Home Physical Sciences Crystal structure of 9-fluoro-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O
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Crystal structure of 9-fluoro-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O

  • Xing-Wei Li , Yu-Hao Miao , Yue-Xia Ding and Gui-Ge Hou ORCID logo EMAIL logo
Published/Copyright: October 29, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 1

Abstract

C18H15FN4O, monoclinic, P21/c (no. 14), a = 18.0993(7) Å, b = 6.8868(3) Å, c = 24.8450(12) Å, β = 90.515(4)°, V = 3,096.7(2) Å3, Z = 8, R gt (F) = 0.0417, wR ref (F 2) = 0.1040, T = 293 K.

CCDC no.: 2283208

The crystal structure is shown in the Figure 1. Displacement ellipsoids are drawn at the 45 % probability level. Tables 1 and 2 contain details on crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Figure 1: A perspective view of title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 45% probability level.
Figure 1:

A perspective view of title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 45% probability level.

Table 1:

Data collection and handling.

Crystal: Courless block
Size: 0.13 × 0.12 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: SuperNova,
θ max, completeness: 25.5°, >99 %
N(hkl)measured, N(hkl)unique, R int: 15,826, 5,761, 0.026
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 4,868
N(param)refined: 451
Programs: CrysAlisPRO 1 , SHELX 2 , 3
Table 2:

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

Atom x y z U iso*/U eq
C1 −0.03912 (8) 0.1422 (2) 0.42574 (6) 0.0143 (3)
C2 0.05644 (8) 0.3612 (2) 0.42541 (6) 0.0140 (3)
C3 0.02607 (8) 0.4551 (2) 0.38067 (6) 0.0156 (3)
C4 −0.03890 (8) 0.3715 (2) 0.35983 (6) 0.0152 (3)
C5 0.05661 (8) 0.6363 (2) 0.35527 (6) 0.0194 (3)
H5A 0.090805 0.600897 0.327078 0.023*
H5B 0.083589 0.710644 0.382162 0.023*
C6 −0.00510 (9) 0.7608 (2) 0.33155 (7) 0.0232 (4)
H6A −0.033274 0.817843 0.360561 0.028*
H6B 0.016332 0.865705 0.310843 0.028*
C7 −0.08857 (9) 0.7211 (3) 0.24936 (7) 0.0269 (4)
H7 −0.076617 0.846538 0.238695 0.032*
C8 −0.13821 (9) 0.6141 (3) 0.21871 (7) 0.0281 (4)
H8 −0.158933 0.665224 0.187394 0.034*
C9 −0.15598 (8) 0.4307 (3) 0.23577 (7) 0.0246 (4)
C10 −0.12537 (8) 0.3476 (2) 0.28105 (6) 0.0199 (4)
H10 −0.138310 0.222397 0.291351 0.024*
C11 −0.07440 (8) 0.4552 (2) 0.31124 (6) 0.0173 (3)
C12 −0.05612 (8) 0.6448 (2) 0.29585 (6) 0.0204 (4)
C13 0.12394 (8) 0.4317 (2) 0.45441 (6) 0.0155 (3)
C14 0.19337 (8) 0.4533 (2) 0.43023 (6) 0.0156 (3)
C15 0.24758 (8) 0.5523 (2) 0.50873 (6) 0.0193 (4)
H15 0.289613 0.594147 0.527146 0.023*
C16 0.18276 (8) 0.5370 (2) 0.53681 (6) 0.0194 (3)
H16 0.180718 0.568256 0.573181 0.023*
C17 0.12038 (8) 0.4732 (2) 0.50899 (6) 0.0178 (3)
H17 0.075965 0.458320 0.527055 0.021*
C18 0.26961 (8) 0.4347 (3) 0.35278 (7) 0.0252 (4)
H18A 0.285957 0.565599 0.358744 0.038*
H18B 0.265530 0.410808 0.314804 0.038*
H18C 0.304670 0.346021 0.368408 0.038*
C19 0.45731 (8) 0.6753 (2) 0.43112 (6) 0.0139 (3)
C20 0.56309 (8) 0.8583 (2) 0.43274 (6) 0.0143 (3)
C21 0.53723 (8) 0.9705 (2) 0.38999 (6) 0.0152 (3)
C22 0.46859 (8) 0.9141 (2) 0.36842 (6) 0.0149 (3)
C23 0.57563 (8) 1.1469 (2) 0.36770 (7) 0.0198 (4)
H23A 0.605236 1.109989 0.336998 0.024*
H23B 0.608284 1.201683 0.394894 0.024*
C24 0.51855 (9) 1.2976 (2) 0.35058 (7) 0.0223 (4)
H24A 0.493357 1.346352 0.382109 0.027*
H24B 0.543223 1.405944 0.333439 0.027*
C25 0.43537 (9) 1.3109 (3) 0.26759 (7) 0.0263 (4)
H25 0.451296 1.436944 0.260953 0.032*
C26 0.38466 (9) 1.2259 (3) 0.23299 (7) 0.0291 (4)
H26 0.367299 1.292140 0.202813 0.035*
C27 0.36041 (9) 1.0406 (3) 0.24421 (7) 0.0263 (4)
C28 0.38481 (8) 0.9368 (3) 0.28813 (6) 0.0211 (4)
H28 0.366814 0.812842 0.295051 0.025*
C29 0.43742 (8) 1.0224 (2) 0.32213 (6) 0.0175 (3)
C30 0.46305 (8) 1.2114 (2) 0.31219 (6) 0.0207 (4)
C31 0.63400 (8) 0.9002 (2) 0.46153 (6) 0.0147 (3)
C32 0.70289 (8) 0.9037 (2) 0.43608 (6) 0.0158 (3)
C33 0.76319 (8) 0.9831 (2) 0.51409 (6) 0.0189 (3)
H33 0.807103 1.013508 0.531894 0.023*
C34 0.69917 (8) 0.9807 (2) 0.54336 (6) 0.0191 (3)
H34 0.699554 1.007443 0.580051 0.023*
C35 0.63372 (8) 0.9367 (2) 0.51619 (6) 0.0168 (3)
H35 0.589527 0.931962 0.534950 0.020*
C36 0.77492 (9) 0.8635 (3) 0.35710 (7) 0.0308 (4)
H36A 0.795326 0.991860 0.359822 0.046*
H36B 0.769046 0.829276 0.319852 0.046*
H36C 0.807616 0.772664 0.374379 0.046*
F1 −0.20482 (5) 0.32482 (16) 0.20577 (4) 0.0330 (3)
F2 0.31151 (5) 0.95573 (17) 0.20961 (4) 0.0363 (3)
N1 0.02456 (6) 0.20589 (18) 0.44820 (5) 0.0149 (3)
N2 −0.07152 (6) 0.21600 (18) 0.38149 (5) 0.0153 (3)
N3 −0.07248 (7) −0.0111 (2) 0.44905 (6) 0.0189 (3)
N4 0.25359 (7) 0.51016 (18) 0.45617 (5) 0.0171 (3)
N5 0.52384 (6) 0.71206 (18) 0.45386 (5) 0.0143 (3)
N6 0.42874 (6) 0.76659 (18) 0.38791 (5) 0.0151 (3)
N7 0.41691 (7) 0.5329 (2) 0.45337 (6) 0.0186 (3)
N8 0.76588 (7) 0.94388 (18) 0.46111 (5) 0.0174 (3)
O1 0.19852 (5) 0.40703 (16) 0.37742 (4) 0.0205 (3)
O2 0.70410 (5) 0.85874 (17) 0.38296 (4) 0.0220 (3)
H7B 0.3709 (10) 0.521 (3) 0.4440 (7) 0.027 (5)*
H7A 0.4342 (9) 0.469 (3) 0.4819 (7) 0.021 (5)*
H1A −0.0568 (9) −0.058 (2) 0.4800 (7) 0.016 (4)*
H1B −0.1206 (11) −0.030 (3) 0.4416 (7) 0.032 (5)*

1 Source of material

The compound (E)-7-fluoro-2-((6-methoxypyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one was prepared according to the literature: 4 , 5 15 mL of anhydrous ethanol and 15 mL of 1,2-dichloroethane were added to a flask to dissolve compound (E)-7-fluoro-2-((6-methoxypyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one (0.70 g, 2.37 mmol), guanidine hydrochloride (1.58 g, 16.59 mmol), and potassium hydroxide (0.93 g, 16.59 mmol). The reactants were heated to reflux for 3.5 h and the reaction was monitored by Thin-Layer Chromatography (TLC). The coarse product was isolated and purified after the reaction and the filtrate was removed by concentration under reduced pressure. The residue was separated and purified by silica gel column using dichloromethane/methanol (3:1, v:v) as eluent. The product was dissolved with 30 mL of dichloromethane and 15 mL of methanol and recrystallized at room temperature to give the title compound.

2 Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms, with d(C–H) = 0.96 Å (methyl), U iso(H) = 1.5U eq(C), and d(C–H) = 0.97 Å (methylene), U iso(H) = 1.2U eq(C), and d(C–H) = 0.93 Å (aromatic), U iso(H) = 1.2U eq(C). H atoms on N atom were located in difference maps and treated as riding.

3 Comment

Previous research revealed that some 3,4-dihydronaphthalen-1(2H)-one (DHN) derivatives have good effects on inflammation. 4 , 5 Some 1,4,5,6-tetrahydrobenzo[h]quinazolin-2-amine derivatives with low toxicity and good activity were further synthesized via a Michael addition reaction between DHN derivatives and guanidine hydrochloride under base catalysis. 6 , 7 , 8 Fluorine atoms with strong electronegativity can improve the lipophilicity of compounds, improve membrane permeability and enhance bioavailability. 9 We designed the reaction of 7-position F-substituted tetrahydronaphthalenone with 5-methoxy-2-pyridinecarboxaldehyde by Claisen–Schmidt condensation to obtain compound (E)-7-fluoro-2-((6-methoxypyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one. Further Michael addition with guanidine hydrochloride afforded the target compound 9-fluoro-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine.

The single crystal structure analysis shows that two drug molecules are present in the asymmetric unit (cf. the figure). The bond lengths and bond angles are within the predicted range. 10 Through Michael addition reaction, the original α,β-unsaturated ketone was condensed with guanidine hydrochloride to obtain a 5,6-dihydrobenzo[h]quinazolin-2-amine compound. The bond lengths of C(1)–N(3) and C(19)–N(7) in two molecules are 1.349(2) Å and 1.345(2) Å, respectively. In a molecule, because of two groups of methylene, C(5), C(6) and C(23), C(24), the coplanarity of pyrimidine and fluorophenone rings is more significant. The dihedral angle between 2-aminopyrimidine and fluorophenone rings is about 18.61(3)° and 23.00(3)° in two molecules, respectively. On the other side of the title molecule, it’s replaced by a 6-methoxypyridine substituent. The dihedral angle between 2-aminopyrimidine and 6-methoxypyridine rings is about 56.05(3)° and 56.34(3)° in two molecules, respectively. At the C(9) and C(27) positions, two fluorine atoms are substituted, and the corresponding C(9)–F(1) and C(27)–F(2) bond lengths are 1.3629(19) Å and 1.3602(19) Å, respectively. Overall, this distorted conformation may increase the possibility of interaction with biologically active molecules, resulting in enhanced biological activity. 11 , 12 , 13

Corresponding author: Gui-Ge Hou, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P.R. China, E-mail:

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

  2. Research funding: Shandong Laboratory Program (No. SYS202205), Shandong Provincial Natural Science Foundation (Nos. ZR2022MH159 and ZR2023MH190) and Shandong Province Science and Technology-based Small and Medium-sized Enterprises Innovation Capacity Enhancement Project (No. 2023TSGC0870).

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

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Received: 2024-08-03
Accepted: 2024-09-17
Published Online: 2024-10-29
Published in Print: 2025-02-25

© 2024 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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  44. Crystal structure of ethyl 4-(4-benzylpiperazin-1-yl)benzoate, C20H24N2O2
  45. The crystal structure of bis(selenocyanato-κ1 N)-bis(methanol)-bis((1E,2E)-1,2-bis (1-(pyridin-4-yl)ethylidene)-hydrazine)iron(II) methanol solvate, C34H44FeN10O4Se2
  46. Crystal structure of (E)-1-(5-bromo-2-hydroxyphenyl)-3-(5-(4-methoxyphenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl)prop-2-en-1-one, C26H21BrN2O4
  47. The crystal structure of methyl 4-(4-(methylsulfonyl)phenyl)-2-methyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C19H21NO5S
  48. Crystal structure of 1′,3′-dihydro-2,2′-spirobi[indene]-1,3-dione, C17H12O2
  49. Crystal structure of (E)-2,2′,3,3′-tetrahydro-[1,1′-biindenylidene]-4,4′-diol, C18H16O2
  50. Crystal structure of di-glycylglycinium squarate dihydrate, C12H22N4O12, at 105 K
  51. Crystal structure of {[(4-fluorophenyl)methyl]triphenylphosphonium}dibromocopper(I), [C25H21FP]+[CuBr2]−
  52. Crystal structure of poly[diaqua-bis(μ2-5-((pyridin-4-yl-methyl)amino)benzene-1,3-dicarboxylato-κ 2 N:O)cadmium(II)], C28H26CdN4O10
https://doi.org/10.1515/ncrs-2024-0330
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of the co-crystal 2,4,6-triamino-1,3,5-triazine-1,3-dioxide — acetic acid (1/2) C7H14N6O6
  4. Crystal structure of the dinuclear mercury(II) complex bis(μ2-bromido)-dibromido-bis{1-[(benzotriazol-1-yl)methyl]-1-H-1,3-(2-ethyl-5-methyl-imidazol)-κ1 N} dimercury(II), C26H30N10Hg2Br4
  5. Crystal structure of poly[hexaqua-pentakis(μ4-2,2′-bipyridine-4,4′-dicarboxylato-κ4 O:O′:O″:O‴)-(μ2-2,2′-bipyridine-4,4′-dicarboxylato-κ2 O:O)tetraytterbium(III)] hydrate, C36H26N6O16Yb2
  6. Hydrothermal synthesis and crystal structure of catena-poly[(1,10-phenanthroline-κ 2 N,N′)-bis(μ 2-nitroisophthalato-κ 3 O,O′:O″)nickel(II)], C20H13NiN3O7
  7. Crystal structure of 72,73,75,76-tetrafluoro-25,44-dimethyl-31,33,36,38-tetraoxo-31,32,33,36,37,38-hexahydro-3(2,7)-benzo[lmn][3,8]phenanthrolina-1,5(4,1)-dipyridin-1-iuma-2,4(1,2),7(1,4)-tribenzenacyclooctaphane-11,51-diium hexafluoridophosphate, [C46H28F4N4O4][PF6]2, a dicationic cyclophane
  8. Crystal structure of (E)-2-(4-(1H-imidazol-1-yl)benzylidene)-7-fluoro-3,4-dihydronaphthalen-1(2H)-one, C20H15FN2O
  9. The salt crystal structure of etoricoxib hydrochloride, C18H16Cl2N2O2S
  10. The structure of t-butyl 7-[2-(4-fluorophenyl)-3-phenyl-4-(phenylcarbamoyl)-5-(propan-2-yl)-1H-pyrrol-1-yl]-3,5-dihydroxyheptanoate, C37H43FN2O5
  11. The crystal structure of (μ4-oxo)-tri(μ4-2,2′-bipyridine-6,6′-bis(olato)-κ5 O,O′:N:N′:O″)tetrazinc(II) – methylformamide (1/1), C33H25N7O8Zn4
  12. The co-crystal structure of 4-chlorobenzophenone–salicylhydrazide(1/1), C20H17ClN2O3
  13. Crystal structure of 9-fluoro-4-(6-methoxypyridin-2-yl)-5,6-dihydrobenzo[h]quinazolin-2-amine, C18H15FN4O
  14. The crystal structure of the co-crystal composed of benzhydrazide and 5-aminoisophthalic acid, C8H7NO4⋅C7H8N2O
  15. The cocrystal structure of praziquantel-hesperetin (1/1), C35H38N2O8
  16. Crystal structure of new barium manganese fluorides dihydrates, Ba10Mn2F25·2H2O
  17. The crystal structure of bis[μ2-(3-(3-(pyridin-2-yl)-1H-pyrazol-1-yl)propanoate-κ2O:N)-bis(2,2′-bipyridine-κ2 N, N′)dicopper(II)]dinitrate, C42H36Cu2N12O10
  18. Crystal structure of (3,6-di(2-pyridyl)-4-phenylaminopyridazine-κ2N,N′)-bis(2-(p-toluene)pyridinyl-κ2C,N)-iridium(III) hexafluorophosphate –dichloromethane (1/1), C45H37Cl2F6IrN7P
  19. The crystal structure of 2-(2′-carboxybenzyl)benzoic acid, C15H12O5
  20. The crystal structure of dichlorido-[(E)-N′,N″-bis((2E,3E)-3-(hydroxyimino)butan-2-ylidene)-2-((E)-3-(hydroxyimino)butan-2-ylidene)hydrazine-1-carbohydrazonhydrazide-κ 4 N 4]cobalt(II), C13H22N9O3Cl2Co
  21. Crystal structure of (−)-flavesine H, C15H22N2O2
  22. Crystal structure of 3-methoxybenzyl 2-(6-methoxynaphthalen-2-yl)propanoate, C22H22O4
  23. Crystal structure of dicarbonyl(2-oxopyridin-1(2H)-olato-κ 2 O,O)iridium(I), C7H4IrNO4
  24. The crystal structure of 4-(3-(triphenylphosphonio)propyl)piperazin-1-ium dibromide trihydrate, C25H37Br2N2O3P
  25. The crystal structure of ethyl 5,6-dihydroxybenzofuran-3-carboxylate, C11H10O5
  26. Crystal structure of 14-(R)-(2′-cyano-phenoxy)-3,19-diacetyl andrographolide, C31H37NO7
  27. The twinned crystal structure of 10-(4-methyl benzoate)-2,8-diethyl-5,5-difluoro-1,3,7,9-tetramethyl-5H-di-pyrrolo[1,2-c:2′,1′-f] [1,3,2]diazaborinin-4-ium-5-uide, C25H29BF2N2O2
  28. The crystal structure of (9H-thioxanthen-9- ylidene)hydrazine monohydrate, C13H11N2SO0.5
  29. The crystal structure of pyridinium diaqua-{1,2-phenylenebis((carboxylatocarbonyl)amido-κ4 N,N′,O,O′)manganese(III), C15H14MnN3O8
  30. Crystal structure of the hydrogen storage active high entropy phase Tb0.82Sm0.18Ni0.83Co0.17Mg
  31. Crystal structure of diaqua-bis[5-methyl-1-(1H-pyrazol-3-yl)-1H-1,2,3-triazole-4-carboxylato-κ 2 N,O)]manganese(II), C14H16MnN10O6
  32. Crystal structures of diiodido-3-((pyridin-2-ylmethylene)amino)-2-(pyridin-3-yl)-2,3-dihydroquinazolin-4(1H)-one-cadmium(II)
  33. Synthesis and crystal structure of methyl 4-(2-ethoxy-2-oxoethoxy)-3,5-dimethoxybenzoate, C14H18O7
  34. Crystal structure of isoxazolo[4,5-b]pyridin-3-amine, C6H5N3O
  35. Crystal structure of 4-chloro-1-isobutyl-1H-imidazo, C14H14ClN3
  36. The crystal structure of 1,1,1,2,2,2-hexakis(2-methyl-2-phenylpropyl)distannane,C60H78Sn2
  37. The crystal structure of (2,7-dimethoxynaphthalene-1,8-diyl)bis((3-nitrophenyl)methanone), C26H18N2O8
  38. Crystal structure of diaqua-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) dinitrate dihydrate, C60H76Cl8N14O14Zn
  39. The crystal structure of diphenyl bis(2-((diphenoxyphosphoryl)amino)ethyl)phosphoramidate monohydrate C40H42N3O10P3
  40. Crystal structure of 4,4′-bis(dibromomethyl)-1,1′-biphenyl, C14H10Br4
  41. Crystal structure of CaPtZn
  42. Crystal structure of 3-chloro-5-(trifluoromethyl)pyridine-2-carboxylic acid, C7H3ClF3NO2
  43. The crystal structure of (3′-(2-bromophenyl)-2-phenyl-[2,2′-bioxiran]-3-yl)(phenyl)methanone, C92H68O12Br4
  44. Crystal structure of ethyl 4-(4-benzylpiperazin-1-yl)benzoate, C20H24N2O2
  45. The crystal structure of bis(selenocyanato-κ1 N)-bis(methanol)-bis((1E,2E)-1,2-bis (1-(pyridin-4-yl)ethylidene)-hydrazine)iron(II) methanol solvate, C34H44FeN10O4Se2
  46. Crystal structure of (E)-1-(5-bromo-2-hydroxyphenyl)-3-(5-(4-methoxyphenoxy)-3-methyl-1-phenyl-1H-pyrazol-4-yl)prop-2-en-1-one, C26H21BrN2O4
  47. The crystal structure of methyl 4-(4-(methylsulfonyl)phenyl)-2-methyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C19H21NO5S
  48. Crystal structure of 1′,3′-dihydro-2,2′-spirobi[indene]-1,3-dione, C17H12O2
  49. Crystal structure of (E)-2,2′,3,3′-tetrahydro-[1,1′-biindenylidene]-4,4′-diol, C18H16O2
  50. Crystal structure of di-glycylglycinium squarate dihydrate, C12H22N4O12, at 105 K
  51. Crystal structure of {[(4-fluorophenyl)methyl]triphenylphosphonium}dibromocopper(I), [C25H21FP]+[CuBr2]−
  52. Crystal structure of poly[diaqua-bis(μ2-5-((pyridin-4-yl-methyl)amino)benzene-1,3-dicarboxylato-κ 2 N:O)cadmium(II)], C28H26CdN4O10
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