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organic compounds
4-(4-Fluorophenyl)-6-(2-furyl)pyrimidin-2-amine
aInstitute of Chemistry, University of the Punjab, Lahore 54590, Pakistan, bDepartment of Chemistry, F. C. College University, Lahore 54600, Pakistan, and cDepartment of Chemistry, The University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
*Correspondence e-mail: mujahid_bk@yahoo.com
Molecules of the title compound, C14H10FN3O, are essentially planar and in the they form dimers via hydrogen bonds, involving pyrimidinyl N atoms and amino H atoms, about inversion centers. The centroids of the furyl and pyrimidinyl rings are separated by 3.489 (2)Å, indicating π–π stacking interactions.
Related literature
For related literature, see: Colorado, & Brodbelt (1996); Bojarski et al. (1985
); Fun et al. (2006
); Gallagher et al. (2004
); Hueso et al. (2003
); Miranda et al. (2006
); Varga et al. (2003
).; Miyazaki et al. (2005
).
Experimental
Crystal data
|
Refinement
|
|
Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997
); data reduction: SCALEPACK (Otwinowski & Minor, 1997
); 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, 1997
); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536808012294/lh2621sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808012294/lh2621Isup2.hkl
3-(4-Fluorophenyl)-1-(furan-2-yl)prop-2-en-1-one (2.5 g, 9.08 mmol), guanidine hydrochloride (1.3 g, 1.5 mmol), ethanol (20 ml) and 50% aqueous KOH solution (4 ml) were mixed together and stirred at reflux temperature for 1 hr. Under the same conditions, 30% aqueous H2O2 (3.1 ml, 27.3 mmol) was added to the above mixture in small portions over a period of I hr. The ethanol was removed under reduced pressure in a rotary evaporator and distilled water (20 ml) was added to the residue. The product was isolated as precipitates, washed repeatedly with pure water and recrystallized from chloroform (yield 58%).
Though all the H atoms could be distinguished in the difference Fourier map the H-atoms bonded to C-atoms were included at geometrically idealized positions and refined in riding-model approximation with the following constraints: C—H distances were set to 0.95 Å and Uiso(H) = 1.2Ueq(C). H-atoms bonded to N3 were taken from the difference map and were allowed to refine with Uiso = 1.2 times Ueq of N3. The final difference map was free of any chemically significant features.
Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997); 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, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C14H10FN3O | F(000) = 528 |
Mr = 255.25 | Dx = 1.498 Mg m−3 |
Monoclinic, P21/c | Melting point = 513–515 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 11.629 (4) Å | Cell parameters from 4617 reflections |
b = 5.992 (3) Å | θ = 3.6–27.5° |
c = 16.389 (6) Å | µ = 0.11 mm−1 |
β = 97.69 (2)° | T = 173 K |
V = 1131.7 (8) Å3 | Prism, colorless |
Z = 4 | 0.24 × 0.20 × 0.16 mm |
Nonius KappaCCD diffractometer | 2567 independent reflections |
Radiation source: fine-focus sealed tube | 1935 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
ω and ϕ scans | θmax = 27.5°, θmin = 3.6° |
Absorption correction: multi-scan (SORTAV; Blessing, 1997) | h = −14→15 |
Tmin = 0.974, Tmax = 0.983 | k = −7→7 |
4617 measured reflections | l = −21→21 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.044 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.123 | w = 1/[σ2(Fo2) + (0.061P)2 + 0.4P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
2567 reflections | Δρmax = 0.25 e Å−3 |
179 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.025 (6) |
C14H10FN3O | V = 1131.7 (8) Å3 |
Mr = 255.25 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.629 (4) Å | µ = 0.11 mm−1 |
b = 5.992 (3) Å | T = 173 K |
c = 16.389 (6) Å | 0.24 × 0.20 × 0.16 mm |
β = 97.69 (2)° |
Nonius KappaCCD diffractometer | 2567 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1997) | 1935 reflections with I > 2σ(I) |
Tmin = 0.974, Tmax = 0.983 | Rint = 0.033 |
4617 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.123 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.25 e Å−3 |
2567 reflections | Δρmin = −0.21 e Å−3 |
179 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
F1 | 1.25524 (8) | −0.3651 (2) | 0.33665 (7) | 0.0417 (3) | |
N1 | 0.78951 (10) | −0.1133 (2) | 0.47173 (8) | 0.0212 (3) | |
N2 | 0.63490 (10) | 0.1576 (2) | 0.46105 (8) | 0.0214 (3) | |
N3 | 0.64102 (12) | −0.1403 (3) | 0.55076 (8) | 0.0260 (3) | |
H31 | 0.5641 (17) | −0.128 (3) | 0.5524 (11) | 0.031* | |
H32 | 0.6685 (16) | −0.273 (4) | 0.5618 (11) | 0.031* | |
O1 | 0.68164 (9) | 0.57384 (19) | 0.30924 (7) | 0.0252 (3) | |
C1 | 0.94793 (12) | −0.0974 (3) | 0.39086 (9) | 0.0209 (3) | |
C2 | 0.98310 (14) | −0.3102 (3) | 0.41767 (10) | 0.0269 (4) | |
H2 | 0.9353 | −0.3948 | 0.4488 | 0.032* | |
C3 | 1.08664 (14) | −0.4012 (3) | 0.39983 (10) | 0.0302 (4) | |
H3 | 1.1108 | −0.5456 | 0.4191 | 0.036* | |
C4 | 1.15313 (13) | −0.2769 (3) | 0.35368 (10) | 0.0282 (4) | |
C5 | 1.12145 (14) | −0.0680 (3) | 0.32395 (10) | 0.0280 (4) | |
H5 | 1.1690 | 0.0130 | 0.2915 | 0.034* | |
C6 | 1.01768 (13) | 0.0212 (3) | 0.34272 (10) | 0.0256 (4) | |
H6 | 0.9939 | 0.1649 | 0.3225 | 0.031* | |
C7 | 0.83900 (12) | −0.0007 (3) | 0.41450 (9) | 0.0203 (3) | |
C8 | 0.79028 (13) | 0.1937 (3) | 0.37932 (9) | 0.0225 (3) | |
H8 | 0.8261 | 0.2737 | 0.3395 | 0.027* | |
C9 | 0.68719 (12) | 0.2674 (3) | 0.40437 (9) | 0.0200 (3) | |
C10 | 0.68960 (12) | −0.0280 (3) | 0.49192 (9) | 0.0208 (3) | |
C11 | 0.62985 (12) | 0.4679 (3) | 0.36912 (9) | 0.0207 (3) | |
C12 | 0.53195 (13) | 0.5788 (3) | 0.38160 (10) | 0.0242 (4) | |
H12 | 0.4803 | 0.5406 | 0.4196 | 0.029* | |
C13 | 0.52194 (14) | 0.7633 (3) | 0.32661 (10) | 0.0279 (4) | |
H13 | 0.4620 | 0.8722 | 0.3206 | 0.033* | |
C14 | 0.61369 (14) | 0.7542 (3) | 0.28479 (10) | 0.0279 (4) | |
H14 | 0.6291 | 0.8584 | 0.2440 | 0.034* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0259 (5) | 0.0527 (7) | 0.0494 (6) | 0.0132 (5) | 0.0156 (4) | −0.0045 (5) |
N1 | 0.0169 (6) | 0.0245 (7) | 0.0224 (6) | 0.0016 (5) | 0.0036 (5) | 0.0019 (5) |
N2 | 0.0184 (6) | 0.0232 (7) | 0.0229 (6) | 0.0012 (5) | 0.0041 (5) | −0.0007 (5) |
N3 | 0.0201 (7) | 0.0296 (8) | 0.0296 (7) | 0.0035 (6) | 0.0085 (5) | 0.0081 (6) |
O1 | 0.0253 (6) | 0.0242 (6) | 0.0270 (6) | 0.0029 (5) | 0.0073 (5) | 0.0040 (5) |
C1 | 0.0165 (7) | 0.0256 (8) | 0.0208 (7) | 0.0008 (6) | 0.0031 (6) | −0.0022 (6) |
C2 | 0.0242 (8) | 0.0277 (9) | 0.0300 (8) | 0.0039 (7) | 0.0078 (6) | 0.0032 (7) |
C3 | 0.0280 (8) | 0.0300 (9) | 0.0330 (9) | 0.0095 (7) | 0.0063 (7) | 0.0016 (7) |
C4 | 0.0185 (7) | 0.0379 (10) | 0.0285 (8) | 0.0071 (7) | 0.0048 (6) | −0.0080 (7) |
C5 | 0.0233 (8) | 0.0341 (10) | 0.0283 (8) | −0.0024 (7) | 0.0100 (6) | −0.0026 (7) |
C6 | 0.0230 (7) | 0.0270 (8) | 0.0272 (8) | 0.0025 (7) | 0.0052 (6) | 0.0006 (7) |
C7 | 0.0178 (7) | 0.0225 (8) | 0.0205 (7) | −0.0013 (6) | 0.0020 (6) | −0.0018 (6) |
C8 | 0.0201 (7) | 0.0245 (8) | 0.0236 (7) | 0.0005 (6) | 0.0052 (6) | 0.0023 (6) |
C9 | 0.0185 (7) | 0.0210 (8) | 0.0203 (7) | −0.0004 (6) | 0.0013 (6) | −0.0023 (6) |
C10 | 0.0179 (7) | 0.0238 (8) | 0.0206 (7) | −0.0004 (6) | 0.0030 (6) | −0.0012 (6) |
C11 | 0.0198 (7) | 0.0218 (8) | 0.0207 (7) | −0.0007 (6) | 0.0033 (6) | −0.0015 (6) |
C12 | 0.0211 (7) | 0.0243 (8) | 0.0272 (8) | 0.0010 (6) | 0.0036 (6) | −0.0025 (7) |
C13 | 0.0271 (8) | 0.0228 (8) | 0.0324 (9) | 0.0047 (7) | −0.0008 (7) | −0.0002 (7) |
C14 | 0.0328 (8) | 0.0216 (8) | 0.0283 (8) | 0.0035 (7) | 0.0004 (7) | 0.0051 (7) |
F1—C4 | 1.3623 (18) | C3—H3 | 0.9500 |
N1—C7 | 1.346 (2) | C4—C5 | 1.376 (3) |
N1—C10 | 1.3503 (19) | C5—C6 | 1.391 (2) |
N2—C10 | 1.346 (2) | C5—H5 | 0.9500 |
N2—C9 | 1.348 (2) | C6—H6 | 0.9500 |
N3—C10 | 1.359 (2) | C7—C8 | 1.387 (2) |
N3—H31 | 0.902 (19) | C8—C9 | 1.390 (2) |
N3—H32 | 0.87 (2) | C8—H8 | 0.9500 |
O1—C14 | 1.3667 (19) | C9—C11 | 1.456 (2) |
O1—C11 | 1.3736 (18) | C11—C12 | 1.357 (2) |
C1—C2 | 1.392 (2) | C12—C13 | 1.421 (2) |
C1—C6 | 1.399 (2) | C12—H12 | 0.9500 |
C1—C7 | 1.491 (2) | C13—C14 | 1.344 (2) |
C2—C3 | 1.388 (2) | C13—H13 | 0.9500 |
C2—H2 | 0.9500 | C14—H14 | 0.9500 |
C3—C4 | 1.372 (2) | ||
C7—N1—C10 | 116.33 (13) | N1—C7—C8 | 121.46 (14) |
C10—N2—C9 | 115.37 (12) | N1—C7—C1 | 116.36 (14) |
C10—N3—H31 | 119.2 (12) | C8—C7—C1 | 122.18 (14) |
C10—N3—H32 | 115.2 (12) | C7—C8—C9 | 117.68 (14) |
H31—N3—H32 | 114.2 (17) | C7—C8—H8 | 121.2 |
C14—O1—C11 | 106.44 (12) | C9—C8—H8 | 121.2 |
C2—C1—C6 | 118.38 (14) | N2—C9—C8 | 122.34 (14) |
C2—C1—C7 | 119.86 (14) | N2—C9—C11 | 116.84 (13) |
C6—C1—C7 | 121.76 (14) | C8—C9—C11 | 120.82 (14) |
C3—C2—C1 | 121.33 (16) | N2—C10—N1 | 126.82 (14) |
C3—C2—H2 | 119.3 | N2—C10—N3 | 117.09 (13) |
C1—C2—H2 | 119.3 | N1—C10—N3 | 116.08 (14) |
C4—C3—C2 | 118.14 (16) | C12—C11—O1 | 109.78 (14) |
C4—C3—H3 | 120.9 | C12—C11—C9 | 133.89 (15) |
C2—C3—H3 | 120.9 | O1—C11—C9 | 116.32 (13) |
F1—C4—C3 | 118.27 (16) | C11—C12—C13 | 106.53 (15) |
F1—C4—C5 | 118.67 (15) | C11—C12—H12 | 126.7 |
C3—C4—C5 | 123.06 (15) | C13—C12—H12 | 126.7 |
C4—C5—C6 | 118.06 (15) | C14—C13—C12 | 106.75 (14) |
C4—C5—H5 | 121.0 | C14—C13—H13 | 126.6 |
C6—C5—H5 | 121.0 | C12—C13—H13 | 126.6 |
C5—C6—C1 | 121.00 (16) | C13—C14—O1 | 110.49 (14) |
C5—C6—H6 | 119.5 | C13—C14—H14 | 124.8 |
C1—C6—H6 | 119.5 | O1—C14—H14 | 124.8 |
C6—C1—C2—C3 | 2.2 (2) | C10—N2—C9—C11 | 179.48 (13) |
C7—C1—C2—C3 | −177.11 (14) | C7—C8—C9—N2 | 0.3 (2) |
C1—C2—C3—C4 | −1.0 (2) | C7—C8—C9—C11 | −178.93 (13) |
C2—C3—C4—F1 | 179.47 (14) | C9—N2—C10—N1 | −0.3 (2) |
C2—C3—C4—C5 | −0.5 (2) | C9—N2—C10—N3 | 178.41 (13) |
F1—C4—C5—C6 | −179.16 (14) | C7—N1—C10—N2 | −0.3 (2) |
C3—C4—C5—C6 | 0.8 (2) | C7—N1—C10—N3 | −178.93 (13) |
C4—C5—C6—C1 | 0.4 (2) | C14—O1—C11—C12 | 0.17 (17) |
C2—C1—C6—C5 | −1.8 (2) | C14—O1—C11—C9 | 179.54 (13) |
C7—C1—C6—C5 | 177.43 (14) | N2—C9—C11—C12 | 1.5 (2) |
C10—N1—C7—C8 | 0.8 (2) | C8—C9—C11—C12 | −179.20 (16) |
C10—N1—C7—C1 | −178.73 (12) | N2—C9—C11—O1 | −177.67 (13) |
C2—C1—C7—N1 | 10.0 (2) | C8—C9—C11—O1 | 1.6 (2) |
C6—C1—C7—N1 | −169.28 (13) | O1—C11—C12—C13 | 0.07 (17) |
C2—C1—C7—C8 | −169.55 (14) | C9—C11—C12—C13 | −179.15 (16) |
C6—C1—C7—C8 | 11.2 (2) | C11—C12—C13—C14 | −0.29 (18) |
N1—C7—C8—C9 | −0.9 (2) | C12—C13—C14—O1 | 0.40 (18) |
C1—C7—C8—C9 | 178.66 (13) | C11—O1—C14—C13 | −0.36 (17) |
C10—N2—C9—C8 | 0.2 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H31···N2i | 0.90 (2) | 2.30 (2) | 3.190 (2) | 168 (2) |
C5—H5···O1ii | 0.95 | 2.58 | 3.474 (2) | 157 |
C2—H2···N1 | 0.95 | 2.46 | 2.789 (2) | 100 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C14H10FN3O |
Mr | 255.25 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 173 |
a, b, c (Å) | 11.629 (4), 5.992 (3), 16.389 (6) |
β (°) | 97.69 (2) |
V (Å3) | 1131.7 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.24 × 0.20 × 0.16 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SORTAV; Blessing, 1997) |
Tmin, Tmax | 0.974, 0.983 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4617, 2567, 1935 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.123, 1.03 |
No. of reflections | 2567 |
No. of parameters | 179 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.25, −0.21 |
Computer programs: COLLECT (Hooft, 1998), DENZO (Otwinowski & Minor, 1997), SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H31···N2i | 0.90 (2) | 2.30 (2) | 3.190 (2) | 168 (2) |
C5—H5···O1ii | 0.95 | 2.58 | 3.474 (2) | 157 |
C2—H2···N1 | 0.95 | 2.46 | 2.789 (2) | 100 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+2, y−1/2, −z+1/2. |
Acknowledgements
The authors gratefully acknowledge the Higher Education Commission of Pakistan for the financial support for the project.
References
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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.
Compounds containing a pyrimidine moiety play a significant role in many biological systems (Hueso et al., 2003). The pyrimidine ring is present in nucleic acids, several vitamins, coenzymes and antibiotics. Pyrimidine based compounds have been reported as anticancer and antiviral agents (Miyazaki et al., 2005). They have been used as hypnotic drugs for the nervous system, e.g., barbiturates act as anaesthetic and sleeping agents and have been in use for the treatment of anxiety, epilepsy and other psychiatric disorders (Colorado & Brodbelt, 1996; Bojarski et al., 1985). We have prepared a series of pyrimidine based compounds from different chalcones following the literature method (Varga et al., 2003). In this paper we report the preparation and structure of the title pyrimidine compound, (I).
The crystal structure of (I) is composed of more or less planar molecules of 4-(4-fluorophenyl)-6-(2-furyl)pyrimidin-2-yl-amine (Fig. 1) wherein the dihedral angle between the mean-planes formed by the furyl and pyrimidinyl rings is 1.91 (12)° and the phenyl ring is oriented at 12.33 (11) and 10.45 (10)° with respect to these rings, respectively. The atoms F1 and N3 are displaced from the mean-planes of the phenyl and pyrimidinyl rings by 0.026 (2) and 0.032 (2) Å, respectively. The bond distances and bond angles in (I) agree well with the corresponding bond distances and angles reported in some compounds closely related to (I)(e.g., Gallagher et al., 2004; Fun et al., 2006; Miranda et al., 2006). The geometry at atom N3 is trigonal pyramidal with sum of the angles about N3 being 348.6°.
It is interesting to note that only one of the amino H-atoms, namely H31 is involved in hydrogen bonding, resulting in dimers about inversion centers (Fig. 2) (details of hydrogen bonding geometry are given in Table 1). In addition, non-classical intermolecular hydrogen bonds, C5–H5···O1, and intramolecular interactions C2–H2···N1 were also observed. The shortest distance between the centroids of furyl and pyrimidinyl rings from adjacent molecules separated by translation along the b axis is 3.489 (2) Å indicating π-π stacking interactions.