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In the structure of the title compound, C20H18N2O2S, the carbonyl group, the naphthyl ring system and the cyclo­pentyl ring are not in the plane of the pyrimidinyl ring. In the crystal structure, pairs of mol­ecules are connected into dimers via N—H...O hydrogen bonding

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806009378/nc6062sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536806009378/nc6062Isup2.hkl
Contains datablock I

CCDC reference: 605133

Key indicators

  • Single-crystal X-ray study
  • T = 295 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.039
  • wR factor = 0.117
  • Data-to-parameter ratio = 13.5

checkCIF/PLATON results

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Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT147_ALERT_1_C su on Symmetry Constrained Cell Angle(s) ....... ? PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ? PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C6 - C12 ... 1.53 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1994); cell refinement: CAD-4; data reduction: XCAD4 (Harms & Wocadlo, 1994); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Version 1.05; Farrugia, 1999); software used to prepare material for publication: SHELXL97.

2-(Cyclopentylsulfanyl)-6-(1-naphthoyl)pyrimidin-4(3H)-one top
Crystal data top
C20H18N2O2SF(000) = 736
Mr = 350.42Dx = 1.344 Mg m3
Monoclinic, P21/nMelting point: 459.4 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 11.920 (2) ÅCell parameters from 25 reflections
b = 10.312 (3) Åθ = 11.7–12.5°
c = 14.855 (4) ŵ = 0.20 mm1
β = 108.43 (2)°T = 295 K
V = 1732.3 (7) Å3Prism, colorless
Z = 40.40 × 0.30 × 0.20 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
1579 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.024
Graphite monochromatorθmax = 25.2°, θmin = 1.9°
ω/2θ scansh = 1413
Absorption correction: ψ scan
(North et al., 1968)
k = 012
Tmin = 0.923, Tmax = 0.961l = 117
3499 measured reflections3 standard reflections every 3600 min
3109 independent reflections intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.117 w = 1/[σ2(Fo2) + (0.0519P)2 + 0.0074P]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
3109 reflectionsΔρmax = 0.24 e Å3
231 parametersΔρmin = 0.20 e Å3
1 restraintExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0037 (10)
Special details top

Experimental. 1H NMR (DMSO): δ 1.27–1.30 (m, 4H), 1.47 (m, 2H), 1.61 (m, 2H), 3.31 (m, 1H), 6.61 (s, 1H), 7.60–8.18 (m, 7H), 13.09 (s, 1H).

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.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

- 10.6942 (0.0075) x - 4.5520 (0.0115) y + 3.9971 (0.0184) z = 0.0234 (0.0048)

* 0.0028 (0.0014) C2 * -0.0049 (0.0014) C4 * 0.0076 (0.0019) C5 * -0.0053 (0.0017) C6 * -0.0002 (0.0018) N1 0.0114 (0.0035) N3 - 0.0293 (0.0044) O1 - 0.0157 (0.0041) S1 0.0420 (0.0048) C12 0.5305 (0.0054) O2

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.00481 (8)0.18801 (7)0.22893 (5)0.0617 (3)
O10.07417 (19)0.15271 (18)0.02306 (12)0.0668 (6)
O20.2278 (2)0.34742 (18)0.35238 (13)0.0701 (7)
N10.12059 (19)0.0314 (2)0.29269 (14)0.0459 (6)
C20.0639 (2)0.0357 (2)0.21810 (17)0.0457 (7)
N30.0467 (2)0.0053 (2)0.12775 (15)0.0465 (6)
H3X0.008 (2)0.046 (2)0.0813 (16)0.071 (10)*
C40.0898 (3)0.1213 (3)0.10683 (19)0.0496 (7)
C50.1511 (2)0.1961 (3)0.18877 (17)0.0491 (7)
H50.18150.27720.18180.059*
C60.1648 (2)0.1483 (2)0.27655 (18)0.0439 (7)
C70.0628 (3)0.2088 (2)0.35652 (17)0.0494 (7)
H70.14470.17770.37800.059*
C80.0042 (3)0.1395 (3)0.41298 (19)0.0616 (8)
H8A0.01190.04710.41640.074*
H8B0.08870.15330.38600.074*
C90.0447 (3)0.2034 (3)0.5103 (2)0.0726 (10)
H9A0.01670.21110.54000.087*
H9B0.10900.15220.55130.087*
C100.0883 (3)0.3357 (3)0.4937 (2)0.0839 (11)
H10A0.17250.34340.52620.101*
H10B0.04760.40270.51710.101*
C110.0623 (3)0.3492 (3)0.3861 (2)0.0668 (9)
H11A0.01390.38960.35630.080*
H11B0.12330.39890.37120.080*
C120.2278 (2)0.2305 (3)0.36325 (18)0.0467 (7)
C130.2848 (2)0.1652 (2)0.45563 (18)0.0452 (7)
C140.3284 (2)0.0420 (3)0.4560 (2)0.0582 (8)
H140.32180.00240.39840.070*
C150.3827 (3)0.0264 (3)0.5403 (2)0.0720 (10)
H150.41100.11010.53840.086*
C160.3933 (3)0.0318 (3)0.6246 (2)0.0726 (9)
H160.42890.01340.68060.087*
C170.3637 (3)0.2167 (3)0.7185 (2)0.0724 (10)
H170.39870.17080.77420.087*
C180.3249 (3)0.3384 (3)0.7235 (2)0.0749 (10)
H180.33340.37560.78230.090*
C190.2722 (3)0.4086 (3)0.6409 (2)0.0674 (9)
H190.24570.49250.64490.081*
C200.2591 (3)0.3553 (3)0.5536 (2)0.0565 (8)
H200.22420.40400.49920.068*
C210.3521 (3)0.1575 (3)0.6297 (2)0.0565 (8)
C220.2975 (2)0.2280 (2)0.54473 (18)0.0452 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0951 (7)0.0496 (4)0.0367 (4)0.0233 (4)0.0157 (4)0.0003 (3)
O10.1044 (17)0.0608 (13)0.0318 (11)0.0181 (11)0.0166 (11)0.0083 (9)
O20.1155 (19)0.0436 (12)0.0491 (12)0.0168 (11)0.0232 (12)0.0002 (9)
N10.0589 (15)0.0435 (13)0.0346 (12)0.0092 (11)0.0140 (11)0.0020 (10)
C20.0584 (19)0.0441 (15)0.0343 (15)0.0042 (14)0.0141 (14)0.0042 (12)
N30.0631 (16)0.0449 (14)0.0299 (12)0.0065 (12)0.0122 (11)0.0011 (11)
C40.065 (2)0.0461 (16)0.0376 (16)0.0051 (14)0.0166 (14)0.0035 (13)
C50.0629 (19)0.0413 (15)0.0414 (16)0.0108 (14)0.0143 (14)0.0016 (13)
C60.0505 (17)0.0431 (16)0.0365 (15)0.0021 (13)0.0117 (13)0.0001 (12)
C70.071 (2)0.0441 (16)0.0317 (14)0.0076 (14)0.0136 (14)0.0052 (12)
C80.084 (2)0.0540 (18)0.0508 (18)0.0018 (16)0.0268 (17)0.0039 (14)
C90.097 (3)0.082 (2)0.0411 (17)0.004 (2)0.0257 (18)0.0041 (17)
C100.121 (3)0.069 (2)0.055 (2)0.003 (2)0.018 (2)0.0198 (17)
C110.099 (3)0.0489 (19)0.0552 (19)0.0016 (17)0.0280 (18)0.0062 (15)
C120.0569 (18)0.0449 (17)0.0409 (16)0.0102 (14)0.0190 (14)0.0023 (13)
C130.0460 (16)0.0444 (16)0.0413 (16)0.0063 (13)0.0082 (13)0.0018 (13)
C140.056 (2)0.0566 (19)0.0544 (19)0.0026 (15)0.0057 (15)0.0101 (15)
C150.073 (2)0.0540 (19)0.075 (2)0.0170 (17)0.0034 (19)0.0007 (18)
C160.077 (2)0.064 (2)0.061 (2)0.0101 (18)0.0012 (18)0.0114 (18)
C170.089 (3)0.081 (3)0.0361 (17)0.001 (2)0.0031 (16)0.0072 (17)
C180.092 (3)0.084 (3)0.0398 (18)0.002 (2)0.0075 (17)0.0133 (17)
C190.086 (2)0.062 (2)0.0464 (19)0.0044 (18)0.0097 (17)0.0109 (16)
C200.068 (2)0.0548 (18)0.0406 (16)0.0015 (15)0.0090 (15)0.0030 (13)
C210.0585 (19)0.0581 (19)0.0442 (16)0.0010 (15)0.0039 (14)0.0051 (15)
C220.0466 (17)0.0457 (16)0.0391 (15)0.0060 (13)0.0075 (13)0.0010 (12)
Geometric parameters (Å, º) top
S1—C21.750 (3)C10—H10A0.9700
S1—C71.813 (2)C10—H10B0.9700
O1—C41.242 (3)C11—H11A0.9700
O2—C121.216 (3)C11—H11B0.9700
N1—C21.300 (3)C12—C131.486 (3)
N1—C61.366 (3)C13—C141.372 (4)
C2—N31.359 (3)C13—C221.438 (3)
N3—C41.375 (3)C14—C151.404 (4)
N3—H3X0.879 (17)C14—H140.9300
C4—C51.431 (4)C15—C161.359 (4)
C5—C61.355 (3)C15—H150.9300
C5—H50.9300C16—C211.396 (4)
C6—C121.527 (4)C16—H160.9300
C7—C81.509 (4)C17—C181.347 (4)
C7—C111.514 (4)C17—C211.420 (4)
C7—H70.9800C17—H170.9300
C8—C91.527 (4)C18—C191.392 (4)
C8—H8A0.9700C18—H180.9300
C8—H8B0.9700C19—C201.370 (4)
C9—C101.508 (4)C19—H190.9300
C9—H9A0.9700C20—C221.410 (4)
C9—H9B0.9700C20—H200.9300
C10—C111.534 (4)C21—C221.424 (4)
C2—S1—C799.82 (12)H10A—C10—H10B108.6
C2—N1—C6116.4 (2)C7—C11—C10101.4 (2)
N1—C2—N3123.5 (2)C7—C11—H11A111.5
N1—C2—S1121.01 (19)C10—C11—H11A111.5
N3—C2—S1115.48 (19)C7—C11—H11B111.5
C2—N3—C4122.9 (2)C10—C11—H11B111.5
C2—N3—H3X117.7 (19)H11A—C11—H11B109.3
C4—N3—H3X119.4 (19)O2—C12—C13123.5 (2)
O1—C4—N3120.3 (2)O2—C12—C6117.3 (2)
O1—C4—C5125.9 (3)C13—C12—C6119.1 (2)
N3—C4—C5113.8 (2)C14—C13—C22118.9 (2)
C6—C5—C4119.7 (2)C14—C13—C12119.1 (2)
C6—C5—H5120.1C22—C13—C12122.0 (2)
C4—C5—H5120.1C13—C14—C15122.5 (3)
C5—C6—N1123.7 (2)C13—C14—H14118.8
C5—C6—C12119.1 (2)C15—C14—H14118.8
N1—C6—C12117.1 (2)C16—C15—C14118.8 (3)
C8—C7—C11103.9 (2)C16—C15—H15120.6
C8—C7—S1115.6 (2)C14—C15—H15120.6
C11—C7—S1112.41 (19)C15—C16—C21121.9 (3)
C8—C7—H7108.2C15—C16—H16119.1
C11—C7—H7108.2C21—C16—H16119.1
S1—C7—H7108.2C18—C17—C21121.1 (3)
C7—C8—C9102.2 (2)C18—C17—H17119.4
C7—C8—H8A111.3C21—C17—H17119.4
C9—C8—H8A111.3C17—C18—C19120.2 (3)
C7—C8—H8B111.3C17—C18—H18119.9
C9—C8—H8B111.3C19—C18—H18119.9
H8A—C8—H8B109.2C20—C19—C18120.7 (3)
C10—C9—C8106.5 (2)C20—C19—H19119.7
C10—C9—H9A110.4C18—C19—H19119.7
C8—C9—H9A110.4C19—C20—C22121.2 (3)
C10—C9—H9B110.4C19—C20—H20119.4
C8—C9—H9B110.4C22—C20—H20119.4
H9A—C9—H9B108.6C16—C21—C17121.1 (3)
C9—C10—C11106.7 (2)C16—C21—C22119.7 (3)
C9—C10—H10A110.4C17—C21—C22119.1 (3)
C11—C10—H10A110.4C20—C22—C21117.6 (2)
C9—C10—H10B110.4C20—C22—C13124.2 (2)
C11—C10—H10B110.4C21—C22—C13118.2 (2)
C6—N1—C2—N30.5 (4)N1—C6—C12—C1326.7 (4)
C6—N1—C2—S1179.04 (19)O2—C12—C13—C14150.5 (3)
C7—S1—C2—N15.9 (3)C6—C12—C13—C1429.8 (4)
C7—S1—C2—N3173.6 (2)O2—C12—C13—C2228.4 (4)
N1—C2—N3—C41.1 (4)C6—C12—C13—C22151.2 (2)
S1—C2—N3—C4178.5 (2)C22—C13—C14—C151.5 (4)
C2—N3—C4—O1178.2 (3)C12—C13—C14—C15179.5 (3)
C2—N3—C4—C51.7 (4)C13—C14—C15—C160.5 (5)
O1—C4—C5—C6178.1 (3)C14—C15—C16—C210.3 (5)
N3—C4—C5—C61.9 (4)C21—C17—C18—C190.1 (5)
C4—C5—C6—N11.5 (4)C17—C18—C19—C200.0 (5)
C4—C5—C6—C12178.6 (2)C18—C19—C20—C220.5 (5)
C2—N1—C6—C50.7 (4)C15—C16—C21—C17179.9 (3)
C2—N1—C6—C12177.9 (2)C15—C16—C21—C220.1 (5)
C2—S1—C7—C880.4 (2)C18—C17—C21—C16179.5 (3)
C2—S1—C7—C11160.6 (2)C18—C17—C21—C220.6 (5)
C11—C7—C8—C942.2 (3)C19—C20—C22—C211.0 (4)
S1—C7—C8—C9165.8 (2)C19—C20—C22—C13178.9 (3)
C7—C8—C9—C1024.9 (3)C16—C21—C22—C20179.0 (3)
C8—C9—C10—C111.1 (4)C17—C21—C22—C201.0 (4)
C8—C7—C11—C1042.5 (3)C16—C21—C22—C131.1 (4)
S1—C7—C11—C10168.2 (2)C17—C21—C22—C13178.9 (3)
C9—C10—C11—C726.4 (4)C14—C13—C22—C20178.4 (3)
C5—C6—C12—O224.3 (4)C12—C13—C22—C200.6 (4)
N1—C6—C12—O2153.0 (3)C14—C13—C22—C211.8 (4)
C5—C6—C12—C13156.0 (2)C12—C13—C22—C21179.3 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3X···O1i0.88 (2)1.90 (2)2.776 (3)177 (3)
Symmetry code: (i) x, y, z.
 

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