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Crystal structure of 6-hy­dr­oxy-5-(2-meth­­oxy­phen­oxy)-2,2′-bipyrimidin-4(3H)-one

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aDepartment of Studies in Chemistry, University of Mysore, Manasagangotri, Mysuru 570 006, India, bDepartment of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435-2001, USA, and cSchool of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, UK
*Correspondence e-mail: yathirajan@hotmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 2 June 2016; accepted 5 June 2016; online 17 June 2016)

In the title compound, C15H12N4O4, the dihedral angle between the heterocyclic rings is 12.60 (8)°, and that between the benzene ring and the adjacent heterocyclic ring is 85.14 (6)°. In the crystal, a combination of N—H⋯O and O—H⋯O hydrogen bonds link mol­ecules related by a glide plane into a C(5) C(6)[R22(9)] chain of rings, which is a distinctly different packing motif to those observed in hydrated modifications of this compound.

1. Chemical context

Pyrimidine derivatives exhibit a wide variety of biological actions (Önal & Yıldırım, 2007[Önal, Z. & Yıldırım, İ. (2007). Heterocycl. Commun. 13, 113-120.]) and specific examples are of particular value in the treatment of cardiovascular diseases (Goldmann & Stoltefuss, 1991[Goldmann, S. & Stoltefuss, J. (1991). Angew. Chem. Int. Ed. Engl. 30, 1559-1578.]). One such derivative is bosentan, 4-tert-butyl-N-[6-(2-hy­droxy­eth­oxy)-5-(2-meth­oxyphen­oxy)-2-(pyrimidin-2-yl)pyrimidin-4-yl]benzene-1-sulfonamide, which is used in the treatment of pulmonary artery hypertension (Pearl et al., 1999[Pearl, J. M., Wellmann, S. A., McNamara, J. L., Lombardi, J. P., Wagner, C. J., Raake, J. L. & Nelson, D. P. (1999). Ann. Thorac. Surg. 68, 1714-21 discussion 1721-1714-21; discussion 1722.]; Hoeper et al., 2003[Hoeper, M., Taha, N., Bekjarova, A., Gatzke, R. & Spiekerkoetter, E. (2003). Eur. Respir. J. 22, 330-334.]; Kenyon & Nappi, 2003[Kenyon, K. W. & Nappi, J. M. (2003). Ann. Pharmacother. 37, 1055-1062.]).

[Scheme 1]

4-Hy­droxy-5-(2-meth­oxy­phen­oxy)-2,2′-bipyrimidin-6(1H)-one (I)[link] (Fig. 1[link]) is an inter­mediate in the synthesis of bosentan (Rebelli et al., 2013[Rebelli, P., Yerrabelly, J. R., Yalamanchili, B. K., Kommera, R., Ghojala, V. R. & Bairy, K. R. (2013). Org. Process Res. Dev. 17, 1021-1026.]; Kompella et al., 2014[Kompella, A., Kasa, S., Balina, V. S., Kusumba, S., Adibhatla, B. R. K. & Muddasani, P. R. (2014). Sci. J. Chem. 2, 9-15.]) and accordingly it is of inter­est to determine its crystal and mol­ecular structure, which we report here. Crystals of the anhydrous title compound (I)[link] were obtained from a solution of a 1:1 mixture of di­methyl­sulfoxide and N,N-di­methyl­formamide in the presence of adipic acid: by contrast, a similar crystallization regime but omitting the adipic acid yielded the corresponding dihydrate (II) (Yamuna et al., 2013[Yamuna, T. S., Jasinski, J. P., Anderson, B. J., Yathirajan, H. S. & Kaur, M. (2013). Acta Cryst. E69, o1707-o1708.]), so permitting comparison of the anhydrous and hydrated forms.

[Figure 1]
Figure 1
The mol­ecular structure of compound (I)[link] showing displacement ellipsoids drawn at the 30% probability level.

2. Structural commentary

The bond distances in the ring containing atom N11 clearly show the presence of localized double bonds in the bonds C12=N13 and C14=C15 as well as the exocyclic C16=O16, fully consistent with the location of the H atoms on atoms N11 and O14, as deduced from difference maps and confirmed by the refinement. By contrast, the bond distances in the other heterocyclic ring indicate conventional aromatic-type delocalization.

At each of the sites C14, C31 and C32, the corresponding pairs of exocyclic O—C—N (at C14) or O—C—C angles (at C31 and C32) differ by almost 10°, as generally observed in the arenes of type ArOR when the substituent R lies close to the plane of the aryl ring (Seip & Seip, 1973[Seip, H. M. & Seip, R. (1973). Acta Chem. Scand. 27, 4024-4027.]; Ferguson et al., 1996[Ferguson, G., Glidewell, C. & Patterson, I. L. J. (1996). Acta Cryst. C52, 420-423.]). Here atoms C15 and C37 (Fig. 1[link]) are displaced from the plane of the aryl ring (C31–C36) by 0.219 (3) and 0.204 (4) Å, respectively, with both substituents displaced to the same side of the aryl ring. The C—O—C angles at atoms O15 and O32, 115.41 (12) and 117.65 (18)° respectively, and the C—O—H angle at atom O14 is 114.2 (16)°; are all significantly larger the the idealized tetra­hedral value of 109.5°.

The dihedral angle between the heterocyclic rings is 12.60 (8)° and that between the ring containing N11 and the aryl ring is 85.14 (6)°. Accordingly, the mol­ecule of (I)[link] exhibits no inter­nal symmetry and thus the compound is conformationally chiral: the centrosymmetric space group confirms that (I)[link] crystallizes as a conformational racemate.

3. Supra­molecular inter­actions

In the crystal, mol­ecules of (I)[link] are linked by a combination of O—H⋯N and N—H⋯N hydrogen bonds (Table 1[link]) to form a C(5) C(6)[R22(9)] chain of rings running parallel to the [001] direction (Fig. 2[link]): adjacent mol­ecules are related by glide-plane symmetry. Two chains of this type, related to one another by inversion, pass through each unit cell, but there are no direction-specific inter­actions between adjacent chains.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N11—H11⋯O15i 0.855 (19) 2.257 (19) 2.9733 (18) 141.4 (17)
O14—H14⋯O16ii 0.85 (2) 1.80 (2) 2.6117 (18) 160 (2)
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].
[Figure 2]
Figure 2
Part of the crystal structure of compound (I)[link] showing the formation of a hydrogen-bonded C(5) C(6)[R22)9)] chain of rings parallel to [001]. For the sake of clarity, the H atoms bonded to C atoms have all been omitted.

4. Database survey

In the dihydrate (II), an extensive series of hydrogen bonds, encompassing N—H⋯O, O—H⋯N and O—H⋯O types links the mol­ecular components into a complex sheet structure (Yamuna et al., 2013[Yamuna, T. S., Jasinski, J. P., Anderson, B. J., Yathirajan, H. S. & Kaur, M. (2013). Acta Cryst. E69, o1707-o1708.]), in contrast to the rather simple chains in (I)[link] reported here. A sheet structure, built from a combination of the same three types of hydrogen bond is found also in the structure of bosentan monohydrate (Kaur et al., 2013[Kaur, M., Jasinski, J. P., Keeley, A. C., Yathirajan, H. S., Betz, R., Gerber, T. & Butcher, R. J. (2013). Acta Cryst. E69, o12-o13.]).

5. Synthesis and crystallization

A sample of compound (I)[link] was a gift from Cadila Pharmaceuticals Ltd, Ahmedabad, Gujarat, India. Colourless plates of the anhydrous compound (I)[link] were grown by slow evaporation, at room temperature of a solution of (I)[link] in a mixture of di­methyl­sulfoxide and N,N-di­methyl­formamide (1:1, v/v) containing an excess of adipic acid (hexane-1,6-dioic acid).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All H atoms were located in difference maps. The H atoms bonded to C atoms were then treated as riding atoms in geometrically idealized positions with C—H distances 0.93 Å (aromatic and heteroaromatic) or 0.96 Å (CH3) and with Uiso(H) = kUeq(C) where k = 1.5 for the methyl group, which was permitted to rotate but not to tilt and 1.2 for all other H atoms bonded to C atoms. For the H atoms bonded to O or N atoms, the atomic coordinates were refined with Uiso(H) = 1.5Ueq(O) or 1.2Ueq(N), giving the O—H and N—H distances shown in Table 1[link].

Table 2
Experimental details

Crystal data
Chemical formula C15H12N4O4
Mr 312.29
Crystal system, space group Monoclinic, P21/c
Temperature (K) 298
a, b, c (Å) 12.1863 (9), 10.7079 (8), 11.1726 (8)
β (°) 105.412 (8)
V3) 1405.48 (19)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.49 × 0.46 × 0.28
 
Data collection
Diffractometer Agilent Xcalibur, Eos, Gemini CCD
Absorption correction Multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. University of Göttingen, Germany.])
Tmin, Tmax 0.812, 0.969
No. of measured, independent and observed [I > 2σ(I)] reflections 7121, 3113, 2311
Rint 0.037
(sin θ/λ)max−1) 0.650
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.134, 1.07
No. of reflections 3113
No. of parameters 215
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.26, −0.25
Computer programs: CrysAlis PRO (Agilent, 2014[Agilent (2014). CrysAlis PRO. Agilent Technologies Ltd, Yarnton, England.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009).

6-Hydroxy-5-(2-methoxyphenoxy)-2,2'-bipyrimidin-4(3H)-one top
Crystal data top
C15H12N4O4F(000) = 648
Mr = 312.29Dx = 1.476 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 12.1863 (9) ÅCell parameters from 3266 reflections
b = 10.7079 (8) Åθ = 3.5–29.2°
c = 11.1726 (8) ŵ = 0.11 mm1
β = 105.412 (8)°T = 298 K
V = 1405.48 (19) Å3Plate, colourles
Z = 40.49 × 0.46 × 0.28 mm
Data collection top
Agilent Xcalibur, Eos, Gemini CCD
diffractometer
2311 reflections with I > 2σ(I)
Detector resolution: 16.0416 pixels mm-1Rint = 0.037
φ and ω scansθmax = 27.5°, θmin = 3.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1515
Tmin = 0.812, Tmax = 0.969k = 1310
7121 measured reflectionsl = 1414
3113 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: mixed
wR(F2) = 0.134H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.0582P)2 + 0.1493P]
where P = (Fo2 + 2Fc2)/3
3113 reflections(Δ/σ)max < 0.001
215 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.25 e Å3
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
xyzUiso*/Ueq
N110.18153 (12)0.35790 (14)0.63063 (13)0.0295 (3)
H110.1817 (15)0.3477 (17)0.7066 (18)0.035*
C120.14803 (12)0.47018 (16)0.58084 (14)0.0257 (4)
N130.15092 (11)0.50269 (13)0.46986 (12)0.0288 (3)
C140.19721 (13)0.41910 (16)0.40542 (14)0.0259 (4)
C150.23862 (13)0.30650 (15)0.45349 (14)0.0246 (4)
C160.22954 (14)0.26765 (16)0.57208 (15)0.0286 (4)
O140.20095 (11)0.45956 (12)0.29445 (11)0.0384 (3)
H140.2235 (18)0.405 (2)0.251 (2)0.058*
O150.29101 (9)0.22750 (11)0.38791 (10)0.0286 (3)
O160.26156 (12)0.16663 (12)0.62240 (11)0.0435 (4)
N210.10457 (13)0.51230 (15)0.77235 (13)0.0382 (4)
C220.11108 (13)0.55897 (16)0.66440 (15)0.0287 (4)
N230.09267 (14)0.67630 (15)0.62621 (15)0.0442 (4)
C240.06898 (19)0.7543 (2)0.7096 (2)0.0534 (6)
H240.05640.83800.68810.064*
C250.06238 (17)0.7179 (2)0.8239 (2)0.0503 (6)
H250.04670.77430.88050.060*
C260.07998 (16)0.5938 (2)0.85148 (18)0.0472 (5)
H260.07460.56530.92830.057*
C310.41008 (14)0.22844 (17)0.42471 (15)0.0305 (4)
C320.46353 (16)0.1335 (2)0.37687 (17)0.0417 (5)
C330.58106 (19)0.1307 (3)0.4082 (2)0.0639 (7)
H330.61840.06780.37710.077*
C340.64289 (19)0.2205 (3)0.4850 (3)0.0713 (8)
H340.72200.21850.50430.086*
C350.59019 (18)0.3127 (3)0.5336 (2)0.0595 (6)
H350.63300.37200.58680.071*
C360.47253 (15)0.3169 (2)0.50285 (17)0.0414 (5)
H360.43580.37950.53510.050*
O320.39382 (13)0.05064 (15)0.30120 (14)0.0585 (5)
C370.4443 (3)0.0572 (3)0.2648 (2)0.0755 (8)
H37A0.48890.03360.20950.113*
H37B0.38570.11430.22330.113*
H37C0.49230.09680.33690.113*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N110.0418 (8)0.0269 (8)0.0233 (7)0.0053 (6)0.0148 (6)0.0020 (6)
C120.0255 (8)0.0249 (9)0.0261 (8)0.0005 (7)0.0059 (6)0.0018 (7)
N130.0345 (7)0.0239 (8)0.0278 (7)0.0035 (6)0.0078 (6)0.0006 (6)
C140.0298 (8)0.0261 (9)0.0216 (7)0.0028 (7)0.0063 (6)0.0010 (7)
C150.0283 (8)0.0233 (9)0.0235 (7)0.0008 (7)0.0090 (6)0.0023 (7)
C160.0342 (9)0.0251 (10)0.0283 (8)0.0022 (7)0.0112 (6)0.0005 (7)
O140.0632 (8)0.0300 (8)0.0255 (6)0.0066 (6)0.0178 (6)0.0038 (5)
O150.0310 (6)0.0293 (7)0.0267 (6)0.0032 (5)0.0098 (4)0.0058 (5)
O160.0722 (9)0.0286 (8)0.0360 (7)0.0176 (7)0.0256 (6)0.0095 (6)
N210.0455 (9)0.0392 (10)0.0327 (8)0.0007 (7)0.0155 (6)0.0068 (7)
C220.0273 (8)0.0283 (10)0.0304 (8)0.0007 (7)0.0074 (6)0.0054 (7)
N230.0592 (10)0.0287 (9)0.0473 (9)0.0076 (8)0.0189 (8)0.0052 (7)
C240.0661 (14)0.0319 (12)0.0638 (14)0.0109 (10)0.0198 (11)0.0135 (10)
C250.0466 (11)0.0519 (14)0.0544 (13)0.0037 (10)0.0169 (9)0.0267 (11)
C260.0511 (11)0.0596 (15)0.0354 (10)0.0023 (11)0.0194 (9)0.0162 (10)
C310.0315 (8)0.0330 (10)0.0278 (8)0.0055 (7)0.0091 (6)0.0059 (7)
C320.0456 (11)0.0453 (13)0.0333 (9)0.0162 (9)0.0092 (8)0.0034 (9)
C330.0484 (13)0.085 (2)0.0592 (14)0.0317 (13)0.0169 (11)0.0048 (14)
C340.0340 (12)0.101 (2)0.0756 (17)0.0110 (13)0.0089 (11)0.0157 (17)
C350.0424 (12)0.0687 (17)0.0600 (14)0.0114 (11)0.0008 (10)0.0076 (13)
C360.0394 (10)0.0399 (12)0.0438 (11)0.0031 (9)0.0089 (8)0.0016 (9)
O320.0649 (9)0.0506 (10)0.0543 (9)0.0259 (8)0.0057 (7)0.0188 (8)
C370.113 (2)0.0547 (16)0.0594 (15)0.0433 (15)0.0238 (14)0.0059 (13)
Geometric parameters (Å, º) top
N11—C121.342 (2)C26—N211.332 (2)
N11—H110.86 (2)C16—O161.234 (2)
C12—N131.297 (2)C26—H260.9300
C12—C221.484 (2)C31—C361.373 (3)
N13—C141.361 (2)C31—C321.389 (3)
C14—C151.361 (2)C32—O321.357 (2)
C15—C161.421 (2)C32—C331.381 (3)
C16—N111.381 (2)C33—C341.373 (4)
C14—O141.3255 (19)C33—H330.9300
C15—O151.3816 (18)C34—C351.367 (4)
O14—H140.85 (2)C34—H340.9300
O15—C311.3990 (19)C35—C361.384 (3)
N21—C221.327 (2)C35—H350.9300
C22—N231.327 (2)C36—H360.9300
N23—C241.339 (2)O32—C371.418 (3)
C24—C251.358 (3)C37—H37A0.9600
C24—H240.9300C37—H37B0.9600
C25—C261.368 (3)C37—H37C0.9600
C25—H250.9300
C12—N11—C16123.44 (14)N21—C26—H26118.8
C12—N11—H11116.5 (13)C25—C26—H26118.8
C16—N11—H11119.4 (13)C36—C31—C32120.81 (17)
N13—C12—N11123.65 (15)O15—C31—C32115.95 (15)
N13—C12—C22121.28 (15)O15—C31—C36123.24 (16)
N11—C12—C22115.02 (14)O32—C32—C31116.00 (16)
C12—N13—C14116.70 (14)O32—C32—C33125.34 (19)
O14—C14—N13113.69 (14)C15—O15—C31115.41 (12)
O14—C14—C15123.87 (15)C32—O32—C37117.65 (18)
C15—C14—N13122.41 (14)C33—C32—C31118.7 (2)
C14—C15—O15120.54 (13)C34—C33—C32120.2 (2)
C14—C15—C16120.98 (15)C34—C33—H33119.9
O15—C15—C16118.47 (14)C32—C33—H33119.9
O16—C16—N11121.35 (15)C35—C34—C33121.1 (2)
O16—C16—C15126.03 (16)C35—C34—H34119.4
N11—C16—C15112.61 (14)C33—C34—H34119.4
C14—O14—H14114.2 (16)C34—C35—C36119.4 (2)
C22—N21—C26115.78 (17)C34—C35—H35120.3
N23—C22—N21127.09 (16)C36—C35—H35120.3
N23—C22—C12117.26 (15)C31—C36—C35119.9 (2)
N21—C22—C12115.59 (15)C31—C36—H36120.1
C22—N23—C24114.59 (17)C35—C36—H36120.1
N23—C24—C25123.6 (2)O32—C37—H37A109.5
N23—C24—H24118.2O32—C37—H37B109.5
C25—C24—H24118.2H37A—C37—H37B109.5
C24—C25—C26116.47 (19)O32—C37—H37C109.5
C24—C25—H25121.8H37A—C37—H37C109.5
C26—C25—H25121.8H37B—C37—H37C109.5
N21—C26—C25122.44 (19)
C16—N11—C12—N134.3 (2)N11—C12—C22—N216.7 (2)
C16—N11—C12—C22173.20 (14)N21—C22—N23—C242.4 (3)
N11—C12—N13—C144.0 (2)C12—C22—N23—C24174.60 (16)
C22—C12—N13—C14173.33 (13)C22—N23—C24—C250.9 (3)
C12—N13—C14—O14177.94 (14)N23—C24—C25—C260.8 (3)
C12—N13—C14—C150.1 (2)C22—N21—C26—C250.0 (3)
O14—C14—C15—O151.7 (2)C24—C25—C26—N211.3 (3)
N13—C14—C15—O15176.13 (13)C15—O15—C31—C3612.1 (2)
O14—C14—C15—C16178.56 (15)C15—O15—C31—C32168.10 (14)
N13—C14—C15—C163.6 (2)C36—C31—C32—O32179.61 (17)
C12—N11—C16—O16178.32 (16)O15—C31—C32—O320.6 (2)
C12—N11—C16—C150.4 (2)C36—C31—C32—C330.8 (3)
C14—C15—C16—O16178.06 (17)O15—C31—C32—C33178.93 (17)
O15—C15—C16—O162.2 (3)O32—C32—C33—C34179.5 (2)
C14—C15—C16—N113.2 (2)C31—C32—C33—C340.1 (3)
O15—C15—C16—N11176.48 (13)C32—C33—C34—C351.1 (4)
C14—C15—O15—C31100.24 (17)C33—C34—C35—C361.2 (4)
C16—C15—O15—C3179.49 (18)C32—C31—C36—C350.7 (3)
C26—N21—C22—N232.0 (3)O15—C31—C36—C35179.05 (17)
C26—N21—C22—C12175.03 (15)C34—C35—C36—C310.3 (3)
N13—C12—C22—N236.9 (2)C33—C32—O32—C379.3 (3)
N11—C12—C22—N23170.67 (15)C31—C32—O32—C37171.21 (19)
N13—C12—C22—N21175.73 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H11···O15i0.855 (19)2.257 (19)2.9733 (18)141.4 (17)
O14—H14···O16ii0.85 (2)1.80 (2)2.6117 (18)160 (2)
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x, y+1/2, z1/2.
 

Acknowledgements

BKS thanks the UGC for the award of a Rajeev Gandhi fellowship and the University of Mysore for research facilities. HSY thanks Cadila Pharmaceuticals Ltd, Ahmedabad, Gujarat, India, for a sample of compound (I)[link]. JPJ acknowledges the NSF–MRI program (grant No. 1039027) for funds to purchase the X-ray diffractometer.

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