Home Crystal structure of the co-crystal N,N′-bis(4-pyridylmethyl)oxalamide and 2,3,5,6-tetrafluoro-1,4-di-iodobenzene (1/1), C14H14N4O2⋅C6F4I2
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Crystal structure of the co-crystal N,N′-bis(4-pyridylmethyl)oxalamide and 2,3,5,6-tetrafluoro-1,4-di-iodobenzene (1/1), C14H14N4O2⋅C6F4I2

  • Sang Loon Tan and Edward R.T. Tiekink ORCID logo EMAIL logo
Published/Copyright: August 29, 2019

Abstract

C20H14F4I2N4O2, triclinic, P1̄ (no. 2), a = 5.0726(1) Å, b = 10.9432(2) Å, c = 19.8090(3) Å, α = 104.475(2)°, β = 90.427(2)°, γ = 92.908(2)°, V = 1063.10(3) Å3, Z = 2, Rgt(F) = 0.0329, wRref(F2) = 0.0907, T = 100 K.

CCDC no.: 1943428

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 prism
Size:0.18 × 0.09 × 0.07 mm
Wavelength:Cu Kα radiation (1.54184 Å)
μ:23.8 mm−1
Diffractometer, scan mode:XtaLAB Synergy, ω
θmax, completeness:76.6°, >99%
N(hkl)measured, N(hkl)unique, Rint:26223, 4449, 0.054
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 4243
N(param)refined:295
Programs:CrysAlisPRO [1], SHELX [2], [3], WinGX/ORTEP [4]
Table 2:

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

AtomxyzUiso*/Ueq
I1−0.93660(3)0.72803(2)0.57419(2)0.01511(9)
I2−1.85947(4)0.96049(2)0.83098(2)0.01554(9)
F1−1.2374(4)0.98419(19)0.61693(10)0.0229(4)
F2−1.5833(5)1.07247(19)0.71513(11)0.0257(5)
F3−1.5620(4)0.69523(19)0.78998(10)0.0231(4)
F4−1.1973(4)0.61157(18)0.69594(10)0.0215(4)
C1−1.2092(6)0.7939(3)0.65246(17)0.0148(6)
C2−1.3121(7)0.9113(3)0.66020(18)0.0170(7)
C3−1.4939(7)0.9564(3)0.71006(17)0.0164(6)
C4−1.5862(6)0.8858(3)0.75486(16)0.0153(6)
C5−1.4846(6)0.7679(3)0.74753(17)0.0158(6)
C6−1.2971(6)0.7243(3)0.69823(17)0.0150(6)
O10.3945(4)0.5968(2)0.22104(11)0.0177(5)
O2−0.1600(4)0.4795(2)0.11436(11)0.0180(5)
N1−0.5684(5)0.6843(3)0.46768(14)0.0192(6)
N2−0.0394(5)0.6170(3)0.24624(14)0.0153(5)
H2N−0.199(3)0.593(3)0.2295(19)0.018*
N30.2693(5)0.4341(2)0.09621(13)0.0141(5)
H3N0.432(3)0.449(4)0.1126(19)0.017*
N40.7928(5)0.1093(3)−0.07489(14)0.0177(5)
C7−0.4752(6)0.7953(3)0.45856(17)0.0187(6)
H7−0.5404220.8700620.4874350.022*
C8−0.2896(6)0.8080(3)0.40965(16)0.0182(6)
H8−0.2275500.8893310.4057870.022*
C9−0.1958(6)0.6994(3)0.36625(16)0.0154(6)
C10−0.2921(6)0.5835(3)0.37495(17)0.0183(6)
H10−0.2334560.5071980.3460430.022*
C11−0.4746(7)0.5803(3)0.42624(17)0.0188(7)
H11−0.5362170.5003140.4322760.023*
C120.0081(6)0.7098(3)0.31267(16)0.0176(6)
H12A0.0091520.7956420.3047600.021*
H12B0.1846080.6987320.3312180.021*
C130.1604(6)0.5721(3)0.20635(15)0.0123(6)
C140.0725(6)0.4876(3)0.13412(15)0.0140(6)
C150.2249(6)0.3760(3)0.02171(15)0.0173(6)
H15A0.2249190.443511−0.0035130.021*
H15B0.0483690.3313200.0147760.021*
C160.4290(6)0.2838(3)−0.00954(16)0.0153(6)
C170.5356(6)0.2013(3)0.02478(16)0.0187(6)
H170.4875560.2030710.0712590.022*
C180.7136(7)0.1161(3)−0.00964(17)0.0178(6)
H180.7832100.0593890.0143510.021*
C190.6897(7)0.1900(3)−0.10696(16)0.0186(6)
H190.7437540.187247−0.1531170.022*
C200.5096(6)0.2775(3)−0.07743(16)0.0165(6)
H200.4418750.332321−0.1029160.020*

Source of material

N,N′-Bis(pyridin-4-ylmethyl)oxalamide, 4LH2, was prepared according to the literature procedure [5] (melting point, m.pt: 474–475 K; lit. [5]: 486–487 K). 1,4-Diiodotetrafluorobenzene was purchased from Aldrich (Gillingham, Dorset, United Kingdom) and used as received without purification. The co-crystal was prepared through solvent drop-assisted grinding of 4LH2 (0.154 g, 1 mmol) and 1,4-C6F4I2 (0.402 g, 1 mmol). The mixture was ground for 15 mins in the presence of few drops of methanol that lead to a beige slurry. This was dissolved in dimethylformamide (2 mL) and carefully layered with the same volume of benzene. Colourless crystals were obtained after about three days. M.pt: 451–453 K. IR (ATR; cm−1): 3282(m) ν(N—H), 3058–2938(w) ν(C—H), 1655–1642(s) ν(C=O), 1603–1511(s) ν(C=C), 1417(s) ν(C—F), 1360(m) ν(C—N), 755(s) δ(C=C), 482(s) ν(C—I).

Experimental details

The C-bound H atoms were geometrically placed (C—H = 0.95–0.99 Å) and refined as riding with Uiso(H) = 1.2Ueq(C). The N-bound H-atoms were located in a difference Fourier map but were refined with a distance restraint of N—H = 0.88 ± 0.01 Å, and with Uiso(H) set to 1.2Uequiv(N). The maximum and minimum residual electron density peaks of 2.65 and 1.59 e Å−3, respectively, were located 1.00 and 0.80 Å from the I1 atom, respectively.

Comment

As noted in a recent bibliographic review [6], isomeric molecules of the general formula (n-C5H4N)CH2N(H)C(=O)C(=O)N(H)CH2(C5H4N-n), for n = 2, 3 and 4, hereafter abbreviated as nLH2, featured prominently in the early days of “crystal engineering.” The isomeric molecules have potential hydrogen bonding functionality in the two terminal n-pyridyl residues (acceptors) and in the central di-amide group (donors and acceptors). Exploiting this functionality and by systematically co-crystallising nLH2 with bi-functional carboxylic acids, two-dimensional sheets could be generated. An example of this is found in the co-crystal comprising equal amounts of 3LH2 and N,N′-dicarboxymethylurea [7]. The 3LH2 molecules self-assembled into supramolecular tapes via amide-N—H⋯O(amide) hydrogen bonding and 10-membered amide synthons {⋯HNC2O}2. Connections between parallel tapes leading to two-dimensional arrays were mediated by bifunctional carboxylic acids forming hydroxy-O—H⋯N(pyridyl) hydrogen bonds [7]. Using the same principles, two-dimensional sheets were generated whereby the supramolecular tapes of 3LH2 formed by amide-N—H⋯O(amide) hydrogen bonding were linked by N⋯I halogen bonds, such as in the 1:1 co-crystal of 3LH2 and 1,4-di-iodobuta-1,3-diyne, that is, I—C≡C—C≡C—I [8]. However, the formation of supramolecular tapes for nLH2 is not always reliable [6]. Thus, in the 1:1 co-crystal formed between 3LH2 and the prototype bridging halogen-bonding molecule, 1,4-diiodotetrafluorobenzene, supramolecular tapes are formed but, mediated by via amide-N—H⋯N(pyridyl) hydrogen bonds and 18-membered {⋯HNC2NC3N}2 synthons [9]. Halogen bonding is also observed but, of the type O⋯I resulting in the formation of a two-dimensional array. As a part of continuing studies of the formation of multi-component crystals of nLH2 [10], [11], [12], the title 1:1 co-crystal containing the co-formers 4LH2 and 1,4-diiodotetrafluorobenzene was prepared and characterised crystallographically.

The molecular structures of the independent molecules comprising the asymmetric unit, each in a general position, are shown in the figure (70% displacement ellipsoids). The central C2N2O2 residue is approximately planar with the r.m.s. deviation of the fitted atoms being 0.0705 Å, and with the maximum deviation from the plane being 0.0948(15) Å for the O2 atom. This is in fact unusual as the central residue is usually considerably more planar [6]. The deviation from planarity arises from a twist about the central C13—C14 bond as seen in the torsion angle of O1—C13—C14—O2 of −167.6(3)°. While the C13—C14 bond length may be considered long at 1.546(4) Å, the distance falls in the usual range for nLH2 molecules, an observation ascribed to the presence of electronegative substituents at each of the carbon atoms [6]. The appended methylene-carbon atoms lie to the same side of the central plane with deviations of 0.074(5) Å, for the C12 atom, and 0.223(5) Å, for C15. The pyridyl rings also lie to the same side of the molecule so that the conformation approximates syn-periplanar. The dihedral angle between the central plane and the N1- and N4-pyridyl rings are 68.32(10) and 63.82(9)°, respectively. The dihedral angle between the pyridyl rings is 47.90(11)°, consistent with a splayed relationship, and emphasises the conformational flexibility of these molecules [6]. As is always observed in the nLH2 molecules [6], intramolecular amide-N—H⋯O(amide) hydrogen bonds are evident which give rise to S(5) loops [N2—H2n⋯O2: H2n⋯O2 = 2.32(4) Å, N2⋯O2 = 2.717(3) Å with angle at H2n = 107(2)° and N3—H3n⋯O1: H3n⋯O1 = 2.36(4) Å, N3⋯O1 = 2.711(3) Å with angle at H3n = 104(2)°].

As evident from the figure, the independent molecules are connected by N⋯I halogen bonds [N1⋯I1 = 2.795(3) Å and, from symmetry, N4⋯I2i = 2.840(3) Å for symmetry operation (i) 3 + x, −1 + y, −1 + z]. The result is a linear supramolecular chain along [3 −1 −1]. Links between chains leading to a two-dimensional array are of the type amide-N—H⋯O(amide) hydrogen bonding and as these occur on either side of the central di-amide residue, a supramolecular tape is sustained by these interactions [N2—H2n⋯O1ii: H2n⋯O1ii = 2.071(16) Å, N2⋯O1ii = 2.899(3) Å with angle at H2n = 158(3)°; N3—H3n⋯O2iii: H3n⋯O2iii = 2.078(17) Å, N3⋯O2iii = 2.917(3) Å with angle at H3n = 160(3)° for (ii) −1 + x, y, z and (iii) 1 + x, y, z]. The aforementioned layers are connected into double-layers via methylene-C—H⋯O(amide) interactions [C15—H15a⋯O2iv: H15a⋯O2iv = 2.57 Å, C15⋯O2iv = 3.471(4) Å with angle at H15a = 152° for (iv) −x, 1−y, −z]. The double layers inter-digitate so that fluoro atoms lie in voids defined by the 1,4-diiodotetrafluorobenzene molecules but, directional interactions are not apparent. Accordingly, in order to understand more about the supramolecular interactions stabilising the crystal, the structure was further evaluated using Crystal Explorer 17 [13] to calculate the Hirshfeld surfaces along with the full and delineated fingerprint plots guided by established procedures [14]. The analysis of the calculated Hirshfeld surface for the complete asymmetric unit of the title structure revealed a myriad of different types of contacts with the most prevalent being F⋯H/H⋯F at 26.2% but, at separations greater than the sum of the van der Waals radii. Other major contributors to the contacts were found to be H⋯H [14.1%], C⋯H/H⋯C [13.4%], O⋯H/H⋯O [9.3%], I⋯C/C⋯I [9.1%] and I⋯H/H⋯I [7.6%], with only the H⋯O contacts being less than the sum of the respective van der Waals radii; I⋯N/N⋯I interactions only amounted to 3.1% of all surface contacts.

The calculations were also performed on the individual co-crystal co-formers. For 4LH2, reflecting the composition of the molecule, the percentage contributions from H⋯H [21.7%], C⋯H/H⋯C [17.3%] and O⋯H/H⋯O [14.7%] contacts all increased in significance while F⋯H/H⋯F [19.9%], I⋯C/C⋯I [2.7%] and [I⋯H/H⋯I [5.0%] decreased. As expected, the opposite trends in surface contacts are evident for the 1,4-diiodotetrafluorobenzene molecule with diminished contributions from H⋯H [0.0%], C⋯H/H⋯C [5.4%] and O⋯H/H⋯O [0.0%] contacts but, significantly increased contributions from F⋯H/H⋯F [33.3%], I⋯C/C⋯I [18.6%] and [I⋯H/H⋯I [16.2%] contacts to the calculated surface.

Acknowledgements

Sunway University Sdn Bhd is thanked for financial support of this work through Grant no. STR-RCTR-RCCM-001-2019.

References

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Received: 2019-07-09
Accepted: 2019-07-26
Published Online: 2019-08-29
Published in Print: 2019-09-25

©2019 Sang Loon Tan et al., published by De Gruyter, Berlin/Boston

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

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  49. The crystal structure of dichlorido-μ2-dichlorido-(η2-1,4-bis(4-vinylbenzyl)-1,4-diazabicyclo[2.2.2]octane-1,4-diium)dicopper(I), C24H30N2Cu2Cl4
  50. Crystal structure of 4-bromobenzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate, C22H29BrN2OS
  51. Crystal structure of (4S,4aS,6aR,6bR,12aS,12bR,14aS,14bR)-3,3,6a,6b,9,9,12a-heptamethyloctadecahydro-1H,3H-4,14b-ethanophenanthro[1,2-h]isochromene-1(6bH)-one, C30H48O2
  52. Crystal structure of 3,5-bis(trifluoromethyl)benzyl (Z)-N′-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate, C30H33F6N3S
  53. The crystal structure of 3-methoxyphenanthridin-6(5H)-one, C14H11NO2
  54. Crystal structure of 4-(5,5-difluoro-1,3,7,9-tetramethyl-3H,5H-5λ4-dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinin-10-yl)pyridin-1-ium tetraiodidoferrate(III), C18H19BF2FeI4N3
  55. Crystal structure of 2-(3-methoxyphenyl)-3-((phenylsulfonyl)methyl)imidazo[1,2-a]pyridine, C21H18N2O3S
  56. Crystal structure of [(2-(2-chlorophenyl)-5-ethyl-1,3-dioxane-5-carboxylato-κ2O,O′) (5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)]nickel(II) perchlorate, C29H50Cl2N4NiO8
  57. Crystal structure of (Z)-6-(dimethylamino)-3,3-bis(4-(dimethylamino)phenyl)-2-(2-(quinoxalin-2-ylmethylene)hydrazinyl)-2,3-dihydroinden-1-one, C35H35N7O
  58. 5-Methyl-N′-[5-methyl-1-(4-methylphenyl)-1H-1,2,3-triazole-4-carbonyl]-1-(4-methylphenyl)-1H-1,2,3-triazole-4-carbohydrazide, C22H22N8O2
  59. Crystal structure of 2,3-dichloro-6-methoxyquinoxaline, C9H6Cl2N2O
  60. Synthesis and crystal structure of 7-chloro-2-(ethylsulfinyl)-6-fluoro-3-(1H-pyrazole-1-yl)-4H-thiochromen-4-one, C13H10FN3OS2
  61. Crystal structure of 4-ethylpiperazine-1-carbothioic dithioperoxyanhydride, C14H26N4S4
  62. Crystal structure of 2-(2-(6-methylpyridin-2-yl)naphthalen-1-yl)pyrimidine, C20H15N3
  63. The crystal structure of N′-((1E,2E)-4-(7-methoxy-2-oxo-2H-chromen-8-yl)-2-methylbut-2-en-1-ylidene)-3-methylbenzohydrazide, C23H22N2O4
  64. Crystal structure of catena-poly[(μ2-isophthalato-κ2O:O′)-(2,5-di(pyrazin-2-yl)-4,4′-bipyridine-κ3N,N′,N′′)zinc(II)] — water (2/5), C26H21N6O6.5Zn
  65. Crystal structure of (3E,5E)-3,5-bis(3-nitrobenzylidene)-1-((4-(trifluoromethyl)phenyl)sulfonyl)piperidin-4-one — dichloromethane (2/1), C53H38Cl2F6N6O14S2
  66. Crystal structure of (μ2-oxido)-bis(N,N′-o-phenylenebis(salicylideneiminato))diiron(III) — N,N′-dimethylformamide, C47H43Fe2N4O9
  67. Crystal structure of N1,N3-bis(2-hydroxyethyl)-N1, N1,N3,N3-tetramethylpropane-1,3-diaminium dibromide, C11H28Br2N2O2
  68. Crystal structure of (E)-N-(4-chlorophenyl)-1-(pyridin-2-yl)methanimine, C12H9ClN2
  69. Crystal structure of 8-bromo-6-oxo-2-phenyl-6H-pyrrolo[3,2,1-ij]quinoline-5-carbaldehyde, C18H11BrNO2
  70. Crystal structure of 1,4-bis(2-azidoethyl)piperazine-1,4-diium dichloride trihydrate, C8H18N8Cl2 ⋅ 3 H2O
  71. Crystal structure of (E)-4-bromo-N-(pyridin-2-ylmethylene)aniline, C12H9BrN2
  72. Crystal structure of bis[(2-(3-bromophenyl)-5-methyl-1,3-dioxane-5-carboxylato-κ-O)-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)]nickel(II), C40H60Br2N4NiO8
  73. The crystal structure of (1E,2E)-2-methyl-4-((7-oxo-7H-furo[3,2-g]chromen-9-yl)oxy)but-2-enal O-isonicotinoyl oxime–trichloromethane (3/1), C67H49Cl3N6O18
  74. Crystal structure of 3-(2-ethoxy-2-oxoethyl)-1-methyl-1H-imidazol-3-ium hexafluoridophosphate(V), C8H13F6N2O2P
  75. Crystal structure of bis[(2-(2-bromophenyl)-5-ethyl-1,3-dioxane-5-carboxylato-κO)-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane-κ4N,N′,N′′,N′′′)]nickel(II) hemihydrate C42H65Br2N4NiO8.5
  76. The crystal structure of N-(7-(4-fluorobenzylidene)-3-(4-fluorophenyl)-3,3a,4,5,6,7-hexahydro-2H-indazole-2-carbonothioyl)benzamide, C28H23F2N3OS
  77. The crystal structure of N1,N4-bis(pyridin-3-yl)cyclohexane-1,4-dicarboxamide, C18H20N4O2
  78. Crystal structure of (E)-2-(3,6-bis(ethylamino)-2,7-dimethyl-9H-xanthen-9-yl)-N′-((6-methylpyridin-2-yl)methylene)benzohydrazide – methanol (1/1), C34H37N5O3
  79. Crystal structure of 2-oxo-1-(pyrimidin-5-ylmethyl)-3-(3-(trifluoromethyl)phenyl)-1,2-dihydro-5l4-pyrido[1,2-a]pyrimidin-4-olate, C20H13F3N4O2
  80. Crystal structure of poly[(μ3-9H-carbazole-3,6-dicarboxylato-κ3O1: O2: O3)(μ2-4-(pyridin-4-yl)pyridine-κ2N1:N1′)zinc(II)], C19H11N2O4Zn
  81. Crystal structure of (E)-N′-((1,8-dihydropyren-1-yl)-methylene)picolinohydrazide, C23H15N3O
  82. Crystal structure of catena-poly{[μ2-1,2-bis(diphenylphosphino)ethane]dichloridocadmium(II)}, C26H24CdCl2P2
  83. Crystal structure of the 1:2 co-crystal between N,N′-bis(4-pyridylmethyl)oxalamide and acetic acid as a dihydrate, C14H14N4O2⋅2 C2H4O2⋅2 H2O
  84. Crystal structure of the co-crystal N,N′-bis(3-pyridylmethyl)oxalamide acetic acid (1/2), C14H14N4O2⋅2C2H4O2
  85. Crystal structure of the co-crystal N,N′-bis(4-pyridylmethyl)oxalamide and 2,3,5,6-tetrafluoro-1,4-di-iodobenzene (1/1), C14H14N4O2⋅C6F4I2
  86. Crystal structure of the co-crystal 4-[(4-carboxyphenyl)disulfanyl]benzoic acid–(1E,4E)-1-N,4-N-bis(pyridin-4-ylmethylidene)cyclohexane-1,4-diamine (1/1), C14H10O4S2⋅C18H20N4
  87. Crystal structure of hexacarbonyl-bis(μ2-di-n-propyldithiocarbamato-κ3S,S′:S3S:S:S′)-di-rhenium(I), C20H28N2O6Re2S4
  88. Crystal structure of fac-tricarbonyl-morpholine-κN-(morpholinocarbamodithioato-κ2S,S′)rhenium(I), C12H17N2O5ReS2
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