alexa Crystal Structure and Hirshfeld Surface Analysis of 1,2-Bis((2-(Bromomethyl)Phenyl)Thio)Ethane and Two Polymorphs of 1,2-Bis((2-((Pyridin-2-ylthio)Methyl)Phenyl)Thio)Ethane | Open Access Journals
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Crystal Structure and Hirshfeld Surface Analysis of 1,2-Bis((2-(Bromomethyl)Phenyl)Thio)Ethane and Two Polymorphs of 1,2-Bis((2-((Pyridin-2-ylthio)Methyl)Phenyl)Thio)Ethane

Simplicio González-Montiel1*, Saray Baca-Téllez1, Diego Martínez-Otero2, Alejandro Álvarez-Hernández1 and Julián Cruz-Borbolla1
1Área Academic Chemistry, Chemical Research Center, University of the State of Hidalgo, 4.5 km. Road Pachuca-Tulancingo, City of Knowledge, CP 42184, Mineral de la Reforma, Hidalgo, Mexico
2Joint Research Centre in Sustainable Chemistry, UNAM UAEM, Toluca-Atlacomulco Highway 14.5 km., C.P. 50200, Toluca, State of Mexico, Mexico
Corresponding Author : Simplicio González-Montiel
Área Académica de Química, Centro de Investigaciones Químicas
Universidad Autónoma del Estado de Hidalgo
km. 4.5 Carretera Pachuca-Tulancingo, Ciudad del Conocimiento
C.P. 42184, Mineral de la Reforma, Hidalgo, México
Tel: +52-771-71-72-000
Fax: +52-771-71-72-000
E-mail: [email protected]
Received May 07, 2015; Accepted June 12, 2015; Published June 17, 2015
Citation: González-Montiel S, Baca-Téllez S, Martínez-Otero D, Álvarez- Hernández A, Cruz-Borbolla J, et al. (2015) Crystal Structure and Hirshfeld Surface Analysis of 1,2-Bis((2-(Bromomethyl)Phenyl)Thio)Ethane and Two Polymorphs of 1,2-Bis((2-((Pyridin-2-ylthio)Methyl)Phenyl)Thio)Ethane. Mod Chem appl 3:154. doi: 10.4172/2329-6798.1000154
Copyright: ©2015 González-Montiel S et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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1,2-Bis((2-(bromomethyl)phenyl)thio)ethane (1) and 1,2-bis((2-((pyridin-2-ylthio)methyl)phenyl)thio)ethane (2) were prepared and characterized by IR and NMR spectroscopy and single-crystal X-ray crystallography. X-ray diffraction studies shown that compound 1 crystallizes in a monoclinic space group P21/n with crystal parameters a=8.3970(3) Å, b=12.4566(2) Å, c=8.9251(3) Å; β=117.911(3)°, V=824.96(5) Å3 and z=2, and compound 2 exists in two monoclinic polymorphs (2a and 2b). Polymorph 2a crystals are in space group P21, with unit cell parameters a=5.3702(2) Å, b=14.4235(6) Å, c=15.4664(7) Å, β=119.97(9)°, V=1197.97(9) Å3 and z=2, while polymorph 2b crystals are in space group P21/c with unit cell parameters a=7.8312(3) Å, b=9.6670(4) Å, c=16.2962(5) Å, β=121.219(3)°; V=1210.12(7) Å3 and z=2. Variations in the crystal packing help to distinguish these two polymorphs via π-π and C−H•••π interactions. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots have been performed to gain insight into the behavior of these interactions in compound 1 and polymorphs 2a and 2b.

Polymorphs; 1,2-bis((2-((pyridin-2-ylthio)methyl) phenyl)thio)ethane; Crystal packing; Hirshfeld surface; π-π and C−H•••π interactions
Polymorphism is the ability of a particular molecule to exist in more than one crystal structure and it has great importance in pharmacology, solid-state chemistry, and material science since different polymorphs may have different physicochemical properties such as thermal behavior, stability, solubility, melting point, and bioavailability, among others [1-6]. Variations in structural units in a crystal leading to polymorphs occur through different intermolecular interactions such as D–H•••A hydrogen bonding, π-π stacking, CH•••π, halogen•••π, halogen•••halogen and anion•••π. These crystal structure modification in each polymorph result in different thermodynamic stability, i.e., the free energy of the crystals, kinetics of nucleation and crystal growth promoted by crystallization conditions (solvent, temperature, concentration, cocrystallization, pressure, etc.) [7-15]. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld’s stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). Hirshfeld surface analysis has gained prominence as a powerful tool to explore and describe a wide variety of intermolecular interactions within a crystal, [16-18] and it is almost always related to its corresponding 2D fingerprint-plot. This plot provides a convenient way to quantify intermolecular interactions within crystal structures and helps to reveal important information both about close contacts and also about more distant interactions and areas where contacts are weak [19-25].
Herewith we report the synthesis and structural study of two polymorphs of 1,2-bis((2-((pyridin-2-ylthio)methyl)phenyl)thio) ethane (2a and 2b) and 1,2-bis((2-(bromomethyl)phenyl)thio)ethane (1) (Scheme 1) as part of our studies concerning the construction of novel metallomacrocycles based on ligands that contain in their structure two 2-mercaptopyridyl groups [26]. The intermolecular interactions that exist in the crystal structure of the two polymorphs have also been investigated by Hirshfeld surface analysis [23-25].
Materials and instrumentation
All reagents are commercially available and were used without further purification. Melting points were measured in a Mel-Temp II instrument and are not corrected. Elemental analyses of the compounds were determined on a Perkin–Elmer Series II CHNS/O Analyzer. IR spectra were recorded on the 4000-400 cm-1 range on a Perkin–Elmer 2000 FTIR spectrometer as KBr pellets. 1H NMR and 13C{1H} NMR spectra were recorded on a Varian Inova 400 NMR spectrometer at 20°C in CDCl3 solutions; 1H, 399.78 MHz and residual protio-solvent signal were utilized as reference. Chemical shifts are quoted in the δ scale (downfield shifts positive) relative to tetramethylsilane (1H). 1,2-bis-(2-hydroxymethylphenylthio)ethane (HOCH2Ph-S-CH2- CH2-S-PhCH2OH) was prepared according to a previously reported protocol [27].
Synthesis of 1,2-bis((2-(bromomethyl)phenyl)thio)ethane (1) and 1,2-bis((2-((2-pyridinylthio)methyl)phenyl)thio)ethane (2)
Preparation of 1,2-bis((2-(bromomethyl)phenyl)thio)ethane (1): 1,2-bis-(2-hydroxymethylphenylthio)ethane (8.15 mmol, 2.5 g) was dissolved in 50 mL of toluene and hydrobromic acid, 48% (25 mL) was added; the mixture was refluxed for 5 days. After cooling to room temperature, the two layers were separated and the organic layer was dried with NaSO4, then filtered through a bed of Celite and the solvent was removed under reduced pressure to give a white solid. Yield: 3.15 g (90%). m.p.=111-115°C. Anal. Calc. for C16H16Br2S2: C, 44.46; H, 3.73. Found: C, 44.16; H, 3.83%. 1H NMR (399.78 MHz, CDCl3): δ=7.45- 7.42 (2H, m, H1), 7.37–7.34 (2H, m, H4), 7.30-7.24 (4H, m, H2 and H3), 4.70 (4H, s, CH2-Br), 3.18 (4H, s, S-CH2) ppm. 13C{1H} NMR (100.53 MHz, CDCl3): δ 138.68 (C6), 135.05 (C5), 131.26 (C4), 130.99 (C1), 129.43 (C2), 127.49 (C3), 33.81 (S-CH2), 32.12 (CH2-Br) ppm. IR (KBr): 3058, 2966, 2920, 2852, 1588, 1567, 1466, 1443, 1431, 1218, 1203, 1194, 1063, 1038, 818, 754, 727, 704, 672, 602, 567, 497, 445 cm-1.
Preparation of 1,2-bis((2-((2-pyridinylthio)methyl)phenyl)thio) ethane (2): 1,2-bis((2-(bromomethyl)phenyl)thio)ethane (4.63 mmol, 2.0 g) and 2-mercaptopyridine (9.26 mmol, 1.03 g) were dissolved in 50 mL toluene, and then Cs2CO3 (4.63 mmol, 1.51 g) was added directly into the solution; the mixture was then refluxed for 16 h. After cooling, the resulting suspension was filtered through Celite and the solvent was removed under reduced pressure to give a white solid. Yield 2.10 g (92%). m.p.=82-87°C. Anal. Calc. for C26H24N2S4: C, 63.38; H, 4.91; Found: C, 62.98; H, 4.83%. 1H NMR (399.78 MHz, CDCl3): δ=8.46 (2H, ddd, 3J=4.96 Hz, 4J=1.84 Hz, 5J=0.94 Hz, H12), 7.49 (2H, dd, 3J=6.18 Hz, 4J=2.96 Hz, H1), 7.45 (2H, ddd, 3J=8.05 Hz, 4J=7.41 Hz, 5J=1.88 Hz, H10), 7.31 (2H, dd, 3J=6.48 Hz, 4J=2.66 Hz, H4), 7.16 (4H, m, H2, H3), 7.13 (2H, dd, 3J=7.14 Hz, 4J=0.98 Hz, H9), 6.98 (2H, ddd, 3J=7.34 Hz, 4J=4.95 Hz, 5J=1.02 Hz, H11), 4.62 (4H, s, H7), 3.14 (2H, s, H8) ppm. 13C NMR (CDCl3): δ=158.80 (C8), 149.42 (C12), 139.01 (C5), 136.11 (C10), 134.79 (C6), 130.82 (C1), 130.61 (C4), 128.10 (C2), 127.07 (C3), 122.36 (C9), 119.69 (11), 33.99 (C13), 32.91 (C7) ppm. IR (KBr): 3056, 2992, 2924, 2847, 1578, 1556, 1453, 1414, 1281, 1242, 1147, 1122, 1062, 1043, 985, 956, 820, 757, 619, 580, 479 cm-1.
X-ray diffraction
Suitable crystals of 1 were grown in toluene by slow evaporation while crystals of 2 were grown in dimethylsulfoxide and were separated by fractional crystallization; the polymorph 2a crystallized first after 2 weeks stored at room temperature and then crystals of polymorph 2b were obtained after 4 weeks at the same solution. All crystal structures were determined by X-ray analysis, and their crystallographic details and structure refinements are presented in Table 1. X-ray diffraction data were collected at room temperature on an Oxford Diffraction Gemini CCD diffractometer, using graphite-monochromated Cu Kα radiation (λ=1.54184 Å) for 1 and Mo Kα radiation (λ=0.71073 Å) for 2a and 2b. Data were processed using the Crysalis software package [28]. Using Olex2 [29], the structures were solved with the XS program [30] employing direct methods and refined with the XL refinement package using Least Squares minimization [30]. All non-hydrogen atoms were refined anisotropically and hydrogen atoms were located at calculated positions and refined using a riding model with isotropic thermal parameters fixed at 1.2 times the Ueq value of the appropriate carrier atom (Table 1).
Computational details
The Hirshfeld surfaces and fingerprint plots were calculated using the Crystal Explorer (version 3.1) software [31].
Results and Discussion
Synthesis of compounds 1 and 2
Compound 1,2-bis((2-((2-pyridinylthio)methyl)phenyl)thio)etane (2) was prepared in good yield using an established route (Scheme 1). Thus, starting from 1,2-bis-(2-hydroxymethylphenylthio)etane [26] bromination using an excess of hydrobromic acid led to 1,2-bis((2- (bromomethyl)phenyl)thio)etane (1). 1,2-bis((2-((2-pyridinylthio) methyl)phenyl)thio)etane was obtained from the reaction between 1,2-bis((2-(bromomethyl)phenyl)thio)ethane and 2-mercaptopyridine in presence of Cs2CO3. Compounds 1 and 2 are soluble in chloroform, dichloromethane, toluene, benzene and acetonitrile, and are insoluble in methanol, ethanol, pentane and n-hexanes.
NMR spectroscopy
The 1H NMR spectrum of compound 1 show three signals at high frequencies corresponding to ortho-substituted benzene rings, two single signals at low frequencies correspond to the bridge ethylene group and the bromomethylene group. The 1H NMR spectrum of compound 2 shows eight signals at high frequencies due to two ABCD patterns corresponding to the ortho-substituted benzene rings and to the ortho-substituted pyridine rings; signals at low frequencies correspond to the methylene groups that link the phenyl and pyridine rings and to the ethylene brigde between both phenyl rings.
The 13C NMR spectrum of compound 1 shows six signals at high frequencies that are attributed to ortho-substituted benzene rings and two single signals at low frequencies corresponding to the methylene group link bromide and the ethylene group that brigde both phenyl rings. The 13C-NMR of compound 2 shows eleven signals at high frequencies which six are attributed to ortho-substituted benzene and pyridine rings, and two signals at low frequencies corresponding to methylene and ethylene groups. In solution, the two −CH2-S-C6H4SCH 2-Br and −CH2-S-C6H4S-CH2-C5H4N units are equivalent.
Molecular and crystal structures
Molecular structures: The molecular structure of 1, 2a and 2b was confirmed by X-ray diffraction studies and their structure are depicted in Figures 1 and 2, and selected bond lengths, angles and torsion angles are given in Table 2.
In all compounds 1, 2a and 2b the aromatic rings on the ethylene group adopt anti-conformation, i.e. the −PhCH2Br fragments in 1 and −Ph-CH2-S-C5H4N fragments in 2a and 2b are positioned on opposite sides of the ethylene bridge with C1−C7---C7i−C1i torsion angles in 1 and 2b equal to 180° and C1−C7---C8−C9 torsion angle in 2a equal to 177.16°. In compounds 1 and 2b the phenyl rings [CgA=C1/C2/C3/C4/ C5/C6 and CgA’=C1’/C2’/C3’/C4’/C5’/C6’, symmetry code: (i) 2‒x, 1‒y, 1‒z for 1 and ‒x, 1‒y, ‒z for 2b] are in an antiparallel manner in relation to each another with centroid-to-centroid distance CgA•••CgA’ of 8.367 Å and 8.149 Å for 1 and 2b, respectively. While in 2a the phenyl rings (CgA=C1/C2/C3/C4/C5/C6 and CgB=C9/C10/C11/C12/C13/C14) are nearly coplanar with the dihedral angle between the two phenyl rings being 9.76° with centroid-to-centroid distance CgA•••CgB of 9.407 Å. The fragments −CH2Br in 1 and −CH2-S-C5H4N in 2a and 2b are displayed in a trans arrangement (Figures 1 and 2).
In polymorph 2a phenyl rings are nearly coplanar while in 2b phenyl rings are positioned in an antiparallel manner and centroid-tocentroid distance increases when phenyl rings are nearly coplanar. In this context the polymorph 2a presents a larger centroid-to-centroid distance compared to polymorph 2b [Δd(Cg•••Cg)=1.258 Å].
Crystal structures: The crystal lattice of 1 exhibits a supramolecular assembly that has a polymeric array via C–H•••π, π•••π interactions of the offset face to face stacking and Br•••π interactions. Thus, in this crystal lattice there is a C–H•••π interaction between one hydrogen atom of the methylene group bonded to bromine with a phenyl ring d(H8a•••Cg)=2.947 Å and image(C8–H8a•••Cg2)=111.78°; also a π•••π offset-stacked interaction is observed with d(H6•••Cg)=3.465 Å, d(Cg•••Cg)=4.655 Å and image(Cg–H6•••Cg)=105.81°; finally Br•••π interactions are also observed with d(Br1•••Cg)=3.465 Å, d(Br1•••C6)=3.600 Å and image(Br1–C6•••Cg)=92.96° (Figure 3).
Crystal analysis of polymorphs 2a and 2b suggests the presence of different π–π and C–H•••π interactions. The crystal lattice of polymorph 2a exhibits the formation of a supramolecular, polymeric array via C–H•••π interactions between one hydrogen atom of the methylene group linking a phenyl ring with a pyridine ring and other interactions between one hydrogen atom of the methylene group that bridges two phenyl rings [C–H•••π interactions with d(H7b•••Cg1)=2.708 Å and image(C7–H7b•••Cg1)=142.92°; d(H8a•••Cg2)=2.868 Å and image(C8–H78a•••Cg2)==143.02°; d(H15b•••Cg3)=3.116 Å and image(C15–H15b•••Cg3)=145.68°; where C1/C2/C3/ C4/C5/C6=Cg1, C9/C10/C11/C12/C13/C14=Cg2 and N1/C16/C17/ C18/C19/C20=Cg3, respectively] (Figure 4). Polymorph 2b presents a supramolecular, tetrameric assembly via π•••π offset-stacked and C–H•••π T-shaped interactions (π•••π offset-stacked interactions between two pyridinic rings with d(H10•••Cg2)=3.434 Å, d(Cg2•••Cg2)=4.446 Å and d(interplanar)=3.380 Å. C–H•••π T-shaped interactions are due to contacts between one hydrogen atom of one phenyl ring and another phenyl ring with d(H3•••Cg1)=3.302 Å, d(Cg1•••Cg1)=5.397 Å and image(C3–H3•••Cg)=148.16°, where C1/C2/C3/C4/C5/C6=Cg1 and N1/C9/C10/ C11/C12/C13=Cg2, respectively) (Figure 5).
Hirshfeld surface analysis
The intermolecular interactions of crystal structures of 1, 2a and 2b were quantified using Hirshfeld surface analysis and fingerprint plots which are illustrated in Figure 6. Surfaces that have been mapped over a norm are shown. The relative contributions of different interactions of compounds 1, 2a and 2b are presented in Figure 7.
In general, the fingerprint plots of compounds 1, 2a and 2b shown that dominant interactions are C•••H (19.2-31.8%) and H•••H (35.5-48.6%), and especially in compound 1 it is observed a Br•••H contribution (28.8%), other significant S•••H interactions have been observed varying from 10.8-17.5%. Hirshfeld surfaces of polymorphs 2a and 2b exhibit significant differences between intermolecular interactions. Thus, in 2b C•••H contributions are 7.6% larger than those for 2a; H•••H contributions in 2b are smaller by 5.1% than in those in 2a, S•••H contributions are quite similar in both polymorphs (17.0% in 2a and 17.5% in 2b), N•••H contributions are also similar (5.8% in 2a and 4.0% in 2b). Finally, polymorph 2b does not present C•••C contributions while in 2a this contribution is 3.3%. These differences in the contributions of all types of interactions found in the crystal structures of compounds 2a and 2b evidence that they are structurally different.
The crystal structure of the compound 1 and polymorphs 2a and 2b show different intermolecular interactions that lead to different types of supramolecular arrays. Quantification of the intermolecular interactions present in compounds 1, 2a and 2b was realized by Hirshfeld surface analysis and 2D fingerprint plots. This analysis of intermolecular contacts present in the crystal packing of 2a and 2b leads to conclude these compounds are true polymorphs.
Supplementary Material
Crystallographic data for the structural analyses have been deposited with the Cambridge Crystallographic Data Center, CCDC Nos. 1037743 for 1, 1037744 for 2a, and 1037745 for 2b. The data can be obtained free of charge from The Director, CCDC, 12 Union Road, Cambridge CB21EZ, UK (Fax: +44-1223-336-033; E-mail: [email protected] or
S.G.M. thankfully acknowledges financial support from CONACyT “México” (Grant CB-2011-01-167873) and S.B.T. is grateful for a graduate fellowship from CONACyT (352507).

Tables and Figures at a glance

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Table 1   Table 2

Figures at a glance

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Figure 1   Figure 2   Figure 3   Figure 4
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Figure 5   Figure 6   Figure 7
Scheme 5
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