Literature DB >> 21577857

1,3-Dimethyl-5-(2-methyl-benzyl-idene)pyrimidine-2,4,6(1H,3H,5H)-trione.

R Panchatcharam, V Dhayalan, A K Mohanakrishnan, G Chakkaravarthi, V Manivannan.   

Abstract

In the title compound, C(14)H(14)N(2)O(3), the dihedral angle between the pyrimidine and benzene rings is 14.9 (1)°. The mol-ecular structure is stabilized by weak intra-molecular C-H⋯O inter-actions and the crystal structure exhibits a weak inter-molecular π-π inter-action [centroid-centroid distance = 3.575 (3) Å].

Entities:  

Year:  2009        PMID: 21577857      PMCID: PMC2970469          DOI: 10.1107/S1600536809035521

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


Related literature

For the biological activity of pyrimidine derivatives, see: Cody et al. (1997 ▶); Li et al. (1995 ▶). For related structures, see: Da Silva et al. (2005 ▶); Rezende et al. (2005 ▶). For graph-set notation, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C14H14N2O3 M = 258.27 Monoclinic, a = 8.182 (5) Å b = 8.334 (4) Å c = 18.202 (5) Å β = 94.267 (5)° V = 1237.7 (10) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 295 K 0.30 × 0.28 × 0.18 mm

Data collection

Bruker Kappa APEXII diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.971, T max = 0.982 16198 measured reflections 3837 independent reflections 2517 reflections with I > 2σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.072 wR(F 2) = 0.238 S = 1.04 3837 reflections 175 parameters H-atom parameters constrained Δρmax = 0.52 e Å−3 Δρmin = −0.34 e Å−3 Data collection: APEX2 (Bruker, 2004 ▶); cell refinement: SAINT (Bruker, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809035521/bt5051sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809035521/bt5051Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C14H14N2O3F(000) = 544
Mr = 258.27Dx = 1.386 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 6022 reflections
a = 8.182 (5) Åθ = 2.2–29.8°
b = 8.334 (4) ŵ = 0.10 mm1
c = 18.202 (5) ÅT = 295 K
β = 94.267 (5)°Block, colourless
V = 1237.7 (10) Å30.30 × 0.28 × 0.18 mm
Z = 4
Bruker Kappa APEXII diffractometer3837 independent reflections
Radiation source: fine-focus sealed tube2517 reflections with I > 2σ(I)
graphiteRint = 0.024
ω and φ scansθmax = 30.7°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −11→11
Tmin = 0.971, Tmax = 0.982k = −8→11
16198 measured reflectionsl = −26→26
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.072Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.238H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.1214P)2 + 0.5641P] where P = (Fo2 + 2Fc2)/3
3837 reflections(Δ/σ)max < 0.001
175 parametersΔρmax = 0.52 e Å3
0 restraintsΔρmin = −0.34 e Å3
xyzUiso*/Ueq
C10.0138 (2)0.2553 (2)0.49118 (10)0.0391 (4)
C2−0.1183 (3)0.2104 (3)0.44177 (12)0.0547 (6)
H2−0.19740.14060.45730.066*
C3−0.1326 (3)0.2681 (4)0.37060 (12)0.0589 (6)
H3−0.22050.23700.33840.071*
C4−0.0168 (3)0.3713 (3)0.34746 (12)0.0548 (6)
H4−0.02850.41470.30030.066*
C50.1166 (3)0.4106 (3)0.39422 (12)0.0519 (5)
H50.19610.47850.37750.062*
C60.1363 (2)0.3521 (3)0.46527 (11)0.0424 (5)
C70.2861 (3)0.4007 (4)0.51198 (15)0.0714 (8)
H7A0.35860.31050.51880.107*
H7B0.25520.43700.55900.107*
H7C0.34080.48590.48810.107*
C80.0343 (3)0.2024 (3)0.56714 (11)0.0447 (5)
H80.14120.21610.58730.054*
C9−0.0641 (2)0.1379 (2)0.61602 (10)0.0390 (4)
C100.0217 (3)0.0920 (3)0.68754 (10)0.0429 (5)
C11−0.2160 (2)−0.0676 (2)0.71455 (10)0.0396 (4)
C12−0.2395 (3)0.1068 (3)0.60570 (11)0.0449 (5)
C130.0281 (3)−0.0647 (3)0.79980 (12)0.0584 (6)
H13A0.1247−0.12230.78850.088*
H13B−0.0416−0.13400.82570.088*
H13C0.05890.02630.83000.088*
C14−0.4706 (3)−0.0581 (4)0.63701 (16)0.0715 (8)
H14A−0.4822−0.16750.65240.107*
H14B−0.5004−0.04960.58510.107*
H14C−0.54090.00930.66360.107*
N1−0.3007 (2)−0.0073 (2)0.65217 (9)0.0433 (4)
N2−0.0600 (2)−0.0100 (2)0.73120 (8)0.0397 (4)
O10.1595 (2)0.1369 (3)0.70726 (9)0.0682 (6)
O2−0.3317 (2)0.1744 (3)0.56044 (11)0.0748 (6)
O3−0.2774 (2)−0.1642 (2)0.75393 (10)0.0587 (5)
U11U22U33U12U13U23
C10.0383 (9)0.0465 (10)0.0326 (8)0.0012 (8)0.0033 (7)0.0046 (7)
C20.0453 (11)0.0775 (16)0.0407 (10)−0.0112 (11)−0.0004 (9)0.0047 (11)
C30.0505 (12)0.0883 (18)0.0367 (10)0.0003 (12)−0.0041 (9)0.0010 (11)
C40.0654 (14)0.0672 (15)0.0323 (9)0.0100 (11)0.0064 (9)0.0082 (9)
C50.0614 (13)0.0556 (13)0.0403 (10)−0.0084 (10)0.0144 (9)0.0035 (9)
C60.0407 (10)0.0498 (11)0.0371 (9)−0.0012 (8)0.0061 (7)−0.0031 (8)
C70.0539 (14)0.104 (2)0.0549 (14)−0.0309 (15)−0.0017 (11)0.0038 (14)
C80.0417 (10)0.0534 (12)0.0382 (9)−0.0060 (9)−0.0016 (8)0.0071 (9)
C90.0413 (10)0.0433 (10)0.0320 (8)−0.0013 (8)−0.0009 (7)0.0049 (7)
C100.0415 (10)0.0535 (11)0.0330 (9)−0.0047 (9)−0.0017 (7)0.0061 (8)
C110.0460 (10)0.0390 (10)0.0350 (9)−0.0009 (8)0.0100 (7)−0.0014 (7)
C120.0391 (10)0.0608 (13)0.0345 (9)0.0025 (9)0.0008 (7)0.0053 (9)
C130.0598 (14)0.0761 (16)0.0384 (10)0.0067 (12)−0.0022 (9)0.0186 (11)
C140.0449 (13)0.108 (2)0.0611 (15)−0.0255 (14)0.0006 (11)−0.0008 (15)
N10.0378 (8)0.0532 (10)0.0387 (8)−0.0071 (7)0.0025 (6)−0.0027 (7)
N20.0408 (8)0.0466 (9)0.0315 (7)0.0021 (7)0.0020 (6)0.0070 (6)
O10.0512 (9)0.1035 (15)0.0473 (9)−0.0257 (9)−0.0139 (7)0.0199 (9)
O20.0443 (9)0.1221 (17)0.0570 (10)0.0125 (10)−0.0022 (8)0.0328 (11)
O30.0673 (11)0.0574 (10)0.0536 (9)−0.0123 (8)0.0186 (8)0.0089 (7)
C1—C61.396 (3)C9—C121.457 (3)
C1—C21.404 (3)C9—C101.482 (3)
C1—C81.449 (3)C10—O11.217 (3)
C2—C31.379 (3)C10—N21.371 (3)
C2—H20.9300C11—O31.212 (2)
C3—C41.369 (4)C11—N21.376 (3)
C3—H30.9300C11—N11.380 (3)
C4—C51.373 (4)C12—O21.214 (3)
C4—H40.9300C12—N11.391 (3)
C5—C61.380 (3)C13—N21.467 (3)
C5—H50.9300C13—H13A0.9600
C6—C71.495 (3)C13—H13B0.9600
C7—H7A0.9600C13—H13C0.9600
C7—H7B0.9600C14—N11.460 (3)
C7—H7C0.9600C14—H14A0.9600
C8—C91.355 (3)C14—H14B0.9600
C8—H80.9300C14—H14C0.9600
C6—C1—C2118.38 (18)C12—C9—C10117.69 (17)
C6—C1—C8117.61 (18)O1—C10—N2120.04 (18)
C2—C1—C8123.97 (19)O1—C10—C9123.19 (19)
C3—C2—C1121.1 (2)N2—C10—C9116.74 (18)
C3—C2—H2119.5O3—C11—N2121.34 (19)
C1—C2—H2119.5O3—C11—N1121.6 (2)
C4—C3—C2119.7 (2)N2—C11—N1117.08 (17)
C4—C3—H3120.1O2—C12—N1119.8 (2)
C2—C3—H3120.1O2—C12—C9124.2 (2)
C3—C4—C5119.7 (2)N1—C12—C9116.06 (17)
C3—C4—H4120.1N2—C13—H13A109.5
C5—C4—H4120.1N2—C13—H13B109.5
C4—C5—C6121.9 (2)H13A—C13—H13B109.5
C4—C5—H5119.0N2—C13—H13C109.5
C6—C5—H5119.0H13A—C13—H13C109.5
C5—C6—C1118.95 (19)H13B—C13—H13C109.5
C5—C6—C7118.1 (2)N1—C14—H14A109.5
C1—C6—C7122.9 (2)N1—C14—H14B109.5
C6—C7—H7A109.5H14A—C14—H14B109.5
C6—C7—H7B109.5N1—C14—H14C109.5
H7A—C7—H7B109.5H14A—C14—H14C109.5
C6—C7—H7C109.5H14B—C14—H14C109.5
H7A—C7—H7C109.5C11—N1—C12124.58 (17)
H7B—C7—H7C109.5C11—N1—C14117.58 (19)
C9—C8—C1135.66 (19)C12—N1—C14117.7 (2)
C9—C8—H8112.2C10—N2—C11124.92 (16)
C1—C8—H8112.2C10—N2—C13117.15 (18)
C8—C9—C12127.86 (18)C11—N2—C13117.91 (18)
C8—C9—C10114.43 (18)
C6—C1—C2—C3−4.0 (4)C10—C9—C12—O2159.2 (2)
C8—C1—C2—C3178.4 (2)C8—C9—C12—N1158.5 (2)
C1—C2—C3—C4−0.2 (4)C10—C9—C12—N1−20.2 (3)
C2—C3—C4—C53.1 (4)O3—C11—N1—C12178.2 (2)
C3—C4—C5—C6−1.7 (4)N2—C11—N1—C12−0.2 (3)
C4—C5—C6—C1−2.5 (4)O3—C11—N1—C142.9 (3)
C4—C5—C6—C7179.6 (3)N2—C11—N1—C14−175.4 (2)
C2—C1—C6—C55.2 (3)O2—C12—N1—C11−166.3 (2)
C8—C1—C6—C5−177.0 (2)C9—C12—N1—C1113.1 (3)
C2—C1—C6—C7−177.0 (3)O2—C12—N1—C148.9 (4)
C8—C1—C6—C70.7 (3)C9—C12—N1—C14−171.7 (2)
C6—C1—C8—C9164.5 (3)O1—C10—N2—C11179.7 (2)
C2—C1—C8—C9−17.9 (4)C9—C10—N2—C11−2.3 (3)
C1—C8—C9—C12−3.4 (4)O1—C10—N2—C13−2.0 (3)
C1—C8—C9—C10175.4 (2)C9—C10—N2—C13176.01 (19)
C8—C9—C10—O114.5 (3)O3—C11—N2—C10176.1 (2)
C12—C9—C10—O1−166.7 (2)N1—C11—N2—C10−5.6 (3)
C8—C9—C10—N2−163.5 (2)O3—C11—N2—C13−2.2 (3)
C12—C9—C10—N215.4 (3)N1—C11—N2—C13176.12 (18)
C8—C9—C12—O2−22.1 (4)
D—H···AD—HH···AD···AD—H···A
C2—H2···O20.932.262.893 (3)125
C8—H8···O10.932.282.732 (3)110
C13—H13B···O30.962.262.706 (4)107
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C2—H2⋯O20.932.262.893 (3)125
  6 in total

1.  Supramolecular structures of five 5-(arylmethylene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-triones: isolated molecules, hydrogen-bonded chains and chains of fused hydrogen-bonded rings.

Authors:  Marcos C Rezende; Moisés Dominguez; James L Wardell; Janet M S Skakle; John N Low; Christopher Glidewell
Journal:  Acta Crystallogr C       Date:  2005-04-23       Impact factor: 1.172

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  5-(1-Hydroxyethylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione and four amino derivatives.

Authors:  Emerson T da Silva; Rodrigo S Ribiero; Edson L S Lima; James L Wardell; Janet M S Skakle; John N Low; Christopher Glidewell
Journal:  Acta Crystallogr C       Date:  2004-12-11       Impact factor: 1.172

4.  1,2-Diarylcyclopentenes as selective cyclooxygenase-2 inhibitors and orally active anti-inflammatory agents.

Authors:  J J Li; G D Anderson; E G Burton; J N Cogburn; J T Collins; D J Garland; S A Gregory; H C Huang; P C Isakson; C M Koboldt
Journal:  J Med Chem       Date:  1995-10-27       Impact factor: 7.446

5.  Comparison of ternary complexes of Pneumocystis carinii and wild-type human dihydrofolate reductase with coenzyme NADPH and a novel classical antitumor furo[2,3-d]pyrimidine antifolate.

Authors:  V Cody; N Galitsky; J R Luft; W Pangborn; A Gangjee; R Devraj; S F Queener; R L Blakley
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-11-01

6.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  6 in total
  1 in total

1.  5-(3,4-Dimeth-oxy-benzyl-idene)-1,3-dimethyl-1,3-diazinane-2,4,6-trione.

Authors:  Mukut Gohain; Theunis J Muller; Barend C B Bezuidenhoudt
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-12-21
  1 in total

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