research communications
Synthesis and N-(5-acetyl-4-methylpyrimidin-2-yl)benzenesulfonamide
ofaChemistry of Natural & Microbial Products Department, National Research Center, Cairo, Egypt, bSchool of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10, 3AT, United Kingdom, and cDepartment of Chemistry, Helwan University, Cairo, Egypt
*Correspondence e-mail: rashaazzam8@gmail.com
This article is part of a collection of articles to commemorate the founding of the African Crystallographic Association and the 75th anniversary of the IUCr.
N-(5-Acetyl-4-methylpyrimidin-2-yl)benzenesulfonamide, C13H13N3O3S, was sythesized and characterized by single-crystal X-ray diffraction. In the crystal, π–π interactions between the phenyl and pyrimidine groups of neighbouring molecules form molecular chains parallel to [010]. Adjacent molecular chains are linked by N—H⋯N hydrogen-bonding interactions between the pyrimidine and amine groups of neighbouring molecules, resulting in a three-dimensional network.
Keywords: synthesis; pyrimidine sulfonamide; crystal structure; X-ray diffraction.
CCDC reference: 2245275
1. Chemical context
Sulfonamide-bearing molecules with one or several pharmacological scaffolds constitute a class of drugs with antiviral, anticancer, anti-carbonic anhydrase (CA), diuretic, cyclooxigenase 2 (COX2) inhibitory, protease inhibitory, and/or antibacterial activities (Supuran, 2003; Scozzafava et al., 2003; Casini & Scozzafava, 2002). It is noteworthy that the sulfonamide moiety is one of the significant, privileged building blocks that medicinal chemists frequently find in potent drugs (Elgemeie et al., 2019). Thus, many widely marketed drugs incorporate this moiety. Several pyrimidine and other pyrimidine analogues that could be incorporated in new designs for bioactive molecules with medicinal applications have already been considered (Azzam, 2019; Azzam & Elgemeie, 2019; Azzam et al., 2017, 2019; Mohamed-Ezzat et al., 2021, 2022; Elgemeie et al., 2015a,b, 2017). The synthesis of N-(5-acetyl-4-methylpyrimidin-2-yl)benzenesulfonamide (AMBS) was reported several decades ago (Gutsche et al., 1964). In this article, we describe an alternative novel one-pot reaction methodology for the synthesis of this compound, which was also crystallized and crystallographically investigated.
2. Structural commentary
N-(5-Acetyl-4-methylpyrimidin-2-yl)benzenesulfonamide (AMBS) crystallizes in the monoclinic system, P21/c and contains four molecules in the (Z = 4). The is shown in Fig. 1. The acetaldehyde group of the molecule is disordered with two components related by a twist of 31.3 (1)° about the Car—C bond. Apart from a slight twist of the aldehyde group associated with the disorder, the 1-(2-amino-4-methylpyrimidin-5-yl)ethan-1-one segment of the molecule is essentially planar, the sulfonamide atom S1 being located only 0.423 (1) Å away from the plane of the pyrimidine group. The molecule exhibits a C7—N1—S1—C1 torsion angle of −79.0 (2)°, while the twist between the planes of the phenyl group and the pyrimidine ring comprises a dihedral angle of 63.07 (7)°.
3. Supramolecular features
The packing of AMBS is shown in Fig. 2. In the crystal, partial π–π overlap is observed between the phenyl group of one molecule and the pyrimidine group of an adjacent one related by 21 symmetry (1 − x, − + y, − z or 1 − x, + y, − z). The dihedral angle between the planes of the rings is 9.04 (10)° with a ring centroid-to-centroid distance of 3.769 (1) Å (Fig. 3). The slippage distances between the overlapping rings are 1.44 Å (1 − x, − + y, − z) and 1.58 Å (1 − x, + y, − z). These π–π interactions form chains in the structure in which one AMBS molecule comprises the linker between two further molecules. The bent nature of the molecule results in a zigzag pattern of chains propagating parallel to [010].
The hydrogen-bonding interactions in the crystal are summarized in Table 1. Two linear N—H⋯N hydrogen bonds, with N⋯N distances of 2.891 (2) Å, occur between two neighbouring molecules related by inversion symmetry (1 − x, 1 − y, 1 − z). A pair of hydrogen bonds is formed between the pyrimidine and amine groups of the two molecules, resulting in a R22(8) geometry (Fig. 2). The hydrogen bonds link the molecular chains formed by the π–π interactions and are perpendicular to the chains' protrusion. Additionally, non-classical hydrogen-bonding contacts of the C—H⋯O type with C⋯O distances in the range of ca 2.7–3.4 Å help to consolidate the structure.
4. Database survey
A survey of the Cambridge Structural Database (Groom et al., 2016; accessed February 2023) using CONQUEST (Bruno et al., 2002) for structures containing the N-(pyrimidin-2-yl)benzenesulfonamide group gave 164 hits, i.e. too many for them all to be analysed in detail.
An example of a closely related compound is 4,5,6-trimethyl-2-[(phenylsulfonyl)amino]pyrimidine (TPAP) (refcode VENKIJ; Li & Yang, 2006). In this structure, the dihedral angle between the planes through the phenyl and pyrimidine rings is 91.9°, larger than that observed for the title compound AMBS [63.07 (7)°]. In contrast to AMBS, π–π interactions are only observed between the pyrimidine rings in TPAP, resulting in stacking along the a-axis with interplanar distances of 3.81 Å.
Another closely related compound is N-(pyrimidin-2-yl)benzenesulfonamide (PBS) (refcode XIFKAZ01; Coles et al., 2000). In PBS, the dihedral angle between the planes through the phenyl and pyrimidine rings is 74.5°, again larger than for AMBS. Also unlike in AMBS, π–π interactions occur in PBS between pairs of molecules involving only the pyrimidine rings and with an interplanar distance of 3.5 Å. Similarly to AMBS, two linear N—H⋯N hydrogen bonds are observed in PBS between the pyrimidine and amine groups of neighbouring molecules, resulting in similar R22(8) motifs.
5. Synthesis and crystallization
Phenylsulfonyl guanidine 1 is a common starting material for the synthesis of several and has been utilized effectively in the generation of a range of biologically active compounds. Our approach was based on synthesizing the substituted sulfonyl derivative 4 by reacting the sulfonyl guanidine 1 with triethylorthoformate 2 and acetyl acetone 3 (Fig. 4). The target product was identified by NMR spectroscopy and X-ray crystallography.
Synthesis of compound 4: Triethylorthoformate (5 ml) was added to a mixture of phenylsulfonyl guanidine (0.05 mol) and acetyl acetone (0.1 mol). The reaction mixture was then refluxed for 6 h. After cooling, the resulting precipitate was filtered and crystallized from ethanol.
Orange crystals; yield 45%; m.p. 469 K. 1H NMR (400 MHz, DMSO-d6): δ 2.49 (s, 3H, CH3), 2.52 (s, 3H, CH3), 7.57–7.66 (m, 3H, Ar-H), 8.00–8.02 (m, 2H, Ar-H), 8.93 (s, 1H, CH-pyrimidine), 12.34 (s, 1H, NH). Analysis calculated for C13H13N3O3S (291.33): C, 53.60; H, 4.50; N, 14.42; S, 11.01. Found: C, 53.60; H, 4.49; N, 14.41; S, 11.00.
6. Refinement
Crystal data, data collection and structure . The N—H hydrogen was refined freely. The remaining hydrogen atoms were positioned geometrically and using a riding model [C—H = 0.93–0.96 Å with Uiso(H) = 1.2 or 1.5 Ueq(C). The acetaldehyde group of the molecule is disordered with two components related by a twist of 31.3 (1)° about the Car—C bond. In the the two components were restrained to have similar geometry (SAME in SHELXL) and atomic displacement parameters (SIMU and ISOR). The occupancies of the two components refined to 0.591 (11)/0.409 (11).
details are summarized in Table 2Supporting information
CCDC reference: 2245275
https://doi.org/10.1107/S2056989023001871/yz2029sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989023001871/yz2029Isup3.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989023001871/yz2029Isup3.cml
Data collection: CrysAlis PRO 1.171.42.54a (Rigaku OD, 2022); cell
CrysAlis PRO 1.171.42.54a (Rigaku OD, 2022); data reduction: CrysAlis PRO 1.171.42.54a (Rigaku OD, 2022); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/1 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020), ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: Mercury (Macrae et al., 2020).C13H13N3O3S | F(000) = 608 |
Mr = 291.32 | Dx = 1.355 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 10.0699 (6) Å | Cell parameters from 5035 reflections |
b = 14.7429 (6) Å | θ = 3.9–27.7° |
c = 10.5212 (7) Å | µ = 0.24 mm−1 |
β = 113.900 (7)° | T = 293 K |
V = 1428.04 (16) Å3 | Block, orange |
Z = 4 | 0.44 × 0.24 × 0.16 mm |
Rigaku SuperNova, Dual, Cu at home/near, Atlas diffractometer | 2548 reflections with I > 2σ(I) |
ω scans | Rint = 0.026 |
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2022) | θmax = 29.5°, θmin = 3.5° |
Tmin = 0.484, Tmax = 1.000 | h = −13→10 |
12642 measured reflections | k = −18→18 |
3532 independent reflections | l = −13→14 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.046 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.125 | w = 1/[σ2(Fo2) + (0.0493P)2 + 0.420P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.001 |
3532 reflections | Δρmax = 0.23 e Å−3 |
216 parameters | Δρmin = −0.29 e Å−3 |
84 restraints |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
C1 | 0.5229 (2) | 0.75192 (12) | 0.26887 (19) | 0.0461 (4) | |
C2 | 0.6205 (2) | 0.76291 (14) | 0.2086 (2) | 0.0552 (5) | |
H2 | 0.630570 | 0.718727 | 0.150041 | 0.066* | |
C3 | 0.7033 (2) | 0.84155 (15) | 0.2374 (3) | 0.0651 (6) | |
H3 | 0.768869 | 0.850929 | 0.196825 | 0.078* | |
C4 | 0.6886 (3) | 0.90550 (15) | 0.3257 (3) | 0.0712 (7) | |
H4 | 0.746248 | 0.957279 | 0.346473 | 0.085* | |
C5 | 0.5901 (3) | 0.89393 (15) | 0.3833 (2) | 0.0696 (6) | |
H5 | 0.579890 | 0.938259 | 0.441639 | 0.083* | |
C6 | 0.5065 (3) | 0.81732 (14) | 0.3555 (2) | 0.0580 (5) | |
H6 | 0.439261 | 0.809307 | 0.394462 | 0.070* | |
C7 | 0.6186 (2) | 0.52796 (12) | 0.37144 (19) | 0.0463 (4) | |
C8 | 0.8002 (2) | 0.49089 (16) | 0.3045 (2) | 0.0579 (5) | |
C10 | 0.7564 (2) | 0.40722 (14) | 0.4752 (2) | 0.0568 (5) | |
H10 | 0.780068 | 0.359996 | 0.539203 | 0.068* | |
C11 | 0.8767 (3) | 0.5141 (2) | 0.2123 (3) | 0.0835 (8) | |
H11A | 0.853870 | 0.469409 | 0.140165 | 0.125* | |
H11B | 0.979663 | 0.514976 | 0.266457 | 0.125* | |
H11C | 0.845364 | 0.572710 | 0.171410 | 0.125* | |
N1 | 0.50291 (19) | 0.58192 (11) | 0.35938 (18) | 0.0508 (4) | |
N2 | 0.69070 (18) | 0.54638 (11) | 0.29291 (17) | 0.0537 (4) | |
N3 | 0.64728 (17) | 0.46152 (10) | 0.46533 (16) | 0.0496 (4) | |
O1 | 0.28821 (16) | 0.67414 (10) | 0.25840 (16) | 0.0653 (4) | |
O2 | 0.39885 (17) | 0.61859 (10) | 0.10316 (14) | 0.0621 (4) | |
S1 | 0.41467 (5) | 0.65419 (3) | 0.23421 (5) | 0.04929 (17) | |
C9 | 0.8367 (2) | 0.41647 (16) | 0.3968 (2) | 0.0600 (5) | 0.591 (11) |
C12 | 0.9420 (7) | 0.3432 (4) | 0.3990 (8) | 0.0750 (19) | 0.591 (11) |
C13 | 0.9860 (17) | 0.2756 (10) | 0.5150 (18) | 0.098 (4) | 0.591 (11) |
H13A | 1.053800 | 0.233375 | 0.505298 | 0.148* | 0.591 (11) |
H13B | 0.901665 | 0.243536 | 0.511702 | 0.148* | 0.591 (11) |
H13C | 1.030623 | 0.306600 | 0.602434 | 0.148* | 0.591 (11) |
O3 | 0.9931 (8) | 0.3397 (4) | 0.3128 (8) | 0.110 (2) | 0.591 (11) |
C9A | 0.8367 (2) | 0.41647 (16) | 0.3968 (2) | 0.0600 (5) | 0.409 (11) |
C12A | 0.9727 (9) | 0.3620 (7) | 0.4306 (12) | 0.079 (3) | 0.409 (11) |
C13A | 0.990 (2) | 0.2750 (12) | 0.509 (3) | 0.089 (4) | 0.409 (11) |
H13D | 1.082486 | 0.248722 | 0.525215 | 0.133* | 0.409 (11) |
H13E | 0.913988 | 0.233796 | 0.454891 | 0.133* | 0.409 (11) |
H13F | 0.983594 | 0.286757 | 0.595831 | 0.133* | 0.409 (11) |
O3A | 1.0616 (8) | 0.3857 (7) | 0.3876 (10) | 0.106 (3) | 0.409 (11) |
H1 | 0.458 (2) | 0.5700 (14) | 0.409 (2) | 0.054 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0557 (11) | 0.0456 (9) | 0.0403 (10) | 0.0056 (8) | 0.0228 (9) | 0.0082 (7) |
C2 | 0.0619 (13) | 0.0559 (11) | 0.0551 (12) | 0.0062 (9) | 0.0311 (10) | 0.0070 (9) |
C3 | 0.0567 (13) | 0.0676 (14) | 0.0760 (16) | 0.0015 (10) | 0.0320 (12) | 0.0183 (11) |
C4 | 0.0695 (15) | 0.0511 (12) | 0.0789 (17) | −0.0026 (10) | 0.0157 (13) | 0.0080 (11) |
C5 | 0.0897 (18) | 0.0535 (12) | 0.0634 (14) | 0.0051 (11) | 0.0287 (13) | −0.0043 (10) |
C6 | 0.0754 (15) | 0.0552 (11) | 0.0510 (12) | 0.0089 (10) | 0.0335 (11) | 0.0040 (9) |
C7 | 0.0469 (11) | 0.0518 (10) | 0.0433 (10) | 0.0003 (8) | 0.0215 (9) | 0.0043 (7) |
C8 | 0.0491 (12) | 0.0804 (14) | 0.0498 (12) | −0.0014 (10) | 0.0258 (10) | 0.0012 (10) |
C10 | 0.0515 (12) | 0.0632 (12) | 0.0570 (12) | 0.0109 (9) | 0.0233 (10) | 0.0133 (9) |
C11 | 0.0691 (16) | 0.125 (2) | 0.0738 (17) | 0.0090 (15) | 0.0472 (14) | 0.0168 (15) |
N1 | 0.0595 (10) | 0.0514 (9) | 0.0521 (10) | 0.0093 (7) | 0.0336 (8) | 0.0141 (7) |
N2 | 0.0550 (10) | 0.0635 (10) | 0.0499 (10) | −0.0001 (8) | 0.0289 (8) | 0.0072 (7) |
N3 | 0.0506 (9) | 0.0558 (9) | 0.0481 (9) | 0.0081 (7) | 0.0259 (8) | 0.0112 (7) |
O1 | 0.0542 (9) | 0.0753 (9) | 0.0733 (10) | 0.0134 (7) | 0.0331 (8) | 0.0233 (8) |
O2 | 0.0792 (11) | 0.0595 (8) | 0.0457 (8) | −0.0060 (7) | 0.0234 (7) | 0.0020 (6) |
S1 | 0.0546 (3) | 0.0506 (3) | 0.0465 (3) | 0.0042 (2) | 0.0244 (2) | 0.00978 (19) |
C9 | 0.0466 (11) | 0.0798 (14) | 0.0577 (13) | 0.0102 (10) | 0.0254 (10) | 0.0069 (10) |
C12 | 0.045 (2) | 0.101 (3) | 0.084 (4) | 0.011 (2) | 0.030 (3) | 0.006 (3) |
C13 | 0.081 (6) | 0.098 (5) | 0.094 (6) | 0.048 (5) | 0.012 (5) | 0.016 (5) |
O3 | 0.096 (4) | 0.128 (4) | 0.144 (5) | 0.037 (3) | 0.087 (4) | 0.017 (3) |
C9A | 0.0466 (11) | 0.0798 (14) | 0.0577 (13) | 0.0102 (10) | 0.0254 (10) | 0.0069 (10) |
C12A | 0.054 (4) | 0.105 (4) | 0.077 (4) | 0.025 (4) | 0.025 (4) | 0.001 (4) |
C13A | 0.072 (7) | 0.107 (8) | 0.086 (7) | 0.025 (7) | 0.032 (6) | −0.007 (7) |
O3A | 0.070 (4) | 0.144 (6) | 0.127 (6) | 0.026 (4) | 0.062 (4) | 0.009 (4) |
C1—C2 | 1.378 (3) | C10—C9 | 1.376 (3) |
C1—C6 | 1.382 (3) | C10—H10 | 0.9300 |
C1—S1 | 1.7538 (19) | C11—H11A | 0.9600 |
C2—C3 | 1.388 (3) | C11—H11B | 0.9600 |
C2—H2 | 0.9300 | C11—H11C | 0.9600 |
C3—C4 | 1.373 (3) | N1—S1 | 1.6465 (16) |
C3—H3 | 0.9300 | N1—H1 | 0.83 (2) |
C4—C5 | 1.367 (3) | O1—S1 | 1.4267 (15) |
C4—H4 | 0.9300 | O2—S1 | 1.4226 (15) |
C5—C6 | 1.368 (3) | C9—C12 | 1.507 (4) |
C5—H5 | 0.9300 | C12—O3 | 1.211 (5) |
C6—H6 | 0.9300 | C12—C13 | 1.497 (6) |
C7—N2 | 1.330 (2) | C13—H13A | 0.9600 |
C7—N3 | 1.337 (2) | C13—H13B | 0.9600 |
C7—N1 | 1.374 (2) | C13—H13C | 0.9600 |
C8—N2 | 1.338 (3) | C9A—C12A | 1.501 (5) |
C8—C9A | 1.412 (3) | C12A—O3A | 1.207 (5) |
C8—C9 | 1.412 (3) | C12A—C13A | 1.495 (6) |
C8—C11 | 1.502 (3) | C13A—H13D | 0.9600 |
C10—N3 | 1.329 (2) | C13A—H13E | 0.9600 |
C10—C9A | 1.376 (3) | C13A—H13F | 0.9600 |
C2—C1—C6 | 121.33 (19) | C7—N1—S1 | 127.69 (14) |
C2—C1—S1 | 120.01 (15) | C7—N1—H1 | 118.2 (14) |
C6—C1—S1 | 118.66 (15) | S1—N1—H1 | 112.6 (15) |
C1—C2—C3 | 118.4 (2) | C7—N2—C8 | 117.10 (17) |
C1—C2—H2 | 120.8 | C10—N3—C7 | 115.02 (17) |
C3—C2—H2 | 120.8 | O2—S1—O1 | 119.43 (10) |
C4—C3—C2 | 120.1 (2) | O2—S1—N1 | 110.41 (9) |
C4—C3—H3 | 120.0 | O1—S1—N1 | 102.84 (9) |
C2—C3—H3 | 120.0 | O2—S1—C1 | 108.71 (9) |
C5—C4—C3 | 120.8 (2) | O1—S1—C1 | 108.55 (9) |
C5—C4—H4 | 119.6 | N1—S1—C1 | 106.06 (9) |
C3—C4—H4 | 119.6 | C10—C9—C8 | 115.92 (19) |
C4—C5—C6 | 120.2 (2) | C10—C9—C12 | 120.0 (3) |
C4—C5—H5 | 119.9 | C8—C9—C12 | 123.6 (3) |
C6—C5—H5 | 119.9 | O3—C12—C13 | 120.4 (5) |
C5—C6—C1 | 119.3 (2) | O3—C12—C9 | 121.9 (4) |
C5—C6—H6 | 120.3 | C13—C12—C9 | 117.6 (5) |
C1—C6—H6 | 120.3 | C12—C13—H13A | 109.5 |
N2—C7—N3 | 126.86 (17) | C12—C13—H13B | 109.5 |
N2—C7—N1 | 118.71 (17) | H13A—C13—H13B | 109.5 |
N3—C7—N1 | 114.43 (16) | C12—C13—H13C | 109.5 |
N2—C8—C9A | 120.86 (18) | H13A—C13—H13C | 109.5 |
N2—C8—C9 | 120.86 (18) | H13B—C13—H13C | 109.5 |
N2—C8—C11 | 114.9 (2) | C10—C9A—C8 | 115.92 (19) |
C9A—C8—C11 | 124.2 (2) | C10—C9A—C12A | 120.4 (3) |
C9—C8—C11 | 124.2 (2) | C8—C9A—C12A | 122.5 (3) |
N3—C10—C9A | 124.15 (19) | O3A—C12A—C13A | 121.1 (5) |
N3—C10—C9 | 124.15 (19) | O3A—C12A—C9A | 120.1 (5) |
N3—C10—H10 | 117.9 | C13A—C12A—C9A | 118.6 (6) |
C9—C10—H10 | 117.9 | C12A—C13A—H13D | 109.5 |
C8—C11—H11A | 109.5 | C12A—C13A—H13E | 109.5 |
C8—C11—H11B | 109.5 | H13D—C13A—H13E | 109.5 |
H11A—C11—H11B | 109.5 | C12A—C13A—H13F | 109.5 |
C8—C11—H11C | 109.5 | H13D—C13A—H13F | 109.5 |
H11A—C11—H11C | 109.5 | H13E—C13A—H13F | 109.5 |
H11B—C11—H11C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···N3i | 0.83 (2) | 2.06 (2) | 2.891 (2) | 179 (2) |
C6—H6···O2ii | 0.93 | 2.62 | 3.338 (3) | 135 |
C10—H10···O1i | 0.93 | 2.54 | 3.243 (3) | 133 |
C11—H11B···O3A | 0.96 | 2.26 | 2.769 (7) | 113 |
C13A—H13E···O1iii | 0.96 | 2.50 | 3.40 (3) | 156 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2; (iii) −x+1, y−1/2, −z+1/2. |
Funding information
We thank Helwan University for funding this research.
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