- Email: [email protected]
N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies
Journal of Molecular Structure xxx (xxxx) xxx
Contents lists available at ScienceDirect
Journal of Molecular Structure journal homepage: http://www.elsevier.com/locate/molstruc
N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies Fatma Aydın a, *, N. Burcu Arslan b, Kadir Aslan c, ** a b c
Department of Chemistry, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, 17100, Çanakkale, Turkey Department of Computer Education and Instructional Technology, Faculty of Education, Giresun University, 28200, Giresun, Turkey Morgan State University, School of Engineering, Department of Civil Engineering, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
a r t i c l e i n f o
a b s t r a c t
Article history: Received 17 May 2019 Received in revised form 11 November 2019 Accepted 12 November 2019 Available online xxx
A new dithiocarbamate molecule, named as N-benzoyl-S-(undecyl)-dithiocarbamate (C19H29NOS2), was synthesized and characterized by 1HNMR, 13CNMR, FT-IR spectroscopic methods. X-ray analysis of the crystal structure of title compound showed the presence of triclinic space group with a ¼ 4.2417 (8) Å, b ¼ 20.010 (4) Å, c ¼ 27.959 (6) Å, Z ¼ 4, V ¼ 2338.9 Å3. Detailed investigation of molecular packing of the molecule indicated the presence of intermolecular hydrogen bond between C1eH1/S4i and C24 eH24/S2v that generates R22 (10) motifs, and intermolecular hydrogen bonds between N1eH111/S4ii and N2eH222/S2iv atoms that forms R22 (7) rings. Thermal properties of the title compound were investigated by thermogravimetric analysis (DTA/TG) and differential scanning calorimetry (DSC). Molecular electrostatic potential (MEP), the HOMO and LUMO energies and thermodynamic parameters of the title compound were calculated using density functional theory (DFT) with B3LYP/6-311G (d,p) level. © 2019 Published by Elsevier B.V.
Keywords: Dithiocarbamate X-ray structure determination HOMO and LUMO analysis Molecular electrostatic potential Thermal properties (DTA/TG/DSC)
1. Introduction Dithiocarbamate (DTC) derivatives are a class of pesticides, and are widely used as agrochemicals, such as, ziram, thiram, ferbam, maneb, zineb, mangozeb etc. for protecting crops against fungal diseases [1e5]. DTCs are also used as organic intermediates in the synthesis of thiazoles [6e8] and metal sulfide nanoparticles [9], additives in rubber industry [10], vulcanization accelerators [11]. Recently, DTCs have also been used as protection groups in peptide synthesis [12], linkers for the formation of self-assembled monolayers [13] and in the synthesis of ionic liquids [14]. Dithiocarbamate ligands used in coordination chemistry has generated a large collection of crystallographic data for metal-dithiocarbamato derivatives and they have been used in wide range of applications such as medicine, industry and agriculture [15]. DTC derivatives containing sulfur (i.e. N, N0 -dialkyldithiocarbamate) are used for the selective removal of heavy metals, such as, copper (II), lead (II),
* Corresponding author. ** Corresponding author. E-mail addresses: [email protected] (F. Aydın), [email protected], [email protected] (K. Aslan).
cadmium (II), and mercury (II) [16,17]. Furthermore, DTCs are employed in medicinal chemistry in cancer therapy [18e21], as pesticides agrochemicals [22] and as reagents in analytical chemistry [23,24]. In the last decade, some gold (III)-dithiocarbamato derivatives as potential anticancer agents have been designed and tested by research groups [25]. New coumarin derivatives bearing dithiocarbamate moiety has been synthesized and used as antimicrobial agents [26]. In the present study, a new aroyl dithiocarbamate was synthesized via the reaction of benzoyl isocyanate and 1-undecanethiol (Scheme 1), and characterized by elemental analysis (CHNS), FTIR, UVevis, 1H NMR, 13C NMR measurements. Single crystal structural property was studied by experimental X-ray diffraction method. The thermal behavior of the title compound was investigated by thermogravimetric and differential thermal (TG/DTA) analysis and differential scanning calorimetric (DSC) analysis. Theoretical calculations for the molecular electrostatic potential, the HOMO and LUMO energies and thermodynamic parameters of the title compound were carried out using DFT with B3LYP/6-311G (d,p) level. The UVevisible spectra of title compound were used for investigation of electronic transitions, and the optical band gaps (Eg, eV) values for the title compound in different solvents were calculated from electronic absorption spectra.
https://doi.org/10.1016/j.molstruc.2019.127414 0022-2860/© 2019 Published by Elsevier B.V.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
2
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Scheme 1. Synthesis pathway of the title compound.
2. Experimental section 2.1. Material and methods Benzoyl chloride, potassium isocyanate, 1-undecanethiol, acetone, tetrahydrofuran was purchased from Sigma-Aldrich, Merck Chemical. All commercial reagents were used without further purification. Melting point of the title compound was determined on Electrothermal 9100® apparatus. Reactions during the synthesis of the title compound were monitored by thin-layer chromatography (TLC) on silica-gel 60 F254 plates (Merck) and an UV lamp. Elemental analysis was conducted on a LECO-932 CHNS analyzer. FT-IR analysis was performed by using a PerkinElmer Spectrum 100FT-IR instrument with an ATR apparatus in the range 4000-650 cm1. 1HNMR and 13CNMR spectra were recorded on a Bruker AVANCE DPX NMR spectrometer operating at 400 and 101.6 MHz, respectively, using TMS as an internal standard and DMSO‑d6 as solvent. UVevisible measurements were carried out with a PerkinElmer WinLab-25 series spectrophotometer in quartz cells of 1 cm path length. SETERAM LABSYS evo 1600 was used for DTA/TG analysis of the title compound. 2.2. The synthesis of the N-Benzoyl-S-(undecyl)-dithiocarbamate Benzoyl chloride (0.700 g, 5 mmol) was added slowly to dry acetone solution (20 mL) containing potassium thiocyanate (0.485 g, 5 mmol). A mixture was refluxed with stirring for 30 min After then, a solution of 1-undecanethiol (0.940 g, 5 mmol) in
acetone (15 mL) was added dropwise to the benzoyl isothiocyanate and refluxed with stirring for 2 h. When the reaction was completed, the solution was poured into a beaker containing some ice. The yellow oil product was separated and washed with distilled water. After drying under vacuum, recrystallized from tetrahydrofuran to give the product. Mp: 52e53 C, Yield 86%. Elemental analysis for C19H29NOS2: calculated, (%): C: 64.91, H: 8.31, N: 3.98, S: 18.24, O: 4.55; Found, (%): C: 64.72, H: 8.32, N: 4.07, S: 18.35, O: 4.54.
2.3. X-ray crystallography A single crystal of title compound was grown by slow evaporation of the solution of products in tetrahydrofuran. Diffraction data of it was collected at Bruker APEX-II CCD diffractometer using MoKa radiation. The crystal structure was solved and refined by SHELXS-97 and SHELXL-97 programs, respectively [27,28]. The refinement was carried out by full-matrix least-squares method on the positional and anisotropic temperature parameters of the nonhydrogen atoms, or equivalently corresponding to 416 crystallographic parameters. All non-hydrogen atoms were refined anisotropically, whereas hydrogen atoms were located geometrically and refined as riding with respective CeH distances of 0.93 A, 0.96 A and 0.97 A corresponding to the aromatic, methylene and methyl CeH bonds. The atomic numbering scheme with displacement ellipsoids of the crystal structure drawing with ORTEP III was depicted at the 30% probability level for clarity (Fig. 1).
Fig. 1. ORTEP III diagram of title compound.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
2.4. Computational studies The molecular structure of title compound was optimized using DFT in the ground state by B3LYP [29] method with the 6-311G (d,p) [30] basis sets included in Gaussian 09 program [31]. Molecular structure of the title compound optimized by 6-311G (d,p) basis set displayed frontier molecular orbitals, and electrostatic potential were simulated. In addition, thermodynamic parameters (i.e., heat capacity, enthalpy and entropy values) for the title molecule were calculated. 3. Results and discussion 3.1. FT-IR and NMR spectral studies The IR spectra of the title compound showed significant absorption of the carbonyl group at 1697 cm1 y (C]O) and the amide group at 3313 cm1 (y NeH), respectively. Vibration bands with the wave numbers of 3055 and 3050 cm1 (y CeH, AreH) and 1553 and 1502 cm1 (y C]C) were observed as the result of the vibration of phenyl ring. The frequencies of 2955, 2918 and 2850 cm1 and 1250 cm1 were assigned to the stretching vibrations (CeH) and (CeC) in undecyl moiety, respectively [32]. The dithiocarbamate compounds exhibit a characteristic band in the range (1580-1450) cm-1 assignable to the y (CeN) [33]. Additional bands at 1431 cm1 (y COeN) and 1207 cm1 (NCS) were observed. The band of 747 cm1 (y C]S) was attributed to thiocarbonyl group (C]S) symmetric stretching vibration [34,35] (Fig. S1). 1 H NMR and 13C NMR spectra for title compound are shown in Figs. S2 and S3 (Supplemental Materials). 1H NMR spectra exhibits
organic solvent (THF, CH3CN and DMSO) in the range of 300e600 nm (Fig. 2), where. two bands were observed. The highdensity bands at 340, 344 and 348 nm for THF, CH3CN and DMSO solvents, respectively, are due to the transition p /p * of the nitrogen-carbon-sulfur (-N-C]S) group on dithiocarbamate moiety conjugated with benzoyl. It also appears as a shoulder on the transition n/p* localized on sulfur connected with undecyl moiety observed at 408, 411 and 415 nm. Optical band gaps (Eg, eV) value from the electronic absorption spectra of the title compound in different solvents were calculated for these transitions and the optical energy were determined from the (ahy)2 versus photon energy (hy) graph using Tauc equation [36], where a is the absorption coefficient (Fig. 3). From the value of Tauc equation, for the title compound in THF, CH3CN and DMSO, the band gaps corresponding to n-p* transitions were calculated 3.59, 3.55 and 3.51 eV, respectively. DFT (B3LYP) calculations and energy levels of the HOMO-1, HOMO and LUMO, LUMOþ1 orbitals was used for determine the low-lying excited states of compound [37,38]. Energy difference HOMO-1, HOMO and LUMO, LUMOþ1 were calculated as 6.5769, 6.2841 and 2.2201, 1.1649 eV, respectively (Fig. 4). Large HOMOLUMO gap energy value of 4.064 eV indicates that the title compound is in steady state. Fig. 4 also showed that the electronic density on the HOMO of the title compound was localized primarily on dithiocarbamate skeleton and carbonyl group, whereas the LUMO orbital of it was localized on dithiocarbamate skeleton along the phenyl ring and its amide group due to intramolecular charge transfer. Energy level of LUMO, which is related to the electron affinity, implies that the title compound is susceptible to nucleophilic attacks [39].
all expected resonances for (CeOeNH) and (CeSeCH2) groups at 12.65 ppm and 3.20 ppm, respectively. The 1H NMR signal for NeH proton of amide or thioureide moiety due to the resonance with the carbonyl (C]O) and thiocarbonyl (C]S) groups shifted downfield to about 12.65 ppm, while that NeH appeared at about ~8.00 ppm. Three signals were appeared at 7.53 (d, 2H), 7.66 (m, 1H) and 7.94 (d, 2H) for phenyl protons. In addition, the title compound has an undecyl moiety and aliphatic protons were assigned at 1.68 (2H, m), 1.40 (2H, m) 1.25 (16 H, m) and 0.86 (3H, t) ppm. In the 13C NMR spectra of the title compound, aromatic proton signals were appeared in the region 133.0, 131.8, 128.7 and 128.4 ppm for phenyl moiety. Functional groups in the structure of aroyl dithiocarbamate derivative were confirmed with at 204.6 d(C]S), 165.3 d(C]O), 35.9 d(SeCH2), 13.9 ppm d(CH3) and (CH2)n) within range of d (31.3e22.1) ppm for title compound, respectively (Scheme 2). 3.2. Electronic spectral studies and HOMO-LUMO analysis High chemical reactivity, more polarizability and the transfer of charge within a molecule are associated with the frontier orbital gap (i.e., energy gap between HOMO and LUMO). The UVeVis spectra of the title compound were recorded in different polarity
3
Fig. 2. UVevis spectra of title compound in THF, CH3CN and DMSO solvents.
Scheme 2. 1H and 13C NMR chemical shifts of the title compound in DMSO‑d6.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
4
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Fig. 5. Molecular electrostatic potential map calculated at B3LYP/6-311þþG (d,p)level for title compound.
Fig. 3. A plot of (ahy)2 versus photon energy (hy) of the title compound in THF, CH3CN and DMSO solvents, a: the absorption coefficient.
3.3. Molecular electrostatic potential (MEP) Molecular electrostatic potential is used for relative reactivates toward electrophilic attack and nucleophilic reactions, for a molecule, plays an important role in determining the electron acceptor and donor sites. MEP also shows the electron cloud distributions for hydrophilic and hydrophobic groups of a molecule. MEP was assessed using the B3LYP/6-311G (d,p) method to investigate the reactive sites of title compound (Fig. 5). In MEP surface, different colors are represented by different values of the electrostatic
potential: red and blue represent the regions of the most negative and positive electrostatic potential whereas green represent the regions of zero potential. As seen in Fig. 5, the negative regions (from red to yellow) are placed around the oxygen and sulfur atoms and it is shown the polar head (hydrophilic) such as dithiocarbamate, carbonyl group. The less positive regions (greenish) are placed around all aliphatic and aromatic carbon and hydrogen atoms and it is shown the long nonpolar groups (hydrophobic) of phenyl and undecyl moiety. These calculations predict that hydrogen bonds are located on medium region of molecule. 3.4. X-ray properties N-Benzoyl-S-(undecyl)-dithiocarbamate is crystallized in the triclinic form with space group P-1 by two symmetric molecules in asymmetric unit with Z ¼ 4 in the unit cell. The title compound consists of dithiocarbamate, carbonyl group, phenyl ring and its amide group and contains an undecyl moiety as hydrophobic group. Molecular packing diagrams of the title compound are displaced along a-axis in Fig. 6. Because of the functional groups of the
Fig. 4. Frontier molecular orbitals diagram for the title compound.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
5
Table 1 Crystal data, data collection and refinement parameters for the title compound. Crystal data Chemical formula Mr Crystal system, space group Temperature (K) a, b, c (Å)
a, b, g ( ) V (Å3) Z Radiation type No. of reflections for cell measurement q range ( ) for cell measurement m (mm1) Crystal shape Crystal size (mm) Data collection Diffractometer Absorption correction Tmin, Tmax No. of measured, independent and observed [I > 2s(I)] reflections Rint (sin q/l)max (Å1) Refinement R [F2 > 2s(F2)], wR (F2), S No. of reflections No. of parameters H-atom treatment
(D/s)max Drmax, Drmin (e Å3)
C19H28NOS2 350.54 Triclinic, P-1 296 4.2417 (8), 20.010 (4), 27.959 (6) 82.422 (6), 86.478 (6), 84.577 (6) 2338.9 (8) 4 MoKa 9907 3.0e28.1 0.23 Block 0.19 0.17 0.14
BrukerAPEX-II CCD Multi-scan 0.676, 0.746 87167, 9171, 5101 0.070 0.617
0.156, 0.526, 1.31 9171 416 H-atom parameters constrained w ¼ 1/[s2(Fo2) þ (0.1249P) 2 þ 30.6399P] where P ¼ (Fo2 þ 2Fc2)/3 0.341 1.42, 0.43
Computer programs: BrukerAPEX2, BrukerSAINT, SHELXT 2014/4 (Sheldrick, 2014), SHELXL2016/6 (Sheldrick, 2016).
3.5. Thermodynamic properties
Fig. 6. A partial view of the crystal packing of title compound, showing the linear arrangement built from (a) NeH …. S- and (b) CeH …. S- hydrogen bonds. The hydrogen bonds are shown as dotted lines.
title compound, b-axis and c-axis (20.010 and 27.959 Å, respectively) are larger than the a-axis (4.2417 Å) in the crystal dimensions. Crystallographic data and the details of X-ray diffraction study of the title compound is shown in Table 1, whereas selected bond lengths and bond angles is compiled in Table 2. The benzamide moiety of the title compound has a closely planar configuration and the maximum deviation from the meanplane belongs to O1 oxygen atom with 0.267 Å. The undecyl group twists slightly due to the consistent of dithiocarbamate group. The torsion angle values about this twist are 4.4 on C7/N1/ C8/S1 atom group and 178.7 on N1/C8/S1/C9 atom group. Detailed investigation of molecular packing of the molecule indicates the intermolecular hydrogen bond C1eH1/S4i and C24eH24/S2v generates R22 (10) motifs. In addition, intermolecular hydrogen bonds occur between N1eH111/S4ii and 2 iv N2eH222/S2 atoms to form R2 (7) rings.
The statistically thermodynamic parameters such as standard heat capacity of constant pressure (Cp), enthalpy (H) and entropy (S) were calculated using the B3LYP/6-311G (d,p) method in ground state by increasing from 100 K to 900 K in gas phase. The results are shown in Fig. 7 and Table S1. Fig. 7 shows that Cp, S and the H of the title compound increase from 100 K to 900 K, which is caused by the rise of molecular vibration intensity with the increasing temperature [40]. Quadratic formulas were used to fit the correlation equations between different parameters heat capacity, enthalpy, entropy and temperature, R being the corresponding fitting factor (R2) for these thermodynamic parameters. The corresponding fitting equations for title compound are as presented below:
C p;m ¼ 11; 3366 þ 0; 3045 T 1; 4282x105 T2 ðR2 ¼ 0; 9973
Sm ¼ 56; 5472 þ 0; 2633 T 5; 5547x105 T2 ðR2 ¼ 0; 9991
DH0m ¼ 3; 95915 þ 0; 0309 T þ 6; 2975x105 T2 ðR2 ¼ 0; 9978
The thermogravimetric measurements and calculations clearly show that the high temperature phase of title compound is
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
6
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Table 2 Hydrogen-bond geometry (Å, ). DdH$$$A
DdH
H$$$A
D$$$A
C1eH1/S4i N1eH111/S4ii C19eH19A$$$O2iii N2eH222/S2iv C24eH24/S2v C38eH38A$$$O1vi
0.93 0.86 0.96 0.86 0.93 0.96
2.89 2.70 2.77 2.72 2.91 2.81
3.777 3.534 3.647 3.546 3.792 3.665
DdH$$$A (14) (9) (18) (9) (14) (19)
160.5 162.6 151.5 162.5 158.9 148.3
Symmetrycodes: (i) xþ1, y, z; (ii) xþ2, y, z; (iii) x, y1, z; (iv) x2, y, z; (v) x1, y, z; (vi) x, yþ1, z.
Fig. 8. Thermo analytical (TG/DTA) curves of title compound.
Fig. 7. Correlation graph of calculated thermodynamic properties and temperatures for the title compound.
thermally unstable and final decomposition stars at about 200 C for compound [41,42]. All the theoretical parameters can be helpful information for the new synthesis of like title compound or thiocarbamate derivatives.
Fig. 9. Differential scanning calorimetric graphs of title compound.
is thermally stable up to 184.08 C [43]. 3.6. Thermal analysis 4. Conclusions Fig. 8 shows the TG and DTA curves of obtained crystal of the title compound. The DTA curve showed three endothermal peaks. The first sharp peak at 53.2 C is a significant endothermic peak corresponding to the melting of the crystal. At the melting point no weight loss was observed in the TG curve. The first decomposition step of the compound was observed in the temperature range 198.1e228.0 C and the approximate weight loss was 17.53%. Above this temperature, a second weight loss of 71.02% (Calc. 70.14%) occurred in the range 292e331 C which indicates elimination of C12H24NS2$. The second decomposition step, which also includes the first-thermal degradation step is observed at Tmax ¼ 318.5 C for the DTA peak. After this at around 458 C, decomposition was about 100% leaving no residue in the crucible. The DSC curve of the compound was obtained at a heating rate of 10 C/min under argon atmosphere (Fig. 9). The melting point of the compound as can be seen in the DSC curve was observed as a sharp endothermic peak at about 50.33 C and the positive enthalpy value of 105.14 J g-1 at 50.33 C can be attributed to the energy absorbed during the (endothermic) melting process. The lower point and sharpness of DSC curve indicated that the compound had good crystallinity and high purity. The degradation of the compound related with the endothermic peak in the DSC curve was observed at 200.45 C with DН ¼ 99.12 J g-1. The DSC curve clearly indicates that the compound
Synthesis, experimental and theoretical characterization of a new dithiocarbamate molecule, called N-benzoyl-S-(undecyl)dithiocarbamate was reported. X-ray analysis revealed that the title compound crystallizes in the triclinic space group P-1, with cell parameters a ¼ 4.2417 (8) Å, b ¼ 20.010 (4) Å, c ¼ 27.959 (6) Å, a ¼ 82.422 (6) , b ¼ 86.478 (6) , g ¼ 84.577 (6) and V ¼ 2338.9 Å3. The presence of intermolecular N…HS, N/HO, C/HO, and C/HN hydrogen bond interactions was confirmed via experimental and theoretical studies. Molecular electrostatic potential surface parameter of the title compound was good agreement with the predicted hydrogen bonds. The energy gap between the HOMOLUMO orbital for the title compound was calculated to be 4.064 eV. Electronic absorption spectra for the title compound was predicted from DFT calculations and were compared to experimental UVevisible spectrum, which showed the presence of n- p* and p- p* bands. The low melting point of the title compound is predicted to be related to the large unit cell and the weak intermolecular H-bonding in the crystal structure of the molecule. TG/ DTA and DSC curves showed that the compound melted at a low temperature (53.2 and 50.33 C, respectively). DTA of the title compound showed that the decomposition was taken place in two steps. Calculated frontier molecular orbital energies were
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
compared with the optical band gaps (Eg, eV) value from electronic absorption spectra. Hydrophilic and hydrophobic groups of the compound were also predicted from the molecular electrostatic potential. We hope that the synthesis, crystallographic and spectroscopic characterization and DFT studies of N-Benzoyl-S-(undecyl)-dithiocarbamate will be helpful for the synthesis of new dithiocarbamates. Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work “N-Benzoyl-S-(undecyl)-dithiocarbamate: synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies” reported in this paper. Appendix A. Supplementary data Supplementary data associated with this article can be found in the online version, at https://doi.org/10.1016/j.molstruc.2019. 127414. These data include MOL file and InChiKeys of the most important compounds described in this article. Author contributions Fatma AYDIN: Investigation;Conducting a research and investigation process, specifically performing the experiments, or data/ evidence collection, Visualization; Preparation (Experimental section), creation and presentation of the published work, specifically visualization/ data presentation, Writing- Review & Editing; Preparation, creation and presentation of the published work by those from the original research group, commentary or revision e including pre-or postpublication stages; N. Burcu ARSLAN: Using Software Programming (DFT with B3LYP/6-311G(d,p) level), X-ray analysis and molecular structure determination; Kadir ASLAN: Review & Editing;Preparation, creation and presentation of the published work, Resources; Provision of study materials, reagents, materials, Funding acquisition;Acquisition of the financial support for the project leading to this publication. References [1] G. Eng, X. Song, Q. Duong, D. Strickman, J. Glass, L. May, Synthesis, structure characterization and insecticidal activity of some triorganotin dithiocarbamates, Appl. Organomet. Chem. 17 (4) (2003) 218e225. [2] M. Mulkey, The Grouping of a Series of Dithiocarbamate Pesticides Based on a Common Mechanism of Toxicity. US Environmental Protection Agency, Office of Pesticide Programs, Office of Prevention, Pesticides and Toxic Substances, SAP Report, Washington, DC, 2001. [3] H. Kidd, D. Hartley, Pesticide index: an index of chemical, common and trade names of pesticides and related crop protection products, R. Soc. Chem. (1988). [4] S. Hurt, J. Ollinger, G. Arce, Q. Bui, A.J. Tobia, B. van Ravenswaay, Dialkyldithiocarbamates (EBDCs), Hayes’ Handbook of Pesticide Toxicology, Elsevier, 2010, pp. 1689e1710. [5] N.L. Botha, P.A. Ajibade, A.O. Ashafa, Synthesis, spectroscopic characterization, antifungal and antibacterial studies of copper (II) dithiocarbamate complexes, J. Pharm. Sci. Res. 10 (8) (2018) 2111e2114. [6] A.A. Aly, A.B. Brown, T.M. Bedair, E.A. Ishak, Dithiocarbamate salts: biological activity, preparation, and utility in organic synthesis, J. Sulfur Chem. 33 (5) (2012) 605e617. [7] F. Aryanasab, A.Z. Halimehjani, M.R. Saidi, Dithiocarbamate as an efficient intermediate for the synthesis of 2-amino-1, 3, 4-thiadiazoles in water, Tetrahedron Lett. 51 (5) (2010) 790e792. [8] A.Z. Halimehjani, L. Hasani, M.A. Alaei, M.R. Saidi, Dithiocarbamates as an efficient intermediate for the synthesis of 2-(alkylsulfanyl) thiazoles in water, Tetrahedron Lett. 57 (8) (2016) 883e886. [9] E.R. Knight, A.R. Cowley, G. Hogarth, J.D. Wilton-Ely, Bifunctional dithiocarbamates: a bridge between coordination chemistry and nanoscale
7
materials, Dalton Trans. 4 (2009) 607e609. [10] R.M. Mariano, H.M. da Costa, M.R. Oliveira, M.M. Rubinger, L.L. Visconte, The behavior of dithiocarbimate derivative as safety accelerator of natural rubber compounds, J. Appl. Polym. Sci. 110 (4) (2008) 1938e1944. [11] M.N. Alam, S.K. Mandal, S.C. Debnath, Effect of zinc dithiocarbamates and thiazole-based accelerators on the vulcanization of natural rubber, Rubber Chem. Technol. 85 (1) (2012) 120e131. [12] T.W. Green, P.G. Wuts, Protective Groups in Organic Synthesis, Wiley, New York, 1999. [13] P. Morf, F. Raimondi, H.-G. Nothofer, B. Schnyder, A. Yasuda, J.M. Wessels, T.A. Jung, Dithiocarbamates: functional and versatile linkers for the formation of self-assembled monolayers, Langmuir 22 (2) (2006) 658e663. [14] D. Zhang, J. Chen, Y. Liang, H. Zhou, Facile synthesis of novel ionic liquids containing dithiocarbamate, Synth. Commun. 35 (4) (2005) 521e526. [15] P.J. Heard, Main group dithiocarbamate complexes, Prog. Inorg. Chem. 53 (2005) 1e69. [16] A.R. Ipeaiyeda, A.J. Odola, Co-precipitation of Ni, Cr, Mn, Pb and Zn in industrial wastewater and sediment samples with copper (II) cyclohexylmethyldithiocarbamate for their flame atomic absorption spectrometric determination, Water Sci. Technol. 66 (1) (2012) 105e112. [17] X. Jing, F. Liu, X. Yang, P. Ling, L. Li, C. Long, A. Li, Adsorption performances and mechanisms of the newly synthesized N, N0 -di (carboxymethyl) dithiocarbamate chelating resin toward divalent heavy metal ions from aqueous media, J. Hazard Mater. 167 (1e3) (2009) 589e596. [18] D. Buac, S. Schmitt, G. Ventro, F.R. Kona, Q.P. Dou, Dithiocarbamate-based coordination compounds as potent proteasome inhibitors in human cancer cells, Mini Rev. Med. Chem. 12 (12) (2012) 1193e1201. [19] W. Huang, Y. Ding, Y. Miao, M.Z. Liu, Y. Li, G.F. Yang, Synthesis and antitumor activity of novel dithiocarbamate substituted chromones, Eur. J. Med. Chem. 44 (9) (2009) 3687e3696. [20] R.D. Li, H.L. Wang, Y.B. Li, Z.Q. Wang, X. Wang, Y.T. Wang, Z.M. Ge, R.T. Li, Discovery and optimization of novel dual dithiocarbamates as potent anticancer agents, Eur. J. Med. Chem. 93 (2015) 381e391. [21] C. Marzano, L. Ronconi, F. Chiara, M.C. Giron, I. Faustinelli, P. Cristofori, A. Trevisan, D. Fregona, Gold (III)-dithiocarbamato anticancer agents: activity, toxicology and histopathological studies in rodents, Int. J. Cancer 129 (2) (2011) 487e496. [22] D. Halls, The properties of dithiocarbamates a review, Microchimica Acta 57 (1) (1969) 62e77. [23] C. Giridhar, S. Kanchi, T. Niranjan, K. Bisetty, N. Naidu, Sensitive determination of nickel (II) using catalytic hydrogen wave in the presence of dithiocarbamates at DME, J, Environ. Anal. Chem. 1 (108) (2014) 2. [24] S. Kanchi, M. Sulochana, K.B. Naidu, K. Saraswathi, N.V. Naidu, Dithiocarbamates as a sensitive electroanalytical reagent: determination of chromium by catalytic hydrogen wave at dme in water systems and vegetables, Food Anal. Methods 4 (4) (2011) 453e464. [25] L. Ronconi, D. Aldinucci, Q. Ping Dou, D. Fregona, Latest insights into the anticancer activity of gold (III)-dithiocarbamato complexes, Anti Cancer Agents Med. Chem. 10 (4) (2010) 283e292. [26] S.N. Mangasuli, K.M. Hosamani, P.B. Managutti, Synthesis of novel coumarin derivatives bearing dithiocarbamate moiety: an approach to microwave, molecular docking, Hirshfeld surface analysis, DFT studies and potent antimicrobial agents, J. Mol. Struct. (2019). [27] G. Sheldrick, SHELXS-97: Program for the Solution of Crystal Structures, 1997, There is no corresponding record for this reference, University of Gottingen, Germany, 1988. [28] G. Sheldrick, SHELXL-97, Program for Crystal Structure Refinement, 1997, There is no corresponding record for this reference, University of Goettingen, Germany, 2008. [29] A.D. Becke, Density-functional thermochemistry .3. The role of exact exchange, J. Chem. Phys. 98 (7) (1993) 5648e5652. [30] R. Ditchfield, W.J. Hehre, J.A. Pople, Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules, J. Chem. Phys. 54 (2) (1971) 724e728. [31] M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. Petersson, GAUSSIAN09. Revision E. 01, Gaussian Inc., Wallingford, CT, USA, 2009. [32] J. Coates, Interpretation of Infrared Spectra, a Practical Approach, Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation, 2006. [33] V. Alverdi, L. Giovagnini, C. Marzano, R. Seraglia, F. Bettio, S. Sitran, R. Graziani, D. Fregona, Characterization studies and cytotoxicity assays of Pt (II) and Pd (II) dithiocarbamate complexes by means of FT-IR, NMR spectroscopy and mass spectrometry, J. Inorg. Biochem. 98 (6) (2004) 1117e1128. [34] N.B. Arslan, C. Kazak, F. Aydın, Experimental and theoretical investigation of N-(4-nitrobenzoyl)-S-(cyclohexyl)-dithiocarbamate, N-(4-nitrobenzoyl)-Sbenzyldithiocarbamate, J. Mol. Struct. 1155 (2018) 646e653. € [35] F. Aydın, N.B. Arslan, N. Ozdemir, Tautomerism in 4-chlorophenyl benzoylcarbamodithioate: experimental and DFT study, J. Mol. Struct. 1137 (2017) 233e239. [36] J. Tauc, R. Grigorovici, A. Vancu, Optical properties and electronic structure of amorphous germanium, Phys. Status Solidi 15 (2) (1966) 627e637. [37] M. Haroon, M. Khalid, T. Akhtar, M.N. Tahir, M.U. Khan, M. Saleem, R. Jawaria, Synthesis, spectroscopic, SC-XRD characterizations and DFT based studies of ethyl2-(substituted-(2-benzylidenehydrazinyl)) thiazole-4-carboxylate
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
8
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
derivatives, J. Mol. Struct. 1187 (2019) 164e171. [38] R. Jawaria, M. Hussain, M. Khalid, M.U. Khan, M.N. Tahir, M.M. Naseer, A.A.C. Braga, Z. Shafiq, Synthesis, crystal structure analysis, spectral characterization and nonlinear optical exploration of potent thiosemicarbazones based compounds: a DFT refine experimental study, Inorg. Chim. Acta 486 (2019) 162e171. [39] T. Helgaker, P. Jorgensen, J. Olsen, Molecular Electronic-Structure Theory, John Wiley & Sons, 2014. [40] J.B. Ott, J. Boerio-Goates, Chemical Thermodynamics: Advanced Applications: Advanced Applications, Elsevier, 2000. ski, [41] M. Wojtas, A. Bil, R. Jakubas, A. Ga˛ gor, A. Pietraszko, O. Czupin
ski, D. Isakov, Organic-inorganic compounds with strong nonlinear Z. Tylczyn optical properties based on 2, 4, 6-trimethylpyridinium and tetrahedral BF 4 networks, Phys. Rev. B 83 (14) (2011) 144103. [42] M. Wojtas, A. Bil, A. Gagor, W. Medycki, A.L. Kholkin, Phase stability and dynamics of hybrid organiceinorganic crystals [(CH 3) 3 PH][SbCl 4] and [(CH 3) 3 PH][SbBr 4]: a computational and NMR approach, CrystEngComm 18 (14) (2016) 2413e2424. [43] S.B. Kalia, R. Puri, A. Thakur, J. Christopher, Synthesis, characterization and thermal degradation studies on some oxovanadium (IV) carbodithioates, J. Therm. Anal. Calorim. 119 (3) (2015) 1619e1632.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
Contents lists available at ScienceDirect
Journal of Molecular Structure journal homepage: http://www.elsevier.com/locate/molstruc
N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies Fatma Aydın a, *, N. Burcu Arslan b, Kadir Aslan c, ** a b c
Department of Chemistry, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, 17100, Çanakkale, Turkey Department of Computer Education and Instructional Technology, Faculty of Education, Giresun University, 28200, Giresun, Turkey Morgan State University, School of Engineering, Department of Civil Engineering, 1700 East Cold Spring Lane, Baltimore, MD, 21251, USA
a r t i c l e i n f o
a b s t r a c t
Article history: Received 17 May 2019 Received in revised form 11 November 2019 Accepted 12 November 2019 Available online xxx
A new dithiocarbamate molecule, named as N-benzoyl-S-(undecyl)-dithiocarbamate (C19H29NOS2), was synthesized and characterized by 1HNMR, 13CNMR, FT-IR spectroscopic methods. X-ray analysis of the crystal structure of title compound showed the presence of triclinic space group with a ¼ 4.2417 (8) Å, b ¼ 20.010 (4) Å, c ¼ 27.959 (6) Å, Z ¼ 4, V ¼ 2338.9 Å3. Detailed investigation of molecular packing of the molecule indicated the presence of intermolecular hydrogen bond between C1eH1/S4i and C24 eH24/S2v that generates R22 (10) motifs, and intermolecular hydrogen bonds between N1eH111/S4ii and N2eH222/S2iv atoms that forms R22 (7) rings. Thermal properties of the title compound were investigated by thermogravimetric analysis (DTA/TG) and differential scanning calorimetry (DSC). Molecular electrostatic potential (MEP), the HOMO and LUMO energies and thermodynamic parameters of the title compound were calculated using density functional theory (DFT) with B3LYP/6-311G (d,p) level. © 2019 Published by Elsevier B.V.
Keywords: Dithiocarbamate X-ray structure determination HOMO and LUMO analysis Molecular electrostatic potential Thermal properties (DTA/TG/DSC)
1. Introduction Dithiocarbamate (DTC) derivatives are a class of pesticides, and are widely used as agrochemicals, such as, ziram, thiram, ferbam, maneb, zineb, mangozeb etc. for protecting crops against fungal diseases [1e5]. DTCs are also used as organic intermediates in the synthesis of thiazoles [6e8] and metal sulfide nanoparticles [9], additives in rubber industry [10], vulcanization accelerators [11]. Recently, DTCs have also been used as protection groups in peptide synthesis [12], linkers for the formation of self-assembled monolayers [13] and in the synthesis of ionic liquids [14]. Dithiocarbamate ligands used in coordination chemistry has generated a large collection of crystallographic data for metal-dithiocarbamato derivatives and they have been used in wide range of applications such as medicine, industry and agriculture [15]. DTC derivatives containing sulfur (i.e. N, N0 -dialkyldithiocarbamate) are used for the selective removal of heavy metals, such as, copper (II), lead (II),
* Corresponding author. ** Corresponding author. E-mail addresses: [email protected] (F. Aydın), [email protected], [email protected] (K. Aslan).
cadmium (II), and mercury (II) [16,17]. Furthermore, DTCs are employed in medicinal chemistry in cancer therapy [18e21], as pesticides agrochemicals [22] and as reagents in analytical chemistry [23,24]. In the last decade, some gold (III)-dithiocarbamato derivatives as potential anticancer agents have been designed and tested by research groups [25]. New coumarin derivatives bearing dithiocarbamate moiety has been synthesized and used as antimicrobial agents [26]. In the present study, a new aroyl dithiocarbamate was synthesized via the reaction of benzoyl isocyanate and 1-undecanethiol (Scheme 1), and characterized by elemental analysis (CHNS), FTIR, UVevis, 1H NMR, 13C NMR measurements. Single crystal structural property was studied by experimental X-ray diffraction method. The thermal behavior of the title compound was investigated by thermogravimetric and differential thermal (TG/DTA) analysis and differential scanning calorimetric (DSC) analysis. Theoretical calculations for the molecular electrostatic potential, the HOMO and LUMO energies and thermodynamic parameters of the title compound were carried out using DFT with B3LYP/6-311G (d,p) level. The UVevisible spectra of title compound were used for investigation of electronic transitions, and the optical band gaps (Eg, eV) values for the title compound in different solvents were calculated from electronic absorption spectra.
https://doi.org/10.1016/j.molstruc.2019.127414 0022-2860/© 2019 Published by Elsevier B.V.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
2
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Scheme 1. Synthesis pathway of the title compound.
2. Experimental section 2.1. Material and methods Benzoyl chloride, potassium isocyanate, 1-undecanethiol, acetone, tetrahydrofuran was purchased from Sigma-Aldrich, Merck Chemical. All commercial reagents were used without further purification. Melting point of the title compound was determined on Electrothermal 9100® apparatus. Reactions during the synthesis of the title compound were monitored by thin-layer chromatography (TLC) on silica-gel 60 F254 plates (Merck) and an UV lamp. Elemental analysis was conducted on a LECO-932 CHNS analyzer. FT-IR analysis was performed by using a PerkinElmer Spectrum 100FT-IR instrument with an ATR apparatus in the range 4000-650 cm1. 1HNMR and 13CNMR spectra were recorded on a Bruker AVANCE DPX NMR spectrometer operating at 400 and 101.6 MHz, respectively, using TMS as an internal standard and DMSO‑d6 as solvent. UVevisible measurements were carried out with a PerkinElmer WinLab-25 series spectrophotometer in quartz cells of 1 cm path length. SETERAM LABSYS evo 1600 was used for DTA/TG analysis of the title compound. 2.2. The synthesis of the N-Benzoyl-S-(undecyl)-dithiocarbamate Benzoyl chloride (0.700 g, 5 mmol) was added slowly to dry acetone solution (20 mL) containing potassium thiocyanate (0.485 g, 5 mmol). A mixture was refluxed with stirring for 30 min After then, a solution of 1-undecanethiol (0.940 g, 5 mmol) in
acetone (15 mL) was added dropwise to the benzoyl isothiocyanate and refluxed with stirring for 2 h. When the reaction was completed, the solution was poured into a beaker containing some ice. The yellow oil product was separated and washed with distilled water. After drying under vacuum, recrystallized from tetrahydrofuran to give the product. Mp: 52e53 C, Yield 86%. Elemental analysis for C19H29NOS2: calculated, (%): C: 64.91, H: 8.31, N: 3.98, S: 18.24, O: 4.55; Found, (%): C: 64.72, H: 8.32, N: 4.07, S: 18.35, O: 4.54.
2.3. X-ray crystallography A single crystal of title compound was grown by slow evaporation of the solution of products in tetrahydrofuran. Diffraction data of it was collected at Bruker APEX-II CCD diffractometer using MoKa radiation. The crystal structure was solved and refined by SHELXS-97 and SHELXL-97 programs, respectively [27,28]. The refinement was carried out by full-matrix least-squares method on the positional and anisotropic temperature parameters of the nonhydrogen atoms, or equivalently corresponding to 416 crystallographic parameters. All non-hydrogen atoms were refined anisotropically, whereas hydrogen atoms were located geometrically and refined as riding with respective CeH distances of 0.93 A, 0.96 A and 0.97 A corresponding to the aromatic, methylene and methyl CeH bonds. The atomic numbering scheme with displacement ellipsoids of the crystal structure drawing with ORTEP III was depicted at the 30% probability level for clarity (Fig. 1).
Fig. 1. ORTEP III diagram of title compound.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
2.4. Computational studies The molecular structure of title compound was optimized using DFT in the ground state by B3LYP [29] method with the 6-311G (d,p) [30] basis sets included in Gaussian 09 program [31]. Molecular structure of the title compound optimized by 6-311G (d,p) basis set displayed frontier molecular orbitals, and electrostatic potential were simulated. In addition, thermodynamic parameters (i.e., heat capacity, enthalpy and entropy values) for the title molecule were calculated. 3. Results and discussion 3.1. FT-IR and NMR spectral studies The IR spectra of the title compound showed significant absorption of the carbonyl group at 1697 cm1 y (C]O) and the amide group at 3313 cm1 (y NeH), respectively. Vibration bands with the wave numbers of 3055 and 3050 cm1 (y CeH, AreH) and 1553 and 1502 cm1 (y C]C) were observed as the result of the vibration of phenyl ring. The frequencies of 2955, 2918 and 2850 cm1 and 1250 cm1 were assigned to the stretching vibrations (CeH) and (CeC) in undecyl moiety, respectively [32]. The dithiocarbamate compounds exhibit a characteristic band in the range (1580-1450) cm-1 assignable to the y (CeN) [33]. Additional bands at 1431 cm1 (y COeN) and 1207 cm1 (NCS) were observed. The band of 747 cm1 (y C]S) was attributed to thiocarbonyl group (C]S) symmetric stretching vibration [34,35] (Fig. S1). 1 H NMR and 13C NMR spectra for title compound are shown in Figs. S2 and S3 (Supplemental Materials). 1H NMR spectra exhibits
organic solvent (THF, CH3CN and DMSO) in the range of 300e600 nm (Fig. 2), where. two bands were observed. The highdensity bands at 340, 344 and 348 nm for THF, CH3CN and DMSO solvents, respectively, are due to the transition p /p * of the nitrogen-carbon-sulfur (-N-C]S) group on dithiocarbamate moiety conjugated with benzoyl. It also appears as a shoulder on the transition n/p* localized on sulfur connected with undecyl moiety observed at 408, 411 and 415 nm. Optical band gaps (Eg, eV) value from the electronic absorption spectra of the title compound in different solvents were calculated for these transitions and the optical energy were determined from the (ahy)2 versus photon energy (hy) graph using Tauc equation [36], where a is the absorption coefficient (Fig. 3). From the value of Tauc equation, for the title compound in THF, CH3CN and DMSO, the band gaps corresponding to n-p* transitions were calculated 3.59, 3.55 and 3.51 eV, respectively. DFT (B3LYP) calculations and energy levels of the HOMO-1, HOMO and LUMO, LUMOþ1 orbitals was used for determine the low-lying excited states of compound [37,38]. Energy difference HOMO-1, HOMO and LUMO, LUMOþ1 were calculated as 6.5769, 6.2841 and 2.2201, 1.1649 eV, respectively (Fig. 4). Large HOMOLUMO gap energy value of 4.064 eV indicates that the title compound is in steady state. Fig. 4 also showed that the electronic density on the HOMO of the title compound was localized primarily on dithiocarbamate skeleton and carbonyl group, whereas the LUMO orbital of it was localized on dithiocarbamate skeleton along the phenyl ring and its amide group due to intramolecular charge transfer. Energy level of LUMO, which is related to the electron affinity, implies that the title compound is susceptible to nucleophilic attacks [39].
all expected resonances for (CeOeNH) and (CeSeCH2) groups at 12.65 ppm and 3.20 ppm, respectively. The 1H NMR signal for NeH proton of amide or thioureide moiety due to the resonance with the carbonyl (C]O) and thiocarbonyl (C]S) groups shifted downfield to about 12.65 ppm, while that NeH appeared at about ~8.00 ppm. Three signals were appeared at 7.53 (d, 2H), 7.66 (m, 1H) and 7.94 (d, 2H) for phenyl protons. In addition, the title compound has an undecyl moiety and aliphatic protons were assigned at 1.68 (2H, m), 1.40 (2H, m) 1.25 (16 H, m) and 0.86 (3H, t) ppm. In the 13C NMR spectra of the title compound, aromatic proton signals were appeared in the region 133.0, 131.8, 128.7 and 128.4 ppm for phenyl moiety. Functional groups in the structure of aroyl dithiocarbamate derivative were confirmed with at 204.6 d(C]S), 165.3 d(C]O), 35.9 d(SeCH2), 13.9 ppm d(CH3) and (CH2)n) within range of d (31.3e22.1) ppm for title compound, respectively (Scheme 2). 3.2. Electronic spectral studies and HOMO-LUMO analysis High chemical reactivity, more polarizability and the transfer of charge within a molecule are associated with the frontier orbital gap (i.e., energy gap between HOMO and LUMO). The UVeVis spectra of the title compound were recorded in different polarity
3
Fig. 2. UVevis spectra of title compound in THF, CH3CN and DMSO solvents.
Scheme 2. 1H and 13C NMR chemical shifts of the title compound in DMSO‑d6.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
4
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Fig. 5. Molecular electrostatic potential map calculated at B3LYP/6-311þþG (d,p)level for title compound.
Fig. 3. A plot of (ahy)2 versus photon energy (hy) of the title compound in THF, CH3CN and DMSO solvents, a: the absorption coefficient.
3.3. Molecular electrostatic potential (MEP) Molecular electrostatic potential is used for relative reactivates toward electrophilic attack and nucleophilic reactions, for a molecule, plays an important role in determining the electron acceptor and donor sites. MEP also shows the electron cloud distributions for hydrophilic and hydrophobic groups of a molecule. MEP was assessed using the B3LYP/6-311G (d,p) method to investigate the reactive sites of title compound (Fig. 5). In MEP surface, different colors are represented by different values of the electrostatic
potential: red and blue represent the regions of the most negative and positive electrostatic potential whereas green represent the regions of zero potential. As seen in Fig. 5, the negative regions (from red to yellow) are placed around the oxygen and sulfur atoms and it is shown the polar head (hydrophilic) such as dithiocarbamate, carbonyl group. The less positive regions (greenish) are placed around all aliphatic and aromatic carbon and hydrogen atoms and it is shown the long nonpolar groups (hydrophobic) of phenyl and undecyl moiety. These calculations predict that hydrogen bonds are located on medium region of molecule. 3.4. X-ray properties N-Benzoyl-S-(undecyl)-dithiocarbamate is crystallized in the triclinic form with space group P-1 by two symmetric molecules in asymmetric unit with Z ¼ 4 in the unit cell. The title compound consists of dithiocarbamate, carbonyl group, phenyl ring and its amide group and contains an undecyl moiety as hydrophobic group. Molecular packing diagrams of the title compound are displaced along a-axis in Fig. 6. Because of the functional groups of the
Fig. 4. Frontier molecular orbitals diagram for the title compound.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
5
Table 1 Crystal data, data collection and refinement parameters for the title compound. Crystal data Chemical formula Mr Crystal system, space group Temperature (K) a, b, c (Å)
a, b, g ( ) V (Å3) Z Radiation type No. of reflections for cell measurement q range ( ) for cell measurement m (mm1) Crystal shape Crystal size (mm) Data collection Diffractometer Absorption correction Tmin, Tmax No. of measured, independent and observed [I > 2s(I)] reflections Rint (sin q/l)max (Å1) Refinement R [F2 > 2s(F2)], wR (F2), S No. of reflections No. of parameters H-atom treatment
(D/s)max Drmax, Drmin (e Å3)
C19H28NOS2 350.54 Triclinic, P-1 296 4.2417 (8), 20.010 (4), 27.959 (6) 82.422 (6), 86.478 (6), 84.577 (6) 2338.9 (8) 4 MoKa 9907 3.0e28.1 0.23 Block 0.19 0.17 0.14
BrukerAPEX-II CCD Multi-scan 0.676, 0.746 87167, 9171, 5101 0.070 0.617
0.156, 0.526, 1.31 9171 416 H-atom parameters constrained w ¼ 1/[s2(Fo2) þ (0.1249P) 2 þ 30.6399P] where P ¼ (Fo2 þ 2Fc2)/3 0.341 1.42, 0.43
Computer programs: BrukerAPEX2, BrukerSAINT, SHELXT 2014/4 (Sheldrick, 2014), SHELXL2016/6 (Sheldrick, 2016).
3.5. Thermodynamic properties
Fig. 6. A partial view of the crystal packing of title compound, showing the linear arrangement built from (a) NeH …. S- and (b) CeH …. S- hydrogen bonds. The hydrogen bonds are shown as dotted lines.
title compound, b-axis and c-axis (20.010 and 27.959 Å, respectively) are larger than the a-axis (4.2417 Å) in the crystal dimensions. Crystallographic data and the details of X-ray diffraction study of the title compound is shown in Table 1, whereas selected bond lengths and bond angles is compiled in Table 2. The benzamide moiety of the title compound has a closely planar configuration and the maximum deviation from the meanplane belongs to O1 oxygen atom with 0.267 Å. The undecyl group twists slightly due to the consistent of dithiocarbamate group. The torsion angle values about this twist are 4.4 on C7/N1/ C8/S1 atom group and 178.7 on N1/C8/S1/C9 atom group. Detailed investigation of molecular packing of the molecule indicates the intermolecular hydrogen bond C1eH1/S4i and C24eH24/S2v generates R22 (10) motifs. In addition, intermolecular hydrogen bonds occur between N1eH111/S4ii and 2 iv N2eH222/S2 atoms to form R2 (7) rings.
The statistically thermodynamic parameters such as standard heat capacity of constant pressure (Cp), enthalpy (H) and entropy (S) were calculated using the B3LYP/6-311G (d,p) method in ground state by increasing from 100 K to 900 K in gas phase. The results are shown in Fig. 7 and Table S1. Fig. 7 shows that Cp, S and the H of the title compound increase from 100 K to 900 K, which is caused by the rise of molecular vibration intensity with the increasing temperature [40]. Quadratic formulas were used to fit the correlation equations between different parameters heat capacity, enthalpy, entropy and temperature, R being the corresponding fitting factor (R2) for these thermodynamic parameters. The corresponding fitting equations for title compound are as presented below:
C p;m ¼ 11; 3366 þ 0; 3045 T 1; 4282x105 T2 ðR2 ¼ 0; 9973
Sm ¼ 56; 5472 þ 0; 2633 T 5; 5547x105 T2 ðR2 ¼ 0; 9991
DH0m ¼ 3; 95915 þ 0; 0309 T þ 6; 2975x105 T2 ðR2 ¼ 0; 9978
The thermogravimetric measurements and calculations clearly show that the high temperature phase of title compound is
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
6
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
Table 2 Hydrogen-bond geometry (Å, ). DdH$$$A
DdH
H$$$A
D$$$A
C1eH1/S4i N1eH111/S4ii C19eH19A$$$O2iii N2eH222/S2iv C24eH24/S2v C38eH38A$$$O1vi
0.93 0.86 0.96 0.86 0.93 0.96
2.89 2.70 2.77 2.72 2.91 2.81
3.777 3.534 3.647 3.546 3.792 3.665
DdH$$$A (14) (9) (18) (9) (14) (19)
160.5 162.6 151.5 162.5 158.9 148.3
Symmetrycodes: (i) xþ1, y, z; (ii) xþ2, y, z; (iii) x, y1, z; (iv) x2, y, z; (v) x1, y, z; (vi) x, yþ1, z.
Fig. 8. Thermo analytical (TG/DTA) curves of title compound.
Fig. 7. Correlation graph of calculated thermodynamic properties and temperatures for the title compound.
thermally unstable and final decomposition stars at about 200 C for compound [41,42]. All the theoretical parameters can be helpful information for the new synthesis of like title compound or thiocarbamate derivatives.
Fig. 9. Differential scanning calorimetric graphs of title compound.
is thermally stable up to 184.08 C [43]. 3.6. Thermal analysis 4. Conclusions Fig. 8 shows the TG and DTA curves of obtained crystal of the title compound. The DTA curve showed three endothermal peaks. The first sharp peak at 53.2 C is a significant endothermic peak corresponding to the melting of the crystal. At the melting point no weight loss was observed in the TG curve. The first decomposition step of the compound was observed in the temperature range 198.1e228.0 C and the approximate weight loss was 17.53%. Above this temperature, a second weight loss of 71.02% (Calc. 70.14%) occurred in the range 292e331 C which indicates elimination of C12H24NS2$. The second decomposition step, which also includes the first-thermal degradation step is observed at Tmax ¼ 318.5 C for the DTA peak. After this at around 458 C, decomposition was about 100% leaving no residue in the crucible. The DSC curve of the compound was obtained at a heating rate of 10 C/min under argon atmosphere (Fig. 9). The melting point of the compound as can be seen in the DSC curve was observed as a sharp endothermic peak at about 50.33 C and the positive enthalpy value of 105.14 J g-1 at 50.33 C can be attributed to the energy absorbed during the (endothermic) melting process. The lower point and sharpness of DSC curve indicated that the compound had good crystallinity and high purity. The degradation of the compound related with the endothermic peak in the DSC curve was observed at 200.45 C with DН ¼ 99.12 J g-1. The DSC curve clearly indicates that the compound
Synthesis, experimental and theoretical characterization of a new dithiocarbamate molecule, called N-benzoyl-S-(undecyl)dithiocarbamate was reported. X-ray analysis revealed that the title compound crystallizes in the triclinic space group P-1, with cell parameters a ¼ 4.2417 (8) Å, b ¼ 20.010 (4) Å, c ¼ 27.959 (6) Å, a ¼ 82.422 (6) , b ¼ 86.478 (6) , g ¼ 84.577 (6) and V ¼ 2338.9 Å3. The presence of intermolecular N…HS, N/HO, C/HO, and C/HN hydrogen bond interactions was confirmed via experimental and theoretical studies. Molecular electrostatic potential surface parameter of the title compound was good agreement with the predicted hydrogen bonds. The energy gap between the HOMOLUMO orbital for the title compound was calculated to be 4.064 eV. Electronic absorption spectra for the title compound was predicted from DFT calculations and were compared to experimental UVevisible spectrum, which showed the presence of n- p* and p- p* bands. The low melting point of the title compound is predicted to be related to the large unit cell and the weak intermolecular H-bonding in the crystal structure of the molecule. TG/ DTA and DSC curves showed that the compound melted at a low temperature (53.2 and 50.33 C, respectively). DTA of the title compound showed that the decomposition was taken place in two steps. Calculated frontier molecular orbital energies were
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
compared with the optical band gaps (Eg, eV) value from electronic absorption spectra. Hydrophilic and hydrophobic groups of the compound were also predicted from the molecular electrostatic potential. We hope that the synthesis, crystallographic and spectroscopic characterization and DFT studies of N-Benzoyl-S-(undecyl)-dithiocarbamate will be helpful for the synthesis of new dithiocarbamates. Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work “N-Benzoyl-S-(undecyl)-dithiocarbamate: synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies” reported in this paper. Appendix A. Supplementary data Supplementary data associated with this article can be found in the online version, at https://doi.org/10.1016/j.molstruc.2019. 127414. These data include MOL file and InChiKeys of the most important compounds described in this article. Author contributions Fatma AYDIN: Investigation;Conducting a research and investigation process, specifically performing the experiments, or data/ evidence collection, Visualization; Preparation (Experimental section), creation and presentation of the published work, specifically visualization/ data presentation, Writing- Review & Editing; Preparation, creation and presentation of the published work by those from the original research group, commentary or revision e including pre-or postpublication stages; N. Burcu ARSLAN: Using Software Programming (DFT with B3LYP/6-311G(d,p) level), X-ray analysis and molecular structure determination; Kadir ASLAN: Review & Editing;Preparation, creation and presentation of the published work, Resources; Provision of study materials, reagents, materials, Funding acquisition;Acquisition of the financial support for the project leading to this publication. References [1] G. Eng, X. Song, Q. Duong, D. Strickman, J. Glass, L. May, Synthesis, structure characterization and insecticidal activity of some triorganotin dithiocarbamates, Appl. Organomet. Chem. 17 (4) (2003) 218e225. [2] M. Mulkey, The Grouping of a Series of Dithiocarbamate Pesticides Based on a Common Mechanism of Toxicity. US Environmental Protection Agency, Office of Pesticide Programs, Office of Prevention, Pesticides and Toxic Substances, SAP Report, Washington, DC, 2001. [3] H. Kidd, D. Hartley, Pesticide index: an index of chemical, common and trade names of pesticides and related crop protection products, R. Soc. Chem. (1988). [4] S. Hurt, J. Ollinger, G. Arce, Q. Bui, A.J. Tobia, B. van Ravenswaay, Dialkyldithiocarbamates (EBDCs), Hayes’ Handbook of Pesticide Toxicology, Elsevier, 2010, pp. 1689e1710. [5] N.L. Botha, P.A. Ajibade, A.O. Ashafa, Synthesis, spectroscopic characterization, antifungal and antibacterial studies of copper (II) dithiocarbamate complexes, J. Pharm. Sci. Res. 10 (8) (2018) 2111e2114. [6] A.A. Aly, A.B. Brown, T.M. Bedair, E.A. Ishak, Dithiocarbamate salts: biological activity, preparation, and utility in organic synthesis, J. Sulfur Chem. 33 (5) (2012) 605e617. [7] F. Aryanasab, A.Z. Halimehjani, M.R. Saidi, Dithiocarbamate as an efficient intermediate for the synthesis of 2-amino-1, 3, 4-thiadiazoles in water, Tetrahedron Lett. 51 (5) (2010) 790e792. [8] A.Z. Halimehjani, L. Hasani, M.A. Alaei, M.R. Saidi, Dithiocarbamates as an efficient intermediate for the synthesis of 2-(alkylsulfanyl) thiazoles in water, Tetrahedron Lett. 57 (8) (2016) 883e886. [9] E.R. Knight, A.R. Cowley, G. Hogarth, J.D. Wilton-Ely, Bifunctional dithiocarbamates: a bridge between coordination chemistry and nanoscale
7
materials, Dalton Trans. 4 (2009) 607e609. [10] R.M. Mariano, H.M. da Costa, M.R. Oliveira, M.M. Rubinger, L.L. Visconte, The behavior of dithiocarbimate derivative as safety accelerator of natural rubber compounds, J. Appl. Polym. Sci. 110 (4) (2008) 1938e1944. [11] M.N. Alam, S.K. Mandal, S.C. Debnath, Effect of zinc dithiocarbamates and thiazole-based accelerators on the vulcanization of natural rubber, Rubber Chem. Technol. 85 (1) (2012) 120e131. [12] T.W. Green, P.G. Wuts, Protective Groups in Organic Synthesis, Wiley, New York, 1999. [13] P. Morf, F. Raimondi, H.-G. Nothofer, B. Schnyder, A. Yasuda, J.M. Wessels, T.A. Jung, Dithiocarbamates: functional and versatile linkers for the formation of self-assembled monolayers, Langmuir 22 (2) (2006) 658e663. [14] D. Zhang, J. Chen, Y. Liang, H. Zhou, Facile synthesis of novel ionic liquids containing dithiocarbamate, Synth. Commun. 35 (4) (2005) 521e526. [15] P.J. Heard, Main group dithiocarbamate complexes, Prog. Inorg. Chem. 53 (2005) 1e69. [16] A.R. Ipeaiyeda, A.J. Odola, Co-precipitation of Ni, Cr, Mn, Pb and Zn in industrial wastewater and sediment samples with copper (II) cyclohexylmethyldithiocarbamate for their flame atomic absorption spectrometric determination, Water Sci. Technol. 66 (1) (2012) 105e112. [17] X. Jing, F. Liu, X. Yang, P. Ling, L. Li, C. Long, A. Li, Adsorption performances and mechanisms of the newly synthesized N, N0 -di (carboxymethyl) dithiocarbamate chelating resin toward divalent heavy metal ions from aqueous media, J. Hazard Mater. 167 (1e3) (2009) 589e596. [18] D. Buac, S. Schmitt, G. Ventro, F.R. Kona, Q.P. Dou, Dithiocarbamate-based coordination compounds as potent proteasome inhibitors in human cancer cells, Mini Rev. Med. Chem. 12 (12) (2012) 1193e1201. [19] W. Huang, Y. Ding, Y. Miao, M.Z. Liu, Y. Li, G.F. Yang, Synthesis and antitumor activity of novel dithiocarbamate substituted chromones, Eur. J. Med. Chem. 44 (9) (2009) 3687e3696. [20] R.D. Li, H.L. Wang, Y.B. Li, Z.Q. Wang, X. Wang, Y.T. Wang, Z.M. Ge, R.T. Li, Discovery and optimization of novel dual dithiocarbamates as potent anticancer agents, Eur. J. Med. Chem. 93 (2015) 381e391. [21] C. Marzano, L. Ronconi, F. Chiara, M.C. Giron, I. Faustinelli, P. Cristofori, A. Trevisan, D. Fregona, Gold (III)-dithiocarbamato anticancer agents: activity, toxicology and histopathological studies in rodents, Int. J. Cancer 129 (2) (2011) 487e496. [22] D. Halls, The properties of dithiocarbamates a review, Microchimica Acta 57 (1) (1969) 62e77. [23] C. Giridhar, S. Kanchi, T. Niranjan, K. Bisetty, N. Naidu, Sensitive determination of nickel (II) using catalytic hydrogen wave in the presence of dithiocarbamates at DME, J, Environ. Anal. Chem. 1 (108) (2014) 2. [24] S. Kanchi, M. Sulochana, K.B. Naidu, K. Saraswathi, N.V. Naidu, Dithiocarbamates as a sensitive electroanalytical reagent: determination of chromium by catalytic hydrogen wave at dme in water systems and vegetables, Food Anal. Methods 4 (4) (2011) 453e464. [25] L. Ronconi, D. Aldinucci, Q. Ping Dou, D. Fregona, Latest insights into the anticancer activity of gold (III)-dithiocarbamato complexes, Anti Cancer Agents Med. Chem. 10 (4) (2010) 283e292. [26] S.N. Mangasuli, K.M. Hosamani, P.B. Managutti, Synthesis of novel coumarin derivatives bearing dithiocarbamate moiety: an approach to microwave, molecular docking, Hirshfeld surface analysis, DFT studies and potent antimicrobial agents, J. Mol. Struct. (2019). [27] G. Sheldrick, SHELXS-97: Program for the Solution of Crystal Structures, 1997, There is no corresponding record for this reference, University of Gottingen, Germany, 1988. [28] G. Sheldrick, SHELXL-97, Program for Crystal Structure Refinement, 1997, There is no corresponding record for this reference, University of Goettingen, Germany, 2008. [29] A.D. Becke, Density-functional thermochemistry .3. The role of exact exchange, J. Chem. Phys. 98 (7) (1993) 5648e5652. [30] R. Ditchfield, W.J. Hehre, J.A. Pople, Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules, J. Chem. Phys. 54 (2) (1971) 724e728. [31] M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. Petersson, GAUSSIAN09. Revision E. 01, Gaussian Inc., Wallingford, CT, USA, 2009. [32] J. Coates, Interpretation of Infrared Spectra, a Practical Approach, Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation, 2006. [33] V. Alverdi, L. Giovagnini, C. Marzano, R. Seraglia, F. Bettio, S. Sitran, R. Graziani, D. Fregona, Characterization studies and cytotoxicity assays of Pt (II) and Pd (II) dithiocarbamate complexes by means of FT-IR, NMR spectroscopy and mass spectrometry, J. Inorg. Biochem. 98 (6) (2004) 1117e1128. [34] N.B. Arslan, C. Kazak, F. Aydın, Experimental and theoretical investigation of N-(4-nitrobenzoyl)-S-(cyclohexyl)-dithiocarbamate, N-(4-nitrobenzoyl)-Sbenzyldithiocarbamate, J. Mol. Struct. 1155 (2018) 646e653. € [35] F. Aydın, N.B. Arslan, N. Ozdemir, Tautomerism in 4-chlorophenyl benzoylcarbamodithioate: experimental and DFT study, J. Mol. Struct. 1137 (2017) 233e239. [36] J. Tauc, R. Grigorovici, A. Vancu, Optical properties and electronic structure of amorphous germanium, Phys. Status Solidi 15 (2) (1966) 627e637. [37] M. Haroon, M. Khalid, T. Akhtar, M.N. Tahir, M.U. Khan, M. Saleem, R. Jawaria, Synthesis, spectroscopic, SC-XRD characterizations and DFT based studies of ethyl2-(substituted-(2-benzylidenehydrazinyl)) thiazole-4-carboxylate
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414
8
F. Aydın et al. / Journal of Molecular Structure xxx (xxxx) xxx
derivatives, J. Mol. Struct. 1187 (2019) 164e171. [38] R. Jawaria, M. Hussain, M. Khalid, M.U. Khan, M.N. Tahir, M.M. Naseer, A.A.C. Braga, Z. Shafiq, Synthesis, crystal structure analysis, spectral characterization and nonlinear optical exploration of potent thiosemicarbazones based compounds: a DFT refine experimental study, Inorg. Chim. Acta 486 (2019) 162e171. [39] T. Helgaker, P. Jorgensen, J. Olsen, Molecular Electronic-Structure Theory, John Wiley & Sons, 2014. [40] J.B. Ott, J. Boerio-Goates, Chemical Thermodynamics: Advanced Applications: Advanced Applications, Elsevier, 2000. ski, [41] M. Wojtas, A. Bil, R. Jakubas, A. Ga˛ gor, A. Pietraszko, O. Czupin
ski, D. Isakov, Organic-inorganic compounds with strong nonlinear Z. Tylczyn optical properties based on 2, 4, 6-trimethylpyridinium and tetrahedral BF 4 networks, Phys. Rev. B 83 (14) (2011) 144103. [42] M. Wojtas, A. Bil, A. Gagor, W. Medycki, A.L. Kholkin, Phase stability and dynamics of hybrid organiceinorganic crystals [(CH 3) 3 PH][SbCl 4] and [(CH 3) 3 PH][SbBr 4]: a computational and NMR approach, CrystEngComm 18 (14) (2016) 2413e2424. [43] S.B. Kalia, R. Puri, A. Thakur, J. Christopher, Synthesis, characterization and thermal degradation studies on some oxovanadium (IV) carbodithioates, J. Therm. Anal. Calorim. 119 (3) (2015) 1619e1632.
Please cite this article as: F. Aydın et al., N-Benzoyl-S-(undecyl)-dithiocarbamate: Synthesis, characterization, X-ray single crystal structure, thermal behavior and computational studies, Journal of Molecular Structure, https://doi.org/10.1016/j.molstruc.2019.127414