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Journal of the Chilean Chemical Society

versão On-line ISSN 0717-9707

J. Chil. Chem. Soc. vol.64 no.2 Concepción jun. 2019

http://dx.doi.org/10.4067/S0717-97072019000204441 

Article

CRYSTAL STRUCTURE AND HIRSHFELD SURFACE ANALYSIS OF (E)-5-PHENYL-3-((4-(TRIFLUOROMETHYL)BENZYLIDENE)AMINO)THIAZOLIDIN-2-IMINIUM BROMIDE

Abel M. MaharramovA 

Gulnara SH. DuruskariA 

Gunay Z. MammadovaA 

Ali N. KhalilovA  B 

Javahir M. AslanovaA 

Jonathan CisternaC 

Alejandro CárdenasD 

Iván BritoC 

1Organic Chemistry Department, Baku State University, Z. Xalilov Str. 23, AZ 1148, Baku, Azerbaijan.

2Department of Physics and Chemistry, “Composite Materials” Scientific Research Center, Azerbaijan State Economic University (UNEC), H.Aliyev str. 135, Az 1063, Baku, Azerbaijan.

3Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Avda. Universidad de Antofagasta 02800, Campus Coloso, Antofagasta, Chile.

4Departamento de Física, Facultad de Ciencias Básicas, Universidad de Antofagasta, Avda. Universidad de Antofagasta 02800, Campus Coloso, Antofagasta, Chile.

ABSTRACT

In the cation of the title salt, the central thiazolidine ring adopts an envelope conformation. In the crystal N-H⋯Br hydrogen bonds link the components into a bi-dimensional network with the cations and anions stacked parallel to plane (101). The molecular structure shows several positional disorders over -CF3 and thiazolidine fragments and these were modeled. The weak intermolecular interactions in the crystal structure are mainly constituted by H⋯F, H⋯π and H⋯Br. Hirshfeld surface analysis were used to verify the contributions of the different intermolecular interactions.

INTRODUCTION

Schiff bases and related N-ligands attract considerable interest and play an important role in the development of the chemistry of chelate systems as potential ligands towards a large number of metal ions18. Growing interest in the synthesis of such a type of compounds are due to their potential application as catalyst in many organic transformations912 and diverse useful properties, such as solvatochromism13, molecular switching14,15, crystal engineering16, etc. Noncovalent interactions (hydrogen, aerogen, halogen, chalcogen, pnictogen, tetrel and icosagen bonds, as well as cation-π, anion-π, lone pair-π, π-π stacking, agostic, pseudo-agostic, anagostic, dispersion-driven, lipophilic, etc.) concern weak forces of attraction formed between different molecules (intermolecular) or fragments of the same molecule (intramolecular). While these weak interactions were firstly taken into consideration by van der Waals in 1873 17, the understanding of their crucial role in synthesis, catalysis, crystal engineering, pharmaceutical design, molecular biology, molecular recognition, materials, etc. has been increasingly explored in the last few decades.

Herein we found strong charge assisted hydrogen bond and halogen bonding in (E)-5-phenyl-3-((4-(trifluoromethyl)benzylidene)amino)thiazolidin-2-iminium bromide (scheme 1).

Scheme 1 

EXPERIMENTAL

NMR spectra were recorded at room temperature on a Bruker Avance II + 300 (UltraShield™ Magnet) spectrometer operating at 300.130 and 75.468 MHz for proton and carbon-13, respectively. All NMR spectra are reported in parts per million (ppm, d) relative to tetramethylsilane (Me4Si) for 1H and 13C NMR spectra, with the residual solvent proton and carbon resonances used as internal standards. Coupling constants (J) are reported in Hertz (Hz), and integrations are reported as number of protons.

The following abbreviations are used to describe peak patterns: s = singlet, d = doublet, t = triplet, m = multiplet, br = broad. 1H and 13C NMR chemical shift assignments are supported by data obtained from 1H-1H COSY, 1H-13C HMQC, and 1H-13C. Electrospray mass spectra (ESI-MS) were run with an ion-trap instrument (Varian 500-MS LC Ion Trap Mass Spectrometer) equipped with an electrospray ion source. For electrospray ionization, the drying gas and flow rate were optimized according to the particular sample with 35 p.s.i. nebulizer pressure. Scanning was performed from m/z 0 to 1100 in methanol solution. The compounds were observed in the positive mode (capillary voltage = 80-105 V).

For the molecular structure of title compound, H atoms were located in the difference Fourier map, refined with fixed individual displacement parameters, using a riding model with C—H distances of 0.93 Å (for aromatic rings), 0.92 Å; 0.96 Å (for CH3, CH2), with U(H) values of 1.2Ueq(C, N) (for CH in aromatic rings and -NH2+), and 1.5Ueq(C, O) (for CH3 and -OH). Solvent molecules were restrained using Rigid body (RIGU) restrains (O1S, C1S). trifluoromethyl moiety (-CF3) was restrained using SADI. All sigma for 1-2 distances of 0.004 Å and sigma for 1-3 distances of 0.004 Å. Finally the several disordered -CF3, was treated with FVAR and SUMP.

X-ray diffraction patterns of title compound were collected using a Bruker SMART APEX-II CCD area detector equipped with graphite-monochromated Mo-Κα radiation (λ = 0.71073 Å) at room temperature. The diffraction frames were integrated using the APEX3 package18. The structure of were solved by intrinsic phasing19 using the OLEX 2 program20.

The structure was then refined with full-matrix least-square methods based on F2 (SHELXL-2014)19. For C14H8BrCl2FN2, non-hydrogen atoms were refined with anisotropic displacement parameters. All hydrogen atoms were included in their calculated positions, assigned fixed isotropic thermal parameters and constrained to ride on their parent atoms. 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 software20. CCDC 1912059 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 title compound. 

Empirical Formula C18H21BrF3N3O2S
Formula mass, g mol−1 480.35
Collection T, K 296.15
crystal system monoclinic
space group P21/n
a (Å) 5.7935(3)
b (Å) 11.6768(9)
c (Å) 31.310(2)
β(°) 95.259(4)
V3) 2109.2(2)
Z 4
ρcalcd (gcm−3) 1.513
Crystal size (mm) 0.52 × 0.31 × 0.17
F(000) 976.0
abs coeff (mm−1) 2.092
range (°) 2.612 – 56.186
range h,k,l -7/7, -14/15, -41/41
No. total refl. 16972
No. unique refl. 5122 [Rint = 0.0504, Rsigma = 0.0613]
Comp. θmax (%) 99.5/28.09
Data/Restraints/Parameters 5122/41/279
Final R [I>2σ(I)] R1 = 0.0783, wR2 = 0.1938
R indices (all data) R1 = 0.1057, wR2 = 0.2136
Goodness of fit / F2 1.132
Largest diff. Peak/hole (eÅ−3) 1.52/-0.86

To the solution of 1 mmol of 3-amino-5-phenylthiazolidin-2-iminium bromide in 20 mL ethanol was added 1 mmol of 4-(trifluoromethyl)benzaldehyde and refluxed for 2 hours. Then the reaction mixture was cooled down. Reaction products was precipitated from reaction mixture as a colorless single crystals, collected by filtration and washed with cold acetone.Yield 73%. Mp 231°C. Anal. Calcd. for C17H15BrF3N3S (Mr =430.29): C, 47.45; H, 3.51; N, 9.77. Found: C, 47.40; H, 3.48; N, 9.71 %. 1H NMR (300MHz, DMSO-d6): 4.58 (k, 1H, CH2, 3JH-H=6.6); 4,89 (t, 1H, CH2, 3JH-H=8.4); 5.60 (t, 1H, CH-Ar, 3JH-H=7.5); 7.39-8.29 (m, 9H, 9Ar-H); 8.51 (s, 1H, CH=); 10.51 (s, 1H, NH=). 13C NMR(75MHz, DMSO-d6): 45.45, 56.03, 125.74, 125.80, 127.86, 128.95, 129.15, 129.22, 130.72, 131.14, 136.85, 137.50, 149.54, 168.62. MS (ESI), m/z: 350.38 [C17H15F3N3S]+ and 79.88 Br.

RESULTS AND DISCUSSION

The cation structure corresponds to the E isomer in the solid state. All the distances and angles are normal21,22. The bond lengths range between measured C-C and C=N values for single and double bonds in C4-C5, C5-N1 and N1-N2 are slightly larger than the reported for similar organic compounds2325, depicted a potential electronic disconnection between the rings in the cation of the title compound.

Figure 1 ORTEP plot of the title compound. Thermal ellipsoid was drawn with 30% of probability. Some hydrogen atoms were omitted for sake. 

In the cation of the title salt, the central thiazolidine ring (S1/N2/C1-C3) adopts an envelope conformation with puckering parameters 0.300(6)Å, and φ(2)= 325,1(12)°. The dihedral angle between the mean plane of the central thiazolidine ring and the (4-trifluoromethyl)benzylidene ring (C5-C10) is 0.4(3) while this plane make a angle 10(2)° with the phenyl ring. The N2-N1-C4-C5 bridge that links the thiazolidine and (4-trifluoromethyl)benzylidene ring is 0.40 (3)° (see tables 3 and 4).

Table 2 Fractional Atomic Coordinates (×104) and Equivalent Isotropic Displacement Parameters (Å2x103) for title compound. Ueq is defined as 1/3 of of the trace of the orthogonalised UIJ tensor. 

Atoms x y z U(eq)
Br1 14384.5(10) 2642.6(5) 7630.0(2) 31.7(2)
S1 5698(2) 5952.5(13) 7912.1(4) 28.4(3)
F1A 13725(9) 2291(6) 5137.4(16) 72(2)
F2A 9940(40) 1910(20) 4957(6) 92(6)
F3A 11190(20) 3418(9) 4903(2) 97(4)
F1B 13110(80) 3170(50) 5005(14) 72(2)
F2B 9970(50) 2870(30) 4861(8) 97(4)
F3B 10770(40) 1435(13) 5094(5) 92(6)
O1S 4010(20) 6087(10) 6154(2) 158(6)
N1 8072(8) 4562(4) 6923.8(13) 24.0(10)
N2 7800(8) 4922(4) 7335.3(15) 24.8(10)
N3 4486(9) 5894(5) 7069.8(16) 35.7(12)
C1 9231(9) 4612(5) 7724.9(17) 24.5(11)
C3 5958(9) 5579(5) 7384.4(17) 25.6(11)
C4 9802(10) 3931(5) 6872.6(18) 26.0(11)
C5 10177(9) 3531(5) 6437.9(16) 25.2(11)
C6 12186(10) 2943(5) 6368.8(18) 31.9(13)
C7 12622(11) 2597(6) 5964.3(19) 35.2(14)
C8 11035(11) 2845(6) 5616.9(18) 38.1(15)
C9 8995(11) 3414(6) 5682.1(19) 40.3(16)
C10 8574(11) 3770(6) 6086.6(19) 37.7(15)
C11 11509(12) 2527(7) 5183(2) 55(2)
C12 9042(10) 5043(6) 8521.8(18) 35.1(14)
C13 11095(10) 4464(6) 8637.2(18) 35.9(14)
C14 11758(12) 4214(7) 9060(2) 49.8(19)
C15 10333(14) 4513(8) 9372(2) 59(2)
C16 8294(13) 5090(7) 9259(2) 49.4(19)
C17 7633(11) 5337(6) 8841.2(19) 39.4(15)
C2A 8686(13) 5497(7) 8052(2) 25.9(15)
C2B 7620(30) 4718(18) 8105(6) 25.9(15)
C1S 3780(20) 5914(9) 5728(3) 88(4)
O2S 9430(30) 7111(8) 6313(3) 169(6)

Table 3 Bond Angles for the title compound. 

Atoms Angle/° Atoms Angle/°
C3 S1 C2A 89.5(3) F2A C11 F3A 91.6(13)
C3 S1 C2B 90.7(6) F2A C11 C8 117.5(11)
C4 N1 N2 117.1(5) F3A C11 C8 112.2(7)
N1 N2 C1 127.0(4) F1B C11 F3B 131(2)
C3 N2 N1 116.4(4) F1B C11 C8 116(2)
C3 N2 C1 116.5(4) F2B C11 F1B 87.5(19)
N2 C1 C2A 105.1(5) F2B C11 F3B 87.3(17)
N2 C1 C2B 106.3(8) F2B C11 C8 116.8(15)
N2 C3 S1 113.3(4) F3B C11 C8 110.2(9)
N3 C3 S1 123.1(4) C13 C12 C17 118.6(6)
N3 C3 N2 123.6(5) C13 C12 C2A 116.6(5)
N1 C4 C5 119.1(5) C13 C12 C2B 118.9(9)
C6 C5 C4 119.9(5) C17 C12 C2A 124.0(6)
C6 C5 C10 118.8(5) C17 C12 C2B 111.8(9)
C10 C5 C4 121.3(5) C14 C13 C12 120.8(6)
C7 C6 C5 121.2(5) C13 C14 C15 119.6(6)
C6 C7 C8 119.7(5) C16 C15 C14 119.8(6)
C7 C8 C11 120.6(6) C17 C16 C15 120.7(6)
C9 C8 C7 119.8(5) C16 C17 C12 120.5(6)
C9 C8 C11 119.6(6) C1 C2A S1 106.9(5)
C10 C9 C8 120.4(5) C1 C2A C12 113.0(6)
C9 C10 C5 120.1(5) C12 C2A S1 111.4(5)
F1A C11 F3A 99.4(7) C1 C2B S1 101.0(10)
F1A C11 C8 114.7(6) C12 C2B S1 109.9(11)
F2A C11 F1A 116.9(13) C12 C2B C1 110.8(12)

Table 4 Bond Lengths for the title compound 

Atoms Length/Å Atoms Length/Å
S1 C3 1.729(5) C4 C5 1.474(7)
S1 C2A 1.826(8) C5 C6 1.386(7)
S1 C2B 1.89(2) C5 C10 1.401(8)
F1A C11 1.334(8) C6 C7 1.375(8)
F2A C11 1.316(12) C7 C8 1.389(8)
F3A C11 1.362(9) C8 C9 1.388(8)
F1B C11 1.356(16) C8 C11 1.458(7)
F2B C11 1.347(14) C9 C10 1.376(8)
F3B C11 1.366(12) C12 C13 1.387(8)
O1S C1S 1.344(11) C12 C17 1.391(8)
N1 N2 1.378(6) C12 C2A 1.560(9)
N1 C4 1.266(7) C12 C2B 1.53(2)
N2 C1 1.456(7) C13 C14 1.374(8)
N2 C3 1.335(7) C14 C15 1.381(9)
N3 C3 1.296(7) C15 C16 1.377(10)
C1 C2A 1.508(9) C16 C17 1.359(8)
C1 C2B 1.581(19)

In the crystal N-H⋯Br hydrogen bonds link the components into a bi-dimensional network with the cations and anions stacked parallel to plane 101. The weak interactions are mainly constituted by H⋯F, Η⋯π and Η⋯Br. Moreover, In crystal structure it is found strong charge assisted hydrogen-halogen bonding and, intermolecular hydrogen-π bonding interaction along to [010] direction with 2.40 Å (Figure 2 and table 5)

Figure 2 Non-covalent interactions in the crystal structure of the title compound. 

Table 5 Hydrogen Bonds for Gul7. 

D H A d(D-H)/Å d(H-A)/Å d(D-A)/Å D-H-A/°
O1S H1S O2S1 0.84 2.21 2.991(16) 154.8
N3 H3A O1S 0.88 2.10 2.863(8) 144.7

1-1+X,+Y,+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 intermolecular interactions in the crystal structure. The Hirshfeld surface analysis 26 was generated by CrystalExplorer 17.5 27 and comprised dnorm surface plots and 2D (two-dimensional) fingerprint plots 28. The plots of the Hirshfeld surface confirms the presence of the non-covalent interaction described below (Figure 3.), taking account the several positional disorder in the molecular structure

Figure 3 The two-dimensional fingerprint plots of the title compound [de and di represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (internal) the surface, respectively]. 

Table 6 Contributions of interatomic contacts to the Hirshfeld surface for the title compound*

Contact Contribution (%)
Br⋯H 6.8%
Br⋯N 0.9%
Br⋯C 0.7%
F⋯F 0.5%
F⋯O 0.1%
F⋯H 24.5%
F⋯C 1.0%
O⋯H 2.9%
O⋯C 0.3%
H⋯H 32.8%
H⋯N 3.8%
Η ⋯C (π - H) 19.3%

*Reciprocal contacts

The weak intermolecular interactions are mainly constituted by H⋯F, Η⋯π and H⋯Br, with a contribution of 24.5, 19.3 and 6.8%, respectively. Where the reciprocal contacts appear as a wide stain for H⋯F, with de + di≃ 2.8 Å, for H⋯Br as a sharp spike with de + di≃ 2.3 Å and, π ⋯H as asymmetrical wings with de + di≃ 3.0. Å, according to the interaction depicted in figure 2. This type of weak interactions are also observed in isostructural compounds recently reported2325.

CONCLUSIONS.

In this study we offer the report of synthesis, characterization and structural studies of the title compounds, showing the E isomer in the solid state. The weaks intermolecular interactions, were successfully verified with Hirshfeld surface analyses, being mainly constituted by H⋯F, Η⋯π and H⋯Br, with a contribution of 24.5, 19.3 and 6.8%, respectively. The chemistry of this compound allow postulate as a good candidate for several applications such as potential biological, pharmacological and analytical applications, moreover heterocyclic amines are also widely used in the synthesis of Schiff bases, which provide different kinds of noncovalent interactions.

ACKNOWLEDGEMENTS.

Ali Khalilov thankful to Baku State University for the “50+50” individual grant support in this work. 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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