Home Crystal structure of the co-crystal N,N′-bis(3-pyridylmethyl)oxalamide acetic acid (1/2), C14H14N4O2⋅2C2H4O2
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Crystal structure of the co-crystal N,N′-bis(3-pyridylmethyl)oxalamide acetic acid (1/2), C14H14N4O2⋅2C2H4O2

  • Sang Loon Tan and Edward R.T. Tiekink EMAIL logo
Published/Copyright: August 23, 2019

Abstract

C18H22N4O6, triclinic, P1̄ (no. 2), a = 5.03050(10) Å, b = 12.4151(4) Å, c = 15.5353(5) Å, α = 96.186(3)°, β = 98.961(2)°, γ = 96.669(2)°, V = 944.05(5) Å3, Z = 2, Rgt(F) = 0.0421, wRref(F2) = 0.1213, T = 100 K.

CCDC no.: 1943424

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:0.12 × 0.06 × 0.03 mm
Wavelength:Cu Kα radiation (1.54184 Å)
μ:0.88 mm−1
Diffractometer, scan mode:XtaLAB Synergy, ω
θmax, completeness:76.4°, >99%
N(hkl)measured, N(hkl)unique, Rint:23452, 3961, 0.046
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3434
N(param)refined:267
Programs:CrysAlisPRO [1], SHELX [2], [3], WinGX/ORTEP [4]
Table 2:

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

AtomxyzUiso*/Ueq
O10.46011(17)0.26057(8)0.44552(7)0.0227(2)
O21.08150(17)0.40313(8)0.56093(7)0.0217(2)
N11.1023(2)−0.08529(10)0.29420(8)0.0229(3)
N20.8899(2)0.25133(9)0.41867(8)0.0181(2)
H2N1.060(2)0.2728(14)0.4409(12)0.022*
N30.6514(2)0.41745(9)0.58355(8)0.0182(2)
H3N0.480(2)0.3944(14)0.5640(12)0.022*
N41.2770(2)0.52811(10)0.85107(9)0.0238(3)
C11.0502(3)0.01818(11)0.29399(10)0.0201(3)
H11.1378450.0628130.2579110.024*
C20.8744(2)0.06351(11)0.34394(9)0.0190(3)
C30.7520(3)−0.00171(12)0.39765(10)0.0225(3)
H30.6321690.0265980.4331740.027*
C40.8059(3)−0.10883(12)0.39916(10)0.0254(3)
H40.725276−0.1546510.4359060.030*
C50.9802(3)−0.14727(12)0.34570(11)0.0255(3)
H51.014323−0.2209450.3457120.031*
C60.8186(3)0.17915(11)0.33567(9)0.0198(3)
H6A0.9230270.2089940.2925410.024*
H6B0.6232580.1780410.3126810.024*
C70.7078(2)0.28844(11)0.46330(9)0.0171(3)
C80.8337(2)0.37563(10)0.54145(9)0.0172(3)
C90.7312(3)0.50968(11)0.65300(10)0.0202(3)
H9A0.5658770.5395010.6662880.024*
H9B0.8447650.5678720.6311900.024*
C100.8865(3)0.48131(11)0.73672(9)0.0192(3)
C111.1326(3)0.54366(11)0.77476(10)0.0200(3)
H111.2019700.6005760.7447780.024*
C121.1788(3)0.44756(13)0.89287(11)0.0290(3)
H121.2793060.4360540.9473780.035*
C130.9373(3)0.38039(13)0.86012(11)0.0299(3)
H130.8739750.3235960.8912840.036*
C140.7890(3)0.39754(11)0.78080(10)0.0242(3)
H140.6225400.3524330.7568790.029*
O31.4448(2)−0.14942(8)0.18767(8)0.0256(2)
H3O1.345(4)−0.1252(17)0.2224(12)0.038*
O41.4014(2)0.00897(9)0.13449(8)0.0319(3)
C151.4974(3)−0.07653(11)0.13447(10)0.0217(3)
C161.6897(3)−0.10963(13)0.07447(10)0.0259(3)
H16A1.649220−0.0785890.0192690.039*
H16B1.668207−0.1895480.0622280.039*
H16C1.876909−0.0822960.1028270.039*
O51.7283(2)0.66193(9)0.92028(7)0.0262(2)
H5O1.589(3)0.6206(15)0.8934(13)0.039*
O61.7052(2)0.72550(8)0.79044(7)0.0252(2)
C171.8173(3)0.72694(11)0.86564(10)0.0205(3)
C182.0714(3)0.80222(13)0.90705(11)0.0279(3)
H18A2.1916220.8107270.8635960.042*
H18B2.1643950.7712370.9569310.042*
H18C2.0238870.8737720.9276220.042*

Source of material

N,N′-Bis(pyridin-3-ylmethyl)oxalamide, 3LH2, was prepared according to the literature procedure [5] (melting point, m.pt: 474–475 K). The title co-crystal was prepared by dissolving 3LH2 (0.154 g, 1 mmol) in an excess of glacial acetic acid (3 mL). Upon its dissolution, benzene (3 mL) was carefully layered on top of the solution. Colourless crystals formed approximately one week after the crystallisation and shown crystallographically to be 3LH2⋅2CH3C(=O)OH. M.pt: 373–374 K. IR (ATR, cm−1): 3323–3282(m) ν(N—H), 3152–2934(w) ν(C—H), 1697–1660(s) ν(C=O), 1516(s) ν(C=C), 1361(m) ν(C—N), 802(s) δ(C=C).

Experimental details

The C-bound H atoms were geometrically placed (C—H = 0.95–0.99 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The O- and N-bound H-atoms were located in a difference Fourier map but were refined with distance restraints of O—H = 0.84 ± 0.01 Å and N—H = 0.88 ± 0.01 Å, respectively, and with Uiso(H) set to 1.5Uequiv(O) and 1.2Uequiv(N), respectively.

Comment

A recent review [6] has summarised the structural chemistry of co-crystals, salts and metal complexes formed by isomeric molecules with 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. Hydrogen bonding functionality is apparent in these molecules, namely in the central di-amide group as well as in the two terminal pyridyl residues. As a part of on-going studies in forming co-crystals and coordination polymers of nLH2 [7], [8], [9], the title 2:1 co-crystal, 3LH2⋅2CH3C(=O)OH, was formed and characterised crystallographically.

The molecular structures of the molecules comprising the asymmetric unit are shown in the figure (70% displacement ellipsoids). The 3LH2 molecule features a planar, central C2N2O2 residue with the r.m.s. deviation of the fitted atoms = 0.0204 Å; the maximum deviation from the plane is 0.0286(7) Å for the N2 atom. The planarity does not extend to the appended methylene-carbon atoms which lie 0.207(2) Å, for the C6 atom, and 0.189(2) Å, for C9, to one side of the plane through the central atoms. Indeed, the pyridyl rings lie to the same side of the molecule so that the conformation is syn-periplanar. The dihedral angles between the central plane and the N1- and N4-pyridyl rings are 71.34(4) and 77.78(4)°, respectively; the dihedral angle between the pyridyl rings is 85.83(4)°. The observed syn-periplanar conformation is found in one of the two polymorphs of 3LH2, the other exhibiting an anti-periplanar conformation in each of the independent molecules [10]. DFT calculations showed the energy difference between the two observed conformations in the polymorphs was less than 1 kcal mol−1, consistent with the conformational flexibility of these molecules [6]. Finally, two intramolecular amide-N—H⋯O(amide) hydrogen bonds are noted [N2—H2n⋯O2: H2n⋯O2 = 2.314(18) Å, N2⋯O2 = 2.7170(16) Å with angle at H2n = 108.4(11)° and N3—H3n⋯O1: H3n⋯O1 = 2.325(18) Å, N3⋯O1 = 2.7091(16) Å with angle at H3n = 106.9(12)°]; each of these gives rise to an S(5) loop using graph-set notation [11]. The acetic acid molecules are attached to 3LH2via hydroxy-O—H⋯N(pyridyl) hydrogen bonds, indicated by dashed bonds in the figure. The great disparity in the C—O bonds confirms the location of the acidic protons in the carboxylic acids [C15—O3, O4 = 1.3213(18) and 1.2163(18) Å; C17—O5, O6 = 1.3244(18) and 1.2129(18) Å].

As mentioned above, conventional hydroxy-O—H⋯N(pyridyl) hydrogen bonds link the components of the asymmetric unit into a three-molecular aggregate [O3—H3o⋯N1: H3o⋯N1 = 1.85(2) Å, O3⋯N1 = 2.6952(16) Å with angle at H3o = 174(2)° and O5—H5o⋯N4: H5o⋯N4 = 1.820(17) Å, O5⋯N4 = 2.6550(16) Å with angle at H5o = 172(2)°]. The di-amide residues self-associate to form a supramolecular tape along the a-axis direction and mediated by 10-membered {⋯HNC2O}2 synthons, as shown in the lower view of the figure [N2—H2n⋯O1i: H2n⋯O1i = 2.027(11) Å, N2⋯O1i = 2.8206(14) Å with angle at H2n = 151.2(16)° and N3—H3n⋯O2ii: H3n⋯O2ii = 2.014(11) Å, N3⋯O2ii = 2.8157(14) Å with angle at H3n = 152.5(16)° for symmetry operations (i) 1 + x, y, z and (ii) −1 + x, y, z]. The tapes are connected into a layer in the ac-plane by methylene-C—H⋯O (carbonyl) [C6—H6a⋯O6iii: H6a⋯O6iii = 2.54 Å, C6⋯O6iii = 3.5045(18) Å with angle at H6a = 165° for (iii) 3 − x, 1 − y, 1 − z] and pyridyl-C—H⋯O (hydroxy) [C12—H12⋯O5iv: H12⋯O5iv = 2.50 Å, C12⋯O5iv = 3.327(2) Å with angle at H12 = 145° for (iv) 3 − x, 1 − y, 2 − z]. The connections between layers along the b-axis direction are also of the type C—H⋯O but at longer separations that is, pyridyl-C—H⋯O (amide) [C4—H4⋯O1v: H4⋯O1v = 2.60 Å, C4⋯O1v = 3.544(2) Å with angle at H4 = 172° for (v) 1 − x, −y, 1 − z] and methyl-C—H⋯O (amide) [C16—H16a⋯O1vi: H16a⋯O1vi = 2.61 Å, C16⋯O1vi = 3.585(2) Å with angle at H16a = 172° for (vi) 3 − x, −y, −z] interactions.

In order to understand more about the supramolecular interactions important in the molecular packing, Crystal Explorer 17 [12] was used for the calculation of the Hirshfeld surfaces as well as of the full and delineated two-dimensional fingerprint plots for the entire three-molecule aggregate using established procedures [13]. Important contributions to the calculated Hirshfeld surface come from H⋯H [44.1%] and O⋯H/H⋯O [30.0%] contacts, the latter reflecting the significant H⋯O contacts identified above. Other important surface contacts come from C⋯H/H⋯C [14.4%] as well as N⋯H/H⋯N [4.7%] and O⋯C/C⋯O [3.2%] contacts but, generally at distances greater than the sum of the respective van der Waals radii. The same calculations were also performed on each of the crystallographically independent components of the asymmetric unit. As anticipated, several differences in percentage contributions to the surface are apparent. For 3LH2, the contributions from H⋯H [40.6%] and O⋯H/H⋯O [25.3%] contacts have decreased significantly while those from N⋯H/H⋯N [11.0%] and C⋯H/H⋯C [16.9%] have increased compared with the overall three-molecule aggregate. A recent study [14] highlighted how the analysis of calculated Hirshfeld surfaces could be employed to distinguish between different molecules in the asymmetric unit. This is also true in the present case of the O3- and O5-carboxylic acids. Hence, differences in the percentage contributions to the overall surfaces for each molecule are apparent in the H⋯H [41.4% compared with 43.7% for the O3- and O5-carboxylic acids, respectively], O⋯H/H⋯O [38.1 and 37.8%] and C⋯H/H⋯C [6.1 and 4.4%]; the contributions from N⋯H/H⋯N contacts remain the same [8.1 and 8.2%].

Similar overall percentage contributions calculated for the three-molecule aggregate in the title co-crystal were noted in a very closely related structure, that is, 4LH2⋅2CH3C(=O)OH, isolated as a dihydrate [15]; the calculations were performed on the overall five-molecule aggregate. Here, despite the presence of water molecules of crystallisation that participate in significant hydrogen bonding interactions, the most important contribution to the Hirshfeld surface still comes from H⋯H contacts [43.4%] with O⋯H/H⋯O [32.5%] contacts being a little more important than in the title structure. Contacts of the type H⋯C/C⋯H [14.4%] also make a significant contribution to the surface but, again at relatively long separations.

Funding source: Sunway University Sdn Bhd

Award Identifier / Grant number: STR-RCTR-RCCM-001-2019

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

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Received: 2019-07-09
Accepted: 2019-07-26
Published Online: 2019-08-23
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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  44. Hydrothermal synthesis and crystal structure of cylo[tetraaqua-bis(μ2-1,4-bis(1H-benzo[d]imidazol-1-yl)but-2-ene-κ2N:N′)-bis(μ2-4-nitro-phthalate-κ2O,O′)dinickel(II)], C26H23N5O8Ni
  45. Crystal structure of 3-[methyl(phenyl)amino]-1-phenylthiourea, C14H15N3S
  46. Crystal structure of 1-(4-chlorophenyl)-3-[methyl(phenyl)amino]thiourea, C14H14ClN3S
  47. Crystal structure of 2-tert-butyl-1H-imidazo[4,5-b]pyridine, C10H13N3
  48. Crystal structure of 5-carboxy-2-(2-carboxyphenyl)-1H-imidazol-3-ium-4-carboxylate dihydrate, C12H8N2O6⋅2(H2O)
  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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