Crystal structure and Hirshfeld surface analysis of 5,5-di­chloro-2-(di­chloro­meth­yl)-6,6-dimethyl-5,6-di­hydro­pyrimidin-4-amine

Gurbanov, A.V.; Akkurt, M.; Manahelohe, G.M.

doi:10.1107/S2056989025009247

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Volume 81| Part 12| December 2025| Pages 1111-1114

https://doi.org/10.1107/S2056989025009247

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Crystal structure and Hirshfeld surface analysis of 5,5-dichloro-2-(dichloromethyl)-6,6-dimethyl-5,6-dihydropyrimidin-4-amine

Atash V. Gurbanov,^a Mehmet Akkurt ^b and Gizachew Mulugeta Manahelohe ^c ^*

^aExcellence Center, Baku State University, Z. Khalilov Str. 33, AZ 1148, Baku, Azerbaijan, ^bDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye, and ^cDepartment of Chemistry, University of Gondar, PO Box 196, Gondar, Ethiopia
^*Correspondence e-mail: [email protected]

Edited by L. Van Meervelt, Katholieke Universiteit Leuven, Belgium (Received 15 October 2025; accepted 21 October 2025; online 6 November 2025)

In the title compound, C₇H₉Cl₄N₃, the central 4,5-dihydropyrimidine ring adopts an approximate twist-boat conformation. In the crystal, molecules are connected in the [101] direction by ribbons of N—H⋯N hydrogen-bonded dimers with an R²₂(8) motif.

Keywords: crystal structure; 4,5-dihydropyrimidine; hydrogen bonds; dimers; Hirshfeld surface analysis.

CCDC reference: 2237849

1. Chemical context

N-containing compounds have attracted much attention due to their properties in the fields of molecular recognition, crystal engineering, catalysis, coordination chemistry and organic synthesis (Gadzhieva et al., 2005 ; Maharramov et al., 2011 ; Gurbanov et al., 2022 ; Polyanskii et al., 2019 ). Depending on the main N-skeleton as well as the attached substituents, the supramolecular arrangements and catalytic activity of the corresponding metal complexes can be regulated (Aliyeva et al., 2024 ; Gurbanov et al., 2018 ; Huseynov et al., 2018 ). Numerous synthetic strategies for the synthesis of new N-containing compounds have been developed including metal-mediated synthesis (Gurbanov et al., 2023 ; Mahmudov et al., 2023 ). Attachment of –Cl and –NH₂ groups on the N-heterocycle can alter the supramolecular mode of the corresponding organic materials. Thus, in the current work we have synthesized the title compound, which provides multiple intermolecular non-covalent interactions.

2. Structural commentary

The central 4,5-dihydropyrimidine ring exhibits an approximate twist-boat conformation. Atoms C1/C2/N1/N2 are almost coplanar (r.m.s. deviation = 0.006 Å) and C3 and C4 deviate from their best plane by 0.824 (2) and 0.317 (2) Å, respectively. The molecule features a short intramolecular N—H⋯Cl contact (Fig. 1; Table 1) forming a C(5) motif (Bernstein et al., 1995 ). The C—N distances in the 4,5-dihydropyrimidine ring are consistent with single- and double-bond characteristics [C1=N2 = 1.276 (2), C4=N1 = 1.307 (2) C2—N2 = 1.473 (2), C1—N1 = 1.387 (2) and C4—N3 = 1.313 (2) Å]. The single C—N bond length [1.313 (2) Å] for the NH₂ group attached to the pyrimidine ring is significantly shorter than a typical C—N single bond (around 1.47 Å). The other bond lengths and angles are comparable to those in the structures discussed in the Database survey section.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N1ⁱ	0.90	2.08	2.978 (2)	174
C5—H5A⋯N2ⁱⁱ	0.98	2.54	3.506 (3)	170
Symmetry codes: (i) ; (ii) .

Figure 1
The title molecule with the atom-labelling scheme and displacement ellipsoids drawn at the 30% probability level. Short intramolecular H⋯Cl contacts are indicated by dashed lines.

3. Supramolecular features and Hirshfeld surface analysis

In the crystal, molecules are linked into dimers with an R₂²(8) motif by N—H⋯N hydrogen bonds, forming ribbons in the [10 $[\overline{1}]$ ] direction, which also feature pairwise C—H⋯N hydrogen bonds (Table 1; Figs. 2, 3 and 4). No C—H⋯π or π–π interactions are found. van der Waals interactions between the ribbons consolidate the crystal structure.

Figure 2
Partial packing of the title compound in the unit cell, showing N—H⋯N and C—H⋯N hydrogen bonds as dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity.

Figure 3
The view of the interactions shown in Fig. 2

from the b-axis.

Figure 4
The view of the interactions shown in Fig. 2

from the c-axis.

Crystal Explorer 17.5 (Spackman et al., 2021 ) was utilized to generate Hirshfeld surfaces (Fig. 5) and two-dimensional fingerprint plots (Fig. 6) in order to quantify the intermolecular interactions in the crystal (Table 1). The most important Cl⋯H/H⋯Cl interactions appear as two symmetrical broad wings with d_e + d_i = 2.85 Å and contribute 42.9% to the Hirshfeld surface (Fig. 6b). The intermolecular H⋯H contacts, contributing 25.9% to the overall crystal packing, are reflected in Fig. 6c as widely scattered points of high density due to the large hydrogen content of the molecule, with the tip at d_e = d_i = 1.25 Å. The observed Cl⋯Cl contact distance of 3.5355 (8) Å is slightly longer than the conventional 3.50 Å van der Waals separation. The Cl⋯Cl contacts (16.2%) have an arrow-shaped distribution of points with the tip at d_e = d_i = 1.75 Å (Fig. 6d). The N⋯H/H⋯N interactions represent 9.5% of the total Hirshfeld surface. These interactions are manifested as two symmetrical sharp spikes at d_e + d_i = 1.95 Å (Fig. 6a). The Cl⋯N/N⋯Cl (4.4%), Cl⋯C/C⋯Cl (0.7%) and C⋯H/H⋯C (0.4%) interactions all contribute in smaller ways.

Figure 5
View of the three-dimensional Hirshfeld surface of the compound plotted over d_norm.

Figure 6
The two-dimensional fingerprint plots, showing (a) all interactions, and delineated into (b) Cl⋯H/H⋯Cl, (c) H⋯H and (d) Cl⋯Cl interactions [d_e and d_i represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (internal) the surface, respectively].

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 6.00, update of April 2025; Groom et al., 2016 ) for 4,5-dihydropyrimidine resulted in 77 hits. Entries KIMHIB (Wan et al., 2023 ) and ZEDLOJ (Mori & Maeda, 1994 ) are the closest analogues of the title compound.

KIMHIB crystallizes with two independent molecules (A and B) in the asymmetric unit of the orthorhombic space group Pna2₁. ZEDLOJ crystallizes in the monoclinic space group A2/a. In KIMHIB, the dihydropyrimidine ring of molecule A adopts a distorted screw-boat conformation with ring puckering parameters Q_T = 0.433 (6) Å, θ = 112.2 (8)° and φ = 328.7 (9)°, whereas the dihydropyrimidine ring of molecule B exhibits a distorted twist-boat conformation [Q_T = 0.459 (6) Å, θ = 109.2 (7)°, φ = 81.1 (8)°]. In ZEDLOJ, the central pyrimidine ring adopts a distorted screw-boat conformation [Q_T = 0.462 (2) Å, θ = 67.2 (2) °, φ = 216.1 (3) °]. Idealized values for screw-boat and twist-boat conformations are: θ = 67.5° and 90°, and φ = (60k + 30)°, respectively, where k is an integer.

In KIMHIB, the molecular conformation may be associated with C—H⋯N intramolecular interactions. In the crystal, molecules form layers parallel to the (100) plane via C—H⋯π interactions with van der Waals interactions between the layers, no π–π interactions are observed. In ZEDLOJ, the molecular conformation may be supported by C—H⋯N hydrogen bonds. Classical intermolecular hydrogen bonds are not observed, with C—H⋯π and van der Waals interactions consolidating of the structure.

5. Synthesis and crystallization

To a mixture of 0.5 ml dichloroacetonitrile and 1.5 ml of NH₄OH (28–30%) solution was added 10 mg of Pd(CH₃COO)₂ in 5 ml acetone. The mixture was stirred for 24 h at r.t. The precipitate was filtered and dissolved in CH₂Cl₂. Light-yellow crystals of the title compound suitable for X-ray structural analysis were obtained after ca 2 d. Yield 60%; IR (ATR, 298 K): 3320 and 3203 ν(N—H), 1641 and 1602 ν(C=N); M_r = 276.97; elemental analysis calculated (%) for C₇H₉Cl₄N₃: C 30.36, H 3.28, N 15.17; found: C 30.33, H 3.27, N 15.14. ¹H NMR in DMSO-d₆, δ(p.p.m.): 1.98 (3H, –CH₃) and 2.07 (3H,–CH₃), 5.91 (1H, –CHCl₂), 8.35 (2H,–NH₂). ¹³C NMR in DMSO-d₆, δ (p.p.m.): 18.62 and 23.65 (–CH₃), 67.02 (–CCH₃), 70.99 (–CHCl₂), 112.44 (–CCl₂–), 150.51 and 165.34 (C=N).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The hydrogen atoms were placed in calculated positions and refined as riding models with fixed isotropic displacement parameters [C—H = 0.96 and 0.98 Å, N—H = 0.90 Å with U_iso(H) = 1.2U_eq(N, C)].

Table 2
Experimental details

Crystal data
Chemical formula	C₇H₉Cl₄N₃
M_r	276.97
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	296
a, b, c (Å)	6.1069 (3), 9.1118 (4), 10.2591 (5)
α, β, γ (°)	90.981 (2), 96.700 (2), 95.980 (2)
V (Å³)	563.63 (5)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	1.01
Crystal size (mm)	0.25 × 0.18 × 0.12

Data collection
Diffractometer	Bruker D8 Quest PHOTON 100 detector
Absorption correction	Multi-scan (SADABS; Krause et al., 2015
T_min, T_max	0.793, 0.874
No. of measured, independent and observed [I > 2σ(I)] reflections	8178, 2272, 1998
R_int	0.037
(sin θ/λ)_max (Å⁻¹)	0.626

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.083, 1.07
No. of reflections	2272
No. of parameters	129
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.39, −0.36
Computer programs: APEX3 and SAINT (Bruker, 2008 ), SHELXS97 (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2020 ).

Supporting information

CCDC reference: 2237849

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989025009247/vm2318sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989025009247/vm2318Isup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989025009247/vm2318Isup3.cml

checkCIF report

Computing details top

5,5-Dichloro-2-(dichloromethyl)-6,6-dimethyl-5,6-dihydropyrimidin-4-amine top

Crystal data top

C₇H₉Cl₄N₃	Z = 2
M_r = 276.97	F(000) = 280
Triclinic, P1	D_x = 1.632 Mg m⁻³
a = 6.1069 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.1118 (4) Å	Cell parameters from 5453 reflections
c = 10.2591 (5) Å	θ = 3.1–26.4°
α = 90.981 (2)°	µ = 1.01 mm⁻¹
β = 96.700 (2)°	T = 296 K
γ = 95.980 (2)°	Plate, light-yellow
V = 563.63 (5) Å³	0.25 × 0.18 × 0.12 mm

Data collection top

Bruker D8 Quest PHOTON 100 detector diffractometer	1998 reflections with I > 2σ(I)
Detector resolution: 0 pixels mm^-1	R_int = 0.037
φ and ω scans	θ_max = 26.4°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Krause et al., 2015	h = −7→7
T_min = 0.793, T_max = 0.874	k = −11→11
8178 measured reflections	l = −12→11
2272 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: structure-invariant direct methods
R[F² > 2σ(F²)] = 0.033	Hydrogen site location: mixed
wR(F²) = 0.083	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0247P)² + 0.3903P] where P = (F_o² + 2F_c²)/3
2272 reflections	(Δ/σ)_max = 0.001
129 parameters	Δρ_max = 0.39 e Å⁻³
0 restraints	Δρ_min = −0.36 e Å⁻³

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
C1	0.2993 (3)	0.46088 (19)	0.77624 (17)	0.0290 (4)
C2	0.1477 (3)	0.2365 (2)	0.85204 (18)	0.0327 (4)
C3	0.1199 (3)	0.18825 (19)	0.70582 (18)	0.0291 (4)
C4	0.0636 (3)	0.3194 (2)	0.62278 (17)	0.0281 (4)
C5	0.4578 (3)	0.5991 (2)	0.8006 (2)	0.0368 (4)
H5A	0.535164	0.597285	0.889662	0.044*
C6	−0.0758 (4)	0.2743 (3)	0.8909 (2)	0.0470 (5)
H6A	−0.053847	0.318689	0.977638	0.071*
H6B	−0.176096	0.185742	0.889584	0.071*
H6C	−0.136976	0.342158	0.829808	0.071*
C7	0.2421 (4)	0.1190 (2)	0.9398 (2)	0.0471 (5)
H7A	0.238776	0.146708	1.030174	0.071*
H7B	0.392426	0.110595	0.924333	0.071*
H7C	0.154603	0.025863	0.920024	0.071*
Cl1	0.65595 (12)	0.60821 (8)	0.68869 (9)	0.0749 (2)
Cl2	0.31392 (11)	0.75861 (6)	0.78797 (6)	0.05086 (18)
Cl3	0.37541 (9)	0.13811 (6)	0.65640 (6)	0.04623 (16)
Cl4	−0.08182 (8)	0.03163 (5)	0.67338 (5)	0.04116 (15)
N1	0.1654 (3)	0.45015 (16)	0.65682 (14)	0.0299 (3)
N2	0.3036 (3)	0.37185 (17)	0.87098 (15)	0.0344 (4)
N3	−0.0794 (3)	0.29820 (18)	0.51650 (16)	0.0399 (4)
H3A	−0.114976	0.373990	0.465988	0.048*
H3B	−0.140745	0.207580	0.487858	0.048*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0314 (9)	0.0258 (8)	0.0287 (9)	0.0033 (7)	−0.0013 (7)	0.0040 (7)
C2	0.0379 (10)	0.0298 (9)	0.0281 (9)	−0.0019 (8)	−0.0017 (7)	0.0068 (7)
C3	0.0288 (8)	0.0252 (8)	0.0320 (9)	0.0023 (7)	−0.0016 (7)	0.0036 (7)
C4	0.0304 (9)	0.0296 (9)	0.0243 (8)	0.0051 (7)	0.0014 (7)	0.0044 (7)
C5	0.0409 (10)	0.0280 (9)	0.0384 (10)	−0.0005 (8)	−0.0062 (8)	0.0081 (8)
C6	0.0519 (13)	0.0490 (13)	0.0421 (12)	0.0011 (10)	0.0176 (10)	0.0011 (10)
C7	0.0578 (13)	0.0369 (11)	0.0411 (12)	−0.0043 (10)	−0.0108 (10)	0.0179 (9)
Cl1	0.0567 (4)	0.0623 (4)	0.1098 (6)	−0.0065 (3)	0.0378 (4)	0.0052 (4)
Cl2	0.0716 (4)	0.0310 (3)	0.0473 (3)	0.0127 (2)	−0.0098 (3)	−0.0047 (2)
Cl3	0.0395 (3)	0.0437 (3)	0.0588 (3)	0.0141 (2)	0.0107 (2)	0.0032 (2)
Cl4	0.0436 (3)	0.0295 (2)	0.0461 (3)	−0.00512 (19)	−0.0052 (2)	0.0032 (2)
N1	0.0350 (8)	0.0266 (7)	0.0266 (7)	0.0031 (6)	−0.0034 (6)	0.0062 (6)
N2	0.0422 (9)	0.0291 (8)	0.0284 (8)	−0.0025 (7)	−0.0062 (7)	0.0064 (6)
N3	0.0512 (10)	0.0306 (8)	0.0330 (9)	0.0007 (7)	−0.0132 (7)	0.0041 (7)

Geometric parameters (Å, º) top

C1—N2	1.276 (2)	C5—Cl1	1.760 (2)
C1—N1	1.387 (2)	C5—Cl2	1.774 (2)
C1—C5	1.504 (2)	C5—H5A	0.9800
C2—N2	1.473 (2)	C6—H6A	0.9600
C2—C7	1.526 (3)	C6—H6B	0.9600
C2—C6	1.536 (3)	C6—H6C	0.9600
C2—C3	1.541 (3)	C7—H7A	0.9600
C3—C4	1.525 (2)	C7—H7B	0.9600
C3—Cl4	1.7851 (18)	C7—H7C	0.9600
C3—Cl3	1.7960 (19)	N3—H3A	0.9000
C4—N1	1.307 (2)	N3—H3B	0.9001
C4—N3	1.313 (2)

N2—C1—N1	129.26 (17)	C1—C5—H5A	108.5
N2—C1—C5	114.72 (16)	Cl1—C5—H5A	108.5
N1—C1—C5	115.98 (15)	Cl2—C5—H5A	108.5
N2—C2—C7	107.95 (15)	C2—C6—H6A	109.5
N2—C2—C6	107.44 (16)	C2—C6—H6B	109.5
C7—C2—C6	111.29 (18)	H6A—C6—H6B	109.5
N2—C2—C3	108.66 (14)	C2—C6—H6C	109.5
C7—C2—C3	111.77 (17)	H6A—C6—H6C	109.5
C6—C2—C3	109.58 (16)	H6B—C6—H6C	109.5
C4—C3—C2	108.96 (15)	C2—C7—H7A	109.5
C4—C3—Cl4	112.61 (12)	C2—C7—H7B	109.5
C2—C3—Cl4	111.15 (13)	H7A—C7—H7B	109.5
C4—C3—Cl3	105.30 (12)	C2—C7—H7C	109.5
C2—C3—Cl3	111.34 (12)	H7A—C7—H7C	109.5
Cl4—C3—Cl3	107.34 (10)	H7B—C7—H7C	109.5
N1—C4—N3	121.44 (17)	C4—N1—C1	116.08 (15)
N1—C4—C3	118.94 (15)	C1—N2—C2	116.41 (15)
N3—C4—C3	119.58 (16)	C4—N3—H3A	121.1
C1—C5—Cl1	110.83 (14)	C4—N3—H3B	122.3
C1—C5—Cl2	110.93 (14)	H3A—N3—H3B	116.6
Cl1—C5—Cl2	109.46 (11)

N2—C2—C3—C4	−51.33 (19)	Cl3—C3—C4—N3	98.37 (18)
C7—C2—C3—C4	−170.35 (16)	N2—C1—C5—Cl1	117.03 (17)
C6—C2—C3—C4	65.79 (19)	N1—C1—C5—Cl1	−64.87 (19)
N2—C2—C3—Cl4	−176.00 (12)	N2—C1—C5—Cl2	−121.15 (17)
C7—C2—C3—Cl4	64.98 (19)	N1—C1—C5—Cl2	56.9 (2)
C6—C2—C3—Cl4	−58.88 (18)	N3—C4—N1—C1	175.14 (18)
N2—C2—C3—Cl3	64.38 (17)	C3—C4—N1—C1	−7.3 (2)
C7—C2—C3—Cl3	−54.64 (19)	N2—C1—N1—C4	−16.6 (3)
C6—C2—C3—Cl3	−178.50 (13)	C5—C1—N1—C4	165.66 (17)
C2—C3—C4—N1	40.3 (2)	N1—C1—N2—C2	1.1 (3)
Cl4—C3—C4—N1	164.11 (14)	C5—C1—N2—C2	178.85 (16)
Cl3—C3—C4—N1	−79.24 (18)	C7—C2—N2—C1	155.08 (19)
C2—C3—C4—N3	−142.10 (18)	C6—C2—N2—C1	−84.8 (2)
Cl4—C3—C4—N3	−18.3 (2)	C3—C2—N2—C1	33.7 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N1ⁱ	0.90	2.08	2.978 (2)	174
N3—H3B···Cl4	0.90	2.53	2.9364 (17)	108
C5—H5A···N2ⁱⁱ	0.98	2.54	3.506 (3)	170
C6—H6B···Cl4	0.96	2.75	3.109 (2)	103
C7—H7B···Cl3	0.96	2.76	3.112 (2)	103
C7—H7C···Cl4	0.96	2.77	3.218 (2)	110

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

Short interatomic contacts (Å) top

Contact	Distance	Symmetry operation
Cl1···H6C	3.15	1+x,y,z
Cl2···H7C	3.07	x,1+y,z
H3A···N1	2.08	-x,1-y,1-z
H6A···Cl2	3.08	-x,1-y,2-z
H5A···N2	2.54	1-x,1-y,2-z

Acknowledgements

This work has been supported by the Baku State University (Azerbaijan). The authors' contributions are as follows. Conceptualization, AVG, MA and GMM; synthesis and X-ray analysis AVG; writing (review and editing of the manuscript) AVG and MA; funding acquisition, AVG; supervision, MA.

References

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