Synthesis, structural characterization and conformational aspects of thenoylthiocarbamic-O-alkylesters

Journal of Molecular Structure 936 (2009) 37–45

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Synthesis, structural characterization and conformational aspects of thenoylthiocarbamic-O-alkylesters Lígia R. Gomes a,b,*, John Nicolson Low c, Antonio Quesada d, Luís M.N.B.F. Santos e, Marisa A.A. Rocha e, Bernd Schröder f a

CIAGEB – Faculdade de Ciências de Saúde, Escola Superior de Saúde da UFP, Universidade Fernando Pessoa, Rua Carlos da Maia, 296, P-4200-150 Porto, Portugal REQUIMTE – Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, P-4169-007 Porto, Portugal Department of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen, AB24 3UE Scotland, UK d Departamento de Didáctica del las Ciencias, Edificio ‘‘Humanidades y Ciencias de Educación” (D2), Universidad de Jaén, 23071 Jaén, Spain e Centro de Investigação em Química, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal f CICECO, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal b c

a r t i c l e

i n f o

Article history: Received 8 May 2009 Received in revised form 16 July 2009 Accepted 17 July 2009 Available online 22 July 2009 Keywords: N-Thenoylthiocarbamic-O-n-alkylester Crystal structure Odd and even effect B3LYP Conformation

a b s t r a c t A set of four N-thenoylthiocarbamic-O-n-alkylesters, where alkylester = propylester, butylester, pentylester and hexylester were structurally characterized in solid state by single crystal X-ray diffractometry. The supramolecular structure for each compound is stabilised by N–H


O hydrogen bonds. For each compound gaseous phase ab initio geometry optimizations for several conformations were performed at the B3LYP/6-311++G(d,p) level of theory in order to evaluate and compare the calculated geometry with the experimental molecular crystal geometry as well as to evaluate the energetic difference between several alkyl conformations. The compounds were further analysed by FTIR spectroscopy and the experimental FTIR spectra were compared with the calculated ones at B3LYP/6-311++G(d,p) level of theory. The structural results for the set were further used in the interpretation of the odd and even effect found previously in their thermophysical properties. Ó 2009 Elsevier B.V. All rights reserved.

1. Introduction Thiocarbamic esters and their derivatives are substances which exhibit important biological activities. In particular, the antifungal activity of carbamic and thiocarbamic esters of thiophenols has been established since 1979 [1]. The structure–activity studies of carbamate and other esters as agonists and antagonists to nicotine have also been made [2]. Thiocarbamate esters and their derivatives have been also investigated in coordination chemistry due to their ability to form stable complexes with transition metals [3] but also because of the cytostatic activity shown by their palladium(II) and platinum(II) halide complexes [4–6]. The applications of aromatic thiocarboxamide ester derivatives drive the study of their coordination [3] and thermochemical properties [7]. In the present work a set of several N-thenoylthiocarbamic-O-n-alkylesters, namely N-thenoylthiocarbamic-O-n-propylester (Httpre), N-thenoylthiocarbamic-O-n-butylester (Httbue), N-thenoylthiocarbamic-O-n-pentylester (Httpte) and N-theno-

ylthiocarbamic-O-n-hexylester (Htthxe), shown schematically in Fig. 1, have been prepared and characterized in solid state and in the gas phase in order to try to establish the role that structural interactions play in their thermodynamic properties such as standard molar enthalpies of formation in the solid and gas phases, and molar entropies of fusion at fusion temperatures, which show a distinctive odd (Httpre and Httpte) and even (Httbue and Htthxe) effect relative to the n(C) carbon atoms in the alkyl chain of the ester group. Accordingly, the X-ray study was performed for the set in order to determine the molecular features present in crystal structures. The structures of the isolated molecules were calculated by B3LYP/6-311++G(d,p) model and the vibrational behaviour studied by FTIR in solid state and by B3LYP/6-311++G(d,p) frequency calculations in gaseous phase.

2. Experimental 2.1. Synthesis of compounds

* Corresponding author. Address: CIAGEB – Faculdade de Ciências de Saúde, Escola Superior de Saúde da UFP, Universidade Fernando Pessoa, Rua Carlos da Maia, 296, P-4200-150 Porto, Portugal. Tel.: +351 225 074 630; fax: +351 225 074 637. E-mail address: [email protected] (L.R. Gomes). 0022-2860/$ - see front matter Ó 2009 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2009.07.013

The studied N-thenoylthiocarbamic-O-n-alkylesters were prepared according to the described procedure [7]. Elemental analysis: for Httpre, C9H11NO2S2, found 100 w(C) = 47.5, 100 w(H) = 4.8, 100 w(N) = 6.3, 100 w(O) = 14.0, 100 w(S) = 27.0, calculated 100

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conditions and refinement parameters for the compounds are all listed in Table 1.

H N

S

O R

O

S

Fig. 1. General formula of the compounds studied. R = –CH2CH2CH3: N-thenoylthiocarbamic-O-n-propylester (Httpre); R = –CH2CH2CH2CH3: N-thenoylthiocarbamic-O-n-butylester (Httbue); R = –CH2CH2CH2CH2CH3: N-thenoylthiocarbamicO-n-pentylester (Httpte); R = –CH2CH2CH2CH2CH2CH3: N-thenoylthiocarbamic-On-hexylester (Htthxe).

w(C) = 47.14, 100 w(H) = 4.83, 100 w(N) = 6.11, 100 w(O) = 13.95, 100 w(S) = 27.97; for Httbue, C10H13NO2S2, found 100 w(C) = 49.1, 100 w(H) = 5.2, 100 w(N) = 5.5, 100 w(O) = 13.3, 100 w(S) = 26.1, calculated 100 w(C) = 49.36, 100 w(H) = 5.38, 100 w(N) = 5.76, 100 w(O) = 13.15, 100 w(S) = 26.35; for Httpte, C11H15NO2S2, found 100 w(C) = 51.7, 100 w(H) = 5.7, 100 w(N) = 5.5, 100 w(O) = 12.9, 100 w(S) = 24.8, calculated 100 w(C) = 51.33, 100 w(H) = 5.87, 100 w(N) = 5.44, 100 w(O) = 12.43, 100 w(S) = 24.92; for Htthxe, C12H17NO2S2, found 100 w(C) = 53.2, 100 w(H) = 6.2, 100 w(N) = 5.0, 100 w(O) = 11.5, 100 w(S) = 23.8, calculated 100 w(C) = 53.11, 100 w(H) = 6.31, 100 w(N) = 5.16, 100 w(O) = 11.79, 100 w(S) = 23.63. 1 H NMR (CDCl3, 300 MHz): for Httpre: 9.06 (br s, 1H, NH), 7.67– 7.64 (m, 2H, Arom), 7.16–7.13 (t, 1H, Arom), 4.56 (t, 2H, CH2), 1.88 (m, 2H, CH2), 1.06 (t, 3H, CH3); for Httbue: 9.02 (br s, 1H, NH), 7.67–7.63 (m, 2H, Arom), 7.17–7.14 (t, 1H, Arom), 4.61 (t, 2H, CH2), 1.83 (m, 2H, CH2), 1.51 (m, 2H, CH2), 0.98 (tr, 3H, CH3); for Httpte: 9.00 (br s, 1H, NH), 7.67–7.63 (m, 2H, Arom), 7.17– 7.14 (t, 1H, Arom), 4.60 (t, 2H, CH2), 1.86 (m, 2H, CH2), 1.54– 1.57 (m, 2H, CH2), 1.47–1.38 (m, 4H, CH2), 0.94 (tr, 3H, CH3); for Htthxe: 9.04 (br s, 1H, NH), 7.67–7.63 (q, 2H, Arom), 7.16–7.13 (t, 1H, Arom), 4.59 (t, 2H, CH2), 1.81 (m, 2H, CH2), 1.69–1.44 (b, 2H, CH2), 1.35–1.30 (b, 4H, CH2), 0.91 (tr, 3H, CH3).

2.3. Computational chemistry For all compounds in the series, ab initio geometry optimization by DFT, for three possible conformers, identified as A, B and C, was performed, differing in the relative position (starting geometry) of the alkyl chain towards the aromatic ring plane as depicted in Fig. 2. The ab initio calculations were made at the B3LYP exchangecorrelation functional, which combines the hybrid exchange functional of Becke [20] with the gradient-correlation functional of Lee et al. [21] and the split-valence polarized 6-311G++(d,p) basis set [22] level of theory. The GaussView 3.0 [23] program was used to get visual animation and the normal modes description. At the same theoretical level, analytical frequency calculations were performed to ensure true minima (Nimg = 0) and to derive some thermochemical parameters such as enthalpic and entropic thermal vibrations. Zero-point vibrational energies (ZPEs) and enthalpy energy correction contributions were taken into account during calculation of the enthalpies of all species at 298.15 K. The scaling factors of 0.9887 and 0.9688 [24] were used for the calculation of the zero-point vibrational energies and fundamental vibrational frequencies, respectively. All the ab initio calculations were performed with the GAUSSIAN 03 program package [25]. 2.4. IR spectra FTIR spectra were obtained, at room temperature, in the range of [4000–400] cm 1, using KBr pellets in a FTIR Mattson 7000 galaxy series spectrometer, with a resolution of 2 cm 1. Density functional theory gas phase vibrational spectra were calculated as previously described at B3LYP/6-311++G(d,p) level of theory . 3. Results and discussion 3.1. Crystal structures

2.2. Structural characterization Crystals for X-ray diffraction were obtained by slow evaporation of ethanolic solutions of Httbue and Httpte and from chloroform solutions of Httpre and Htthxe. The intensity data were collected by a Bruker–Nonius CCD diffractometer. Data collection, cell refinement and data reduction were made with the software package of the diffractometer: COLLECT [8] for data collection; DIRAX/LSQ [9] and SAINT [10] for cell refinement; and EVALCCD [11] for data reduction. Absorption corrections were performed with SADABS [12]. The structures were solved using the software: SIR2004 [13,14] and refined with OSCAIL [15] and SHELXL97 [16]. H atoms were treated as riding atoms with C–H(aromatic), 0.95 Å, C–H(CH2), 0.99 Å, with Uiso(H) = 1.2Ueq(C), C–H(methyl), 0.98 Å, with Uiso(H) = 1.5Ueq(C); N–H, 0.88 Å, with Uiso = 1.2Ueq(N). In Httpre atoms C231, C241, C251 and C331, C341, C351 belonging to one of the propyl groups are disordered. They were refined with two site occupancies of 0.615(12) and 0.385(12). Hydrogen atoms attached to the disordered carbon atoms were calculated in the basis of the disorder. The C341–C351 bond distances were restrained to 1.55(1) Å. The extinction and Flack parameters were refined to 0.0040(9) and 0.08(10) as implemented in SHELXL [17]. Molecular graphics were produced by ORTEP [18] and PLATON [19]. The complete set of structural parameters in CIF format is available as an Electronic Supplementary Publication from the Cambridge Crystallographic Data Centre (CCDC 715889-690630690631-715294). Information about crystal data, data acquisition

N-Thenoylthiocarbamic-O-n-propylester (Httpre) crystallizes in the triclinic space group P1, with four molecules in the asymmetric unit. The asymmetric unit was chosen such that the four molecules form a hydrogen-bonded set. N-Thenoylthiocarbamic-O-n-hexylester (Htthxe) crystallizes in the monoclinic P21/c. Both N-thenoylthiocarbamic-O-n-butylester (Httbue) and N-thenoylthiocarbamic-O-n-pentylester (Httpte) crystallize in the monoclinic space group P21/n and their structural features are indicative of isomorphism. The corresponding asymmetric units are depicted in Figs. 3–6. The main bond lengths and angles between atoms of the compounds are listed in Table 2. The Csp2 = Csp2 and the Csp2–S bond lengths are the expected for thiophene rings. For Httpre the mean bond distances between the C–O (carbonyl) group of the set is 1.224(4) Å; the C–N(amide) group of 1.382(4) Å and the S–C from thiocarbamic residue of 1.627(3) Å. The crystal quality was poor and as a result the data completeness was low, 0.90 at 50° 2h. As mentioned above one of the propyl groups was disordered and treated as such in the refinement. The thermal parameters for the atoms in the propyl groups in the other three molecules are high indicating a high degree of thermal disorder. This disorder could not be resolved as separate disordered groups. Nevertheless, the data are of sufficient quality to allow the description of the connectivity within the supramolecular structure for this compound. For the remaining compounds, the bond lengths of N(2)–C21 [1.377(4); 1.379(4); 1.382(3) Å], N(2)–C(22) [1.367(4); 1.363(3);

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L.R. Gomes et al. / Journal of Molecular Structure 936 (2009) 37–45 Table 1 Crystal data, data acquisition conditions and refinement parameters for the studied compounds.

Empirical formula Formula weight (g mol 1) Temperature (K) Wavelength (Mo Ka) (Å) Crystal system, space group Unit cell dimensions

Volume (Å3) Z, calc. density (g cm 3) Absorption coefficient (mm 1) Max. and min. transmission Crystal size (mm) F(0 0 0) h range for data collection (°) Index ranges

Reflection collected/independent reflections/ reflections with I > 2r(I) Completeness to h = 27.5° (%) Absorption correction Refinement method GooF Data/parameters/restrains Final R indices (I > 2r(I)) R indices (all data) Maximum and minimum difference peaks (e Å

3

)

Httpre

Httbue

Httpte

Htthxe

C9H11NO2S2 Mr = 229.33 T = 150(2) 0.71073 Triclinic, P1 a = 10.9540(12) Å b = 11.021(2) Å c = 11.7453(14) Å a = 115.584(6)° b = 117.171(4)° c = 91.456(6)° V = 1093.1(3) Z = 4, q = 1.393 l = 0.461 Tmin = 0.9135, Tmax = 0.9954 0.20  0.20  0.01 480.0 2.25–28.38 11 6 h 6 14 13 6 k 6 14 12 6 l 6 14 10,948/5474/1641; Rint = 0.023 84 Multi-scan Full-matrix least squares on F2 S = 1.052 3899/486/4 R = 0.0574, wR = 0.1067 R = 0.1095, wR = 0.1277 Dqmax = 0.389 Dqmin = 0.517

C10H13NO2S2 Mr = 243.33 T = 120(2) 0.71073 Monoclinic, P21/n a = 8.352(2) Å b = 16.856(5) Å c = 9.2110(14) Å b = 115.450(16)

C11H15NO2S2 Mr = 253.36 T = 120(2) 0.71073 Monoclinic, P21/n a = 8.5961(10) Å b = 17.009(2) Å c = 9.1461(10) Å b = 112.983(8)

C12H17NO2S2 Mr = 271.48 T = 150(2) 0.71073 Monoclinic, P21/c a = 8.8626(4) Å b = 16.8527(8) Å c = 9.5552(5) Å b = 102.518(2)

V = 1170.9(5) Z = 4, q = 1.380 l = 0.434 Tmin = 0.7836, Tmax = 0.9417 0.59  0.16  0.14 512.0 5.03–27.52 10 6 h 6 10 21 6 k 6 21 11 6 l 6 11 34,786/2669/1641; Rint = 0.069 99 Multi-scan Full-matrix least squares on F2 S = 1.038 2669/137/0 R = 0.0542, wR = 0.1274 R = 0.1068, wR = 0.1543 Dqmax = 0.449 Dqmin = 0.515

V = 1231.1(2) Z = 4, q = 1.389 l = 0.417 Tmin = 0.8312, Tmax = 0.9876 0.46  0.16  0.03 544.0 5.11–27.15 11 6 h 6 11 22 6 k 6 22 11 6 l 6 11 37,392/2801/1861; Rint = 0.047 99 Multi-scan Full-matrix least squares on F2 S = 1.043 2801/149/0 R = 0.0548, wR = 0.1283 R = 0.0988, wR = 0.1577 Dqmax = 0.578 Dqmin = 0.536

V = 1393.23(12) Z = 4, q = 1.294 l = 0.372 Tmin = 0.9094, Tmax = 0.9926 0.26  0.08  0.02 576.0 3.09–33.19 12 6 h 6 13 24 6 k 6 21 14 6 l 6 14 15,713/5099/3531; Rint = 0.041 99 Multi-scan Full-matrix least squares on F2 S = 1.013 5099/156/0 R = 0.0416, wR = 0.0919 R = 0.0737, wR = 0.1045 Dqmax = 0.385 Dqmin = 0.270

1.381(3) Å] and of O21–C21 [1.212(3); 1.215(3); 1.331(3) Å] for Httbue, Httpte and Htthxe molecules, respectively, are almost the same except for N(2)–C(22) in Htthxe. These are in good agreement with those reported earlier for similar compounds [26] and show a partial double bond character. The S22–C22, [1.622(3); 1.627(3) Å] for Httbue and Httpte bond lengths are slightly shorter than those found earlier in phenyl-thiocarbamic acid-O-pyridin-4-ylmethyl ester [1.646(3) Å], [27] and for a series of O-isopropyl-N-aryl-thioc-

Fig. 2. Representation of the overlapped geometric optimized molecules with conformations A, B and C (hydrogen atoms are omitted). Here Httbue is shown as example.

arbamates [26], indicating a stronger double bond character for the C–S bond (thione form) in the studied compounds. The remaining bond lengths and bond angles are in the normal range. Crystal structure analysis of this thiocarbamic esters shows that the heteroatom S1 of the thenoyl group adopts a cis conformation relative to the carbonyl oxygen O21. This conformation is assumed in other compounds containing the thenoyl functional group, e.g. in N,N-dialkyl-(2-thienylcarbonyl)thiourea [28]. In opposite, in the furyl analogous [29] the trans conformation seems to be more stable due probably to the electrostatic repulsion between the oxygen atoms that can occur in the cis form. The supramolecular structure in each of these compounds is based on a hydrogen bond interaction between the amide N atom, N2(x) and the amide O atom, O21(x), where x = 1–4 in the case of Httpre. In each structure the molecules are linked to form a C(4) chain [30]. The supramolecular structures are further stabilised by a weak C3–H3


O21 hydrogen bond in the case of Httbue, Httpte and Htthxe, forming a spiro-linked R21(7) ring as shown in Fig. 7, where the packing diagram obtained for Httbue is given as example. This stabilisation although present is much weaker in the case of Httpre. Hydrogen bond distances and angles are given in Table 3. In Httpre the asymmetric unit chains are linked by unit translations via the N24–H24


O213 (1 + x, 1 + y, 2 + z) hydrogen bond and form chains which run parallel to [1 1 2]. In Httbue and Httpte the, N2–H2


O21( 1/2 + x, 1/2 y, 1/2 + z), C(4) chains run parallel to [1 0 1]. In Htthxe the, N2–H2


O21(x, 1/2 y, 1/2 + z), C4 chains run parallel to [0 0 1]. In these structures, as in similar N-cycloacylylthiocarbamic-O-esters, [31,32] the amide oxygen atom plays the most important role on the definition of the supramolecular structure. In contrast, studies performed with O-aryl-N-

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aryl-thiocarbamides indicate that it is the N–H


S interaction, involving the thioamide [33,34] the responsible for the crystal packing arrangement. The study of the thermodynamic (concerning the energetics in the crystalline and gaseous phase) and thermophysical properties (such as standard molar enthalpies of sublimation and standard molar enthalpies and entropies of fusion determinations) has been made for these compounds. This study shows that these parameters are markedly different depending on the odd and even number of carbon atoms of the alkyl chain (even and odd effect) [7]. The series of compounds with odd number of (alkyl) carbon atoms have higher standard molar entropy of fusion Dlcr Som , than the even series. This is indicative of lower absolute entropy in crystalline phase for the odd series. Since X-ray analysis reveals some pattern involving hydrogen bonding in the definition of the supramolecular structures, it became appropriate to search for aspects related with the structure packing and geometry which could explain the lower absolute entropy of the odd series based in the higher degree of order observed in the crystal structure. The zig–zag chain formed by the aliphatic carbon atoms C23 ? C26 is mostly planar for Httbue (the mean deviation of the atoms to the best plane is 0.0063(17) Å) while the deviations for atoms in C23 ? C27 atoms of Httpte to the best plane formed by themselves is higher (the mean deviation of the atoms is 0.0279(30) Å). For Htthxe the aliphatic chain C23 ? C28 is not planar with a deviation of fitted atoms of 0.2383(17) Å, showing that the higher the number of the carbon atoms in the chain the lower the planarity. Nevertheless, the dihedral angle, H, formed between least squares planes of the aromatic ring and the C23 ? C2x alkyl chain (x = 5, 6, 7 or 8 for Httpre, Httbue, Httpte and Htthxe,) are 78.55(1.50)°; (mean value of the four molecules), 46.05(19)°, 50.43(16)° and 17.78(9)°, respectively. These values are higher for Httpre and Httpte, the compounds with odd number of carbon atoms indicating a higher planarity of the whole molecule in the case of Httbue and Htthxe. The calculated density follows the same trend (see values in Table 1): q (Httpre) > q (Httpte) > q (Httbue) > q (Htthxe). The relative planarity of the even carbon atom chain compounds may condition the density of the crystal packing allowing for more freedom of the packing modes that can, eventually, lower the solid state entropy. Table 4 lists the standard molar enthalpies of fusion and the standard molar entropies of fusion, crystallographic density and the dihedral angles formed between the aromatic ring and the alkyl chain, for Httpre, Httbue, Httpte and Htthxe [7]. These observations are summarized in Fig. 8 which consists of a graphical representation of standard molar entropies of fusion Dlcr Som , standard molar enthalpies of fusion Dlcr Hom , dihedral angles, H, and calculated density, q, as a function of the number of carbon atoms in the alkyl chain, n(C), where the odd (Httpre and Httpte) and even (Httbue and Htthxe) effect is evidenced.

3.2. Gaseous phase ab initio study

Fig. 3. ORTEP view of molecules 1–4 (from top to bottom) of Httpre showing the atom labelling. Ellipsoids represent the 30% probability level.

3.2.1. Geometries optimization DFT calculations were performed at B3LYP/6-311++G(d,p) level of theory. One of the objectives of this study was the evaluation of the influence of the alkyl chain in the definition of the conformation assumed in solid and gaseous state, three different local minimum conformations of the alkyl chain were explored. Those conformations were identified as A, B and C and are schematically depicted in Fig. 2 in which Httpte is given as example. Geometric optimizations were made for all the derived conformations as well as the theoretical frequencies calculations allowing for the derivation of thermodynamic parameters. The total electronic energies, Eo, zero-point energies correction, ZPE,

L.R. Gomes et al. / Journal of Molecular Structure 936 (2009) 37–45

41

Fig. 4. ORTEP view of Httbue showing the atom labelling. Ellipsoids represent the 30% probability level.

enthalpies thermal correction, Hcorr, and enthalpic energies plus thermal correction, H298.15 K, for T = 298.15 K obtained for geometric optimizations of the different conformers are presented in Table 5. For all compounds the ab initio calculations show that conformations A and B are the most stable in gaseous phase. Conformation C, corresponding to the geometry obtained when the original conformation resulting from X-ray analysis was run is less stable. Nevertheless, the gaseous phase, ab initio energetic difference between the different alkyl conformers is very small (maximum 3.7 kJ mol 1), supporting the existence of several accessible molecular geometries and energetic pathways that will allow the existence of different crystal packing solutions according the odd and even alkyl group type.

A summary of selected optimized geometric parameters are listed in Table 2. This shows the predicted values for bond lengths and angles in the gas phase and those in the crystal structures for the thiocarbamic ester functional group. The bond lengths and angles are almost identical in all theoretical predictions and do not change with the molecular species or even with the conformation that the alkyl chain assumes. Most of the bond lengths, obtained for the N-thenoylthiocarbamic residue in gaseous phase are higher than those obtained by single crystal diffractometry. These features point for the existence of more delocalization of the electronic density in solid state. Exceptions are made for C21–O21 bonds, in which O21 is involved in the hydrogen bond interactions which define the supramolecular solid state structures. As far as the bond angles are concerned, most of the calculated values are

Fig. 5. ORTEP view of Httpte showing the arbitrary atom labelling. Ellipsoids represent the 30% probability level.

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Fig. 6. ORTEP view of Htthxe showing the arbitrary atom labelling. Ellipsoids represent the 30% probability level.

Table 2 Selected geometric parameters for the studied compounds (Å, °) obtained by X-ray diffractometry, and from ab initio geometry optimizations at B3LYP/6-311++G(d,p) for the conformations A, B and C. Httpre*

Httbue

Httpte

Htthxe

X-ray A, B, C X-ray A, B, C X-ray A, B, C X-ray A, B, C X-ray A, B, C X-ray A, B, C

1.456(6) 1.482 1.224(5) 1.209 1.379(5) 1.385 1.383(5) 1.404 1.336(5) 1.350 1.627(4) 1.642

1.456(4) 1.482 1.212(3) 1.209 1.367(4) 1.385 1.377(4) 1.404 1.328(3) 1.350 1.622(3) 1.641

1.452(4) 1.482 1.215(3) 1.209 1.363(4) 1.385 1.369(4) 1.404 1.331(3) 1.350 1.627(3) 1.642

1.4695(18) 1.482 1.2218(14) 1.209 1.3819(16) 1.385 1.3805(16) 1.404 1.3315(15) 1.350 1.6368(13) 1.642

X-ray A, B, C X-ray A, B, C X-ray A, B, C X-ray A, B, C X-ray A, B, C

115.1(14) 113.1 123.2(14) 124.4 129.1(14) 129.6 128.0(14) 127.8 106.5(12) 106.1

114.9(2) 113.2 123.5(2) 124.4 126.9(2) 126.6 127.6(2) 127.9 106.5(2) 106.1

115.1(2) 113.1 123.3(2) 124.5 127.2(2) 129.6 127.6(2) 127.8 107.1(2) 106.1

115.29(10) 113.2 123.63(12) 124.4 126.97(10) 129.6 127.42(9) 127.9 106.94(10) 106.1

Parameters Bond lengths (Å) C2–C21 C21–O21 N2–C22 C21–N2 C22–O2 C22–S22 Bond angles (°) C2–C21–N2 O21–C21–N2 C21–N2–C22 N2–C22–S22 N2–C22–O2 *

Fig. 7. H bonding diagram for Httpte showing a C(4) chain running parallel to [1 0 1]. The molecules labelled , $ and # are at ( 1/2 + x, 1/2 y, 1/2 + z), (1/ 2 + x, 1/2 y, 1/2 + z) and (1 x, y, 1 z), respectively.

For Httpre the X-ray parameters were taken as the average of the four molecules.

similar to the experimental ones. The Mulliken atomic charges of the compounds calculated at B3LYP/6-311++G(d,p) level are presented in Table 6. Once atomic charge distributions and thermodynamic properties were calculated based on the optimized geometries, they could be analyzed bearing these differences in mind. The atomic charge distributions in the thenoyl [C4H3S(CO)] molecular region is hardly affected by the alkyl chain increase in length. Progressively more negative Mulliken atomic charges are observed in the S(thioamide) and O(amide) atoms of the thiocarbamic ester residue with the increase of the alkyl chain size as a result of the increase of the inductive effect of the by the alkyl group. The effect described previously is also supported by the observed [35] increase of coordination ability with the alkyl chain length

which is more pronounced in the first members of the alkyl chain series. 3.3. FTIR analysis The frequencies obtained from theoretical predictions were examined and assigned using the graphical user interface GaussView [23] and compared with the experimental frequencies. The FTIR experimental data and the theoretical frequencies assignments are given as Supplementary information, Tables S1–S4. In Fig. 9, the experimental solid state vibrational frequencies are plotted against the DFT gas phase unscaled vibrational frequencies where Httpte is given as an example. A reasonably good linear correlation is obtained, since DFT gas phase and experimental solid

43

L.R. Gomes et al. / Journal of Molecular Structure 936 (2009) 37–45 Table 3 Geometric parameters for the intermolecular contacts (Å, °) for all the compounds. D–H

Httpre N21–H21. . .O214 N22–H22. . .O211 N23–H23. . .O212 N24–H24. . .O213_$1 Equiv $1 (x + 1, y + 1, z + 2)

Httpte N2–H2


O21_$1 C3–H3


O21_$1 Equiv $1 ( 1/2 + x, 1/2

1.40

<(DHA)

0.88 0.88 0.88 0.88

2.05 1.99 2.01 2.05

2.836(9) 2.833(8) 2.848(8) 2.846(8)

148.7 159.5 159.8 149.4

1.98 2.52

2.816(3) 3.194(4)

158 128

y,

0.88 0.95 1/2 + z)

2.07 2.60

2.904(3) 3.328(4)

158 134

y,

0.88 0.95 1/2 + z) 0.85 0.95

2.03 2.43

2.8714(14) 3.1722(16)

173 135

Httpre Httbue Httpte Htthxe

1.32

80 60 40

y, 1/2 + z)

n(C)

3 4 5 6

q (g cm 3) 1.393 1.380 1.389 1.294

Ha (o) 78.55 46.05 50.43 17.78

Dlcr Hom [7] (kJ mol 1)

Dlcr Som [7] (J K 1 mol

26.10 ± 0.46 23.89 ± 0.39 24.59 ± 0.44 22.48 ± 0.37

70.5 ± 1.2 65.6 ± 1.1 69.4 ± 1.2 64.9 ± 1.1

ΔlcrSom / J·K–1·mol–1

20

Table 4 Calculated densities, dihedral angles, and standard molar enthalpies of fusion and standard molar entropies of fusion of Httpre, Httbue, Httpte and Htthxe. Compound

1.36

1.28

70

68

66

26

1

)

a The dihedral angle, formed between least squares planes of the aromatic ring and the C23 ? C2x alkyl chain (x = 5, 6, 7 or 8 for Httpre, Httbue, Httpte and Htthxe).

ΔlcrHom / kJ·mol–1

Htthxe N2–H2


O21_$1 C3–H3


O21_$1 Equiv $1 (x, 1/2

D


A

Θ/o

Httbue N2–H2


O21_$1 C3–H3


O21_$1 Equiv $1 ( 1/2 + x, 1/2

H


A

ρ / g·cm–3

D_H


A

25 24 23 22 3

4

5

6

n(C)

state vibrational frequencies are directly compared. The simple scaling factor (k) correlation between the experimental wavelengths, mexp, and the theoretical predictions, mtheo, in the form mexp = k
mtheo (k = 0.98) is in agreement with the typical recommendation for the vibrational frequency scaling factor (0.96– 0.97) for the B3LYP with a Gaussian triple zeta basis set [24]. The IR spectra of the studied N-thenoylthiocarbamic-O-n-alkylesters show four valence vibrations of special interest: mNH (3240– 3251 cm 1), mC@O (1680–1686 cm 1), mCN (1511–1516 cm 1) and mC@S (1295–1305 cm 1), which are very similar to the ones found in analogous N-benzoylthiocarbamic-O-alkylesters (mNH (3219– 3300 cm 1), mC@O (1690–1715 cm 1), mCN (1450–1490 cm 1) and mC@S (1260–1290 cm 1) [35].

4. Conclusions These structural studies of a series four N-thenoylthiocarbamic-O-n-alkylesters using spectroscopic and non-spectroscopic techniques, namely by infrared spectroscopy and X-ray crystallography were complemented by a theoretical approach using ab initio calculations. The discrete solid state molecules exhibit a stronger double bond character for the C–S bond (thione form) as compared with similar dithiocarbamates and show the heteroatom S1 of the thenoyl group in a cis conformation relative to the carbonyl oxygen of the monothiocarbamate residue. The ab initio geometrical optimizations in gas phase at B3LYP/6311++G(d,p) level of theory made for the discrete molecules

Fig. 8. Graphic representation of calculated density, q, dihedral angles, H, standard molar enthalpies of fusion, Dlcr Hom , and standard molar entropies of fusion Dlcr Som , as a function of the number of carbon atoms in the alkyl chain, n(C), showing a distinctive odd (Httpe and Httpene) and even (Httbe and Htthe) effect.

showed two aspects for consideration, namely, (i) most of the bond lengths, obtained for the N-thenoylthiocarbamic residue are higher than those obtained by single crystal diffractometry, suggesting that the electronic density in solid state is more delocalized than in the gas phase; this feature is also seen in the IR results where some differences in the experimental wavelengths, mexp and the scaled theoretical predictions, mtheo are observed and (ii) the alkyl chain conformation found in solid state is not necessary the most stable, nevertheless, ab initio energetic difference between the different alkyl conformers is very small, supporting the existence of several accessible molecular geometries that will allow the existence of different crystal packing solutions according the odd and even alkyl group type. Crystal packing for these compounds is dominated by an intermolecular N–H


O hydrogen bond and by a weak C–H (thenoyl ring)


O interaction. These interactions do not involve atoms belonging to the alkyl chain. However, the compounds show a marked even/odd effect (a function of the number of carbon atoms in the alkyl chain) in some of their thermodynamic properties for example in their standard molar entropies of fusion and standard molar enthalpies of fusion indicating that these chains play an important role in the definition of the entropy of the solid state. Geometrical

44

L.R. Gomes et al. / Journal of Molecular Structure 936 (2009) 37–45

Table 5 Total electronic energies, Eo, zero-point energies correction, ZPE, enthalpies thermal correction, Hcorr, and enthalpic energies plus thermal correction, H298.15 K, for T = 298.15 K (in hartree), for the conformers A, B and C of Httpre, Httbue, Httpte and Htthxe, calculated at B3LYP/6-311++G(d,p) level of theory. Parameters A

Httpre (RX = B; C)

Httbue (RX = C)

Httpte (RX = C)

Htthxe (RX = A)

1390.694107 ( 0.25) 1390.694069 ( 0.15) 1390.694011 (0.00) 1390.694011

1430.018519 ( 0.34) 1430.018458 ( 0.18) 1430.018388 (0.00) 1430.018388

1469.342825 (0.00) 1469.342801 (0.06) 1469.341474 (3.55) 1469.342825

RX

1351.369768 ( 0.35) 1351.369633 (0.00) 1351.369633 (0.00) 1351.369633

ZPE

A B C RX

0.187814 0.187924 0.187924 0.187923

0.215871 0.216019 0.215888 0.215888

0.243831 0.243967 0.243848 0.243848

0.271958 0.271887 0.272098 0.271961

Hcorr

A B C RX

0.016012 0.015890 0.015890 0.015890

0.017395 0.017227 0.017296 0.017296

0.018815 0.018652 0.018694 0.018694

0.020072 0.020080 0.019992 0.020072

H298.15 K

A

1351.1659415 ( 0.32) 1351.1658189 (0.00) 1351.1658189 (0.00) 1351.1658199

1390.4608416 ( 0.04) 1390.4608230 (0.01) 1390.4608278 (0.00) 1390.4608278

1429.7558723 ( 0.07) 1429.7558397 (0.02) 1429.7558462 (0.00) 1429.7558462

1469.0507951 (0.01) 1469.0508339 ( 0.11) 1469.0493836 (3.70) 1469.0507921

Eo

B C

B C RX

Below the correspondent Eo and H298.15 K are presented the difference between the values obtained for the conformer A, B and C and the obtained values for the conformer using the starting geometry X-ray data [(A, B or C) (RX)] (values in kJ mol 1). ZPE – zero-point correction; Eo – total electronic energy; H298.15 K – total electronic energy + zero-point energy + enthalpy correction. The zero-point energy correction was scaled using the 0.9887 scaling factor and the enthalpy correction using the 0.9688 scaling factor.

Table 6 Dipole moments (D) and charge distributions (e) for conformers A, B and C of Httpre, Httbue, Httpte and Htthxe, calculated at B3LYP/6-311++G(d,p) level of theory.

Conformer

Httpre B

Httbue C

Httpte C

Htthxe A

Dipole (D)

6.1243

6.1669

6.2061

6.2263

Mulliken charge distributions Thiophene ring S1 0.351 C1 +0.397 C2 0.993 C3 +1.412 C4 +0.568

0.354 +0.397 0.999 +1.430 +0.601

0.353 +0.382 0.986 +1.404 +0.591

0.355 +0.384 0.994 +1.437 +0.625

Thiocarbamic ester C5 O1 N1 C6 S2 O2

1.733 0.213 0.033 +0.046 0.229 +0.036

1.781 0.211 0.037 +0.094 0.259 +0.056

1.740 0.211 0.041 +0.092 0.262 +0.064

1.800 0.210 0.040 +0.108 0.279 +0.069

0.112 0.312 0.435

0.263 0.312 +0.025 0.588

0.364 0.246 +0.027 0.155 0.614

0.463 0.203 +0.030 0.184 0.148 0.637

Alkyl chain C7 C8 C9 C10 C11 C12

of the solid state as compared with the less planar odd compounds. Attempts were made to prepare single crystals of the N-thenoylthiocarbamic-O-n-ethylester but the reaction produced 2-thiophenecarboxamide. Details of the preparation and the crystal structure for this compound are given in [36].

Acknowledgements The authors thank ‘‘Servicios Técnicos de Investigacion of Universidad de Jaén” and the staff for data collection. The authors also thank Dr. Manuel Melguizo for helpful discussion and advice and are also grateful to Maria Celeste Coimbra de Azevedo for the FTIR data acquisition and Hilário Rodrigues Tavares for the 1H NMR measurements. B.S. thanks FCT and the European Social Fund (ESF) under the third Community Support Framework (CSF) for the award of a Post-Doctoral Research Grant (SFRH/BPD/38637/2007). Thanks are also due to FCT, the Programa Operacional Ciência e Inovação 2010 (POCI2010) and FEDER for financial support to Project POCI/ QUI/61873/2004.

Appendix A. Supplementary data

analysis based on the dihedral angle, H, formed between the aromatic ring planes and the C23 ? C2x alkyl chain planes showed a greater degree of planarity of the whole molecule in the case of the even compounds. This planarity of the even carbon atom chain compounds may lower the density of the crystal packing, allowing for more freedom of the packing modes which contributes to an increase of the absolute entropy

The FTIR data and frequencies assignment are available as supporting information (S1–S4). All crystallographic data for this paper are deposited in Cambridge Crystallographic Data Centre (CCDC 715889-690630-690631-715294). The data can be obtained free of charge at www.ccdc.cam.ac.uk or from Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 (0) 1223 336033, e-mail: [email protected]. Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.molstruc.2009.07.013.

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L.R. Gomes et al. / Journal of Molecular Structure 936 (2009) 37–45

3500

Experimental Vibrational Frequencies / cm-1

3000

2500

2000

1500

1000

500

0 0

500

1000

1500

2000

2500

3000

3500

Calculated Vibrational Frequencies / cm-1 Fig. 9. Correlation between the experimental solid state vibrational frequencies and the calculated [B3LYP/6-311++G (d,p)] gas phase unscaled vibrational frequencies for Httpte. Scaling equations: mscal = 7.936 + 0.9787mcalc (—, fitting line) and mscal = 0.9825mcalc (- - -, fitting line).

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