Synthesis and Molecular Structure Investigation by DFT and X-Ray Diffraction of ARNO

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Abstract We report here the synthesis of (Z)-5-(4-nitrobenzyliden)-3-N(2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (ARNO) compound. The crystal structure has been determined by X-ray diffraction. The compound crystallizes in the triclinic system with
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  ORIGINAL PAPER Synthesis and Molecular Structure Investigation by DFTand X-Ray Diffraction of ARNO Nadia Benhalima  • Khaled Toubal  • Abdelkader Chouaih  • Giuseppe Chita  • Sabino Maggi  • Ayada Djafri  • Fodil Hamzaoui Received: 30 March 2011/Accepted: 29 June 2011/Published online: 14 July 2011   Springer Science+Business Media, LLC 2011 Abstract  We report here the synthesis of (  Z  )-5-(4-nitro-benzyliden)-3-  N  (2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one(ARNO) compound. The crystal structure has been deter-mined by X-ray diffraction. The compound crystallizes inthetriclinicsystemwithspacegroup P  1andcellparameters: a = 9.1289(19), b = 9.3717(7), c = 12.136(3) A˚, a = 102.133(11)  ,  b  =  90.99(2)  ,  c  =  117.165(9)  ,  V   =  895.4(3) A˚ 3 and  Z   =  2.ThestructurehasbeenrefinedtoafinalR  =  0.05for 2591 observed reflections. The refined structure wasfound to be significantly non planar. The molecule exhibitsintermolecular hydrogen bond of type C–H _ O andC–H _ S. ab initio calculations were also were performed atHartree–Fock and density functional theory levels. The fullHF and DFT geometry optimization was carried out usingLANL2DZ, 6-31G* and B3LYP/6-31 ? G** basis sets. Theoptimized geometry of the title compound was found to beconsistent structure determined by X-ray diffraction. Theminimumenergyofgeometricalstructureisobtainedbyusinglevel HF/LANL2DZ basis sets. Keywords  Structure    X-ray diffraction    Thiazolidin-4-one    Ab initio calculations    ARNO Introduction Research on new materials exhibiting nonlinear optical(NLO) behavior continues to be of primary interest forbasic research as well as for industrial applications. Theresearch on new materials with NLO properties for tele-communications and optoelectronics is directly related tothe determination of their three-dimensional structure.Polymers represent a large family of interesting materialsfor nonlinear optics applications. In particular, compoundsderived from thiazoles have recently received particularattention due to their NLO properties [1–3]. Density functional theory (DFT) is presently consideredone of the most successful models in the world of compu-tational chemistry since it yields accurate results for severalphysico-chemicalproperties,especiallywhenhybridDFTisused. The hybrid DFT functional offers reliable informationfor the excited state properties of small molecules [4], donorand acceptor systems [5], as well as metal complexes [6]. In this paper we present a structural study of the (  Z  )-5-(4-nitrobenzyliden)-3-  N  (2-ethoxyphenyl)-2-thioxo-thiazo-lidin-4-one compound, hereafter known as ARNO (to avoidrewriting the IUPAC name every time), by single-crystalX-ray diffraction to determine the most stable conformationin the crystalline state. To gain a better picture of the con-formational profile of the given compound, we have alsoperformed theoretical calculations using classical ab initiomethods based on self-consistent field-molecular-orbitalHartree–Fock (HF) theory and Density Functional Theory(DFT) with the LANL2DZ, 6-31G* and 6-31 ? G** basissets. N. Benhalima    A. Chouaih ( & )    F. HamzaouiLaboratoire de Structure, Elaboration et Applications desMate´riaux Mole´culaires (SEA2M), De´partement de Ge´niedes Proce´de´s, Faculte´ des Sciences et de la Technologie,University of Mostaganem, 27000 Mostaganem, Algeriae-mail: achouaih@gmail.comK. Toubal    A. DjafriLaboratoire de Synthe`se Organique Applique´e (LSOA),De´partement de Chimie, Faculte´ de Sciences,University of Oran–Es-Se´nia, 31000 Oran, AlgeriaG. Chita    S. MaggiCNR-IC Institute of Crystallography, Via Amendola 122/O,70126 Bari, Italy  1 3 J Chem Crystallogr (2011) 41:1729–1736DOI 10.1007/s10870-011-0165-9  The results from X-ray diffraction have been comparedto those obtained from ab initio DFT and HF calculations,finding a good agreement with the structure determinedfrom the single-crystal measurements. Experiment and Computational Methods SynthesisThe title compound was prepared by reaction of   N  -aryl-rhodanine (0.01 M), aldehyde (0.01 M), 5 mL of aceticacid and sodium acetate (0.02 M) in a 150 mL boilingflask. Then 2 mL of triethylamine are added to this mix-ture. The system is refluxed for 4 h, forming a yellow solid.The crystals obtained are filtered and recrystallized inethanol. Synthesis of the compound was performed asfollows (Fig. 1).Spectral AnalysisAll reagents and solvents for synthesis and spectroscopicstudies were commercially available and used as receivedwithout further purification. The IR spectra was recordedon a JASCO 4200 FT-IR spectrometer as a KBr pellet. The 1 H and  13 C NMR spectra were measured in CDCl 3  with aBRUKER Ac DPX-200 (300 MHz) spectrometer at 25   C.Spectral Data of ARNO(  Z  )-5-(4-nitrobenzyliden)-3-  N  (2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (2g, yield 75%, yellow solid, M.p.210   C). IR (KBr, cm - 1 ): 3407 broad band, 3035 (C–N),1710 (C=O),1256 (C=S). 1 H NMR, (CDCl 3 , 300 MHz)  d  (ppm) J (Hz): 1, 42 (t,3H, –O–CH 2 –CH 3 , J 3 =  6.97), 4.06 (oct, 1H, J 2 =  2.2,J 3 =  6.95) (–O–CH 2 –CH 3 ), 4.11 (oct, 1H, J 2 =  2.2;J 3 =  6.95), (–O–CH 2 –CH 3 ), 7.53–7.08 (m, 4H), 7.71 (d,2H, J  =  8.75) 7.79 (s, 1H, –CH=C–), 8.53 (d, 2H,J  =  8.80). 13 C NMR, (CDCl 3 , 300 MHz)  d  (ppm): 14.17 (O–CH 2 –CH 3 ), 64.43 (–O–CH 2 –CH 3 ), 113.48, 121.00, 123.26,124.46, 128.35, 129.12, 129.77, 130.95, 131.63, 139.44,147.96, 154.21, 167.19 (C=S), 191.65 (C=O).X-Ray Structure DeterminationA yellow prismatic crystal with approximate dimensions of 0.20  9  0.15  9  0.10 mm was selected for data collection.The X-ray diffraction data were collected on a Kappa CCDNonius diffractometer. Reflection data were measured at298 K using graphite monochromated Mo K  a  radiation( k  =  0.71073 A˚). Intensities for 4080 reflections weremeasured with indices  - 11 \ h \ 11,  - 12 \ k  \ 11, - 15 \ l \ 15. The structure was determined by consider-ing 2591 reflections with  I    4 r  I  ð Þ . The structure wassolved by direct methods using the SHELXS-97 [7]. A Fourier synthesis revealed the complete structure, whichwas refined by full-matrix least squares. All non-H atomsrefined anisotropically. The positions of the H atoms bon-ded to C atoms were calculated. The H atoms were locatedfrom a difference Fourier map and included in the refine-ment with the isotropic temperature factor of the carrieratom. The final least-squares cycle using SHELXL-97 [8] gave  R  =  0.05 for the observed reflections with  S   =  0.95,( D q ) min =- 0.425 e/A˚ 3 , ( D q ) max  = 0.219 e/A˚ 3 . An ORTEP[9] view of the molecular structure with the atomic num-bering is shown in Fig. 2. Atomic scattering factors forheavy atoms were taken from International Tables forX-ray Crystallography [10] while the factors for H were Fig. 1  Preparation and chemical structure of (  Z  )-5-(4-nitrobenzyliden)-3-  N  (2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (ARNO). Reagents andconditions: ( a ) ClCH 2 CO 2 H, 70   C; ( b ) NO 2 C 6 H 4 CHO, CH 3 COOH, CH 3 COONa, 90   C Fig. 2  General view of molecule with atomic numbering scheme(thermal ellipsoids drawn at 50% probability). H atoms are shown assmall spheres of arbitrary radii1730 J Chem Crystallogr (2011) 41:1729–1736  1 3  those of Stewart et al. [11]. The details of crystal data andrefinement are given in Table 1.Computational MethodFor calculations involving hydrogen-bonding interactionsystems it is very important to select an appropriatemethod, and carefully considering and evaluating itsaccuracy and speed of calculation. DFT methods are fastand can be used to compute mid-sized and even largemolecular systems. In this work, full geometry optimiza-tion has been performed using the GAUSSIAN03 package[12] and the Gauss-View molecular visualization program[13], at the Becke3-parameter hybrid exchange functionsand Lee-Young–Parr correlation functional (B3LYP) level[14, 15] and HF theory [16], using the LANL2DZ, 6-31G* and 6-31 ? G** basis sets by the Berny method [17, 18]. Results and Discussion Description of the Crystal StructureA general view of the molecule with atomic labeling(thermal ellipsoids are drawn at 50% probability) is shownin Fig. 2. Figure 3 shows a perspective view of the crystal packing in the unit cell. Selected bond lengths, bond anglesand torsion angles for all non-hydrogen atoms by X-raydiffraction are listed in Tables 2, 3, and 4, together with the calculated parameters, respectively. The average values of bond distances and angles in the two benzene rings for bothexperimental and calculated are in good agreement withliterature values. The three C–S distances, S1–C8, S1–C10and S2  =  C10 [1.753(3), 1.753(3) and 1.626(3) A˚],respectively in the thiazole ring have values intermediatebetween those reported for C(Sp3)–S single [1.81 A˚] anddouble [1.61 A˚] bonds [10]. The mean value of bondangles in thiazole ring is 107.96(2)  . The crystal structureexhibits intermolecular interaction of the type C–H _ O andC–H _ S in which C atoms (C2, C4, C5, C7, C13 and C14)act as donors and O (O1, O2 and O3) and S1 atoms acts asacceptors. In the crystalline state, these intermolecularinteractions stabilize the crystal structure. The geometry of the hydrogen-bonded interactions is listed in Table 5.Figure 4 shows some hydrogen bonds in the crystal. Allbond angles C–C–C, C–N–C and C–C–N are close to 120  ,indicating that the  p  electrons in the ARNO molecule aredelocalized.Crystallographic data (excluding structure factors) forthe structure reported in this article have been depositedwith the Cambridge Crystallographic Data Centre as sup-plementary publication number CCDC 805892. 1 Table 1  Crystal data and structure refinement detailsCompound ARNOEmpirical formula C 18 H 14 O 4 N 2 S 2 CCDC reference no. 805892Formula weight 386.45Crystal size (mm) 0.20  9  0.15  9  0.10Temperature (K) 298(2)Crystal system, space group Triclinic,  P  1Unit cell dimensionsa (A˚) 9.1289(19)b (A˚) 9.3717(7)c (A˚) 12.136(3) a  (  ) 102.133(11) b  (  ) 90.99(2) c  (  ) 117.165(9)Wavelength (A˚) 0.71073Volume (A˚ 3 ) 895.4(3)  Z  , calculated density (mg/m 3 ) 2/1.433 F  (000) 400 h  range for data collection 5.01–27.50Limiting indices  - 11  B  h  B  11,  - 12  B  k   B  11, - 15  B  l  B  15Reflections collected/unique 4080/2591Refinement method Full-matrix least-squares on F 2 dataParameters 227Goodness of fit on F 2 0.935Final R indices  F  0 [ 4 r ð F  0 Þ½   R 1  0.0523 wR 2  0.1316  R  indices (all data)  R 1  0.0994 wR 2  0.1607 Fig. 3  A perspective view of the crystal packing in the unit cell 1 Copies of the data can be obtained free of charge on application toCCDC, 12 Union Road, Cambridge CB2 1EZ, UK. Fax:  ? 44 1223336033; e-mail: deposit@ccdc.cam.ac.uk.J Chem Crystallogr (2011) 41:1729–1736 1731  1 3  Geometry Optimization The ground state geometries were optimized by theHartree Fock and DFT levels of theory, usingLANL2DZ, 6-31G(d) and 6-31 ? G(d,p) basis sets. Theoptimized structure of ARNO is illustrated in Fig. 5 andthe corresponding main geometrical parameters (bondslengths, bond angles and torsion angles) are listed inTables 2, 3, and 4, as we can see there is a good agreement between the calculated and the experimentalvalues. We also checked the effect of basis sets on thecalculations. The largest deviation between X-ray dataand theoretical calculations at the HF/LANL2DZ level isthe S1–C10 distance, around 0.06 A˚, and the C16–O4–C17 angle, which is larger than 3  . The B3LYP/ LANL2DZ results deviate in the range from 0.001 to0.9 A˚for bond lengths, and from 0.02   to 2.56   (C8–C7–C6) for bond angles. The difference between theexperimental and calculated bond lengths calculated atthe HF level with 6-31G(d) basis set does not exceed0.037 A˚(O4–C17), whereas in the case of B3LYP withsame basis set, the largest difference between theobserved and the calculated values is about 0.03 A˚. Thebond angles for HF/631G(d) calculations are very closeto the experimental values (Table 3), and the maximumdifference is about 2.42  . For DFT with 6-31G(d) basisthe bond angle difference does not exceed 2.67  . TheHF/6-31 ? G(d,p) and B3LYP/6-31 ? G(d,p) results deviatein the range from 0.001 to 0.035 A˚(O4–C17) and 0.001to 0.029 A˚for the bond lengths, and from 0.04   to 2.57  (C16–O4–C17) and 0.04   to 2.48   (C8–C7–C6) for thebond angles, respectively. X-ray structure of the titlecompound is compared with its optimized counterparts(see Fig. 6).In summary, the optimized bond lengths and bondangles obtained using the DFT method are in good Table 2  Bond distances fornon-hydrogen atoms by X-rayand theoretical calculations(e.s.d.’s are given inparenthesis)Bond distances (A˚) X-ray HF B3LYPLANL2DZ 6-31G* 6-31 ? G** LANL2DZ 6-31G* 6-31 ? G**S1–C10 1.753(3) 1.809 1.760 1.760 1.846 1.785 1.782S1–C8 1.753(3) 1.807 1.761 1.760 1.820 1.761 1.761S2–C10 1.626(3) 1.667 1.629 1.629 1.678 1.640 1.640O1–N1 1.223(3) 1.238 1.193 1.194 1.280 1.231 1.232O2–N1 1.227(4) 1.239 1.193 1.194 1.280 1.231 1.232O3–C9 1.211(3) 1.216 1.186 1.187 1.244 1.213 1.215O4–C16 1.364(3) 1.368 1.340 1.339 1.388 1.356 1.357O4–C17 1.447(4) 1.447 1.410 1.412 1.471 1.432 1.435N1–C3 1.473(4) 1.461 1.458 1.461 1.474 1.470 1.471N2–C10 1.384(3) 1.371 1.362 1.364 1.388 1.378 1.380N2–C9 1.398(4) 1.403 1.394 1.393 1.424 1.412 1.410N2–C11 1.439(3) 1.438 1.432 1.433 1.447 1.437 1.437C1–C2 1.383(4) 1.388 1.380 1.382 1.398 1.387 1.389C1–C6 1.392(4) 1.404 1.395 1.396 1.423 1.413 1.414C2–C3 1.382(4) 1.390 1.383 1.383 1.406 1.394 1.395C3–C4 1.379(4) 1.390 1.382 1.382 1.406 1.394 1.395C4–C5 1.394(4) 1.389 1.382 1.383 1.399 1.389 1.390C5–C6 1.390(4) 1.404 1.394 1.395 1.422 1.412 1.413C6–C7 1.472(4) 1.472 1.474 1.474 1.462 1.455 1.456C7–C8 1.331(4) 1.334 1.327 1.328 1.361 1.353 1.354C8–C9 1.494(4) 1.487 1.491 1.493 1.492 1.492 1.493C11–C12 1.373(4) 1.383 1.376 1.377 1.398 1.389 1.389C11–C16 1.404(4) 1.397 1.394 1.395 1.414 1.408 1.408C12–C13 1.390(4) 1.395 1.386 1.388 1.407 1.395 1.397C13–C14 1.378(5) 1.392 1.381 1.383 1.406 1.393 1.395C14–C15 1.380(5) 1.396 1.388 1.389 1.407 1.397 1.398C15–C16 1.399(4) 1.393 1.386 1.388 1.409 1.399 1.401C17–C18 1.493(6) 1.519 1.514 1.514 1.524 1.518 1.5181732 J Chem Crystallogr (2011) 41:1729–1736  1 3  agreement with the corresponding X-ray structuralparameters. It is worth noting that some of the optimizedtorsion angles have slightly different values from the cor-responding experimental ones, due to the fact that thetheoretical calculations consider only isolated molecules inthe gaseous phase while the experimental results refer tomolecules in the crystal environment. Conclusions In this study, we have synthesized the (  Z  )-5-(4-nitroben-zyliden)-3-  N  (2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one(ARNO) compound and its crystal structure was deter-mined by X-ray diffraction. This compound belongs tothe centrosymmetric space group  P  1. From the crystal Table 3  Bond angles for non-hydrogen atoms by X-ray andtheoretical calculations (e.s.d.’sare given in parenthesis)Bond angles (  ) X-ray HF B3LYPLANL2DZ 6-31G* 6-31 ? G** LANL2DZ 6-31G* 6-31 ? G**C10–S1–C8 93.12(13) 91.65 92.44 92.47 91.43 92.85 92.90C16–O4–C17 118.0(2) 121.95 120.42 120.57 119.20 118.92 119.14O1–N1–O2 124.2(3) 123.71 124.85 124.88 123.78 124.79 124.57O1–N1–C3 118.3(3) 118.18 117.60 117.58 118.15 117.63 117.74O2–N1–C3 117.5(3) 118.11 117.56 117.54 118.08 117.58 117.68C10–N2–C9 117.1(2) 118.15 117.36 117.28 118.41 117.51 117.43C10–N2–C11 122.1(2) 122.02 122.58 122.55 121.93 122.42 122.26C9–N2–C11 120.8(2) 119.43 119.77 119.87 119.46 119.85 120.14C2–C1–C6 121.4(3) 121.34 121.04 121.06 121.57 121.56 121.58C3–C2–C1 118.6(3) 118.35 118.52 118.48 118.43 118.55 118.56C2–C3–C4 122.1(3) 122.03 121.99 122.04 121.86 121.79 121.77C2–C3–N1 119.6(3) 118.97 119.00 118.97 119.07 119.11 119.13C4–C3–N1 118.3(3) 119.00 119.01 118.99 119.08 119.09 119.10C3–C4–C5 118.0(3) 118.95 118.86 118.85 119.03 119.06 119.06C6–C5–C4 121.6(3) 120.69 120.66 120.66 120.91 121.00 121.03C5–C6–C1 118.2(3) 118.64 118.91 118.90 118.21 118.03 118.01C5–C6–C7 123.1(3) 124.63 123.28 123.41 124.70 124.62 124.64C1–C6–C7 118.7(3) 116.72 117.79 117.68 117.09 117.35 117.35C8–C7–C6 128.8(3) 131.44 129.42 129.48 131.36 131.47 131.28C7–C8–C9 121.8(3) 120.03 119.80 119.79 120.02 119.18 119.45C7–C8–S1 128.5(2) 130.89 130.88 130.94 130.04 131.03 130.83C9–C8–S1 109.47(19) 109.08 109.28 109.23 109.94 109.79 109.71O3–C9–N2 122.8(3) 123.54 124.05 124.04 123.32 123.70 123.73O3–C9–C8 127.2(3) 125.27 125.75 125.69 125.70 126.17 126.05N2–C9–C8 110.0(2) 111.19 110.19 110.26 110.97 110.13 110.21N2–C10–S2 128.0(2) 127.90 127.74 127.61 128.43 128.11 127.85N2–C10–S1 110.13(19) 109.89 110.69 110.72 109.22 109.68 109.72S2–C10–S1 121.91(17) 122.21 121.57 121.66 122.35 122.21 122.43C12–C11–C16 121.4(3) 121.12 121.16 121.18 121.00 121.13 121.12C12–C11–N2 120.9(2) 120.92 120.35 120.31 120.62 120.42 120.25C16–C11–N2 117.7(2) 117.96 118.48 118.50 118.37 118.43 118.62C11–C12–C13 119.5(3) 119.86 120.14 120.16 119.92 120.0 120.05C14–C13–C12 119.7(3) 119.22 118.94 118.92 119.34 119.22 119.17C13–C14–C15 121.4(3) 121.02 121.27 121.25 120.97 121.13 121.11C14–C15–C16 119.6(3) 119.54 119.78 119.77 119.68 119.87 119.87O4–C16–C15 125.7(3) 124.90 125.16 125.11 125.04 125.36 125.25O4–C16–C11 115.9(2) 115.86 116.13 116.18 115.88 115.98 116.08C15–C16–C11 118.4(3) 119.24 118.70 118.71 119.08 118.65 118.66O4–C17–C18 106.9(3) 107.03 107.43 107.58 106.92 107.42 107.59J Chem Crystallogr (2011) 41:1729–1736 1733  1 3
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