organic compounds
6-Chloro-1-(3,5-dimethylphenylsulfonyl)-1H-benzimidazol-2(3H)-one
aInstitute of Pharmaceutical and Toxicological Chemistry, "P. Pratesi", University of Milano, via L. Mangiagalli, 25, 20133-Milano, Italy, and bDepartment of Pharmaceutical Chemistry, University of Messina, viale Annunziata, 98168-Messina, Italy
*Correspondence e-mail: fiorella.meneghetti@unimi.it
The title compound, C15H13ClN2O3S, is one of a series of N1-benzyl-1,3-dihydro-2H-benzimidazol-2-one derivatives, a new class of non-nucleoside HIV-1 reverse transcriptase inhibitors. The dihedral angle between the two pharmacophoric groups, the dimethylbenzene ring and the benzimidazolone ring system, is 88 (1)°, giving a butterfly-like conformation to the molecule. The molecular packing is characterized by a bifurcated N—H⋯(O,O) hydrogen bond and short Cl⋯O contacts of 3.122 (2) Å. In addition, π–π stacking of the benzimidazolone rings is also present, with interplanar separations of 3.95 (1) Å.
Related literature
For the role of the substituents on the benzene nucleus in anti-HIV-1 compounds, see: Barreca et al. (2007). For related literature, see: Barreca et al. (2005); Beddoes et al. (1986); Liu et al. (2007).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536808042694/fj2178sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808042694/fj2178Isup2.hkl
The compound I has been synthesized as previously reported (Barreca et al., 2007). Single crystals were obtained at room temperature by slow evaporation of a CHCl3 solution.
All non-H-atoms were refined anisotropically. Hydrogen atoms were introduced at calculated positions, in their described geometries and allowed to ride on the attached carbon atom with fixed isotropic thermal parameters (1.2Ueq and 1.5Ueq of the parent carbon atom for aromatic H-atoms and methyls H-atoms, respectively).
Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell
SHELXL97 (Sheldrick, 2008); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).C15H13ClN2O3S | F(000) = 696 |
Mr = 336.78 | Dx = 1.470 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 25 reflections |
a = 12.173 (3) Å | θ = 9–10° |
b = 14.036 (3) Å | µ = 0.40 mm−1 |
c = 8.949 (2) Å | T = 293 K |
β = 95.77 (2)° | Prism, colourless |
V = 1521.3 (6) Å3 | 0.5 × 0.4 × 0.3 mm |
Z = 4 |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.014 |
Radiation source: fine-focus sealed tube | θmax = 28.0°, θmin = 3.3° |
Graphite monochromator | h = −16→15 |
Non–profiled ω/2θ scans | k = 0→18 |
3964 measured reflections | l = 0→11 |
3634 independent reflections | 3 standard reflections every 120 min |
3214 reflections with I > 2σ(I) | intensity decay: 1% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.057 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.19 | w = 1/[σ2(Fo2) + (0.0188P)2 + 1.7615P] where P = (Fo2 + 2Fc2)/3 |
3634 reflections | (Δ/σ)max = 0.003 |
199 parameters | Δρmax = 0.23 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
C15H13ClN2O3S | V = 1521.3 (6) Å3 |
Mr = 336.78 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 12.173 (3) Å | µ = 0.40 mm−1 |
b = 14.036 (3) Å | T = 293 K |
c = 8.949 (2) Å | 0.5 × 0.4 × 0.3 mm |
β = 95.77 (2)° |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.014 |
3964 measured reflections | 3 standard reflections every 120 min |
3634 independent reflections | intensity decay: 1% |
3214 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.057 | 0 restraints |
wR(F2) = 0.133 | H-atom parameters constrained |
S = 1.19 | Δρmax = 0.23 e Å−3 |
3634 reflections | Δρmin = −0.27 e Å−3 |
199 parameters |
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. |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.78957 (6) | 0.45343 (4) | 0.18441 (6) | 0.04124 (17) | |
Cl1 | 0.89540 (9) | 0.73749 (6) | 0.67132 (11) | 0.0776 (3) | |
O3 | 0.81132 (18) | 0.55252 (13) | 0.1756 (2) | 0.0524 (5) | |
O1 | 0.80048 (19) | 0.25911 (13) | 0.3298 (2) | 0.0545 (5) | |
N2 | 0.85398 (19) | 0.32965 (15) | 0.5597 (2) | 0.0426 (5) | |
H2 | 0.8602 | 0.2802 | 0.6166 | 0.051* | |
N1 | 0.83211 (18) | 0.42285 (14) | 0.3607 (2) | 0.0371 (4) | |
O2 | 0.83888 (19) | 0.38810 (15) | 0.0896 (2) | 0.0567 (5) | |
C2 | 0.8705 (2) | 0.42257 (18) | 0.6105 (3) | 0.0387 (5) | |
C8 | 0.6470 (2) | 0.4341 (2) | 0.1704 (3) | 0.0508 (6) | |
C7 | 0.85543 (19) | 0.48366 (17) | 0.4866 (2) | 0.0351 (5) | |
C1 | 0.8269 (2) | 0.32671 (17) | 0.4093 (3) | 0.0417 (5) | |
C4 | 0.9024 (2) | 0.5555 (2) | 0.7717 (3) | 0.0519 (7) | |
H4 | 0.9177 | 0.5817 | 0.8670 | 0.062* | |
C6 | 0.8637 (2) | 0.58080 (18) | 0.5011 (3) | 0.0425 (5) | |
H6 | 0.8547 | 0.6215 | 0.4188 | 0.051* | |
C3 | 0.8955 (2) | 0.4574 (2) | 0.7537 (3) | 0.0464 (6) | |
H3 | 0.9074 | 0.4166 | 0.8356 | 0.056* | |
C5 | 0.8864 (2) | 0.61419 (19) | 0.6469 (3) | 0.0491 (6) | |
C13 | 0.6006 (3) | 0.3614 (3) | 0.0822 (4) | 0.0734 (10) | |
H13 | 0.6452 | 0.3204 | 0.0334 | 0.088* | |
C9 | 0.5842 (3) | 0.4951 (3) | 0.2471 (4) | 0.0671 (9) | |
H9 | 0.6174 | 0.5437 | 0.3060 | 0.081* | |
C11 | 0.4255 (4) | 0.4091 (4) | 0.1443 (5) | 0.0941 (15) | |
H11 | 0.3495 | 0.3998 | 0.1362 | 0.113* | |
C10 | 0.4705 (3) | 0.4829 (4) | 0.2352 (5) | 0.0858 (12) | |
C12 | 0.4884 (4) | 0.3499 (3) | 0.0666 (6) | 0.0954 (15) | |
C15 | 0.4332 (5) | 0.2721 (4) | −0.0324 (8) | 0.152 (2) | |
H15A | 0.3928 | 0.2305 | 0.0274 | 0.229* | |
H15B | 0.4884 | 0.2362 | −0.0772 | 0.229* | |
H15C | 0.3835 | 0.3005 | −0.1099 | 0.229* | |
C14 | 0.4004 (4) | 0.5506 (5) | 0.3165 (7) | 0.1339 (17) | |
H14A | 0.4464 | 0.5843 | 0.3924 | 0.201* | |
H14B | 0.3454 | 0.5152 | 0.3626 | 0.201* | |
H14C | 0.3650 | 0.5953 | 0.2462 | 0.201* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0549 (4) | 0.0401 (3) | 0.0290 (3) | 0.0002 (3) | 0.0055 (2) | 0.0037 (2) |
Cl1 | 0.1068 (7) | 0.0451 (4) | 0.0801 (6) | −0.0057 (4) | 0.0058 (5) | −0.0229 (4) |
O3 | 0.0702 (13) | 0.0436 (10) | 0.0431 (10) | −0.0050 (9) | 0.0043 (9) | 0.0112 (8) |
O1 | 0.0876 (15) | 0.0359 (9) | 0.0394 (10) | −0.0034 (9) | 0.0039 (9) | −0.0019 (8) |
N2 | 0.0592 (13) | 0.0362 (10) | 0.0325 (10) | 0.0004 (9) | 0.0044 (9) | 0.0061 (8) |
N1 | 0.0522 (12) | 0.0326 (9) | 0.0266 (9) | 0.0025 (8) | 0.0046 (8) | 0.0029 (7) |
O2 | 0.0803 (14) | 0.0593 (12) | 0.0319 (9) | 0.0065 (11) | 0.0119 (9) | −0.0046 (8) |
C2 | 0.0415 (12) | 0.0424 (13) | 0.0326 (11) | −0.0008 (10) | 0.0060 (9) | 0.0002 (9) |
C8 | 0.0551 (16) | 0.0537 (16) | 0.0421 (14) | −0.0006 (13) | −0.0025 (12) | 0.0088 (12) |
C7 | 0.0357 (11) | 0.0383 (12) | 0.0316 (11) | 0.0015 (9) | 0.0055 (8) | −0.0022 (9) |
C1 | 0.0570 (15) | 0.0357 (12) | 0.0327 (11) | 0.0021 (11) | 0.0068 (10) | 0.0021 (9) |
C4 | 0.0551 (16) | 0.0606 (17) | 0.0398 (13) | −0.0041 (13) | 0.0039 (11) | −0.0130 (12) |
C6 | 0.0491 (14) | 0.0375 (12) | 0.0410 (13) | 0.0005 (11) | 0.0051 (10) | −0.0003 (10) |
C3 | 0.0521 (15) | 0.0540 (15) | 0.0332 (12) | −0.0012 (12) | 0.0040 (10) | 0.0017 (11) |
C5 | 0.0524 (15) | 0.0400 (13) | 0.0557 (16) | −0.0051 (11) | 0.0096 (12) | −0.0138 (12) |
C13 | 0.076 (2) | 0.0580 (19) | 0.080 (2) | −0.0021 (17) | −0.0227 (19) | 0.0045 (17) |
C9 | 0.0559 (18) | 0.089 (3) | 0.0559 (18) | −0.0019 (17) | 0.0029 (14) | −0.0021 (17) |
C11 | 0.060 (2) | 0.121 (4) | 0.096 (3) | −0.021 (2) | −0.016 (2) | 0.039 (3) |
C10 | 0.063 (2) | 0.123 (4) | 0.072 (2) | 0.008 (2) | 0.0080 (19) | 0.015 (2) |
C12 | 0.081 (3) | 0.079 (3) | 0.117 (4) | −0.011 (2) | −0.033 (3) | 0.016 (3) |
C15 | 0.138 (5) | 0.115 (4) | 0.186 | −0.035 (4) | −0.075 (4) | −0.004 (4) |
C14 | 0.080 (3) | 0.185 | 0.140 (5) | 0.021 (4) | 0.027 (3) | −0.019 (5) |
S1—O3 | 1.419 (2) | C6—C5 | 1.388 (4) |
S1—O2 | 1.423 (2) | C6—H6 | 0.9300 |
S1—N1 | 1.6667 (19) | C3—H3 | 0.9300 |
S1—C8 | 1.749 (3) | C13—C12 | 1.368 (6) |
Cl1—C5 | 1.746 (3) | C13—H13 | 0.9300 |
O1—C1 | 1.210 (3) | C9—C10 | 1.388 (5) |
N2—C1 | 1.354 (3) | C9—H9 | 0.9300 |
N2—C2 | 1.389 (3) | C11—C12 | 1.367 (7) |
N2—H2 | 0.8600 | C11—C10 | 1.395 (7) |
N1—C7 | 1.419 (3) | C11—H11 | 0.9300 |
N1—C1 | 1.421 (3) | C10—C14 | 1.512 (7) |
C2—C3 | 1.376 (3) | C12—C15 | 1.520 (7) |
C2—C7 | 1.399 (3) | C15—H15A | 0.9600 |
C8—C13 | 1.375 (4) | C15—H15B | 0.9600 |
C8—C9 | 1.376 (5) | C15—H15C | 0.9600 |
C7—C6 | 1.372 (3) | C14—H14A | 0.9600 |
C4—C5 | 1.385 (4) | C14—H14B | 0.9600 |
C4—C3 | 1.389 (4) | C14—H14C | 0.9600 |
C4—H4 | 0.9300 | ||
O3—S1—O2 | 120.41 (13) | C4—C3—H3 | 121.1 |
O3—S1—N1 | 105.25 (11) | C4—C5—C6 | 123.8 (3) |
O2—S1—N1 | 106.81 (11) | C4—C5—Cl1 | 119.1 (2) |
O3—S1—C8 | 109.74 (14) | C6—C5—Cl1 | 117.1 (2) |
O2—S1—C8 | 109.40 (14) | C12—C13—C8 | 119.6 (4) |
N1—S1—C8 | 103.86 (12) | C12—C13—H13 | 120.2 |
C1—N2—C2 | 111.5 (2) | C8—C13—H13 | 120.2 |
C1—N2—H2 | 124.2 | C8—C9—C10 | 119.0 (4) |
C2—N2—H2 | 124.2 | C8—C9—H9 | 120.5 |
C7—N1—C1 | 109.87 (18) | C10—C9—H9 | 120.5 |
C7—N1—S1 | 127.94 (16) | C12—C11—C10 | 122.8 (4) |
C1—N1—S1 | 120.99 (16) | C12—C11—H11 | 118.6 |
C3—C2—N2 | 130.5 (2) | C10—C11—H11 | 118.6 |
C3—C2—C7 | 121.3 (2) | C9—C10—C11 | 117.8 (4) |
N2—C2—C7 | 108.2 (2) | C9—C10—C14 | 119.5 (5) |
C13—C8—C9 | 122.0 (3) | C11—C10—C14 | 122.7 (4) |
C13—C8—S1 | 120.2 (3) | C11—C12—C13 | 118.7 (4) |
C9—C8—S1 | 117.7 (2) | C11—C12—C15 | 119.7 (5) |
C6—C7—C2 | 122.1 (2) | C13—C12—C15 | 121.5 (5) |
C6—C7—N1 | 132.8 (2) | C12—C15—H15A | 109.5 |
C2—C7—N1 | 105.1 (2) | C12—C15—H15B | 109.5 |
O1—C1—N2 | 129.2 (2) | H15A—C15—H15B | 109.5 |
O1—C1—N1 | 125.6 (2) | C12—C15—H15C | 109.5 |
N2—C1—N1 | 105.1 (2) | H15A—C15—H15C | 109.5 |
C5—C4—C3 | 119.6 (2) | H15B—C15—H15C | 109.5 |
C5—C4—H4 | 120.2 | C10—C14—H14A | 109.5 |
C3—C4—H4 | 120.2 | C10—C14—H14B | 109.5 |
C7—C6—C5 | 115.5 (2) | H14A—C14—H14B | 109.5 |
C7—C6—H6 | 122.3 | C10—C14—H14C | 109.5 |
C5—C6—H6 | 122.3 | H14A—C14—H14C | 109.5 |
C2—C3—C4 | 117.7 (2) | H14B—C14—H14C | 109.5 |
C2—C3—H3 | 121.1 |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.86 | 2.18 | 2.852 (3) | 135 (1) |
N2—H2···O2i | 0.86 | 2.39 | 3.075 (3) | 138 (1) |
Symmetry code: (i) x, −y+1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C15H13ClN2O3S |
Mr | 336.78 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 12.173 (3), 14.036 (3), 8.949 (2) |
β (°) | 95.77 (2) |
V (Å3) | 1521.3 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.40 |
Crystal size (mm) | 0.5 × 0.4 × 0.3 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3964, 3634, 3214 |
Rint | 0.014 |
(sin θ/λ)max (Å−1) | 0.661 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.057, 0.133, 1.19 |
No. of reflections | 3634 |
No. of parameters | 199 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.23, −0.27 |
Computer programs: CAD-4 Software (Enraf–Nonius, 1989), SHELXL97 (Sheldrick, 2008), XCAD4 (Harms & Wocadlo, 1995), SIR92 (Altomare et al., 1994), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.86 | 2.18 | 2.852 (3) | 134.8 (9) |
N2—H2···O2i | 0.86 | 2.39 | 3.075 (3) | 137.5 (9) |
Symmetry code: (i) x, −y+1/2, z+1/2. |
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
In the course of previous studies on new anti-HIV agents, some of us reported the synthesis and anti-HIV activity of a series of N1-benzyl-1,3-dihydro-2H-benzimidazol-2-ones, a new class of non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) (Barreca et al. 2005). More recently molecular modeling studies led to the discovery of N1-phenylsulfonyl-1,3-dihydro-2H-benzimidazol-2-ones as highly potent NNRTIs active at nanomolar concentration (Barreca et al. 2007). In this paper we report the results of the X-ray structure determination of 6-chloro-1-(3,5-dimethylphenylsulfonyl)-1,3-dihydro-2H-benzimidazol-2-one (I) the most potent derivative of the series, active against wild-type and mutant HIV-1 strains (Barreca et al., 2007). On this respect, its geometrical features defined by X-ray analysis (Fig. 1), could be an useful tool to understand the structure-activity relationship of this class of compounds. The bicyclic part of the molecule consists of an aromatic ring (C2 to C7) and an imidazol-2(3H)-one nucleus approximately planar. This bicyclic fragment makes a dihedral angle of 88 (1)° with the dimethylphenyl ring. Such geometry is in agreement with the best docked conformation previously calculated (Barreca et al., 2007) and match well with the pharmacophoric model proposed for the interactions with the macromolecule. As previously observed in other N-(phenylsulfonyl)indoles (Liu et al., 2007) and N-phenylsulfonamides, (Beddoes et al., 1986) the N atom lone pair eclipses the sulfonyl group; accordingly the corresponding torsion angle O(2)—S(1)—N(1)—C(7) is 48.4 (2)°. In the crystal packing are present two intermolecular hydrogen bonds (Fig. 2) between N2—H2 and O1I at a distance of 2.18 (2) Å, angle 134.2 (2)° and N2—H2 with O2I of 2.39 (2) Å, angle 137.9 (4)°, forming a biforcated linkage with the adjacent molecule at x; 1/2 - y; z + 1/2. The crystal structure is also stabilized by π-π stacking of the benzimidazolone moieties [3.95 (1) Å] and by short intermolecular Cl(1)···O(3)I contacts [3.122 (2) Å].