, S.; Torambetov, B.

doi:10.1107/S2056989025002440

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ISSN: 2056-9890

Volume 81| Part 4| April 2025| Pages 328-331

https://doi.org/10.1107/S2056989025002440

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Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-dimethylbenzyl)sulfanyl]pyrimidine-4,6-diamine

Gulrukh Salieva,^a,^b Tursunali Kholikov,^a Rasul Ya Okmanov,^c Alimjon Matchanov,^d Khamid U Khodjaniyazov,^d Shakhnoza Kadirova ^a and Batirbay Torambetov ^a ^*

^aNational University of Uzbekistan named after Mirzo Ulugbek, 4 University St, Tashkent, 100174, Uzbekistan, ^bTashkent Medical Academy, 2 Farabi St, Tashkent, 100109, Uzbekistan, ^cS. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek St 77, Tashkent 100170, Uzbekistan, and ^dInstitute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, M. Ulugbek St, 83, Tashkent, 100125, Uzbekistan
^*Correspondence e-mail: torambetov_b@mail.ru

Edited by J. Ellena, Universidade de Sâo Paulo, Brazil (Received 21 February 2025; accepted 17 March 2025; online 25 March 2025)

The title compound, C₁₃H₁₆N₄S (DAMP-DMB), was synthesized through the reaction of 2,4-dimethylbenzyl chloride with diaminopyrimidine-thiol. Single-crystal X-ray diffraction analysis confirmed that the compound crystallizes in the monoclinic crystal system, space group P2₁/c. The asymmetric unit contains a single molecular entity. Structural examination revealed the presence of a dimeric arrangement consolidated by N—H⋯N hydrogen-bonding interactions. Additionally, Hirshfeld surface analysis indicated that H⋯H, N⋯H, C⋯H, and S⋯H contacts account for 98.9% of the total intermolecular interactions to the Hirshfeld surface.

Keywords: crystal structure; molecular structure; diaminopyrimidine-thiol; 2,4-dimethylbenzyl; Hirshfeld surface analysis.

CCDC reference: 2431935

1. Chemical context

Diamino-substituted pyrimidines are pyrimidine derivatives with important applications in pharmaceuticals and organic synthesis (Tolba et al., 2022 ; Rosowsky et al., 2004 ). These compounds play a crucial role in medicinal chemistry, in particular because of their antiviral (Hocková et al., 2004 ), antibacterial (Kandeel et al., 1994 ), antimalarial (Neekhara et al., 2006 ) and antimicrobial activities (Holla et al., 2006 ). Similarly, a 4,6-diaminopyrimidine-based derivative has showed potential antiviral activity against dengue by targeting the NS2B/NS3 protease (Subasri et al., 2017 ). Some organometallic complexes of diaminopyrimidine-thiol with tin and ruthenium exhibit anticancer activity (Grześkiewicz et al., 2017 ; Silva et al., 2020 ). Herein we report the crystal structure and Hirshfeld surface analysis of a newly synthesized organic compound, namely 2-[(2,4-dimethylbenzyl)sulfanyl]pyrimidine-4,6-diamine (DAMP-DMB).

2. Structural commentary

DAMP-DMB (Fig. 1) crystallizes in the monoclinic crystal system, space group P2₁/c (14), with a single molecule in the asymmetric unit. The amine groups on the pyrimidine ring are co-planar and the dihedral angle between the pyrimidine and phenyl rings is 63.03 (14)°. The torsion angles for the groups are N1—C4—S1—C5 = −6.7 (3)° and C11—C6—C5—S1 = −104.2 (3)° respectively. DAMP-DMB contains several hydrogen-bond donor and acceptor groups. However, due to the twisted conformation of the diaminopyrimidine group, the molecule does not exhibit any intramolecular hydrogen-bonding or π-stacking interactions.

Figure 1
The molecular structure of DAMP-DMB, with atomic displacement ellipsoids drawn at the 30% probability level, showing the atom labeling. Hydrogen atoms are represented as small spheres with arbitrary radii.

3. Supramolecular features

The crystal structure of DAMP-DMB reveals a dimeric association of molecules around the inversion center, where the molecules are connected through moderately strong N4—H4B⋯N2 [H⋯A = 2.19 (3) Å] hydrogen bonds (Fig. 2a, Table 1) (Steiner, 2002 ). In the dimeric association of DAMP-DMB molecules, the ring pattern contains a total of eight atoms, two of them are donors, two are acceptors, hence the graph-set notation is R₂² (8) (Bernstein et al., 1995 ). These dimeric units are further stabilized by N—H⋯π interactions, specifically between the amine hydrogen atom of the pyrimidine ring and the π-electron cloud of the benzene ring [N3—H3A⋯Cg2, H⋯Cg = 2.89 (4) Å]. Similarly, as observed in the 2D finger print plots (see Section 4), the crystal structure also contains hydrogen-bonding interactions specifically, N—H⋯N interactions [N4—H4A⋯N1, H⋯A = 2.56 (3) Å]. Furthermore, the crystal structure exhibits intermolecular H⋯H interactions involving the methyl hydrogen and and the hydrogen atom of the methylene spacer. (Fig. 2b). This hierarchical organization, governed by multiple weak intermolecular interactions, including H⋯H, N⋯H, C⋯H, and S⋯H, plays a crucial role in the overall packing and cohesion of the crystal structure.

Table 1
Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C6–C11 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C10—H10⋯C1ⁱ	0.93	2.82	3.623 (4)	145
N3—H3B⋯N4ⁱⁱ	0.82 (3)	2.54 (3)	3.340 (5)	168 (3)
N4—H4A⋯N1ⁱⁱⁱ	0.87 (3)	2.56 (3)	3.372 (4)	156 (3)
N4—H4A⋯C4ⁱⁱⁱ	0.87 (3)	2.70 (4)	3.540 (4)	164 (3)
N4—H4B⋯N2^iv	0.86 (3)	2.19 (3)	3.039 (3)	172 (3)
N3—H3A⋯Cg2^v	0.85 (4)	2.89 (4)	3.561 (3)	137 (3)
Symmetry codes: (i) ; (ii) $[x, -y-{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) ; (v) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
(a) The association between the molecules of DAMP-DMB to form a dimer involving N4—H4B⋯N2 interactions and (b) view of the packing of molecules and association of dimeric units along the c axis in the crystal structure of DAMP-DMB.

4. Hirshfeld surface analysis

A Hirshfeld surface analysis (Spackman & Jayatilaka, 2009 ) was performed and fingerprint plots (Spackman & McKinnon, 2002 ) generated using CrystalExplorer 21.5 (Spackman et al., 2021 ) to investigate the interactions contributing to the cohesion of the crystal structure. The Hirshfeld surface and fingerprint plots are shown in Figs. 3 and 4. The presence of red spots on the Hirshfeld surface indicates close N⋯H contacts, which are also reflected in the corresponding 2D fingerprint plots. The molecule predominantly engages in H⋯H, C⋯H, N⋯H, and S⋯H interactions, contributing 51.6%, 23.0%, 15.8%, and 8.5%, respectively to the Hirshfeld surface, accounting for 98.9% of the total interactions. In contrast, interactions such as C⋯C and C⋯N collectively account for only 0.9%, indicating their minimal role in crystal-structure cohesion. The 2D fingerprint plots reveals the presence of distinct hydrogen-bonding spikes corresponding to N—H⋯N interactions. The lower right spike at (d_i, d_e) = (1.2, 0.8), represents the hydrogen-bond acceptor, while the upper left spike at (d_i, d_e) = (0.8, 1.8) corresponds to the hydrogen-bond donor. Similarly, a sharp feature along the diagonal in the lower left region indicates a close H⋯H contact, shorter than 2.4 Å, where d_i = d_e ≃ 1.2 Å (Figs. 3 and 4).

Figure 3
Visualization of the three-dimensional Hirshfeld surfaces for DAMP-DMB.

Figure 4
Two-dimensional fingerprint plots of the Hirshfeld surfaces for DAMP-DMB showing the contributions of various hydrogen-bonding interactions.

5. Database survey

A survey of the Cambridge Structural Database (CSD, Version 5.45, last updated March 2024; Groom et al., 2016 ) using ConQuest (Bruno et al., 2002 ) revealed 32 crystal structures for the diaminopyrimidine-thiol (DAMP) fragment; among which, eleven structures are related to organometallic compounds. Out of the eleven structures, two complexes of the diaminopyrimidine thiol ligand with triphenyl tin and one with trimethyl tin are reported where the sulfur atom binds monodentately with the metal atom (CEHZIB, Grześkiewicz et al., 2017; VUFTAT, VUFTEX, Ioannidou et al., 2013 ). Similarly, three structures with ruthenium and two with cobalt metal centers are reported where the metal is coordinated bidentately with N and S atoms (FEGQER, Silva et al., 2020; JACCAV, Ribeiro et al., 2020 ; XOTDAO, da Silva et al., 2019 ; TIYJUG01, Yamanari et al., 2002 ; COHBEK, Gioftsidou et al., 2024 ). Interestingly, one crystal structure with a Cu metal atom is reported where the diaminopyrimidine thiol derivative binds with the metal atom in a bidentate fashion through the nitrogen atoms (DEDRAI, Moyaert et al., 2017 ). Two structures of a diaminopyrimidine thiol derivative containing zinc are also deposited (TAGBUY, Romero et al., 1990 ; ZIKFII, Salas et al., 1995 ). Similarly, twelve crystal structures of DAMP with amides have been reported. In addition, one crystal structure having two DAMP fragments connected via a bridging methylene (–CH₂–) group are reported. There are also structures for methyl and ethyl derivatives directly connected to the thiol group of the DAMP fragment. However, no crystal structures of DAMP derivatives with 2,4-dimethylbenzyl have been reported.

6. Synthesis and crystallization

A round-bottomed flask equipped with a magnetic stirrer was charged with diaminopyrimidine-thiol (50.0 mg, 0.351 mmol) dissolved in a mixture of 1.0 N aqueous NaOH (0.35 mL, 0.35 mmol) and methanol (5.0 mL). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo to afford a tan solid. The resulting solid was dissolved in DMF (5.0 mL), treated with 2,4-dimethylbenzyl chloride (50.0 µL, 0.35 mmol), and stirred at room temperature for 2 h. The reaction progress was monitored by TLC. Upon completion, the DMF was removed in vacuo, and the residue was partitioned between water (50 mL) and chloroform (3 × 50 mL). The combined organic extracts were dried over Na₂SO₄, filtered, and concentrated under vacuum. The residue was further dried at room temperature for 48 h, yielding the product as colorless crystals (90%) (Salieva et al., 2025 ).

¹H-NMR (600 MHz, CD₃OD) δ: 2.23 (s, 3H, CH₃), 2.30 (s, 3H, CH₃), 4.27 (s, 2H, S-CH₂) 5.29 (s, 1H, CH pyrimidine), 6.88 (d, J = 6 Hz, 1H, Ar), 6.93 (s, 1H, Ar), 7.17 (d, J = 12 Hz, H, CH Ar) ¹³C NMR (150 MHz, CD₃OD) δ: 18.0, 19.7, 32.4, 79.2, 126.3, 129.7, 130.6, 132.3, 136.4, 136.7, 163.8, 169.6. LC-MC (Q-TOF) m/z; [M+H+] calculated C₁₃H₁₇N₄S⁺ = 261.116, found 261.118.

Elemental analysis: calculated; C₁₃H₁₆N₄S = 260.1168, C, 59.97; H, 6.19; N, 21.52; S, 12.31%. Found; C₁₃H₁₆N₄S = 260.1168, C, 59.8882; H, 6.0750; N, 21.3749; S, 12.3001%.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were refined isotropically by a mixture of independent and constrained refinement.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₆N₄S
M_r	260.36
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	14.482 (3), 9.3850 (19), 10.590 (2)
β (°)	108.07 (3)
V (Å³)	1368.3 (5)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	2.00
Crystal size (mm)	0.2 × 0.1 × 0.07

Data collection
Diffractometer	Bruker D8 VENTURE dual wavelength Mo/Cu
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.64, 0.87
No. of measured, independent and observed [I > 2σ(I)] reflections	37911, 2329, 2057
R_int	0.040
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.149, 1.08
No. of reflections	2329
No. of parameters	181
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.57, −0.21
Computer programs: APEX5 and SAINT (Bruker, 2016 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2431935

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989025002440/ex2091sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989025002440/ex2091Isup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989025002440/ex2091Isup3.cml

checkCIF report

Computing details top

2-[(2,4-Dimethylbenzyl)sulfanyl]pyrimidine-4,6-diamine top

Crystal data top

C₁₃H₁₆N₄S	F(000) = 552
M_r = 260.36	D_x = 1.264 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 14.482 (3) Å	Cell parameters from 9926 reflections
b = 9.3850 (19) Å	θ = 5.7–66.3°
c = 10.590 (2) Å	µ = 2.00 mm⁻¹
β = 108.07 (3)°	T = 293 K
V = 1368.3 (5) Å³	Prism, colourless
Z = 4	0.2 × 0.1 × 0.07 mm

Data collection top

Bruker D8 VENTURE dual wavelength Mo/Cu diffractometer	2329 independent reflections
Radiation source: microfocus sealed X-ray tube, INCOATEC IµS	2057 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.040
Detector resolution: 7.3910 pixels mm^-1	θ_max = 66.6°, θ_min = 5.7°
φ and ω scans	h = −16→16
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −11→11
T_min = 0.64, T_max = 0.87	l = −12→12
37911 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.149	w = 1/[σ²(F_o²) + (0.068P)² + 0.8542P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
2329 reflections	Δρ_max = 0.57 e Å⁻³
181 parameters	Δρ_min = −0.21 e Å⁻³
0 restraints

Special details top

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) top

	x	y	z	U_iso*/U_eq
S1	0.70925 (6)	0.22323 (8)	0.45344 (7)	0.0692 (3)
N2	0.58768 (15)	0.0155 (2)	0.4032 (2)	0.0564 (5)
N1	0.66759 (16)	0.0540 (2)	0.2395 (2)	0.0577 (5)
N3	0.6348 (2)	−0.0867 (4)	0.0539 (3)	0.0772 (8)
N4	0.4784 (2)	−0.1665 (3)	0.3859 (3)	0.0711 (7)
C4	0.64938 (18)	0.0803 (3)	0.3523 (2)	0.0531 (6)
C1	0.61661 (19)	−0.0562 (3)	0.1686 (2)	0.0562 (6)
C2	0.5520 (2)	−0.1347 (3)	0.2127 (3)	0.0598 (7)
H2	0.518848	−0.211765	0.164224	0.072*
C3	0.53829 (19)	−0.0950 (3)	0.3309 (2)	0.0555 (6)
C6	0.81963 (19)	0.4397 (3)	0.4079 (3)	0.0598 (7)
C7	0.88069 (19)	0.4817 (3)	0.5314 (3)	0.0623 (7)
C8	0.8975 (2)	0.6268 (4)	0.5536 (3)	0.0770 (8)
H8	0.937665	0.657394	0.635863	0.092*
C9	0.8560 (3)	0.7274 (3)	0.4561 (4)	0.0847 (10)
C10	0.7976 (2)	0.6828 (4)	0.3357 (4)	0.0923 (11)
H10	0.770351	0.749011	0.269275	0.111*
C11	0.7789 (2)	0.5421 (4)	0.3123 (4)	0.0805 (9)
H11	0.737651	0.513470	0.230042	0.097*
C5	0.7966 (2)	0.2853 (3)	0.3734 (3)	0.0692 (8)
H5A	0.855552	0.228946	0.403493	0.083*
H5B	0.769744	0.274625	0.277885	0.083*
C12	0.9274 (3)	0.3764 (4)	0.6386 (3)	0.0899 (10)
H12A	0.980309	0.421258	0.704739	0.135*
H12B	0.951482	0.297020	0.600929	0.135*
H12C	0.880392	0.343347	0.678883	0.135*
C13	0.8798 (4)	0.8847 (4)	0.4839 (6)	0.1331 (18)
H13A	0.849016	0.939278	0.405419	0.200*
H13B	0.948811	0.898122	0.508998	0.200*
H13C	0.856385	0.915894	0.554811	0.200*
H3A	0.675 (3)	−0.036 (4)	0.030 (3)	0.085 (11)*
H3B	0.603 (2)	−0.150 (4)	0.007 (3)	0.070 (10)*
H4A	0.437 (2)	−0.222 (3)	0.332 (3)	0.071 (9)*
H4B	0.466 (2)	−0.124 (3)	0.450 (3)	0.072 (9)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0831 (5)	0.0680 (5)	0.0734 (5)	−0.0215 (3)	0.0488 (4)	−0.0164 (3)
N2	0.0670 (13)	0.0534 (12)	0.0586 (12)	−0.0058 (10)	0.0338 (10)	−0.0031 (10)
N1	0.0677 (13)	0.0592 (12)	0.0537 (12)	−0.0022 (10)	0.0296 (10)	0.0014 (10)
N3	0.096 (2)	0.0867 (19)	0.0632 (15)	−0.0224 (16)	0.0454 (15)	−0.0157 (14)
N4	0.0889 (18)	0.0677 (15)	0.0719 (16)	−0.0251 (14)	0.0468 (14)	−0.0155 (13)
C4	0.0594 (14)	0.0509 (13)	0.0554 (14)	0.0026 (11)	0.0274 (11)	0.0025 (11)
C1	0.0633 (15)	0.0597 (15)	0.0500 (13)	0.0048 (12)	0.0240 (11)	0.0012 (11)
C2	0.0680 (16)	0.0579 (15)	0.0597 (15)	−0.0052 (12)	0.0288 (12)	−0.0069 (12)
C3	0.0626 (15)	0.0524 (14)	0.0581 (14)	0.0009 (11)	0.0286 (12)	0.0027 (11)
C6	0.0559 (15)	0.0639 (16)	0.0697 (17)	−0.0036 (12)	0.0345 (13)	0.0030 (13)
C7	0.0552 (15)	0.0678 (17)	0.0722 (17)	−0.0032 (12)	0.0317 (13)	0.0024 (13)
C8	0.0640 (18)	0.083 (2)	0.089 (2)	−0.0123 (15)	0.0304 (15)	−0.0116 (17)
C9	0.077 (2)	0.0590 (18)	0.129 (3)	0.0018 (15)	0.047 (2)	0.0057 (19)
C10	0.067 (2)	0.086 (2)	0.119 (3)	0.0026 (17)	0.023 (2)	0.031 (2)
C11	0.0671 (18)	0.085 (2)	0.089 (2)	−0.0080 (16)	0.0251 (16)	0.0186 (18)
C5	0.0748 (18)	0.0703 (18)	0.0786 (19)	−0.0111 (14)	0.0473 (15)	−0.0064 (14)
C12	0.080 (2)	0.111 (3)	0.078 (2)	−0.0021 (19)	0.0240 (17)	0.020 (2)
C13	0.129 (4)	0.072 (2)	0.197 (5)	−0.006 (2)	0.048 (4)	−0.008 (3)

Geometric parameters (Å, º) top

S1—C4	1.767 (3)	C7—C8	1.390 (4)
S1—C5	1.823 (3)	C7—C12	1.500 (4)
N2—C4	1.326 (3)	C8—H8	0.9300
N2—C3	1.354 (3)	C8—C9	1.390 (5)
N1—C4	1.323 (3)	C9—C10	1.359 (5)
N1—C1	1.354 (3)	C9—C13	1.524 (5)
N3—C1	1.351 (3)	C10—H10	0.9300
N3—H3A	0.85 (4)	C10—C11	1.355 (5)
N3—H3B	0.82 (3)	C11—H11	0.9300
N4—C3	1.362 (3)	C5—H5A	0.9700
N4—H4A	0.87 (3)	C5—H5B	0.9700
N4—H4B	0.86 (3)	C12—H12A	0.9600
C1—C2	1.381 (4)	C12—H12B	0.9600
C2—H2	0.9300	C12—H12C	0.9600
C2—C3	1.379 (4)	C13—H13A	0.9600
C6—C7	1.390 (4)	C13—H13B	0.9600
C6—C11	1.388 (4)	C13—H13C	0.9600
C6—C5	1.505 (4)

C4—S1—C5	103.99 (13)	C9—C8—H8	119.1
C4—N2—C3	115.2 (2)	C8—C9—C13	119.7 (4)
C4—N1—C1	114.6 (2)	C10—C9—C8	119.2 (3)
C1—N3—H3A	119 (2)	C10—C9—C13	121.1 (4)
C1—N3—H3B	118 (2)	C9—C10—H10	119.9
H3A—N3—H3B	122 (3)	C11—C10—C9	120.2 (3)
C3—N4—H4A	115 (2)	C11—C10—H10	119.9
C3—N4—H4B	115 (2)	C6—C11—H11	119.1
H4A—N4—H4B	122 (3)	C10—C11—C6	121.7 (3)
N2—C4—S1	111.56 (18)	C10—C11—H11	119.1
N1—C4—S1	119.41 (19)	S1—C5—H5A	109.8
N1—C4—N2	129.0 (2)	S1—C5—H5B	109.8
N1—C1—C2	122.0 (2)	C6—C5—S1	109.16 (19)
N3—C1—N1	115.8 (3)	C6—C5—H5A	109.8
N3—C1—C2	122.1 (3)	C6—C5—H5B	109.8
C1—C2—H2	121.1	H5A—C5—H5B	108.3
C3—C2—C1	117.8 (2)	C7—C12—H12A	109.5
C3—C2—H2	121.1	C7—C12—H12B	109.5
N2—C3—N4	115.5 (2)	C7—C12—H12C	109.5
N2—C3—C2	121.4 (2)	H12A—C12—H12B	109.5
N4—C3—C2	123.0 (3)	H12A—C12—H12C	109.5
C7—C6—C5	122.0 (3)	H12B—C12—H12C	109.5
C11—C6—C7	119.5 (3)	C9—C13—H13A	109.5
C11—C6—C5	118.5 (3)	C9—C13—H13B	109.5
C6—C7—C8	117.7 (3)	C9—C13—H13C	109.5
C6—C7—C12	122.1 (3)	H13A—C13—H13B	109.5
C8—C7—C12	120.2 (3)	H13A—C13—H13C	109.5
C7—C8—H8	119.1	H13B—C13—H13C	109.5
C7—C8—C9	121.8 (3)

N1—C1—C2—C3	1.8 (4)	C7—C6—C5—S1	76.3 (3)
N3—C1—C2—C3	−179.9 (3)	C7—C8—C9—C10	−0.2 (5)
C4—S1—C5—C6	154.6 (2)	C7—C8—C9—C13	−177.8 (3)
C4—N2—C3—N4	176.9 (2)	C8—C9—C10—C11	1.1 (5)
C4—N2—C3—C2	−0.4 (4)	C9—C10—C11—C6	−1.3 (5)
C4—N1—C1—N3	−179.1 (3)	C11—C6—C7—C8	0.4 (4)
C4—N1—C1—C2	−0.8 (4)	C11—C6—C7—C12	−179.7 (3)
C1—N1—C4—S1	−178.90 (18)	C11—C6—C5—S1	−104.2 (3)
C1—N1—C4—N2	−1.1 (4)	C5—S1—C4—N2	175.2 (2)
C1—C2—C3—N2	−1.2 (4)	C5—S1—C4—N1	−6.7 (3)
C1—C2—C3—N4	−178.3 (3)	C5—C6—C7—C8	179.9 (2)
C3—N2—C4—S1	179.62 (18)	C5—C6—C7—C12	−0.2 (4)
C3—N2—C4—N1	1.7 (4)	C5—C6—C11—C10	−179.0 (3)
C6—C7—C8—C9	−0.6 (4)	C12—C7—C8—C9	179.5 (3)
C7—C6—C11—C10	0.5 (5)	C13—C9—C10—C11	178.8 (4)

Hydrogen-bond geometry (Å, º) top

Cg2 is the centroid of the C6–C11 ring.

D—H···A	D—H	H···A	D···A	D—H···A
C10—H10···C1ⁱ	0.93	2.82	3.623 (4)	145
N3—H3B···N4ⁱⁱ	0.82 (3)	2.54 (3)	3.340 (5)	168 (3)
N4—H4A···N1ⁱⁱⁱ	0.87 (3)	2.56 (3)	3.372 (4)	156 (3)
N4—H4A···C4ⁱⁱⁱ	0.87 (3)	2.70 (4)	3.540 (4)	164 (3)
N4—H4B···N2^iv	0.86 (3)	2.19 (3)	3.039 (3)	172 (3)
N3—H3A···Cg2^v	0.85 (4)	2.89 (4)	3.561 (3)	137 (3)

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

Acknowledgements

BT is grateful to the Frank H. Allen International Research and Education (FAIRE) programme, provided by the Cambridge Crystallographic Data Centre (CCDC), for the opportunity to use the Cambridge Structural Database (CSD)

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-di­methyl­benz­yl)sulfan­yl]pyrimidine-4,6-di­amine

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Hirshfeld surface analysis

5. Database survey

6. Synthesis and crystallization

7. Refinement

Supporting information

Acknowledgements

References

research communications

Synthesis, crystal structure and Hirshfeld surface analysis of 2-[(2,4-dimethylbenzyl)sulfanyl]pyrimidine-4,6-diamine

3. Supramolecular features