Home The crystal structure of 1-((1-methyl-1H-1,2,4-triazol-3-yl) methyl)-3-(2,4,5-trifluorobenzyl)-1,3,5-triazinane-2,4,6-trione, C14H11F3N6O3
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The crystal structure of 1-((1-methyl-1H-1,2,4-triazol-3-yl) methyl)-3-(2,4,5-trifluorobenzyl)-1,3,5-triazinane-2,4,6-trione, C14H11F3N6O3

  • Yi-Jing Du , Hong-Shun Sun ORCID logo EMAIL logo , Jian-Qiang Wang and Jia-Ying Xu
Published/Copyright: February 14, 2023

Abstract

C14H11F3N6O3, orthorhombic, Pbca (no. 61), a = 8.08620(10) Å, b = 15.4730(2) Å, c = 23.5892(2) Å, V = 2951.43(6) Å3, Z = 8, R gt (F) = 0.0463, wR ref (F 2) = 0.1395, T = 293 K.

CCDC no.: 2238122

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: Colorless block
Size: 0.20 × 0.10 × 0.10 mm
Wavelength: Cu Kα radiation (1.54178 Å)
μ: 1.28 mm−1
Diffractometer, scan mode: Rigaku Mercury
θ max, completeness: 74.4°, >99%
N(hkl)measured, N(hkl)unique, R int: 50,285, 2991, 0.065
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 2712
N(param)refined: 235
Programs: Rigaku [1], Olex2 [2], SHELX [3, 4]
Table 2:

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

Atom x y z U iso*/U eq
N1 0.20256 (18) 0.07419 (9) 0.36883 (6) 0.0180 (3)
N2 0.11187 (19) 0.02902 (10) 0.28007 (6) 0.0206 (3)
H2A 0.0939 −0.0120 0.2563 0.025*
N3 0.11168 (18) 0.17574 (9) 0.30152 (6) 0.0180 (3)
N4 −0.12391 (19) 0.38431 (10) 0.29917 (6) 0.0216 (3)
N5 −0.29975 (18) 0.31259 (10) 0.35155 (6) 0.0199 (3)
N6 −0.17560 (19) 0.25533 (10) 0.34046 (6) 0.0205 (3)
O1 0.21541 (18) −0.06774 (9) 0.34285 (6) 0.0274 (3)
O2 −0.00009 (17) 0.12553 (9) 0.21859 (5) 0.0258 (3)
O3 0.19661 (16) 0.21725 (8) 0.38928 (5) 0.0229 (3)
F1 0.32191 (15) 0.14838 (9) 0.52638 (5) 0.0336 (3)
F2 0.89419 (15) 0.14513 (9) 0.49200 (5) 0.0351 (3)
F3 0.84506 (14) 0.05513 (8) 0.39638 (5) 0.0337 (3)
C1 0.4189 (2) 0.07909 (11) 0.44397 (7) 0.0204 (4)
C2 0.4512 (2) 0.12507 (12) 0.49312 (7) 0.0234 (4)
C3 0.6076 (3) 0.14877 (13) 0.51088 (8) 0.0266 (4)
H3A 0.6237 0.1798 0.5442 0.032*
C4 0.7382 (2) 0.12455 (13) 0.47719 (8) 0.0250 (4)
C5 0.7112 (2) 0.07786 (13) 0.42787 (8) 0.0243 (4)
C6 0.5551 (2) 0.05499 (12) 0.41111 (8) 0.0221 (4)
H6B 0.5397 0.0235 0.3779 0.027*
C7 0.2442 (2) 0.05469 (13) 0.42821 (7) 0.0224 (4)
H7A 0.2290 −0.0067 0.4348 0.027*
H7B 0.1681 0.0854 0.4528 0.027*
C8 0.1810 (2) 0.00649 (11) 0.33122 (7) 0.0196 (4)
C9 0.0687 (2) 0.11135 (12) 0.26347 (7) 0.0196 (4)
C10 0.1720 (2) 0.15992 (11) 0.35567 (7) 0.0180 (4)
C11 0.0846 (2) 0.26610 (11) 0.28568 (8) 0.0204 (4)
H11A 0.0826 0.2707 0.2447 0.025*
H11B 0.1761 0.3007 0.2995 0.025*
C12 −0.0737 (2) 0.30146 (11) 0.30907 (7) 0.0183 (4)
C13 −0.2670 (2) 0.38735 (12) 0.32676 (8) 0.0225 (4)
H13A −0.3352 0.4357 0.3284 0.027*
C14 −0.4433 (2) 0.28671 (13) 0.38477 (8) 0.0264 (4)
H14A −0.4301 0.2279 0.3970 0.040*
H14B −0.4533 0.3237 0.4173 0.040*
H14C −0.5411 0.2915 0.3619 0.040*

Source of material

All chemicals were obtained from commercial sources and used as purchased. To a solution of 6-(ethylthio)-3-((1-methyl-1H-1,2,4-triazol-3-yl)methyl)-1-(2,4,5-trifluorobenzyl)-1,3,5-triazine-2,4(1H,3H)-dione (0.41 g, 1 mmol) in dichloromethane (20 mL), 3-chloroperoxybenzoic acid (0.51 g, 3 mmol) was added. Then the mixture was stirred at room temperature for 3 h. After the reaction was completed, the solution was washed with saturated NaHSO3 and NaHCO3, respectively. The organic layer was dried over anhydrous magnesium sulfate, filtered, and concentrated under reduced pressure. The crude products were purified by flash column chromatography. Colorless block crystals of the title compound were obtained by slow evaporation of a solution in ethyl acetate. 1 H NMR (400 MHz, DMSO-d 6): δ 12.08 (s, 1H), 8.39 (s, 1H), 7.60 (m, 1H), 7.49 (m, 1H), 4.95 (s, 4H), 3.83 (s, 3H).

Experimental details

Absorption corrections were applied using a multi-scan program [1]. Using Olex2 [2], the structure was solved with the ShelXT [3] package and refined with the ShelXL [4] program. H atoms were positioned geometrically and allowed to ride on their parent atoms, with C–H = 0.93 Å (phenyl and triazolyl), 0.96 Å (methyl) or 0.97 Å (methylene) and with U iso(H) = 1.2U eq(C), and N–H = 0.86 Å and U iso(H) = 1.2U eq(N).

Comment

The 1,3,5-triazinane-2,4,6-trione, known as isocyanurate, is used to be a human gonadotropin-releasing hormone receptor antagonist [5, 6]. Many references showed crystal structures of the derivatives with 1,3,5-triazinane-2,4,6-trione as parent structure [7], [8], [9], [10]. In this work, we report the single crystal structure of 1-((1-methyl-1H-1,2,4-triazol-3-yl) methyl)-3-(2,4,5-trifluorobenzyl)-1,3,5-triazinane-2,4,6-trione, which is an intermediate for the synthesis of ensitrelvir, a novel oral drug for the treatment of coronavirus disease 2019 (COVID-19) [11].

Single-crystal structure analysis revealed that the asymmetric unit consists one 1-((1-methyl-1H-1,2,4-triazol-3-yl)methyl)-3-(2,4,5-trifluorobenzyl)-1,3,5-triazinane-2,4,6-trione molecule. The central six-membered heterocyclic ring lies on a general position, which is evidently different from that observed in the symmetric tri-substituted compounds (lying on a 3-fold totation axis) [7], [8], [9]. The dihedral angles between the least-squares plane of the central triazinane ring of the title molecule and those of the terminal triazole/benzene ring groups are 80.5(4)° (C12/N4/C13/N5/N6) and 78.0(2)° (C1–C6), respectively. The two planes of the terminal ring of the title molecule are oriented with respect to each other at 78.4(3)° [(C12/N4/C13/N5/N6) and (C1–C6)]. In the solid state structure, numerous classical N–H⃛N and weak C–H⃛F, C–H⃛N and C–H⃛O hydrogen-bonding interactions result in a one-dimensional supramolecular chain along the [0 1 0] direction.


Corresponding author: Hong-Shun Sun, Targeted MRI Contrast Agents Laboratory of Jiangsu Province, Nanjing Polytechnic Institute, Nanjing 210048, 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: Natural Science Foundation of Jiangsu Province (No. BK20181486), Natural Science Foundation of Jiangsu Higher Education Institutions (No. 17KJB320001), Key Program of Nanjing Polytechnic Institute (No. NJPI-2022-02) and Qinglan Project of Jiangsu Province (2019).

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

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Received: 2023-01-05
Accepted: 2023-01-26
Published Online: 2023-02-14
Published in Print: 2023-04-25

© 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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  74. The crystal structure of trichlorido[N-[(2-oxyphenyl)methylidene]phenylglycinemethylester-κ3O,N,O′]-tin(IV) – methylene chloride (1/1), C16H14Cl3NO3Sn·CH2Cl2
  75. The crystal structure of furan-2,5-diylbis((4-chlorophenyl)methanol), C18H14Cl2O3
  76. The crystal structure of hexalithium decavanadate hexadecahydrate, H32Li6O44V10
  77. Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S
  78. Crystal structure of aqua(μ2-2,2′,2″-((nitrilo)tris(ethane-2,1-diyl(nitrilo)methylylidene))tris (6-ethoxyphenolato))(pentane-2,4-dionato-κ2O,O′)-dinickel(II), C38H48N4Ni2O9
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