Home 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
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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

  • Sang Loon Tan and Edward R.T. Tiekink ORCID logo EMAIL logo
Published/Copyright: August 17, 2019

Abstract

C18H26N4O8, triclinic, P1̄ (no. 2), a = 4.7975(2) Å, b = 9.8725(3) Å, c = 11.0244(3) Å, α = 85.312(3)°, β = 79.872(3)°, γ = 87.600(3)°, V = 512.09(3) Å3, Z = 1, Rgt(F) = 0.0381, wRref(F2) = 0.1064, T = 100(2) K.

CCDC no.: 1943404

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:0.13 × 0.08 × 0.06 mm
Wavelength:Cu Kα radiation (1.54184 Å)
μ:0.93 mm−1
Diffractometer, scan mode:XtaLAB Synergy, ω
θmax, completeness:76.4°, >99%
N(hkl)measured, N(hkl)unique, Rint:12778, 2132, 0.024
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2064
N(param)refined:152
Programs:CrysAlisPRO [1], SHELX [2], [3], WinGX/ORTEP [4]
Table 2:

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

AtomxyzUiso*/Ueq
O1−0.0316(2)0.67171(9)0.39091(9)0.0215(2)
H1O0.069(4)0.691(2)0.4434(15)0.032*
O20.0344(2)0.88746(9)0.31598(9)0.0208(2)
C1−0.2532(3)0.74917(15)0.22251(13)0.0221(3)
H1A−0.4509520.7718510.2563320.033*
H1B−0.2351500.6527730.2063260.033*
H1C−0.1942540.8049180.1452360.033*
C2−0.0687(3)0.77664(13)0.31375(12)0.0161(3)
O30.32813(19)0.84427(9)1.01777(8)0.0177(2)
N10.2813(2)0.71711(11)0.55318(10)0.0173(2)
N20.7261(2)0.91165(10)0.88469(10)0.0144(2)
H2N0.823(3)0.9833(13)0.8508(14)0.017*
C30.3408(3)0.84326(13)0.57505(12)0.0178(3)
H30.2706650.9178990.5280720.021*
C40.5003(3)0.86942(13)0.66329(12)0.0168(3)
H40.5377810.9603030.6764730.020*
C50.6050(3)0.76099(12)0.73235(11)0.0139(3)
C60.5454(3)0.62963(13)0.70875(12)0.0170(3)
H60.6156200.5530510.7533200.020*
C70.3828(3)0.61228(13)0.61955(12)0.0184(3)
H70.3411750.5225090.6046330.022*
C80.7810(3)0.78179(12)0.83007(12)0.0152(3)
H8A0.7434130.7077250.8964660.018*
H8B0.9839350.7748630.7927440.018*
C90.5066(3)0.92940(12)0.97453(11)0.0132(3)
O1W0.2347(3)0.55775(10)1.03265(11)0.0319(3)
H1W0.244(5)0.6434(10)1.020(2)0.048*
H2Wa0.103(6)0.530(3)1.000(4)0.048*
H3Wa0.390(4)0.522(3)1.000(4)0.048*
  1. aOccupancy: 0.5.

Source of material

N,N′-Bis(pyridin-4-ylmethyl)oxalamide, 4LH2, was prepared according to the literature procedure [5] (melting point, m.pt: 485–486 K; lit. [5]: 486–487 K). The title co-crystal solvate was prepared by dissolving 4LH2 (0.154 g, 1 mmol) in an excess of glacial acetic acid (3 mL). Upon 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 4LH2⋅2CH3C(=O)OH⋅2H2O. M.pt: 374–376 K. IR (ATR, cm−1): 3278(s) ν(N—H), 3168–2919(w) ν(C—H), 1710–1649(s) ν(C=O), 1524(s) ν(C=C), 1357(m) ν(C—N), 710(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 a 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. One of the water-bound hydrogen atoms was statistically disordered over two sites. Difference Fourier maps appear to indicate partial proton transfer to give a pyridinium cation and acetate anion in a ca. 0.3 : 0.7 ratio. On the basis of the great disparity in the C2—O1, O2 bond lengths (see below) the molecules were modelled as neutral. Further multi-temperature experiments would clarify whether proton transfer occurs as a function of temperature or whether the above observation is an artefact of the data.

Comment

The structural chemistry of 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, abbreviated as nLH2, and their co-crystals, salts and metal complexes has been reviewed recently [6]. The key feature of the molecules in terms of co-crystal formation is the presence of a central di-amide functionality as well as two terminal pyridyl residues, both of which are capable of participating in conventional hydrogen bonding. Continuing interest in examining co-crystal formation of 4LH2 and their ability to generate coordination polymers [7], [8], [9], lead to the isolation of the title 2:1 co-crystal di-hydrate, 4LH2⋅2CH3C(=O)OH⋅2H2O.

The molecular structure of the constituents of the crystal are shown in the figure (70% displacement ellipsoids; the full molecule of 4LH2 and symmetry-related acetic acid and water molecules are generated by the symmetry-operation (i) 1 − x, 2 − y, 2 − z; in the Figure the water is shown as ordered). The 4LH2 molecule is disposed about a centre of inversion so the pyridyl rings adopt an anti-periplanar disposition. The central C2N2O2 atoms are co-planar [r.m.s. deviation = 0.0034 Å], with the adjacent C8 atoms lying 0.065(2) Å to either side of the plane. An intramolecular amide-N—H⋯O(amide) hydrogen bond is noted [N2—H2n⋯O3i: H2n⋯O3i = 2.335(14) Å, N2⋯O3i = 2.7025(13) Å, with angle at H2n = 105.1(11)°] which gives rise to an S(5) loop using graph-set notation [10]. An orthogonal relationship between the central plane and each terminal pyridyl ring is evident as seen in the dihedral angle between the planes of 87.28(3)°. Suggestive evidence that the carboxylic acid is just that, an acid, is found in the great disparity in the C2—O1, O2 bond lengths of 1.3122(16) and 1.2232(16) Å, respectively; see Experimental details for the possibility of partial proton transfer.

Significant hydrogen bonding is evident in the molecular packing. As seen from the figure, there are acetic acid-O—H⋯N(pyridyl) [O1—H1o⋯N1: H1o⋯N1 = 1.754(18) Å, O1⋯N1 = 2.6051(14) Å with angle at H1o = 175.6(19)°] and water-O—H⋯O(amide) [O1w—H1w⋯O3: H1w⋯O3 = 2.038(11) Å, O1w⋯O3 = 2.8694(14) Å with angle at H1w = 167(2)°] hydrogen bonds. The aforementioned hydrogen bonds give rise to a five-molecule aggregate. In the crystal, the acetic acid-O—H⋯N(pyridyl), mentioned above, combine with amide-N—H⋯O(carbonyl-acetic acid) hydrogen bonds [N2—H2n⋯O2ii: H2n⋯O2ii = 2.174(15) Å, N2⋯O2ii = 2.9542(14) Å with angle at H2n = 147.2(13)° for (iii) 1 − x, 2 − y, 1 − z] to give rise to 22-membered, centrosymmetric {⋯HNC4N⋯OHCO}2 synthons and supramolecular tapes along the c-axis direction. The water molecules are connected to the chains laterally (along the b-axis direction) and are linked to each other normal to the tapes via water-O—H⋯O(water) hydrogen bonds to form chains along the a-axis and therefore, stabilise a three-dimensional architecture. As noted in the Experimental details, the second water-bound hydrogen atom is disordered over two positions, in a 50:50 ratio for H2w and H3w, and so there are two such connections to consider [O1w—H2w⋯O1wiii: H2w⋯O1wiii = 1.97(3) Å, O1w⋯O1wiii = 2.7945(19) Å with angle at H2w = 165(4)° and O1w—H3w⋯O1wiv: H3w⋯O1wiv = 1.92(2) Å, O1w⋯O1wiv = 2.7468(19) Å with angle at H3w = 165(4)° for (iii) −x, 1 − y, 2 − z and (iv) 1 − x, 1 − y, 2 − z]. In order to gain further insight into the supramolecular association in the crystal, Crystal Explorer 17 [11] was employed to calculate the Hirshfeld surfaces as well as the full and delineated two-dimensional fingerprint plots which was analysed following established procedures [12]. Initially, the calculations were performed on the five-molecule aggregate illustrated in the upper view of the figure; the reported values are the average of the results calculated for the individual disorder components. The most important contribution to the Hirshfeld surface comes from H⋯H contacts [40.6%]. However, O⋯H/H⋯O contacts make a notable contribution to the calculated surface, at 35.5%, which is consistent with the significant H⋯O contacts identified above. The other major contribution comes from C⋯H/H⋯C contacts [15.1%]. Other contributions >2% to the surface are due to N⋯H/H⋯N [3.2%] and O⋯O [1.6%]. Very similar percentage contributions are noted in a closely related structure, 3LH2⋅2CH3C(=O)OH [13], that is with the isomeric 3-pyridyl base and lacking solvent water molecules. Hence, in this latter structure, H⋯H and O⋯H/H⋯O contacts are calculated to contribute 44.1 and 30.0%, respectively, to the overall surface. Contacts of the type C⋯H/H⋯C [14.4%] also make a significant contribution, followed by N⋯H/H⋯N [4.7%] and O⋯C/C⋯O [3.2%] but at long separations. Calculations were also performed on the individual 4LH2 and acid molecules. For the former, the major contributions to the calculated Hirshfeld surface were H⋯H [38.7%], O⋯H/H⋯O [28.5%], C⋯H/H⋯C [19.1%] and N⋯H/H⋯N [9.4%], together contributing to over 95% of all contacts to the overall surface. The remaining contacts are O⋯N/N⋯O [1.5%], N⋯C/C⋯N [1.1%], O⋯C/C⋯O [1.0%] and C⋯C [0.7%]. For the molecule of acetic acid, hydrogen atoms are involved in over 96% of all surface contacts: O⋯H/H⋯O [41.4%], H⋯H [38.4%], N⋯H/H⋯N [8.5%] and C⋯H/H⋯C [8.0%].

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: 2019-07-08
Accepted: 2019-07-26
Published Online: 2019-08-17
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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  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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