organic compounds
5-[Bis(cyclopropanecarbonyl)amino]-4,6-dichloropyrimidine containing a short cyclopropyl C—H⋯O interaction
aDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
*Correspondence e-mail: w.harrison@abdn.ac.uk
The title compound, C12H11Cl2N3O2, possesses normal intramolecular geometrical parameters. The crystal packing is influenced by C—H⋯O and possible weak π–π stacking interactions.
Comment
A great deal of research has been carried out on pyrimidine systems, fuelled by their important biological applications and properties (Brown, 1994). Various dihaloaminopyridines and dihaloaminopyrimidines have proven to be useful in terms of their antiviral activity, particularly for their action towards the Herpes virus (Giovanninetti et al., 1980). As part of our general investigations in this area, the title compound, (I), C12H11Cl2N3O2, has been synthesized, albeit in moderate yield. Similarly low yields have also been observed by Giovanninetti et al. (1980) in acylation reactions of dichloroaminopyrimidines.
Compound (I) possesses normal intramolecular geometrical parameters (Table 1). The 4,6-dichloropyrimidine moiety (C1–C4/N1/N2/Cl1/Cl2) is close to being planar; for the non-H atoms, the r.m.s. deviation from the least-squares plane is 0.031 Å. Atom N3 is significantly displaced from the mean plane by 0.204 (3) Å. The dihedral angle between the aromatic ring and the C5/N3/C9 group is 74.81 (10)°. The major conformational difference in the cyclopropanecarbonyl `arms' of (I) concerns the amide carbonyl (C5=O1 and C9=O2) groups. The first of these is close to being eclipsed with respect to the N3—C3 bond, whereas the second is almost anti with respect to the same pair of atoms (Table 1). The cyclopropyl rings [mean C—C = 1.504 (3) Å; mean C—C—C = 60.0 (2)°] are unexceptional.
As well as ) appears to be influenced by C—H⋯O interactions (Table 2). The first of these bonds involves the atoms C1—H1⋯O1ii (see Table 2 for symmetry code), i.e. the aromatic H atom and an amide carbonyl O-atom acceptor. These bonds help stabilize the [001] stacks of (I) and are generated by c-glide symmetry. The second, with a near-linear C7—H4⋯O2i bond angle of 173° and a very short H⋯O separation of 2.35 Å, involves a cyclopropyl H atom and the other amide carbonyl O atom as the acceptor species, the acceptor generated by inversion symmetry (Fig. 2), which results in dimers of (I). Allen et al. (1996) have shown that C—H⋯O hydrogen bonds from cyclopropyl methylene groups are enhanced because strain inherent in the C3 ring tends to increase the acidity of the CH moieties involved, although the example here appears to be a particularly strong bond.
the crystal packing in (IThere may be π–π stacking effects involving the pyrimidine rings (C1–C4/N1/N2, with centroid Cg) in (I). The Cg⋯Cgiii [symmetry code: (iii) x, − y, + z; i.e. the c-glide] separation is 3.7160 (12) Å, but the centroids are laterally displaced by the large value of 1.87 Å, suggesting that this is a very weak interaction.
In combination, these effects result (Fig. 3) in stacks of molecules of (I) propagating along [001]. The stacks are crosslinked along [010] by the proposed C7—H4⋯O2i (Table 2) bonds, whereas along [100] only van der Waals interactions hold the adjacent stacks together. In this direction, the N1⋯Cl2iv [symmetry code (iv) x − 1, y, z] contact of 3.252 (2) Å is slightly less than the van der Waals radius sum of 3.30 Å for these species (Spek, 2003).
Experimental
To prepare (I), 4,6-dichloro-5-aminopyrimidine (0.412 g, 2.512 mmol) was placed in a twin-necked flask and was stirred in dry dichloromethane (35 ml) under a nitrogen atmosphere. The reaction mixture was cooled to 273 K, whereupon Hünig's base (7.54 mmol, 1.30 ml) was added, and the reaction was stirred for approximately 10 min. Cyclopropane carbonyl chloride (7.54 mmol, 0.68 ml) was then added, and the reaction was warmed to room temperature and stirred for 24 h. The progress of the reaction was monitored using (TLC, solvent dichloromethane), showing the product with an RF of 0.19 The reaction mixture was then washed with saturated brine (3 × 20 ml) and dried with magnesium sulfate, and the solvent was removed at reduced pressure. The resultant organic liquor was purified using flash (solvent 3:0.1 chloroform/methanol). Overlap of the starting material with the product required the use of a different solvent system (2:2:0.1 dichloromethane/hexane/methanol) to further purify the product (RF = 0.17). Vapour diffusion crystallization was used to obtain white crystals of (I); dichloromethane was used as the solvent and hexane was used as the precipitant. The yield obtained was 0.063 g (8.4%). M.p. 406–409 K. FT–IR (KBr, cm−1): νmax 3062 (w, CH, cyclopropane), 1697, 1713 (C=O, carbonyl), 1517, 1413 (s, C=N, conjugated, cyclic, pyrimidine), 1541 (m, C—N, tertiary amine), 1174 (s, pyrimidine-NR2), 813 (s, pyrimidine-Cl); 1H (400 MHz; CDCl3): δ 0.96 (4H, ddd), 1.20 (4H, ddd), 2.01 (2H, tt), 8.76 (1H, s); 13C (100 MHz, CDCl3): δ 11.2, 15.7, 131.4, 157.3, 161.9, 174.1. Elemental analysis data were consistent with the crystallographic results: found: C 47.93, H 3.58, N 13.75, Cl 22.78%; calculated for C12H11Cl2N3O2: C 48.02, H 3.69, N 14.00, Cl 23.62%.
Crystal data
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Refinement
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All H atoms were placed in calculated positions (C—H = 0.95–1.00 Å) and refined as riding on their carrier atoms, with Uiso(H) = 1.2Ueq(carrier atom).
Data collection: COLLECT (Nonius, 1998); cell HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO (Otwinowski & Minor, 1997) and SCALEPACK, and SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
Supporting information
https://doi.org/10.1107/S1600536804012577/hg6054sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804012577/hg6054Isup2.hkl
Data collection: Collect (Nonius BV, 1998); cell
HKL SCALEPACK (Otwinowski & Minor 1997); data reduction: HKL DENZO (Otwinowski & Minor, 1997) and SCALEPACK, and SORTAV (Blessing 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.C12H11Cl2N3O2 | F(000) = 616 |
Mr = 300.14 | Dx = 1.548 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 14708 reflections |
a = 7.6677 (3) Å | θ = 2.9–27.5° |
b = 26.7366 (12) Å | µ = 0.51 mm−1 |
c = 6.6477 (3) Å | T = 120 K |
β = 109.065 (2)° | Rod, colourless |
V = 1288.08 (10) Å3 | 0.50 × 0.10 × 0.10 mm |
Z = 4 |
Enraf–Nonius KappaCCD diffractometer | 2937 independent reflections |
Radiation source: fine-focus sealed tube | 1960 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.077 |
ω and φ scans | θmax = 27.5°, θmin = 3.1° |
Absorption correction: multi-scan (SORTAV; Blessing, 1995) | h = −9→9 |
Tmin = 0.787, Tmax = 0.951 | k = −34→34 |
13247 measured reflections | l = −8→8 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.043 | H-atom parameters constrained |
wR(F2) = 0.104 | w = 1/[σ2(Fo2) + (0.0514P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.98 | (Δ/σ)max = 0.001 |
2937 reflections | Δρmax = 0.30 e Å−3 |
172 parameters | Δρmin = −0.35 e Å−3 |
0 restraints |
Experimental. Melting points were determined using a Kofler hot-stage apparatus and are uncorrected. Infrared spectra were recorded using a Nicolet Avatar 320 F T–IR spectrometer, using KBr discs. NMR spectra were determined using a Varian Unity Inova spectrometer (400 MHz, 1H and 100 MHz, 13C) using deuterated (2H)-chloroform as solvent, with the presence of residual CHCl3, as the reference at 7.26 p.p.m., with J values in Hz). Flash chromatography was carried out using silica gel (230–400 mesh), TLC was performed on plates cut from 20x20 cm aluminium sheets, coated with Merck Kieselgel 60 silica with F254 indicator. Dry dichloromethane was distilled under argon, from calcium hydride prior to use. All glassware was pre-dried in the oven before use and cooled in an argon atmosphere. |
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 | ||
C1 | 0.5414 (3) | 0.76193 (9) | 0.1288 (3) | 0.0203 (5) | |
H1 | 0.4834 | 0.7937 | 0.1158 | 0.024* | |
C2 | 0.7893 (3) | 0.71636 (9) | 0.1331 (3) | 0.0179 (5) | |
C3 | 0.6997 (3) | 0.67255 (8) | 0.1500 (3) | 0.0174 (5) | |
C4 | 0.5243 (3) | 0.67875 (9) | 0.1631 (3) | 0.0188 (5) | |
C5 | 0.6995 (3) | 0.59998 (9) | −0.0595 (4) | 0.0214 (5) | |
C6 | 0.7272 (4) | 0.54607 (9) | −0.0764 (4) | 0.0304 (6) | |
H2 | 0.8099 | 0.5282 | 0.0513 | 0.037* | |
C7 | 0.7186 (4) | 0.52743 (11) | −0.2948 (5) | 0.0357 (7) | |
H3 | 0.7035 | 0.5526 | −0.4083 | 0.043* | |
H4 | 0.7968 | 0.4984 | −0.3017 | 0.043* | |
C8 | 0.5606 (4) | 0.51833 (11) | −0.2210 (4) | 0.0374 (7) | |
H5 | 0.5399 | 0.4837 | −0.1816 | 0.045* | |
H6 | 0.4467 | 0.5379 | −0.2883 | 0.045* | |
C9 | 0.9288 (3) | 0.60715 (9) | 0.3131 (4) | 0.0227 (5) | |
C10 | 0.9574 (3) | 0.63209 (9) | 0.5189 (4) | 0.0240 (6) | |
H7 | 0.8567 | 0.6543 | 0.5322 | 0.029* | |
C11 | 1.0718 (3) | 0.60382 (11) | 0.7154 (4) | 0.0303 (6) | |
H8 | 1.0402 | 0.6082 | 0.8473 | 0.036* | |
H9 | 1.1149 | 0.5699 | 0.6949 | 0.036* | |
C12 | 1.1561 (3) | 0.64675 (10) | 0.6412 (4) | 0.0294 (6) | |
H10 | 1.2513 | 0.6395 | 0.5743 | 0.035* | |
H11 | 1.1766 | 0.6778 | 0.7267 | 0.035* | |
Cl1 | 0.40433 (8) | 0.62739 (2) | 0.20502 (9) | 0.02528 (17) | |
Cl2 | 1.01125 (7) | 0.71437 (2) | 0.12343 (9) | 0.02406 (17) | |
O1 | 0.6038 (2) | 0.62476 (6) | −0.2070 (3) | 0.0257 (4) | |
O2 | 1.0293 (2) | 0.57489 (7) | 0.2855 (3) | 0.0340 (5) | |
N1 | 0.4413 (3) | 0.72255 (7) | 0.1495 (3) | 0.0203 (4) | |
N2 | 0.7137 (2) | 0.76143 (7) | 0.1244 (3) | 0.0196 (4) | |
N3 | 0.7750 (2) | 0.62417 (7) | 0.1419 (3) | 0.0187 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0216 (12) | 0.0217 (13) | 0.0163 (12) | 0.0038 (10) | 0.0043 (10) | −0.0021 (9) |
C2 | 0.0177 (11) | 0.0222 (13) | 0.0122 (11) | 0.0003 (10) | 0.0027 (9) | −0.0016 (9) |
C3 | 0.0185 (12) | 0.0173 (12) | 0.0147 (11) | 0.0038 (9) | 0.0030 (9) | −0.0024 (9) |
C4 | 0.0194 (12) | 0.0205 (13) | 0.0142 (11) | −0.0002 (10) | 0.0021 (9) | −0.0009 (9) |
C5 | 0.0195 (12) | 0.0216 (13) | 0.0242 (13) | −0.0016 (10) | 0.0085 (11) | −0.0016 (10) |
C6 | 0.0339 (14) | 0.0179 (14) | 0.0322 (14) | 0.0018 (11) | 0.0008 (12) | −0.0021 (11) |
C7 | 0.0346 (15) | 0.0275 (16) | 0.0449 (16) | 0.0030 (13) | 0.0128 (13) | −0.0144 (13) |
C8 | 0.0444 (17) | 0.0226 (15) | 0.0414 (16) | −0.0055 (12) | 0.0088 (14) | −0.0082 (12) |
C9 | 0.0195 (12) | 0.0199 (13) | 0.0272 (13) | 0.0005 (10) | 0.0056 (10) | 0.0026 (10) |
C10 | 0.0198 (12) | 0.0288 (15) | 0.0212 (12) | 0.0062 (11) | 0.0035 (10) | 0.0023 (10) |
C11 | 0.0244 (13) | 0.0388 (17) | 0.0237 (13) | 0.0016 (12) | 0.0023 (11) | 0.0069 (11) |
C12 | 0.0242 (13) | 0.0341 (16) | 0.0258 (13) | −0.0036 (12) | 0.0024 (11) | −0.0019 (11) |
Cl1 | 0.0214 (3) | 0.0248 (3) | 0.0300 (3) | −0.0029 (2) | 0.0089 (2) | 0.0013 (3) |
Cl2 | 0.0185 (3) | 0.0255 (3) | 0.0294 (3) | 0.0003 (2) | 0.0095 (2) | 0.0012 (2) |
O1 | 0.0276 (9) | 0.0220 (9) | 0.0232 (9) | 0.0040 (8) | 0.0025 (7) | −0.0026 (7) |
O2 | 0.0275 (10) | 0.0310 (11) | 0.0375 (10) | 0.0120 (8) | 0.0022 (8) | −0.0055 (8) |
N1 | 0.0183 (10) | 0.0234 (12) | 0.0180 (10) | 0.0032 (9) | 0.0043 (8) | −0.0005 (8) |
N2 | 0.0213 (10) | 0.0177 (11) | 0.0182 (10) | 0.0013 (8) | 0.0044 (8) | 0.0006 (8) |
N3 | 0.0183 (10) | 0.0139 (10) | 0.0214 (10) | 0.0022 (8) | 0.0033 (8) | −0.0013 (8) |
C1—N2 | 1.331 (3) | C7—C8 | 1.468 (4) |
C1—N1 | 1.336 (3) | C7—H3 | 0.9900 |
C1—H1 | 0.9500 | C7—H4 | 0.9900 |
C2—N2 | 1.330 (3) | C8—H5 | 0.9900 |
C2—C3 | 1.381 (3) | C8—H6 | 0.9900 |
C2—Cl2 | 1.725 (2) | C9—O2 | 1.209 (3) |
C3—C4 | 1.386 (3) | C9—N3 | 1.420 (3) |
C3—N3 | 1.425 (3) | C9—C10 | 1.473 (3) |
C4—N1 | 1.322 (3) | C10—C11 | 1.516 (3) |
C4—Cl1 | 1.725 (2) | C10—C12 | 1.526 (3) |
C5—O1 | 1.212 (3) | C10—H7 | 1.0000 |
C5—N3 | 1.428 (3) | C11—C12 | 1.479 (4) |
C5—C6 | 1.467 (3) | C11—H8 | 0.9900 |
C6—C7 | 1.516 (4) | C11—H9 | 0.9900 |
C6—C8 | 1.518 (4) | C12—H10 | 0.9900 |
C6—H2 | 1.0000 | C12—H11 | 0.9900 |
N2—C1—N1 | 127.0 (2) | C7—C8—H6 | 117.7 |
N2—C1—H1 | 116.5 | C6—C8—H6 | 117.7 |
N1—C1—H1 | 116.5 | H5—C8—H6 | 114.8 |
N2—C2—C3 | 123.4 (2) | O2—C9—N3 | 120.7 (2) |
N2—C2—Cl2 | 116.61 (17) | O2—C9—C10 | 123.7 (2) |
C3—C2—Cl2 | 119.98 (17) | N3—C9—C10 | 115.6 (2) |
C2—C3—C4 | 115.0 (2) | C9—C10—C11 | 116.3 (2) |
C2—C3—N3 | 123.3 (2) | C9—C10—C12 | 115.5 (2) |
C4—C3—N3 | 121.6 (2) | C11—C10—C12 | 58.16 (16) |
N1—C4—C3 | 123.8 (2) | C9—C10—H7 | 117.8 |
N1—C4—Cl1 | 116.51 (17) | C11—C10—H7 | 117.8 |
C3—C4—Cl1 | 119.64 (17) | C12—C10—H7 | 117.8 |
O1—C5—N3 | 117.6 (2) | C12—C11—C10 | 61.25 (16) |
O1—C5—C6 | 122.7 (2) | C12—C11—H8 | 117.6 |
N3—C5—C6 | 119.5 (2) | C10—C11—H8 | 117.6 |
C5—C6—C7 | 115.7 (2) | C12—C11—H9 | 117.6 |
C5—C6—C8 | 114.5 (2) | C10—C11—H9 | 117.6 |
C7—C6—C8 | 57.87 (17) | H8—C11—H9 | 114.7 |
C5—C6—H2 | 118.2 | C11—C12—C10 | 60.59 (16) |
C7—C6—H2 | 118.2 | C11—C12—H10 | 117.7 |
C8—C6—H2 | 118.2 | C10—C12—H10 | 117.7 |
C8—C7—C6 | 61.13 (18) | C11—C12—H11 | 117.7 |
C8—C7—H3 | 117.7 | C10—C12—H11 | 117.7 |
C6—C7—H3 | 117.7 | H10—C12—H11 | 114.8 |
C8—C7—H4 | 117.7 | C4—N1—C1 | 115.17 (19) |
C6—C7—H4 | 117.7 | C2—N2—C1 | 115.5 (2) |
H3—C7—H4 | 114.8 | C9—N3—C3 | 120.09 (18) |
C7—C8—C6 | 60.99 (18) | C9—N3—C5 | 125.63 (19) |
C7—C8—H5 | 117.7 | C3—N3—C5 | 113.66 (18) |
C6—C8—H5 | 117.7 | ||
N2—C2—C3—C4 | −1.6 (3) | C9—C10—C12—C11 | −106.3 (2) |
Cl2—C2—C3—C4 | 178.07 (15) | C3—C4—N1—C1 | −2.2 (3) |
N2—C2—C3—N3 | 174.74 (19) | Cl1—C4—N1—C1 | 176.46 (16) |
Cl2—C2—C3—N3 | −5.6 (3) | N2—C1—N1—C4 | −1.3 (3) |
C2—C3—C4—N1 | 3.5 (3) | C3—C2—N2—C1 | −1.3 (3) |
N3—C3—C4—N1 | −172.92 (19) | Cl2—C2—N2—C1 | 178.99 (16) |
C2—C3—C4—Cl1 | −175.10 (15) | N1—C1—N2—C2 | 2.9 (3) |
N3—C3—C4—Cl1 | 8.5 (3) | O2—C9—N3—C3 | −156.7 (2) |
O1—C5—C6—C7 | 30.2 (3) | C10—C9—N3—C3 | 22.0 (3) |
N3—C5—C6—C7 | −155.0 (2) | O2—C9—N3—C5 | 13.8 (3) |
O1—C5—C6—C8 | −34.4 (3) | C10—C9—N3—C5 | −167.6 (2) |
N3—C5—C6—C8 | 140.4 (2) | C2—C3—N3—C9 | 70.4 (3) |
C5—C6—C7—C8 | −104.0 (3) | C4—C3—N3—C9 | −113.5 (2) |
C5—C6—C8—C7 | 106.1 (3) | C2—C3—N3—C5 | −101.1 (2) |
O2—C9—C10—C11 | −22.5 (4) | C4—C3—N3—C5 | 75.0 (2) |
N3—C9—C10—C11 | 158.9 (2) | O1—C5—N3—C9 | −160.4 (2) |
O2—C9—C10—C12 | 42.9 (3) | C6—C5—N3—C9 | 24.5 (3) |
N3—C9—C10—C12 | −135.7 (2) | O1—C5—N3—C3 | 10.6 (3) |
C9—C10—C11—C12 | 105.0 (2) | C6—C5—N3—C3 | −164.5 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C7—H4···O2i | 0.99 | 2.35 | 3.339 (3) | 173 |
C1—H1···O1ii | 0.95 | 2.51 | 3.203 (3) | 130 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x, −y+3/2, z+1/2. |
Acknowledgements
We thank the EPSRC UK National Crystallography Service (University of Southampton) for the data collection.
References
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