Home The crystal structure of N,N′-(1,2-phenylene)bis (2-((2-oxopropyl)selanyl)benzamide), C26H24N2O4Se2
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The crystal structure of N,N′-(1,2-phenylene)bis (2-((2-oxopropyl)selanyl)benzamide), C26H24N2O4Se2

  • Shuxiao Feng ORCID logo EMAIL logo , Xuan Zhong , Kaiyan Qi , Yafei Guo ORCID logo , Junling Wang ORCID logo , Guangna Gu and Junying Ma
Published/Copyright: May 31, 2023
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 238 Issue 4

Abstract

C26H24N2O4Se2, monoclinic, C2/c (no. 15), a = 22.9092(7) Å, b = 5.8900(2) Å, c = 36.6209(9) Å, β = 91.983(3)°, V = 4938.5(3) Å3, Z = 8, R gt (F) = 0.0419, wR ref (F 2) = 0.1162, T = 293 K.

CCDC no.: 2103258

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: Yellow block
Size: 0.13 × 0.10 × 0.08 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 4.04 mm−1
Diffractometer, scan mode: Xcalibur, ω
θ max, completeness: 67.1°, >99 %
N(hkl) measured, N(hkl)unique, R int: 14,718, 4379, 0.038
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3327
N(param)refined: 325
Programs: CrysAlisPRO [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
Se1 0.47870 (2) 0.15546 (9) 0.54004 (2) 0.05475 (16)
Se2 0.67807 (2) 0.24397 (10) 0.70607 (2) 0.06457 (18)
O1 0.54585 (14) −0.1959 (6) 0.55983 (8) 0.0692 (9)
O2 0.69068 (13) −0.1167 (5) 0.66263 (7) 0.0609 (8)
O3 0.34211 (14) 0.4608 (7) 0.55843 (9) 0.0793 (10)
O4a 0.5843 (8) 0.376 (4) 0.7620 (6) 0.114 (5)
N1 0.61238 (15) −0.2067 (6) 0.60686 (9) 0.0522 (9)
H1 0.6263 (13) −0.146 (5) 0.6258 (6) 0.023 (8)*
N2 0.73920 (15) −0.1431 (6) 0.61037 (9) 0.0511 (8)
H2 0.7670 (15) −0.081 (8) 0.5996 (12) 0.075 (16)*
C1 0.48852 (16) 0.1790 (7) 0.59245 (10) 0.0477 (10)
C2 0.45913 (17) 0.3427 (8) 0.61201 (11) 0.0570 (11)
H2A 0.4339 0.4427 0.5997 0.068*
C3 0.4670 (2) 0.3584 (9) 0.64949 (12) 0.0693 (14)
H3 0.4469 0.4680 0.6623 0.083*
C4 0.5041 (2) 0.2143 (10) 0.66775 (12) 0.0756 (15)
H4 0.5088 0.2242 0.6930 0.091*
C5 0.53459 (19) 0.0541 (10) 0.64891 (11) 0.0685 (13)
H5 0.5602 −0.0430 0.6615 0.082*
C6 0.52753 (16) 0.0357 (8) 0.61088 (10) 0.0510 (10)
C7 0.56201 (18) −0.1334 (8) 0.59053 (11) 0.0530 (10)
C8 0.65061 (18) −0.3665 (7) 0.59201 (11) 0.0495 (10)
C9 0.6284 (2) −0.5589 (8) 0.57457 (13) 0.0637 (12)
H9 0.5884 −0.5861 0.5743 0.076*
C10 0.6644 (2) −0.7101 (8) 0.55764 (15) 0.0719 (14)
H10 0.6486 −0.8346 0.5452 0.086*
C11 0.7234 (3) −0.6761 (9) 0.55926 (14) 0.0735 (14)
H11 0.7477 −0.7780 0.5478 0.088*
C12 0.7472 (2) −0.4924 (8) 0.57771 (12) 0.0600 (11)
H12 0.7875 −0.4730 0.5790 0.072*
C13 0.71138 (18) −0.3356 (7) 0.59446 (10) 0.0485 (9)
C14 0.72992 (17) −0.0506 (8) 0.64348 (10) 0.0514 (10)
C15 0.76875 (17) 0.1409 (8) 0.65555 (10) 0.0515 (10)
C16 0.8228 (2) 0.1760 (9) 0.64032 (13) 0.0682 (13)
H16 0.8354 0.0758 0.6226 0.082*
C17 0.8581 (2) 0.3555 (10) 0.65077 (14) 0.0748 (14)
H17 0.8938 0.3780 0.6399 0.090*
C18 0.8402 (2) 0.5000 (10) 0.67731 (15) 0.0799 (16)
H18 0.8639 0.6209 0.6846 0.096*
C19 0.7878 (2) 0.4692 (9) 0.69329 (13) 0.0699 (13)
H19 0.7765 0.5689 0.7114 0.084*
C20 0.75093 (18) 0.2906 (8) 0.68283 (11) 0.0545 (11)
C21 0.43181 (18) 0.4280 (8) 0.52876 (11) 0.0566 (11)
H21A 0.4443 0.5513 0.5447 0.068*
H21B 0.4376 0.4743 0.5037 0.068*
C22 0.36861 (18) 0.3790 (8) 0.53385 (11) 0.0552 (11)
C23 0.3393 (2) 0.2172 (10) 0.50735 (13) 0.0763 (15)
H23A 0.3208 0.0981 0.5206 0.114*
H23B 0.3679 0.1528 0.4919 0.114*
H23C 0.3105 0.2972 0.4927 0.114*
C24 0.6748 (2) 0.5241 (9) 0.73489 (14) 0.0801 (15)
H24A 0.7024 0.5181 0.7556 0.096*
H24B 0.6838 0.6549 0.7200 0.096*
C25 0.6130 (3) 0.5370 (11) 0.74766 (14) 0.0823 (16)
C26a 0.5823 (8) 0.763 (3) 0.7458 (6) 0.116 (5)
H26Aa 0.5658 0.7854 0.7216 0.174*
H26Ba 0.6099 0.8818 0.7514 0.174*
H26Ca 0.5519 0.7654 0.7631 0.174*
O4Ab 0.6046 (11) 0.439 (5) 0.7728 (8) 0.114 (5)
C26Ab 0.5757 (11) 0.678 (4) 0.7240 (7) 0.116 (5)
H26Db 0.5831 0.6445 0.6989 0.174*
H26Eb 0.5841 0.8353 0.7288 0.174*
H26Fb 0.5355 0.6476 0.7287 0.174*

  1. aOccupancy: 0.565 (15), bOccupancy: 0.435 (15).

1 Source of material

To a 50 mL round bottom flask, add 2-chloroselenylbenzoyl chloride (0.5 mmoL) and 3 mL acetone and the mixture was kept for 18 h under anhydrous condition at room temperature. After the reactant completely reacts, o–phenylenediamine (0.5 mmoL) is added and the reaction continues for 15 min. Add 5 mL water slowly to quench the reaction, and let it stand to precipitate crystals. For the crude product without crystal precipitation, use ethyl acetate Ester (3 × 20 mL) extraction, column chromatography (petroleum ether/ethyl acetate = 3:1) separation and purification to obtain the target product.

2 Experimental details

Using Olex2 [2], the structure was solved with the ShelXS [3] structure solution program and refined with the ShelXL [4] refinement package.

3 Comment

As an organic selenium compound with antioxidant and anti-inflammatory properties, Ebselen is a mimic of glutathione peroxidase (GPX) and an excellent scavenger of peroxynitrite [5]. The crystals that it combines with various organic amino acids have attracted much attention [6, 7] and its analogues were extensively studied [8, 9]. The title crystal is symmetric Ebselen analogue of open loop mother nucleus, it is the latest discovery based on previous research [10]. The crystal structure is shown in the Figure which includes that the two open loop mother nucleus of Ebselen are connected to acetone by Se–C and they are connected to the ortho benzene ring. The dihedral angles between the C8–C9–C10 plane and other two benzene planes where the C1–C2–C3 and C15–C16–C17 are located were found to be 65.1 ° and 23.8 ° respecticely. The angle between the benzene rings on both sides is 81.4 ° , the C(1)–Se(1)–C(21) and the C(20)–Se(2)–C(24) bond angles are 101.21 ( 18 ) ° and 99.7 ( 2 ) ° , and the C(7)–N(1)–C(8)–C(9) and the C(14)–N(2)–C(13)–C(12) torsion angles are − 42.2 ( 6 ) ° and 174.6 ( 4 ) ° . The bond lengths of Se(1)–C(21), Se(2)–C(24), N(1)–C(8), N(2)–C(13) are 1.967(4) Å, 1.961(5) Å, 1.408(5) Å, 1.416(5) Å, respectively. The crystal data of bond lengths and angles are completely according to expected data [11, 12].

Corresponding author: Shuxiao Feng, School of Chemistry and Chemical Engineering, Henan University of Science and Technology, Luoyang, Henan 471003, P.R. 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: None declared.

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

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Received: 2023-04-12
Accepted: 2023-05-11
Published Online: 2023-05-31
Published in Print: 2023-08-28

© 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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https://doi.org/10.1515/ncrs-2023-0181
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of a polymorph of potassium picrate, C6H2KN3O7
  4. The crystal structure of (1E,2E)-1,2-bis(quinolin-2-ylmethylene)hydrazine, C20H14N4
  5. 5-Amino-2-chloro-4-fluoro-N-(N-isopropyl-N-methylsulfamoyl) benzamide, C11H15O3ClFN3S
  6. Crystal structure of trans-N 1,N 8-bis(2-cyanoethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H42N6
  7. The crystal structure of [N-{[2-(oxy)-4-methoxyphenyl](phenyl)methylidene}alaninato]-diphenyl-silicon(IV) – chloroform (1/1), C29H25NO4Si·CHCl3
  8. Crystal structure of tetracarbonyl-{μ-[N-(diphenylphosphanyl)-N,P,P-triphenylphosphinous amide]}-bis[μ-(phenylmethanethiolato)]diiron (Fe–Fe), C48H39Fe2NO4P2S2
  9. Crystal structure of baryte from Mine du Pradet (France)
  10. The crystal structure of [(2,2′-bipyridine-6-carboxylato-κ3 N,N,O)-(6-phenylpyridine-2-carboxylate-κ2 N,O)copper(II)] monohydrate, C23H17N3O5Cu
  11. Crystal structure of bis(μ-benzeneselenolato)-(μ-[N-benzyl-N-(diphenylphosphanyl)-P,P-diphenylphosphinous amide])-tetracarbonyl diiron (Fe–Fe), C47H37Fe2NO4P2Se2
  12. The crystal structure of diaqua-methanol-κ1 O- (3-thiophenecarboxylato-κO)-(2,2′-dipyridyl-κ2 N,N′)manganese(II) 3-thiophenecarboxylate, C21H22N2O7S2Mn
  13. Crystal structure of catena-poly[tetrakis(butyl)-μ2-2-((oxido(phenyl)methylene)hydrazineylidene)propanoato-κ4 O:O,O′,N-μ2-2-((oxido(phenyl)methylene)hydrazineylidene)propanoato-κ4 O,N,O′:N′-ditin(IV)], C34H50N6O6Sn2
  14. Crystal structure of 4-chloro-N′-[(1E)-(2-nitrophenyl)methylidene]benzohydrazide, C14H10ClN3O3
  15. The crystal structure of 3-(1′-deoxy-3′,5′-O-dibenzy-β-d-ribosyl)adenine dichloromethane solvate, C49H52Cl2N10O6
  16. The crystal structure of (Z)-4-amino-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H17N3O
  17. The co-crystal structure of etoricoxib–phthalic acid (1/1), C18H15ClN2O2S·C8H6O4
  18. Crystal structure of (glycinto-κ 2 O,N ′)-[5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ 4 N,N ′,N ″,N ‴]nickel(II) perchlorate monohydrate C18H42ClN5NiO7
  19. The crystal structure of catena-poly[bis(1-ethylimidazole-k1 N)-(μ 2-benzene-1-carboxyl-3,5-dicarboxylato-κ 2 O, O′)zinc(II)], C19H20N4O6Zn
  20. Crystal structure of 3-(thiazol-2-ylcarbamoyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid, C11H12N2O4S
  21. Rietveld structure analysis of keatite, a rare, metastable SiO2 polymorph
  22. Crystal structure of catena-poly[(μ2-isophthalato-k3 O,O′:O″)(4-(4-pyridyl)-2,5-dipyrazylpyridine-k3 N,N′,N″)cobalt(II)] trihydrate C26H22N6O7Co1
  23. Crystal structure of 3,5–di-O-benzoyl-1,2-O-isopropylidene-α–D-ribose, C22H22O7
  24. The crystal structure of fac-tricarbonyl(6-bromo-2,2-bipyridine-κ2 N,N)-(nitrato-κO)rhenium(I), C13H7BrN3O6Re
  25. The crystal structure of (E)-N′-(4-hydroxy-3-methoxybenzylidene)-2-naphthohydrazide monohydrate, C19H18N2O4
  26. The crystal structure of 5,5′-diselanediyl-bis(2-hydroxybenzaldehyde), C14H10O4Se2
  27. The crystal structure of catena-poly[diaqua-m2-dicyanido-κ2 C:N-dicyanido-κ1 C-bis(4-(pyridin-4-yl)benzaldehyde-κ1N)iron(II)-platinum(II), C28H22N6O4PtFe
  28. Redetermination of the crystal structure of 5,14-dihydro-6,17-dimethyl-8,15-diphenyldibenzo(b,i)(1,4,8,11)tetra-azacyclotetradecine, C32H28N4
  29. Crystal structure of poly[(μ3-2-(3,5-dicarboxyphenyl) benzimidazole-6-carboxylato-κ4O:O:O′:O″)lead(II)] monohydrate, C16H10N2O7Pb
  30. The crystal structure of fac-tricarbonyl(2-pyridin-2-yl-quinoline-κ2 N,N′)-(pyrazole-κN)rhenium(I)nitrate, C20H14N4O3ReNO3
  31. Crystal structure of dibromo-dicarbonyl-bis(tricyclohexylphosphine)-osmium(II) dichloromethane solvate, C38H66Br2O2OsP2
  32. Crystal structure of poly[bis(μ 2-2,6-bis(1-imidazoly)pyridine-κ 2 N:N′)copper(II)] diperchlorate dihydrate, C22H22Cl2CuN10O10
  33. The crystal structure of fac-tricarbonyl(N-benzoyl-N,N-cyclohexylmethylcarbamimidothioato-κ2 S,O)-(pyridine-κN)rhenium(I), C23H24N3O4ReS
  34. Crystal structure of (E)-7-fluoro-2-(4-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C17H12F2O
  35. Synthesis and crystal structure of 1-((3R,10S,13S, 17S)-3-((2-methoxyphenyl)amino)-10,13-dimethylhexadecahydro-1H-cyclopenta[α]phenanthren-17-yl)ethan-1-one, C28H41NO2
  36. The crystal structure of fac-tricarbonyl((pyridin-2-yl)methanamino-κ2 N,N′)-((pyridin-2-yl)methanamino-κN)rhenium(I) nitrate, C15H16O3N4Re
  37. The crystal structure of (1-(pyridin-2-yl)-N-(pyridin-2-ylmethyl)-N-((1-(4-vinylbenzyl)-1H-benzo[d]imidazol-2-yl)methyl)methanamine-κ 4 N,N′,N″,N‴)tris(nitrato-kO,O′)-erbium(III), C29H27ErN8O9
  38. Crystal structure of tetracene-5,12-dione, C18H10O2
  39. Crystal structure of (3R,3aS,6R,6aR)-6-hexyl-3-methyltetrahydrofuro[3,4-b]furan-2,4-dione, C13H20O4
  40. The crystal structure of N′1,N′3-bis((E)-thiophen-2-ylmethylene)isophthalohydrazide monohydrate, C18H16N4O3S2
  41. Crystal structure of methyl ((4-aminobenzyl)sulfonyl)-L-prolinate, C13H18N2O4S
  42. Crystal structure of (E)-3-(3-methoxybenzylidene)benzofuran-2(3H)-one, C16H12O3
  43. Synthesis and crystal structure (E)-1-(4-bromo-2-hydroxyphenyl)-3-(dimethylamino)prop-2-en-1-one, C11H12BrNO2
  44. Synthesis and crystal structure of (S,E)-4-hydroxy-3-(2-((4aR,6aS,7R,10aS,10bR)-3,3,6a,10b-tetramethyl-8-methylenedecahydro-1H-naphtho[2,1-d][1,3]dioxin-7-yl)ethylidene)dihydrofuran-2(3H)-one, C23H34O5
  45. The crystal structure of N,N′-(1,2-phenylene)bis (2-((2-oxopropyl)selanyl)benzamide), C26H24N2O4Se2
  46. The crystal structure of 1-ethyl-2-nitro-imidazole oxide, C5H7N3O3
  47. The crystal structure of 2-(2-fluorophenyl)naphtho[2,1-d]thiazole, C17H10FNS
  48. Crystal structure of (E)-2,4-di-tert-butyl-6-(((2-fluorophenyl)imino) methyl)phenol, C21H26FNO
  49. Synthesis and crystal structure of 3-methyl-2-(methylthio)-4H-chromen-4-one, C12H12O2S
  50. Crystal structure of dithieno[2,3-d:2′,3′-d′]benzo[1,2-b:4,5-b′]dithiophene-5,10-dione, C14H4O2S4
  51. The crystal structure of dimethyl 2,2ʹ-((adamantane-1,3-diylbis(4,1-phenylene)) bis(oxy))diacetate, C28H32O6
  52. The crystal structure of N-(6-chloro-2-methyl-2H-indazol-5-yl)acetamide, C10H10ClN3O
  53. Crystal structure of triaqua-(5-bromoisophthalato-κ1 O)-(2,2′-bipyridine-κ2 N:N′)nickel(II) hydrate, C18H19BrN2NiO8
  54. The crystal structure of 2-amino-4-carboxypyridin-1-ium perchlorate, C6H7ClN2O6
  55. The crystal structure of catena-poly[5-aminonicotinic acid-k1 N-m2-bromido-copper(I)], Cu(C6N2H6O2)Br
  56. The crystal structure of 2,2-bis(3-methoxyphenyl)-1-tosyl-1,2-dihydro- 2λ4,3λ4  -[1,3,2]diazaborolo[4,5,1-ij]quinoline - dichloromethane (1/1)
  57. The crystal structure of catena-poly[bis(6-phenylpyridine-2-carboxylato-κ2 N,O)-(μ2-4,4′-bipyridne-κ2 N:N)cadmium(II)], C34H24N4O4Cd
  58. The crystal structure of 5,7-dinitropyrazolo[5,1-b]quinazolin-9(4H)-one, C10H5N5O5
  59. Crystal structure of rac-1,8-bis(2-carbamoylethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H46N6O2
  60. The crystal structure of (E)-N ′-(2-bromobenzylidene)-2-naphthohydrazide, C36H26Br2N4O2
  61. The crystal structure of 5-nitronaphthoquinone, C10H5NO4
  62. The crystal structure of (S, R p )-4–benzhydrylideneamino-12-(4-tert-butyl oxazolin-2-yl)[2.2]paracyclophane, C36H36N2O
  63. Synthesis and crystal structure of 2-(2-oxo-2-(o-tolyl)ethyl)-4H-chromen-4-one, C18H14O3
  64. Crystal structure of 2-(thiazol-2-yl)hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C11H10N2O3S
  65. Crystal structure of N-(diaminomethylene)-1-(dimethylamino)-1-iminiomethanaminium dichloride, C4H13Cl2N5
  66. Crystal structure of poly[(μ3-3, 5-dichloro-2-hydroxy-benzoato-κ4 Cl,O:O′:O″) silver(I)], C7H3AgCl2O3
  67. The crystal structure of tetrakis(1-isopropylimidazole-κ1 N)-[μ2- imidazole-4,5-dicarboxylato-κ4 O,N,O′,N′)]- trioxido-divanadium, C29H41N10O7V2
  68. Crystal structure of catena-[(μ3-bromido)-(1H-1,2,4-triazol-1-yl)benzoato-κ1 N)copper(I)], C9H7BrCuN3O2
  69. The crystal structure of (E)-4-fluoro-N′-(1-(2-hydroxyphenyl)propylidene)benzohydrazide, C16H15FN2O2
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