Computational Sciences Congress, Amasya, TURKEY26-28 October 2018

Investigation of structural and spectroscopic properties of C12H12N2SCH3OH molecule by using theoretical methods

Name Surname 1,*

1Department of Physics, Faculty of Arts and Sciences, Amasya University, 05100, Amasya, Turkey*aaaaaaa@amasya.edu.tr

Abstract— In this work, we have investigated Schiff-bases compound due to the chemical important. The Schiff-bases compound C12H12N2SCH3OH molecular geometry, vibrational frequencies and molecular electrostatic potential (MEP) in the ground state were investigated by theoretical calculations. The calculated results show that the optimized geometry can well reproduce the crystal structure, and the theoretical vibrational frequencies and chemical shift values show good agreement with experimental values.

Keywords— Schiff base; crystal structure; hydrogen bonding, FT-IR spectra; DFT

I. INTRODUCTION

Compounds that contain N- and S-donor atoms have exhibited antibacterial properties. Besides this type N,S-compounds can be useful ligands to form transition metal complexesyridine derivatives are involved in bioactivities with applications in pharmaceutical drugs and agricultural products [1]. They also reported the X-ray structure of 2-methylsulfanyl-N-[(1H-pyrrol-2-yl)methylidene]aniline methanol mono solvate which features an aryl methyl thioether group and an imino-2-pyrrole motif. The imine pendant prevents the reversible formation of the benzothiazoline, a transformation that was evident in the structure. Firstly they reported that featured a free amino group and was bonded to a palladium centre [2]. In experimental literature, title molecule was synthesed [3]. .Basuli et. al[4] reported 1H and 13C NMR data and they rerults were aggrement Richards et. al. results[1]. In addition to some experimental compound data such as FT–IR, we now computed some theoretical calculations (structural characteristics, vibrational spectroscopic analysis and molecular electrostatic potential (MEP). Therefore, properties of the title compound have been studied for the first time theoretically.

II. MATERIAL METHODS

The geometry optimizations of the title compound were calculated by gradient corrected density functional theory (DFT) method with a hybrid functional B3LYP and HF level of theory using Gaussian 09 [5] program package with the 6-311++G (d,p) basis sets. The molecular structure, vibrational and electronic absorption spectra were visualized by GaussView 05 [6] program. The harmonic vibrational frequencies were calculated at the same level of theory for the optimized structure and the obtained frequencies were scaled by 0.961 (B3LYP) and 0.892 (HF). Also, the electronic properties, such as MEP properties of the title molecule are also computed.

III. RESULTS AND DISCUSSION

A. Optimized geometriesThe optimized parameters (bond lengths, bond angles and

dihedral angles) of the title compound have been obtained using the B3LYP and HF/(6-311++G(d,p)) methods in gas phase(see Fig. 1).

Fig. 1 (top) 2-methylsulfanyl-N-[(1H-pyrrol-2-yl) methylidene] aniline molecule and anearby solvent methanol molecule[1]; (middle, down) The theoretical geometric structure of title (with B3LYP, HF).

Then a comparison was made between the experimental and the calculated geometry parameters, see Table 1. As seen from Table 1, most of the optimized theoretical bond lengths agree with each other while experimental bond lengths is slightly shorter than them. Similar results also observed both bond angles and dihedral angles. From the Tabke 1, we see that the calculated bond angles as much torsion angles are in agreement with the each other.

We have also compaired optimized energies: B3LYP(-29609,84 eV) < HF(-29471,05 eV). According to these results, it may be concluded that the B3LYP method well reproduce the geometry of the title compound.

TABLE I

Computational Sciences Congress, Amasya, TURKEY26-28 October 2018

Selected molecular structure parameter

ParametersExp. [1]

CalculatedB3LYP HF

Bond Angles (Å)S—C1 1.7586 (13) 1.78 1.78S—C7 1.7968 (14) 1.82 1.81N1—C8 1.2829 (17) 1.29 1.26N2—C9 1.3714 (17) 1.38 1.36N2—H2N 0.884 (18) 1.03 1.00C2—C3 1.3915 (18) 1.40 1.39C9—C10 1.3806 (18) 1.40 1.37O1S—C1S 1.4120 (2) 1.42 1.40O1S—H1SO 0.83 00(3) 0.98 0.94Bond angles (º)C1—S—C7 103.05 (7) 102.85 103.73C8—N1—C2 119.01 (12) 118.93 119.75C12—N2—C9 109.42 (11) 109.41 109.23C6—C1—S 124.24 (10) 124.20 123.78N1—C8—C9 122.40 (13) 125.80 123.39N2—C9—C10 107.17 (12) 107.21 107.97Torsion angles (º)C7—S—C1—C6 −7.76 (13) -8.05 -10.52C7—S—C1—C2 172.43 (10) 173.71 170.99C6—C1—C2—N1 177.62 (11) 178.14 178.74S—C1—C2—N1 −2.55 (15) -3.53 -2.71C8—N1—C2—C3 −41.88 (18) -45.66 -46.79N1—C8—C9—N2 −0.60 (2) -3.66 -1.58N1—C8—C9—C10 179.65 (14) 176.27 178.22

B. Vibrational spectraIn order to facilitate assignment of the observed peaks, we

investigated the vibrational frequencies as theoretical.. The compound C12H12N2SCH3OH includes 33 atoms and therefore undergoes 93 normal modes of vibrations. Among the 93 normal modes of vibrations, 61 modes of vibrations are in plane and remaining 32 modes are out of plane. In IR spectra, there are some characteristic stretching vibrations: O-H, N-H, C-N, C-H, C=N, C=C, C-C, O-CH3 and S-CH3 groups.

The N–H stretching vibrations generally give rise to bands at 3500–3300 cm_1 [7-9]. The very weak band observed in the IR spectrum at 3377cm-1 (B3LYP) and 3013cm-1 (HF) are assigned to the N–H stretching mode. The C–N stretching vibrations are observed in 1266-1382 cm-1 [10]. The strong bands located at 1381 and 1182 cm-1 for B3LYP (1232 and 1054 cm-1 for HF) are assigned to the C–N in-plane bending mode. The medium intensity band observed at at 851 and 643 cm-1 for B3LYP (759 and 573 cm-1 for HF) in the IR spectrum are assigned to the C–N out-of plane bending mode. The aromatic C−H stretching vibrations are generally found between 3000 and 3100 cm−1, which is the characteristic region for the ready identification of v(CH) vibrations in plane [11]. The asymmetric C–H stretching vibration are observed at 3042 (2714) cm-1 while the CH stretching vibrations is assigned to strong bands at 3130 (2792) cm−1 for B3LYP

(HF). The substitution sensitive CH in plane bending vibrations are assigned to the some strong bands, in the region at 1437-1021(1282-911) cm−1 and also a strong IR bands observed CH out-of-plane bending vibrationat at 1306-725(1165-647) cm−1 for B3LYP (HF). Other essential characteristic vibrations of the title compound are O-H, C=N, C-O and CC stretching. Some of these modes, corresponding to the experimental modes, such as C=N and CC stretching were observed to be 1714 and in the region 1280-1625 cm−1

[12, 13]. C=N modes have been calculated at 1594 cm−1 (1422 cm−1) and 1537 cm−1 (1371 cm−1) for B3LYP(HF). Similarly CC modes have observed in the region 1265-1547 cm−1

(1128-1380 cm−1) for B3LYP(HF). All these calculated values are in good agreement with the experimental and theoretical data [1].

C. Molecular electrostatic potentialMolecular electrostatic potential (MEP) mapping is very

useful descriptor for predicting favorable sites of electrophilic and nucleophilic reactions or revealing preferential sites of electrostatically dominated noncovalent interactions [14]. Red-electron rich or partially negative charge regions of MEP were related to electrophilic reactivity and the blue-electron deficient or partially positive charge regions of MEP were related to nucleophilic reactivity shown in Fig. 2.

Fig. 2. Molecular electrostatic potential map of molecule.

In the both B3LYP and HF method, the MEP indicate the most electron rich centre were found around the O, S and N atom, -0.045, -0.033 and -0.022 a.u value, respectively. On the other hand, a maximum positive regions are localized on the H atoms (around +0.020 a.u. for both methods). These sites give information concerning the region from where the compound can have metallic bonding and intermolecular interactions.

IV. CONCLUSIONS

In this study, we have learned structural, vibrational and MEP properties of this compound due to biological significance have been made in theoreticaly detailed for the first time. The calculated theoretical structural parameters were well agreed with the experimental data; however, the intermolecular interactions have some influences on the molecular geometry in the solid state. FT-IR theoretical spectra analyses show that the predicted vibrational frequencies can be comparable the experimental values. The MEP of compound indicates hydrogen atoms is more positive in the molecule. Besides the O atom is more negative than S

Computational Sciences Congress, Amasya, TURKEY26-28 October 2018

and N atoms in title molecule. All calculations were computed B3LYP and HF method and comparable each other.

ACKNOWLEDGMENT

This work was supported by Amasya University Research Fun for financial support through Project number FMB-BAP 15-092.

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