Home Crystal structure of trans-N 1,N 8-bis(2-cyanoethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H42N6
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Crystal structure of trans-N 1,N 8-bis(2-cyanoethyl)-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, C22H42N6

  • Saswata Rabi ORCID logo , Lucky Dey , Ismail M. M. Rahman ORCID logo EMAIL logo , Edward R. T. Tiekink ORCID logo EMAIL logo and Tapashi Ghosh Roy ORCID logo EMAIL logo
Published/Copyright: May 5, 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

C22H42N6, triclinic, P 1 ‾ (no. 2), a = 8.3115(2) Å, b = 8.8263(2) Å, c = 9.7688(2) Å, α =  111.490 ( 2 ) ° , β =  115.056 ( 2 ) ° , γ =  93.681 ( 2 ) ° , V = 583.25(3) Å3, Z = 1, R gt (F) = 0.0465, wR ref (F 2) = 0.1351, T = 294 K.

CCDC no.: 2257384

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: Colourless block
Size: 0.16 × 0.11 × 0.07 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.52 mm−1
Diffractometer, scan mode: XtaLAB Synergy, ω
θ max, completeness: 67.1°, >99 %
N(hkl)measured , N(hkl)unique, R int: 13,649, 2075, 0.034
Criterion for I obs, N(hkl)gt: I obs > 2σ(I obs), 1928
N(param)refined: 130
Programs: CrysAlisPRO  [1], SHELX [2, 3], WinGX/ORTEP [4]
Table 2:

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

Atom x y z U iso*/U eq
N1 0.25155 (14) 0.64361 (13) 0.78500 (12) 0.0392 (3)
N2 0.09668 (14) 0.63110 (13) 0.44208 (13) 0.0399 (3)
H2N 0.079 (2) 0.6321 (19) 0.5235 (15) 0.048*
N3 −0.0730 (3) 0.9230 (3) 0.7599 (2) 0.0890 (5)
C1 0.41794 (17) 0.74675 (17) 0.80962 (16) 0.0443 (3)
H1 0.414383 0.864536 0.857784 0.053*
C2 0.42117 (18) 0.71433 (18) 0.64616 (17) 0.0472 (3)
H2A 0.414904 0.595849 0.591858 0.057*
H2B 0.539675 0.777984 0.675326 0.057*
C3 0.27230 (18) 0.75613 (16) 0.51628 (16) 0.0438 (3)
C4 −0.06654 (19) 0.65103 (17) 0.31906 (18) 0.0486 (4)
H4A −0.057710 0.625263 0.217452 0.058*
H4B −0.071656 0.767527 0.362875 0.058*
C5 −0.24211 (18) 0.53737 (17) 0.27652 (18) 0.0466 (3)
H5A −0.256766 0.573082 0.376085 0.056*
H5B −0.345163 0.553591 0.191829 0.056*
C6 0.22886 (19) 0.71069 (19) 0.93481 (16) 0.0506 (4)
H6A 0.310087 0.823248 1.009622 0.061*
H6B 0.264383 0.640267 0.993298 0.061*
C7 0.0307 (2) 0.7179 (2) 0.89235 (19) 0.0553 (4)
H7A −0.050866 0.605779 0.815547 0.066*
H7B 0.020344 0.754019 0.994125 0.066*
C8 −0.0271 (2) 0.8322 (2) 0.8169 (2) 0.0581 (4)
C9 0.5997 (2) 0.7334 (2) 0.9360 (2) 0.0609 (4)
H9A 0.701336 0.802967 0.945872 0.091*
H9B 0.604645 0.770563 1.043532 0.091*
H9C 0.606339 0.618284 0.897435 0.091*
C10 0.3248 (2) 0.7361 (2) 0.3789 (2) 0.0648 (5)
H10A 0.438823 0.817019 0.426245 0.097*
H10B 0.338405 0.624311 0.332689 0.097*
H10C 0.230010 0.754533 0.291709 0.097*
C11 0.2638 (2) 0.93911 (18) 0.5961 (2) 0.0567 (4)
H11A 0.381147 1.014363 0.642046 0.085*
H11B 0.171415 0.963152 0.512237 0.085*
H11C 0.233529 0.954165 0.684010 0.085*

1 Source of material

The precursor molecule, tet-a, was prepared following a literature procedure [5]. Thus, the condensation of ethylenediamine with acetone in the presence of a quantitative amount of perchloric acid, yielded the hexamethyl derivative of the 14-membered tetraazamacrocycle, Me6[14]diene·2HClO4. The diene ligand, on reduction with NaBH4, followed by extraction with CHCl3 at pH above 12, resulted in a mixture of isomeric macrocycles, the Me6[14]anes. These were separated by fractional crystallisation from xylene and designated as tet-a and tet-b. The reaction of tet-a with excess acrylonitrile was stereoselective and gave the N-pendent derivative, tet-ax, in which two ethylcyano groups are attached to less crowded nitrogen atom. Elemental analysis (Leco CHNS-932 elemental analyzer; %) for C22H42N6: C, 67.65; H, 10.84; N, 21.51. Found: C, 67.82; H, 10.95; N, 21.35. IR (Shimadzu IR 20 spectrophotometer, KBr, cm −1 ): 3227 (w) ν(N–H), 1361 (s) ν(CH3), 2965 (m) ν(C–H), 1141 (w) ν(C–C), 1177 (m) ν(N–C), 2241(s) ν(C–N). 1 H NMR (Bruker AVANCE 400 NMR spectrometer, DMSO-d 6 , ppm) δ: Mehtyl–H: 0.92 (d, e, 6H), 1.05 (s, e, 6H), 1.15 (s, a, 6H). Methylene–H: 1.19 (m), 2.55 (m), 2.75 (m), 2.98 (m). Methine–H: 3.10 (m). Amine–H: 7.26 (s). 13 C{1 H} NMR (Bruker AVANCE 400 NMR spectrometer, DMSO-d 6 , ppm) δ: Methyl–C: 14.66, 18.69, 25.92. Ring–C: 28.73, 40.29, 45.64, 47.55, 49.55. Ethylcyano–C: 52.62, 54.31, 119.92.

2 Experimental details

The C–bond H atoms were geometrically placed (C–H = 0.93–0.98 Å) and refined as riding with U iso (H) = 1.2–1.5U eq (C). The N–bond H atom was located in a difference map and refined with N–H = 0.86 ± 0.01 Å, and with U iso (H) = 1.2U eq (N).

3 Comment

Cyclam (1,4,8,11-tetraazacyclotetradecane) is a 14-membered macrocycle, is classified as an aza-crown ether and its ability to complex metal ions is well known [6]. Being readily substituted at practically all positions in the ring and being flexible in its coordination potential, isomerism gives rise to fascinating structural chemistry, e.g. for 2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane, 30 different configurations may be envisaged when this molecule is coordinated to nickel(II) [7]. The determination of pharmaceutical potential has motivated on-going interest in this area, such as the recent report of the evaluation of the anti-microbial activity of cadmium derivatives of the N-bond bis-cyanoethyl derivative of a related octa-methyl macrocycle [8]. In continuation of this work, herein the crystal structure determination of a related bis-cyanoethyl substituted macrocycle lacking methyl substituents in the ethylene link, (I), is described.

The molecular structure is shown in the figure (35 % probability ellipsoids). The unlabelled atoms in the figure are related by the symmetry operation −x, 1 − y, 1 − z as the molecule is disposed about an inversion centre. The four nitrogen atoms define a plane and participate in intramolecular secondary-amine–N–H⃛N (teriary amine) hydrogen bonds [N2–H2n⃛N1: H2n⃛N1 = 2.298(13) Å, N2⃛N1 = 2.9916(15) Å with angle at H2n =  137.3 ( 15 ) ° ]; this interaction serves to close a slightly twisted, six-membered {⃛NC3NH} synthon. When viewed side-on through the N4 plane, the ethylene bridges lie to either side of the plane as do the N–bond ethylcyano substituents. Further, the four N–bond carbon atoms of the propylene links are close to co-planar with the N4 plane. This latter configuration is in stark contrast to that observed in the methanol solvate of the compound [9], where the C3 links are kinked with respect to the N4 plane. This change in conformation in the literature precedent is correlated with the influence of methanol–O–H⃛N (secondary amine) hydrogen bonding interactions.

In accord with an analysis of the molecular packing of (I), employing Platon [10], the crystal is largely devoid of directional interactions between molecules, partially owing to the intramolecular N–H⃛N hydrogen bonds, precluding these atom from forming intermolecular contacts. This conclusion is confirmed by an analysis of the calculated Hirshfeld surfaces, employing CrystalExplorer [11] and standard procedures [12]. This analysis shows that 77.5 % of all surface contacts are H⃛H contacts. The other contributors are N⃛H/H⃛N [18.3 %] and N⃛C/C⃛N [3.6 %] contacts.

Corresponding authors: Ismail M. M. Rahman, Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima 960-1296, Japan, E-mail: . Edward R. T. Tiekink, Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia, E-mail: ; and Tapashi Ghosh Roy, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram 4331, Bangladesh, E-mail:

Funding source: Environmental Radioactivity Research Network Center

Award Identifier / Grant number: ERAN: I-23–13

Funding source: Japan Society for the Promotion of Science (JSPS)

Award Identifier / Grant number: Grants-in–Aid for Scientific Research (21K12287)

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

  2. Research funding: Environmental Radioactivity Research Network Center (ERAN: I-23–13) and Grants-in–Aid for Scientific Research (21K12287) from the Japan Society for the Promotion of Science (JSPS).

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

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Received: 2023-03-05
Accepted: 2023-04-19
Published Online: 2023-05-05
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-2023-0103
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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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