Home The crystal structure of 5-(2-fluoro-3-methoxyphenyl)-1-(2-fluoro-6-(trifluoromethyl)benzyl)-6-methylpyrimidine-2,4(1H,3H)-dione, C20H15F5N2O3
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The crystal structure of 5-(2-fluoro-3-methoxyphenyl)-1-(2-fluoro-6-(trifluoromethyl)benzyl)-6-methylpyrimidine-2,4(1H,3H)-dione, C20H15F5N2O3

  • Yundeng Wu ORCID logo EMAIL logo , Jun Xie , Hui Wan , Xiangyang Xu and Jian Li
Published/Copyright: September 12, 2022
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 237 Issue 6

Abstract

C20H15F5N2O3, orthorhombic, Pbca (no. 61), a = 10.9913 (4) Å, b = 11.0451(5) Å, c = 30.3925(14) Å, V = 3689.6 (3) Å3, Z = 8, R gt (F) = 0.0360, wR ref (F 2) = 0.0927, T = 170 K.

CCDC no.: 2203655

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 needle
Size: 0.45 × 0.15 × 0.09 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.14 mm−1
Diffractometer, scan mode: Bruker D8 Venture, φ and ω
θ max, completeness: 27.1°, >99%
N (hkl)measured, N(hkl)unique, R int: 55,383, 4080, 0.061
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3247
N(param)refined: 273
Programs: Bruker [1], SHELX [2, 3], Olex2 [4], PLATON [5–8], Publcif [9]
Table 2:

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

Atom x y z U iso∗/U eq
F1 0.37628 (8) 0.80102 (8) 0.47806 (3) 0.0324 (2)
F2 0.74812 (9) 1.00525 (10) 0.40788 (4) 0.0463 (3)
F3 0.67307 (11) 1.17325 (9) 0.38586 (4) 0.0540 (3)
F4 0.63691 (10) 1.01055 (9) 0.34989 (3) 0.0443 (3)
F5 0.43702 (8) 0.39478 (8) 0.30865 (3) 0.0299 (2)
O1 0.33282 (10) 0.38100 (9) 0.40013 (3) 0.0289 (2)
O2 0.57698 (10) 0.62480 (9) 0.48081 (3) 0.0290 (2)
O3 0.30526 (11) 0.33727 (11) 0.23971 (4) 0.0408 (3)
N1 0.45547 (11) 0.50533 (10) 0.43923 (4) 0.0240 (3)
H1 0.459553 0.449340 0.459778 0.029∗
N2 0.51251 (11) 0.69585 (10) 0.41403 (4) 0.0215 (2)
C1 0.38539 (13) 0.47809 (12) 0.40245 (5) 0.0227 (3)
C2 0.51841 (13) 0.60935 (12) 0.44684 (5) 0.0230 (3)
C3 0.44309 (13) 0.67822 (12) 0.37608 (4) 0.0221 (3)
C4 0.38118 (13) 0.57386 (12) 0.36975 (5) 0.0223 (3)
C5 0.58291 (13) 0.80739 (12) 0.42148 (5) 0.0234 (3)
H5A 0.630002 0.825759 0.394531 0.028∗
H5B 0.641898 0.792528 0.445502 0.028∗
C6 0.50685 (12) 0.91762 (12) 0.43330 (4) 0.0219 (3)
C7 0.40719 (13) 0.91045 (13) 0.46109 (5) 0.0246 (3)
C8 0.33650 (14) 1.00785 (14) 0.47336 (5) 0.0305 (3)
H8 0.269244 0.997414 0.492625 0.037∗
C9 0.36547 (15) 1.12070 (15) 0.45708 (5) 0.0344 (4)
H9 0.316582 1.188805 0.464291 0.041∗
C10 0.46622 (15) 1.13428 (14) 0.43017 (5) 0.0329 (4)
H10 0.487401 1.212313 0.419480 0.040∗
C11 0.53637 (14) 1.03493 (13) 0.41871 (5) 0.0261 (3)
C12 0.64715 (16) 1.05584 (14) 0.39083 (5) 0.0347 (4)
C13 0.44151 (15) 0.77978 (13) 0.34335 (5) 0.0302 (3)
H13A 0.400238 0.850032 0.356199 0.045∗
H13B 0.398055 0.753894 0.316812 0.045∗
H13C 0.525217 0.801802 0.335643 0.045∗
C14 0.30323 (13) 0.55042 (12) 0.33062 (5) 0.0235 (3)
C15 0.19568 (14) 0.61467 (14) 0.32290 (5) 0.0316 (3)
H15 0.172129 0.678158 0.342188 0.038∗
C16 0.12383 (15) 0.58558 (16) 0.28717 (6) 0.0381 (4)
H16 0.050912 0.629636 0.282136 0.046∗
C17 0.15589 (15) 0.49354 (15) 0.25854 (5) 0.0361 (4)
H17 0.104958 0.474570 0.234244 0.043∗
C18 0.26243 (15) 0.42904 (14) 0.26536 (5) 0.0297 (3)
C19 0.33338 (13) 0.45918 (13) 0.30163 (5) 0.0240 (3)
C20 0.2214 (2) 0.28483 (18) 0.20942 (6) 0.0528 (5)
H20A 0.201834 0.343773 0.186374 0.079∗
H20B 0.146795 0.261971 0.225009 0.079∗
H20C 0.257859 0.212714 0.196046 0.079∗

Source of material

In a representative experiment, approximately 0.4 g (1 mmol) of the title compound was dissolved in a mixed solvent of xylene (5 mL) and dichloromethane (5 mL) placed in a glass vial sealed with perforated tape. Solvent was evaporated slowly at room temperature and the product was obtained as a needle crystals in about two weeks.

Experimental details

Using Olex2 [4], the structure was solved with the ShelXT [2] using intrinsic phasing and refined with the ShelXL [3] refinement package.

Coordinates of hydrogen atoms were included using constraints or restraints. Their U iso values were set to 1.2 U eq of the parent atoms for all C(H) groups, all C(H, H) groups, all N(H) groups, and 1.5 U eq for all C(H, H, H) groups.

The secondary CH2, C5(H5A, H5B), were refined with riding coordinates.

The aromatic/amide H, N1(H1), C8(H8), C9(H9), C10(H10), C15(H15), C16(H16), C17(H17), were refined with riding coordinates.

Idealised Me, C13(H13A, H13B, H13C), C20(H20A, H20B, H20C), were refined as rotating group.

Comment

The title compound is an intermediate of products reported by literature [10], which are the most recent synthetic class of antimicrobials active against a number of pathogenic microorganisms and has been approved for a treatment of select gram-positive infections. This research is also part of our continuing interest in synthesis, characterisation and understanding of hydrogen bonding schemes of related compounds [11–13].

The asymmetric unit of the title structure contains one title molecule (cf. left part of the figure). There are four intramolecular non-classical hydrogen bonds.

C5 participates in three intramolecular hydrogen bonds (cf. left part of the figure). These bonds are C5–H5A⃛F2, D⃛A = 2.8713 (17) Å; C5–H5A⃛F4, D⃛A = 3.1814 (17) Å; and C5–H5B⃛O2, D⃛A = 2.7061 (17) Å. C10 participates in an intramolecular hydrogen bond (C10–H10⃛F3, D⃛A = 2.677 (2) Å; cf. left part of the figure).

The intermolecular hydrogen bonds (N1–H1⃛O2′; ′ = 1 − x, 1 − y, 1 − z; D⃛A = 2.8459 (15) Å; cf. right part of the figure) connect N1 and O2 of two adjacent molecules to form an eight-membered ring.

Non-classical intermolecular hydrogen bonds (C9–H9⃛F1′′; ″ = ½ − x, ½ + y, z; D⃛A = 3.3814 (19) Å) and (C10–H10⃛O1′′′; ′′′ = x, 1 + y, z; D⃛A = 3.2263 (19) Å) run along the b axis (cf. right part of the figure. Some atoms are omitted for clarity purpose).

Non-classical intermolecular hydrogen bonds (C17–H17⃛F5′′′′; ′′′′ = −½ + x, y, ½ − z, D⃛A = 3.3387 (18) Å) run along a axis (cf. right part of the figure).

In total, the three intermolecular hydrogen bonding interactions construct a network parallel to the ab plane (cf. right part of the figure).

Corresponding author: Yundeng Wu, Technique Center, Jinling Pharmaceutical Company Limited, Nanjing, 210046, Jiangsu Province, People’s Republic of China, E-mail:

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

  2. Research funding: Jinling Pharmaceutical Company Limited.

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

References

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Received: 2022-07-30
Accepted: 2022-08-26
Published Online: 2022-09-12
Published in Print: 2022-12-16

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

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

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  69. The crystal structure of dimethanol-5,15-diphenylporphyrin-21,23-diido-κ4 N,Nʹ,Nʺ,Nʹʺ-manganese(III) trans-dicyanido-bis(acetylacetonato-κ2O,Oʹ)ruthenium(III), C46H42N6O6RuMn
  70. Crystal structure of 1,4,8,11-tetraazacyclotetradecane-1,8-diium bis(3,5-dicarboxybenzoate), C28H36N4O12
  71. Bifurcated halogen bonds in the crystal structure of 2,2′-bi(1,8-naphthyridine)—1,4-diiodotetrafluorobenzene (1/1), C22H10F4I2N4
https://doi.org/10.1515/ncrs-2022-0391
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of 1,5-bis(4-chlorophenyl)-3-(3-methylphenyl)pentane- 1,5-dione, C48H40Cl4O4
  4. Crystal structure of (bis(1,10-phenanthroline-κ 2 N,N′))-(3,5-dinitrosalicylato-κ 2 O,O′)nickel(II), C31H18N6NiO7
  5. Crystal structure of {N,N′-bis(4-fluoro-salicylaldehyde)-3,6-dioxa-1,8-diaminooctane-κ4 O,N,N′,O′}zinc(II), C20H20F2N2O4Zn
  6. [5-Bromo-2-(2-(dimethylamino)ethyliminomethyl)phenolato-κ3 N,N′,O]-isothiocyanato-nickel(II), C12H14BrN3NiOS
  7. Crystal structure of 9-bromo-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin- 2-amine, C18H15BrN4O
  8. The crystal structure of imidazolium nitrate, C3H5O3N3
  9. Crystal structure of diiodido-bis(6,6′-dimethoxy-2,2′-(ethane-1,2-diylbis(nitrilomethanylylidene)) diphenolato)tricadmium(II), C36H36Cd3I2N4O8
  10. Crystal structure of [diaqua-bis(2-((1H-tetrazol-1-yl)methyl)-5-carboxy-1H-imidazole-4-carboxylato-κ2 N,O) manganese(II)] dihydrate, C14H18MnN12O12
  11. Crystal structure of Diaqua[5,5′-dicarboxy-2,2′-(propane-1,3-diyl)bis(1H-imidazole-4-carboxylato-k4 O,O′,N,N′)]iron(II), C13H14FeN4O10
  12. Crystal structure of poly[dimethanol-κ1O-(µ2-(E)-2-((2-oxidobenzylidene)amino)acetato)-(µ3-(E)-2-((2-oxidobenzylidene)amino)acetato)dicadmium(II)], C20H22Cd2N2O8
  13. Crystal structure of N 2,N 6-bis(2-(((E)-quinolin-8-ylmethylene)amino)phenyl)pyridine-2,6-dicarboxamide, C39H27N7O2
  14. An I 6 2 − anion in the crystal structure of theophyllinium triiodide monohydrate, C7H11I3N4O3
  15. The crystal structure of poly[6,6′-oxybis(4-(pyridin-1-ium-1-yl)-1,3,5,2,4,6-trioxatriborinan-2-olate)], [B6O9](C5H5N)2
  16. The crystal structure of (carbonato κ2 O,O′)(2-oxopyridin-1(2H)-olato-κN)tris(trimethylphosphine)rhodium(III) water solvate, C15H33NO5P3Rh
  17. The crystal structure of dibromido-bis((RS)-2-(4-chlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)hexanenitrile-κ1 N)zinc(II), C30H34Br2Cl2N8Zn
  18. Synthesis and crystal structure of 3-(((7-hydroxy-3-(4-hydroxy-3,5-dinitrophenyl)-4-oxo-4H-chromen-8-yl)methyl)(nitroso)amino)propanoic acid, C19H14N4O11
  19. The crystal structure of 3-((4-chloro-N-(2-methoxyethyl)benzamido)methyl)phenyl methanesulfonate, C18H20ClNO5S
  20. Crystal structure of di([1,1′:3′,1″-terphenyl]-2′-yl)tellane, C36H26Te
  21. The crystal structure of diaqua-bis(pyrazolo[1,5-a]-pyrimidine-3-carboxylato-κ2 N,O)zinc(II), C14H12N6O6Zn
  22. Crystal structure of N′,N‴-((1E,2E)-1,2-diphenylethane-1,2-diylidene)bis(4-methylbenzohydrazide) – water – methanol (1/1/1), C31H32N4O4
  23. Crystal structure of 3-((2,4-dichlorobenzyl)thio)-5-methyl-7-(trifluoromethyl)-[1,2,4]triazolo [4,3-c]pyrimidine, C14H9Cl2F3N4S
  24. Crystal structure of 3,5,6,7-tetramethoxy-3′,4′-methylenedioxy-flavone, C20H18O8
  25. Crystal structure of catena-poly[(5,5′-dimethyl-2,2′-bipyridine-κ 2 N,N′)-(μ 3-hydrogen-1,1′,1″-(1,3,5-triazine-2,4,6-triyl)tris(piperidine-4-carboxylato)- κ 5 O:O,O′:O″,O‴)-cadmium(II)], C33H40CdN8O6
  26. The crystal structure of 3,5-bis(propan-2-yl)-1H-pyrazol-4-amine, C9H17N3
  27. Crystal structure of [(1,4,7,10-tetraoxacyclododecane-κ 4 O,O′,O″, O‴)-tris(nitrato-κ 2 O,O′)gadolinium(III)], C8H16N3O13Gd
  28. The crystal structure of 2,2′-((pyridine-2,6-diylbis(methylene))bis(sulfanediyl))-bis(4,5-dihydro-1H-imidazol-3-ium) bromide, C13H19Br2N5S2
  29. Crystal structure of E-2-chloro-N′-(1-(5-chloro-2-hydroxyphenyl)propylidene)benzohydrazide, C16H14Cl2N2O2
  30. Crystal structure of 3-(adamantan-1-yl)-4-methyl-5-{[(4-nitrophenyl)methyl]sulfanyl}-4H-1,2,4-triazole, C20H24N4O2S
  31. The crystal structure of dimethanol-κ1O-(5,10,15,20-tetrakis(4-nitrophenyl)porphyrin-21,23-diido-κ4 O,O′,O″,O′″)manganese(III) trans-dicyanido-κ1C-bis(acetylacetonato-κ2 O,O′)ruthenium(III), C58H46N10O14RuMn
  32. The crystal structure of nitroxyl-κ N-{hydridotris(3-trifluoromethyl-5-methylpyrazolyl-1-yl-κN 3)borato}nickel(II), C15H13BF9N7NiO
  33. The crystal structure of [(2,2′-bipyridine-κ2 N,N)-bis(6-phenylpyridine-2-carboxylato- κ2 N,O)nickel(II)] monohydrate, C34H26N4O5Ni
  34. The crystal structure of 5-(2-fluoro-3-methoxyphenyl)-1-(2-fluoro-6-(trifluoromethyl)benzyl)-6-methylpyrimidine-2,4(1H,3H)-dione, C20H15F5N2O3
  35. The crystal structure of ethyl 2,3,5-trifluoro-4-(4-oxo-3,4-dihydropyridin-1(2H)-yl)benzoate, C14H12F3NO3
  36. [2,2′-{Ethane-1,2-diylbis[(azanylylidene)methanylylidene]}bis(3-bromo-2-hydroxyphenyl)]iron(III) nitrate, C20H12Br2CuN2O2
  37. The crystal structure of 1-(2-iodophenyl)-4-phenyl-1H-1,2,3-triazole, C14H10IN3
  38. Synthesis and crystal structure of 2-(2-oxo-2-(thiophen-2-yl)ethyl)-4H-chromen-4-one, C15H10O3S
  39. {6,6′-((1E,1′E)-((2,2-dimethylpropane-1,3-diyl)bis(azaneylylidene))bis(methaneylylidene))bis(2-bromo-4-chlorophenolate)-κ4N,N′,O,O′}copper(II), C19H16Br2Cl2CuN2O2
  40. The crystal structure of N′-[bis(2-hydroxyphenyl)methylidene]pyridine-4-carbohydrazide, C19H15N3O3
  41. Crystal structure of 2-chloro-6-formylphenolato-κ2O,O′-(6,6′-(((2,2-dimethylpropane-1,3-diyl)bis(azaneylylidene))bis(methaneylylidene))bis(2-chlorophenolato)κ4 N,N,O,O′)cobalt(III), C26H22Cl3CoN2O4
  42. The crystal structure of tetrakis(6-phenylpyridine-2-carboxylate-κ 2 N,O)-bis(μ2-6-phenylpyridine-2-carboxylate-κ 2 O:O′)-bis(μ2-6-phenylpyridine-2-carboxylate-κ 3N,O:O)tetralead(II) C48H32N4O8Pb2
  43. The crystal structure of 3,7-dihydroxy-9-methoxy-4a-methyl-4aH-benzo[c] chromene-2,6-dione —dichloromethane (1/1), C16H14Cl2O6
  44. The crystal structure of (Z)-6-(((5-chloro-2-hydroxyphenyl)amino)methylene)- 4-nitrocyclohexa, C13H9ClN2O4
  45. Crystal structure of dichlorido-tetra((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ1 N)zinc(II), C60H68O4N12Cl10Zn
  46. The crystal structure of 4-(2-bromoethoxy)-2-hydroxybenzaldehyde, C9H9BrO3
  47. The crystal structure of 5-azido-1-methyl-4-nitroimidazole, C4H4O2N6
  48. Crystal structure of dibromido-tetra((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ 1 N)zinc(II), C60H68O4N12Br2Cl8Zn
  49. Crystal structure of tetrasodium-bis(μ 2-oxido)-hexafluoro-didioxo-molybdenum(V), Na2(Mo2O4F6)
  50. Crystal structure of (E)-N′-(2-chloro-6-hydroxybenzylidene)-4- hydroxybenzohydrazide-water (1/1), C14H13Cl1N2O4
  51. Crystal structure of (E)-N-(4-morpholinophenyl)-1-(quinolin-2-yl)methanimine, C20H19N3O
  52. The crystal structure of catena-poly[(1,10-phenanthroline-κ2 N,N′)-(μ3-2-hydroxybenzene-1,3-dicarboxylato-κ5 O,O′:O″,O‴:O‴)cadmium(II)], C20H12CdN2O5
  53. The crystal structure of 2,6-di-tert-butyl-4-(4-(methylthio)benzylidene)cyclohexa-2,5-dien-1-one, C22H28OS
  54. La3.65Mg30Sb1.07 as a disordered derivative of Th2Ni17-type structure
  55. Crystal structure of (E)-N-(4-morpholinophenyl)-1-(quinoxalin-2-yl)methanimine, C19H18N4O
  56. The crystal structure of 2,2′-(1,2-phenylenebis(methylene))bis(1,3-dimethylisothiouronium) bromide, C14H24Br2N4S2
  57. Crystal structure of tetraaqua-bis[4-(1H-1,2,4-triazol-1-yl)benzoato-κ1 N]zinc(II), C18H20ZnN6O8
  58. Crystal structure of bis(tricarbonyl)-{(S)-(tert-butoxycarbonyl)(1-methoxy-1-oxo-3-sulfido-k2 S:S′-propan-2-yl)amido-k2N:N′}diiron(I) (Fe—Fe), C15H15Fe2NO10S
  59. Crystal structure of (E)-3-((4-chlorophenyl)thio)-4-hydroxypent-3-en-2-one, C11H11ClO2S
  60. The crystal structure of (E)-3′,6′-bis(diethylamino)-2-((5-(diethylamino)-2-hydroxybenzylidene)amino)spiro[isoindoline-1,9′-xanthen]-3-one, C39H45N5O3
  61. The crystal structure of 2-(4-methoxynaphthalen-1-yl)-4H-chromen-4-one, C20H14O3
  62. The crystal structure of trans-dichlorido-(ethylenediamine-κ 2 N,N′)-bis(triphenylphosphine-κ 1 P)ruthenium(II), C38H38Cl2N2P2Ru
  63. The double polymeric chain of catena-poly[(μ2-6-bromopyridine-3-carboxylato-κ2 O,O′) (6-bromopyridine-3-carboxylato-κ2 O,O′) (μ2-1,2-bis(4-pyridyl)ethylene-κ2 N:N′)cobalt(II)], C24H16CoBr2N4O4
  64. The crystal structure of tert-butyl 2-(4-(12-bromo [2.2]paracyclophanyl)carbamoyl)pyrrolidine-1-carboxylate, C26H31BrN2O3
  65. The crystal structure of (Z)-2-(2,3-dimethoxybenzylidene)naphtho[1,2-b]furan-3(2H)-one, C21H16O4
  66. Crystal structure of 2-hydroxy-1-tosylindolin-3-yl- 2-naphthoate, C26H21N1S1O5
  67. The crystal structure of 1-methyl-N-(1-methyl-1H-imidazole-2-carbonyl)-1H-imidazole-2-carboxamide, C10H11N5O2
  68. The crystal structure of (E)-2-((5-bromo-2-hydroxybenzylidene)amino)-3′,6′-bis(ethylamino)-2′, 7′-dimethylspiro[isoindoline-1,9′-xanthen]-3-one, C33H31BrN4O3
  69. The crystal structure of dimethanol-5,15-diphenylporphyrin-21,23-diido-κ4 N,Nʹ,Nʺ,Nʹʺ-manganese(III) trans-dicyanido-bis(acetylacetonato-κ2O,Oʹ)ruthenium(III), C46H42N6O6RuMn
  70. Crystal structure of 1,4,8,11-tetraazacyclotetradecane-1,8-diium bis(3,5-dicarboxybenzoate), C28H36N4O12
  71. Bifurcated halogen bonds in the crystal structure of 2,2′-bi(1,8-naphthyridine)—1,4-diiodotetrafluorobenzene (1/1), C22H10F4I2N4
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