Literature DB >> 22199686

N-(2-Fluoro-phen-yl)-5-[(4-meth-oxy-phen-yl)amino-meth-yl]-6-methyl-2-phenyl-pyrimidin-4-amine.

Jerzy Cieplik, Janusz Pluta, Iwona Bryndal, Tadeusz Lis.

Abstract

The conformation of the title mol-ecule, C(25)H(23)FN(4)O, is mainly determined by an intra-molecular N-H⋯N hydrogen bond closing a six-membered ring and the dihedral angles between the pyrimidine ring and the three benzene rings which are 12.8 (2), 12.0 (2) and 86.1 (2)°. An intra-molecular N-H⋯F inter-action also occurs. The crystal stucture is stabilized by weak C-H⋯O and C-H⋯π inter-actions. An inter-molecular N-H⋯N inter-action is also observed.

Entities: Chemical Disease Gene Species

Year: 2011 PMID： 22199686 PMCID： PMC3238833 DOI： 10.1107/S1600536811045028

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For antibacterial activity of 6-methyl-2-phenyl-5-substituted pyrimidine derivatives, see: Cieplik et al. (1995 ▶, 2003 ▶, 2008 ▶); Pluta et al. (1996 ▶). For related structures, see: Cieplik et al. (2006 ▶).

Experimental

Crystal data

C25H23FN4O M = 414.47 Monoclinic, a = 27.075 (11) Å b = 8.922 (4) Å c = 22.983 (10) Å β = 132.22 (5)° V = 4112 (3) Å3 Z = 8 Mo Kα radiation μ = 0.09 mm−1 T = 85 K 0.53 × 0.17 × 0.14 mm

Data collection

Oxford Diffraction Xcalibur PX κ-geometry diffractometer 28521 measured reflections 10469 independent reflections 7196 reflections with I > 2σ(I) R int = 0.025

Refinement

R[F 2 > 2σ(F 2)] = 0.044 wR(F 2) = 0.121 S = 1.01 10469 reflections 288 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.61 e Å−3 Δρmin = −0.22 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811045028/gk2418sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811045028/gk2418Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811045028/gk2418Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₂₅H₂₃FN₄O	F(000) = 1744
M_r = 414.47	D_x = 1.339 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 14660 reflections
a = 27.075 (11) Å	θ = 4.2–38.5°
b = 8.922 (4) Å	µ = 0.09 mm⁻¹
c = 22.983 (10) Å	T = 85 K
β = 132.22 (5)°	Block, light yellow
V = 4112 (3) Å³	0.53 × 0.17 × 0.14 mm
Z = 8

Oxford Diffraction Xcalibur PX κ-geometry diffractometer	7196 reflections with I > 2σ(I)
Radiation source: normal-focus sealed tube	R_int = 0.025
graphite	θ_max = 38.5°, θ_min = 4.2°
φ and ω scans	h = −46→40
28521 measured reflections	k = −12→15
10469 independent reflections	l = −35→39

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.044	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.121	H atoms treated by a mixture of independent and constrained refinement
S = 1.01	w = 1/[σ²(F_o²) + (0.070P)²] where P = (F_o² + 2F_c²)/3
10469 reflections	(Δ/σ)_max = 0.001
288 parameters	Δρ_max = 0.61 e Å⁻³
0 restraints	Δρ_min = −0.22 e Å⁻³

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are onlyused when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

	x	y	z	U_iso*/U_eq
N1	0.23426 (3)	0.36669 (7)	0.40998 (3)	0.01317 (11)
C2	0.17473 (4)	0.43335 (8)	0.36504 (4)	0.01210 (12)
C21	0.12462 (4)	0.39073 (8)	0.28059 (4)	0.01287 (12)
C22	0.14297 (4)	0.30769 (8)	0.24607 (4)	0.01447 (13)
H22	0.1884	0.2809	0.2763	0.017*
C23	0.09517 (4)	0.26420 (9)	0.16781 (4)	0.01767 (14)
H23	0.1081	0.2075	0.1449	0.021*
C24	0.02852 (4)	0.30321 (9)	0.12281 (5)	0.02034 (16)
H24	−0.0041	0.2721	0.0695	0.024*
C25	0.00996 (4)	0.38787 (10)	0.15623 (5)	0.02228 (16)
H25	−0.0354	0.4157	0.1256	0.027*
C26	0.05782 (4)	0.43180 (10)	0.23455 (4)	0.01855 (14)
H26	0.0449	0.4904	0.2570	0.022*
N3	0.15437 (3)	0.53341 (7)	0.38901 (3)	0.01317 (11)
C4	0.19708 (4)	0.56283 (8)	0.46609 (4)	0.01252 (12)
N4	0.17917 (3)	0.66198 (7)	0.49490 (4)	0.01472 (12)
H4	0.2030 (5)	0.6531 (12)	0.5456 (6)	0.018*
C41	0.11961 (4)	0.74116 (8)	0.45602 (4)	0.01369 (12)
C42	0.11209 (4)	0.81165 (8)	0.50421 (4)	0.01637 (14)
F4	0.16300 (3)	0.79604 (6)	0.58317 (3)	0.02284 (11)
C43	0.05679 (4)	0.89387 (9)	0.47602 (5)	0.02065 (15)
H43	0.0539	0.9390	0.5111	0.025*
C44	0.00524 (4)	0.90943 (10)	0.39507 (5)	0.02180 (16)
H44	−0.0338	0.9642	0.3740	0.026*
C45	0.01153 (4)	0.84392 (10)	0.34542 (5)	0.02132 (16)
H45	−0.0233	0.8563	0.2902	0.026*
C46	0.06771 (4)	0.76038 (9)	0.37476 (4)	0.01719 (14)
H46	0.0708	0.7165	0.3396	0.021*
C5	0.26157 (4)	0.49669 (8)	0.52009 (4)	0.01261 (12)
C57	0.30861 (4)	0.53792 (9)	0.60615 (4)	0.01576 (13)
H571	0.3492	0.4750	0.6358	0.019*
H572	0.3223	0.6440	0.6127	0.019*
N5	0.27693 (3)	0.51636 (7)	0.63795 (4)	0.01484 (12)
H5	0.2652 (5)	0.4199 (13)	0.6350 (6)	0.018*
C51	0.30334 (4)	0.58811 (8)	0.70885 (4)	0.01285 (12)
C52	0.33894 (4)	0.72198 (8)	0.73410 (4)	0.01505 (13)
H52	0.3495	0.7634	0.7055	0.018*
C53	0.35944 (4)	0.79668 (8)	0.80092 (4)	0.01564 (13)
H53	0.3834	0.8882	0.8171	0.019*
C54	0.34466 (4)	0.73683 (8)	0.84340 (4)	0.01471 (13)
O5	0.36179 (3)	0.80239 (6)	0.90928 (3)	0.02145 (13)
C58	0.39084 (5)	0.94760 (9)	0.92941 (5)	0.02204 (16)
H581	0.4332	0.9422	0.9417	0.033*
H582	0.3990	0.9848	0.9753	0.033*
H583	0.3604	1.0159	0.8850	0.033*
C55	0.30912 (4)	0.60230 (8)	0.81897 (4)	0.01540 (13)
H55	0.2988	0.5610	0.8478	0.018*
C56	0.28893 (4)	0.52895 (8)	0.75279 (4)	0.01431 (13)
H56	0.2650	0.4374	0.7369	0.017*
C6	0.27830 (4)	0.40137 (8)	0.48783 (4)	0.01261 (12)
C61	0.34603 (4)	0.33005 (9)	0.53604 (4)	0.01562 (13)
H611	0.3474	0.2675	0.5021	0.023*
H612	0.3547	0.2678	0.5772	0.023*
H613	0.3801	0.4084	0.5602	0.023*

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0143 (3)	0.0145 (3)	0.0130 (2)	0.0007 (2)	0.0101 (2)	0.00032 (19)
C2	0.0143 (3)	0.0121 (3)	0.0127 (3)	0.0001 (2)	0.0103 (2)	0.0006 (2)
C21	0.0147 (3)	0.0129 (3)	0.0128 (3)	−0.0003 (2)	0.0100 (2)	0.0001 (2)
C22	0.0167 (3)	0.0139 (3)	0.0142 (3)	0.0011 (2)	0.0110 (3)	−0.0002 (2)
C23	0.0225 (4)	0.0154 (3)	0.0152 (3)	0.0009 (3)	0.0127 (3)	−0.0015 (2)
C24	0.0219 (4)	0.0185 (3)	0.0149 (3)	−0.0009 (3)	0.0101 (3)	−0.0025 (3)
C25	0.0154 (3)	0.0271 (4)	0.0175 (3)	0.0011 (3)	0.0082 (3)	−0.0034 (3)
C26	0.0158 (3)	0.0227 (4)	0.0172 (3)	0.0004 (3)	0.0111 (3)	−0.0031 (3)
N3	0.0159 (3)	0.0133 (3)	0.0130 (2)	0.0015 (2)	0.0108 (2)	0.00088 (19)
C4	0.0158 (3)	0.0115 (3)	0.0136 (3)	0.0006 (2)	0.0112 (2)	0.0008 (2)
N4	0.0171 (3)	0.0160 (3)	0.0125 (2)	0.0041 (2)	0.0105 (2)	0.0012 (2)
C41	0.0165 (3)	0.0115 (3)	0.0168 (3)	0.0010 (2)	0.0127 (3)	0.0006 (2)
C42	0.0215 (3)	0.0143 (3)	0.0186 (3)	0.0011 (3)	0.0156 (3)	0.0005 (2)
F4	0.0304 (3)	0.0232 (3)	0.0176 (2)	0.0073 (2)	0.0172 (2)	0.00160 (18)
C43	0.0261 (4)	0.0173 (3)	0.0278 (4)	0.0026 (3)	0.0219 (3)	−0.0006 (3)
C44	0.0181 (3)	0.0187 (4)	0.0292 (4)	0.0020 (3)	0.0162 (3)	−0.0018 (3)
C45	0.0167 (3)	0.0206 (4)	0.0214 (3)	0.0021 (3)	0.0106 (3)	−0.0014 (3)
C46	0.0166 (3)	0.0177 (3)	0.0170 (3)	0.0017 (3)	0.0112 (3)	−0.0008 (2)
C5	0.0141 (3)	0.0130 (3)	0.0123 (3)	−0.0001 (2)	0.0094 (2)	0.0003 (2)
C57	0.0149 (3)	0.0204 (3)	0.0134 (3)	−0.0007 (3)	0.0100 (3)	−0.0023 (2)
N5	0.0194 (3)	0.0149 (3)	0.0129 (2)	−0.0030 (2)	0.0120 (2)	−0.0010 (2)
C51	0.0133 (3)	0.0143 (3)	0.0114 (3)	0.0012 (2)	0.0085 (2)	0.0012 (2)
C52	0.0196 (3)	0.0153 (3)	0.0144 (3)	−0.0015 (3)	0.0131 (3)	0.0006 (2)
C53	0.0201 (3)	0.0143 (3)	0.0156 (3)	−0.0019 (3)	0.0132 (3)	−0.0004 (2)
C54	0.0194 (3)	0.0143 (3)	0.0143 (3)	0.0017 (2)	0.0129 (3)	0.0012 (2)
O5	0.0370 (3)	0.0165 (3)	0.0200 (3)	−0.0041 (2)	0.0229 (3)	−0.0029 (2)
C58	0.0306 (4)	0.0176 (4)	0.0187 (3)	−0.0027 (3)	0.0169 (3)	−0.0031 (3)
C55	0.0204 (3)	0.0145 (3)	0.0173 (3)	0.0018 (3)	0.0151 (3)	0.0025 (2)
C56	0.0165 (3)	0.0138 (3)	0.0163 (3)	−0.0007 (2)	0.0125 (3)	0.0009 (2)
C6	0.0142 (3)	0.0128 (3)	0.0134 (3)	0.0001 (2)	0.0103 (2)	0.0010 (2)
C61	0.0153 (3)	0.0176 (3)	0.0154 (3)	0.0025 (3)	0.0109 (3)	0.0014 (2)

N1—C2	1.3345 (13)	C45—H45	0.9500
N1—C6	1.3607 (15)	C46—H46	0.9500
C2—N3	1.3461 (10)	C5—C6	1.3890 (11)
C2—C21	1.4878 (16)	C5—C57	1.5112 (16)
C21—C26	1.3974 (15)	C57—N5	1.4661 (11)
C21—C22	1.3984 (11)	C57—H571	0.9900
C22—C23	1.3899 (16)	C57—H572	0.9900
C22—H22	0.9500	N5—C51	1.4178 (12)
C23—C24	1.3925 (16)	N5—H5	0.904 (11)
C23—H23	0.9500	C51—C52	1.3931 (12)
C24—C25	1.3900 (13)	C51—C56	1.4073 (11)
C24—H24	0.9500	C52—C53	1.4019 (12)
C25—C26	1.3921 (16)	C52—H52	0.9500
C25—H25	0.9500	C53—C54	1.3868 (11)
C26—H26	0.9500	C53—H53	0.9500
N3—C4	1.3384 (14)	C54—O5	1.3807 (11)
C4—N4	1.3739 (10)	C54—C55	1.3985 (12)
C4—C5	1.4230 (15)	O5—C58	1.4220 (12)
N4—C41	1.4004 (13)	C58—H581	0.9800
N4—H4	0.879 (11)	C58—H582	0.9800
C41—C46	1.4018 (17)	C58—H583	0.9800
C41—C42	1.4024 (11)	C55—C56	1.3867 (12)
C42—F4	1.3605 (16)	C55—H55	0.9500
C42—C43	1.3770 (13)	C56—H56	0.9500
C43—C44	1.3924 (18)	C6—C61	1.5050 (15)
C43—H43	0.9500	C61—H611	0.9800
C44—C45	1.3905 (13)	C61—H612	0.9800
C44—H44	0.9500	C61—H613	0.9800
C45—C46	1.3948 (13)

C2—N1—C6	116.86 (8)	C6—C5—C4	115.94 (8)
N1—C2—N3	126.33 (7)	C6—C5—C57	123.87 (7)
N1—C2—C21	117.65 (8)	C4—C5—C57	120.10 (8)
N3—C2—C21	115.98 (7)	N5—C57—C5	111.08 (8)
C26—C21—C22	118.80 (8)	N5—C57—H571	109.4
C26—C21—C2	120.16 (9)	C5—C57—H571	109.4
C22—C21—C2	121.03 (8)	N5—C57—H572	109.4
C23—C22—C21	120.35 (8)	C5—C57—H572	109.4
C23—C22—H22	119.8	H571—C57—H572	108.0
C21—C22—H22	119.8	C51—N5—C57	120.10 (7)
C22—C23—C24	120.43 (9)	C51—N5—H5	113.4 (6)
C22—C23—H23	119.8	C57—N5—H5	112.4 (7)
C24—C23—H23	119.8	C52—C51—C56	118.06 (7)
C25—C24—C23	119.65 (8)	C52—C51—N5	122.64 (7)
C25—C24—H24	120.2	C56—C51—N5	119.11 (7)
C23—C24—H24	120.2	C51—C52—C53	121.18 (7)
C24—C25—C26	119.96 (8)	C51—C52—H52	119.4
C24—C25—H25	120.0	C53—C52—H52	119.4
C26—C25—H25	120.0	C54—C53—C52	119.94 (8)
C25—C26—C21	120.79 (9)	C54—C53—H53	120.0
C25—C26—H26	119.6	C52—C53—H53	120.0
C21—C26—H26	119.6	O5—C54—C53	124.45 (7)
C4—N3—C2	116.40 (7)	O5—C54—C55	115.93 (7)
N3—C4—N4	119.57 (7)	C53—C54—C55	119.61 (7)
N3—C4—C5	122.37 (8)	C54—O5—C58	116.58 (6)
N4—C4—C5	118.05 (7)	O5—C58—H581	109.5
C4—N4—C41	130.19 (7)	O5—C58—H582	109.5
C4—N4—H4	113.6 (7)	H581—C58—H582	109.5
C41—N4—H4	113.3 (7)	O5—C58—H583	109.5
N4—C41—C46	127.26 (8)	H581—C58—H583	109.5
N4—C41—C42	116.00 (8)	H582—C58—H583	109.5
C46—C41—C42	116.73 (8)	C56—C55—C54	120.20 (7)
F4—C42—C43	119.27 (8)	C56—C55—H55	119.9
F4—C42—C41	116.93 (8)	C54—C55—H55	119.9
C43—C42—C41	123.80 (9)	C55—C56—C51	121.01 (8)
C42—C43—C44	118.59 (9)	C55—C56—H56	119.5
C42—C43—H43	120.7	C51—C56—H56	119.5
C44—C43—H43	120.7	N1—C6—C5	121.95 (7)
C45—C44—C43	119.27 (8)	N1—C6—C61	115.44 (8)
C45—C44—H44	120.4	C5—C6—C61	122.62 (8)
C43—C44—H44	120.4	C6—C61—H611	109.5
C44—C45—C46	121.54 (9)	C6—C61—H612	109.5
C44—C45—H45	119.2	H611—C61—H612	109.5
C46—C45—H45	119.2	C6—C61—H613	109.5
C45—C46—C41	120.04 (8)	H611—C61—H613	109.5
C45—C46—H46	120.0	H612—C61—H613	109.5
C41—C46—H46	120.0

C6—N1—C2—N3	1.13 (11)	C44—C45—C46—C41	−0.17 (13)
C6—N1—C2—C21	−176.79 (6)	N4—C41—C46—C45	−179.60 (8)
N1—C2—C21—C26	166.64 (7)	C42—C41—C46—C45	−1.20 (11)
N3—C2—C21—C26	−11.50 (10)	N3—C4—C5—C6	1.19 (10)
N1—C2—C21—C22	−12.51 (10)	N4—C4—C5—C6	−177.79 (6)
N3—C2—C21—C22	169.35 (7)	N3—C4—C5—C57	177.97 (7)
C26—C21—C22—C23	−1.44 (11)	N4—C4—C5—C57	−1.00 (10)
C2—C21—C22—C23	177.72 (7)	C6—C5—C57—N5	−129.73 (8)
C21—C22—C23—C24	0.23 (12)	C4—C5—C57—N5	53.76 (10)
C22—C23—C24—C25	0.84 (12)	C5—C57—N5—C51	−161.21 (6)
C23—C24—C25—C26	−0.68 (13)	C57—N5—C51—C52	27.18 (11)
C24—C25—C26—C21	−0.55 (13)	C57—N5—C51—C56	−157.88 (7)
C22—C21—C26—C25	1.60 (12)	C56—C51—C52—C53	−0.53 (11)
C2—C21—C26—C25	−177.57 (7)	N5—C51—C52—C53	174.46 (7)
N1—C2—N3—C4	−3.45 (11)	C51—C52—C53—C54	0.40 (12)
C21—C2—N3—C4	174.50 (6)	C52—C53—C54—O5	−179.13 (7)
C2—N3—C4—N4	−178.93 (6)	C52—C53—C54—C55	−0.22 (12)
C2—N3—C4—C5	2.12 (10)	C53—C54—O5—C58	6.20 (11)
N3—C4—N4—C41	1.78 (12)	C55—C54—O5—C58	−172.75 (7)
C5—C4—N4—C41	−179.22 (7)	O5—C54—C55—C56	179.18 (7)
C4—N4—C41—C46	−13.42 (13)	C53—C54—C55—C56	0.17 (12)
C4—N4—C41—C42	168.17 (7)	C54—C55—C56—C51	−0.31 (11)
N4—C41—C42—F4	−0.01 (10)	C52—C51—C56—C55	0.48 (11)
C46—C41—C42—F4	−178.59 (7)	N5—C51—C56—C55	−174.69 (7)
N4—C41—C42—C43	−179.89 (8)	C2—N1—C6—C5	2.61 (10)
C46—C41—C42—C43	1.53 (12)	C2—N1—C6—C61	−177.14 (6)
F4—C42—C43—C44	179.69 (7)	C4—C5—C6—N1	−3.64 (10)
C41—C42—C43—C44	−0.43 (13)	C57—C5—C6—N1	179.71 (7)
C42—C43—C44—C45	−1.00 (13)	C4—C5—C6—C61	176.09 (7)
C43—C44—C45—C46	1.31 (13)	C57—C5—C6—C61	−0.56 (11)

Cg1, Cg2 and Cg3 are the centroids of the N1–C6, C41–C46 and C21–C26 rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···N5	0.88 (1)	2.07 (1)	2.794 (2)	139 (1)
N4—H4···F4	0.88 (1)	2.19 (1)	2.633 (1)	111 (1)
C61—H611···O5ⁱ	0.98	2.49	3.426 (2)	159
C61—H612···Cg1ⁱⁱ	0.98	2.69	3.381 (3)	128
C61—H613···Cg2ⁱⁱⁱ	0.98	2.73	3.657 (3)	159
C53—H53···Cg3ⁱⁱ	0.95	2.74	3.634 (3)	156
N5—H5···N1ⁱⁱⁱ	0.90 (1)	2.76 (1)	3.541 (2)	145 (1)

Table 1

Hydrogen-bond geometry (Å, °)

Cg1, Cg2 and Cg3 are the centroids of the N1–C6, C41–C46 and C21–C26 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4⋯N5	0.88 (1)	2.07 (1)	2.794 (2)	139 (1)
N4—H4⋯F4	0.88 (1)	2.19 (1)	2.633 (1)	111 (1)
C61—H611⋯O5ⁱ	0.98	2.49	3.426 (2)	159
C61—H612⋯Cg1ⁱⁱ	0.98	2.69	3.381 (3)	128
C61—H613⋯Cg2ⁱⁱⁱ	0.98	2.73	3.657 (3)	159
C53—H53⋯Cg3ⁱⁱ	0.95	2.74	3.634 (3)	156
N5—H5⋯N1ⁱⁱⁱ	0.90 (1)	2.76 (1)	3.541 (2)	145 (1)

Symmetry codes: (i) ; (ii) ; (iii) .

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