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Acta Cryst. (2007). E63, o3942    [ doi:10.1107/S1600536807037610 ]

2-(Benzoylmethylsulfanyl)-6-benzyl-5-isopropylpyrimidin-4(3H)-one

Z.-K. Rao, S.-S. Zhang, Y.-P. He, Y.-T. Zheng and C. Li

Abstract top

The title compound, C22H22N2O2S, shows remarkable activity against HIV-1. The benzoyl and benzyl rings form dihedral angles of 85.7 (2) and 77.4 (3)°, respectively, with the pyrimidine ring. The dihedral angle between the two phenyl rings is 19.3 (3)°. Intramolecular C-H...N and C-H...O hydrogen bonds stabilize the molecular structure. Centrosymmetrically related molecules are linked by N-H...O hydrogen bonds into a dimer. In addition, intermolecular C-H...O hydrogen bonds are observed

Comment top

As part of our ongoing investigation on the 2-arylcarbonylmethyl S-DABOs analogues (He et al., 2004), the title compound was synthesized as a novel inhibitor, and it shows remarkable activity against HIV-1. Its molecular structure contains a pyrimidine and two phenyl rings (Fig. 1). The C1–C6 and C17–C22 phenyl rings form dihedral angles of 85.7 (2)° and 77.4 (3)°, respectively, with the pyrimidine ring. The dihedral angle between the two phenyl rings is 19.3 (3)°. The C17—C16—C12 bond angle between the pyrimidine and C17–C22 rings is 114.2 (3)°.

Intramolecular C—H···N and C—H···O type hydrogen bonds stabilize the molecular structure. The centrosymmetrically related molecules are linked by N—H···O hydrogen bonds into a dimer (Fig. 2). In addition, intermolecular C—H···O hydrogen bonds are observed (Table 1).

Related literature top

For related literature, see: He et al. (2004).

Experimental top

The title compound was prepared according to the procedure of He et al. (2004). Single crystals were obtained from an ethyl acetate solution by slow evaporation at room temperature.

Refinement top

Methyl H atoms were placed in calculated positions with C—H = 0.96 Å and torsion angle was refined to fit the electron density with Uiso(H) = 1.5Ueq(C). Other H were placed in calculated positions with C—H = 0.93–0.97 Å and N—H = 0.86 Å, and refined in riding mode, Uiso(H) = 1.2Ueq(C,N). Owing to the poor diffraction quality of the crystal, the ratio of observed to unique reflections is low (31%) and the Rint value is high (0.103).

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1998); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1998); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atom-labelling scheme and 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. A view of a N—H···O hydrogen-bonded dimer. Hydrogen bonds are shown as dashed lines. Atoms labelled with the suffix A are generated by the symmetry operation (1 − x, −y, 1 − z).
2-(Benzoylmethylsulfanyl)-6-benzyl-5-isopropylpyrimidin-4(3H)-one top
Crystal data top
C22H22N2O2SZ = 4
Mr = 378.48F000 = 800
Monoclinic, P21/nDx = 1.254 Mg m−3
Hall symbol: -P 2ynMo Kα radiation
λ = 0.71073 Å
a = 8.691 (2) Åθ = 1.8–27.0º
b = 23.223 (6) ŵ = 0.18 mm−1
c = 10.705 (3) ÅT = 298 (2) K
β = 111.949 (4)ºPlate, colourless
V = 2004.1 (9) Å30.30 × 0.19 × 0.08 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		4358 independent reflections
Radiation source: fine-focus sealed tube1348 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.103
T = 298(2) Kθmax = 27.0º
φ and ω scansθmin = 1.8º
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		h = −11→11
Tmin = 0.961, Tmax = 0.987k = −24→29
12473 measured reflectionsl = −11→13
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)] = 0.065H-atom parameters constrained
wR(F2) = 0.138  w = 1/[σ2(Fo2) + (0.039P)2]
where P = (Fo2 + 2Fc2)
S = 1.00(Δ/σ)max = 0.001
4358 reflectionsΔρmax = 0.19 e Å−3
244 parametersΔρmin = −0.18 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C22H22N2O2SV = 2004.1 (9) Å3
Mr = 378.48Z = 4
Monoclinic, P21/nMo Kα
a = 8.691 (2) ŵ = 0.18 mm−1
b = 23.223 (6) ÅT = 298 (2) K
c = 10.705 (3) Å0.30 × 0.19 × 0.08 mm
β = 111.949 (4)º
Data collection top
Bruker SMART CCD area-detector
diffractometer		4358 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1998)		1348 reflections with I > 2σ(I)
Tmin = 0.961, Tmax = 0.987Rint = 0.103
12473 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.065244 parameters
wR(F2) = 0.138H-atom parameters constrained
S = 1.00Δρmax = 0.19 e Å−3
4358 reflectionsΔρmin = −0.18 e Å−3
Special details top

Geometry. 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.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.74405 (15)0.14324 (5)0.58050 (11)0.0803 (4)
O10.5071 (3)0.23901 (12)0.4777 (3)0.0893 (10)
O20.3701 (3)−0.00995 (11)0.5886 (2)0.0705 (8)
N10.5429 (4)0.06432 (13)0.6032 (3)0.0591 (9)
H1A0.57340.04790.54420.071*
N20.5769 (4)0.14324 (13)0.7453 (3)0.0720 (10)
C10.6581 (5)0.31823 (17)0.5976 (4)0.0521 (10)
C20.5386 (5)0.3564 (2)0.5210 (4)0.0753 (13)
H2B0.44430.34260.45230.090*
C30.5575 (6)0.4147 (2)0.5452 (5)0.0975 (16)
H3A0.47630.44010.49270.117*
C40.6947 (7)0.4352 (2)0.6456 (6)0.1010 (17)
H4A0.70710.47460.66110.121*
C50.8153 (6)0.3981 (2)0.7244 (4)0.0914 (15)
H5A0.90890.41220.79340.110*
C60.7952 (5)0.33933 (19)0.6994 (4)0.0718 (12)
H6A0.87600.31400.75250.086*
C70.6320 (5)0.25571 (18)0.5645 (4)0.0577 (11)
C80.7706 (5)0.21571 (14)0.6419 (4)0.0666 (12)
H8A0.78110.21540.73530.080*
H8B0.87350.23070.63910.080*
C90.6094 (5)0.11632 (16)0.6528 (4)0.0594 (11)
C100.4286 (5)0.03664 (18)0.6432 (4)0.0588 (11)
C110.3910 (5)0.06488 (17)0.7479 (4)0.0591 (11)
C120.4662 (6)0.11664 (18)0.7929 (4)0.0717 (13)
C130.2691 (5)0.03583 (18)0.7980 (4)0.0761 (13)
H13A0.26760.05800.87540.091*
C140.3136 (5)−0.02547 (18)0.8449 (4)0.0980 (15)
H14A0.2296−0.04130.87280.147*
H14B0.4184−0.02600.91930.147*
H14C0.3212−0.04810.77230.147*
C150.0966 (6)0.0379 (2)0.6919 (5)0.143 (2)
H15A0.06930.07690.66210.215*
H15B0.01880.02380.72890.215*
H15C0.09160.01430.61690.215*
C160.4398 (6)0.15025 (17)0.9048 (4)0.1119 (18)
H16A0.33140.14070.90530.134*
H16B0.52210.13810.99040.134*
C170.4508 (7)0.21374 (19)0.8932 (5)0.0658 (12)
C180.3165 (7)0.2464 (3)0.8216 (5)0.0944 (16)
H18A0.21480.22830.77860.113*
C190.3263 (9)0.3049 (4)0.8110 (6)0.118 (2)
H19A0.23220.32620.76240.142*
C200.4709 (11)0.3311 (3)0.8706 (7)0.112 (2)
H20A0.47790.37070.86100.135*
C210.6078 (7)0.3015 (3)0.9445 (6)0.1028 (18)
H21A0.70780.32050.98800.123*
C220.5972 (7)0.2424 (3)0.9547 (4)0.0835 (14)
H22A0.69190.22171.00460.100*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.1087 (9)0.0565 (8)0.1015 (9)−0.0011 (7)0.0689 (8)−0.0034 (7)
O10.070 (2)0.086 (2)0.088 (2)−0.0099 (18)0.0023 (17)−0.0288 (18)
O20.094 (2)0.0537 (19)0.079 (2)−0.0062 (16)0.0503 (17)−0.0155 (15)
N10.086 (2)0.045 (2)0.060 (2)0.0038 (19)0.0430 (19)−0.0075 (18)
N20.115 (3)0.051 (2)0.072 (2)−0.011 (2)0.061 (2)−0.0165 (19)
C10.057 (3)0.051 (3)0.051 (3)0.005 (2)0.023 (2)0.008 (2)
C20.085 (3)0.071 (3)0.073 (3)−0.003 (3)0.032 (3)−0.004 (3)
C30.098 (4)0.085 (5)0.108 (4)0.021 (4)0.036 (3)0.017 (3)
C40.137 (6)0.058 (4)0.127 (5)0.001 (4)0.071 (4)0.002 (4)
C50.109 (4)0.071 (4)0.087 (4)−0.032 (3)0.029 (3)−0.018 (3)
C60.081 (3)0.065 (3)0.064 (3)−0.014 (3)0.022 (3)−0.003 (2)
C70.064 (3)0.058 (3)0.054 (3)−0.005 (3)0.026 (2)−0.002 (2)
C80.081 (3)0.052 (3)0.069 (3)−0.005 (2)0.030 (2)0.000 (2)
C90.082 (3)0.045 (3)0.062 (3)0.007 (2)0.039 (2)0.003 (2)
C100.071 (3)0.052 (3)0.061 (3)0.006 (3)0.033 (2)0.004 (2)
C110.084 (3)0.049 (3)0.059 (3)0.004 (2)0.043 (2)−0.004 (2)
C120.121 (4)0.048 (3)0.067 (3)0.008 (3)0.058 (3)−0.001 (2)
C130.103 (4)0.063 (3)0.090 (3)0.002 (3)0.068 (3)−0.009 (3)
C140.129 (4)0.076 (4)0.107 (4)−0.016 (3)0.065 (3)0.011 (3)
C150.078 (4)0.191 (6)0.177 (5)0.037 (4)0.068 (4)0.058 (5)
C160.220 (6)0.054 (3)0.107 (4)−0.017 (4)0.112 (4)−0.029 (3)
C170.096 (4)0.057 (3)0.064 (3)−0.002 (3)0.053 (3)−0.016 (3)
C180.095 (4)0.113 (5)0.072 (4)0.007 (4)0.027 (3)−0.022 (4)
C190.128 (6)0.142 (7)0.089 (4)0.068 (5)0.045 (4)0.021 (5)
C200.175 (7)0.079 (5)0.121 (6)0.024 (5)0.098 (6)0.004 (4)
C210.101 (5)0.104 (5)0.121 (5)−0.031 (4)0.061 (4)−0.047 (4)
C220.089 (4)0.084 (4)0.078 (3)0.019 (3)0.033 (3)−0.011 (3)
Geometric parameters (Å, °) top
S1—C91.743 (4)C11—C131.514 (5)
S1—C81.790 (3)C12—C161.518 (5)
O1—C71.199 (4)C13—C151.506 (5)
O2—C101.244 (4)C13—C141.511 (5)
N1—C91.358 (4)C13—H13A0.98
N1—C101.379 (4)C14—H14A0.96
N1—H1A0.86C14—H14B0.96
N2—C91.288 (4)C14—H14C0.96
N2—C121.391 (4)C15—H15A0.96
C1—C61.370 (5)C15—H15B0.96
C1—C21.379 (5)C15—H15C0.96
C1—C71.491 (5)C16—C171.486 (5)
C2—C31.376 (5)C16—H16A0.97
C2—H2B0.93C16—H16B0.97
C3—C41.358 (5)C17—C181.362 (6)
C3—H3A0.93C17—C221.367 (5)
C4—C51.376 (5)C18—C191.370 (7)
C4—H4A0.93C18—H18A0.93
C5—C61.389 (5)C19—C201.325 (7)
C5—H5A0.93C19—H19A0.93
C6—H6A0.93C20—C211.344 (6)
C7—C81.502 (5)C20—H20A0.93
C8—H8A0.97C21—C221.383 (6)
C8—H8B0.97C21—H21A0.93
C10—C111.438 (4)C22—H22A0.93
C11—C121.367 (5)
C9—S1—C8100.97 (18)N2—C12—C16113.0 (4)
C9—N1—C10122.9 (3)C15—C13—C14109.9 (4)
C9—N1—H1A118.5C15—C13—C11110.5 (4)
C10—N1—H1A118.5C14—C13—C11114.3 (3)
C9—N2—C12116.5 (3)C15—C13—H13A107.3
C6—C1—C2118.8 (4)C14—C13—H13A107.3
C6—C1—C7123.2 (4)C11—C13—H13A107.3
C2—C1—C7118.1 (4)C13—C14—H14A109.5
C3—C2—C1120.7 (4)C13—C14—H14B109.5
C3—C2—H2B119.7H14A—C14—H14B109.5
C1—C2—H2B119.7C13—C14—H14C109.5
C4—C3—C2120.1 (5)H14A—C14—H14C109.5
C4—C3—H3A119.9H14B—C14—H14C109.5
C2—C3—H3A119.9C13—C15—H15A109.5
C3—C4—C5120.5 (5)C13—C15—H15B109.5
C3—C4—H4A119.7H15A—C15—H15B109.5
C5—C4—H4A119.7C13—C15—H15C109.5
C4—C5—C6119.0 (4)H15A—C15—H15C109.5
C4—C5—H5A120.5H15B—C15—H15C109.5
C6—C5—H5A120.5C17—C16—C12114.2 (3)
C1—C6—C5120.9 (4)C17—C16—H16A108.7
C1—C6—H6A119.5C12—C16—H16A108.7
C5—C6—H6A119.5C17—C16—H16B108.7
O1—C7—C1120.8 (4)C12—C16—H16B108.7
O1—C7—C8122.3 (4)H16A—C16—H16B107.6
C1—C7—C8116.8 (4)C18—C17—C22116.6 (4)
C7—C8—S1114.4 (3)C18—C17—C16122.1 (6)
C7—C8—H8A108.7C22—C17—C16121.3 (5)
S1—C8—H8A108.7C17—C18—C19122.1 (6)
C7—C8—H8B108.7C17—C18—H18A118.9
S1—C8—H8B108.7C19—C18—H18A118.9
H8A—C8—H8B107.6C20—C19—C18119.5 (7)
N2—C9—N1123.3 (3)C20—C19—H19A120.3
N2—C9—S1122.9 (3)C18—C19—H19A120.3
N1—C9—S1113.8 (3)C19—C20—C21121.4 (7)
O2—C10—N1118.4 (4)C19—C20—H20A119.3
O2—C10—C11126.2 (4)C21—C20—H20A119.3
N1—C10—C11115.4 (4)C20—C21—C22118.9 (6)
C12—C11—C10117.2 (4)C20—C21—H21A120.6
C12—C11—C13124.9 (4)C22—C21—H21A120.6
C10—C11—C13117.8 (4)C17—C22—C21121.5 (5)
C11—C12—N2124.5 (3)C17—C22—H22A119.3
C11—C12—C16122.5 (4)C21—C22—H22A119.3
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O2i0.861.892.747 (4)177
C6—H6A···O1ii0.932.563.388 (5)148
C8—H8A···N20.972.472.879 (5)105
C14—H14C···O20.962.342.984 (5)124
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x+1/2, −y+1/2, z+1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O2i0.861.892.747 (4)177
C6—H6A···O1ii0.932.563.388 (5)148
C8—H8A···N20.972.472.879 (5)105
C14—H14C···O20.962.342.984 (5)124
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x+1/2, −y+1/2, z+1/2.
Acknowledgements top

The authors thank the National Natural Science Foundation of China (grant No. 30530179) for financial support.

references
References top

Bruker (1998). SMART, SAINT, SADABS and SHELXTL. Bruker AXS, Inc., Madison, Wisconsin, USA.

He, Y. P., Chen, F. E., Yu, X. J., Wang, Y. P. De., Clercq, E., Balzarini, J. & Pannecouque, C. (2004). Bioorg. Chem. 32, 536–548.

Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.