Home Crystal structure of 2-amino-4-(2-fluoro-3-(trifluoromethyl)phenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, C20H18ClF4N3O
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Crystal structure of 2-amino-4-(2-fluoro-3-(trifluoromethyl)phenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-3-ium chloride, C20H18ClF4N3O

  • Lu Yu , Qing-Guo Meng , Gui-Ge Hou ORCID logo , Yong-Jun Liu and Zi-Kai Geng EMAIL logo
Published/Copyright: October 11, 2023

Abstract

C20H18ClF4N3O, orthorhombic, Pbca (no. 61), a = 12.5254(4) Å, b = 12.6845(5) Å, c = 24.1490(11) Å, V = 3836.8(3) Å3, Z = 8, R gt (F) = 0.0485, wR ref (F2) = 0.1343, T = 293 K.

CCDC no.: 2272279

The crystal structure is shown in the Figure. Displacement ellipsoids are drawn at the 30 % 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.

Table 1:

Data collection and handling.

Crystal: Yellow block
Size: 0.15 × 0.14 × 0.12 mm
Wavelength: Cu Kα radiation (1.54178 Å)
μ: 2.27 mm−1
Diffractometer, scan mode: XtaLAB AFC12 (RINC)
θmax, completeness: 73.9°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 15,274, 3805, 0.054
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 3361
N(param)refined: 267
Programs: CrysAlisPRO [1], SHELX [2, 3]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.30840 (16) 0.12858 (17) 0.96703 (8) 0.0246 (4)
C2 0.23258 (17) −0.03005 (17) 0.92281 (9) 0.0254 (4)
H2 0.196956 −0.087685 0.942537 0.031*
C3 0.42679 (17) 0.00620 (16) 0.92360 (8) 0.0242 (4)
C4 0.34727 (17) −0.06157 (17) 0.91374 (8) 0.0255 (4)
C5 0.37032 (17) −0.17070 (18) 0.89178 (9) 0.0288 (5)
H5A 0.307908 −0.197654 0.872669 0.035*
H5B 0.386304 −0.217742 0.922342 0.035*
C6 0.46457 (17) −0.16732 (19) 0.85214 (10) 0.0300 (5)
H6A 0.486494 −0.238748 0.843386 0.036*
H6B 0.442855 −0.133391 0.817949 0.036*
C7 0.66270 (18) −0.13206 (18) 0.86310 (10) 0.0303 (5)
H7 0.676359 −0.191188 0.841456 0.036*
C8 0.74780 (17) −0.07028 (18) 0.88084 (9) 0.0295 (5)
H8 0.817419 −0.088135 0.871275 0.035*
C9 0.72789 (17) 0.01795 (18) 0.91283 (9) 0.0272 (5)
C10 0.62408 (17) 0.04198 (17) 0.92874 (9) 0.0267 (4)
H10 0.611432 0.099480 0.951717 0.032*
C11 0.53901 (16) −0.01928 (17) 0.91057 (8) 0.0243 (4)
C12 0.55823 (17) −0.10792 (18) 0.87679 (9) 0.0270 (4)
C13 0.17654 (16) −0.01599 (18) 0.86689 (9) 0.0262 (4)
C14 0.20727 (17) 0.06165 (17) 0.82983 (9) 0.0269 (5)
C15 0.16062 (19) 0.07353 (19) 0.77779 (9) 0.0330 (5)
C16 0.0802 (2) 0.0040 (2) 0.76248 (10) 0.0407 (6)
H16 0.047463 0.010721 0.728103 0.049*
C17 0.0488 (2) −0.0752 (2) 0.79826 (11) 0.0405 (6)
H17 −0.004475 −0.122119 0.787646 0.049*
C18 0.09643 (18) −0.0851 (2) 0.85013 (9) 0.0326 (5)
H18 0.074436 −0.138563 0.873875 0.039*
C19 0.2015 (2) 0.1571 (2) 0.73930 (10) 0.0400 (6)
C20 0.90917 (17) 0.07421 (19) 0.90861 (10) 0.0318 (5)
H20A 0.939270 0.008785 0.921084 0.048*
H20B 0.953645 0.131551 0.920490 0.048*
H20C 0.904789 0.074016 0.868927 0.048*
Cl1 0.53974 (4) 0.31046 (4) 0.97499 (2) 0.02830 (16)
F1 0.28703 (10) 0.12832 (10) 0.84377 (5) 0.0310 (3)
F2 0.30268 (14) 0.13926 (13) 0.72382 (7) 0.0561 (5)
F3 0.20003 (13) 0.25397 (12) 0.76144 (6) 0.0452 (4)
F4 0.14390 (17) 0.16261 (15) 0.69268 (6) 0.0643 (5)
N1 0.40529 (14) 0.10538 (14) 0.94739 (7) 0.0251 (4)
H1A 0.458166 0.152892 0.953256 0.033 (7)*
N2 0.22689 (14) 0.06415 (14) 0.95774 (7) 0.0261 (4)
H2A 0.164557 0.082781 0.970729 0.031 (7)*
N3 0.29398 (14) 0.21691 (15) 0.99561 (8) 0.0279 (4)
H3A 0.347756 0.251484 1.003201 0.045 (8)*
H3B 0.229409 0.229185 1.008687 0.042 (8)*
O1 0.80455 (12) 0.08656 (13) 0.93148 (7) 0.0316 (4)

1 Source of material

Based on literature synthetic techniques [4, 5], using 20 % sodium hydroxide solution (5.0 mL) as a catalyst, 7-methoxy-3,4-dihydronaphthalen-1(2H)-one (0.70 g, 4.00 mmol) was mixed with 2-fluoro-3-(trifluoromethyl)benzaldehyde (0.77 g, 4.00 mmol) in 25 mL of methanol with stirring for 3 h at room temperature to produce a yellow precipitate. Filtration gave an intermediate: (E)-2-(2-fluoro-3-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one. The intermediate (0.830 g, 2.37 mmol), guanidine hydrochloride (1.58 g, 16.59 mmol) and potassium hydroxide (0.931 g, 16.59 mmol) were added to a mixture of anhydrous ethanol (10 mL) and dichloroethane (10 mL), and the reaction was carried out at 90 °C for 2 h. The reaction was monitored by Thin–Layer Chromatography (TLC, PE:EA = 8:1, v/v). The filtered filtrate is depressurized to remove the solvent. Dichloromethane/methanol (20:1, v/v) was used as eluent to separate and purify by the silica gel column. The obtained product was dissolved in a solution of dichloromethane (5 mL) and methanol (5 mL), and slowly evaporated at room temperature to achieve appropriate yellow crystals.

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), Uiso(H) = 1.5Ueq(C), and d(C–H) = 0.97 Å(methylene), Uiso(H) = 1.2Ueq(C), and d(C–H) = 0.98 Å(methyne), Uiso(H) = 1.2Ueq(C), and d(C–H) = 0.93 Å(aromatic), Uiso(H) = 1.2Ueq(C). H atoms on N atom were located in different maps and treated as riding.

3 Comment

3,4–Dihydronaphthalene-1(2H)-one derivatives have been used in previous studies as formulations and inhibitors of novel anti-allergic, anti-inflammatory drugs and retinoic acid metabolic enzymes [6]. It contains two pharmacophores: 3,4-dihydronaphthalen-1(2H)-one and an α,β-unsaturated token. These two pharmacophores can be used as the main binding sites [4]. The 1,4,5,6-tetrahydrobenzo[h]quinazoline-2-amine skeleton structure formed by the condensation of α,β-unsaturated ketones with guanidinium chloride that can effectively improve the water solubility [7]. The substitution of the trifluoromethyl group can transform the substituent into a powerful electron-withdrawing group, which can slightly increase lipophilicity [8]. In this study, the Claisen–Schmidt reaction of 7-methoxy-3,4-dihydronaphthalene-1(2H)-one with 2-fluoro-3-(trifluoromethyl)benzaldehyde to form the intermediate (E)-2-(2-fluoro-3-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalene-1(2H)-one was investigated. The target product: 4-(2-fluoro-4-(trifluoromethyl)phenyl)-9-methoxy-1,4,5,6-tetrahydrobenzo[h]quinazolin-2-amine was obtained by the condensation of the intermediate with guanidinium chloride hydrochloride.

Single crystals were obtained by evaporation from dichloromethane/methanol solution at room temperature. The single crystal structure analysis shows that 2-fluoro-4-(trifluoromethyl)phenyl and carbonyl groups adopt E stereochemistry. There is a chiral C(2) atom at the bridgehead position of 1,4,5,6-tetrahydrobenzo[h]quinazoline-2-amine. In the solid state, the molecules crystallize in an orthorhombic group Pbca, and the whole does not show chiral properties. However, the crystal generates two isomers, which one is the S configuration and the other is the R configuration [9]. The benzene ring at C(2) atom is substituted by electron-withdrawing substituents (–F and –CF3). Because of the chiral structural characteristics and the substituent effect, there is a large dihedral angle between the central parent nucleus and the substituted benzene ring, with the dihedral angle of about 84.98(3)°. This twisting structure may increase the possibility of interaction with bioactive molecules [10]. In addition, the pyrimidine ring is non-aromatic ring, which is different from aromatic pyrimidine ring in 5,6-dihydrobenzo[h]quinazolin-2-amine derivatives [11, 12]. In this study, the non-aromatic pyrimidine ring has different bond lengths, i.e. bond lengths of C(1)–N(1), C(1)–N(2), C(2)–N(2), C(2)–C(4), C(3)–C(4), C(3)–N(1) are 1.336(3), 1.327(3), 1.464(3), 1.507(3), 1.337(3) and 1.409(3) Å, respectively. Interestingly, 1,4,5,6-tetrahydrobenzo[h]quinazoline-2-amine has a positive charge and forms a stable structure with a chloride ion [13, 14]. The chloride ion, as a hydrogen-bond acceptor, was stabilized by three groups of hydrogen bonds, viz. N(1)–H(1A)⋯Cl(1), N(3)–H(3A)⋯Cl(1) and C(10)–H(10)⋯Cl(1) bonds.


Corresponding author: Zi-Kai Geng, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P.R. China, E-mail:

Funding source: Shandong Provincial Natural Science Foundation

Award Identifier / Grant number: ZR2023MH190

Funding source: Project of Improving Innovation Ability of Small and Medium-Sized Sci-Tech Enterprises in Shandong Province

Award Identifier / Grant number: 2023TSGC0870

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

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

  3. Research funding: This work was supported by Shandong Provincial Natural Science Foundation (No. ZR2023MH190) and Project of Improving Innovation Ability of Small and Medium-Sized Sci-Tech Enterprises in Shandong Province (No. 2023TSGC0870).

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Received: 2023-08-16
Accepted: 2023-09-29
Published Online: 2023-10-11
Published in Print: 2023-12-15

© 2023 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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  48. Crystal structure of (1E,1′E)-4,4′-(9,9-diethyl-9H-fluorene-2,7-diyl)dibenzaldehyde dioxime, C31H28N2O2
  49. Crystal structure of diethyl 1,9-bis(4-fluorophenyl)-4,6-diphenylhexahydro-3H-2,7,3,5-(epimethanetriyliminomethanetriyl)cyclopenta [b]pyridine-3,7(2H)-dicarboxylate, C40H36F2N2O4
  50. Crystal structure of bis(benzene-1 carboxylato-O 3,5-carboxyl-κ1O)-[(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)nickel(II) ─ benzene-1,3,5-tricarboxylic acid ─ water (1/2/4), C52H66N4NiO28
  51. Crystal structure of 1,4-dibromo-2,5-bis(2-methoxyethoxy)benzene-1,4-diol, C12H16Br2O4
  52. Crystal structure of dicarbonyl[N,N′-(1,2-dimethyl-1,2-ethanediylidene)bis[2,6-bis(1-methylethyl)benzenamine]-N,N′]nickel(0), C30H40N2NiO2
  53. Crystal structure of 1,4-dibromo-2,5-bis(prop-2-yn-1-yloxy)benzene, C12H8Br2O2
  54. Crystal structure of O-(3-(benzo[d]thiazol-2-yl)naphthalen-2-yl) O-phenyl carbonothioate, C24H15NO2S2
  55. The crystal structure of (E)-4-fluoro-N′-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H15FN2O2
  56. Crystal structure of (E)-1-(benzo[d]thiazol-2-yl)-N-(4,5-dihydropyren-2-yl)methanimine, C24H16N2S
  57. Crystal structure of 3-((4-bromophenyl)thio)-1H-indole, C14H10BrNS
  58. Synthesis and crystal structure of 1-((7-hydroxy-3-(4-hydroxy-3-nitrophenyl)-4-oxo-4H-chromen-8-yl)methyl)piperidin-1-ium-4-carboxylate monohydrate, C22H22N2O9
  59. Synthesis and crystal structure of (3E,5S,10S,13S,14S,17Z)-17-ethylidene-10,13-dimethylhexadecahydro-3H-cyclopenta[α]phenanthren-3-one O-(methacryloyl) oxime, C50H74N2O4
  60. Crystal structure of the hydrogen storage active phase La12Mg46LiMn
  61. The crystal structure of the salt: 4-((1,3-dioxoisoindolin-2-yl)carbamoyl)pyridine-1-ium 2-carboxybenzoate, C14H10N3O3·C8H5O4
  62. Crystal structure of (2-(2-pyridine)-benzimidazole-κ2 N,N′)-bis(1-phenylpyrazole-κ2 C,N)iridium(III) hexafluorophosphate, C30H22F6IrN7P
  63. Crystal structure of dichlorido-bis[2-(2,4-difluorophenyl)pyridine-κ1N]platinum(II), C22H14Cl2F4N2Pt
  64. Crystal structure of (5R,8R,9R,10R,12R,13R,14R, 17S,17Z)-2-((3-fluoropyridin-4-yl)methylene)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl)hexadecahydro-3H-cyclopenta[a]phenanthren-3-one, C36H52FNO3
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