Literature DB >> 23795129

5-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetra-hydropyrimidin-5-yl)-1,3-dimethyl-1H-chromeno[2,3-d]pyrim-idine-2,4(3H,5H)-dione 3.5-hydrate.

Subhadip Roy1, Subrata Das.   

Abstract

The title compound, C19H19N5O5·3.5H2O, crystallizes with 3.5 mol-ecules of water in the asymmetric unit, one of which lies on a mirror plane. One of the water mol-ecules links the mol-ecules, forming centrosymmetric dimers. These dimers are then linked through further N-H⋯O and O-H⋯O hydrogen bonding, leading to the observed three-dimensional structure.

Entities:  

Year:  2013        PMID: 23795129      PMCID: PMC3685110          DOI: 10.1107/S1600536813013986

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


Related literature

Many chromene derivatives occur in natural products, see: Hatakeyama et al. (1988 ▶). For the biological activity of functionalized chromenes, see: Brooks (1998 ▶); Valenti et al. (1993 ▶); Tang et al. (2007 ▶). For the use of 6-amino-uracil derivatives as precursors in the synthesis of biologically significant fused uracils, see: Shaw (1996 ▶). The fusion of a chromene unit to the uracil ring is found to increase the biological activity, see: Sabry et al. (2011 ▶).

Experimental

Crystal data

C19H19N5O5·3.5H2O M = 460.45 Monoclinic, a = 29.993 (4) Å b = 7.9105 (6) Å c = 21.458 (3) Å β = 119.860 (16)° V = 4415.3 (10) Å3 Z = 8 Mo Kα radiation μ = 0.11 mm−1 T = 298 K 0.32 × 0.12 × 0.06 mm

Data collection

Oxford Diffraction Xcalibur (Eos, Gemini) diffractometer Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007 ▶) T min = 0.93, T max = 1.00 9327 measured reflections 4554 independent reflections 2538 reflections with I > 2σ(I) R int = 0.069

Refinement

R[F 2 > 2σ(F 2)] = 0.060 wR(F 2) = 0.137 S = 0.98 4554 reflections 308 parameters H-atom parameters constrained Δρmax = 0.24 e Å−3 Δρmin = −0.25 e Å−3 Data collection: CrysAlis PRO (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: OLEX.SOLVE (Bourhis et al., 2013 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶); software used to prepare material for publication: OLEX2. Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813013986/go2089sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813013986/go2089Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536813013986/go2089Isup3.cdx Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H19N5O5·3.5H2OZ = 8
Mr = 460.45F(000) = 1944
Monoclinic, C2/cDx = 1.385 Mg m3
a = 29.993 (4) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.9105 (6) ŵ = 0.11 mm1
c = 21.458 (3) ÅT = 298 K
β = 119.860 (16)°Block, clear colourless
V = 4415.3 (10) Å30.32 × 0.12 × 0.06 mm
Oxford Diffraction Xcalibur (Eos, Gemini) diffractometer4554 independent reflections
Radiation source: Enhance (Mo) X-ray Source2538 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.069
Detector resolution: 16.1511 pixels mm-1θmax = 26.5°, θmin = 2.8°
ω scansh = −37→36
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007)k = −9→5
Tmin = 0.93, Tmax = 1.00l = −26→26
9327 measured reflections
Refinement on F2H-atom parameters constrained
Least-squares matrix: fullw = 1/[σ2(Fo2) + (0.037P)2] where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.060(Δ/σ)max = 0.001
wR(F2) = 0.137Δρmax = 0.24 e Å3
S = 0.98Δρmin = −0.25 e Å3
4554 reflectionsExtinction correction: SHELXL2013 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
308 parametersExtinction coefficient: 0.0029 (2)
0 restraints
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.
xyzUiso*/Ueq
O10.20391 (8)1.0426 (2)0.41093 (10)0.0553 (6)
O20.36262 (7)0.8244 (2)0.56168 (9)0.0444 (5)
O30.51160 (8)0.8412 (3)0.44642 (10)0.0579 (6)
O40.34405 (7)0.6704 (2)0.34016 (8)0.0442 (5)
O50.24740 (6)0.5527 (2)0.34356 (8)0.0378 (5)
N10.28226 (8)0.9305 (3)0.48757 (10)0.0350 (5)
N20.22732 (8)0.8001 (3)0.37727 (10)0.0374 (6)
N30.42861 (9)0.7489 (3)0.39256 (11)0.0399 (6)
N40.48358 (8)0.7140 (3)0.51612 (10)0.0359 (6)
N60.45814 (8)0.5830 (3)0.58939 (10)0.0469 (7)
H6A0.43580.53370.59720.056*
H6B0.48910.59750.62400.056*
C10.23592 (11)0.9317 (4)0.42411 (14)0.0398 (7)
C20.26390 (10)0.6756 (3)0.39378 (12)0.0316 (6)
C30.31020 (9)0.6787 (3)0.45432 (12)0.0289 (6)
C40.32143 (10)0.8121 (3)0.50451 (12)0.0323 (6)
C50.47635 (11)0.7709 (3)0.45087 (14)0.0394 (7)
C60.44477 (10)0.6371 (3)0.52362 (12)0.0307 (6)
C70.39607 (9)0.6201 (3)0.46424 (11)0.0284 (6)
C80.38635 (11)0.6784 (3)0.39612 (12)0.0338 (6)
C90.35107 (9)0.5470 (3)0.46939 (11)0.0297 (6)
H90.36450.50810.51890.036*
C100.32640 (10)0.3965 (3)0.42059 (12)0.0294 (6)
C110.27754 (10)0.4047 (3)0.36074 (12)0.0307 (6)
C120.25456 (11)0.2707 (3)0.31460 (13)0.0418 (7)
H120.22170.28110.27510.050*
C130.28154 (13)0.1200 (4)0.32827 (14)0.0484 (8)
H130.26690.02840.29750.058*
C140.33003 (12)0.1059 (4)0.38743 (15)0.0466 (8)
H140.34800.00470.39660.056*
C150.35207 (11)0.2422 (3)0.43328 (13)0.0384 (7)
H150.38460.23060.47330.046*
C160.17779 (11)0.7988 (4)0.30914 (13)0.0573 (9)
H16A0.17950.71930.27660.086*
H16B0.17090.90960.28810.086*
H16C0.15080.76670.31840.086*
C170.29347 (11)1.0725 (3)0.53773 (14)0.0498 (8)
H17A0.31801.03700.58560.075*
H17B0.26231.10770.53630.075*
H17C0.30741.16510.52400.075*
C180.53408 (11)0.7462 (4)0.57937 (14)0.0517 (8)
H18A0.52960.80030.61590.078*
H18B0.55380.81840.56620.078*
H18C0.55190.64100.59740.078*
C190.41982 (13)0.8013 (4)0.32181 (13)0.0627 (10)
H19A0.39100.74040.28510.094*
H19B0.44990.77750.31830.094*
H19C0.41280.92040.31570.094*
O6W0.40247 (8)1.3900 (3)0.65089 (12)0.0588 (6)
H6WA0.37071.39370.63860.088*
H6WB0.41041.28910.64700.088*
O7W0.43622 (9)1.0753 (3)0.62611 (10)0.0552 (6)
H7WA0.45311.10060.60550.083*
H7WB0.41550.99490.60360.083*
O8W0.54970 (10)0.6130 (4)0.72984 (11)0.0811 (8)
H8WA0.53500.69630.73730.122*
H8WB0.55790.54010.76310.122*
O9W0.50000.8957 (5)0.75000.1228 (18)
H9W0.48270.96120.71460.184*
U11U22U33U12U13U23
O10.0445 (13)0.0462 (12)0.0788 (14)0.0148 (11)0.0333 (12)0.0016 (11)
O20.0366 (12)0.0490 (12)0.0398 (10)−0.0016 (10)0.0131 (9)−0.0123 (9)
O30.0455 (14)0.0749 (15)0.0645 (13)−0.0121 (12)0.0357 (11)0.0036 (11)
O40.0348 (12)0.0556 (12)0.0329 (9)−0.0022 (10)0.0098 (9)0.0056 (9)
O50.0291 (10)0.0419 (11)0.0321 (9)−0.0001 (9)0.0075 (8)−0.0069 (8)
N10.0314 (13)0.0298 (12)0.0480 (12)0.0017 (11)0.0229 (11)−0.0050 (10)
N20.0227 (12)0.0441 (14)0.0399 (12)0.0061 (11)0.0114 (10)−0.0007 (11)
N30.0388 (15)0.0482 (14)0.0377 (12)−0.0051 (12)0.0229 (11)0.0031 (11)
N40.0251 (13)0.0444 (13)0.0371 (11)0.0000 (11)0.0146 (10)0.0003 (10)
N60.0248 (13)0.0726 (17)0.0309 (11)−0.0112 (13)0.0044 (10)0.0060 (11)
C10.0354 (16)0.0398 (16)0.0509 (16)0.0040 (14)0.0266 (14)0.0040 (14)
C20.0241 (14)0.0342 (14)0.0349 (13)−0.0023 (12)0.0134 (12)−0.0023 (11)
C30.0232 (14)0.0298 (14)0.0326 (12)−0.0032 (11)0.0131 (11)−0.0041 (11)
C40.0302 (15)0.0366 (15)0.0333 (13)−0.0059 (13)0.0181 (12)−0.0033 (11)
C50.0329 (17)0.0404 (16)0.0521 (17)0.0039 (14)0.0268 (14)0.0025 (14)
C60.0263 (14)0.0345 (14)0.0327 (13)0.0023 (12)0.0158 (11)−0.0005 (12)
C70.0222 (14)0.0303 (14)0.0312 (12)0.0054 (11)0.0121 (11)0.0025 (11)
C80.0340 (16)0.0348 (15)0.0313 (13)0.0019 (13)0.0153 (12)−0.0010 (11)
C90.0246 (14)0.0342 (14)0.0260 (12)−0.0001 (12)0.0094 (11)−0.0015 (11)
C100.0302 (15)0.0307 (14)0.0333 (13)−0.0038 (12)0.0204 (12)−0.0032 (11)
C110.0312 (15)0.0337 (14)0.0284 (12)0.0008 (12)0.0157 (11)−0.0024 (11)
C120.0442 (18)0.0456 (17)0.0338 (14)−0.0154 (15)0.0182 (13)−0.0104 (13)
C130.065 (2)0.0394 (17)0.0512 (17)−0.0101 (17)0.0370 (17)−0.0134 (14)
C140.060 (2)0.0339 (16)0.0600 (18)−0.0009 (15)0.0404 (17)−0.0045 (14)
C150.0395 (17)0.0361 (15)0.0443 (15)0.0054 (14)0.0243 (13)0.0037 (13)
C160.0357 (19)0.069 (2)0.0505 (17)0.0128 (17)0.0093 (15)−0.0031 (16)
C170.057 (2)0.0424 (17)0.0625 (18)−0.0016 (16)0.0394 (17)−0.0147 (15)
C180.0275 (16)0.069 (2)0.0514 (17)−0.0142 (16)0.0140 (14)−0.0073 (16)
C190.073 (3)0.080 (2)0.0452 (16)−0.018 (2)0.0366 (17)0.0045 (17)
O6W0.0444 (14)0.0660 (15)0.0617 (13)−0.0016 (12)0.0231 (12)−0.0009 (12)
O7W0.0469 (15)0.0627 (15)0.0571 (12)−0.0127 (12)0.0267 (11)−0.0025 (11)
O8W0.0576 (17)0.114 (2)0.0506 (13)0.0053 (16)0.0110 (12)0.0133 (14)
O9W0.157 (4)0.076 (3)0.060 (2)0.000−0.002 (2)0.000
O1—C11.225 (3)C10—C111.388 (3)
O2—C41.238 (3)C10—C151.396 (3)
O3—C51.240 (3)C11—C121.378 (3)
O4—C81.240 (3)C12—H120.9300
O5—C21.349 (3)C12—C131.388 (4)
O5—C111.411 (3)C13—H130.9300
N1—C11.379 (3)C13—C141.379 (4)
N1—C41.401 (3)C14—H140.9300
N1—C171.474 (3)C14—C151.385 (3)
N2—C11.379 (3)C15—H150.9300
N2—C21.383 (3)C16—H16A0.9600
N2—C161.477 (3)C16—H16B0.9600
N3—C51.365 (3)C16—H16C0.9600
N3—C81.421 (3)C17—H17A0.9600
N3—C191.465 (3)C17—H17B0.9600
N4—C51.381 (3)C17—H17C0.9600
N4—C61.392 (3)C18—H18A0.9600
N4—C181.468 (3)C18—H18B0.9600
N6—H6A0.8600C18—H18C0.9600
N6—H6B0.8600C19—H19A0.9600
N6—C61.331 (3)C19—H19B0.9600
C2—C31.349 (3)C19—H19C0.9600
C3—C41.424 (3)O6W—H6WA0.8524
C3—C91.516 (3)O6W—H6WB0.8486
C6—C71.386 (3)O7W—H7WA0.8449
C7—C81.418 (3)O7W—H7WB0.8516
C7—C91.522 (3)O8W—H8WA0.8524
C9—H90.9800O8W—H8WB0.8519
C9—C101.513 (3)O9W—H9W0.8500
C2—O5—C11117.17 (18)C11—C10—C9122.1 (2)
C1—N1—C4124.3 (2)C11—C10—C15116.6 (2)
C1—N1—C17117.8 (2)C15—C10—C9121.4 (2)
C4—N1—C17117.6 (2)C10—C11—O5121.6 (2)
C1—N2—C2121.0 (2)C12—C11—O5115.1 (2)
C1—N2—C16117.2 (2)C12—C11—C10123.3 (2)
C2—N2—C16121.8 (2)C11—C12—H12120.7
C5—N3—C8123.9 (2)C11—C12—C13118.6 (3)
C5—N3—C19118.6 (2)C13—C12—H12120.7
C8—N3—C19117.5 (2)C12—C13—H13120.0
C5—N4—C6122.8 (2)C14—C13—C12120.0 (3)
C5—N4—C18116.7 (2)C14—C13—H13120.0
C6—N4—C18120.4 (2)C13—C14—H14119.9
H6A—N6—H6B120.0C13—C14—C15120.2 (3)
C6—N6—H6A120.0C15—C14—H14119.9
C6—N6—H6B120.0C10—C15—H15119.3
O1—C1—N1121.4 (3)C14—C15—C10121.3 (3)
O1—C1—N2122.1 (3)C14—C15—H15119.3
N1—C1—N2116.4 (2)N2—C16—H16A109.5
O5—C2—N2112.3 (2)N2—C16—H16B109.5
O5—C2—C3125.1 (2)N2—C16—H16C109.5
C3—C2—N2122.6 (2)H16A—C16—H16B109.5
C2—C3—C4119.0 (2)H16A—C16—H16C109.5
C2—C3—C9121.9 (2)H16B—C16—H16C109.5
C4—C3—C9119.1 (2)N1—C17—H17A109.5
O2—C4—N1119.9 (2)N1—C17—H17B109.5
O2—C4—C3123.5 (2)N1—C17—H17C109.5
N1—C4—C3116.6 (2)H17A—C17—H17B109.5
O3—C5—N3122.2 (2)H17A—C17—H17C109.5
O3—C5—N4121.0 (3)H17B—C17—H17C109.5
N3—C5—N4116.8 (2)N4—C18—H18A109.5
N6—C6—N4115.8 (2)N4—C18—H18B109.5
N6—C6—C7124.5 (2)N4—C18—H18C109.5
C7—C6—N4119.7 (2)H18A—C18—H18B109.5
C6—C7—C8119.9 (2)H18A—C18—H18C109.5
C6—C7—C9122.5 (2)H18B—C18—H18C109.5
C8—C7—C9117.6 (2)N3—C19—H19A109.5
O4—C8—N3118.5 (2)N3—C19—H19B109.5
O4—C8—C7124.6 (3)N3—C19—H19C109.5
C7—C8—N3116.9 (2)H19A—C19—H19B109.5
C3—C9—C7112.1 (2)H19A—C19—H19C109.5
C3—C9—H9107.4H19B—C19—H19C109.5
C7—C9—H9107.4H6WA—O6W—H6WB109.1
C10—C9—C3109.15 (19)H7WA—O7W—H7WB109.8
C10—C9—C7113.24 (19)H8WA—O8W—H8WB109.1
C10—C9—H9107.4
O5—C2—C3—C4−176.7 (2)C7—C9—C10—C1568.9 (3)
O5—C2—C3—C95.0 (4)C8—N3—C5—O3−176.0 (2)
O5—C11—C12—C13−179.4 (2)C8—N3—C5—N42.7 (4)
N2—C2—C3—C42.1 (4)C8—C7—C9—C3−65.0 (3)
N2—C2—C3—C9−176.2 (2)C8—C7—C9—C1059.0 (3)
N4—C6—C7—C81.1 (4)C9—C3—C4—O2−2.4 (4)
N4—C6—C7—C9−176.3 (2)C9—C3—C4—N1179.7 (2)
N6—C6—C7—C8−178.3 (2)C9—C7—C8—O4−1.7 (4)
N6—C6—C7—C94.3 (4)C9—C7—C8—N3179.0 (2)
C1—N1—C4—O2177.3 (2)C9—C10—C11—O5−2.3 (4)
C1—N1—C4—C3−4.7 (4)C9—C10—C11—C12178.7 (2)
C1—N2—C2—O5176.3 (2)C9—C10—C15—C14−178.2 (2)
C1—N2—C2—C3−2.6 (4)C10—C11—C12—C13−0.2 (4)
C2—O5—C11—C10−11.2 (3)C11—O5—C2—N2−168.9 (2)
C2—O5—C11—C12167.9 (2)C11—O5—C2—C310.0 (4)
C2—N2—C1—O1−179.3 (2)C11—C10—C15—C141.2 (4)
C2—N2—C1—N1−0.5 (4)C11—C12—C13—C140.7 (4)
C2—C3—C4—O2179.3 (2)C12—C13—C14—C15−0.2 (4)
C2—C3—C4—N11.4 (4)C13—C14—C15—C10−0.8 (4)
C2—C3—C9—C7109.6 (3)C15—C10—C11—O5178.3 (2)
C2—C3—C9—C10−16.7 (3)C15—C10—C11—C12−0.7 (4)
C3—C9—C10—C1115.2 (3)C16—N2—C1—O10.9 (4)
C3—C9—C10—C15−165.5 (2)C16—N2—C1—N1179.7 (2)
C4—N1—C1—O1−176.9 (2)C16—N2—C2—O5−4.0 (3)
C4—N1—C1—N24.3 (4)C16—N2—C2—C3177.1 (2)
C4—C3—C9—C7−68.7 (3)C17—N1—C1—O1−3.3 (4)
C4—C3—C9—C10165.0 (2)C17—N1—C1—N2177.9 (2)
C5—N3—C8—O4177.1 (2)C17—N1—C4—O23.7 (4)
C5—N3—C8—C7−3.5 (4)C17—N1—C4—C3−178.4 (2)
C5—N4—C6—N6177.5 (2)C18—N4—C5—O32.0 (4)
C5—N4—C6—C7−2.0 (4)C18—N4—C5—N3−176.7 (2)
C6—N4—C5—O3178.9 (3)C18—N4—C6—N6−5.8 (4)
C6—N4—C5—N30.1 (4)C18—N4—C6—C7174.7 (2)
C6—C7—C8—O4−179.2 (2)C19—N3—C5—O33.7 (4)
C6—C7—C8—N31.5 (3)C19—N3—C5—N4−177.6 (2)
C6—C7—C9—C3112.4 (3)C19—N3—C8—O4−2.5 (4)
C6—C7—C9—C10−123.6 (2)C19—N3—C8—C7176.8 (2)
C7—C9—C10—C11−110.4 (3)
D—H···AD—HH···AD···AD—H···A
N6—H6A···O6Wi0.862.183.009 (3)161
N6—H6B···O8W0.862.092.905 (3)158
O6W—H6WA···O1ii0.852.012.830 (3)162
O6W—H6WB···O7W0.852.002.835 (3)167
O7W—H7WA···O3iii0.841.942.781 (3)177
O7W—H7WB···O20.851.932.773 (3)170
O8W—H8WA···O9W0.851.992.838 (4)177
O8W—H8WB···O6Wiv0.852.012.840 (3)164
O9W—H9W···O7W0.851.932.772 (3)170
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
N6—H6A⋯O6W i 0.862.183.009 (3)161
N6—H6B⋯O8W 0.862.092.905 (3)158
O6W—H6WA⋯O1ii 0.852.012.830 (3)162
O6W—H6WB⋯O7W 0.852.002.835 (3)167
O7W—H7WA⋯O3iii 0.841.942.781 (3)177
O7W—H7WB⋯O20.851.932.773 (3)170
O8W—H8WA⋯O9W 0.851.992.838 (4)177
O8W—H8WB⋯O6W iv 0.852.012.840 (3)164
O9W—H9W⋯O7W 0.851.932.772 (3)170

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  3 in total

1.  A short history of SHELX.

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

2.  Benzo-gamma-pyrone analogues of geiparvarin: synthesis and biological evaluation against B16 melanoma cells.

Authors:  P Valenti; P Da Re; A Rampa; P Montanari; M Carrara; L Cima
Journal:  Anticancer Drug Des       Date:  1993-10

3.  Synthesis of 4H-chromene, coumarin, 12H-chromeno[2,3-d]pyrimidine derivatives and some of their antimicrobial and cytotoxicity activities.

Authors:  Nermien M Sabry; Hany M Mohamed; Essam Shawky A E H Khattab; Shymaa S Motlaq; Ahmed M El-Agrody
Journal:  Eur J Med Chem       Date:  2010-12-21       Impact factor: 6.514

  3 in total

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