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Journal of the Chilean Chemical Society

versão On-line ISSN 0717-9707

J. Chil. Chem. Soc. vol.64 no.3 Concepción set. 2019

http://dx.doi.org/10.4067/S0717-97072019000304496 

Article

CRYSTAL STRUCTURE OF (E)-N′-((1H-PYRROL-2-YL)METHYLENE)-4-HYDROXYBENZOHYDRAZIDE

Ghodrat Mahmoudia 

Sadegh Rostamniaa 

Guillermo Zaragozab 

Iván Britoc 

Jonathan Cisternac 

Alejandro Cárdenasd 

aDepartment of Chemistry, Faculty of Science, University of Maragheh, P.O. Box 55181 −83111, Maragheh, Iran

bUnidad de RX, Edificio CACTUS, Campus Vida, Santiago Compostela, 15782, Spain

cDepartamento de Quιmica, Universidad de Antofagasta, Avda. Universidad de Antofagasta 02800, Campus Coloso Antofagasta–Chile, Antofagasta 1240000, Chile,

dDepartamento de Física, Universidad de Antofagasta, Avda. Universidad de Antofagasta 02800, Campus Coloso Antofagasta – Chile, Antofagasta 1240000, Chile,

ABSTRACT

The title compound corresponds to an enaminone E isomer in the solid state. X-ray structure shows that this crystallizes in the orthorrombic system, with space group Pna21 with 2 independent molecules in the asymmetric unit in a non-centrosymmetric setting. The CNNC unit forms dihedral angles of 5.9(3)/2.1(3); 19.7(3)/17.6(3)° with the pyrrole and phenol rings for molecules A and B respectively. The main differences between both molecules is the dihedral torsion between rings, their mean planes form dihedral angles of 25.45(15) and 15.38(15)° for the molecules A and B. In the asymmetric unit, molecules are linked by two weak N – H⋯O hydrogen bonds with set graph-motif R22 (16). The crystal structure of title compound generates a two dimensional supramolecular network lying parallel (110) with hydrogen bonds interactions between O – H⋯O and N – H⋯O along to [100] and [001] direction with graph set motifs R12 (5), R22 (10), C11 (8) and C11 (12). π stacking interactions are not observed. Hirshfeld surface analysis were used to verify the contributions of the different intermolecular interactions. Both molecules are essentially overlaid between them with RMSD = 0.0574; max D = 0.1211 Å considering inversion and flexibility.

Keywords: Hydrazide; X-ray diffracction; non-covalent interactions; Hirshfeld surface; energy framework

1. INTRODUCTION

Weak interactions, such as hydrogen, halogen, chalcogen, pnicogen, tetrel and picosagen bonds were extensively used in the synthesis, catalysis, crystal engineering, drug delivery, etc. 111. Among those, hydrogen bonding has turned out to be particularly suitable for design of organic and coordination compounds1219. Herein, we found strong intermolecular hydrogen bonds in (E)-N'-((1H-pyrrol-2-yl)methylene)-4-hydroxybenzohydrazide (I) and other weak non-covalent interactions, which were analized by Hirshfeld surface analysis to observe all contributions of the different intermolecular interactions stabilizing final 2D organic framework network (Scheme 1).

Scheme 1 

2. EXPERIMENTAL

High purity (E)-N'-((1H-pyrrol-2-yl)methylene)-4-hydroxybenzohydrazide was prepared in the laboratory following the literature method20. A possible future solution to our inability to grow single-crystals is the use of very interesting and unusual glassware for reaction/crystallization apparatus (branched tube) recently developed by us21. For the molecular structure of title compound, H atoms were located in the difference Fourier map and refined freely with distances in the range of 0.88(4) – 0.99(3) Å, except for the atoms H5A and H3B, which were treated has riding model, with distances C5A–H5A and N3B–H3B of 0.951 and 0.88 Å and Uiso(H) fixed at 1.2Ueq of the parent C and N atoms respectively.

X-ray diffraction patterns of title compound were collected using a Bruker SMART APEX-II CCD area detector equipped with graphite-monochromated Mo-Kα radiation (λ = 0.71073 Å) at 100 K. The diffraction frames were integrated using the APEX3 package22. The structure of were solved by intrinsic phasing23 using the OLEX 2 program24. The structure was then refined with full-matrix least-square methods based on F2 (SHELXL-2014)23. For (I), non-hydrogen atoms were refined with anisotropic displacement parameters. A summary of the details about crystal data, collection parameters and refinement are documented in Table 1, and additional crystallographic details are in the CIF files. ORTEP views were drawn using OLEX2 software24. CCDC 1917875 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via www.ccdc.cam.as.uk/data_request/cif.

Table 1 Crystal data parameters for compound (I) 

Empirical Formula C12H11N3O2
Formula mass, g mol-1 229.24
Collection T, K 99.99
crystal system orthorhombic
space group Pna21
a (Å) 15.3668(9)
b (Å) 11.0969(8)
c (Å) 12.7075(10)
α, β, γ (°) 90
V3) 2166.9(3)
Z 8
ρcalcd (gcm-3) 1.405
Crystal size (mm) 0.29 x 0.21 x 0.14
F(000) 960.0
abs coeff (mm-1) 0.099
range (°) 4.528 to 52.024
range h,k,l -17/18, −13/13, −15/15
No. total refl. 4264
No. unique refl. 4264
Comp. θmax (%) 1.00/26.00
Max/min transmission 0.943,1.000
Data/Restraints/Parameters 4264/1/387
Final R [I>2σ(I)] R1 = 0.0368, wR2 = 0.0820
R indices (all data) R1 = 0.0529, wR2 = 0.0907
Goodness of fit / F2 1.038
Largest diff. Peak/hole (eÅ-3) 0.18/-0.24

3. RESULTS AND DISCUSSIONS

The title compound corresponds to an enaminone E isomer in the solid state. The crystal structure can be described in terms of discrete molecules with two independent molecules in the asymmetric unit. An analysis of normal probability plot25 indicates that differences in the bond lengths and angles of these molecules are statistically insignificant. The average values will therefore be discussed. The sum of the angles around the N1 and N3 atoms [358.9 (3); 359.7(3)°] reflects a planar sp2 geometry. All the distances and angles are normal26,27 and comparable with similar compounds, refcode JOVQUI28 and VETPAO29, included in CCDC data base30. The CNNC unit forms dihedral angles of 5.9(3)/2.1(3)°; 19.7(3)/17.6(3)° with the pyrrole and phenol rings for molecules A and B respectively. The main differences between both molecules is the dihedral torsion between rings, their mean planes form dihedral angles of 25.45(15) and 15.38(15)° for the molecules A and B. In the asymmetric unit, molecules are linked by two weak N–H⋯O hydrogen bonds with set graph-motif R22 (16). The crystal structure of title compound generates a two dimensional supramolecular network lying parallel (110) with hydrogen bonds interactions between O – H⋯O and N – H⋯O along to [100] and [001] direction with graph set motifs R12 (5), R22 (10), C11 (8) and C11 (12). π-π stacking interactions are not observed. Both molecules are essentially overlaid between them with RMSD = 0.0574; max D = 0.1211 Å considering inversion and flexibility.

The molecular structure shows average dihedral angles of 20.1(4)° and 16.0(4)° between 4-hidroxyphenyl ring and -C(O)-NH- moiety and, 3.90(4)° between pyrrole ring and N2 atoms, 4.50(4)°, between carbonyl and -NH-N= fragment, respectively.

Figure 1 ORTEP plot of the title compound. Thermal ellipsoids were drawn with 30% of probability. 

Half-normal probability plot analysis was used to (i) investigate the reliability of the s.u.'s and (ii) identify systematic geometrical differences in two molecules. A comparison of the bond distances and angles of the fitted residues, reveals that the two molecules do not show any significant geometrical differences (see Table 2)31. The slope plot of the bond angles is 0.4910 and the intercept is −0.0016, showed a straight line with an intercept of almost zero and a slope of less than unity indicating that the s.u.s are slightly overestimated. The largest difference (-0.80°) is between the C8A -C9A -C10A angle in the first molecule and C8B -C9B -C10B in the second molecule, with Diff/Sig of −1.89, (RMS Angle Fit = 0.336°, sample size of 23)32.

Table 2 Bond distances and angles of the title compound. 

Atom Length/Å Atom Length/Å Atom Angle/° Atom Angle/°
O1A C7A 1.238(4) O1B C7B 1.236(4) C5A N1A C2A 109.0(3) C5B N1B C2B 109.2(3)
O2A C11A 1.360(4) O2B C11B 1.357(4) C6A N2A N3A 116.0(3) C6B N2B N3B 116.5(3)
N1A C2A 1.373(5) N1B C2B 1.373(5) C7A N3A N2A 118.5(3) C7B N3B N2B 118.0(2)
N1A C5A 1.363(4) N1B C5B 1.362(4) N1A C2A C3A 107.9(3) N1B C2B C3B 107.4(3)
N2A N3A 1.380(4) N2B N3B 1.379(3) N1A C2A C6A 122.6(3) N1B C2B C6B 122.4(3)
N2A C6A 1.278(4) N2B C6B 1.278(4) C3A C2A C6A 129.4(3) C3B C2B C6B 129.6(3)
N3A C7A 1.353(5) N3B C7B 1.356(4) C2A C3A C4A 107.2(3) C2B C3B C4B 107.2(3)
C2A C3A 1.378(5) C2B C3B 1.383(5) C5A C4A C3A 107.6(3) C5B C4B C3B 108.0(3)
C2A C6A 1.440(5) C2B C6B 1.441(5) N1A C5A C4A 108.3(3) C4B C5B N1B 108.2(3)
C3A C4A 1.406(5) C3B C4B 1.401(5) N2A C6A C2A 119.6(3) N2B C6B C2B 119.3(3)
C4A C5A 1.369(5) C4B C5B 1.362(5) O1A C7A N3A 121.3(3) O1B C7B N3B 121.4(3)
C7A C8A 1.482(5) C7B C8B 1.487(5) O1A C7A C8A 122.3(3) O1B C7B C8B 122.1(3)
C8A C9A 1.393(5) C8B C9B 1.388(5) N3A C7A C8A 116.4(3) N3B C7B C8B 116.4(3)
C8A C13A 1.401(4) C8B C13B 1.397(4) C9A C8A C7A 118.6(3) C9B C8B C7B 118.5(3)
C9A C10A 1.384(4) C9B C10B 1.383(5) C9A C8A C13A 118.9(3) C9B C8B C13B 118.6(3)
C10A C11A 1.394(4) C10B C11B 1.397(4) C13A C8A C7A 122.5(3) C13B C8B C7B 122.9(3)
C11A C12A 1.392(5) C11B C12B 1.390(5) C10A C9A C8A 120.5(3) C10B C9B C8B 121.3(3)
C12A C13A 1.380(5) C12B C13B 1.384(5) C9A C10A C11A 120.0(3) C9B C10B C11B 119.5(3)
O2A C11A C10A 117.8(3) O2B C11B C10B 117.6(3)
O2A C11A C12A 122.3(3) O2B C11B C12B 122.6(3)
C12A C11A C10A 120.0(3) C12B C11B C10B 119.8(3)
C13A C12A C11A 119.8(3) C13B C12B C11B 119.9(3)
C12A C13A C8A 120.8(3) C12B C13B C8B 120.8(3)

The crystal structure of title compound generates a two dimensional supramolecular network with hydrogen bonds interactions between O – H⋯O and N – H⋯O along to [100] and [001] direction with graph set motifs33 visible R12 (5), R22 (10), C11 (8) and 11(12) (see Figure 2 and Table 3)

Figure 2 Crystal packing of the title compound showing graph set motifs (top) and intermolecular hydrogen bond between neighbor molecules (bottom). 

Table 3 Hydrogen Bonds Interactions for title compound. 

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°
O2A H2A O1A1 0.88(4) 1.95(4) 2.819(3) 168(4)
N1A H1A O2A2 0.90(4) 2.25(4) 3.097(4) 156(4)
C6A H6A N1B3 0.97(3) 2.73(3) 3.389(5) 126(2)
C12A H12A O1A1 0.97(3) 2.35(3) 3.132(4) 137(3)
O2B H2B O1B4 0.90(5) 1.96(5) 2.814(3) 159(4)
O2B H2B N2B4 0.90(5) 2.31(5) 2.913(3) 124(4)
N1B H1B O2B5 0.88(4) 2.25(4) 3.103(4) 163(4)
C6B H6B N1A6 0.99(3) 2.67(4) 3.419(5) 133(3)
C12B H12B O1B4 0.94(3) 2.47(4) 3.179(4) 132(3)

11/2+X,3/2-Y,+Z

2-1/2+X,3/2-Y,+Z

33/2-X,-1/2+Y,-1/2+Z

4-1/2+X,1/2-Y,+Z

51/2+X,1/2-Y,+Z

61-X,1-Y,1/2+Z

A Hirshfeld surface analysis was conducted to verify the contributions of the different intermolecular interactions. This analysis was used to investigate the presence of hydrogen bonds and other weak intermolecular interactions in the crystal structure. The Hirshfeld surface analysis34 was generated by CrystalExplorer 17.535 and comprised dnorm surface plots and 2D (two-dimensional) fingerprint plots36. The plots of the Hirshfeld surface confirms the presence of the non-covalent interaction described below (Figure 3), taking account that in the asymmetrical unit there are two units (A and B) a procedure described previously in the literature was used to a better analysis and understanding of this interactions37. As described above, a strong hydrogen bonding interaction is observed in the crystal structure generating a 2D-network in the crystal structure, where units “A” and “B” are interacting with N – H⋯O hydrogen bond interaction, despite of both units are in different planes of the crystal, according to the symmetry elements on it. This are depicted in the Figure 3, where the both units are well defined and are interacting between them.

Figure 3 2-D network generated for the title compound. Units A and B are defined by red and blue colours respectively. 

In order to visualize and quantify the similarities and differences in intermolecular contacts across the crystal structure the Hirshfeld surface analysis was made for the molecules A and B present in the asymmetric unit independently (see Figure 4.).

Figure 4 Hirshfeld surface of the title compound for each unit. 

The weak intermolecular interactions are mainly constituted by H⋯O, H⋯N and H⋯C, the contribution for both units are depicted in Figure 5. Where the reciprocal contacts appear as a sharp wing for H⋯O, with de + di ≃ 1.8 Å, for H⋯N as a diffuse wing with de + di ≃ 2.1 Å and, H⋯C as asymmetrical wings with de + di ≃ 2.9 Å. In general, both units show a similar fingerprint plots except the H ⋯ C interaction. We can assume that this difference in the plot could be due to chirality of the crystal structure (non-centrosymmetric setting) or the antiparallel direction generated by the interactions in the both units.

Figure 5 Fingerprint plots for units A and B (top) and weak interactions contributions (bottom). 

Finally, energy framework was analysed to a better understanding of the packing of crystal structure and the supramolecular rearrangement. According to the tube direction, it can conclude that the formation of the framework is directed by the translational symmetry elements in each unit a long of a – axis due the strong hydrogen bond interaction O – H ⋯O and N – H ⋯O type directing the crystal structure layer by layer in the (110) plane disposing the molecular structure in an antiparallel zig-zag setting, according to the electrostatic (Eele). The dispersion (Edis) energy shows a hexagonal cage as a component of the framework energy being less dominating than (Eele) (see Figure 6). This rearrangement allows the formation of another weak interactions in the crystal structure such as H ⋯π between the pyrrole ring and the H – CNN – H fragment. To the best of our knowledge already exists little examples of H ⋯ π weaks interactions between hydrogen and heterocycles38,39.

Figure 6 Energy framework diagrams for (Eele), (Edis) and (Etot) for title compound. 

CONCLUSIONS

In this study we offer the report of structural studies of the title compound, showing the E isomer in the solid state. The weak intermolecular interactions show a 2D supramolecular network. Both molecules are essentially overlaid between them with RMSD = 0.0574; max D = 0.1211 Å considering inversion and flexibility. The understanding of the crystal packing of this molecule allows to postulate this compound in some applications such as synthesis, catalysis, crystal engineering, pharmaceutical design, molecular biology, molecular recognition, materials.

ACKNOWLEDGEMENTS

Iván Brito, Alejandro Cárdenas and Jonathan Cisterna, thank to Universidad de Antofagasta for purchase license for the Cambridge Structural Database and for the financial support. Jonathan Cisterna acknowledge to Universidad de Antofagasta for postdoctoral fellowship.

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