Literature DB >> 21583061

Ethyl 4-(2,4-difluoro-phen-yl)-6-methyl-2-oxo-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

Hoong-Kun Fun, Chin Sing Yeap, M Babu, B Kalluraya.   

Abstract

In the title compound, C(14)H(14)F(2)N(2)O(3), the dihydro-pyrimidin-one ring adopts a flattened boat conformation. The difluoro-phenyl group is disordered over two orientations with occupancies of 0.544 (3) and 0.456 (3). The methoxy-carbonyl group is disordered over two positions with occupancies of 0.580 (8) and 0.420 (8). In the crystal, mol-ecules are linked into centrosymmetric dimers by paired N-H⋯O hydrogen bonds and the dimers are linked into a ribbon-like structure along [100] by further N-H⋯O hydrogen bonds.

Entities:  

Year:  2009        PMID: 21583061      PMCID: PMC2969791          DOI: 10.1107/S1600536809015918

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


Related literature

For general background and pharmaceutical applications of pyrimidinones, see: Kalluraya & Rai (2003 ▶); Atwal (1990 ▶); Sadanandam et al. (1992 ▶); Steele et al. (1998 ▶); Manjula et al. (2004 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C14H14F2N2O3 M = 296.27 Triclinic, a = 7.5176 (1) Å b = 8.0483 (1) Å c = 11.9323 (2) Å α = 90.147 (1)° β = 100.839 (1)° γ = 108.421 (1)° V = 671.25 (2) Å3 Z = 2 Mo Kα radiation μ = 0.12 mm−1 T = 100 K 0.43 × 0.32 × 0.13 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (; Bruker, 2005 ▶) T min = 0.949, T max = 0.985 17515 measured reflections 3075 independent reflections 2703 reflections with I > 2σ(I) R int = 0.028

Refinement

R[F 2 > 2σ(F 2)] = 0.068 wR(F 2) = 0.173 S = 1.08 3075 reflections 266 parameters 45 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.66 e Å−3 Δρmin = −0.84 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809015918/ci2792sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809015918/ci2792Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C14H14F2N2O3Z = 2
Mr = 296.27F(000) = 308
Triclinic, P1Dx = 1.466 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.5176 (1) ÅCell parameters from 7927 reflections
b = 8.0483 (1) Åθ = 2.7–34.4°
c = 11.9323 (2) ŵ = 0.12 mm1
α = 90.147 (1)°T = 100 K
β = 100.839 (1)°Plate, colourless
γ = 108.421 (1)°0.43 × 0.32 × 0.13 mm
V = 671.25 (2) Å3
Bruker SMART APEXII CCD area-detector diffractometer3075 independent reflections
Radiation source: fine-focus sealed tube2703 reflections with I > 2σ(I)
graphiteRint = 0.028
φ and ω scansθmax = 27.5°, θmin = 2.7°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −9→9
Tmin = 0.949, Tmax = 0.985k = −10→10
17515 measured reflectionsl = −15→15
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.068Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.173H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.0607P)2 + 0.8775P] where P = (Fo2 + 2Fc2)/3
3075 reflections(Δ/σ)max = 0.001
266 parametersΔρmax = 0.66 e Å3
45 restraintsΔρmin = −0.84 e Å3
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1)K.
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.
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 > 2sigma(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.
xyzUiso*/UeqOcc. (<1)
F1A0.7550 (6)0.3028 (5)0.3410 (3)0.0598 (8)0.544 (3)
F1B0.8268 (7)0.8571 (6)0.2813 (4)0.0598 (8)0.456 (3)
O10.3876 (2)0.1588 (2)0.01956 (16)0.0352 (4)
O21.2723 (2)0.5461 (2)0.14780 (15)0.0298 (4)
O31.1456 (2)0.7375 (2)0.20789 (18)0.0428 (5)
N10.5906 (2)0.4172 (2)0.10712 (14)0.0207 (4)
N20.7014 (2)0.1862 (2)0.07956 (16)0.0234 (4)
F2A0.7967 (7)0.7696 (9)0.6102 (3)0.0959 (19)0.544 (3)
C1A0.7750 (7)0.4770 (8)0.3704 (4)0.0279 (8)0.544 (3)
C2A0.7792 (9)0.5355 (13)0.4811 (5)0.0557 (19)0.544 (3)
H2AA0.77190.45860.53940.067*0.544 (3)
C3A0.7941 (12)0.7054 (15)0.5035 (6)0.061 (2)0.544 (3)
C4A0.8048 (8)0.8278 (10)0.4216 (5)0.0520 (16)0.544 (3)
H4AA0.81310.94330.43810.062*0.544 (3)
C5A0.8022 (7)0.7640 (8)0.3129 (5)0.0332 (10)0.544 (3)
H5AA0.81070.84230.25540.040*0.544 (3)
C6A0.788 (3)0.5949 (12)0.2835 (7)0.0180 (17)0.544 (3)
F2B0.7660 (6)0.6163 (6)0.6323 (2)0.0479 (11)0.456 (3)
C1B0.8051 (8)0.7153 (9)0.3476 (5)0.0279 (8)0.456 (3)
C2B0.8046 (11)0.7414 (8)0.4604 (6)0.0255 (14)0.456 (3)
H2BA0.82650.85190.49450.031*0.456 (3)
C3B0.7694 (10)0.5921 (9)0.5204 (5)0.0275 (13)0.456 (3)
C4B0.7384 (11)0.4271 (8)0.4734 (5)0.0345 (14)0.456 (3)
H4BA0.71250.33260.51930.041*0.456 (3)
C5B0.7443 (9)0.3954 (11)0.3573 (5)0.0332 (10)0.456 (3)
H5BA0.73010.28530.32560.040*0.456 (3)
C6B0.774 (3)0.5502 (15)0.2934 (11)0.025 (3)0.456 (3)
C70.7793 (3)0.5371 (3)0.16198 (16)0.0182 (4)
H7A0.79950.64330.11950.022*0.580 (8)
H7B0.79850.63850.11780.022*0.420 (8)
C80.5505 (3)0.2516 (3)0.06653 (18)0.0234 (4)
C90.8906 (3)0.2904 (3)0.11002 (16)0.0197 (4)
C100.9344 (3)0.4608 (3)0.14452 (15)0.0179 (4)
C111.1330 (3)0.5786 (3)0.16561 (16)0.0198 (4)
C121.3361 (4)0.8646 (4)0.2385 (3)0.0541 (9)
H12A1.37170.92510.17180.065*0.580 (8)
H12B1.42830.80570.26700.065*0.580 (8)
H12C1.42230.82590.20190.065*0.420 (8)
H12D1.33320.97630.20930.065*0.420 (8)
C13A1.3350 (6)0.9926 (6)0.3285 (4)0.0367 (13)0.580 (8)
H13A1.46291.07000.35590.055*0.580 (8)
H13B1.28660.93050.39080.055*0.580 (8)
H13C1.25461.05990.29700.055*0.580 (8)
C13B1.4024 (9)0.8870 (8)0.3480 (5)0.0355 (17)0.420 (8)
H13D1.43070.78410.37500.053*0.420 (8)
H13E1.30850.90700.38610.053*0.420 (8)
H13F1.51700.98660.36400.053*0.420 (8)
C141.0280 (3)0.1943 (3)0.09888 (19)0.0242 (4)
H14A1.13890.23650.15910.036*
H14B1.06570.21380.02620.036*
H14C0.96760.07100.10420.036*
H1N10.493 (4)0.458 (4)0.105 (2)0.034 (7)*
H1N20.674 (4)0.081 (4)0.052 (2)0.035 (7)*
U11U22U33U12U13U23
F1A0.078 (2)0.0668 (19)0.0584 (16)0.0393 (16)0.0423 (15)0.0248 (14)
F1B0.078 (2)0.0668 (19)0.0584 (16)0.0393 (16)0.0423 (15)0.0248 (14)
O10.0139 (7)0.0315 (8)0.0586 (11)0.0057 (6)0.0059 (7)−0.0174 (8)
O20.0166 (7)0.0307 (8)0.0447 (9)0.0085 (6)0.0107 (6)0.0018 (7)
O30.0160 (8)0.0346 (9)0.0721 (13)−0.0006 (7)0.0104 (8)−0.0262 (9)
N10.0141 (8)0.0243 (9)0.0253 (8)0.0088 (7)0.0032 (6)−0.0036 (7)
N20.0160 (8)0.0206 (8)0.0350 (10)0.0063 (7)0.0081 (7)−0.0045 (7)
F2A0.081 (3)0.165 (5)0.0359 (19)0.034 (3)0.0086 (18)−0.043 (3)
C1A0.0253 (17)0.047 (2)0.0141 (15)0.0144 (16)0.0068 (12)0.0079 (16)
C2A0.039 (3)0.102 (6)0.023 (3)0.018 (4)0.008 (2)0.002 (4)
C3A0.039 (3)0.112 (7)0.026 (4)0.018 (5)0.003 (3)−0.023 (4)
C4A0.030 (3)0.071 (4)0.049 (3)0.012 (3)0.002 (2)−0.039 (3)
C5A0.0261 (18)0.051 (3)0.0162 (16)0.0024 (17)0.0063 (13)−0.0106 (19)
C6A0.010 (3)0.031 (5)0.012 (2)0.004 (4)0.0039 (16)−0.003 (2)
F2B0.079 (3)0.073 (3)0.0113 (13)0.051 (2)0.0125 (14)0.0029 (15)
C1B0.0253 (17)0.047 (2)0.0141 (15)0.0144 (16)0.0068 (12)0.0079 (16)
C2B0.040 (3)0.017 (2)0.025 (3)0.019 (2)0.002 (3)−0.002 (2)
C3B0.041 (3)0.036 (3)0.015 (3)0.023 (3)0.008 (2)0.005 (2)
C4B0.058 (4)0.028 (3)0.028 (3)0.023 (3)0.016 (3)0.011 (2)
C5B0.0261 (18)0.051 (3)0.0162 (16)0.0024 (17)0.0063 (13)−0.0106 (19)
C6B0.016 (4)0.025 (5)0.036 (5)0.008 (5)0.005 (3)−0.005 (3)
C70.0150 (9)0.0218 (9)0.0189 (9)0.0073 (7)0.0039 (7)−0.0009 (7)
C80.0159 (9)0.0252 (10)0.0304 (10)0.0067 (8)0.0080 (8)−0.0038 (8)
C90.0156 (9)0.0262 (10)0.0196 (9)0.0084 (8)0.0062 (7)0.0020 (7)
C100.0144 (9)0.0250 (10)0.0159 (8)0.0081 (7)0.0043 (7)0.0012 (7)
C110.0173 (9)0.0269 (10)0.0162 (8)0.0082 (8)0.0041 (7)0.0013 (7)
C120.0205 (12)0.0508 (17)0.078 (2)−0.0088 (11)0.0148 (13)−0.0355 (15)
C13A0.033 (2)0.028 (2)0.042 (2)0.0054 (17)−0.0014 (18)−0.0057 (17)
C13B0.032 (3)0.035 (3)0.034 (3)0.007 (2)−0.001 (2)−0.006 (2)
C140.0198 (10)0.0261 (10)0.0308 (11)0.0112 (8)0.0085 (8)0.0002 (8)
F1A—C1A1.398 (6)C3B—C4B1.373 (8)
F1B—C1B1.375 (7)C4B—C5B1.418 (8)
O1—C81.238 (3)C4B—H4BA0.93
O2—C111.211 (2)C5B—C6B1.441 (12)
O3—C111.342 (3)C5B—H5BA0.93
O3—C121.451 (3)C6B—C71.579 (12)
N1—C81.337 (3)C7—C101.524 (3)
N1—C71.468 (2)C7—H7A0.98
N1—H1N10.89 (3)C7—H7B0.96
N2—C81.379 (3)C9—C101.349 (3)
N2—C91.382 (3)C9—C141.496 (3)
N2—H1N20.86 (3)C10—C111.467 (3)
F2A—C3A1.367 (7)C12—C13B1.299 (7)
C1A—C2A1.392 (8)C12—C13A1.490 (5)
C1A—C6A1.404 (9)C12—H12A0.97
C2A—C3A1.358 (11)C12—H12B0.97
C2A—H2AA0.93C12—H12C0.97
C3A—C4A1.384 (11)C12—H12D0.97
C4A—C5A1.388 (7)C13A—H12D1.4259
C4A—H4AA0.93C13A—H13A0.96
C5A—C6A1.371 (11)C13A—H13B0.96
C5A—H5AA0.93C13A—H13C0.96
C6A—C71.505 (8)C13B—H13D0.96
F2B—C3B1.355 (6)C13B—H13E0.96
C1B—C2B1.362 (8)C13B—H13F0.96
C1B—C6B1.409 (12)C14—H14A0.96
C2B—C3B1.378 (7)C14—H14B0.96
C2B—H2BA0.93C14—H14C0.96
C11—O3—C12116.68 (18)C10—C7—H7B104.8
C8—N1—C7126.65 (17)C6B—C7—H7B121.4
C8—N1—H1N1117.3 (18)O1—C8—N1123.06 (19)
C7—N1—H1N1115.9 (18)O1—C8—N2120.41 (19)
C8—N2—C9123.28 (18)N1—C8—N2116.53 (18)
C8—N2—H1N2115 (2)C10—C9—N2119.93 (18)
C9—N2—H1N2120 (2)C10—C9—C14126.95 (18)
C2A—C1A—F1A122.6 (6)N2—C9—C14113.12 (17)
C2A—C1A—C6A119.6 (7)C9—C10—C11120.89 (17)
F1A—C1A—C6A117.9 (5)C9—C10—C7121.08 (17)
C3A—C2A—C1A119.6 (6)C11—C10—C7118.04 (17)
C3A—C2A—H2AA120.2O2—C11—O3121.61 (18)
C1A—C2A—H2AA120.2O2—C11—C10127.53 (19)
C2A—C3A—F2A122.2 (8)O3—C11—C10110.85 (16)
C2A—C3A—C4A123.8 (6)C13B—C12—O3113.2 (4)
F2A—C3A—C4A114.0 (8)C13B—C12—C13A46.9 (3)
C3A—C4A—C5A114.5 (6)O3—C12—C13A108.3 (3)
C3A—C4A—H4AA122.7C13B—C12—H12A135.7
C5A—C4A—H4AA122.7O3—C12—H12A110.0
C6A—C5A—C4A125.2 (7)C13A—C12—H12A110.0
C6A—C5A—H5AA117.4C13B—C12—H12B64.7
C4A—C5A—H5AA117.4O3—C12—H12B110.0
C5A—C6A—C1A117.2 (6)C13A—C12—H12B110.0
C5A—C6A—C7121.1 (7)H12A—C12—H12B108.4
C1A—C6A—C7121.6 (7)C13B—C12—H12C108.9
C2B—C1B—F1B118.1 (6)O3—C12—H12C108.9
C2B—C1B—C6B124.0 (7)C13A—C12—H12C141.9
F1B—C1B—C6B117.9 (6)H12A—C12—H12C63.9
C1B—C2B—C3B115.2 (5)H12B—C12—H12C48.0
C1B—C2B—H2BA122.4C13B—C12—H12D109.0
C3B—C2B—H2BA122.4O3—C12—H12D109.0
F2B—C3B—C4B120.2 (5)C13A—C12—H12D67.0
F2B—C3B—C2B115.7 (6)H12A—C12—H12D46.1
C4B—C3B—C2B124.1 (5)H12B—C12—H12D139.4
C3B—C4B—C5B122.4 (6)H12C—C12—H12D107.8
C3B—C4B—H4BA118.8C12—C13A—H13A109.5
C5B—C4B—H4BA118.8H12D—C13A—H13A100.8
C4B—C5B—C6B113.6 (8)C12—C13A—H13B109.5
C4B—C5B—H5BA123.2H12D—C13A—H13B143.5
C6B—C5B—H5BA123.2C12—C13A—H13C109.5
C1B—C6B—C5B120.6 (9)H12D—C13A—H13C77.8
C1B—C6B—C7119.2 (7)C12—C13B—H13D109.5
C5B—C6B—C7120.1 (8)C12—C13B—H13E109.5
N1—C7—C6A113.1 (6)H13D—C13B—H13E109.5
N1—C7—C10109.82 (15)C12—C13B—H13F109.5
C6A—C7—C10115.3 (7)H13D—C13B—H13F109.5
N1—C7—C6B105.6 (8)H13E—C13B—H13F109.5
C10—C7—C6B110.0 (8)C9—C14—H14A109.5
N1—C7—H7A105.9C9—C14—H14B109.5
C6A—C7—H7A105.9H14A—C14—H14B109.5
C10—C7—H7A105.9C9—C14—H14C109.5
C6B—C7—H7A119.3H14A—C14—H14C109.5
N1—C7—H7B104.8H14B—C14—H14C109.5
C6A—C7—H7B108.1
F1A—C1A—C2A—C3A−178.4 (6)C5A—C6A—C7—C6B−168 (8)
C6A—C1A—C2A—C3A0.7 (12)C1A—C6A—C7—C6B10 (5)
C1A—C2A—C3A—F2A179.2 (6)C1B—C6B—C7—N1−120.8 (15)
C1A—C2A—C3A—C4A0.3 (12)C5B—C6B—C7—N160.9 (18)
C2A—C3A—C4A—C5A−1.0 (11)C1B—C6B—C7—C6A5(5)
F2A—C3A—C4A—C5A−180.0 (5)C5B—C6B—C7—C6A−173 (8)
C3A—C4A—C5A—C6A0.8 (12)C1B—C6B—C7—C10120.7 (15)
C4A—C5A—C6A—C1A0.1 (18)C5B—C6B—C7—C10−57.6 (18)
C4A—C5A—C6A—C7177.7 (8)C7—N1—C8—O1−178.9 (2)
C2A—C1A—C6A—C5A−0.9 (17)C7—N1—C8—N21.3 (3)
F1A—C1A—C6A—C5A178.2 (9)C9—N2—C8—O1166.8 (2)
C2A—C1A—C6A—C7−178.4 (9)C9—N2—C8—N1−13.3 (3)
F1A—C1A—C6A—C70.6 (17)C8—N2—C9—C109.5 (3)
F1B—C1B—C2B—C3B175.8 (6)C8—N2—C9—C14−169.96 (19)
C6B—C1B—C2B—C3B−0.7 (16)N2—C9—C10—C11−173.48 (17)
C1B—C2B—C3B—F2B−179.1 (5)C14—C9—C10—C116.0 (3)
C1B—C2B—C3B—C4B0.7 (12)N2—C9—C10—C76.1 (3)
F2B—C3B—C4B—C5B−178.7 (6)C14—C9—C10—C7−174.45 (18)
C2B—C3B—C4B—C5B1.5 (12)N1—C7—C10—C9−15.5 (2)
C3B—C4B—C5B—C6B−3.4 (14)C6A—C7—C10—C9113.7 (5)
C2B—C1B—C6B—C5B−1(3)C6B—C7—C10—C9100.3 (6)
F1B—C1B—C6B—C5B−178.0 (13)N1—C7—C10—C11164.14 (16)
C2B—C1B—C6B—C7−179.8 (10)C6A—C7—C10—C11−66.7 (5)
F1B—C1B—C6B—C74(2)C6B—C7—C10—C11−80.1 (6)
C4B—C5B—C6B—C1B3(2)C12—O3—C11—O2−4.1 (3)
C4B—C5B—C6B—C7−178.4 (12)C12—O3—C11—C10176.8 (2)
C8—N1—C7—C6A−118.4 (5)C9—C10—C11—O26.0 (3)
C8—N1—C7—C1012.0 (3)C7—C10—C11—O2−173.63 (19)
C8—N1—C7—C6B−106.5 (7)C9—C10—C11—O3−174.99 (18)
C5A—C6A—C7—N1−109.7 (12)C7—C10—C11—O35.4 (2)
C1A—C6A—C7—N167.8 (15)C11—O3—C12—C13B−104.0 (4)
C5A—C6A—C7—C10122.8 (12)C11—O3—C12—C13A−154.2 (3)
C1A—C6A—C7—C10−59.7 (14)
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O2i0.89 (3)2.14 (3)3.007 (2)165 (2)
N2—H1N2···O1ii0.86 (3)1.99 (3)2.840 (2)177 (3)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N1⋯O2i0.89 (3)2.14 (3)3.007 (2)165 (2)
N2—H1N2⋯O1ii0.86 (3)1.99 (3)2.840 (2)177 (3)

Symmetry codes: (i) ; (ii) .

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