Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
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

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807037610/ci2429sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807037610/ci2429Isup2.hkl
Contains datablock I

CCDC reference: 663677

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.007 Å
  • R factor = 0.065
  • wR factor = 0.138
  • Data-to-parameter ratio = 17.9

checkCIF/PLATON results

No syntax errors found



Alert level B PLAT026_ALERT_3_B Ratio Observed / Unique Reflections too Low .... 31 Perc. PLAT230_ALERT_2_B Hirshfeld Test Diff for C1 - C2 .. 8.23 su PLAT241_ALERT_2_B Check High Ueq as Compared to Neighbors for C16 PLAT242_ALERT_2_B Check Low Ueq as Compared to Neighbors for C17
Alert level C RINTA01_ALERT_3_C The value of Rint is greater than 0.10 Rint given 0.103 PLAT020_ALERT_3_C The value of Rint is greater than 0.10 ......... 0.10 PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.74 Ratio PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.03 Ratio PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for S1 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C1 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C13 PLAT331_ALERT_2_C Small Average Phenyl C-C Dist. C17 -C22 1.36 Ang. PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 7 PLAT410_ALERT_2_C Short Intra H...H Contact H13A .. H16A .. 1.99 Ang.
0 ALERT level A = In general: serious problem 4 ALERT level B = Potentially serious problem 10 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 9 ALERT type 2 Indicator that the structure model may be wrong or deficient 5 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

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).

Structure description 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).

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

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 = 378.48F(000) = 800
Monoclinic, P21/nDx = 1.254 Mg m3
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 8.691 (2) Åθ = 1.8–27.0°
b = 23.223 (6) ŵ = 0.18 mm1
c = 10.705 (3) ÅT = 298 K
β = 111.949 (4)°Plate, 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)
Graphite monochromatorRint = 0.103
φ and ω scansθmax = 27.0°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Bruker, 1998)
h = 1111
Tmin = 0.961, Tmax = 0.987k = 2429
12473 measured reflectionsl = 1113
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.138H-atom parameters constrained
S = 1.00 w = 1/[σ2(Fo2) + (0.039P)2]
where P = (Fo2 + 2Fc2)
4358 reflections(Δ/σ)max = 0.001
244 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.18 e Å3
Crystal data top
C22H22N2O2SV = 2004.1 (9) Å3
Mr = 378.48Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.691 (2) ŵ = 0.18 mm1
b = 23.223 (6) ÅT = 298 K
c = 10.705 (3) Å0.30 × 0.19 × 0.08 mm
β = 111.949 (4)°
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)] = 0.0650 restraints
wR(F2) = 0.138H-atom parameters constrained
S = 1.00Δρmax = 0.19 e Å3
4358 reflectionsΔρmin = 0.18 e Å3
244 parameters
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 > 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
S10.74405 (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)
H14A0.22960.04130.87280.147*
H14B0.41840.02600.91930.147*
H14C0.32120.04810.77230.147*
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, º) 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, º) 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.

Experimental details

Crystal data
Chemical formulaC22H22N2O2S
Mr378.48
Crystal system, space groupMonoclinic, P21/n
Temperature (K)298
a, b, c (Å)8.691 (2), 23.223 (6), 10.705 (3)
β (°) 111.949 (4)
V3)2004.1 (9)
Z4
Radiation typeMo Kα
µ (mm1)0.18
Crystal size (mm)0.30 × 0.19 × 0.08
Data collection
DiffractometerBruker SMART CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 1998)
Tmin, Tmax0.961, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections
12473, 4358, 1348
Rint0.103
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.065, 0.138, 1.00
No. of reflections4358
No. of parameters244
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.19, 0.18

Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 1998), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1998), SHELXTL.

Hydrogen-bond geometry (Å, º) 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.
 

Subscribe to Acta Crystallographica Section E: Crystallographic Communications

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email support@iucr.org for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds