Startseite Crystal structure of 4-ethyl-2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-1,6-dihydropyrimidine-5-carbonitrile, C14H12N4O3S
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Crystal structure of 4-ethyl-2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-1,6-dihydropyrimidine-5-carbonitrile, C14H12N4O3S

  • Ali A. El-Emam ORCID logo EMAIL logo , Lamya H. Al-Wahaibi , Olivier Blacque und Edward R. T. Tiekink
Veröffentlicht/Copyright: 5. Juli 2022

Abstract

C14H12N4O3S, monoclinic, P21/n (no. 14), a = 12.2777(3) Å, b = 9.4312(2) Å, c = 12.9412(2) Å, β = 107.945(2)°, V = 1425.61(5) Å3, Z = 4, R gt (F) = 0.0305, wR ref (F 2) = 0.0837, T = 160 K.

CCDC no.: 2059188

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless block
Size: 0.27 × 0.22 × 0.10 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 2.20 mm−1
Diffractometer, scan mode: XtaLAB Synergy, ω
θ max, completeness: 74.5°, >99%
N(hkl)measured, N(hkl)unique, R int: 14,965, 2903, 0.015
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 2866
N(param)refined: 203
Programs: CrysAlisPRO [1], SHELX [2, 3], WinGX/ORTEP [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
S1 0.90018 (2) 0.88851 (3) 0.44589 (3) 0.02485 (11)
O1 0.88985 (7) 0.37185 (9) 0.43821 (7) 0.0259 (2)
O2 0.58994 (12) 1.00783 (15) 0.82809 (10) 0.0571 (4)
O3 0.73808 (13) 1.14015 (17) 0.89395 (10) 0.0612 (4)
N1 0.59363 (10) 0.25275 (13) 0.32561 (11) 0.0383 (3)
N2 0.88179 (9) 0.61296 (10) 0.42934 (8) 0.0211 (2)
H2N 0.9557 (8) 0.6164 (16) 0.4686 (11) 0.025*
N3 0.70988 (9) 0.73915 (11) 0.35590 (8) 0.0242 (2)
N4 0.67383 (11) 1.07119 (14) 0.82016 (10) 0.0353 (3)
C1 0.64715 (11) 0.35453 (14) 0.33928 (11) 0.0277 (3)
C2 0.70985 (10) 0.48497 (13) 0.35747 (10) 0.0236 (3)
C3 0.83199 (10) 0.48011 (12) 0.41035 (9) 0.0212 (2)
C4 0.82020 (10) 0.73396 (12) 0.40587 (9) 0.0208 (2)
C5 0.65455 (11) 0.61319 (13) 0.33133 (10) 0.0251 (3)
C6 0.52736 (12) 0.62386 (15) 0.27902 (13) 0.0369 (3)
H6A 0.500585 0.543255 0.228556 0.044*
H6B 0.509062 0.712690 0.236411 0.044*
C7 0.46546 (13) 0.62242 (18) 0.36451 (17) 0.0499 (5)
H7A 0.383469 0.638330 0.329430 0.075*
H7B 0.496242 0.697665 0.417729 0.075*
H7C 0.476845 0.530330 0.401382 0.075*
C8 0.78959 (11) 1.02412 (13) 0.42600 (10) 0.0247 (3)
H8A 0.819023 1.115372 0.407696 0.030*
H8B 0.722190 0.996837 0.364393 0.030*
C9 0.75399 (10) 1.04231 (12) 0.52650 (10) 0.0229 (2)
C10 0.66152 (11) 0.96726 (14) 0.53959 (10) 0.0268 (3)
H10 0.617580 0.908086 0.482518 0.032*
C11 0.63263 (11) 0.97772 (14) 0.63494 (11) 0.0278 (3)
H11 0.568987 0.927480 0.643696 0.033*
C12 0.69928 (11) 1.06341 (14) 0.71671 (10) 0.0266 (3)
C13 0.79025 (11) 1.14236 (14) 0.70558 (11) 0.0288 (3)
H13 0.833660 1.201804 0.762731 0.035*
C14 0.81617 (11) 1.13236 (13) 0.60914 (11) 0.0266 (3)
H14 0.876936 1.187378 0.599095 0.032*

Source of material

To a solution of the 6-ethyl-4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile [5] (1.81 g, 0.01 mol) in DMF (10 mL), 4-nitrobenzyl bromide (2.16 g, 0.01 mol) and anhydrous potassium carbonate (1.38 gm, 0.01 mol) were added. The mixture was stirred at room temperature for 12 h after which water (15 mL) was added and the mixture stirred for further 30 min at room temperature. The precipitated crude product was filtered, washed with cold water, dried and crystallized from its ethanol solution to yield 2.78 g (88%) of (I) as transparent blocks. M.pt.: 465–467 K (uncorrected). 1H NMR (DMSO-d6, 500.13 MHz): δ 1.18 (t, 3H, CH3, J = 7.5 Hz), 2.67 (q, 2H, CH2, J = 7.5 Hz), 4.60 (s, 2H, CH2S), 7.71 (d, 2H, Ar–H, J = 8.5 Hz), 8.18 (d, 2H, Ar–H, J = 8.5), 13.66 (s, 1H, NH). 13C{ 1H} NMR (DMSO-d6, 125.76 MHz): δ 12.22 (CH3), 29.98 (CH2), 33.58 (CH2S), 95.87 (pyrimidine C-5), 115.24 (CN), 123.97, 130.76, 145.88, 147.14 (Ar–C), 162.40 (pyrimidine C-2), 167.0 (pyrimidine C=O), 178.82 (pyrimidine C-4). ESI–MS (m/z): 315.2 [M–H+].

Experimental details

The C-bound H atoms were geometrically placed (C–H = 0.95–0.99 Å) and refined as riding with U iso (H) = 1.2 or 1.5U eq (C). The N-bound H atom was located in a difference map and refined with N–H = 0.88 ± 0.01 Å, and with U iso (H) = 1.2U eq (N).

Comment

Pyrimidine heterocycles and related derivatives such as uracil, thymine and cytosine represent the cores of several potent chemotherapeutic agents [6]. The chemotherapeutic efficacy of pyrimidine-based drugs is accredited to their inhibitory effect on the biosynthesis of pivotal enzymes responsible for the synthesis of nucleic acids such as thymidine phosphorylase, thymidylate synthetase, dihydrofolate reductase and reverse transcriptase [7]. Numerous pyrimidine-based drugs are presently used as effective anti-cancer [8, 9], anti viral [10] and anti-microbial agents [11]. The title compound, (I), was developed and investigated crystallographically in the context of recent studies into the potential of related pyrimidyl derivatives as anti-microbial agents [5] and dihydrofolate reductase inhibitors [12, 13].

The molecular structure of (I) is shown in the upper image of the figure (50% probability ellipsoids). The central sulphur atom is in a V-shaped geometry [C4–S1–C8 = 102.55(6)°] within a C2 donor set. This is obvious, since the C4 and C8 atoms have different hybridizations. The dihedral angle between the pyrimidyl and phenyl rings is 84.11(6)°, indicative of a near to orthogonal relationship. The nitro substituent is co-planar with the ring it is connected to, forming a dihedral angle of 5.20(12)°. Globally, with reference to the substituted pyrimidyl ring, the ethyl and nitrophenyl residues lie to the same side of the molecule.

There are two literature precedents which are particularly worthy of mention, namely the n-propyl and 2-methylpropyl [13] analogues, whereby these groups substitute for the ethyl group in (I). While the n-propyl derivative is isostructural with (I), the 2-methylpropyl analogue is not. The other structure worthy of mention is one with 2-methylpropyl and 4-fluorophenyl substituents [14] instead of the ethyl and 4-nitrophenyl substituents of (I). The literature precedents adopt molecular conformations akin to that just described for (I).

In the molecular packing of (I), hydrogen bonding of the type amide–N–H⃛O(amide) features within centrosymmetric, eight-membered {⃛HNCO} synthons [N2–H2n⃛O1 i : H2n⃛O1 i  = 1.911(12) Å, N2⃛O1 i  = 2.8032(14) Å with angle at H2n = 175.6(11)° for symmetry operation (i): 2 − x, 1 − y, 1 − z]. Chains are formed along the b-axis direction whereby the aforementioned rings are linked by short S1⃛S1 ii interactions of 3.2057(4) Å cf. with the sum of the van der Waals radii of 3.60 Å [15] for symmetry operation (ii): 2 − x, 2 − y, 1 − z. A view of the supramolecular chain is illustrated in the lower image of the figure. Contributing to the stability of the chain are long benzyl–C–H⃛O(amide) [C8–H8A⃛O1 iii : H8a⃛O1 iii  = 2.56 Å, C8⃛O1 iii  = 3.4894(15) Å with angle at H8a = 156° for (iii): x, 1 + y, z]; these are not shown in the figure. The connections leading to a three-dimensional architecture involve the substituted pyrimidyl ring. Thus, one of the nitro–O atoms approaches the ring in a side-on fashion [N4–O3⃛Cg(pyrimidyl) iv  = 2.9404(14) Å with angle at O3 = 120.98(11)° for (iv): 3/2 − x, 1/2 + y, 3/2 − z] as does the nitrile–N atom [C1–N1⃛Cg(pyrimidyl) v  = 3.8321(14) Å with angle at N1 = 92.53(10)° for (v): 3/2 − x, −1/2 + y, 1/2 − z], but on the other side of the ring.

The supramolecular chain along the b-axis described for (I) also occurs in the crystals of isostructural n-propyl (II) and non-isostructural 2-methylpropyl (III) analogues, respectively [13]. With this in mind, it was thought of interest to compute the Hirshfeld surfaces and to evaluate the full and decomposed two-dimensional fingerprint plots for (I)–(III). This exercise was conducted with Crystal Explorer 17.5 [16] in accord with established procedures [17]. In the analysis, the major contribution to the calculated Hirshfeld surface of (I) is due to O⃛H/H⃛O contacts at 25.4% with almost equivalent contributions from H⃛H [18.6%] and C⃛H/H⃛C [18.5%] contacts. While the percentage contribution from O⃛H/H⃛O contacts is rather high, most occur at separations greater than the sum of the van der Waals radii. The next most significant contributing contacts are of the type S⃛H/H⃛S at 6.4%. The remaining contacts beyond 1.3% involve carbon, i.e. O⃛C/C⃛O [5.8%] and N⃛C/C⃛N [3.1%]. It is noted that despite the identification of S⃛S secondary bonding in the crystal of (I), the contribution to the overall surface is only 0.9%.

When analogous calculations were conducted for each of (II) and (III), there were significant perturbations in terms of increased participation of hydrogen in the most significant surface contacts, a correlation readily related to the increased hydrogen content for (I) < (II) < (III). This trend was most evident for the H⃛H which increased from 18.6, 20.3 and 25.8% for (I)–(III), respectively. A similar trend was evident for the O⃛H/H⃛O contacts, i.e. 25.4, 25.4 and 27.9%, respectively. To compensate these increases, there was a small downward trend in the N⃛H/H⃛N contacts, i.e. 13.9, 13.5 and 13.2%. Downward trends were also noted for the N⃛C/C⃛N [3.1, 2.8 and 1.8%, respectively], and in the O⃛C/C⃛O [5.8, 4.6 and 2.6%] contacts. Of the other contacts, the C⃛H/H⃛C [18.5, 19.1, 16.8%] and S⃛H/H⃛S [6.4, 6.6 and 5.9%] contacts varied in a non-systematic fashion.


Corresponding author: Ali A. El-Emam, Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt, E-mail:

Funding source: Princess Nourah bint Abdulrahman University

Award Identifier / Grant number: PNURSP2022R3

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This research was funded by the Princess Nourah bint Abdulrahman University Researchers Supporting Project No. PNURSP2022R3, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2022-05-30
Accepted: 2022-06-20
Published Online: 2022-07-05
Published in Print: 2022-10-26

© 2022 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
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  4. Crystal structure of chlorido-(η 6-toluene)(5,5′-dimethyl-2,2′-bipyridine-κ2 N,N′)ruthenium(II) hexafluoridophosphate(V) ─ acetone (1/1) C22H26ClN2ORuPF6
  5. Crystal structure of 4-(((2-(3-(1-(3-(3-cyanophenyl)-6-oxopyridazin-1(6H)-yl)ethyl)phenyl) pyrimidin-5-yl)oxy)methyl)-1-methylpiperidin-1-ium chloride monohydrate, C30H33N6O2Cl
  6. The crystal structure of 2-chloro-N-((2-chlorophenyl)carbamoyl)nicotinamide, C13H9Cl2N3O2
  7. Crystal structure of 9-(t-butyl)-3,11-dihydro-6H-pyrazolo [1,5-a]pyrrolo[3′,2′:5,6]pyrido[4,3-d]pyrimidin-6-one hemihydrate, C30H32N10O3
  8. Crystal structure of di-μ2-hydroxido-tetrakis(6-methylpyridine-2-carboxylato-k2 N,O) diiron(III) trihydrate C28H32Fe2N4O13
  9. Crystal structure of catena-poly[qua-(μ2-2-aminoisophthalat-κ3 O,O′:O′′)(1,10-phenanthroline-κ2 N,N′)manganese(II)] C20H15MnN3O5
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  14. Synthesis and crystal structure of 1-((3R,10S,13R,17S)-10,13-dimethyl-3- (phenylamino)hexadecahydro-1H-cyclopenta[α] phenanthren-17-yl)ethan-1-one, C27H39NO
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  16. Crystal structure of 2-(adamantan-1-yl)-5-(3,5-dinitrophenyl)-1,3,4-oxadiazole, C18H18N4O5
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  28. The crystal structure of diaqua-bis(pyrazolo[1,5-a]pyrimidine-3-carboxylato-κ2N,O)nickel(II) dihydrate, C14H16N6O8Ni
  29. Crystal structure of poly[μ2-aqua-aqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2 N:N′)-(μ2-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ2 O:O′)-(μ4-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ5 O,O′:O″:O′″:O′″)dicobalt(II)] – water – dimethylformamide (1/1/1) C44H43N11O12Co2
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  31. The crystal structure of Chrysosplenol D, C18H16O8
  32. Crystal structure of poly[deca aqua-bis(μ 4-2-(triazol-1-yl)-benzene-1,3,5-tricarboxylato)- bis(μ 5-2-(triazol-1-yl)-benzene-1,3-dicarboxylato-5-carboxyl acid) pentamanganese(II)] dihydrate, C44H42Mn5N12O36
  33. Synthesis and crystal structure of (E)-1-(4-(((E)-3-(tert-butyl)-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-methyl oxime, C20H24N2O2
  34. The crystal structure of 4,4′-dichloro-6,6′-dimethoxy-2,2′,3,3′,5,5′- hexanitroazobenzene, C14H6N8O14Cl2
  35. Crystal structure of N 2,N 4-dimesitylpentane-2,4-diamine, C23H34N2
  36. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ 6O6)potassium(2-methylphenylamino)ethyl-2-methylphenylamide ammoniate (1/3.5), [K(18-crown-6)](o-CH3C6H4)NH(CH2)2N(o-CH3C6H4) 3.5 NH3, C28H53.5KN5.5O6
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  38. Crystal structure of (E)-7-bromo-2-(3,5-dimethoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C19H17BrO3
  39. Crystal structure of (E)-N′-(1-(5-chloro-2-hydroxyphenyl) ethylidene)-4-hydroxybenzohydrazide, C15H13ClN2O3
  40. {2-(((2-aminoethyl)imino)methyl)-6-bromophenolato-κ3 N,N′,O}iron(III) nitrate, C18H20Br2FeN5O5
  41. Crystal structure of 2-(tert-pentyl)anthracene-9,10-dione, C19H18O2
  42. Crystal structure of 5,5′-(1,4-phenylene)bis(1H-imidazol-3-ium) bis(2-(2-(carboxymethyl)phenyl)acetate), C32H30N4O8
  43. Crystal structure of N 2,N 6-bis(2-(((E)-naphthalen-1-ylmethylene)amino)phenyl)pyridine-2,6-dicarboxamide, C41H29N5O2
  44. The crystal structure of 3-amino-1,2,4-triazolium 2,4,5-trinitroimidazolate, C5H5O6N9
  45. Hydrogen bonded dimers in the crystal structure of 2-chloro-N-(phenylcarbamoyl)nicotinamide, C26H20Cl2N6O4
  46. The crystal structure of 4,4′-bipyridine-5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one-water(1/2/2), C40H32N2O12
  47. Crystal structure of N,N'-bis(4-fluoro-salicylaldehyde)-3,6-dioxa-1,8-diaminooctane, C20H22F2N2O4
  48. Crystal structure of 3-(1,3-dinitropropan-2-yl)-4H-chromen-4-one, C12H10N2O6
  49. The crystal structure of (4-(2-bromoethoxy)-phenyl)(phenyl)methanone, C15H13BrO2
  50. Crystal structure of (E)-7-bromo-2-(4-methoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C18H15BrO2
  51. Crystal structure of dichlorido-tetrakis((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ 1 N)cadmium(II), C60H68O4N12Cl10Cd
  52. Crystal structure of diaqua-diphenanthroline-κ2 N,N′-bis(μ2-2-carboxy-3,4,5,6-tetrafluorobenzoato-κ2 O:O′)-bis(μ2-tetrafluorophthalato-κ3 O,O′:O′)didysprosium(III) – phenanthroline (1/2), C80H38Dy2F16N8O18
  53. Crystal structure of bis(μ2-2-oxido-2-phenylacetato-κ3 O,O′:O′)-bis(N-oxido-benzamide-κ2 O,O′)-bis(propan-2-olato-κ1 O)dititanium(IV), C36H38N2O12Ti2
  54. Crystal structure of poly[diaqua-(μ2-1H-benzo[d][1,2,3]triazole-5-carboxylato-κ2 O:O′)(μ2-oxalato-κ4O,O:O″,O′″)europium(III)] monohydrate, C9H10N3O9Eu
  55. Crystal structure of bis((N-methyl-2-oxyethyl)amine)-bis(μ 2-N,N,N-tris(2-oxoethyl)amine)-bis(isopropoxy)-bis(μ 3-oxo)tetratitanium(IV)– isopropanol (1/2), C34H76N4O16Ti4
  56. Synthesis and crystal structure of ethyl 4-((4-iodobenzyl)amino)benzoate, C16H16INO2
  57. Crystal structure of (Z)-2-(tert-butyl)-5-((5-(tert- butyl)-2H-pyrrol-2-ylidene)(mesityl)methyl)-1H-pyrrole, C26H34N2
  58. Crystal structure of dimethylammonium poly[μ4-1,1′-(1,4- phenylenebis(methylene))bis(1H-pyrazole-3,5-dicarboxylato-κ6 N,O:O′:N′,O″:O‴) manganese(II)], C22H26MnN6O8
Heruntergeladen am 7.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2022-0272/html
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