A concise and efficient synthesis of amino-substituted (1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the mol­ecular and supra­molecular structures of six examples

Vicentes, D.E.; Rodríguez, R.; Ochoa, P.; Cobo, J.; Glidewell, C.

doi:10.1107/S2053229619012087

A concise and efficient synthesis of amino-substituted (1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of six examples

D. E. Vicentes, R. Rodríguez, P. Ochoa, J. Cobo and C. Glidewell

A concise and efficient synthesis of a series of amino-substituted benzimidazole–pyrimidine hybrids has been developed, starting from the readily available N⁴-(2-aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine. In each of N⁵-benzyl-6-methoxy-4-(2-phenyl-1H-benzo[d]imidazol-1-yl)pyrimidine-2,5-diamine, C₂₅H₂₂N₆O, (I), 6-methoxy-N⁵-(4-methoxybenzyl)-4-[2-(4-methoxyphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine, C₂₇H₂₆N₆O₃, (III), 6-methoxy-N⁵-(4-nitrobenzyl)-4-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine, C₂₅H₂₀N₈O₅, (IV), the molecules are linked into three-dimensional framework structures, using different combinations of N—H

N, N—H

O, C—H

N and C—H

π hydrogen bonds in each case. Oxidative cleavage of 6-methoxy-N⁵-(4-methylbenzyl)-4-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine, (II), with diiodine gave 6-methoxy-4-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine, which crystallized as a monohydrate, C₁₉H₁₈N₆O·H₂O, (V), and reaction of (V) with trifluoroacetic acid gave two isomeric products, namely N-{5-amino-6-methoxy-6-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-2-yl}-2,2,2-trifluoroacetamide, which crystallized as an ethyl acetate monosolvate, C₂₁H₁₇F₃N₆O₂·C₄H₈O₂, (VI), and N-{2-amino-6-methoxy-4-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidin-5-yl}-2,2,2-trifluoroacetamide, which crystallized as a methanol monosolvate, C₂₁H₁₇F₃N₆O₂·CH₄O, (VIIa). For each of (V), (VI) and (VIIa), the supramolecular assembly is two-dimensional, based on different combinations of O—H

N, N—H

O, N—H

N, C—H

O and C—H

π hydrogen bonds in each case. Comparisons are made with some related structures.

Keywords: pyrimidine; benzimidazole; synthesis; NMR spectra; crystal structure; disorder; molecular conformation; hydrogen bonding; supramolecular assembly.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229619012087/ov3133sup1.cif Contains datablocks global, I, III, IV, V, VI, VIIa
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133Isup2.hkl Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133IIIsup3.hkl Contains datablock III
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133IVsup4.hkl Contains datablock IV
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133Vsup5.hkl Contains datablock V
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133VIsup6.hkl Contains datablock VI
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229619012087/ov3133VIIasup7.hkl Contains datablock VIIa
	Text file https://doi.org/10.1107/S2053229619012087/ov3133sup8.txt Spectroscopic details

CCDC references: 1950912; 1950913; 1950914; 1950915; 1950916; 1950917

Computing details top

For all structures, data collection: APEX3 (Bruker, 2018); cell refinement: SAINT (Bruker, 2017); data reduction: SAINT (Bruker, 2017); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b) and PLATON (Spek, 2009).

N⁴-(2-Aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine (I) top

Crystal data top

C₂₅H₂₂N₆O	F(000) = 888
M_r = 422.48	D_x = 1.281 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 9.7167 (10) Å	Cell parameters from 5059 reflections
b = 16.1179 (17) Å	θ = 2.5–27.6°
c = 13.9936 (16) Å	µ = 0.08 mm⁻¹
β = 91.395 (4)°	T = 100 K
V = 2190.9 (4) Å³	Block, yellow
Z = 4	0.17 × 0.12 × 0.07 mm

Data collection top

Bruker D8 Venture diffractometer	5058 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	3855 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.074
φ and ω scans	θ_max = 27.6°, θ_min = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −12→12
T_min = 0.804, T_max = 0.994	k = −20→20
29495 measured reflections	l = −17→18

Refinement top

Refinement on F²	Primary 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) = 0.122	w = 1/[σ²(F_o²) + (0.0386P)² + 1.5187P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max < 0.001
5058 reflections	Δρ_max = 0.27 e Å⁻³
300 parameters	Δρ_min = −0.30 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
N1	0.44106 (14)	0.28049 (9)	0.50796 (10)	0.0183 (3)
C2	0.46897 (15)	0.36310 (10)	0.50340 (11)	0.0141 (3)
N3	0.59427 (13)	0.39568 (8)	0.49381 (9)	0.0140 (3)
C4	0.69692 (15)	0.34142 (10)	0.48068 (11)	0.0140 (3)
C5	0.67928 (16)	0.25686 (10)	0.47145 (11)	0.0153 (3)
C6	0.54478 (17)	0.23081 (10)	0.49149 (12)	0.0177 (3)
N21	0.36176 (15)	0.41520 (9)	0.51036 (11)	0.0181 (3)
H21A	0.276 (2)	0.3974 (13)	0.5106 (14)	0.022*
H21B	0.377 (2)	0.4703 (14)	0.5079 (14)	0.022*
N41	0.83032 (13)	0.37716 (8)	0.47263 (9)	0.0143 (3)
C42	0.95045 (16)	0.35362 (10)	0.52036 (12)	0.0162 (3)
N43	1.06045 (14)	0.38499 (9)	0.48187 (10)	0.0183 (3)
C43A	1.01278 (16)	0.43055 (10)	0.40369 (12)	0.0175 (3)
C44	1.08609 (18)	0.47550 (11)	0.33630 (13)	0.0219 (4)
H44	1.1836	0.4792	0.3404	0.026*
C45	1.01237 (19)	0.51431 (11)	0.26371 (13)	0.0237 (4)
H45	1.0601	0.5448	0.2168	0.028*
C46	0.86878 (18)	0.50971 (11)	0.25777 (12)	0.0218 (4)
H46	0.8212	0.5375	0.2070	0.026*
C47	0.79399 (17)	0.46577 (10)	0.32380 (12)	0.0173 (3)
H47	0.6964	0.4624	0.3196	0.021*
C47A	0.86921 (16)	0.42699 (10)	0.39650 (12)	0.0153 (3)
C421	0.95487 (17)	0.30023 (10)	0.60518 (12)	0.0173 (3)
C422	0.84803 (18)	0.29808 (11)	0.67042 (12)	0.0211 (4)
H422	0.7696	0.3326	0.6613	0.025*
C423	0.8573 (2)	0.24526 (12)	0.74844 (13)	0.0276 (4)
H423	0.7851	0.2436	0.7929	0.033*
C424	0.9715 (2)	0.19489 (12)	0.76175 (13)	0.0294 (4)
H424	0.9764	0.1579	0.8146	0.035*
C425	1.0785 (2)	0.19806 (11)	0.69859 (14)	0.0274 (4)
H425	1.1573	0.1640	0.7086	0.033*
C426	1.07071 (18)	0.25088 (11)	0.62068 (13)	0.0214 (4)
H426	1.1447	0.2534	0.5776	0.026*
N51	0.78425 (14)	0.19982 (9)	0.45195 (11)	0.0184 (3)
H51	0.754 (3)	0.1504 (17)	0.4562 (18)	0.049 (7)*
C57	0.85661 (19)	0.20990 (11)	0.36183 (13)	0.0234 (4)
H57A	0.9099	0.2622	0.3636	0.028*
H57B	0.7887	0.2133	0.3081	0.028*
C51	0.95252 (16)	0.13792 (10)	0.34601 (12)	0.0180 (3)
C52	0.97164 (18)	0.10869 (11)	0.25391 (12)	0.0212 (4)
H52	0.9248	0.1345	0.2014	0.025*
C53	1.05844 (18)	0.04218 (12)	0.23798 (13)	0.0241 (4)
H53	1.0715	0.0231	0.1746	0.029*
C54	1.12609 (18)	0.00345 (11)	0.31372 (14)	0.0234 (4)
H54	1.1849	−0.0425	0.3027	0.028*
C55	1.10746 (18)	0.03214 (11)	0.40543 (13)	0.0242 (4)
H55	1.1535	0.0058	0.4578	0.029*
C56	1.02152 (18)	0.09950 (11)	0.42152 (13)	0.0230 (4)
H56	1.0101	0.1192	0.4848	0.028*
O61	0.52698 (12)	0.14793 (7)	0.49352 (10)	0.0279 (3)
C61	0.3919 (2)	0.11880 (13)	0.5156 (2)	0.0550 (8)
H61A	0.3249	0.1411	0.4689	0.082*
H61B	0.3683	0.1373	0.5798	0.082*
H61C	0.3903	0.0580	0.5131	0.082*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0146 (7)	0.0152 (7)	0.0250 (8)	−0.0016 (5)	0.0029 (5)	0.0015 (6)
C2	0.0139 (7)	0.0157 (8)	0.0128 (7)	−0.0002 (6)	0.0006 (6)	0.0004 (6)
N3	0.0126 (6)	0.0136 (7)	0.0158 (7)	0.0003 (5)	0.0011 (5)	−0.0012 (5)
C4	0.0122 (7)	0.0149 (8)	0.0149 (8)	−0.0016 (6)	0.0004 (6)	0.0011 (6)
C5	0.0143 (8)	0.0138 (8)	0.0177 (8)	0.0010 (6)	0.0003 (6)	0.0000 (6)
C6	0.0180 (8)	0.0127 (8)	0.0225 (9)	−0.0017 (6)	0.0011 (6)	0.0008 (6)
N21	0.0110 (7)	0.0158 (7)	0.0277 (8)	−0.0011 (5)	0.0018 (6)	−0.0012 (6)
N41	0.0116 (6)	0.0130 (6)	0.0184 (7)	−0.0004 (5)	0.0007 (5)	0.0009 (5)
C42	0.0142 (8)	0.0144 (8)	0.0201 (8)	0.0010 (6)	−0.0003 (6)	−0.0027 (6)
N43	0.0148 (7)	0.0177 (7)	0.0224 (7)	−0.0005 (5)	0.0028 (5)	0.0004 (6)
C43A	0.0159 (8)	0.0153 (8)	0.0214 (8)	−0.0006 (6)	0.0021 (6)	−0.0023 (6)
C44	0.0179 (8)	0.0231 (9)	0.0249 (9)	−0.0037 (7)	0.0056 (7)	−0.0003 (7)
C45	0.0283 (10)	0.0218 (9)	0.0214 (9)	−0.0049 (7)	0.0073 (7)	0.0024 (7)
C46	0.0280 (9)	0.0176 (8)	0.0197 (9)	0.0010 (7)	0.0003 (7)	0.0023 (7)
C47	0.0167 (8)	0.0142 (8)	0.0211 (8)	−0.0002 (6)	0.0011 (6)	−0.0017 (6)
C47A	0.0167 (8)	0.0105 (7)	0.0188 (8)	−0.0002 (6)	0.0029 (6)	−0.0012 (6)
C421	0.0183 (8)	0.0152 (8)	0.0182 (8)	−0.0029 (6)	−0.0034 (6)	−0.0005 (6)
C422	0.0222 (9)	0.0199 (9)	0.0210 (9)	−0.0023 (7)	−0.0018 (7)	−0.0013 (7)
C423	0.0355 (11)	0.0274 (10)	0.0201 (9)	−0.0088 (8)	0.0018 (8)	−0.0008 (7)
C424	0.0464 (12)	0.0201 (9)	0.0213 (9)	−0.0055 (8)	−0.0096 (8)	0.0041 (7)
C425	0.0326 (10)	0.0203 (9)	0.0287 (10)	0.0021 (7)	−0.0111 (8)	−0.0003 (8)
C426	0.0207 (9)	0.0184 (9)	0.0249 (9)	−0.0006 (7)	−0.0036 (7)	−0.0011 (7)
N51	0.0174 (7)	0.0121 (7)	0.0258 (8)	0.0010 (5)	0.0041 (6)	0.0007 (6)
C57	0.0283 (9)	0.0202 (9)	0.0221 (9)	0.0059 (7)	0.0043 (7)	0.0002 (7)
C51	0.0162 (8)	0.0144 (8)	0.0233 (9)	−0.0020 (6)	0.0020 (6)	−0.0029 (7)
C52	0.0213 (9)	0.0225 (9)	0.0198 (9)	0.0006 (7)	0.0016 (7)	−0.0015 (7)
C53	0.0230 (9)	0.0263 (9)	0.0234 (9)	0.0004 (7)	0.0063 (7)	−0.0078 (7)
C54	0.0175 (8)	0.0192 (9)	0.0337 (10)	0.0016 (7)	0.0061 (7)	−0.0052 (7)
C55	0.0224 (9)	0.0221 (9)	0.0281 (10)	0.0035 (7)	−0.0011 (7)	0.0006 (7)
C56	0.0249 (9)	0.0220 (9)	0.0220 (9)	0.0030 (7)	0.0006 (7)	−0.0052 (7)
O61	0.0191 (6)	0.0117 (6)	0.0533 (9)	−0.0037 (5)	0.0061 (6)	0.0007 (6)
C61	0.0238 (11)	0.0193 (10)	0.123 (2)	−0.0071 (8)	0.0183 (13)	0.0063 (13)

Geometric parameters (Å, º) top

N1—C6	1.312 (2)	C422—C423	1.386 (3)
N1—C2	1.361 (2)	C422—H422	0.9500
C2—N3	1.336 (2)	C423—C424	1.384 (3)
C2—N21	1.343 (2)	C423—H423	0.9500
N3—C4	1.343 (2)	C424—C425	1.382 (3)
C4—C5	1.379 (2)	C424—H424	0.9500
C4—N41	1.4254 (19)	C425—C426	1.384 (3)
C5—N51	1.405 (2)	C425—H425	0.9500
C5—C6	1.407 (2)	C426—H426	0.9500
C6—O61	1.347 (2)	N51—C57	1.468 (2)
N21—H21A	0.88 (2)	N51—H51	0.85 (3)
N21—H21B	0.90 (2)	C57—C51	1.508 (2)
N41—C42	1.384 (2)	C57—H57A	0.9900
N41—C47A	1.394 (2)	C57—H57B	0.9900
C42—N43	1.310 (2)	C51—C56	1.384 (2)
C42—C421	1.466 (2)	C51—C52	1.389 (2)
N43—C43A	1.388 (2)	C52—C53	1.385 (2)
C43A—C47A	1.397 (2)	C52—H52	0.9500
C43A—C44	1.398 (2)	C53—C54	1.382 (3)
C44—C45	1.379 (3)	C53—H53	0.9500
C44—H44	0.9500	C54—C55	1.380 (3)
C45—C46	1.398 (3)	C54—H54	0.9500
C45—H45	0.9500	C55—C56	1.391 (2)
C46—C47	1.384 (2)	C55—H55	0.9500
C46—H46	0.9500	C56—H56	0.9500
C47—C47A	1.387 (2)	O61—C61	1.434 (2)
C47—H47	0.9500	C61—H61A	0.9800
C421—C426	1.391 (2)	C61—H61B	0.9800
C421—C422	1.399 (2)	C61—H61C	0.9800

C6—N1—C2	115.73 (14)	C421—C422—H422	120.2
N3—C2—N21	118.15 (15)	C424—C423—C422	120.21 (18)
N3—C2—N1	124.94 (14)	C424—C423—H423	119.9
N21—C2—N1	116.90 (14)	C422—C423—H423	119.9
C2—N3—C4	116.08 (14)	C425—C424—C423	120.36 (17)
N3—C4—C5	124.43 (14)	C425—C424—H424	119.8
N3—C4—N41	115.31 (13)	C423—C424—H424	119.8
C5—C4—N41	120.21 (14)	C424—C425—C426	119.93 (18)
C4—C5—N51	125.15 (15)	C424—C425—H425	120.0
C4—C5—C6	112.96 (14)	C426—C425—H425	120.0
N51—C5—C6	121.70 (15)	C425—C426—C421	120.21 (17)
N1—C6—O61	120.12 (15)	C425—C426—H426	119.9
N1—C6—C5	125.02 (15)	C421—C426—H426	119.9
O61—C6—C5	114.85 (14)	C5—N51—C57	117.37 (14)
C2—N21—H21A	122.1 (13)	C5—N51—H51	110.3 (17)
C2—N21—H21B	119.1 (12)	C57—N51—H51	109.6 (17)
H21A—N21—H21B	118.4 (18)	N51—C57—C51	110.59 (14)
C42—N41—C47A	106.60 (13)	N51—C57—H57A	109.5
C42—N41—C4	127.52 (13)	C51—C57—H57A	109.5
C47A—N41—C4	123.87 (13)	N51—C57—H57B	109.5
N43—C42—N41	112.51 (14)	C51—C57—H57B	109.5
N43—C42—C421	123.46 (15)	H57A—C57—H57B	108.1
N41—C42—C421	124.02 (14)	C56—C51—C52	118.91 (16)
C42—N43—C43A	105.57 (13)	C56—C51—C57	121.46 (15)
N43—C43A—C47A	110.39 (14)	C52—C51—C57	119.62 (15)
N43—C43A—C44	129.81 (15)	C53—C52—C51	120.49 (17)
C47A—C43A—C44	119.80 (16)	C53—C52—H52	119.8
C45—C44—C43A	117.91 (16)	C51—C52—H52	119.8
C45—C44—H44	121.0	C54—C53—C52	120.41 (16)
C43A—C44—H44	121.0	C54—C53—H53	119.8
C44—C45—C46	121.31 (16)	C52—C53—H53	119.8
C44—C45—H45	119.3	C55—C54—C53	119.39 (16)
C46—C45—H45	119.3	C55—C54—H54	120.3
C47—C46—C45	121.80 (16)	C53—C54—H54	120.3
C47—C46—H46	119.1	C54—C55—C56	120.32 (17)
C45—C46—H46	119.1	C54—C55—H55	119.8
C46—C47—C47A	116.38 (15)	C56—C55—H55	119.8
C46—C47—H47	121.8	C51—C56—C55	120.47 (16)
C47A—C47—H47	121.8	C51—C56—H56	119.8
C47—C47A—N41	132.26 (15)	C55—C56—H56	119.8
C47—C47A—C43A	122.79 (15)	C6—O61—C61	116.59 (14)
N41—C47A—C43A	104.92 (14)	O61—C61—H61A	109.5
C426—C421—C422	119.63 (16)	O61—C61—H61B	109.5
C426—C421—C42	118.00 (15)	H61A—C61—H61B	109.5
C422—C421—C42	122.36 (15)	O61—C61—H61C	109.5
C423—C422—C421	119.61 (17)	H61A—C61—H61C	109.5
C423—C422—H422	120.2	H61B—C61—H61C	109.5

C6—N1—C2—N3	−7.4 (2)	C42—N41—C47A—C47	177.95 (17)
C6—N1—C2—N21	173.46 (15)	C4—N41—C47A—C47	13.0 (3)
N21—C2—N3—C4	−175.69 (14)	C42—N41—C47A—C43A	−0.24 (17)
N1—C2—N3—C4	5.2 (2)	C4—N41—C47A—C43A	−165.17 (14)
C2—N3—C4—C5	3.7 (2)	N43—C43A—C47A—C47	−178.79 (15)
C2—N3—C4—N41	−178.72 (13)	C44—C43A—C47A—C47	0.8 (3)
N3—C4—C5—N51	175.94 (15)	N43—C43A—C47A—N41	−0.39 (18)
N41—C4—C5—N51	−1.5 (2)	C44—C43A—C47A—N41	179.17 (15)
N3—C4—C5—C6	−9.0 (2)	N43—C42—C421—C426	−29.8 (2)
N41—C4—C5—C6	173.53 (14)	N41—C42—C421—C426	150.88 (16)
C2—N1—C6—O61	−179.38 (15)	N43—C42—C421—C422	149.67 (17)
C2—N1—C6—C5	1.0 (2)	N41—C42—C421—C422	−29.7 (2)
C4—C5—C6—N1	6.6 (2)	C426—C421—C422—C423	−1.6 (2)
N51—C5—C6—N1	−178.22 (16)	C42—C421—C422—C423	178.95 (16)
C4—C5—C6—O61	−173.10 (15)	C421—C422—C423—C424	0.0 (3)
N51—C5—C6—O61	2.1 (2)	C422—C423—C424—C425	1.4 (3)
N3—C4—N41—C42	131.28 (16)	C423—C424—C425—C426	−1.0 (3)
C5—C4—N41—C42	−51.1 (2)	C424—C425—C426—C421	−0.6 (3)
N3—C4—N41—C47A	−67.0 (2)	C422—C421—C426—C425	2.0 (3)
C5—C4—N41—C47A	110.63 (18)	C42—C421—C426—C425	−178.58 (16)
C47A—N41—C42—N43	0.84 (18)	C4—C5—N51—C57	−60.8 (2)
C4—N41—C42—N43	165.05 (15)	C6—C5—N51—C57	124.62 (18)
C47A—N41—C42—C421	−179.74 (15)	C5—N51—C57—C51	−172.72 (14)
C4—N41—C42—C421	−15.5 (3)	N51—C57—C51—C56	−34.8 (2)
N41—C42—N43—C43A	−1.06 (18)	N51—C57—C51—C52	144.62 (16)
C421—C42—N43—C43A	179.52 (15)	C56—C51—C52—C53	0.0 (3)
C42—N43—C43A—C47A	0.89 (19)	C57—C51—C52—C53	−179.46 (16)
C42—N43—C43A—C44	−178.61 (17)	C51—C52—C53—C54	0.7 (3)
N43—C43A—C44—C45	178.74 (17)	C52—C53—C54—C55	−0.6 (3)
C47A—C43A—C44—C45	−0.7 (3)	C53—C54—C55—C56	−0.1 (3)
C43A—C44—C45—C46	0.6 (3)	C52—C51—C56—C55	−0.7 (3)
C44—C45—C46—C47	−0.4 (3)	C57—C51—C56—C55	178.74 (17)
C45—C46—C47—C47A	0.4 (2)	C54—C55—C56—C51	0.7 (3)
C46—C47—C47A—N41	−178.49 (17)	N1—C6—O61—C61	−0.9 (3)
C46—C47—C47A—C43A	−0.6 (2)	C5—C6—O61—C61	178.82 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21A···N43ⁱ	0.88 (2)	2.13 (2)	2.985 (2)	162.6 (19)
N21—H21B···N3ⁱⁱ	0.90 (2)	2.18 (2)	3.079 (2)	177.4 (16)
C424—H424···Cg1ⁱⁱⁱ	0.95	2.67	3.336 (2)	128

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

6-Methoxy-N⁵-(4-methoxybenzyl)-4-[2-(4-methoxyphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine (III) top

Crystal data top

C₂₇H₂₆N₆O₃	F(000) = 1016
M_r = 482.54	D_x = 1.317 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 15.8911 (13) Å	Cell parameters from 6049 reflections
b = 9.6209 (7) Å	θ = 2.5–28.3°
c = 15.9244 (11) Å	µ = 0.09 mm⁻¹
β = 91.581 (3)°	T = 100 K
V = 2433.7 (3) Å³	Plate, colourless
Z = 4	0.21 × 0.15 × 0.06 mm

Data collection top

Bruker D8 Venture diffractometer	6049 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	5172 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.051
φ and ω scans	θ_max = 28.3°, θ_min = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −21→21
T_min = 0.959, T_max = 0.995	k = −12→12
66322 measured reflections	l = −21→21

Refinement top

Refinement on F²	Primary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.051	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.128	w = 1/[σ²(F_o²) + (0.0494P)² + 1.899P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
6049 reflections	Δρ_max = 0.38 e Å⁻³
337 parameters	Δρ_min = −0.28 e Å⁻³
0 restraints

Special details top

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

	x	y	z	U_iso*/U_eq
N1	0.69672 (8)	0.57588 (13)	0.60730 (8)	0.0183 (3)
C2	0.62603 (9)	0.54024 (14)	0.56163 (9)	0.0182 (3)
N3	0.59642 (8)	0.41021 (12)	0.55319 (8)	0.0181 (3)
C4	0.63921 (9)	0.31034 (14)	0.59488 (9)	0.0170 (3)
C5	0.70884 (9)	0.33344 (15)	0.64651 (9)	0.0183 (3)
C6	0.73466 (9)	0.47496 (15)	0.64820 (9)	0.0184 (3)
N21	0.58499 (9)	0.64311 (14)	0.52100 (10)	0.0262 (3)
H21A	0.5984 (13)	0.730 (2)	0.5321 (13)	0.031*
H21B	0.5344 (14)	0.628 (2)	0.4999 (13)	0.031*
N41	0.60482 (8)	0.17383 (12)	0.58461 (8)	0.0178 (3)
C42	0.64158 (9)	0.05602 (14)	0.55215 (9)	0.0184 (3)
N43	0.59730 (8)	−0.05674 (13)	0.56527 (8)	0.0212 (3)
C43A	0.52760 (10)	−0.01297 (16)	0.60871 (10)	0.0213 (3)
C44	0.45981 (11)	−0.08966 (18)	0.63842 (11)	0.0281 (4)
H44	0.4559	−0.1872	0.6297	0.034*
C45	0.39908 (12)	−0.0185 (2)	0.68070 (12)	0.0334 (4)
H45	0.3519	−0.0679	0.7007	0.040*
C46	0.40471 (12)	0.1250 (2)	0.69509 (12)	0.0332 (4)
H46	0.3620	0.1698	0.7257	0.040*
C47	0.47110 (11)	0.20336 (18)	0.66579 (10)	0.0263 (3)
H47	0.4753	0.3006	0.6753	0.032*
C47A	0.53085 (9)	0.13064 (16)	0.62174 (9)	0.0198 (3)
C421	0.72194 (10)	0.05637 (15)	0.50931 (10)	0.0200 (3)
C422	0.74991 (10)	0.16830 (15)	0.46289 (10)	0.0207 (3)
H422	0.7161	0.2496	0.4585	0.025*
C423	0.82631 (10)	0.16390 (16)	0.42272 (10)	0.0228 (3)
H423	0.8446	0.2415	0.3912	0.027*
C424	0.87557 (10)	0.04543 (17)	0.42907 (11)	0.0263 (3)
C425	0.84799 (11)	−0.06908 (18)	0.47422 (13)	0.0319 (4)
H425	0.8816	−0.1507	0.4778	0.038*
C426	0.77212 (11)	−0.06387 (16)	0.51362 (12)	0.0273 (3)
H426	0.7534	−0.1424	0.5441	0.033*
O421	0.95281 (8)	0.03106 (14)	0.39365 (9)	0.0356 (3)
C427	0.99011 (12)	0.1535 (2)	0.36183 (13)	0.0364 (4)
H47A	0.9576	0.1857	0.3123	0.055*
H47B	1.0480	0.1336	0.3461	0.055*
H47C	0.9904	0.2260	0.4051	0.055*
N51	0.75636 (9)	0.23497 (14)	0.69262 (9)	0.0244 (3)
H51	0.7899 (13)	0.280 (2)	0.7264 (13)	0.029*
C57	0.71527 (11)	0.12267 (17)	0.73915 (11)	0.0258 (3)
H57A	0.6885	0.0561	0.6993	0.031*
H57B	0.6710	0.1619	0.7747	0.031*
C51	0.78076 (10)	0.04907 (16)	0.79344 (10)	0.0225 (3)
C52	0.75966 (10)	−0.00917 (16)	0.87007 (10)	0.0233 (3)
H52	0.7029	−0.0060	0.8873	0.028*
C53	0.82029 (11)	−0.07166 (17)	0.92157 (10)	0.0252 (3)
H53	0.8049	−0.1112	0.9736	0.030*
C54	0.90386 (10)	−0.07676 (16)	0.89735 (10)	0.0233 (3)
C55	0.92575 (11)	−0.02100 (17)	0.82077 (10)	0.0257 (3)
H55	0.9825	−0.0243	0.8035	0.031*
C56	0.86372 (11)	0.04001 (17)	0.76919 (10)	0.0255 (3)
H56	0.8787	0.0762	0.7162	0.031*
O541	0.96003 (8)	−0.13820 (13)	0.95243 (8)	0.0304 (3)
C541	1.04397 (12)	−0.1556 (3)	0.92368 (14)	0.0455 (5)
H54A	1.0424	−0.2077	0.8708	0.068*
H54B	1.0775	−0.2068	0.9659	0.068*
H54C	1.0694	−0.0642	0.9147	0.068*
O61	0.80307 (7)	0.50128 (12)	0.69806 (7)	0.0246 (2)
C61	0.82886 (11)	0.64414 (18)	0.70656 (13)	0.0322 (4)
H61A	0.8466	0.6792	0.6521	0.048*
H61B	0.8759	0.6506	0.7474	0.048*
H61C	0.7816	0.6999	0.7260	0.048*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0175 (6)	0.0132 (5)	0.0242 (6)	−0.0012 (4)	0.0004 (5)	−0.0003 (5)
C2	0.0200 (7)	0.0121 (6)	0.0224 (7)	0.0002 (5)	−0.0017 (5)	−0.0002 (5)
N3	0.0196 (6)	0.0113 (5)	0.0232 (6)	−0.0003 (4)	−0.0033 (5)	0.0008 (5)
C4	0.0195 (7)	0.0113 (6)	0.0202 (7)	0.0000 (5)	0.0000 (5)	−0.0002 (5)
C5	0.0204 (7)	0.0138 (6)	0.0206 (7)	0.0012 (5)	−0.0014 (5)	0.0010 (5)
C6	0.0166 (6)	0.0171 (7)	0.0214 (7)	−0.0006 (5)	0.0001 (5)	−0.0015 (5)
N21	0.0275 (7)	0.0095 (6)	0.0407 (8)	−0.0011 (5)	−0.0130 (6)	0.0024 (5)
N41	0.0190 (6)	0.0121 (6)	0.0222 (6)	−0.0003 (5)	−0.0013 (5)	0.0014 (5)
C42	0.0225 (7)	0.0115 (6)	0.0209 (7)	0.0000 (5)	−0.0046 (5)	0.0013 (5)
N43	0.0242 (6)	0.0133 (6)	0.0259 (6)	−0.0029 (5)	−0.0027 (5)	0.0025 (5)
C43A	0.0235 (7)	0.0187 (7)	0.0214 (7)	−0.0025 (6)	−0.0043 (6)	0.0036 (6)
C44	0.0339 (9)	0.0221 (8)	0.0281 (8)	−0.0089 (7)	−0.0022 (7)	0.0066 (6)
C45	0.0328 (9)	0.0357 (10)	0.0321 (9)	−0.0126 (8)	0.0060 (7)	0.0078 (7)
C46	0.0300 (9)	0.0367 (10)	0.0333 (9)	0.0000 (7)	0.0106 (7)	0.0029 (8)
C47	0.0295 (8)	0.0225 (8)	0.0270 (8)	−0.0003 (6)	0.0025 (6)	0.0021 (6)
C47A	0.0203 (7)	0.0193 (7)	0.0195 (7)	−0.0031 (6)	−0.0029 (5)	0.0051 (5)
C421	0.0201 (7)	0.0153 (7)	0.0242 (7)	−0.0004 (5)	−0.0037 (6)	−0.0027 (5)
C422	0.0234 (7)	0.0149 (7)	0.0238 (7)	0.0022 (6)	−0.0024 (6)	−0.0024 (5)
C423	0.0246 (8)	0.0192 (7)	0.0245 (7)	−0.0021 (6)	−0.0007 (6)	−0.0016 (6)
C424	0.0215 (8)	0.0228 (8)	0.0347 (9)	−0.0007 (6)	0.0017 (6)	−0.0081 (7)
C425	0.0264 (8)	0.0177 (8)	0.0515 (11)	0.0046 (6)	0.0006 (8)	−0.0013 (7)
C426	0.0256 (8)	0.0149 (7)	0.0414 (9)	0.0004 (6)	−0.0013 (7)	0.0020 (6)
O421	0.0257 (6)	0.0287 (6)	0.0531 (8)	0.0017 (5)	0.0106 (6)	−0.0060 (6)
C427	0.0328 (9)	0.0358 (10)	0.0410 (10)	−0.0007 (8)	0.0123 (8)	−0.0044 (8)
N51	0.0235 (7)	0.0174 (6)	0.0316 (7)	−0.0007 (5)	−0.0102 (6)	0.0058 (5)
C57	0.0274 (8)	0.0215 (7)	0.0282 (8)	0.0011 (6)	−0.0039 (6)	0.0066 (6)
C51	0.0264 (8)	0.0169 (7)	0.0239 (7)	0.0032 (6)	−0.0052 (6)	0.0002 (6)
C52	0.0236 (7)	0.0181 (7)	0.0282 (8)	0.0011 (6)	−0.0005 (6)	0.0005 (6)
C53	0.0306 (8)	0.0199 (7)	0.0252 (8)	0.0001 (6)	−0.0002 (6)	0.0053 (6)
C54	0.0270 (8)	0.0171 (7)	0.0255 (7)	0.0024 (6)	−0.0056 (6)	0.0033 (6)
C55	0.0265 (8)	0.0235 (8)	0.0272 (8)	0.0063 (6)	0.0009 (6)	0.0026 (6)
C56	0.0323 (9)	0.0234 (8)	0.0209 (7)	0.0052 (6)	0.0004 (6)	0.0034 (6)
O541	0.0271 (6)	0.0310 (6)	0.0327 (6)	0.0027 (5)	−0.0056 (5)	0.0127 (5)
C541	0.0280 (9)	0.0642 (14)	0.0442 (11)	0.0150 (9)	−0.0021 (8)	0.0206 (10)
O61	0.0216 (5)	0.0189 (5)	0.0329 (6)	−0.0040 (4)	−0.0082 (5)	0.0002 (4)
C61	0.0262 (8)	0.0225 (8)	0.0473 (11)	−0.0077 (7)	−0.0084 (7)	−0.0037 (7)

Geometric parameters (Å, º) top

N1—C6	1.3071 (19)	C424—O421	1.372 (2)
N1—C2	1.3651 (19)	C424—C425	1.393 (2)
C2—N21	1.3418 (19)	C425—C426	1.375 (3)
C2—N3	1.3420 (18)	C425—H425	0.9500
N3—C4	1.3421 (18)	C426—H426	0.9500
C4—C5	1.378 (2)	O421—C427	1.419 (2)
C4—N41	1.4302 (18)	C427—H47A	0.9800
C5—N51	1.4057 (19)	C427—H47B	0.9800
C5—C6	1.422 (2)	C427—H47C	0.9800
C6—O61	1.3524 (18)	N51—C57	1.473 (2)
N21—H21A	0.88 (2)	N51—H51	0.86 (2)
N21—H21B	0.87 (2)	C57—C51	1.511 (2)
N41—C42	1.3819 (19)	C57—H57A	0.9900
N41—C47A	1.3937 (19)	C57—H57B	0.9900
C42—N43	1.3130 (19)	C51—C56	1.387 (2)
C42—C421	1.464 (2)	C51—C52	1.392 (2)
N43—C43A	1.387 (2)	C52—C53	1.385 (2)
C43A—C47A	1.398 (2)	C52—H52	0.9500
C43A—C44	1.399 (2)	C53—C54	1.394 (2)
C44—C45	1.375 (3)	C53—H53	0.9500
C44—H44	0.9500	C54—O541	1.3684 (19)
C45—C46	1.402 (3)	C54—C55	1.385 (2)
C45—H45	0.9500	C55—C56	1.395 (2)
C46—C47	1.388 (2)	C55—H55	0.9500
C46—H46	0.9500	C56—H56	0.9500
C47—C47A	1.386 (2)	O541—C541	1.432 (2)
C47—H47	0.9500	C541—H54A	0.9800
C421—C422	1.386 (2)	C541—H54B	0.9800
C421—C426	1.406 (2)	C541—H54C	0.9800
C422—C423	1.388 (2)	O61—C61	1.4395 (19)
C422—H422	0.9500	C61—H61A	0.9800
C423—C424	1.385 (2)	C61—H61B	0.9800
C423—H423	0.9500	C61—H61C	0.9800

C6—N1—C2	116.13 (12)	C426—C425—C424	119.93 (15)
N21—C2—N3	118.35 (13)	C426—C425—H425	120.0
N21—C2—N1	116.98 (13)	C424—C425—H425	120.0
N3—C2—N1	124.65 (13)	C425—C426—C421	120.73 (16)
C2—N3—C4	116.51 (12)	C425—C426—H426	119.6
N3—C4—C5	124.55 (13)	C421—C426—H426	119.6
N3—C4—N41	114.46 (12)	C424—O421—C427	116.77 (14)
C5—C4—N41	120.94 (13)	O421—C427—H47A	109.5
C4—C5—N51	127.86 (13)	O421—C427—H47B	109.5
C4—C5—C6	113.08 (13)	H47A—C427—H47B	109.5
N51—C5—C6	119.00 (13)	O421—C427—H47C	109.5
N1—C6—O61	120.37 (13)	H47A—C427—H47C	109.5
N1—C6—C5	124.96 (13)	H47B—C427—H47C	109.5
O61—C6—C5	114.66 (13)	C5—N51—C57	121.19 (13)
C2—N21—H21A	119.6 (14)	C5—N51—H51	107.8 (14)
C2—N21—H21B	119.7 (14)	C57—N51—H51	109.1 (14)
H21A—N21—H21B	116.4 (19)	N51—C57—C51	108.89 (13)
C42—N41—C47A	106.52 (12)	N51—C57—H57A	109.9
C42—N41—C4	129.18 (13)	C51—C57—H57A	109.9
C47A—N41—C4	123.33 (12)	N51—C57—H57B	109.9
N43—C42—N41	112.59 (13)	C51—C57—H57B	109.9
N43—C42—C421	123.65 (13)	H57A—C57—H57B	108.3
N41—C42—C421	123.75 (13)	C56—C51—C52	118.21 (14)
C42—N43—C43A	105.51 (13)	C56—C51—C57	121.01 (14)
N43—C43A—C47A	110.32 (13)	C52—C51—C57	120.77 (15)
N43—C43A—C44	129.89 (15)	C53—C52—C51	120.88 (15)
C47A—C43A—C44	119.78 (15)	C53—C52—H52	119.6
C45—C44—C43A	117.42 (16)	C51—C52—H52	119.6
C45—C44—H44	121.3	C52—C53—C54	120.26 (15)
C43A—C44—H44	121.3	C52—C53—H53	119.9
C44—C45—C46	121.88 (16)	C54—C53—H53	119.9
C44—C45—H45	119.1	O541—C54—C55	123.80 (15)
C46—C45—H45	119.1	O541—C54—C53	116.58 (14)
C47—C46—C45	121.70 (17)	C55—C54—C53	119.62 (14)
C47—C46—H46	119.2	C54—C55—C56	119.39 (16)
C45—C46—H46	119.2	C54—C55—H55	120.3
C47A—C47—C46	115.72 (16)	C56—C55—H55	120.3
C47A—C47—H47	122.1	C51—C56—C55	121.61 (15)
C46—C47—H47	122.1	C51—C56—H56	119.2
C47—C47A—N41	131.46 (14)	C55—C56—H56	119.2
C47—C47A—C43A	123.45 (15)	C54—O541—C541	116.26 (14)
N41—C47A—C43A	105.06 (13)	O541—C541—H54A	109.5
C422—C421—C426	118.39 (15)	O541—C541—H54B	109.5
C422—C421—C42	123.14 (14)	H54A—C541—H54B	109.5
C426—C421—C42	118.44 (14)	O541—C541—H54C	109.5
C421—C422—C423	121.29 (14)	H54A—C541—H54C	109.5
C421—C422—H422	119.4	H54B—C541—H54C	109.5
C423—C422—H422	119.4	C6—O61—C61	117.14 (12)
C424—C423—C422	119.41 (15)	O61—C61—H61A	109.5
C424—C423—H423	120.3	O61—C61—H61B	109.5
C422—C423—H423	120.3	H61A—C61—H61B	109.5
O421—C424—C423	124.28 (16)	O61—C61—H61C	109.5
O421—C424—C425	115.49 (15)	H61A—C61—H61C	109.5
C423—C424—C425	120.23 (15)	H61B—C61—H61C	109.5

C6—N1—C2—N21	178.29 (14)	N43—C43A—C47A—C47	−177.86 (14)
C6—N1—C2—N3	−3.4 (2)	C44—C43A—C47A—C47	2.3 (2)
N21—C2—N3—C4	−179.95 (14)	N43—C43A—C47A—N41	0.16 (16)
N1—C2—N3—C4	1.7 (2)	C44—C43A—C47A—N41	−179.70 (14)
C2—N3—C4—C5	1.8 (2)	N43—C42—C421—C422	150.21 (15)
C2—N3—C4—N41	179.42 (13)	N41—C42—C421—C422	−31.1 (2)
N3—C4—C5—N51	179.41 (15)	N43—C42—C421—C426	−28.1 (2)
N41—C4—C5—N51	2.0 (2)	N41—C42—C421—C426	150.63 (15)
N3—C4—C5—C6	−3.3 (2)	C426—C421—C422—C423	−1.2 (2)
N41—C4—C5—C6	179.31 (13)	C42—C421—C422—C423	−179.52 (14)
C2—N1—C6—O61	−177.13 (13)	C421—C422—C423—C424	0.0 (2)
C2—N1—C6—C5	1.6 (2)	C422—C423—C424—O421	−178.43 (15)
C4—C5—C6—N1	1.4 (2)	C422—C423—C424—C425	1.1 (2)
N51—C5—C6—N1	179.02 (14)	O421—C424—C425—C426	178.63 (16)
C4—C5—C6—O61	−179.76 (13)	C423—C424—C425—C426	−0.9 (3)
N51—C5—C6—O61	−2.2 (2)	C424—C425—C426—C421	−0.3 (3)
N3—C4—N41—C42	120.12 (16)	C422—C421—C426—C425	1.4 (2)
C5—C4—N41—C42	−62.2 (2)	C42—C421—C426—C425	179.76 (16)
N3—C4—N41—C47A	−72.71 (18)	C423—C424—O421—C427	11.7 (2)
C5—C4—N41—C47A	104.97 (17)	C425—C424—O421—C427	−167.85 (17)
C47A—N41—C42—N43	0.22 (17)	C4—C5—N51—C57	−42.8 (2)
C4—N41—C42—N43	169.06 (14)	C6—C5—N51—C57	140.03 (15)
C47A—N41—C42—C421	−178.61 (13)	C5—N51—C57—C51	−170.69 (14)
C4—N41—C42—C421	−9.8 (2)	N51—C57—C51—C56	−30.5 (2)
N41—C42—N43—C43A	−0.12 (17)	N51—C57—C51—C52	148.27 (15)
C421—C42—N43—C43A	178.71 (13)	C56—C51—C52—C53	1.5 (2)
C42—N43—C43A—C47A	−0.03 (17)	C57—C51—C52—C53	−177.31 (15)
C42—N43—C43A—C44	179.81 (16)	C51—C52—C53—C54	0.2 (2)
N43—C43A—C44—C45	179.39 (16)	C52—C53—C54—O541	178.93 (15)
C47A—C43A—C44—C45	−0.8 (2)	C52—C53—C54—C55	−1.1 (2)
C43A—C44—C45—C46	−1.0 (3)	O541—C54—C55—C56	−179.72 (15)
C44—C45—C46—C47	1.4 (3)	C53—C54—C55—C56	0.3 (2)
C45—C46—C47—C47A	0.0 (3)	C52—C51—C56—C55	−2.3 (2)
C46—C47—C47A—N41	−179.29 (16)	C57—C51—C56—C55	176.48 (15)
C46—C47—C47A—C43A	−1.8 (2)	C54—C55—C56—C51	1.4 (3)
C42—N41—C47A—C47	177.57 (16)	C55—C54—O541—C541	−6.0 (2)
C4—N41—C47A—C47	7.9 (2)	C53—C54—O541—C541	173.98 (17)
C42—N41—C47A—C43A	−0.22 (15)	N1—C6—O61—C61	2.8 (2)
C4—N41—C47A—C43A	−169.88 (13)	C5—C6—O61—C61	−176.06 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21A···N43ⁱ	0.88 (2)	2.119 (19)	2.9777 (19)	165.2 (19)
N21—H21B···N3ⁱⁱ	0.88 (2)	2.25 (2)	3.1276 (19)	179 (2)
C425—H425···O541ⁱⁱⁱ	0.95	2.42	3.355 (2)	167
C423—H423···Cg2^iv	0.95	2.73	3.6060 (17)	154

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

6-Methoxy-N⁵-(4-nitrobenzyl)-4-[2-(4-nitrophenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine (IV) top

Crystal data top

C₂₅H₂₀N₈O₅	F(000) = 1064
M_r = 512.49	D_x = 1.487 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 7.6614 (6) Å	Cell parameters from 5246 reflections
b = 16.6048 (11) Å	θ = 2.5–27.5°
c = 18.1311 (13) Å	µ = 0.11 mm⁻¹
β = 97.101 (3)°	T = 100 K
V = 2288.9 (3) Å³	Block, orange
Z = 4	0.17 × 0.15 × 0.10 mm

Data collection top

Bruker D8 Venture diffractometer	5246 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	4667 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.039
φ and ω scans	θ_max = 27.5°, θ_min = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −9→9
T_min = 0.937, T_max = 0.984	k = −21→21
58336 measured reflections	l = −23→23

Refinement top

Refinement on F²	Primary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.043	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.114	w = 1/[σ²(F_o²) + (0.0473P)² + 1.8641P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
5246 reflections	Δρ_max = 0.37 e Å⁻³
353 parameters	Δρ_min = −0.43 e Å⁻³
0 restraints

Special details top

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

	x	y	z	U_iso*/U_eq
N1	0.48756 (15)	0.81443 (7)	0.68882 (6)	0.0146 (2)
C2	0.62442 (18)	0.80687 (8)	0.64864 (8)	0.0148 (3)
N3	0.61248 (15)	0.79614 (7)	0.57479 (6)	0.0153 (2)
C4	0.44918 (18)	0.78690 (8)	0.54030 (7)	0.0136 (3)
C5	0.29790 (17)	0.78807 (8)	0.57449 (7)	0.0140 (3)
C6	0.32969 (18)	0.80507 (8)	0.65162 (8)	0.0142 (3)
N21	0.78733 (16)	0.81348 (8)	0.68643 (7)	0.0193 (3)
H21A	0.798 (2)	0.8068 (11)	0.7348 (11)	0.023*
H21B	0.877 (3)	0.8004 (11)	0.6609 (11)	0.023*
N41	0.43952 (15)	0.78111 (7)	0.46137 (6)	0.0137 (2)
C42	0.36591 (17)	0.72343 (8)	0.41202 (7)	0.0145 (3)
N43	0.37124 (16)	0.74409 (7)	0.34230 (7)	0.0169 (2)
C43A	0.44908 (19)	0.81959 (9)	0.34455 (8)	0.0173 (3)
C44	0.4840 (2)	0.87041 (10)	0.28656 (8)	0.0242 (3)
H44	0.4574	0.8547	0.2360	0.029*
C45	0.5588 (2)	0.94445 (10)	0.30585 (9)	0.0281 (4)
H45	0.5838	0.9802	0.2676	0.034*
C46	0.5991 (2)	0.96841 (10)	0.38037 (9)	0.0245 (3)
H46	0.6490	1.0201	0.3912	0.029*
C47	0.56752 (19)	0.91834 (9)	0.43844 (8)	0.0188 (3)
H47	0.5947	0.9341	0.4889	0.023*
C47A	0.49375 (18)	0.84374 (8)	0.41858 (8)	0.0152 (3)
C421	0.29762 (18)	0.64495 (8)	0.43257 (8)	0.0159 (3)
C422	0.35900 (19)	0.60603 (9)	0.49895 (8)	0.0182 (3)
H422	0.4385	0.6330	0.5351	0.022*
C423	0.3047 (2)	0.52811 (9)	0.51256 (8)	0.0206 (3)
H423	0.3450	0.5015	0.5579	0.025*
C424	0.1902 (2)	0.49038 (9)	0.45830 (9)	0.0212 (3)
C425	0.1225 (2)	0.52835 (9)	0.39307 (9)	0.0230 (3)
H425	0.0410	0.5014	0.3577	0.028*
C426	0.1757 (2)	0.60616 (9)	0.38024 (8)	0.0201 (3)
H426	0.1296	0.6334	0.3360	0.024*
N44	0.14400 (19)	0.40542 (8)	0.46861 (8)	0.0263 (3)
O441	0.05373 (19)	0.37147 (8)	0.41637 (8)	0.0371 (3)
O442	0.19797 (18)	0.37238 (7)	0.52743 (8)	0.0345 (3)
N51	0.12807 (16)	0.77767 (7)	0.53523 (7)	0.0159 (2)
H51	0.067 (2)	0.7404 (11)	0.5551 (10)	0.019*
C57	0.02756 (19)	0.85190 (9)	0.51743 (8)	0.0182 (3)
H57A	0.0750	0.8953	0.5516	0.022*
H57B	−0.0969	0.8430	0.5248	0.022*
C51	0.03723 (18)	0.87764 (9)	0.43807 (8)	0.0173 (3)
C52	−0.0157 (2)	0.82320 (9)	0.38102 (9)	0.0230 (3)
H52	−0.0560	0.7712	0.3929	0.028*
C53	−0.0101 (2)	0.84395 (10)	0.30743 (9)	0.0260 (3)
H53	−0.0425	0.8063	0.2687	0.031*
C54	0.0436 (2)	0.92092 (9)	0.29170 (8)	0.0221 (3)
C55	0.0966 (2)	0.97679 (9)	0.34606 (9)	0.0213 (3)
H55	0.1325	1.0293	0.3337	0.026*
C56	0.09556 (19)	0.95360 (9)	0.41978 (8)	0.0195 (3)
H56	0.1355	0.9903	0.4584	0.023*
N54	0.0453 (2)	0.94243 (9)	0.21334 (8)	0.0274 (3)
O541	0.0520 (2)	0.88772 (9)	0.16802 (7)	0.0450 (4)
O542	0.0417 (2)	1.01342 (8)	0.19625 (7)	0.0371 (3)
O61	0.18690 (13)	0.81298 (6)	0.68725 (5)	0.0184 (2)
C61	0.2153 (2)	0.84133 (10)	0.76322 (8)	0.0207 (3)
H61A	0.2848	0.8016	0.7942	0.031*
H61B	0.1015	0.8489	0.7818	0.031*
H61C	0.2787	0.8927	0.7652	0.031*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0150 (6)	0.0168 (6)	0.0118 (5)	0.0000 (4)	0.0007 (4)	0.0017 (4)
C2	0.0151 (6)	0.0155 (6)	0.0136 (6)	−0.0002 (5)	0.0007 (5)	0.0016 (5)
N3	0.0142 (6)	0.0187 (6)	0.0129 (5)	0.0000 (4)	0.0012 (4)	0.0006 (4)
C4	0.0153 (6)	0.0135 (6)	0.0117 (6)	−0.0001 (5)	0.0007 (5)	0.0002 (5)
C5	0.0131 (6)	0.0140 (6)	0.0145 (6)	−0.0009 (5)	−0.0002 (5)	0.0002 (5)
C6	0.0139 (6)	0.0137 (6)	0.0152 (6)	−0.0002 (5)	0.0032 (5)	0.0011 (5)
N21	0.0141 (6)	0.0318 (7)	0.0117 (6)	0.0004 (5)	0.0003 (5)	0.0012 (5)
N41	0.0144 (5)	0.0147 (5)	0.0117 (5)	−0.0017 (4)	0.0006 (4)	−0.0001 (4)
C42	0.0130 (6)	0.0170 (6)	0.0133 (6)	0.0000 (5)	0.0007 (5)	−0.0018 (5)
N43	0.0179 (6)	0.0196 (6)	0.0132 (5)	−0.0017 (5)	0.0016 (4)	−0.0004 (4)
C43A	0.0167 (7)	0.0208 (7)	0.0144 (6)	−0.0016 (5)	0.0013 (5)	0.0005 (5)
C44	0.0271 (8)	0.0311 (8)	0.0141 (7)	−0.0062 (6)	0.0008 (6)	0.0038 (6)
C45	0.0306 (8)	0.0310 (9)	0.0219 (8)	−0.0100 (7)	0.0001 (6)	0.0104 (6)
C46	0.0251 (8)	0.0215 (7)	0.0256 (8)	−0.0073 (6)	−0.0026 (6)	0.0054 (6)
C47	0.0176 (7)	0.0198 (7)	0.0181 (7)	−0.0023 (5)	−0.0010 (5)	0.0004 (5)
C47A	0.0132 (6)	0.0182 (7)	0.0141 (6)	0.0003 (5)	0.0013 (5)	0.0020 (5)
C421	0.0161 (6)	0.0157 (6)	0.0166 (6)	0.0001 (5)	0.0050 (5)	−0.0018 (5)
C422	0.0204 (7)	0.0176 (7)	0.0166 (7)	0.0008 (5)	0.0021 (5)	−0.0021 (5)
C423	0.0237 (7)	0.0188 (7)	0.0201 (7)	0.0022 (6)	0.0062 (6)	0.0013 (6)
C424	0.0219 (7)	0.0155 (7)	0.0282 (8)	−0.0025 (5)	0.0107 (6)	−0.0019 (6)
C425	0.0219 (7)	0.0225 (7)	0.0247 (7)	−0.0064 (6)	0.0033 (6)	−0.0053 (6)
C426	0.0207 (7)	0.0221 (7)	0.0172 (7)	−0.0027 (6)	0.0011 (5)	−0.0012 (6)
N44	0.0282 (7)	0.0192 (6)	0.0337 (8)	−0.0033 (5)	0.0129 (6)	−0.0012 (6)
O441	0.0477 (8)	0.0258 (6)	0.0388 (7)	−0.0170 (6)	0.0094 (6)	−0.0050 (5)
O442	0.0417 (7)	0.0222 (6)	0.0407 (7)	−0.0029 (5)	0.0089 (6)	0.0074 (5)
N51	0.0132 (6)	0.0181 (6)	0.0157 (6)	−0.0031 (4)	−0.0004 (4)	0.0005 (5)
C57	0.0152 (6)	0.0236 (7)	0.0153 (6)	0.0026 (5)	0.0005 (5)	−0.0015 (5)
C51	0.0136 (6)	0.0207 (7)	0.0169 (6)	0.0029 (5)	−0.0006 (5)	−0.0013 (5)
C52	0.0311 (8)	0.0177 (7)	0.0190 (7)	−0.0018 (6)	−0.0017 (6)	0.0002 (6)
C53	0.0374 (9)	0.0216 (8)	0.0174 (7)	−0.0005 (6)	−0.0028 (6)	−0.0024 (6)
C54	0.0244 (8)	0.0234 (7)	0.0182 (7)	0.0035 (6)	0.0023 (6)	0.0018 (6)
C55	0.0202 (7)	0.0187 (7)	0.0255 (8)	0.0004 (5)	0.0050 (6)	0.0005 (6)
C56	0.0163 (7)	0.0203 (7)	0.0216 (7)	−0.0004 (5)	0.0013 (5)	−0.0038 (6)
N54	0.0330 (8)	0.0278 (7)	0.0218 (7)	0.0025 (6)	0.0041 (6)	0.0026 (6)
O541	0.0782 (11)	0.0365 (7)	0.0195 (6)	0.0000 (7)	0.0035 (6)	−0.0028 (5)
O542	0.0528 (8)	0.0285 (6)	0.0323 (7)	0.0053 (6)	0.0137 (6)	0.0103 (5)
O61	0.0140 (5)	0.0274 (5)	0.0141 (5)	−0.0009 (4)	0.0032 (4)	−0.0018 (4)
C61	0.0196 (7)	0.0284 (8)	0.0149 (7)	−0.0001 (6)	0.0050 (5)	−0.0029 (6)

Geometric parameters (Å, º) top

N1—C6	1.3192 (18)	C423—C424	1.385 (2)
N1—C2	1.3546 (18)	C423—H423	0.9500
C2—N3	1.3426 (17)	C424—C425	1.383 (2)
C2—N21	1.3520 (18)	C424—N44	1.4719 (19)
N3—C4	1.3366 (18)	C425—C426	1.383 (2)
C4—C5	1.3804 (19)	C425—H425	0.9500
C4—N41	1.4270 (17)	C426—H426	0.9500
C5—N51	1.4144 (17)	N44—O442	1.2248 (19)
C5—C6	1.4179 (19)	N44—O441	1.2376 (19)
C6—O61	1.3439 (17)	N51—C57	1.4680 (18)
N21—H21A	0.88 (2)	N51—H51	0.879 (19)
N21—H21B	0.90 (2)	C57—C51	1.5116 (19)
N41—C42	1.3825 (17)	C57—H57A	0.9900
N41—C47A	1.3914 (18)	C57—H57B	0.9900
C42—N43	1.3153 (18)	C51—C56	1.392 (2)
C42—C421	1.4694 (19)	C51—C52	1.396 (2)
N43—C43A	1.3867 (19)	C52—C53	1.384 (2)
C43A—C44	1.400 (2)	C52—H52	0.9500
C43A—C47A	1.4021 (19)	C53—C54	1.383 (2)
C44—C45	1.383 (2)	C53—H53	0.9500
C44—H44	0.9500	C54—C55	1.378 (2)
C45—C46	1.406 (2)	C54—N54	1.466 (2)
C45—H45	0.9500	C55—C56	1.392 (2)
C46—C47	1.386 (2)	C55—H55	0.9500
C46—H46	0.9500	C56—H56	0.9500
C47—C47A	1.390 (2)	N54—O542	1.2184 (19)
C47—H47	0.9500	N54—O541	1.230 (2)
C421—C422	1.395 (2)	O61—C61	1.4465 (17)
C421—C426	1.403 (2)	C61—H61A	0.9800
C422—C423	1.391 (2)	C61—H61B	0.9800
C422—H422	0.9500	C61—H61C	0.9800

C6—N1—C2	115.83 (12)	C422—C423—H423	120.9
N3—C2—N21	117.45 (13)	C425—C424—C423	122.60 (14)
N3—C2—N1	125.93 (13)	C425—C424—N44	118.36 (14)
N21—C2—N1	116.57 (12)	C423—C424—N44	118.98 (14)
C4—N3—C2	115.23 (12)	C426—C425—C424	118.87 (14)
N3—C4—C5	125.28 (12)	C426—C425—H425	120.6
N3—C4—N41	113.98 (12)	C424—C425—H425	120.6
C5—C4—N41	120.60 (12)	C425—C426—C421	120.02 (14)
C4—C5—N51	122.92 (12)	C425—C426—H426	120.0
C4—C5—C6	113.22 (12)	C421—C426—H426	120.0
N51—C5—C6	123.77 (12)	O442—N44—O441	123.98 (14)
N1—C6—O61	119.48 (12)	O442—N44—C424	118.65 (14)
N1—C6—C5	124.24 (12)	O441—N44—C424	117.37 (14)
O61—C6—C5	116.28 (12)	C5—N51—C57	115.66 (11)
C2—N21—H21A	117.6 (13)	C5—N51—H51	112.5 (12)
C2—N21—H21B	115.8 (12)	C57—N51—H51	112.9 (12)
H21A—N21—H21B	119.9 (17)	N51—C57—C51	111.13 (11)
C42—N41—C47A	106.43 (11)	N51—C57—H57A	109.4
C42—N41—C4	131.47 (12)	C51—C57—H57A	109.4
C47A—N41—C4	121.79 (11)	N51—C57—H57B	109.4
N43—C42—N41	112.51 (12)	C51—C57—H57B	109.4
N43—C42—C421	121.96 (12)	H57A—C57—H57B	108.0
N41—C42—C421	125.44 (12)	C56—C51—C52	118.87 (14)
C42—N43—C43A	105.76 (12)	C56—C51—C57	122.54 (13)
N43—C43A—C44	130.11 (13)	C52—C51—C57	118.59 (13)
N43—C43A—C47A	109.88 (12)	C53—C52—C51	120.84 (14)
C44—C43A—C47A	120.00 (14)	C53—C52—H52	119.6
C45—C44—C43A	117.24 (14)	C51—C52—H52	119.6
C45—C44—H44	121.4	C54—C53—C52	118.31 (14)
C43A—C44—H44	121.4	C54—C53—H53	120.8
C44—C45—C46	121.97 (14)	C52—C53—H53	120.8
C44—C45—H45	119.0	C55—C54—C53	122.92 (14)
C46—C45—H45	119.0	C55—C54—N54	119.48 (14)
C47—C46—C45	121.48 (14)	C53—C54—N54	117.60 (14)
C47—C46—H46	119.3	C54—C55—C56	117.69 (14)
C45—C46—H46	119.3	C54—C55—H55	121.2
C46—C47—C47A	116.18 (14)	C56—C55—H55	121.2
C46—C47—H47	121.9	C55—C56—C51	121.29 (14)
C47A—C47—H47	121.9	C55—C56—H56	119.4
C47—C47A—N41	131.40 (13)	C51—C56—H56	119.4
C47—C47A—C43A	123.11 (13)	O542—N54—O541	123.10 (15)
N41—C47A—C43A	105.40 (12)	O542—N54—C54	118.65 (14)
C422—C421—C426	119.72 (13)	O541—N54—C54	118.25 (14)
C422—C421—C42	122.47 (13)	C6—O61—C61	117.01 (11)
C426—C421—C42	117.64 (13)	O61—C61—H61A	109.5
C423—C422—C421	120.51 (14)	O61—C61—H61B	109.5
C423—C422—H422	119.7	H61A—C61—H61B	109.5
C421—C422—H422	119.7	O61—C61—H61C	109.5
C424—C423—C422	118.18 (14)	H61A—C61—H61C	109.5
C424—C423—H423	120.9	H61B—C61—H61C	109.5

C6—N1—C2—N3	4.6 (2)	N43—C43A—C47A—N41	−0.50 (16)
C6—N1—C2—N21	−177.75 (13)	C44—C43A—C47A—N41	179.02 (14)
N21—C2—N3—C4	177.58 (13)	N43—C42—C421—C422	149.75 (14)
N1—C2—N3—C4	−4.8 (2)	N41—C42—C421—C422	−26.4 (2)
C2—N3—C4—C5	0.3 (2)	N43—C42—C421—C426	−25.5 (2)
C2—N3—C4—N41	175.96 (11)	N41—C42—C421—C426	158.37 (14)
N3—C4—C5—N51	−179.77 (13)	C426—C421—C422—C423	2.1 (2)
N41—C4—C5—N51	4.9 (2)	C42—C421—C422—C423	−173.01 (13)
N3—C4—C5—C6	3.5 (2)	C421—C422—C423—C424	0.7 (2)
N41—C4—C5—C6	−171.85 (12)	C422—C423—C424—C425	−2.9 (2)
C2—N1—C6—O61	−178.90 (12)	C422—C423—C424—N44	174.41 (13)
C2—N1—C6—C5	0.0 (2)	C423—C424—C425—C426	2.2 (2)
C4—C5—C6—N1	−3.7 (2)	N44—C424—C425—C426	−175.09 (14)
N51—C5—C6—N1	179.60 (13)	C424—C425—C426—C421	0.7 (2)
C4—C5—C6—O61	175.28 (12)	C422—C421—C426—C425	−2.8 (2)
N51—C5—C6—O61	−1.4 (2)	C42—C421—C426—C425	172.56 (13)
N3—C4—N41—C42	125.40 (15)	C425—C424—N44—O442	−177.24 (15)
C5—C4—N41—C42	−58.8 (2)	C423—C424—N44—O442	5.3 (2)
N3—C4—N41—C47A	−61.90 (17)	C425—C424—N44—O441	3.5 (2)
C5—C4—N41—C47A	113.94 (15)	C423—C424—N44—O441	−173.89 (15)
C47A—N41—C42—N43	0.74 (16)	C4—C5—N51—C57	−99.47 (15)
C4—N41—C42—N43	174.27 (13)	C6—C5—N51—C57	76.92 (17)
C47A—N41—C42—C421	177.20 (13)	C5—N51—C57—C51	99.45 (14)
C4—N41—C42—C421	−9.3 (2)	N51—C57—C51—C56	−124.40 (14)
N41—C42—N43—C43A	−1.04 (16)	N51—C57—C51—C52	56.08 (17)
C421—C42—N43—C43A	−177.63 (13)	C56—C51—C52—C53	0.2 (2)
C42—N43—C43A—C44	−178.52 (16)	C57—C51—C52—C53	179.69 (15)
C42—N43—C43A—C47A	0.94 (16)	C51—C52—C53—C54	−2.1 (3)
N43—C43A—C44—C45	177.90 (16)	C52—C53—C54—C55	1.9 (3)
C47A—C43A—C44—C45	−1.5 (2)	C52—C53—C54—N54	−178.78 (15)
C43A—C44—C45—C46	0.1 (3)	C53—C54—C55—C56	0.2 (2)
C44—C45—C46—C47	0.8 (3)	N54—C54—C55—C56	−179.06 (14)
C45—C46—C47—C47A	−0.2 (2)	C54—C55—C56—C51	−2.2 (2)
C46—C47—C47A—N41	−177.19 (15)	C52—C51—C56—C55	2.1 (2)
C46—C47—C47A—C43A	−1.3 (2)	C57—C51—C56—C55	−177.44 (13)
C42—N41—C47A—C47	176.32 (15)	C55—C54—N54—O542	−21.6 (2)
C4—N41—C47A—C47	2.0 (2)	C53—C54—N54—O542	159.07 (16)
C42—N41—C47A—C43A	−0.11 (15)	C55—C54—N54—O541	157.66 (16)
C4—N41—C47A—C43A	−174.41 (12)	C53—C54—N54—O541	−21.6 (2)
N43—C43A—C47A—C47	−177.31 (13)	N1—C6—O61—C61	7.45 (19)
C44—C43A—C47A—C47	2.2 (2)	C5—C6—O61—C61	−171.57 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21A···N43ⁱ	0.88 (2)	2.14 (2)	2.9774 (18)	160.7 (16)
N21—H21B···O61ⁱⁱ	0.90 (2)	2.37 (2)	3.0595 (16)	133.1 (16)
N51—H51···O441ⁱⁱⁱ	0.879 (17)	2.166 (18)	3.0241 (18)	165.0 (16)
C53—H53···N1^iv	0.95	2.50	3.396 (2)	157
C422—H422···O541ⁱ	0.95	2.48	3.236 (2)	136

Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) x+1, y, z; (iii) −x, −y+1, −z+1; (iv) x−1/2, −y+3/2, z−1/2.

6-Methoxy-4-[2-(4-methylphenyl)-1H-benzo[d]imidazol-1-yl]pyrimidine-2,5-diamine monohydrate (V) top

Crystal data top

C₁₉H₁₈N₆O·H₂O	Z = 2
M_r = 364.41	F(000) = 384
Triclinic, P1	D_x = 1.361 Mg m⁻³
a = 8.1992 (7) Å	Mo Kα radiation, λ = 0.71073 Å
b = 11.0160 (8) Å	Cell parameters from 4063 reflections
c = 11.4240 (9) Å	θ = 2.3–27.5°
α = 109.105 (3)°	µ = 0.09 mm⁻¹
β = 109.171 (3)°	T = 100 K
γ = 97.138 (3)°	Block, colourles
V = 889.35 (12) Å³	0.25 × 0.25 × 0.22 mm

Data collection top

Bruker D8 Venture diffractometer	4062 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	3658 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.036
φ and ω scans	θ_max = 27.5°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −10→10
T_min = 0.964, T_max = 0.980	k = −14→14
45501 measured reflections	l = −14→14

Refinement top

Refinement on F²	Primary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.099	w = 1/[σ²(F_o²) + (0.0447P)² + 0.5045P] where P = (F_o² + 2F_c²)/3
S = 1.03	(Δ/σ)_max < 0.001
4062 reflections	Δρ_max = 0.31 e Å⁻³
264 parameters	Δρ_min = −0.35 e Å⁻³
0 restraints

Special details top

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

	x	y	z	U_iso*/U_eq
N1	0.40225 (13)	0.33365 (9)	0.92094 (9)	0.0143 (2)
C2	0.25364 (15)	0.36368 (11)	0.85219 (11)	0.0137 (2)
N3	0.20172 (13)	0.35272 (9)	0.72400 (9)	0.01378 (19)
C4	0.31130 (15)	0.31190 (10)	0.66318 (11)	0.0129 (2)
C5	0.46866 (15)	0.28374 (11)	0.72253 (11)	0.0135 (2)
C6	0.50625 (15)	0.29744 (10)	0.85722 (11)	0.0137 (2)
N21	0.14698 (14)	0.40296 (10)	0.91704 (10)	0.0171 (2)
H21A	0.056 (2)	0.4355 (15)	0.8766 (15)	0.021*
H21B	0.183 (2)	0.4186 (15)	1.0037 (16)	0.021*
N41	0.25100 (13)	0.29007 (9)	0.52339 (9)	0.01324 (19)
C42	0.21619 (14)	0.38007 (11)	0.46339 (11)	0.0130 (2)
N43	0.12910 (13)	0.32076 (9)	0.33160 (9)	0.0145 (2)
C43A	0.10150 (15)	0.18494 (11)	0.30189 (11)	0.0144 (2)
C44	0.01439 (16)	0.07561 (12)	0.17852 (12)	0.0184 (2)
H44	−0.0347	0.0875	0.0965	0.022*
C45	0.00212 (16)	−0.05079 (12)	0.17997 (12)	0.0197 (2)
H45	−0.0566	−0.1263	0.0974	0.024*
C46	0.07440 (16)	−0.06958 (11)	0.30048 (12)	0.0184 (2)
H46	0.0623	−0.1575	0.2978	0.022*
C47	0.16313 (15)	0.03751 (11)	0.42343 (12)	0.0166 (2)
H47	0.2127	0.0254	0.5053	0.020*
C47A	0.17567 (15)	0.16383 (11)	0.42058 (11)	0.0138 (2)
C421	0.27619 (15)	0.52499 (11)	0.53883 (11)	0.0134 (2)
C422	0.43789 (15)	0.58486 (11)	0.65114 (12)	0.0161 (2)
H422	0.5103	0.5315	0.6813	0.019*
C423	0.49301 (16)	0.72227 (12)	0.71887 (12)	0.0182 (2)
H423	0.6038	0.7619	0.7946	0.022*
C424	0.38859 (16)	0.80323 (11)	0.67770 (12)	0.0182 (2)
C425	0.22742 (16)	0.74242 (11)	0.56505 (12)	0.0167 (2)
H425	0.1547	0.7959	0.5354	0.020*
C426	0.17137 (15)	0.60504 (11)	0.49551 (11)	0.0145 (2)
H426	0.0618	0.5655	0.4186	0.017*
C427	0.4488 (2)	0.95229 (13)	0.75377 (15)	0.0284 (3)
H47A	0.3440	0.9877	0.7489	0.043*
H47B	0.5175	0.9921	0.7136	0.043*
H47C	0.5240	0.9738	0.8483	0.043*
N51	0.59367 (14)	0.25492 (10)	0.66395 (11)	0.0178 (2)
H51A	0.657 (2)	0.2022 (16)	0.6950 (15)	0.021*
H51B	0.546 (2)	0.2219 (15)	0.5727 (17)	0.021*
O61	0.65871 (11)	0.26926 (8)	0.91703 (8)	0.01699 (18)
C61	0.70010 (17)	0.27876 (13)	1.05313 (12)	0.0209 (3)
H61A	0.6157	0.2071	1.0526	0.031*
H61B	0.6906	0.3650	1.1079	0.031*
H61C	0.8221	0.2706	1.0914	0.031*
O1	0.15431 (12)	0.48181 (9)	0.18498 (9)	0.01827 (18)
H1A	0.144 (2)	0.4325 (17)	0.2297 (17)	0.027*
H1B	0.225 (2)	0.5596 (18)	0.2457 (17)	0.027*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0166 (5)	0.0127 (4)	0.0125 (4)	0.0034 (4)	0.0044 (4)	0.0053 (4)
C2	0.0166 (5)	0.0105 (5)	0.0135 (5)	0.0021 (4)	0.0057 (4)	0.0048 (4)
N3	0.0153 (4)	0.0136 (4)	0.0127 (4)	0.0044 (3)	0.0053 (4)	0.0055 (4)
C4	0.0167 (5)	0.0104 (5)	0.0117 (5)	0.0022 (4)	0.0055 (4)	0.0049 (4)
C5	0.0154 (5)	0.0111 (5)	0.0144 (5)	0.0029 (4)	0.0069 (4)	0.0046 (4)
C6	0.0143 (5)	0.0097 (5)	0.0145 (5)	0.0017 (4)	0.0032 (4)	0.0048 (4)
N21	0.0194 (5)	0.0213 (5)	0.0132 (5)	0.0089 (4)	0.0077 (4)	0.0075 (4)
N41	0.0171 (4)	0.0112 (4)	0.0119 (4)	0.0039 (3)	0.0059 (4)	0.0048 (4)
C42	0.0135 (5)	0.0145 (5)	0.0143 (5)	0.0052 (4)	0.0074 (4)	0.0074 (4)
N43	0.0168 (5)	0.0144 (5)	0.0136 (5)	0.0045 (4)	0.0071 (4)	0.0057 (4)
C43A	0.0160 (5)	0.0145 (5)	0.0154 (5)	0.0051 (4)	0.0082 (4)	0.0066 (4)
C44	0.0214 (6)	0.0185 (6)	0.0140 (5)	0.0051 (4)	0.0064 (4)	0.0056 (4)
C45	0.0220 (6)	0.0154 (5)	0.0166 (6)	0.0025 (4)	0.0063 (5)	0.0021 (4)
C46	0.0201 (6)	0.0132 (5)	0.0217 (6)	0.0038 (4)	0.0088 (5)	0.0062 (5)
C47	0.0193 (6)	0.0153 (5)	0.0165 (5)	0.0048 (4)	0.0073 (4)	0.0076 (4)
C47A	0.0150 (5)	0.0139 (5)	0.0128 (5)	0.0040 (4)	0.0069 (4)	0.0041 (4)
C421	0.0163 (5)	0.0134 (5)	0.0137 (5)	0.0040 (4)	0.0089 (4)	0.0063 (4)
C422	0.0161 (5)	0.0161 (5)	0.0176 (5)	0.0050 (4)	0.0071 (4)	0.0077 (4)
C423	0.0179 (5)	0.0166 (5)	0.0175 (6)	0.0007 (4)	0.0066 (4)	0.0052 (4)
C424	0.0238 (6)	0.0133 (5)	0.0203 (6)	0.0035 (4)	0.0130 (5)	0.0063 (4)
C425	0.0217 (6)	0.0160 (5)	0.0199 (6)	0.0088 (4)	0.0127 (5)	0.0102 (4)
C426	0.0159 (5)	0.0163 (5)	0.0143 (5)	0.0048 (4)	0.0082 (4)	0.0071 (4)
C427	0.0361 (7)	0.0139 (6)	0.0301 (7)	0.0033 (5)	0.0114 (6)	0.0052 (5)
N51	0.0180 (5)	0.0215 (5)	0.0182 (5)	0.0086 (4)	0.0098 (4)	0.0091 (4)
O61	0.0163 (4)	0.0187 (4)	0.0161 (4)	0.0069 (3)	0.0044 (3)	0.0081 (3)
C61	0.0235 (6)	0.0220 (6)	0.0156 (6)	0.0076 (5)	0.0027 (5)	0.0096 (5)
O1	0.0219 (4)	0.0200 (4)	0.0148 (4)	0.0052 (3)	0.0078 (3)	0.0087 (4)

Geometric parameters (Å, º) top

N1—C6	1.3108 (15)	C47—C47A	1.3944 (15)
N1—C2	1.3612 (14)	C47—H47	0.9500
C2—N3	1.3425 (14)	C421—C422	1.3966 (16)
C2—N21	1.3456 (15)	C421—C426	1.3985 (15)
N3—C4	1.3410 (14)	C422—C423	1.3884 (16)
C4—C5	1.3723 (16)	C422—H422	0.9500
C4—N41	1.4329 (14)	C423—C424	1.3962 (17)
C5—N51	1.4112 (14)	C423—H423	0.9500
C5—C6	1.4178 (15)	C424—C425	1.3964 (17)
C6—O61	1.3417 (13)	C424—C427	1.5093 (17)
N21—H21A	0.920 (16)	C425—C426	1.3903 (16)
N21—H21B	0.884 (16)	C425—H425	0.9500
N41—C42	1.3860 (14)	C426—H426	0.9500
N41—C47A	1.3913 (14)	C427—H47A	0.9800
C42—N43	1.3182 (14)	C427—H47B	0.9800
C42—C421	1.4694 (15)	C427—H47C	0.9800
N43—C43A	1.3922 (14)	N51—H51A	0.908 (16)
C43A—C44	1.4004 (16)	N51—H51B	0.906 (17)
C43A—C47A	1.4007 (15)	O61—C61	1.4428 (14)
C44—C45	1.3895 (17)	C61—H61A	0.9800
C44—H44	0.9500	C61—H61B	0.9800
C45—C46	1.4038 (17)	C61—H61C	0.9800
C45—H45	0.9500	O1—H1A	0.872 (18)
C46—C47	1.3873 (16)	O1—H1B	0.880 (18)
C46—H46	0.9500

C6—N1—C2	116.27 (10)	N41—C47A—C47	131.39 (10)
N3—C2—N21	117.55 (10)	N41—C47A—C43A	105.48 (9)
N3—C2—N1	125.45 (10)	C47—C47A—C43A	123.10 (10)
N21—C2—N1	116.95 (10)	C422—C421—C426	119.22 (10)
C4—N3—C2	115.36 (9)	C422—C421—C42	121.38 (10)
N3—C4—C5	125.10 (10)	C426—C421—C42	119.38 (10)
N3—C4—N41	115.97 (9)	C423—C422—C421	120.15 (11)
C5—C4—N41	118.85 (10)	C423—C422—H422	119.9
C4—C5—N51	125.17 (10)	C421—C422—H422	119.9
C4—C5—C6	113.76 (10)	C422—C423—C424	121.21 (11)
N51—C5—C6	120.85 (10)	C422—C423—H423	119.4
N1—C6—O61	121.15 (10)	C424—C423—H423	119.4
N1—C6—C5	123.97 (10)	C423—C424—C425	118.19 (11)
O61—C6—C5	114.87 (10)	C423—C424—C427	120.61 (11)
C2—N21—H21A	117.5 (10)	C425—C424—C427	121.20 (11)
C2—N21—H21B	119.1 (10)	C426—C425—C424	121.21 (11)
H21A—N21—H21B	121.0 (14)	C426—C425—H425	119.4
C42—N41—C47A	106.59 (9)	C424—C425—H425	119.4
C42—N41—C4	129.12 (9)	C425—C426—C421	120.01 (11)
C47A—N41—C4	122.72 (9)	C425—C426—H426	120.0
N43—C42—N41	112.29 (10)	C421—C426—H426	120.0
N43—C42—C421	124.39 (10)	C424—C427—H47A	109.5
N41—C42—C421	123.28 (10)	C424—C427—H47B	109.5
C42—N43—C43A	105.73 (9)	H47A—C427—H47B	109.5
N43—C43A—C44	130.53 (10)	C424—C427—H47C	109.5
N43—C43A—C47A	109.88 (10)	H47A—C427—H47C	109.5
C44—C43A—C47A	119.58 (10)	H47B—C427—H47C	109.5
C45—C44—C43A	117.83 (11)	C5—N51—H51A	112.1 (10)
C45—C44—H44	121.1	C5—N51—H51B	114.1 (10)
C43A—C44—H44	121.1	H51A—N51—H51B	111.3 (14)
C44—C45—C46	121.60 (11)	C6—O61—C61	116.75 (9)
C44—C45—H45	119.2	O61—C61—H61A	109.5
C46—C45—H45	119.2	O61—C61—H61B	109.5
C47—C46—C45	121.37 (11)	H61A—C61—H61B	109.5
C47—C46—H46	119.3	O61—C61—H61C	109.5
C45—C46—H46	119.3	H61A—C61—H61C	109.5
C46—C47—C47A	116.50 (11)	H61B—C61—H61C	109.5
C46—C47—H47	121.8	H1A—O1—H1B	105.8 (15)
C47A—C47—H47	121.8

C6—N1—C2—N3	3.53 (16)	C43A—C44—C45—C46	−0.10 (18)
C6—N1—C2—N21	−179.02 (10)	C44—C45—C46—C47	−0.73 (19)
N21—C2—N3—C4	−179.31 (10)	C45—C46—C47—C47A	0.26 (17)
N1—C2—N3—C4	−1.88 (16)	C42—N41—C47A—C47	−176.73 (12)
C2—N3—C4—C5	−1.03 (16)	C4—N41—C47A—C47	−9.82 (18)
C2—N3—C4—N41	175.46 (9)	C42—N41—C47A—C43A	1.19 (12)
N3—C4—C5—N51	−172.67 (10)	C4—N41—C47A—C43A	168.09 (10)
N41—C4—C5—N51	10.94 (16)	C46—C47—C47A—N41	178.65 (11)
N3—C4—C5—C6	1.92 (16)	C46—C47—C47A—C43A	1.05 (17)
N41—C4—C5—C6	−174.47 (9)	N43—C43A—C47A—N41	−0.63 (12)
C2—N1—C6—O61	178.12 (9)	C44—C43A—C47A—N41	179.98 (10)
C2—N1—C6—C5	−2.41 (16)	N43—C43A—C47A—C47	177.50 (10)
C4—C5—C6—N1	−0.07 (16)	C44—C43A—C47A—C47	−1.89 (17)
N51—C5—C6—N1	174.78 (10)	N43—C42—C421—C422	−143.75 (11)
C4—C5—C6—O61	179.43 (9)	N41—C42—C421—C422	33.89 (16)
N51—C5—C6—O61	−5.72 (15)	N43—C42—C421—C426	34.72 (16)
N3—C4—N41—C42	62.21 (15)	N41—C42—C421—C426	−147.63 (11)
C5—C4—N41—C42	−121.08 (12)	C426—C421—C422—C423	0.20 (17)
N3—C4—N41—C47A	−101.53 (12)	C42—C421—C422—C423	178.68 (10)
C5—C4—N41—C47A	75.18 (14)	C421—C422—C423—C424	0.60 (17)
C47A—N41—C42—N43	−1.42 (12)	C422—C423—C424—C425	−0.78 (17)
C4—N41—C42—N43	−167.19 (10)	C422—C423—C424—C427	178.95 (11)
C47A—N41—C42—C421	−179.32 (10)	C423—C424—C425—C426	0.18 (17)
C4—N41—C42—C421	14.91 (17)	C427—C424—C425—C426	−179.56 (11)
N41—C42—N43—C43A	1.01 (12)	C424—C425—C426—C421	0.61 (17)
C421—C42—N43—C43A	178.88 (10)	C422—C421—C426—C425	−0.80 (16)
C42—N43—C43A—C44	179.09 (12)	C42—C421—C426—C425	−179.31 (10)
C42—N43—C43A—C47A	−0.21 (12)	N1—C6—O61—C61	0.98 (15)
N43—C43A—C44—C45	−177.90 (11)	C5—C6—O61—C61	−178.54 (9)
C47A—C43A—C44—C45	1.35 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···N43	0.873 (19)	1.970 (19)	2.8421 (15)	178.1 (17)
O1—H1B···N51ⁱ	0.880 (19)	2.08 (2)	2.9243 (16)	161.7 (16)
N21—H21A···O1ⁱⁱ	0.920 (17)	2.076 (17)	2.9881 (16)	170.7 (14)
N21—H21B···O1ⁱⁱⁱ	0.884 (16)	2.061 (16)	2.8729 (14)	152.4 (16)

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

N-{5-Amino-6-methoxy-6-[2-(4-methylphenyl)-1H-\ benzo[d]imidazol-1-yl]pyrimidin-2-yl}-2,2,2-trifluoroacetamide ethyl acetate monosolvate (VI) top

Crystal data top

C₂₁H₁₇F₃N₆O₂·C₄H₈O₂	F(000) = 1104
M_r = 530.51	D_x = 1.363 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 9.1818 (8) Å	Cell parameters from 6413 reflections
b = 21.0771 (16) Å	θ = 2.4–28.3°
c = 13.3610 (11) Å	µ = 0.11 mm⁻¹
β = 91.777 (3)°	T = 100 K
V = 2584.5 (4) Å³	Block, colourless
Z = 4	0.22 × 0.18 × 0.18 mm

Data collection top

Bruker D8 Venture diffractometer	6413 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	5692 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.049
φ and ω scans	θ_max = 28.3°, θ_min = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −12→12
T_min = 0.919, T_max = 0.980	k = −27→28
78171 measured reflections	l = −17→17

Refinement top

Refinement on F²	Primary 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) = 0.120	w = 1/[σ²(F_o²) + (0.0415P)² + 2.1776P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
6413 reflections	Δρ_max = 0.54 e Å⁻³
372 parameters	Δρ_min = −0.44 e Å⁻³
15 restraints

Special details top

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
N1	0.70736 (13)	0.32326 (6)	0.67797 (9)	0.0191 (2)
C2	0.62855 (15)	0.37693 (7)	0.67827 (10)	0.0172 (3)
N3	0.54458 (13)	0.39966 (6)	0.60503 (9)	0.0169 (2)
C4	0.54441 (15)	0.36631 (6)	0.51893 (10)	0.0157 (3)
C5	0.62436 (16)	0.31175 (7)	0.50506 (11)	0.0204 (3)
C6	0.70376 (16)	0.29179 (7)	0.59323 (11)	0.0208 (3)
N21	0.63969 (14)	0.41655 (6)	0.76410 (9)	0.0207 (3)	0.753 (4)
H21	0.6084	0.4558	0.7573	0.025*	0.753 (4)
C21	0.6938 (9)	0.39956 (17)	0.8550 (3)	0.0312 (7)	0.753 (4)
O21	0.7528 (3)	0.34839 (8)	0.88204 (13)	0.0397 (6)	0.753 (4)
C22	0.7133 (8)	0.4569 (2)	0.9265 (4)	0.0303 (5)	0.753 (4)
F21	0.6081 (10)	0.5001 (3)	0.9167 (4)	0.0409 (7)	0.753 (4)
F22	0.8364 (11)	0.4876 (5)	0.9061 (11)	0.0583 (6)	0.753 (4)
F23	0.7217 (13)	0.4388 (4)	1.0204 (4)	0.0597 (14)	0.753 (4)
N31	0.63969 (14)	0.41655 (6)	0.76410 (9)	0.0207 (3)	0.247 (4)
H31	0.5996	0.4544	0.7598	0.025*	0.247 (4)
C31	0.707 (3)	0.4007 (5)	0.8513 (9)	0.0312 (7)	0.247 (4)
O31	0.6623 (11)	0.3501 (3)	0.8895 (4)	0.0397 (6)	0.247 (4)
C32	0.724 (3)	0.4557 (7)	0.9276 (12)	0.0303 (5)	0.247 (4)
F31	0.609 (3)	0.4938 (10)	0.9321 (14)	0.0409 (7)	0.247 (4)
F32	0.837 (3)	0.4919 (15)	0.906 (3)	0.0583 (6)	0.247 (4)
F33	0.746 (4)	0.4327 (14)	1.0184 (12)	0.0597 (14)	0.247 (4)
N41	0.45323 (12)	0.38991 (5)	0.43855 (8)	0.0153 (2)
C42	0.48539 (15)	0.43454 (6)	0.36654 (10)	0.0150 (3)
N43	0.37204 (13)	0.44782 (6)	0.30671 (9)	0.0161 (2)
C43A	0.25907 (15)	0.41008 (6)	0.34022 (10)	0.0158 (3)
C44	0.11293 (16)	0.40642 (7)	0.30745 (11)	0.0193 (3)
H44	0.0774	0.4308	0.2520	0.023*
C45	0.02185 (16)	0.36619 (7)	0.35840 (12)	0.0225 (3)
H45	−0.0783	0.3640	0.3386	0.027*
C46	0.07366 (17)	0.32850 (7)	0.43859 (12)	0.0230 (3)
H46	0.0086	0.3005	0.4704	0.028*
C47	0.21845 (16)	0.33142 (7)	0.47231 (11)	0.0198 (3)
H47	0.2543	0.3062	0.5266	0.024*
C47A	0.30785 (15)	0.37328 (6)	0.42236 (10)	0.0160 (3)
C421	0.62823 (14)	0.46485 (6)	0.35734 (10)	0.0159 (3)
C422	0.71016 (15)	0.48617 (7)	0.44070 (10)	0.0167 (3)
H422	0.6794	0.4767	0.5063	0.020*
C423	0.83616 (15)	0.52114 (7)	0.42784 (11)	0.0191 (3)
H423	0.8912	0.5353	0.4849	0.023*
C424	0.88322 (16)	0.53592 (7)	0.33238 (12)	0.0222 (3)
C425	0.80315 (17)	0.51304 (8)	0.24966 (12)	0.0241 (3)
H425	0.8356	0.5216	0.1842	0.029*
C426	0.67658 (16)	0.47793 (7)	0.26146 (11)	0.0207 (3)
H426	0.6230	0.4629	0.2043	0.025*
C427	1.01832 (19)	0.57542 (9)	0.32094 (14)	0.0320 (4)
H47A	1.0209	0.5918	0.2523	0.048*
H47B	1.1047	0.5492	0.3349	0.048*
H47C	1.0173	0.6110	0.3681	0.048*
N51	0.6318 (2)	0.27866 (8)	0.41829 (12)	0.0403 (4)
H51A	0.586 (3)	0.2915 (12)	0.3655 (19)	0.048*
H51B	0.676 (3)	0.2407 (12)	0.4173 (18)	0.048*
O61	0.77832 (14)	0.23785 (6)	0.58267 (9)	0.0296 (3)
C61	0.8521 (2)	0.21279 (9)	0.67127 (13)	0.0361 (4)
H61A	0.7816	0.2066	0.7239	0.054*
H61B	0.9274	0.2427	0.6946	0.054*
H61C	0.8974	0.1721	0.6553	0.054*
C71	0.3647 (2)	0.27537 (8)	0.20733 (13)	0.0308 (4)
C72	0.3096 (3)	0.22030 (10)	0.26512 (15)	0.0419 (5)
H72A	0.3763	0.2117	0.3222	0.063*
H72B	0.3038	0.1829	0.2217	0.063*
H72C	0.2126	0.2302	0.2894	0.063*
O71	0.48004 (15)	0.30265 (6)	0.22485 (9)	0.0356 (3)
O72	0.27230 (16)	0.29191 (6)	0.13288 (10)	0.0371 (3)
C73	0.3180 (3)	0.34448 (9)	0.07135 (15)	0.0455 (5)
H73A	0.4026	0.3320	0.0316	0.055*
H73B	0.3463	0.3812	0.1139	0.055*
C74	0.1899 (3)	0.36150 (11)	0.00293 (17)	0.0568 (7)
H74A	0.1104	0.3779	0.0428	0.085*
H74B	0.1566	0.3236	−0.0337	0.085*
H74C	0.2195	0.3940	−0.0448	0.085*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0177 (6)	0.0228 (6)	0.0168 (6)	−0.0013 (5)	−0.0023 (4)	0.0026 (5)
C2	0.0163 (6)	0.0212 (7)	0.0141 (6)	−0.0043 (5)	0.0010 (5)	0.0004 (5)
N3	0.0162 (5)	0.0189 (6)	0.0156 (5)	−0.0012 (4)	0.0009 (4)	−0.0007 (4)
C4	0.0155 (6)	0.0171 (6)	0.0143 (6)	0.0003 (5)	−0.0015 (5)	0.0011 (5)
C5	0.0228 (7)	0.0207 (7)	0.0174 (6)	0.0050 (5)	−0.0039 (5)	−0.0012 (5)
C6	0.0194 (7)	0.0220 (7)	0.0209 (7)	0.0037 (5)	−0.0030 (5)	0.0018 (5)
N21	0.0214 (6)	0.0253 (6)	0.0154 (6)	−0.0011 (5)	0.0004 (4)	−0.0028 (5)
C21	0.0562 (19)	0.0231 (8)	0.0141 (7)	−0.0171 (8)	−0.0008 (9)	0.0021 (6)
O21	0.0759 (18)	0.0198 (7)	0.0223 (7)	−0.0080 (10)	−0.0170 (11)	0.0061 (5)
C22	0.0470 (15)	0.0285 (8)	0.0152 (7)	−0.0018 (8)	−0.0031 (7)	−0.0018 (6)
F21	0.0589 (8)	0.0411 (15)	0.0223 (19)	0.0097 (11)	−0.0037 (16)	−0.0013 (12)
F22	0.0575 (8)	0.0537 (16)	0.0642 (9)	−0.0243 (9)	0.0080 (7)	−0.0335 (12)
F23	0.122 (5)	0.0424 (19)	0.0139 (5)	0.0191 (16)	−0.0107 (12)	−0.0021 (7)
N31	0.0214 (6)	0.0253 (6)	0.0154 (6)	−0.0011 (5)	0.0004 (4)	−0.0028 (5)
C31	0.0562 (19)	0.0231 (8)	0.0141 (7)	−0.0171 (8)	−0.0008 (9)	0.0021 (6)
O31	0.0759 (18)	0.0198 (7)	0.0223 (7)	−0.0080 (10)	−0.0170 (11)	0.0061 (5)
C32	0.0470 (15)	0.0285 (8)	0.0152 (7)	−0.0018 (8)	−0.0031 (7)	−0.0018 (6)
F31	0.0589 (8)	0.0411 (15)	0.0223 (19)	0.0097 (11)	−0.0037 (16)	−0.0013 (12)
F32	0.0575 (8)	0.0537 (16)	0.0642 (9)	−0.0243 (9)	0.0080 (7)	−0.0335 (12)
F33	0.122 (5)	0.0424 (19)	0.0139 (5)	0.0191 (16)	−0.0107 (12)	−0.0021 (7)
N41	0.0151 (5)	0.0154 (5)	0.0154 (5)	0.0018 (4)	−0.0011 (4)	−0.0003 (4)
C42	0.0162 (6)	0.0150 (6)	0.0136 (6)	0.0027 (5)	0.0004 (5)	−0.0022 (5)
N43	0.0157 (5)	0.0175 (5)	0.0150 (5)	0.0009 (4)	−0.0009 (4)	−0.0017 (4)
C43A	0.0173 (6)	0.0153 (6)	0.0147 (6)	0.0011 (5)	−0.0003 (5)	−0.0037 (5)
C44	0.0184 (6)	0.0225 (7)	0.0166 (6)	0.0015 (5)	−0.0038 (5)	−0.0036 (5)
C45	0.0172 (7)	0.0262 (7)	0.0240 (7)	−0.0023 (6)	−0.0026 (5)	−0.0082 (6)
C46	0.0224 (7)	0.0218 (7)	0.0249 (7)	−0.0067 (6)	0.0035 (6)	−0.0039 (6)
C47	0.0237 (7)	0.0167 (6)	0.0190 (7)	−0.0012 (5)	0.0002 (5)	−0.0009 (5)
C47A	0.0158 (6)	0.0160 (6)	0.0161 (6)	0.0012 (5)	−0.0014 (5)	−0.0035 (5)
C421	0.0138 (6)	0.0162 (6)	0.0179 (6)	0.0028 (5)	0.0012 (5)	−0.0012 (5)
C422	0.0158 (6)	0.0178 (6)	0.0166 (6)	0.0023 (5)	0.0019 (5)	−0.0013 (5)
C423	0.0153 (6)	0.0194 (6)	0.0225 (7)	0.0016 (5)	−0.0001 (5)	−0.0041 (5)
C424	0.0171 (7)	0.0222 (7)	0.0277 (8)	−0.0002 (5)	0.0060 (6)	−0.0008 (6)
C425	0.0226 (7)	0.0299 (8)	0.0201 (7)	−0.0008 (6)	0.0066 (6)	0.0017 (6)
C426	0.0189 (7)	0.0263 (7)	0.0168 (6)	0.0014 (6)	0.0003 (5)	−0.0017 (5)
C427	0.0255 (8)	0.0358 (9)	0.0353 (9)	−0.0103 (7)	0.0101 (7)	−0.0031 (7)
N51	0.0582 (11)	0.0382 (9)	0.0234 (7)	0.0317 (8)	−0.0162 (7)	−0.0121 (6)
O61	0.0364 (6)	0.0281 (6)	0.0239 (6)	0.0166 (5)	−0.0073 (5)	0.0007 (5)
C61	0.0407 (10)	0.0395 (10)	0.0277 (8)	0.0212 (8)	−0.0078 (7)	0.0070 (7)
C71	0.0421 (10)	0.0271 (8)	0.0229 (8)	0.0116 (7)	−0.0023 (7)	−0.0067 (6)
C72	0.0589 (13)	0.0381 (10)	0.0284 (9)	0.0033 (9)	−0.0033 (9)	0.0017 (8)
O71	0.0401 (7)	0.0396 (7)	0.0268 (6)	0.0104 (6)	−0.0044 (5)	−0.0037 (5)
O72	0.0542 (8)	0.0284 (6)	0.0278 (6)	0.0023 (6)	−0.0131 (6)	−0.0035 (5)
C73	0.0744 (15)	0.0295 (9)	0.0317 (10)	0.0013 (9)	−0.0151 (10)	0.0016 (8)
C74	0.0933 (19)	0.0365 (11)	0.0389 (11)	0.0125 (12)	−0.0259 (12)	−0.0018 (9)

Geometric parameters (Å, º) top

N1—C6	1.3117 (19)	C47—C47A	1.390 (2)
N1—C2	1.3429 (19)	C47—H47	0.9500
C2—N3	1.3171 (18)	C421—C426	1.396 (2)
C2—N21	1.4196 (18)	C421—C422	1.3987 (19)
N3—C4	1.3481 (18)	C422—C423	1.387 (2)
C4—C5	1.3800 (19)	C422—H422	0.9500
C4—N41	1.4303 (17)	C423—C424	1.394 (2)
C5—N51	1.357 (2)	C423—H423	0.9500
C5—C6	1.4293 (19)	C424—C425	1.394 (2)
C6—O61	1.3369 (18)	C424—C427	1.506 (2)
N21—C21	1.346 (3)	C425—C426	1.391 (2)
N21—H21	0.8800	C425—H425	0.9500
C21—O21	1.255 (5)	C426—H426	0.9500
C21—C22	1.548 (3)	C427—H47A	0.9800
C22—F23	1.312 (3)	C427—H47B	0.9800
C22—F21	1.330 (3)	C427—H47C	0.9800
C22—F22	1.338 (3)	N51—H51A	0.86 (3)
C31—O31	1.256 (11)	N51—H51B	0.90 (3)
C31—C32	1.549 (7)	O61—C61	1.4457 (19)
C32—F33	1.316 (7)	C61—H61A	0.9800
C32—F31	1.325 (8)	C61—H61B	0.9800
C32—F32	1.333 (8)	C61—H61C	0.9800
N41—C42	1.3838 (17)	C71—O71	1.221 (2)
N41—C47A	1.3906 (17)	C71—O72	1.334 (2)
C42—N43	1.3225 (17)	C71—C72	1.491 (3)
C42—C421	1.4674 (19)	C72—H72A	0.9800
N43—C43A	1.3922 (18)	C72—H72B	0.9800
C43A—C44	1.4007 (19)	C72—H72C	0.9800
C43A—C47A	1.4057 (19)	O72—C73	1.449 (2)
C44—C45	1.385 (2)	C73—C74	1.510 (3)
C44—H44	0.9500	C73—H73A	0.9900
C45—C46	1.405 (2)	C73—H73B	0.9900
C45—H45	0.9500	C74—H74A	0.9800
C46—C47	1.392 (2)	C74—H74B	0.9800
C46—H46	0.9500	C74—H74C	0.9800

C6—N1—C2	115.43 (12)	N41—C47A—C43A	105.27 (12)
N3—C2—N1	127.38 (13)	C426—C421—C422	119.25 (13)
N3—C2—N21	114.34 (13)	C426—C421—C42	118.25 (12)
N1—C2—N21	118.20 (12)	C422—C421—C42	122.22 (12)
C2—N3—C4	115.44 (12)	C423—C422—C421	120.15 (13)
N3—C4—C5	124.23 (13)	C423—C422—H422	119.9
N3—C4—N41	116.40 (12)	C421—C422—H422	119.9
C5—C4—N41	119.37 (12)	C422—C423—C424	121.02 (13)
N51—C5—C4	125.75 (14)	C422—C423—H423	119.5
N51—C5—C6	121.02 (14)	C424—C423—H423	119.5
C4—C5—C6	113.23 (13)	C425—C424—C423	118.49 (14)
N1—C6—O61	121.46 (13)	C425—C424—C427	121.78 (14)
N1—C6—C5	124.13 (13)	C423—C424—C427	119.73 (14)
O61—C6—C5	114.39 (13)	C426—C425—C424	121.07 (14)
C21—N21—C2	126.0 (2)	C426—C425—H425	119.5
C21—N21—H21	117.0	C424—C425—H425	119.5
C2—N21—H21	117.0	C425—C426—C421	119.97 (13)
O21—C21—N21	129.2 (4)	C425—C426—H426	120.0
O21—C21—C22	117.0 (3)	C421—C426—H426	120.0
N21—C21—C22	112.4 (3)	C424—C427—H47A	109.5
F23—C22—F21	108.3 (3)	C424—C427—H47B	109.5
F23—C22—F22	108.1 (4)	H47A—C427—H47B	109.5
F21—C22—F22	105.4 (4)	C424—C427—H47C	109.5
F23—C22—C21	111.4 (3)	H47A—C427—H47C	109.5
F21—C22—C21	113.8 (3)	H47B—C427—H47C	109.5
F22—C22—C21	109.5 (4)	C5—N51—H51A	120.3 (17)
O31—C31—C32	113.3 (12)	C5—N51—H51B	120.3 (15)
F33—C32—F31	106.4 (11)	H51A—N51—H51B	119 (2)
F33—C32—F32	108.2 (12)	C6—O61—C61	116.93 (13)
F31—C32—F32	107.0 (11)	O61—C61—H61A	109.5
F33—C32—C31	109.9 (10)	O61—C61—H61B	109.5
F31—C32—C31	114.8 (10)	H61A—C61—H61B	109.5
F32—C32—C31	110.3 (11)	O61—C61—H61C	109.5
C42—N41—C47A	106.72 (11)	H61A—C61—H61C	109.5
C42—N41—C4	128.74 (12)	H61B—C61—H61C	109.5
C47A—N41—C4	124.46 (12)	O71—C71—O72	123.20 (17)
N43—C42—N41	112.54 (12)	O71—C71—C72	124.98 (17)
N43—C42—C421	123.08 (12)	O72—C71—C72	111.82 (17)
N41—C42—C421	124.38 (12)	C71—C72—H72A	109.5
C42—N43—C43A	105.35 (11)	C71—C72—H72B	109.5
N43—C43A—C44	130.32 (13)	H72A—C72—H72B	109.5
N43—C43A—C47A	110.11 (12)	C71—C72—H72C	109.5
C44—C43A—C47A	119.52 (13)	H72A—C72—H72C	109.5
C45—C44—C43A	117.86 (13)	H72B—C72—H72C	109.5
C45—C44—H44	121.1	C71—O72—C73	115.75 (16)
C43A—C44—H44	121.1	O72—C73—C74	106.93 (19)
C44—C45—C46	121.73 (14)	O72—C73—H73A	110.3
C44—C45—H45	119.1	C74—C73—H73A	110.3
C46—C45—H45	119.1	O72—C73—H73B	110.3
C47—C46—C45	121.29 (14)	C74—C73—H73B	110.3
C47—C46—H46	119.4	H73A—C73—H73B	108.6
C45—C46—H46	119.4	C73—C74—H74A	109.5
C47A—C47—C46	116.43 (13)	C73—C74—H74B	109.5
C47A—C47—H47	121.8	H74A—C74—H74B	109.5
C46—C47—H47	121.8	C73—C74—H74C	109.5
C47—C47A—N41	131.59 (13)	H74A—C74—H74C	109.5
C47—C47A—C43A	123.13 (13)	H74B—C74—H74C	109.5

C6—N1—C2—N3	3.0 (2)	C421—C42—N43—C43A	−179.47 (12)
C6—N1—C2—N21	−173.61 (13)	C42—N43—C43A—C44	177.12 (14)
N1—C2—N3—C4	−3.4 (2)	C42—N43—C43A—C47A	−0.15 (15)
N21—C2—N3—C4	173.25 (12)	N43—C43A—C44—C45	−176.92 (14)
C2—N3—C4—C5	0.3 (2)	C47A—C43A—C44—C45	0.1 (2)
C2—N3—C4—N41	179.61 (12)	C43A—C44—C45—C46	−1.9 (2)
N3—C4—C5—N51	−176.87 (17)	C44—C45—C46—C47	2.0 (2)
N41—C4—C5—N51	3.8 (2)	C45—C46—C47—C47A	−0.1 (2)
N3—C4—C5—C6	2.7 (2)	C46—C47—C47A—N41	176.89 (14)
N41—C4—C5—C6	−176.62 (13)	C46—C47—C47A—C43A	−1.7 (2)
C2—N1—C6—O61	179.48 (14)	C42—N41—C47A—C47	−179.30 (14)
C2—N1—C6—C5	0.7 (2)	C4—N41—C47A—C47	−2.3 (2)
N51—C5—C6—N1	176.38 (17)	C42—N41—C47A—C43A	−0.54 (14)
C4—C5—C6—N1	−3.2 (2)	C4—N41—C47A—C43A	176.45 (12)
N51—C5—C6—O61	−2.5 (2)	N43—C43A—C47A—C47	179.33 (13)
C4—C5—C6—O61	177.89 (13)	C44—C43A—C47A—C47	1.7 (2)
N3—C2—N21—C21	166.2 (4)	N43—C43A—C47A—N41	0.44 (15)
N1—C2—N21—C21	−16.8 (5)	C44—C43A—C47A—N41	−177.17 (12)
C2—N21—C21—O21	4.9 (10)	N43—C42—C421—C426	−37.18 (19)
C2—N21—C21—C22	170.6 (3)	N41—C42—C421—C426	143.65 (14)
O21—C21—C22—F23	−32.1 (8)	N43—C42—C421—C422	136.72 (14)
N21—C21—C22—F23	160.3 (7)	N41—C42—C421—C422	−42.5 (2)
O21—C21—C22—F21	−154.9 (7)	C426—C421—C422—C423	1.5 (2)
N21—C21—C22—F21	37.5 (7)	C42—C421—C422—C423	−172.37 (13)
O21—C21—C22—F22	87.5 (8)	C421—C422—C423—C424	0.3 (2)
N21—C21—C22—F22	−80.1 (8)	C422—C423—C424—C425	−2.0 (2)
O31—C31—C32—F33	26 (2)	C422—C423—C424—C427	178.41 (14)
O31—C31—C32—F31	−94 (2)	C423—C424—C425—C426	2.0 (2)
O31—C31—C32—F32	145 (2)	C427—C424—C425—C426	−178.39 (15)
N3—C4—N41—C42	87.21 (17)	C424—C425—C426—C421	−0.3 (2)
C5—C4—N41—C42	−93.41 (18)	C422—C421—C426—C425	−1.5 (2)
N3—C4—N41—C47A	−89.09 (16)	C42—C421—C426—C425	172.63 (13)
C5—C4—N41—C47A	90.29 (17)	N1—C6—O61—C61	5.5 (2)
C47A—N41—C42—N43	0.49 (15)	C5—C6—O61—C61	−175.58 (15)
C4—N41—C42—N43	−176.33 (12)	O71—C71—O72—C73	1.0 (2)
C47A—N41—C42—C421	179.73 (12)	C72—C71—O72—C73	−178.99 (16)
C4—N41—C42—C421	2.9 (2)	C71—O72—C73—C74	−171.64 (16)
N41—C42—N43—C43A	−0.21 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21···N43ⁱ	0.88	2.21	3.0121 (18)	151
N31—H31···N43ⁱ	0.88	2.26	3.0121 (18)	143
N51—H51A···O71	0.85 (3)	2.10 (3)	2.942 (2)	168 (2)
N51—H51B···O21ⁱⁱ	0.90 (3)	2.07 (3)	2.945 (3)	166 (2)
N51—H51B···O31ⁱⁱ	0.90 (3)	1.95 (3)	2.757 (7)	148 (2)
C47—H47···O72ⁱⁱⁱ	0.95	2.51	3.397 (2)	155
C422—H422···Cg3ⁱ	0.95	2.90	3.3906 (15)	113
C423—H423···Cg4ⁱ	0.95	2.68	3.3562 (16)	129

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

N-{2-Amino-6-methoxy-4-[2-(4-methylphenyl)-1H-\ benzo[d]imidazol-1-yl]pyrimidin-5-yl}-2,2,2-trifluoroacetamide (VIIa) top

Crystal data top

C₂₁H₁₇F₃N₆O₂·CH₄O	F(000) = 984
M_r = 474.45	D_x = 1.466 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 12.6296 (8) Å	Cell parameters from 4939 reflections
b = 11.2206 (7) Å	θ = 2.3–27.5°
c = 15.648 (1) Å	µ = 0.12 mm⁻¹
β = 104.180 (2)°	T = 100 K
V = 2149.9 (2) Å³	Block, colourless
Z = 4	0.23 × 0.17 × 0.10 mm

Data collection top

Bruker D8 Venture diffractometer	4939 independent reflections
Radiation source: INCOATEC high brilliance microfocus sealed tube	4034 reflections with I > 2σ(I)
Multilayer mirror monochromator	R_int = 0.062
φ and ω scans	θ_max = 27.5°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2016)	h = −16→16
T_min = 0.906, T_max = 0.988	k = −14→14
35768 measured reflections	l = −20→20

Refinement top

Refinement on F²	Primary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.098	w = 1/[σ²(F_o²) + (0.0381P)² + 1.4265P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
4939 reflections	Δρ_max = 0.36 e Å⁻³
322 parameters	Δρ_min = −0.30 e Å⁻³
0 restraints

Special details top

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

	x	y	z	U_iso*/U_eq
N1	0.44822 (10)	0.59122 (10)	0.56152 (8)	0.0139 (2)
C2	0.35695 (12)	0.55122 (12)	0.50427 (9)	0.0134 (3)
N3	0.29446 (10)	0.45941 (11)	0.51707 (8)	0.0139 (2)
C4	0.32968 (11)	0.40147 (12)	0.59311 (9)	0.0124 (3)
C5	0.42117 (12)	0.43252 (12)	0.65738 (9)	0.0129 (3)
C6	0.47812 (11)	0.53297 (12)	0.63687 (9)	0.0128 (3)
N21	0.32390 (11)	0.60912 (12)	0.42659 (9)	0.0171 (3)
H21A	0.3703 (15)	0.6564 (17)	0.4073 (12)	0.020*
H21B	0.2750 (16)	0.5731 (17)	0.3866 (13)	0.020*
N41	0.26399 (10)	0.30299 (10)	0.60547 (8)	0.0132 (2)
C42	0.29557 (12)	0.18581 (12)	0.62382 (10)	0.0147 (3)
N43	0.21546 (10)	0.11940 (11)	0.63715 (8)	0.0166 (3)
C43A	0.12565 (12)	0.19508 (13)	0.62662 (10)	0.0155 (3)
C44	0.01885 (13)	0.17056 (14)	0.63136 (11)	0.0197 (3)
H44	−0.0021	0.0927	0.6446	0.024*
C45	−0.05517 (13)	0.26339 (15)	0.61613 (11)	0.0210 (3)
H45	−0.1284	0.2488	0.6187	0.025*
C46	−0.02464 (13)	0.37901 (14)	0.59695 (10)	0.0187 (3)
H46	−0.0776	0.4408	0.5872	0.022*
C47	0.08095 (12)	0.40481 (13)	0.59187 (10)	0.0164 (3)
H47	0.1021	0.4828	0.5793	0.020*
C47A	0.15405 (12)	0.31017 (13)	0.60619 (9)	0.0140 (3)
C421	0.40413 (12)	0.13980 (12)	0.62209 (10)	0.0142 (3)
C422	0.45522 (12)	0.05504 (13)	0.68408 (10)	0.0168 (3)
H422	0.4207	0.0286	0.7282	0.020*
C423	0.55623 (13)	0.00967 (13)	0.68101 (10)	0.0188 (3)
H423	0.5911	−0.0464	0.7243	0.023*
C424	0.60792 (12)	0.04435 (13)	0.61583 (10)	0.0180 (3)
C425	0.55521 (12)	0.12752 (13)	0.55353 (10)	0.0172 (3)
H425	0.5885	0.1516	0.5081	0.021*
C426	0.45542 (12)	0.17567 (13)	0.55667 (10)	0.0158 (3)
H426	0.4216	0.2333	0.5142	0.019*
C427	0.71716 (13)	−0.00621 (15)	0.61208 (12)	0.0240 (4)
H42A	0.7293	0.0073	0.5534	0.036*
H42B	0.7183	−0.0920	0.6241	0.036*
H42C	0.7749	0.0331	0.6564	0.036*
N51	0.45019 (10)	0.37407 (11)	0.74001 (8)	0.0135 (2)
H51	0.3981 (15)	0.3683 (15)	0.7723 (12)	0.016*
C51	0.54677 (12)	0.31925 (12)	0.76959 (9)	0.0141 (3)
O51	0.62094 (8)	0.31068 (9)	0.73298 (7)	0.0169 (2)
C52	0.55994 (13)	0.26709 (14)	0.86307 (10)	0.0194 (3)
F51	0.47358 (8)	0.20306 (9)	0.86958 (7)	0.0277 (2)
F52	0.57112 (11)	0.35418 (10)	0.92225 (7)	0.0396 (3)
F53	0.64625 (9)	0.19812 (12)	0.88476 (8)	0.0481 (4)
O61	0.56582 (8)	0.56787 (9)	0.69838 (7)	0.0156 (2)
C61	0.62461 (13)	0.66997 (14)	0.67725 (11)	0.0200 (3)
H61A	0.6519	0.6522	0.6252	0.030*
H61B	0.6862	0.6881	0.7272	0.030*
H61C	0.5755	0.7388	0.6650	0.030*
O71	0.27979 (10)	0.38202 (10)	0.81511 (8)	0.0217 (2)
H71	0.2760 (17)	0.453 (2)	0.8345 (14)	0.033*
C71	0.23100 (16)	0.29836 (16)	0.86160 (13)	0.0303 (4)
H71A	0.2694	0.2994	0.9241	0.045*
H71B	0.2357	0.2185	0.8375	0.045*
H71C	0.1542	0.3194	0.8553	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0142 (6)	0.0126 (6)	0.0159 (6)	0.0004 (5)	0.0060 (5)	0.0012 (5)
C2	0.0129 (7)	0.0130 (6)	0.0156 (7)	0.0027 (5)	0.0063 (5)	0.0000 (5)
N3	0.0146 (6)	0.0130 (6)	0.0145 (6)	0.0006 (5)	0.0041 (5)	0.0013 (5)
C4	0.0131 (7)	0.0103 (6)	0.0155 (7)	0.0010 (5)	0.0066 (5)	−0.0003 (5)
C5	0.0138 (7)	0.0127 (6)	0.0129 (7)	0.0022 (5)	0.0045 (5)	0.0004 (5)
C6	0.0123 (7)	0.0122 (6)	0.0149 (7)	0.0011 (5)	0.0052 (5)	−0.0022 (5)
N21	0.0154 (6)	0.0195 (6)	0.0162 (6)	−0.0013 (5)	0.0034 (5)	0.0046 (5)
N41	0.0131 (6)	0.0122 (6)	0.0143 (6)	−0.0006 (5)	0.0033 (5)	0.0011 (4)
C42	0.0189 (7)	0.0123 (6)	0.0136 (7)	−0.0017 (6)	0.0050 (5)	0.0007 (5)
N43	0.0169 (6)	0.0152 (6)	0.0186 (6)	−0.0008 (5)	0.0061 (5)	0.0022 (5)
C43A	0.0177 (7)	0.0161 (7)	0.0131 (7)	−0.0004 (6)	0.0046 (5)	0.0003 (5)
C44	0.0198 (8)	0.0191 (7)	0.0221 (8)	−0.0043 (6)	0.0085 (6)	0.0021 (6)
C45	0.0159 (7)	0.0264 (8)	0.0227 (8)	−0.0023 (6)	0.0083 (6)	0.0021 (6)
C46	0.0178 (8)	0.0208 (7)	0.0186 (7)	0.0044 (6)	0.0066 (6)	0.0013 (6)
C47	0.0188 (8)	0.0154 (7)	0.0156 (7)	0.0008 (6)	0.0056 (6)	0.0015 (5)
C47A	0.0147 (7)	0.0164 (7)	0.0114 (6)	−0.0024 (5)	0.0041 (5)	−0.0004 (5)
C421	0.0146 (7)	0.0113 (6)	0.0165 (7)	−0.0010 (5)	0.0032 (6)	−0.0013 (5)
C422	0.0195 (8)	0.0137 (7)	0.0174 (7)	−0.0014 (6)	0.0046 (6)	0.0010 (5)
C423	0.0192 (8)	0.0147 (7)	0.0199 (8)	0.0008 (6)	0.0000 (6)	0.0004 (6)
C424	0.0163 (7)	0.0144 (7)	0.0219 (8)	−0.0009 (6)	0.0023 (6)	−0.0056 (6)
C425	0.0180 (7)	0.0166 (7)	0.0181 (7)	−0.0024 (6)	0.0065 (6)	−0.0025 (6)
C426	0.0187 (7)	0.0129 (6)	0.0154 (7)	0.0000 (5)	0.0037 (6)	0.0003 (5)
C427	0.0173 (8)	0.0240 (8)	0.0297 (9)	0.0033 (6)	0.0040 (7)	−0.0040 (7)
N51	0.0156 (6)	0.0139 (6)	0.0120 (6)	−0.0003 (5)	0.0053 (5)	0.0018 (4)
C51	0.0150 (7)	0.0138 (6)	0.0134 (7)	−0.0020 (5)	0.0032 (5)	−0.0002 (5)
O51	0.0155 (5)	0.0191 (5)	0.0174 (5)	−0.0001 (4)	0.0063 (4)	0.0013 (4)
C52	0.0167 (7)	0.0248 (8)	0.0173 (7)	0.0016 (6)	0.0055 (6)	0.0060 (6)
F51	0.0276 (5)	0.0310 (5)	0.0253 (5)	−0.0068 (4)	0.0079 (4)	0.0120 (4)
F52	0.0644 (8)	0.0391 (6)	0.0141 (5)	−0.0164 (6)	0.0072 (5)	−0.0021 (4)
F53	0.0329 (6)	0.0763 (9)	0.0401 (7)	0.0320 (6)	0.0188 (5)	0.0403 (6)
O61	0.0160 (5)	0.0153 (5)	0.0151 (5)	−0.0048 (4)	0.0029 (4)	0.0005 (4)
C61	0.0215 (8)	0.0180 (7)	0.0202 (8)	−0.0088 (6)	0.0044 (6)	0.0001 (6)
O71	0.0263 (6)	0.0155 (5)	0.0287 (6)	−0.0006 (5)	0.0170 (5)	−0.0021 (5)
C71	0.0349 (10)	0.0234 (8)	0.0400 (10)	0.0000 (7)	0.0233 (8)	0.0047 (7)

Geometric parameters (Å, º) top

N1—C6	1.3198 (19)	C422—C423	1.385 (2)
N1—C2	1.3516 (19)	C422—H422	0.9500
C2—N3	1.3423 (19)	C423—C424	1.394 (2)
C2—N21	1.3511 (19)	C423—H423	0.9500
N3—C4	1.3331 (18)	C424—C425	1.395 (2)
C4—C5	1.378 (2)	C424—C427	1.506 (2)
C4—N41	1.4231 (18)	C425—C426	1.383 (2)
C5—C6	1.416 (2)	C425—H425	0.9500
C5—N51	1.4156 (18)	C426—H426	0.9500
C6—O61	1.3357 (17)	C427—H42A	0.9800
N21—H21A	0.90 (2)	C427—H42B	0.9800
N21—H21B	0.86 (2)	C427—H42C	0.9800
N41—C42	1.3835 (18)	N51—C51	1.3431 (19)
N41—C47A	1.3937 (19)	N51—H51	0.925 (19)
C42—N43	1.3138 (19)	C51—O51	1.2156 (18)
C42—C421	1.472 (2)	C51—C52	1.546 (2)
N43—C43A	1.3940 (19)	C52—F53	1.3119 (19)
C43A—C44	1.396 (2)	C52—F52	1.330 (2)
C43A—C47A	1.398 (2)	C52—F51	1.3307 (18)
C44—C45	1.381 (2)	O61—C61	1.4468 (17)
C44—H44	0.9500	C61—H61A	0.9800
C45—C46	1.407 (2)	C61—H61B	0.9800
C45—H45	0.9500	C61—H61C	0.9800
C46—C47	1.386 (2)	O71—C71	1.418 (2)
C46—H46	0.9500	O71—H71	0.86 (2)
C47—C47A	1.389 (2)	C71—H71A	0.9800
C47—H47	0.9500	C71—H71B	0.9800
C421—C426	1.398 (2)	C71—H71C	0.9800
C421—C422	1.398 (2)

C6—N1—C2	116.02 (12)	C423—C422—H422	120.1
N3—C2—N21	116.09 (13)	C421—C422—H422	120.1
N3—C2—N1	126.38 (13)	C422—C423—C424	121.53 (14)
N21—C2—N1	117.52 (13)	C422—C423—H423	119.2
C4—N3—C2	115.31 (12)	C424—C423—H423	119.2
N3—C4—C5	124.40 (13)	C423—C424—C425	117.97 (14)
N3—C4—N41	114.95 (12)	C423—C424—C427	121.38 (14)
C5—C4—N41	120.64 (13)	C425—C424—C427	120.64 (15)
C4—C5—C6	114.69 (13)	C426—C425—C424	121.30 (14)
C4—C5—N51	122.19 (13)	C426—C425—H425	119.4
C6—C5—N51	122.93 (13)	C424—C425—H425	119.4
N1—C6—O61	120.25 (13)	C425—C426—C421	120.22 (14)
N1—C6—C5	123.14 (13)	C425—C426—H426	119.9
O61—C6—C5	116.60 (12)	C421—C426—H426	119.9
C2—N21—H21A	120.3 (12)	C424—C427—H42A	109.5
C2—N21—H21B	115.8 (12)	C424—C427—H42B	109.5
H21A—N21—H21B	116.3 (17)	H42A—C427—H42B	109.5
C42—N41—C47A	106.88 (12)	C424—C427—H42C	109.5
C42—N41—C4	128.18 (12)	H42A—C427—H42C	109.5
C47A—N41—C4	124.84 (12)	H42B—C427—H42C	109.5
N43—C42—N41	112.21 (13)	C51—N51—C5	122.48 (13)
N43—C42—C421	124.14 (13)	C51—N51—H51	119.1 (11)
N41—C42—C421	123.51 (13)	C5—N51—H51	118.2 (11)
C42—N43—C43A	105.77 (12)	O51—C51—N51	127.84 (14)
N43—C43A—C44	129.97 (14)	O51—C51—C52	119.95 (13)
N43—C43A—C47A	110.05 (13)	N51—C51—C52	112.18 (13)
C44—C43A—C47A	119.96 (14)	F53—C52—F52	108.28 (14)
C45—C44—C43A	117.66 (14)	F53—C52—F51	107.84 (13)
C45—C44—H44	121.2	F52—C52—F51	107.02 (13)
C43A—C44—H44	121.2	F53—C52—C51	110.98 (13)
C44—C45—C46	121.54 (14)	F52—C52—C51	110.43 (12)
C44—C45—H45	119.2	F51—C52—C51	112.12 (12)
C46—C45—H45	119.2	C6—O61—C61	116.67 (11)
C47—C46—C45	121.53 (14)	O61—C61—H61A	109.5
C47—C46—H46	119.2	O61—C61—H61B	109.5
C45—C46—H46	119.2	H61A—C61—H61B	109.5
C46—C47—C47A	116.23 (14)	O61—C61—H61C	109.5
C46—C47—H47	121.9	H61A—C61—H61C	109.5
C47A—C47—H47	121.9	H61B—C61—H61C	109.5
C47—C47A—N41	131.85 (13)	C71—O71—H71	111.5 (14)
C47—C47A—C43A	123.06 (14)	O71—C71—H71A	109.5
N41—C47A—C43A	105.09 (12)	O71—C71—H71B	109.5
C426—C421—C422	119.08 (14)	H71A—C71—H71B	109.5
C426—C421—C42	120.89 (13)	O71—C71—H71C	109.5
C422—C421—C42	119.97 (13)	H71A—C71—H71C	109.5
C423—C422—C421	119.89 (14)	H71B—C71—H71C	109.5

C6—N1—C2—N3	0.4 (2)	C42—N41—C47A—C47	−179.74 (15)
C6—N1—C2—N21	179.81 (13)	C4—N41—C47A—C47	3.6 (2)
N21—C2—N3—C4	178.43 (13)	C42—N41—C47A—C43A	0.87 (15)
N1—C2—N3—C4	−2.2 (2)	C4—N41—C47A—C43A	−175.77 (13)
C2—N3—C4—C5	2.1 (2)	N43—C43A—C47A—C47	179.92 (13)
C2—N3—C4—N41	−178.95 (12)	C44—C43A—C47A—C47	1.5 (2)
N3—C4—C5—C6	−0.4 (2)	N43—C43A—C47A—N41	−0.62 (16)
N41—C4—C5—C6	−179.30 (12)	C44—C43A—C47A—N41	−179.02 (13)
N3—C4—C5—N51	174.74 (13)	N43—C42—C421—C426	135.26 (16)
N41—C4—C5—N51	−4.2 (2)	N41—C42—C421—C426	−40.1 (2)
C2—N1—C6—O61	−178.40 (12)	N43—C42—C421—C422	−41.9 (2)
C2—N1—C6—C5	1.5 (2)	N41—C42—C421—C422	142.77 (15)
C4—C5—C6—N1	−1.6 (2)	C426—C421—C422—C423	1.2 (2)
N51—C5—C6—N1	−176.65 (13)	C42—C421—C422—C423	178.42 (13)
C4—C5—C6—O61	178.39 (12)	C421—C422—C423—C424	−1.6 (2)
N51—C5—C6—O61	3.3 (2)	C422—C423—C424—C425	0.5 (2)
N3—C4—N41—C42	124.55 (15)	C422—C423—C424—C427	−179.30 (14)
C5—C4—N41—C42	−56.5 (2)	C423—C424—C425—C426	0.9 (2)
N3—C4—N41—C47A	−59.54 (18)	C427—C424—C425—C426	−179.31 (14)
C5—C4—N41—C47A	119.46 (16)	C424—C425—C426—C421	−1.2 (2)
C47A—N41—C42—N43	−0.87 (17)	C422—C421—C426—C425	0.1 (2)
C4—N41—C42—N43	175.62 (13)	C42—C421—C426—C425	−177.03 (13)
C47A—N41—C42—C421	174.97 (13)	C4—C5—N51—C51	121.97 (16)
C4—N41—C42—C421	−8.5 (2)	C6—C5—N51—C51	−63.29 (19)
N41—C42—N43—C43A	0.47 (16)	C5—N51—C51—O51	−0.1 (2)
C421—C42—N43—C43A	−175.34 (13)	C5—N51—C51—C52	177.62 (12)
C42—N43—C43A—C44	178.29 (16)	O51—C51—C52—F53	−12.2 (2)
C42—N43—C43A—C47A	0.11 (16)	N51—C51—C52—F53	169.85 (14)
N43—C43A—C44—C45	−178.64 (15)	O51—C51—C52—F52	107.89 (16)
C47A—C43A—C44—C45	−0.6 (2)	N51—C51—C52—F52	−70.06 (16)
C43A—C44—C45—C46	−0.3 (2)	O51—C51—C52—F51	−132.87 (14)
C44—C45—C46—C47	0.4 (2)	N51—C51—C52—F51	49.18 (17)
C45—C46—C47—C47A	0.4 (2)	N1—C6—O61—C61	−0.51 (19)
C46—C47—C47A—N41	179.32 (15)	C5—C6—O61—C61	179.54 (12)
C46—C47—C47A—C43A	−1.4 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N21—H21A···O51ⁱ	0.896 (19)	2.255 (18)	2.8952 (17)	128.1 (15)
N51—H51···O71	0.925 (19)	1.788 (18)	2.6944 (18)	166.1 (17)
O71—H71···N43ⁱⁱ	0.86 (2)	1.92 (2)	2.7640 (17)	169 (2)

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1/2, y+1/2, −z+3/2.

Selected torsion and dihedral angles (°) top

Parameter	φ₁	φ₂	φ₃	φ₄	φ₅
(I)	131.28 (16)	-60.8 (2)	-172.72 (14)	144.62 (16)	29.79 (9)
(III)	120.12 (16)	-42.8 (2)	-170.69 (14)	148.27 (15)	29.71 (8)
(IV)	125.40 (15)	-99.47 (15)	99.45 (14)	56.08 (17)	26.79 (8)
(V)	62.21 (15)				34.54 (7)
(VI)	87.21 (17)				40.12 (7)
(VIIa)	124.55 (15)				41.58 (8)
(VIIb)	119.8 (3)				31.96 (8)

φ₁–φ₄ represent the torsion angles N3—C4—N41—C42, C4—C5—N51—C57, C5—N51—C57—C51 and N51—C57—C51—C53, respectively, and φ₅ represents the dihedral angle between the planes of the imidazole ring and C421–C426 aryl ring.

Parameters (Å, °) for hydrogen bonds and short intermolecular contacts top

Compound	D—H···A	D—H	H···A	D···A	D—H···A
(I)	N21—H21A···N43ⁱ	0.88 (2)	2.13 (2)	2.985 (2)	162.6 (19)
	N21—H21B···N3ⁱⁱ	0.90 (2)	2.18 (2)	3.079 (2)	177.4 (16)
	C424—H424···Cg1ⁱⁱⁱ	0.95	2.67	3.336 (2)	128
(III)	N21–H21A···N43^iv	0.88 (2)	2.119 (19)	2.9777 (19)	165.2 (19)
	N21—H21B···N3ⁱⁱ	0.88 (2)	2.25 (2)	3.1276 (19)	179 (2)
	C425—H425···O541^v	0.95	2.42	3.335 (2)	167
	C423—H423···Cg2^vi	0.95	2.73	3.6060 (17)	154
(IV)	N21—H21A···N43^vii	0.88 (2)	2.14 (2)	2.9774 (18)	160.7 (16)
	N21—H21B···O61^viii	0.90 (2)	2.37 (2)	3.0595 (16)	133.1 (16)
	N51—H51···O441^ix	0.879 (17)	2.166 (18)	3.0241 (18)	165.0 (16)
	C53—H53···N1^x	0.95	2.50	3.396 (2)	157
	C422—H422···O541^vii	0.95	2.48	3.236 (2)	136
(V)	O1—H1A···N43	0.873 (19)	1.970 (19)	2.8421 (15)	178.1 (17)
	O1—H1B···N51ⁱⁱ	0.880 (19)	2.08 (2)	2.9243 (16)	161.7 (16)
	N21—H21A···O1^ix	0.920 (17)	2.076 (17)	2.9881 (16)	170.7 (14)
	N21—H21B···O1^xi	0.884 (16)	2.061 (16)	2.8729 (14)	152.4 (16)
(VI)	N21—H21···N43ⁱⁱ	0.88	2.21	3.0121 (18)	151
	N31—H31···N43ⁱⁱ	0.88	2.26	3.0121 (18)	143
	N51—H51A···O71	0.85 (3)	2.10 (3)	2.942 (2)	168 (2)
	N51—H51B···O21^v	0.90 (3)	2.07 (3)	2.945 (3)	166 (2)
	N51—H51B···O31^v	0.90 (3)	1.95 (3)	2.757 (3)	148 (2)
	C47—H47···O72^xii	0.95	2.51	3.397 (2)	155
	C422—H422···Cg3ⁱⁱ	0.95	2.90	3.3906 (15)	113
	C423—H423···Cg4ⁱⁱ	0.95	2.68	3.3562 (16)	129
(VIIa)	N21—H21A···O51ⁱⁱ	0.896 (19)	2.255 (18)	2.8952 (17)	128.1 (15)
	N51—H51···O71	0.925 (19)	1.788 (18)	2.6944 (18)	166.1 (17)
	O71—H71···N43^xiii	0.86 (2)	1.92 (2)	2.7640 (17)	169 (2)
(VIIb)	N21—H21A···N43^iv	0.86 (5)	2.07 (5)	2.903 (4)	166 (3)
	N21—H21B···N3^xiv	0.93 (4)	2.16 (4)	3.073 (4)	170 (3)
	N51—H251···O71	0.88	1.91	2.760 (4)	163

Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y+1, -z+1; (iii) x+1/2, -y+1/2, z+1/2; (iv) x, y+1, z; (v) x, -y-1/2, z-1/2; (vi) x, -y+1/2, z-1/2; (vii) x+1/2, -y+3/2, z+1/2; (viii) x+1, y, z; (ix) -x, -y+1, -z+1; (x) x-1/2, -y+3/2, z-1/2; (xi) x, y, z+1; (xii) x, -y+1/2, z+1/2; (xiii) -x+1/2, y+1/2, -z+3/2; (xiv) -x+1, -y+2, -z+1.

Cg1–Cg4 epresent the centroids of the N1/C2/N3,C4–C6, C51–C56, N41/C42/N43/C43A/C47A and C43A/C44–C47/C47A rings, respectively.

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A concise and efficient synthesis of amino-substituted (1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the mol­ecular and supra­molecular structures of six examples

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A concise and efficient synthesis of amino-substituted (1H-benzo[d]imidazol-1-yl)pyrimidine hybrids: synthetic sequence and the molecular and supramolecular structures of six examples