Crystal structure of 5,5′-[(4-fluoro­phen­yl)methyl­ene]bis­[6-amino-1,3-di­methyl­pyrimidine-2,4(1H,3H)-dione]

Sharma, N.; Brahmachari, G.; Banerjee, B.; Kant, R.; Gupta, V.K.

doi:10.1107/S1600536814019886

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 70| Part 10| October 2014| Pages o1098-o1099

doi:10.1107/S1600536814019886

Open

access

Crystal structure of 5,5′-[(4-fluorophenyl)methylene]bis[6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione]

Naresh Sharma,^a Goutam Brahmachari,^b Bubun Banerjee,^b Rajni Kant ^a and Vivek K. Gupta ^a ^*

^aPost-Graduate Department of Physics & Electronics, University of Jammu, Jammu Tawi 180 006, India, and ^bLaboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati University, Santiniketan 731 235, West Bengal, India
^*Correspondence e-mail: vivek_gupta2k2@hotmail.com

Edited by A. J. Lough, University of Toronto, Canada (Received 20 August 2014; accepted 3 September 2014; online 10 September 2014)

In the title molecule, C₁₉H₂₁FN₆O₄, the dihedral angles between the benzene ring and essentially planar pyrimidine rings [maximum deviations of 0.036 (2) and 0.056 (2) Å] are 73.32 (7) and 63.81 (8)°. The dihedral angle between the mean planes of the pyrimidine rings is 61.43 (6)°. In the crystal, N—H⋯O hydrogen bonds link molecules, forming a two-dimensional network parallel to (001) and in combination with weak C—H⋯O hydrogen bonds, a three-dimensional network is formed. Weak C—H⋯π interactions and π–π interactions, with a centroid–centroid distance of 3.599 (2) Å are also observed.

Keywords: crystal structure; uracil derivatives; biological activity; pyrimidine scaffolds; bis-uracil derivatives.

CCDC reference: 973485

1. Related literature

For the biological activity of uracil derivatives, see: Muller et al. (1993 ); Buckle et al. (1994 ). For drugs containing purine moieties, see: Zhi et al. (2003 ); Devi & Bhuyan (2005 ). For the biological activity of pyrimidine scaffolds, see: Makarov et al. (2005 ); Deshmukh et al. (2009 ); Ibrahim & El-Metwally (2010 ). For the synthesis of bis-uracil derivatives, see: Karimi et al. (2013 ). For a related structure, see: Das et al. (2009 ).

2. Experimental

2.1. Crystal data

C₁₉H₂₁FN₆O₄
M_r = 416.42
Orthorhombic, P b c a
a = 14.6208 (6) Å
b = 11.3324 (7) Å
c = 22.6410 (12) Å
V = 3751.4 (3) Å³
Z = 8
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 293 K
0.30 × 0.20 × 0.20 mm

2.2. Data collection

Oxford Diffraction Xcalibur Sapphire3 diffractometer
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ) T_min = 0.862, T_max = 1.000
9655 measured reflections
3665 independent reflections
2208 reflections with I > 2σ(I)
R_int = 0.047

2.3. Refinement

R[F² > 2σ(F²)] = 0.052
wR(F²) = 0.130
S = 1.04
3665 reflections
291 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C7–C12 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N15—H40⋯O3A′	0.96 (3)	1.96 (3)	2.916 (3)	174 (2)
N18—H50⋯O3A	0.93 (3)	1.88 (3)	2.803 (3)	170 (2)
N15—H30⋯O3Aⁱ	0.86 (3)	2.26 (3)	3.083 (3)	161 (3)
N18—H60⋯O3A′ⁱⁱ	0.91 (3)	2.14 (3)	3.007 (3)	159 (2)
C13—H13A⋯O3Aⁱ	0.96	2.41	3.154 (3)	134
C13—H13A⋯Cgⁱⁱⁱ	0.96	2.98	3.744 (3)	138
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]$ ; (iii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ .

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ); software used to prepare material for publication: PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 973485

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536814019886/lh5725sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814019886/lh5725Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814019886/lh5725Isup3.cml

checkCIF report

Structural commentary top

Uracil derivatives represent a "privileged" structural motif in a wide variety of natural and synthetic compounds with a broad spectrum of significant biological activities (Muller et al., 1993). 6-Aminouracils are the important starting compounds for the synthesis of medicinally useful xanthines and theophyllines, which are now routinely used as a phosphodiesterase inhibitor for the treatment of asthma (Buckle et al., 1994). 6-Aminouracils are regarded as the key intermediates for the synthesis of purine-based drugs, such as penciclovir, caffeine, theophylline, and theobromine (Zhi et al., (2003); Devi & Bhuyan, 2005). In addition, pyrimidine scaffolds are reported to exhibit diverse biological and pharmaceutical activities (Ibrahim & El-Metwally, 2010; Deshmukh et al., 2009), Makarov et al., 2005). Herein, we report the synthesis and crystal structure of a new arylmethylene-bis uracil derivative, namely 5,5'-((4-fluorophenyl)methylene) bis(6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione) synthesized via one-pot pseudo multicomponent reaction at room temperature using iodine as inexpensive and eco-friendly catalyst.

The molecular structure of the title compound is shown in Fig. 1. The distances are in the normal ranges and correspond to those observed in a related structure (Das et al., 2009). The pyrimidine rings are essentially planar with maximum deviations of 0.036 (2) and 0.056 (2) Å for C6 and N1', respectively. The dihedral angle between the mean plane of benzene ring [C7—C12] and pyrimidine rings-A and B are 73.32 (7) ° and 63.81 (8) ° respectively. The dihedral angle between the two pyrimidine rings is 61.43 (6) °. The planarity of the phenyl group confirms its aromatic character. From the least-squares plane calculations of the phenyl moiety, the maximum deviation observed is 0.014 (2) Å for atom C8. The double bond distances C2—O2 = 1.220 (4) Å, C3—O3A = 1.257 (3) Å (ring-A) and C2'- O2' = 1.217 (4) Å, C3A'- O3A' = 1.261 (4) Å (ring-B), are significantly larger than the standard value for carbonyl group (1.192 Å) and lengthening of the C═O double bond is due their involvment in N—H···O and C—H···O hydrogen bonds. In the crystal, N—H···O hydrogen bonds link molecules forming a two-dimensional network parallel to (001) (Fig. 2) and in combination with weak C—H···O hydrogen bonds a three-dimensional network is formed. Weak C—H···π interactions and π–π interactions with a centroid–centroid distance of 3.599 (2) Å between pyrimidine ring-B and benzene ring-C at (1/2 - x, -1/2 + y, z) are also observed.

Synthesis and crystallization top

An oven-dried screw cap test tube was charged with a magnetic stir bar, 6-amino-1,3-dimethyluracil (0.155 g, 1.0 mmol), 4-fluorobenzaldehyde (0.062 g, 0.5 mmol), iodine (0.025 g, 10 mol % as catalyst), and EtOH:H₂O (1:1 v/v; 4 ml) in a sequential manner. The reaction mixture was then stirred vigorously at room temperature and the stirring was continued for 4 h; the progress of the reaction was monitored by TLC. On completion of the reaction, a solid mass precipitated out, which was filtered, and washed with aqueous ethanol to obtain the crude product that was purified just by recrystallization from ethanol without carrying out column chromatography (72% yield). The title compound forms as a White solid. Yield 72%. Mp: 537–539 K. IR (KBr) ν_max cm^-1: 3430, 3104, 2956, 1690, 1603, 1498, 1247, 1216, 1142, 1070, 870, 789, 756. ¹H NMR (400 MHz, DMSO-d₆) δ/p.p.m.: 7.42 (4H, s, –NH₂), 7.11 (2H, dd, J = 8.4 & 5.6 Hz, aromatic H), 6.99 (2H, t, J = 8.8 Hz, aromatic H), 5.56 (1H, s, –CH–), 3.32 (6H, s, 2 × NCH₃), 3.14 (6H, s, 2 × NCH₃). TOF-MS: 439.1513 [M+Na]⁺. The structure of 5,5'-((4-fluorophenyl)methylene)bis(6-amino-1, 3-dimethylpyrimidine-2,4(1H,3H)-dione) was characterized by means of spectral studies including FT—IR, ¹H NMR, and TOF-MS. Crystals suitable for X-ray diffraction were grown by dissolving 50 mg of the title compound in 5 ml DMSO and after several days at ambient temperature colourless block-shaped crystals were formed.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. Atoms H30, H40 attached to N15 and H50, H60 attached to N18 were located in a difference Fourier map and refined isotropically. All the remaining H atoms were geometrically fixed and allowed to ride on their parent C atoms, with C—H distances of 0.93–0.98 Å; and with U_iso(H) = 1.2U_eq(C), except for the methyl group where U_iso(H) = 1.5U_eq(C).

Related literature top

For the biological activity of uracil derivatives, see: Muller et al. (1993); Buckle et al. (1994). For drugs containing purine moieties, see: Zhi et al. (2003); Devi & Bhuyan (2005). For the biological activity of pyrimidine scaffolds, see: Makarov et al. (2005); Deshmukh et al. (2009); Ibrahim & El-Metwally (2010). For the synthesis of bis-uracil derivatives, see: Karimi et al. (2013). For a related structure, see: Das et al. (2009).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure with displacement ellipsoids drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. Part of the crystal structure viewed along the a axis. Hydrogen bonds are shown as dashed lines.

5,5'-[(4-Fluorophenyl)methylene]bis[6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione] top

Crystal data top

C₁₉H₂₁FN₆O₄	F(000) = 1744
M_r = 416.42	D_x = 1.475 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 2766 reflections
a = 14.6208 (6) Å	θ = 4.0–29.0°
b = 11.3324 (7) Å	µ = 0.11 mm⁻¹
c = 22.6410 (12) Å	T = 293 K
V = 3751.4 (3) Å³	Rectangular, white
Z = 8	0.30 × 0.20 × 0.20 mm

Data collection top

Oxford Diffraction Xcalibur Sapphire3 diffractometer	3665 independent reflections
Radiation source: fine-focus sealed tube	2208 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.047
Detector resolution: 16.1049 pixels mm^-1	θ_max = 26.0°, θ_min = 3.4°
ω scans	h = −17→18
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	k = −13→10
T_min = 0.862, T_max = 1.000	l = −27→27
9655 measured reflections

Refinement top

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ²(F_o²) + (0.0402P)² + 0.280P] where P = (F_o² + 2F_c²)/3
3665 reflections	(Δ/σ)_max < 0.001
291 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₁₉H₂₁FN₆O₄	V = 3751.4 (3) Å³
M_r = 416.42	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 14.6208 (6) Å	µ = 0.11 mm⁻¹
b = 11.3324 (7) Å	T = 293 K
c = 22.6410 (12) Å	0.30 × 0.20 × 0.20 mm

Data collection top

Oxford Diffraction Xcalibur Sapphire3 diffractometer	3665 independent reflections
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	2208 reflections with I > 2σ(I)
T_min = 0.862, T_max = 1.000	R_int = 0.047
9655 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.052	0 restraints
wR(F²) = 0.130	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	Δρ_max = 0.19 e Å⁻³
3665 reflections	Δρ_min = −0.20 e Å⁻³
291 parameters

Special details top

Experimental. CrysAlis PRO, Agilent Technologies, Version 1.171.36.28 (release 01–02-2013 CrysAlis171. NET) (compiled Feb 1 2013,16:14:44) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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 only used 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.

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

	x	y	z	U_iso*/U_eq
O3A	0.12040 (11)	0.70286 (16)	0.47999 (8)	0.0448 (5)
O3A'	0.41972 (12)	0.90382 (17)	0.35851 (8)	0.0481 (5)
N3	0.21150 (13)	0.67789 (19)	0.56011 (9)	0.0385 (5)
N1'	0.27279 (15)	0.63863 (19)	0.28860 (9)	0.0445 (6)
C5'	0.28708 (16)	0.7846 (2)	0.36460 (10)	0.0336 (6)
N1	0.35782 (12)	0.7609 (2)	0.56448 (9)	0.0388 (5)
C5	0.26609 (15)	0.7945 (2)	0.47801 (10)	0.0317 (6)
N18	0.16272 (16)	0.6468 (2)	0.36253 (12)	0.0445 (6)
O2	0.29971 (14)	0.6586 (2)	0.64250 (9)	0.0697 (7)
C4	0.25464 (16)	0.8542 (2)	0.41822 (10)	0.0337 (6)
H4	0.2992	0.9187	0.4203	0.040*
C6	0.34765 (15)	0.8050 (2)	0.50801 (10)	0.0328 (6)
C6'	0.24099 (18)	0.6903 (2)	0.34020 (11)	0.0374 (6)
N15	0.42224 (15)	0.8593 (2)	0.48533 (11)	0.0410 (6)
C7	0.16385 (16)	0.9204 (2)	0.41091 (11)	0.0323 (6)
C3A'	0.37186 (18)	0.8189 (2)	0.34004 (11)	0.0393 (6)
N3'	0.40473 (15)	0.7555 (2)	0.29207 (9)	0.0465 (6)
C3A	0.19584 (17)	0.7257 (2)	0.50409 (11)	0.0366 (6)
F20	−0.06866 (11)	1.12341 (16)	0.39325 (9)	0.0834 (7)
C2	0.28952 (18)	0.6969 (3)	0.59256 (12)	0.0437 (7)
O2'	0.39032 (16)	0.60699 (19)	0.22495 (9)	0.0746 (7)
C2'	0.3585 (2)	0.6640 (3)	0.26558 (12)	0.0503 (8)
C13	0.44207 (17)	0.7825 (3)	0.59804 (11)	0.0499 (8)
H13A	0.4918	0.7404	0.5801	0.075*
H13B	0.4341	0.7558	0.6380	0.075*
H13C	0.4554	0.8655	0.5980	0.075*
C12	0.13307 (17)	0.9921 (2)	0.45682 (12)	0.0441 (7)
H12	0.1651	0.9932	0.4923	0.053*
C8	0.11561 (17)	0.9230 (2)	0.35843 (12)	0.0405 (7)
H8	0.1362	0.8786	0.3265	0.049*
C10	0.00938 (18)	1.0575 (2)	0.39853 (15)	0.0505 (8)
C11	0.05596 (19)	1.0616 (3)	0.45075 (14)	0.0510 (8)
H11	0.0363	1.1098	0.4815	0.061*
C9	0.03704 (18)	0.9907 (2)	0.35245 (14)	0.0502 (8)
H9	0.0040	0.9900	0.3174	0.060*
C14	0.14123 (18)	0.6033 (3)	0.58682 (13)	0.0536 (8)
H14A	0.1677	0.5579	0.6183	0.080*
H14B	0.1167	0.5509	0.5575	0.080*
H14C	0.0931	0.6519	0.6022	0.080*
C17	0.4962 (2)	0.7837 (3)	0.26916 (14)	0.0683 (10)
H17A	0.5409	0.7351	0.2885	0.102*
H17B	0.5096	0.8653	0.2766	0.102*
H17C	0.4979	0.7690	0.2274	0.102*
C16	0.2188 (2)	0.5502 (3)	0.25638 (13)	0.0626 (9)
H16A	0.2378	0.5486	0.2158	0.094*
H16B	0.1551	0.5704	0.2585	0.094*
H16C	0.2283	0.4739	0.2738	0.094*
H60	0.1393 (18)	0.576 (3)	0.3509 (12)	0.057 (9)*
H50	0.1483 (16)	0.675 (2)	0.4000 (13)	0.049 (8)*
H40	0.4206 (17)	0.880 (2)	0.4441 (13)	0.060 (9)*
H30	0.476 (2)	0.856 (3)	0.5011 (13)	0.069 (10)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O3A	0.0359 (10)	0.0609 (13)	0.0376 (10)	−0.0095 (9)	−0.0013 (8)	0.0047 (10)
O3A'	0.0439 (10)	0.0557 (12)	0.0446 (11)	−0.0059 (10)	0.0066 (9)	0.0039 (11)
N3	0.0360 (11)	0.0470 (14)	0.0326 (11)	−0.0023 (10)	0.0028 (10)	0.0068 (12)
N1'	0.0635 (15)	0.0365 (13)	0.0335 (12)	0.0040 (11)	0.0064 (11)	0.0008 (11)
C5'	0.0385 (14)	0.0364 (15)	0.0259 (12)	0.0042 (12)	0.0025 (11)	0.0036 (12)
N1	0.0311 (11)	0.0530 (15)	0.0322 (11)	0.0047 (10)	−0.0026 (9)	0.0040 (12)
C5	0.0263 (12)	0.0375 (15)	0.0313 (12)	0.0021 (11)	0.0015 (11)	0.0023 (12)
N18	0.0511 (15)	0.0398 (15)	0.0424 (14)	−0.0043 (12)	0.0052 (13)	−0.0045 (13)
O2	0.0658 (14)	0.1013 (19)	0.0420 (12)	−0.0168 (13)	−0.0105 (11)	0.0299 (13)
C4	0.0340 (13)	0.0350 (15)	0.0320 (13)	0.0015 (12)	−0.0005 (11)	0.0012 (12)
C6	0.0320 (13)	0.0355 (14)	0.0310 (13)	0.0041 (11)	−0.0008 (11)	−0.0001 (12)
C6'	0.0450 (15)	0.0349 (15)	0.0324 (13)	0.0090 (13)	0.0004 (12)	0.0048 (13)
N15	0.0305 (12)	0.0565 (15)	0.0361 (13)	−0.0035 (11)	−0.0025 (11)	0.0055 (12)
C7	0.0302 (13)	0.0315 (14)	0.0352 (14)	0.0001 (11)	0.0000 (11)	0.0043 (12)
C3A'	0.0466 (16)	0.0409 (16)	0.0306 (13)	0.0059 (13)	0.0038 (13)	0.0092 (14)
N3'	0.0534 (14)	0.0510 (15)	0.0349 (12)	0.0043 (12)	0.0139 (11)	0.0073 (12)
C3A	0.0380 (14)	0.0399 (16)	0.0320 (13)	0.0041 (12)	0.0000 (12)	−0.0005 (13)
F20	0.0666 (12)	0.0682 (13)	0.1154 (17)	0.0373 (10)	−0.0044 (11)	0.0026 (13)
C2	0.0443 (16)	0.0500 (18)	0.0366 (15)	0.0012 (14)	0.0019 (13)	0.0050 (15)
O2'	0.1086 (18)	0.0632 (15)	0.0521 (13)	0.0067 (13)	0.0384 (13)	−0.0086 (13)
C2'	0.071 (2)	0.0446 (18)	0.0354 (15)	0.0101 (16)	0.0139 (15)	0.0097 (15)
C13	0.0360 (14)	0.078 (2)	0.0360 (14)	0.0019 (15)	−0.0102 (12)	0.0074 (16)
C12	0.0468 (16)	0.0436 (17)	0.0420 (16)	0.0021 (13)	0.0006 (13)	−0.0035 (14)
C8	0.0459 (15)	0.0344 (15)	0.0414 (15)	0.0067 (12)	−0.0041 (13)	0.0006 (13)
C10	0.0418 (16)	0.0333 (16)	0.076 (2)	0.0096 (13)	0.0004 (16)	0.0073 (17)
C11	0.0578 (18)	0.0398 (17)	0.0554 (19)	0.0045 (14)	0.0075 (16)	−0.0067 (16)
C9	0.0519 (17)	0.0431 (17)	0.0556 (18)	0.0095 (14)	−0.0143 (15)	0.0051 (16)
C14	0.0539 (18)	0.060 (2)	0.0474 (17)	−0.0143 (15)	0.0038 (14)	0.0125 (17)
C17	0.0648 (19)	0.082 (3)	0.0577 (18)	0.0027 (18)	0.0337 (16)	0.008 (2)
C16	0.095 (3)	0.0499 (19)	0.0431 (17)	−0.0025 (18)	0.0072 (17)	−0.0099 (17)

Geometric parameters (Å, º) top

O3A—C3A	1.257 (3)	C7—C12	1.394 (3)
O3A'—C3A'	1.261 (3)	C3A'—N3'	1.388 (3)
N3—C2	1.374 (3)	N3'—C2'	1.376 (3)
N3—C3A	1.398 (3)	N3'—C17	1.470 (3)
N3—C14	1.462 (3)	F20—C10	1.369 (3)
N1'—C2'	1.387 (3)	O2'—C2'	1.217 (3)
N1'—C6'	1.387 (3)	C13—H13A	0.9600
N1'—C16	1.469 (3)	C13—H13B	0.9600
C5'—C6'	1.379 (3)	C13—H13C	0.9600
C5'—C3A'	1.413 (3)	C12—C11	1.382 (4)
C5'—C4	1.523 (3)	C12—H12	0.9300
N1—C6	1.381 (3)	C8—C9	1.388 (3)
N1—C2	1.388 (3)	C8—H8	0.9300
N1—C13	1.468 (3)	C10—C9	1.351 (4)
C5—C6	1.377 (3)	C10—C11	1.365 (4)
C5—C3A	1.419 (3)	C11—H11	0.9300
C5—C4	1.522 (3)	C9—H9	0.9300
N18—C6'	1.345 (3)	C14—H14A	0.9600
N18—H60	0.91 (3)	C14—H14B	0.9600
N18—H50	0.93 (3)	C14—H14C	0.9600
O2—C2	1.220 (3)	C17—H17A	0.9600
C4—C7	1.533 (3)	C17—H17B	0.9600
C4—H4	0.9800	C17—H17C	0.9600
C6—N15	1.354 (3)	C16—H16A	0.9600
N15—H40	0.96 (3)	C16—H16B	0.9600
N15—H30	0.87 (3)	C16—H16C	0.9600
C7—C8	1.382 (3)

C2—N3—C3A	124.1 (2)	O2—C2—N3	122.8 (3)
C2—N3—C14	116.9 (2)	O2—C2—N1	121.5 (3)
C3A—N3—C14	119.0 (2)	N3—C2—N1	115.7 (2)
C2'—N1'—C6'	122.1 (2)	O2'—C2'—N3'	122.8 (3)
C2'—N1'—C16	116.1 (2)	O2'—C2'—N1'	121.3 (3)
C6'—N1'—C16	121.8 (2)	N3'—C2'—N1'	115.9 (2)
C6'—C5'—C3A'	119.0 (2)	N1—C13—H13A	109.5
C6'—C5'—C4	124.6 (2)	N1—C13—H13B	109.5
C3A'—C5'—C4	116.4 (2)	H13A—C13—H13B	109.5
C6—N1—C2	122.4 (2)	N1—C13—H13C	109.5
C6—N1—C13	120.6 (2)	H13A—C13—H13C	109.5
C2—N1—C13	117.0 (2)	H13B—C13—H13C	109.5
C6—C5—C3A	118.0 (2)	C11—C12—C7	121.4 (3)
C6—C5—C4	119.7 (2)	C11—C12—H12	119.3
C3A—C5—C4	122.3 (2)	C7—C12—H12	119.3
C6'—N18—H60	122.2 (17)	C7—C8—C9	121.2 (3)
C6'—N18—H50	114.3 (16)	C7—C8—H8	119.4
H60—N18—H50	119 (2)	C9—C8—H8	119.4
C5—C4—C5'	116.4 (2)	C9—C10—C11	122.6 (3)
C5—C4—C7	114.11 (19)	C9—C10—F20	119.2 (3)
C5'—C4—C7	115.9 (2)	C11—C10—F20	118.2 (3)
C5—C4—H4	102.5	C10—C11—C12	118.3 (3)
C5'—C4—H4	102.5	C10—C11—H11	120.9
C7—C4—H4	102.5	C12—C11—H11	120.9
N15—C6—C5	123.3 (2)	C10—C9—C8	118.8 (3)
N15—C6—N1	115.4 (2)	C10—C9—H9	120.6
C5—C6—N1	121.2 (2)	C8—C9—H9	120.6
N18—C6'—C5'	123.3 (2)	N3—C14—H14A	109.5
N18—C6'—N1'	116.6 (2)	N3—C14—H14B	109.5
C5'—C6'—N1'	120.1 (2)	H14A—C14—H14B	109.5
C6—N15—H40	117.4 (16)	N3—C14—H14C	109.5
C6—N15—H30	124 (2)	H14A—C14—H14C	109.5
H40—N15—H30	116 (3)	H14B—C14—H14C	109.5
C8—C7—C12	117.6 (2)	N3'—C17—H17A	109.5
C8—C7—C4	123.0 (2)	N3'—C17—H17B	109.5
C12—C7—C4	119.0 (2)	H17A—C17—H17B	109.5
O3A'—C3A'—N3'	117.6 (2)	N3'—C17—H17C	109.5
O3A'—C3A'—C5'	124.5 (2)	H17A—C17—H17C	109.5
N3'—C3A'—C5'	118.0 (2)	H17B—C17—H17C	109.5
C2'—N3'—C3A'	124.1 (2)	N1'—C16—H16A	109.5
C2'—N3'—C17	117.2 (2)	N1'—C16—H16B	109.5
C3A'—N3'—C17	118.6 (2)	H16A—C16—H16B	109.5
O3A—C3A—N3	117.2 (2)	N1'—C16—H16C	109.5
O3A—C3A—C5	124.6 (2)	H16A—C16—H16C	109.5
N3—C3A—C5	118.2 (2)	H16B—C16—H16C	109.5

C6—C5—C4—C5'	86.2 (3)	C5'—C3A'—N3'—C17	−175.0 (2)
C3A—C5—C4—C5'	−92.6 (3)	C2—N3—C3A—O3A	−178.5 (2)
C6—C5—C4—C7	−134.7 (2)	C14—N3—C3A—O3A	1.2 (4)
C3A—C5—C4—C7	46.5 (3)	C2—N3—C3A—C5	2.5 (4)
C6'—C5'—C4—C5	75.3 (3)	C14—N3—C3A—C5	−177.9 (2)
C3A'—C5'—C4—C5	−102.8 (3)	C6—C5—C3A—O3A	−175.5 (2)
C6'—C5'—C4—C7	−63.1 (3)	C4—C5—C3A—O3A	3.4 (4)
C3A'—C5'—C4—C7	118.8 (2)	C6—C5—C3A—N3	3.5 (4)
C3A—C5—C6—N15	173.9 (2)	C4—C5—C3A—N3	−177.7 (2)
C4—C5—C6—N15	−4.9 (4)	C3A—N3—C2—O2	176.5 (3)
C3A—C5—C6—N1	−6.9 (4)	C14—N3—C2—O2	−3.2 (4)
C4—C5—C6—N1	174.3 (2)	C3A—N3—C2—N1	−4.8 (4)
C2—N1—C6—N15	−176.2 (2)	C14—N3—C2—N1	175.5 (2)
C13—N1—C6—N15	5.1 (3)	C6—N1—C2—O2	−180.0 (3)
C2—N1—C6—C5	4.6 (4)	C13—N1—C2—O2	−1.3 (4)
C13—N1—C6—C5	−174.1 (2)	C6—N1—C2—N3	1.3 (4)
C3A'—C5'—C6'—N18	176.0 (2)	C13—N1—C2—N3	−179.9 (2)
C4—C5'—C6'—N18	−2.1 (4)	C3A'—N3'—C2'—O2'	−177.2 (3)
C3A'—C5'—C6'—N1'	−6.9 (4)	C17—N3'—C2'—O2'	0.2 (4)
C4—C5'—C6'—N1'	175.0 (2)	C3A'—N3'—C2'—N1'	1.8 (4)
C2'—N1'—C6'—N18	−171.0 (2)	C17—N3'—C2'—N1'	179.3 (2)
C16—N1'—C6'—N18	6.6 (4)	C6'—N1'—C2'—O2'	170.1 (2)
C2'—N1'—C6'—C5'	11.7 (4)	C16—N1'—C2'—O2'	−7.6 (4)
C16—N1'—C6'—C5'	−170.7 (2)	C6'—N1'—C2'—N3'	−8.9 (4)
C5—C4—C7—C8	−142.5 (2)	C16—N1'—C2'—N3'	173.4 (2)
C5'—C4—C7—C8	−3.2 (3)	C8—C7—C12—C11	1.4 (4)
C5—C4—C7—C12	44.9 (3)	C4—C7—C12—C11	174.4 (2)
C5'—C4—C7—C12	−175.8 (2)	C12—C7—C8—C9	−2.7 (4)
C6'—C5'—C3A'—O3A'	179.7 (2)	C4—C7—C8—C9	−175.4 (2)
C4—C5'—C3A'—O3A'	−2.0 (4)	C9—C10—C11—C12	−1.6 (4)
C6'—C5'—C3A'—N3'	0.1 (4)	F20—C10—C11—C12	177.9 (2)
C4—C5'—C3A'—N3'	178.3 (2)	C7—C12—C11—C10	0.7 (4)
O3A'—C3A'—N3'—C2'	−177.2 (2)	C11—C10—C9—C8	0.3 (4)
C5'—C3A'—N3'—C2'	2.4 (4)	F20—C10—C9—C8	−179.2 (2)
O3A'—C3A'—N3'—C17	5.4 (3)	C7—C8—C9—C10	1.9 (4)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the C7–C12 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N15—H40···O3A′	0.96 (3)	1.96 (3)	2.916 (3)	174 (2)
N18—H50···O3A	0.93 (3)	1.88 (3)	2.803 (3)	170 (2)
N15—H30···O3Aⁱ	0.86 (3)	2.26 (3)	3.083 (3)	161 (3)
N18—H60···O3A′ⁱⁱ	0.91 (3)	2.14 (3)	3.007 (3)	159 (2)
C13—H13A···O3Aⁱ	0.96	2.41	3.154 (3)	134
C13—H13A···Cgⁱⁱⁱ	0.96	2.98	3.744 (3)	138

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

Experimental details

Crystal data
Chemical formula	C₁₉H₂₁FN₆O₄
M_r	416.42
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	14.6208 (6), 11.3324 (7), 22.6410 (12)
V (Å³)	3751.4 (3)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.30 × 0.20 × 0.20

Data collection
Diffractometer	Oxford Diffraction Xcalibur Sapphire3 diffractometer
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2010)
T_min, T_max	0.862, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	9655, 3665, 2208
R_int	0.047
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.052, 0.130, 1.04
No. of reflections	3665
No. of parameters	291
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.20

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the C7–C12 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N15—H40···O3A'	0.96 (3)	1.96 (3)	2.916 (3)	174 (2)
N18—H50···O3A	0.93 (3)	1.88 (3)	2.803 (3)	170 (2)
N15—H30···O3Aⁱ	0.86 (3)	2.26 (3)	3.083 (3)	161 (3)
N18—H60···O3A'ⁱⁱ	0.91 (3)	2.14 (3)	3.007 (3)	159 (2)
C13—H13A···O3Aⁱ	0.96	2.41	3.154 (3)	134
C13—H13A···Cgⁱⁱⁱ	0.96	2.98	3.744 (3)	138

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

Acknowledgements

RK acknowledges the Department of Science & Technology for the single-crystal X-ray diffractometer sanctioned as a National Facility under project No. SR/S2/CMP-47/2003. GB is thankful to the CSIR, New Delhi, for financial support [grant No. 02 (110)/12/EMR-II]. BB is grateful to the UGC, New Delhi, for the award of a Senior Research Fellowship.

References

Buckle, D. R., Arch, J. R. S., Connolly, B. J., Fenwick, A. E., Foster, K. A., Murray, K. J., Readshaw, S. A., Smallridge, M. & Smith, D. G. (1994). J. Med. Chem. 37, 476–480. CrossRef CAS PubMed Web of Science Google Scholar
Das, S., Saikia, B. K., Das, B., Saikia, L. & Thakur, A. J. (2009). Acta Cryst. E65, o2416–o2417. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Deshmukh, M. B., Salunkhe, S. M., Patil, D. R. & Anbhule, P. V. (2009). Eur. J. Med. Chem. 44, 2651–2654. Web of Science CrossRef PubMed CAS Google Scholar
Devi, I. & Bhuyan, P. J. (2005). Tetrahedron Lett. 46, 5727–5729. Web of Science CrossRef CAS Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Ibrahim, D. A. & El-Metwally, A. M. (2010). Eur. J. Med. Chem. 45, 1158–1166. Web of Science CrossRef CAS PubMed Google Scholar
Karimi, A. R., Dalirnasab, Z., Karimi, M. & Bagherian, F. (2013). Synthesis, 45, 3300–3304. Web of Science CrossRef CAS Google Scholar
Makarov, V. A., Riabova, O. B., Granik, V. G., Dahse, H., -, M., Stelzner, A., Wutzlerc, P. & Schmidtke, M. (2005). Bioorg. Med. Chem. Lett. 15, 37–39. Web of Science CrossRef PubMed CAS Google Scholar
Muller, C. E., Shi, D., Manning, M. & Daly, J. W. (1993). J. Med. Chem. 36, 3341–3349. CAS PubMed Web of Science Google Scholar
Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Zhi, C., Long, Z.-Y., Gambino, J., Xu, W.-C., Brown, N. C., Barnes, M., Butler, M., LaMarr, W. & Wright, G. E. (2003). J. Med. Chem. 46, 2731–2739. Web of Science CrossRef PubMed CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 70| Part 10| October 2014| Pages o1098-o1099

doi:10.1107/S1600536814019886

Open

access

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structure of 5,5′-[(4-fluoro­phen­yl)methyl­ene]bis­­[6-amino-1,3-di­methyl­pyrimidine-2,4(1H,3H)-dione]

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of 5,5′-[(4-fluorophenyl)methylene]bis[6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione]