Home Crystal structure of 2-chloro-3-((thiophen-2-ylmethyl)amino)naphthalene-1,4-dione, C30H20O4N2Cl2S2
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Crystal structure of 2-chloro-3-((thiophen-2-ylmethyl)amino)naphthalene-1,4-dione, C30H20O4N2Cl2S2

  • Li-Mei Jia , Peng Luo and Wei-Gao Pan ORCID logo EMAIL logo
Published/Copyright: November 17, 2021

Abstract

C30H20O4N2Cl2S2, Orthorhombic, Pca21, a = 16.9808(14) Å, b = 7.5227(6) Å, c = 20.8027(16) Å, V = 2657.4(4) Å3, Z = 4, R gt (F) = 0.0642, wRref(F2) = 0.1809, T = 293 K.

CCDC no.: 2113047

One of the two crystallographically independent molecules of the title crystal 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: Red block
Size: 0.35 × 0.29 × 0.21 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.44 mm−1
Diffractometer, scan mode: Bruker APEX3, φ and ω-scans
θmax, completeness: 27.5°, >99%
N(hkl)measuredN(hkl)uniqueRint: 39,478, 6092, 0.060
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 4101
N(param)refined: 341
Programs: Bruker programs [1], OLEX2 [2, 3], SUPERFLIP [4], EDMA [5, 6], SHELX [7]
Table 2:

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

Atom x y z Uiso*/Ueq
Cl1 −0.19535 (13) 0.0023 (2) −0.08712 (12) 0.0551 (6)
S1Aa −0.4205 (4) 0.4825 (8) −0.1413 (3) 0.0572 (9)
S1Bb −0.3088 (4) 0.3830 (7) −0.0421 (2) 0.0572 (9)
O1 −0.2790 (3) 0.2241 (7) −0.3049 (2) 0.0509 (12)
O2 −0.0461 (3) 0.0888 (9) −0.1424 (3) 0.0714 (17)
N1 −0.3209 (3) 0.1229 (7) −0.1912 (3) 0.0392 (12)
H1 −0.348883 0.099891 −0.224556 0.047*
C1 −0.1265 (3) 0.3137 (6) −0.3464 (2) 0.0484 (17)
H1A −0.167155 0.337263 −0.375116 0.058*
C2 −0.14331 (19) 0.2425 (6) −0.2863 (2) 0.0398 (17)
C3 −0.0826 (2) 0.2073 (6) −0.2433 (2) 0.0443 (17)
C4 −0.0051 (2) 0.2432 (6) −0.2604 (3) 0.064 (2)
H4 0.035524 0.219673 −0.231691 0.076*
C5 0.0117 (2) 0.3145 (7) −0.3206 (3) 0.075 (3)
H5 0.063524 0.338538 −0.332028 0.090*
C6 −0.0490 (3) 0.3497 (7) −0.3635 (2) 0.068 (2)
H6 −0.037815 0.397334 −0.403741 0.081*
C7 −0.2253 (3) 0.2047 (7) −0.2686 (3) 0.0354 (14)
C8 −0.2425 (3) 0.1411 (7) −0.2011 (3) 0.0307 (12)
C9 −0.1820 (4) 0.1018 (8) −0.1612 (3) 0.0381 (14)
C10 −0.0999 (4) 0.1308 (8) −0.1789 (4) 0.0454 (16)
C11 −0.3637 (4) 0.1380 (9) −0.1299 (3) 0.0391 (14)
H11A −0.339189 0.060979 −0.098350 0.047*
H11B −0.417472 0.097800 −0.136060 0.047*
C12 −0.3646 (3) 0.3238 (9) −0.1049 (3) 0.0389 (16)
C13Aa −0.3055 (17) 0.421 (3) −0.0564 (12) 0.0572 (9)
H13Aa −0.260820 0.371588 −0.037770 0.069*
C13Bb −0.4039 (16) 0.465 (3) −0.1255 (11) 0.0572 (9)
H13Bb −0.440066 0.458116 −0.158958 0.069*
C14 −0.3325 (5) 0.5899 (12) −0.0472 (5) 0.069 (2)
H14a −0.315837 0.664645 −0.014319 0.082*
H14Ab −0.309934 0.674803 −0.020466 0.082*
C15 −0.3865 (5) 0.6346 (13) −0.0919 (5) 0.072 (3)
H15a −0.404455 0.751174 −0.094774 0.086*
H15Ab −0.407988 0.746210 −0.099887 0.086*
Cl2 −0.05384 (12) 0.9930 (2) −0.47863 (11) 0.0534 (6)
S2Ac 0.0555 (5) 0.5925 (11) −0.5214 (5) 0.0483 (7)
S2Bd 0.17186 (17) 0.5038 (3) −0.42562 (17) 0.0483 (7)
O3 0.0315 (3) 0.7682 (7) −0.2609 (2) 0.0526 (13)
O4 −0.2030 (3) 0.9040 (8) −0.4229 (3) 0.0653 (15)
N2 0.0727 (3) 0.8673 (7) −0.3768 (3) 0.0413 (12)
H2 0.101284 0.890664 −0.343725 0.050*
C16 −0.1210 (2) 0.6810 (6) −0.21950 (19) 0.0477 (17)
H16 −0.080097 0.655324 −0.191214 0.057*
C17 −0.10454 (18) 0.7534 (5) −0.2795 (2) 0.0365 (15)
C18 −0.1656 (2) 0.7918 (5) −0.32177 (18) 0.0411 (16)
C19 −0.2431 (2) 0.7578 (6) −0.3041 (2) 0.053 (2)
H19 −0.283933 0.783530 −0.332339 0.064*
C20 −0.2595 (2) 0.6854 (6) −0.2441 (3) 0.062 (2)
H20 −0.311327 0.662666 −0.232203 0.074*
C21 −0.1984 (3) 0.6470 (6) −0.2018 (2) 0.059 (2)
H21 −0.209410 0.598562 −0.161640 0.071*
C22 −0.0223 (4) 0.7878 (8) −0.2975 (3) 0.0352 (14)
C23 −0.0053 (3) 0.8517 (7) −0.3653 (3) 0.0334 (13)
C24 −0.0672 (4) 0.8932 (8) −0.4045 (3) 0.0382 (14)
C25 −0.1492 (3) 0.8664 (8) −0.3866 (3) 0.0407 (15)
C26 0.1156 (4) 0.8500 (9) −0.4376 (3) 0.0418 (15)
H26A 0.169278 0.890456 −0.431589 0.050*
H26B 0.091109 0.925967 −0.469581 0.050*
C27 0.1167 (3) 0.6627 (10) −0.4622 (2) 0.0401 (16)
C28Ac 0.142 (2) 0.510 (2) −0.4309 (10) 0.0483 (7)
H28Ac 0.157516 0.508141 −0.388066 0.058*
C29 0.1409 (5) 0.3505 (10) −0.4730 (4) 0.059 (2)
H29d 0.157910 0.233581 −0.468600 0.071*
H29Ac 0.168864 0.244904 −0.468470 0.071*
C28Bd 0.0812 (7) 0.5920 (13) −0.5164 (6) 0.0483 (7)
H28Bd 0.054888 0.658046 −0.547458 0.058*
C30 0.0911 (5) 0.3955 (9) −0.5179 (4) 0.064 (2)
H30d 0.065959 0.317940 −0.546068 0.077*
H30Ac 0.075901 0.311728 −0.548380 0.077*
  1. aOccupancy: 0.501(6), bOccupancy: 0.499(6), cOccupancy: 0.209(6), dOccupancy: 0.791(6).

Source of materials

2,3-Dichloro-1,4-naphthoquinone (0.22 mmol) and NaHCO3 (0.44 mmol) were mixed uniformly and moved to a 100 mL double mouth flask. Thiophen-2-ylmethan-amine (0.22 mmol, dissolved with 40 mL of anhydrous methanol) was added to the above mixed solid to start reaction with magnetic stirring at 0 °C in anhydrous environment. The reaction process was monitored by TLC using petroleum ether (60–90 °C boiling range)/acetic ether (6:1 v/v) as developing phase. After 24 h, the reacting mixture was concentrated by a rotary evaporator (60 °C) to achieve a crude solid. This solid was subsequently dissolved in a mixed solvent of methanol-tetrahydrofuran to give a clear red solution after filtration, from which red flat crystals were obtained during the course of volatilization at room temperature. The melting point was determined as 411–412 K using a XT-4 melting point instrument (Beijing Taike Instrument Co., Ltd, China). NMR spectra were performed on a DRX-400 Bruker NMR spectrometer (Bruker, Germany). HRAPCI-MS: [M+H] found 304.01892; C15H11O2NClS [M+H]+ requires 304.01935. 1 H NMR (400 MHz, CDCl3) δ: [ppm] 8.15 (dd, J = 7.6, 1.3 Hz, 1H, H-4), 8.04 (dd, J = 7.6, 1.4 Hz, 1H, H-1), 7.73 (td, J = 7.6, 1.4 Hz, 1H, H-5), 7.64 (td, J = 7.6, 1.3 Hz, 1H, H-6), 7.29 (dd, J = 5.1, 1.2 Hz, 1H, H-15), 7.07 (dd, J = 3.5, 1.2 Hz, 1H, H-13), 7.00 (dd, J = 5.1, 3.5 Hz, 1H, H-14), 6.19 (s, 1H, N–H), 5.23 (d, J = 6.1 Hz, 2H, H-11). 13 C NMR (101 MHz, CDCl3) δ: [ppm] 180.3 (C-10), 176.9 (C-7), 143.6 (C-8), 140.2 (C-12), 134.9 (C-6), 132.6 (C-5), 132.5 (C-3), 129.8 (C-2), 127.2 (C-15), 126.9 (C-1), 126.5 (C-4, 13), 125.9 (C-14), C-9 (signal absence), 43.7 (C-11).

Experimental details

Using Olex2 [2], the structure was solved with the olex2.solve [3] structure solution program using Charge Flipping and refined with the SHELXL [7] refinement package using Least Squares minimization. The H atoms were placed in idealized positions and treated as riding on their parent atoms, with d(C–H) = (0.97) Å (methylene), Uiso(H) = 1.2Ueq(C), d(C–H) = (0.93) Å (aromatic), Uiso(H) = 1.2Ueq(C), and d(N–H) = (0.86) Å, Uiso(H) = 1.2Ueq(N).

Comment

Derivatives with similar structure to that of the title compound have been reported to possess various bioactivities: 2-chloro-3-((furan-2-ylmethyl)amino)-1,4-naphthoquinone showed high antifungal activity against Candida albicans and Aspergillus niger, while 2-chloro-3-((pyridin-2-ylmethyl) or (pyridin-3-ylmethyl) amino)-1,4-naphthoquinone manifested excellent activity against gram positive bacteria (Staphylococcus aureus, Bacillus subtilis) [8]. The compound 2-chloro-3-(benzylamino)-naphthalene-1,4-dione is one of the best performing multitarget-directed molecules in the anti-Alzheimer’s Disease agents screening, which experienced a high potency profile in inhibiting β-amyloid (Aβ40) aggregation, PHF6 tau fragment, AChE enzyme jointly with a remarkable inhibitory activity against MAO B [9]. It also had some effect on neutrophil degranulation in anti-inflammatory investigation and significant inhibitory effect on mast cell degranulation in antiallergic assay [10]. In our group, the title compound was synthesized for anticancer assay and further to investigate its interactions with Caspase-3 and Topoisomerase-II α/β, so it is necessary to study the single crystal structure.

The asymmetric unit of the title structure contains two molecules 2-chloro-3-((thiophen-2-ylmethyl)amino)naphthalene-1,4-dione, in which the thiophene moieties are disordered, but all other values of the geometric parameters are normal. The crystal packing is stabilized by intermolecular hydrogen bonds: N1–H1…O3 (d(N1–H1…O3) = 3.010 Å; ∠ N1–H1…O3 = 130°), N2–H2A…O1 (d(N2–H2A…O1) = 3.008 Å; ∠ N2–H2A…O1 = 133°).

By a search for a similar molecular scaffold three similar compounds, 2-chloro-3-((2-thienylethyl) amino)-1,4-naphtho-quinone [11], 2-bromo-3-((2-thienylmethyl)amino)-1,4-na-phthoquinone [12] and 2-chloro-3-((2-furylmethyl) amino)-1,4-naphthoquinone [8] were found, in which, the first one owned one more methylene than the title compound at the fatty-thienyl moiety [11], the second one was not 2-chloro but 2-bromo substituent [12], while the third one had a furan ring instead of the thienyl group in the title compound [8]. Furthermore, amazing difference among them was the number of molecules in the asymmetric unit of crystal structure, the three reported crystals had only one molecules in their asymmetric units [8, 11, 12].


Corresponding author: Wei-Gao Pan, Guangxi University of Chinese Medicine, Nanning 530001, China, E-mail:

Funding source: Education Department of Guangxi Zhuang Autonomous Region

Award Identifier / Grant number: 2019KY0329

Funding source: Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine

Award Identifier / Grant number: GXZYZZ2019-7

Funding source: Education Department of Guangxi Zhuang Autonomous Region

Award Identifier / Grant number: J16067-11

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

  2. Research funding: This work was supported by grants from Promotion of Young and Middle-aged Teachers’ Basic Scientific Research Ability in Guangxi Universities, Education Department of Guangxi Zhuang Autonomous Region (grant no. 2019KY0329), Key laboratory opening topic fund, Guangxi Key Laboratory of Zhuang and Yao Ethnic Medicine (grant no. GXZYZZ2019-7), Opening topic fund of Key Laboratory of TCM Extraction and Purification and Quality Analysis (Guangxi University of Chinese Medicine), Education Department of Guangxi Zhuang Autonomous Region (grant no. J16067-11).

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

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Received: 2021-10-08
Accepted: 2021-11-05
Published Online: 2021-11-17
Published in Print: 2022-02-23

© 2021 Li-Mei Jia et al., published by De Gruyter, Berlin/Boston

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

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  39. Crystal structure of bis(μ3-oxido)-bis(μ2-2-formylbenzoato-k2O:O′)-bis(2-(dimethoxymethyl)-benzoato-κO)-oktakismethyl-tetratin(IV)
  40. Crystal structure of 2-((E)-(((E)-2-hydroxy-4-methylbenzylidene) hydrazineylidene)methyl)-4-methylphenol, C16H16N2O2
  41. Crystal structure of (E)-amino(2-((5-methylfuran-2-yl)methylene)hydrazinyl) methaniminium nitrate monohydrate, C14H26N10O10
  42. The crystal structure of N′-(2-chloro-6-hydroxybenzylidene)thiophene-2-carbohydrazide monohydrate, C12H11ClN2O3S
  43. Crystal structure of catena-poly[(μ2-1,1′-(biphenyl-4,4-diyl)bis(1H-imidazol)-κ2N:N′)-bis(4-bromobenzoate-κ1O)zinc(II)], C64H44Br4N8O8Zn2
  44. The crystal structure of catena-poly[(1-(4-carboxybenzyl)pyridin-1-ium-4-carboxylato-κ1O)-(μ2-oxalato-κ4 O:O′:O″:O‴)dioxidouranium(VI)], C16H11NO10U
  45. Crystal structure of 3-allyl-4-(2-bromoethyl)-5-(4-methoxyphenyl)-2-phenylfuran, C22H21BrO2
  46. Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3
  47. Crystal structure of 2-(1H-indol-3-yl)ethan-1-aminium 2-(4-acetylphenoxy)acetate, C20H22N2O4
  48. Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se
  49. The crystal structure of 1,4-bis((1H-benzimidazol-2-yl)methyl)-piperazine-2,5-dione dihydrate, C20H22N6O4
  50. The crystal structure of C19H20O8
  51. The crystal structure of KNa3Te8O18·5H2O exhibiting a 2[Te4O9]2− layer
  52. Erratum
  53. Erratum to: Crystal structure of (Z)-3-(6-bromo-1H-indol-3-yl)-1,3-diphenylprop-2-en-1-one, C23H16BrNO
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