JOURNAL OF CHEMICAL RESEARCH 2008
MARCH, 157–158
RESEARCH PAPER 157
The X-ray crystal structure of 2,4-bis(4-methoxyphenoxy) pyrimidine
Amitabha Dea*, Goutam Biswasb and Heikki Muhonenc
aDepartment of Physics, Khalisani College, Chandannagar, Hooghly, India
bDepartment of Physics, Ramananda College, Bishnupur, India
cDepartment of Chemistry, University of Helsinki, Vuorikatu 20, Fin – 00014, Finland
The X-ray crystal structure of 2,4-bis(4-methoxyphenoxy)pyrimidine, C18H16N2O4 was stabilised by the hydrogen
bonding and van der Waal forces. The C–N bond in the pyrimidine moiety is shortened indicating of immonium
character and good hydrogen bond donor potential. Both the phenyl rings are nearly perpendicular to the
pyrimidine rings. The dihedral angles between the phenyl rings and the pyrimidine ring are 85.6(1) and 87.2(1)°.
In the crystal packing, the pyrimidine rings stack with the pyrimidine rings and phenyl rings stack with the phenyl rings.
The weak C–H…O interactions and p–p stacking interactions generate chains of molecules that are linked into sheets
about the inversion centres.
Keywords: 2,4-bis(4-methoxyphenoxy) pyrimidine, X-ray crystal structure
A large number of 2,4-diaminopyrimidines with hydrogen,
alkyl or aryl substituted in 5 and 6 positions were synthesised
fortheirpossiblechemotherapeuticvalues.1 2,4-Bis(arylamino)
and 2,4-bis(aryloxy) pyrimidines are potent antimicrobial
and antifungal agent.2 Various substituted compounds were
tested against some gram-positive and gram-negative bacteria
and a pathogenic strain of yeast and their activity compared.
It was observed that, in contrast to bis-arylamino substituted
pyrimidines, the biological activity of the bisarylpyrimidines
does not depend on the nature of the substituent in the phenyl
ring.2 In continuation of our structural investigations on
various nucleic acid components,3 the structure of the title
compound was determined.
Fig. 1 The molecule.
2,4-Dichloropyrimidine (0.01 mole) and substituted phenol
(0.025 mole) was mixed as a melt and subsequently cooled
to room temperature. Finely powdered anhydrous K2CO3
(0.025 mole) was added to the reactants and mixed well.
The mixture was heated on an oil bath at the optimum reaction
temperature of 120°C for 30 minutes and cooled; on addition
of 5 ml of toluene an oily substance separated out. The oil was
extracted with hexane-ether, washed (dilute KOH, H2O), and
dried (Na2SO4). Crystals (m.p. 116°C lit. m.p. 116–117°C)
appeared on evaporating the solvent.1
Experimental
C18H16N2O4, Mr = 324.33, crystals by slow evaporation from water/
Fig.
2
Molecular structure showing 50% probability
methanol mixture, crystals dimensions 0.60 ¥ 0.55 ¥ 0.25 mm,
monoclinic, a = 8.394(3), b = 8.284(3), c = 23.083(7)Å, b = 92.60(3)°,
U = 1603.4(10)Å3, Z = 4, Dc = 1.351 g cm-3, space group P21/n,
MoKα radiation(l = 0.7107)Å, µ = 0.10 mm-1, F(000) = 680. Three-
dimensional room temperature X-ray data were collected in the range
0 < 2s < 50° on a AFC7 Rigaku diffractometer by the 2q–w scan mode
(h from 0 to 9, k from 0 to 9, l from –27 to 27). Of the 2702 reflections
measured, there were 2569 unique reflections, all of which were
corrected for Lorentz and polarisation effects (but not for absorption),
2442 independent reflections exceeded the significance level I >
2s (I). The structure was solved by direct methods4 and refined5 by
full matrix least squares on F2. Hydrogen atoms were fixed at ideal
positions and refined in riding mode with common isotropic thermal
vibration parameters Uiso = 0.08 Å2 and for methyl hydrogen Uiso
= 0.10 Å2. Three methyl hydrogen of C(20) atom were constrained
with an O–H distance 0.97 and refined in riding mode. Refinement
converged at a final R = 0.046 (wR2 = 0.111, for all 2569 data, 217
parameters, maximum and mean Δ/σ (0.001, 0.000), with allowance
for the thermal anisotropy of all the non-hydrogen atoms. Minimum
and maximum final electron density –0.17 and 0.12 eA-3. A weighting
scheme w = 1/[s2(Fo2) + (0.0706P)2] where P = (Fo2 + 2Fc2)/3 was
used in the later stages of refinement. Geometric calculations were
performed using PARST6 program. Plots were produced with the
ORTEP7 programs. Complex scattering factors were taken from the
program package SHELXL97.5 See CCDC679236 for further details.
displacement ellipsoids.
Fig. 3 Packing diagram of the molecule viewed down the
a-axis.
The bond angles and distances are comparable to those reported
for the related compounds 2,6-bis{[2-(dimethoxymethyl)phenoxy]
methyl}pyridine8 and 2,6-bis{[2-(hydroxymethyl)phenoxy]methyl}
pyridine.8 In the structure, two phenyl rings are planar and almost
* Correspondent. Email: amitde03@yahoo.com
PAPER: 07/4964
De, Amitabha
