Vibrational spectroscopic (FT-IR, FT-Raman) studies, Hirshfeld surfaces analysis, and quantum chemical calculations of m-acetotoluidide and m-thioacetotoluidide

Accepted Manuscript Vibrational spectroscopic (FT-IR, FT-Raman) studies, Hirshfeld surfaces analysis, and quantum chemical calculations of m-acetotoluidide and m-thioacetotoluidide Wioleta Edyta Śmiszek-Lindert, Elżbieta Chełmecka, Stefan Góralczyk, Marian Kaczmarek PII:

S0022-2860(16)30902-4

DOI:

10.1016/j.molstruc.2016.08.072

Reference:

MOLSTR 22898

To appear in:

Journal of Molecular Structure

Received Date: 5 May 2016 Revised Date:

24 August 2016

Accepted Date: 26 August 2016

Please cite this article as: W.E. Śmiszek-Lindert, E. Chełmecka, S. Góralczyk, M. Kaczmarek, Vibrational spectroscopic (FT-IR, FT-Raman) studies, Hirshfeld surfaces analysis, and quantum chemical calculations of m-acetotoluidide and m-thioacetotoluidide, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.08.072. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT Vibrational spectroscopic (FT-IR, FT-Raman) studies, Hirshfeld surfaces analysis, and quantum chemical calculations of m-acetotoluidide and m-thioacetotoluidide Wioleta Edyta Śmiszek-Linderta1, Elżbieta Chełmeckab, Stefan Góralczyka, Marian Kaczmareka Building Materials Technologies Group, Institute of Mechanized Construction & Rock Mining, W. Korfantego

193A Street, 40-157 Katowice, Poland b

RI PT

a

School of Pharmacy with Division of Laboratory Medicine, Department of Statistics, Medical University of

Silesia, 30 Ostrogórska Street, 41-200 Sosnowiec, Poland

SC

Abstract

M AN U

Theoretical calculations of the m-acetotoluidide and m-thioacetotoluidide isolated molecules were performed by using density functional theory (DFT) method at B3LYP/6-311++G(d,p) and B3LYP/6-311++G(3df,2pd) basis set levels. The Hirshfeld surfaces analysis and FT-IR and FT-Raman spectroscopy studies have been reported. The geometrical parameters of the title amide and thioamide are in a good agreement with the XRD experiment. The vibrational frequencies were calculated and scaled, and subsequently values have been compared with the

TE D

experimental Infrared and Raman spectra. The observed and calculated frequencies are found to be in good agreement. The analysis of the Hirshfeld surface has been well correlated to the spectroscopic studies. Additionally, the highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital

EP

energy (ELUMO) and the energy gap between EHOMO and ELUMO (∆EHOMO–LUMO) have been calculated.

AC C

Keywords: Vibrational spectra, Hydrogen bond, Hirshfeld surfaces, DFT, HOMO-LUMO

*Corresponding author. E-mail address: [email protected], [email protected] (W.E. Śmiszek-Lindert)

ACCEPTED MANUSCRIPT 1. Introduction An aromatic amides are derivatives of carboxylic acid, which containing the functional group –CO–NH–. The review of the literature shows that amides and their derivatives play very important and specific role in the various areas such as medicine or pharmacology [1-4], biology, and even building construction [5]. The amide group is a significant functional group in organic chemistry creates the linkage in proteins, polypeptides, as well

RI PT

as synthetic polymers. Proteins and peptides (biological molecules) play a vital role in the natural biological processes [6]. In the case of chemistry, the interest in amides is very high among chemists, particularly secondary amides, which are preferred models for in-depth researches of the conformational isomerism of the – CO–NH grouping [7]. Aromatic amides are also used for the synthesis of the technological materials. Thioamide

SC

is formed by the substitute of the carbonyl oxygen by sulphur in amide bond (–CS–NH–). The synthesis of the

of thiopeptide were extensively studied [8].

M AN U

biologically important thioamide-containing peptides are widely execute, as well the conformational properties

Inter- and intramolecular hydrogen bonds are the next aspect related to the molecular structure of amides and thioamides, because these interactions play an important and often key role to stabilize molecular structure, as well as in determine their spectral properties. The characteristic interactions between –CO–NH group which is basic structural element in peptides and proteins set the conformational stability and binding

TE D

affinity of their crystal packing. The nature of the hydrogen bond in amides and thioamides is extensively investigated experimentally and theoretically for many years [9, 10]. The quantitative information on the hydrogen bonding abilities of thioamide and amide can help understand the biochemical processes.

EP

In the present work, the spectroscopic studies (FT-IR and FT-Raman), intermolecular interactions in the crystal structure via Hirshfeld surfaces analysis, theoretical calculations (DFT) of the geometries, harmonic

AC C

vibrational frequencies and molecular orbitals (HOMO–LUMO) of amide: m-acetotoluidide and thioamide: mthioacetotoluidide have been presented.

2. Experimental

2.1. Materials and physical measurements m-Acetotoluidide (1) has been obtained commercially (Sigma-Aldrich), and used without further purification. Its crystal structure has been determined by Śmiszek-Lindert et al. in 2008 [11]. In turn, the m-thioacetotoluidide (2)

1

ACCEPTED MANUSCRIPT has been synthesized according to the method described previously [12]. The crystal structure of 2 has been also determined by the authors mentioned above [12]. The IR spectra of 1 and 2 powdered in KBr pellets and the spectra of single crystals were recorded on a FT-IR Nicolet Magna 560 spectrometer (at 2 cm-1 resolution; the spectra were collected in the spectral range of 4000-400 cm-1) at two temperatures, i.e. at room temperature and at liquid nitrogen temperature. Raman spectra

RI PT

of polycrystalline, commercial samples of the m-acetotoluidide and m-thioacetotoluidide were measured at room temperature on a Bio-Rad FTS-175C FT-IR spectrometer at 1 cm-1 resolution. The FT-Raman spectrum has been measured in the range 4000-120 cm-1.

SC

The single crystals of 1 and 2 were obtained by cooling the molten substance, between two closely placed CaF2 plates. The details of experimental techniques of the preparing and the selection of single crystals

2.2. Hirshfeld Surface (HS) analysis

M AN U

have been already described previously [13].

In order to visualize and analyze intermolecular contacts in the crystal lattice of both compounds, the CrystalExplorer program [14] has been used, which accepts a structure input file in the CIF format (Crystallographic Information File). This method is increasingly popular in a discussion of intermolecular

TE D

interactions in a molecular crystals, and is based on the calculation of the promolecular electron density both crystal and in gas phase. Directions and strengths of intermolecular interactions within the crystal of the macetotoluidide and m-thioacetotoluidide were mapped onto the HS using the descriptor dnorm (normalized contact distance; dnorm is a ratio encompassing the distances of any surface point to the nearby interior (di) and exterior

EP

(de) atoms and the van der Waals radii (rvdW) of the atoms). The value of the dnorm is negative or positive when intermolecular contacts are shorter/longer than vdW separations [15]. Besides, the CrystalExplorer program has

AC C

been used to obtain the 2D fingerprint plots (FPs), which are generated, based on the de and di distances. 2-D fingerprint plots are derived from the HS by plotting the fraction of points on the surface as a function of the pair (di, de). Each point on the standard 2D graph represents a bin formed by discrete intervals of di and de (0.01x0.01 Å), and the points are colored as a function of the fraction of surface points in that bin (essentially a pixel), with a range from blue (few points) through green (moderate fraction) to red (highest fraction) [16]. The 2-D fingerprint plots have been also used for visualizing, exploring and quantifying intermolecular interactions in the crystal lattice of the analyzed compounds. Besides, it should be pointed that these plots are visual representation of all intermolecular contacts simultaneously, and are unique and particular for a given crystal structure. 2.3. Quantum chemical calculations 2

ACCEPTED MANUSCRIPT The quantum chemical calculations were performed by means of the Gaussian 09 [17] software package, using hybrid density functional theory (DFT) at the B3LYP (Becke three – parameter hybrid functional combined with Lee-Yang-Parr correlation functional) level and with 6-311++G(d, p) and 6-311++G(3df, 2pd) basis sets for 1 and 2 [18, 19]. The harmonic vibrational frequencies have been calculated at the same level of theory. All the computations have been carried out in gas phase. The initial molecular structure of 1 and 2 compound has been

Results and discussion

SC

3.

RI PT

taken from the X-ray crystallographic data.

3.1 Hirshfeld Surface (HS) analysis

M AN U

The molecular structure of 1 and 2 has been presented in Fig. 1a and c, respectively. In turn, the molecular Hirshfeld surface, which has been mapped over dnorm range from -0.557 to 1.113 Å and -0.404 to 1.199 Å for 1 and 2, respectively, has been illustrated in Fig. 1b and d, respectively. Figures 2a and b show the intermolecular contacts between the molecules compound of 1 and 2, respectively via Hirshfeld surface analysis. Additionally, the fingerprint plots of 1 and 2 have been showed in Fig. 3a to d and 4a to d, respectively. The large circular depressions (deep red; see Fig. 1b and d), which are visible on the front and back

TE D

views of the surface of the analyzed compounds, are indicative of the hydrogen bond contacts (a strong hydrogen bond is characterized by a long spikes). In 1, the H···O intermolecular contacts, comprising 12.9%, appear as a pair of symmetrical large sharp spikes with the shortest distribution points in the fingerprint plots in the region of

EP

di = 1.12 Å, de = 0.78 Å and di = 0.78 Å, de = 1.12 Å for right (bottom area) and left (upper area), respectively (see Fig. 3c). Complementary regions are observable in the 2-D fingerprint plots where one molecule acts as a

AC C

donor (de > di) and the other as an acceptor (de < di) [20]. In the case of 2 (Fig. 4b) the H···S interactions comprise 19.9% of the total Hirshfeld surfaces and also represent two sharp spikes with di + de = ~2.33 Å. The other visible light-white regions in the dnorm surfaces of both compounds are indicative of weaker as well as longer contacts other than hydrogen bonds viz. H···H interactions. In 1, the H···H interactions comprise 59.5% of the total Hirshfeld surface area. Whilst in compound 2 these interactions are characterized by slightly smaller percentage of 56.8% to the total HS in comparison with 1. The 2-D fingerprint plots illustrate a large surface of scattered points; Fig. 3d and 4c. It should be noted that the H···H interactions have significant contribution to the total HS in analyzed amide and thioamide.

3

ACCEPTED MANUSCRIPT Other significant interactions, which have been observed, are H···C contacts. In 1, the H···C/C···H intermolecular interactions comprise 23.7% of the total HS and represent two characteristic wings (di + de = ~3.21 Å; Fig. 3b). Unlike 1, the H···C/C···H interactions are shorter in 2 (di + de = ~2.88 Å), with the smaller percentage of 18.6% to the total HS. The N···H/H···N interactions are less dominant in the crystal structure of the m-acetotoluidide and m-thioacetotoluidide (1.8% and 1.2%, respectively). The sum of di + de = ~3.21 Å and di +

RI PT

de = ~3.08 Å for 1 and 2, respectively, distance is longer than rvdW separation atoms (the sum of the van der Waals radii from Bondi [21] for the N···H is 2.75 Å) and indicates the absence of any N-H···N. Additionally, in the case of 1 the presence of C···N/N···C, C···O/O···C, O···O, C···C (π···π), and N···N contribute only 0.5, 0.4,

SC

0.1, 0.5 and 0.6% to the total HS, respectively, has been confirmed. These interactions are no significant interactions in the crystal structure of this compound. In compound 2, the C···N/N···C and C···C (π···π) intercontacts are also minimal and comprise 1.5% and 2.0%, respectively. It should be noted that, in 1 and 2, the π···π

M AN U

stacking interactions (between the benzene rings of the molecules belonging to the neighbouring chains) have a distance in the range 3.70-4.10 Å and 3.45-4.95 Å, respectively. Generally, the C…C (π···π) van der Waals distance of 3.40 Å has been adopted as the reference distance for chemical stability [22]. In addition, the electrostatic potential of 1 and 2 has been mapped on the Hirshfeld surfaces using density functional theory (DFT). All calculations were performed using 6-311G(d,p) basis set. The electrostatic

TE D

potential molecular surface shows that the surface of the m-acetotoluidide and m-thioacetotoluidide, see Fig. 5a and b, has one positive and two negative areas. In 1 and 2 the C=O and C=S group, respectively, creates a negative region (the most negative), whereas the N-H group creates a positive region (the most positive). The

EP

positive electrostatic potential indicates hydrogen donor potential (N-H group), whereas the hydrogen bond acceptors are represented by negative electrostatic potential (atoms of oxygen and sulphur). Besides, it should be

AC C

noted that in the case of both compounds the phenyl group also creates a negative region, but it is not the most negative region. In 1 this region is more negative than compared with compound 2. The formation of the hydrogen bonds N-H···O in the m-acetotoluidide and N-H···S in the m-thioacetotoluidide has been substantiated by the IR spectroscopic data and described below in the infrared spectral studies.

3.2. IR and Raman spectral studies The IR and Raman spectrum of polycrystalline sample of the m-acetotoluidide and m-thioacetotoluidide measured with the use of the KBr pellet technique at room temperature (298 K) has been shown in Fig. 6a and c, respectively. In turn, the Raman spectrum for additional identification of the νC-H band positions, which are

4

ACCEPTED MANUSCRIPT attributed to the C-H bond stretching vibrations in the molecules, has been also used. The spectrum of 1 and 2 single crystals measured at 77 K, in the frequency ranges of the ~3300-1350 cm-1 and ~3200-1100 cm-1, respectively, is illustrated in Figure 6e and f, respectively. The vibrations of 1 can be divided into following main types: N-H stretching band (~3290 cm-1; intense), C=O stretching band (amide I band) (~1664 cm-1), N-H bending (the in-plane N-H bend) (~1570 cm-1;

RI PT

amide II band) and C-N stretching band (~1327-1260 cm-1), aromatic C-H stretching in the region ~3113–3057 cm-1 and C-H bending bands (in-plane bending) (~1327-1000 cm-1). As evident from Figure 6a the N-H bending band (amide II band) is intense, almost as intense as the C=O stretch. Here, it should be pointed out that the secondary amide out-of-plane N-H bend is not as important as the in plane bend [23]. In Fig. 6a has been also

SC

shown the skeletal vibrations representing C=C stretching appears in the region ~1555-1397 cm-1. The analysis of the IR and Raman spectrum indicated that the skeletal vibrations of C-C bands in aromatic nucleus are much

M AN U

weaker in the IR spectrum than in the Raman spectrum (see Fig. 6a). These data are also based on the experimental data reported in the literature [24]. The studies of the IR spectrum of 1 indicate a medium-strong and relatively narrow band extending over the frequency range ~3300–3054 cm-1. This region and essential features of the band prove the presence of the intermolecular N-H···O interactions in the crystal lattice of the macetotoluidide. A part of the molecular framework of the analyzed amide, viewed along the a axis, demonstrating

TE D

the hydrogen-bonded chains has been shown in Fig. 6b.

In the case of the m-thioacetotoluidide the characteristic IR bands in six regions of the spectrum have been illustrated in Fig. 6c. The main types of vibration are N-H stretching vibration (~3242-2818cm-1), N-H

EP

bending vibration (~1541 cm-1), C=S stretching vibration (the C=S group connected with the nitrogen atom of NH group; ~1139 cm-1 ), (aromatic)C-H stretching vibration (~3100-2900 cm-1), C=C stretching vibration (~1636

AC C

cm-1) as well as (Ar)C-H bending vibration (~1169-1000 cm-1). In turn, the ~3244-2830 cm-1 region is attributed of the hydrogen bond N-H…S. In turn, a part of the molecular framework of 2, viewed along the b axis, presenting the hydrogen-bonded chains has been illustrated in Fig. 6d. Our results indicate that the formation of the hydrogen bonds in the crystals of 1 and 2 influences

strongly the N-H vibrations. The band of the unbounded N-H group is shifted towards lower frequencies by about 190 cm-1 and 259 cm-1 for 1 and 2, respectively, in comparison to the calculated spectrum (see Table 3). Besides, the frequency of the N-H stretching vibration, for both compounds, is lower in the result of the hydrogen bond generates. In the case of the m-acetotoluidide the shift towards lower frequency can be also observed for the C=O stretching band from 1684 cm-1 to ~1664 cm-1. This band is also involved in the generation

5

ACCEPTED MANUSCRIPT of the N-H···O interactions in the crystal lattices of 1. In turn, the N-H bending band (amide II band) has been shifted towards higher frequencies from 1564 cm-1 to 1570 cm-1. From the data collected in Table 3, one can see that the N-H bending band for the m-thioacetotoluidide is also shifted towards higher frequencies (from 1530 cm-1 to 1541 cm-1). The C-H stretching vibrations in the region 3100-3000 cm-1 is the characteristic region for ready

RI PT

identification of these type vibrations. In the present investigation the calculated frequencies, for compound 1, line in the region 3037-2992 cm-1 have been assigned to the C-H stretching vibrations (see Tab. 3) and their experimental counterpart appear in the region ~3067-2940 cm-1 of the Raman spectrum (see Fig. 6a). For compound 2 the C-H stretching vibrations are observed in the region 3100-2900 cm-1 in FT-IR and ~3060-2900

SC

cm-1 in FT-Raman. The DFT calculations give the C-H stretching vibrations at 3087-3105 cm-1 IR and ~30902900 cm-1 in Raman. In general, for both compounds, the C-H stretching vibrations computed by B3LYP/6-

M AN U

311++G(3df,2pd) shows good agreement with the experimental data.

The assignment of band due to the C-S stretching vibration in the m-thioacetotoluidide is generally difficult in the infrared. The C=S group is less polar than C=O group in the m-acetotoluidide and has a considerably weaker band (see Fig. 6a and c). This band is not intense, and it falls at lower frequencies, where it is much more susceptible to coupling effects. It should be pointed, that the absorption of C=S group with other

TE D

substituent usually appears in the range of 1250-1020 cm-1. In the present investigation the experimental frequencies line in the region ~1139 cm-1 of the IR spectrum have been assigned to the C-S stretching vibrations, and their calculated counterpart appear in the region 1122 cm-1. In comparison to the calculated spectrum, the νCis shifted towards the lower frequencies by about 17 cm-1 (Table 3). It should be emphasized that opposite

EP

S band

effect is predicted for compound 1, where the νC-O band is shifted towards the higher frequencies from 1664 cm-1

AC C

to 1684 cm-1 (about 20 cm-1). Stretching band of the carbonyl group is the most intense band, which has been observed in the IR spectrum (see Fig. 6c). In aromatic compounds, the νC-N bands usually lay in the region 1400-1200 cm-1. It should be noted that

the identification of the C-N stretching frequencies was a rather difficult because in this region are observable other vibrations. In the analyzed title amide, the C-N frequencies have been established in the region ~1327-1260 cm-1 in the infrared spectrum. In the case of the title thioamide, the same frequencies have been identified at ~1253 cm-1 in the IR spectrum. Thus, it can be concluded that the experimental results have been supported by theoretical calculations. The comparison experimental IR spectra and DFT calculated results of compound 1 and

6

ACCEPTED MANUSCRIPT 2 show that the C-N stretching vibrations are shifted towards lower frequencies by ~34 cm-1 and higher frequencies by approximately 46 cm-1, respectively. As expected, the quantum mechanical calculations of isolated molecules gave very limited information for the identification of the intermolecular interactions. Thus, the use of the Vibrational Spectroscopy is very helpful and ideally suited to the interpretation of this kind of interactions. Additionally, it should be noted that

RI PT

the measurements of the polarized IR crystalline spectra have provided the crucial informations about the hydrogen bonds character in the molecular crystals of the title compounds. These kinds of researches have been

SC

carried out previously [13, 25].

3.3. DFT calculations

M AN U

The experimental data on the geometric structure of the related molecule of the m-acetotoluidide and mthioacetotoluidide was compared with the calculated geometry parameters and have been listed in Table 1 and 2, respectively. From comparisons of the quantum mechanical studies and X-ray diffraction measurements can see a good compatibility. In 1, the largest deviation of the geometrically optimized bond-lengths/angles from the corresponding experimental values has been observed for the dihedral angle C6-C1-N-C8. In the case of torsion

TE D

angle C6-C1-N-C8 the experimental value is 15.95°. According to the theoretical calculations the abovementioned angles have the following values: 0.00° (B3LYP/6-311++G(d,p)) and -0.01° (B3LYP/6311++G(3df,2pd)). In the case of the compound 2 the significant differences in the DFT and XRD geometries are observed only for the C1-C2-C3-C6, C6-C1-N-C8 and C1-N-C8-S dihedral angles (see Table 2). It should be

EP

noted that the small differences between the calculated and observed geometrical parameters can be assigned to the fact that the theoretical calculations were performed with isolated molecules in the gaseous phase while the

AC C

experimental values have been based on the molecules in the solid state (crystalline state), as well as the inadequacies of the DFT method. Our studies indicate that both the use of B3LYP/6-311++G(d,p) and B3LYP/6311++G(3df,2pd) level gives practically similar values of the geometrical parameters to the experimental ones. Besides, the results show that in the case of the computational values most of the optimized bond-lengths/angles are slightly shorter and longer than the experimental values. These discrepancies have been expounded above. View of the fact that the calculated geometrical parameters showed a good approximation they were the basis for the calculating of the vibrational frequencies. The comparison of the calculated (B3LYP/6311++G(3df,2pd)) IR spectrum of the m-acetotoluidide and m-thioacetotoluidide with the experimental IR spectrum has been presented in Figure 7a and b, respectively. In turn, the comparison of the observed FT-Raman 7

ACCEPTED MANUSCRIPT with the calculated vibrational frequencies of 1 and 2 has been illustrated in Figure 7c and d, respectively. The simulated IR and Raman spectrum have been undergone the scaling procedure. For amide, a corrective vibrational scaling factor of 0.96 to B3LYP calculated frequencies has been applied. In the case of the thioamide the theoretical frequencies have been scaled by the factor 0.98. Our results show that the theoretical model satisfactorily reproduced the experimental FT-IR and FT-Raman spectra. The calculated and experimental

RI PT

vibrational wavenumbers using B3LYP/6-311++G(3df,2pd) method have been shown in Table 3.

The energy profile of the internal rotation of the m-acetotoluidide and m-thioacetotoluidide has been illustrated in Fig. 8. Our study show that the –NH–CO–CH3 and –NH–CS–CH3 group in the molecular structure

SC

of compound 1 and 2, respectively, rotates about the C1-N1 single bond. These internal rotations are not perturbed of the steric hindrance. The results present that the energy profile for the internal rotation of the analyzed compounds has two equally low energy minima at torsion angles of 0° and -180° or 180°. In turn, the

M AN U

barrier to –NH–CO–CH3 and –NH–CS–CH3 rotation about the single bond C-N is approximately 3.9 kcal/mol and 1.49 kcal/mol for m-acetotoluidide and m-thioacetotoluidide, respectively. Our results show that the rotation barrier is twice higher in the case of the compound 1. In 1, the distance between oxygen atom (O1) of –NH–CO– CH3 group and H6-atom of the benzene ring has value approximately 2.248 Å. While the longer steric interactions between 6-H the aromatic ring and the sulphur atom (S1) of –NH–CS–CH3 group in compound 2

TE D

has been observed (2.830 Å); see Fig. 8; marked fragment on the molecules. Furthermore, is worth noticing that the conformations of amides and thioamides have been extensively studied [26-29]. Additionally, in our work, in the Table 4, the DFT results on the highest occupied molecular orbital

EP

(HOMO), lowest unoccupied molecular orbital (LUMO) energies, and their energy gaps (Egap) for the compound 1 and 2 have been presented.

AC C

The LUMO as an electron acceptor depicts the ability to obtain an electron, while HOMO represents the ability to donate an electron. The high-lying occupied MO’s is bonding and the low-lying unoccupied MO’s is antibonding. The HOMO and LUMO molecular orbitals have been named as frontier molecular orbitals (FMO), which play important role in the electric as well as optical properties, and in the quantum chemistry. In turn, the Egap determines the chemical reactivity, kinetic stability, optical polarizability, and chemical hardness-softness of a molecule [30, 31]. Furthermore, it should be noted that interactions between the HOMO and LUMO molecular orbitals of organic molecules are very helpful for organic chemists due to the fact that play important and decisive role in chemical reactions [32, 33]. The HOMO and LUMO energies of compound 1 and 2 have been calculated by the DFT/6-311++G(d,p)/6-311++(3df,2pd) method. In the m-acetotoluidide, the calculated energy

8

ACCEPTED MANUSCRIPT value of HOMO is -6.25 eV and energy of LUMO is -0.74 eV in the case of B3LYP/6-311++(3df,2pd) level (the highest basis set). In the case of m-thioacetotoluidide, the calculated energy value of HOMO is -5.83 eV and energy of LUMO is -1.56 eV. The HOMO-LUMO energy gap, very important stability index, has been also calculated by the use abovementioned method [34]. The theoretical calculations show that in the m-acetotoluidide the frontier orbital

compound 2 the value of the ∆E

HOMO-LUMO gap

RI PT

energy gap is found to be -5.5096 eV in the gas phase (B3LYP/6-311++(3df,2pd) level); (see Tab. 4). In turn, for is -4.2769 eV (B3LYP/6-311++(3df,2pd) level). Thus, values of

the ∆E HOMO-LUMO gap clearly indicate that charge transfer take place within the molecule, and which influences in

SC

the biological activity of the compound 1 and 2. Besides, the values of the band gap (∆E) for both compounds (see Tab. 4) demonstrate that the analyzed molecules are stable and less reactive in different chemical reactions

M AN U

[35, 36]. It should be stressed that a molecule with a large orbital gap is much less polarizable, and is substantially related with low chemical reactivity as well as high kinetic stability.

4. Conclusions

In summary, we demonstrated that the calculated geometrical parameters, using of B3LYP/6-

TE D

311++G(d,p) and B3LYP/6-311++G(3df,2pd) level, are in good agreement with the experimental values obtained from the crystallographic data. All the vibrational wavenumbers are calculated and scaled values (with 6-311++G(3df,2pd) basis set) are compared with experimental FT-IR and FT-Raman spectra. Experimentally observed frequencies are in good agreement with the calculated values. The significant changes in fundamental

EP

frequencies have been observed only in the case of compound 2. Besides, we find that the steric hindrance between aromatic ring and the –CO–NH– as well as –CO–NH– for 1 and 2, respectively, is avoided. The rotation

AC C

barrier of the C-N amide and thioamide bond in the case of 1 and 2 has value 3.9 and 1.49 kcal/mol, respectively. The data shows that in the crystal structure of compound 1 molecules are connected by a long chains of

the N-H···O hydrogen bonds. In addition, the H···H and C···H intermolecular interactions have an important influence on the stabilization of the crystal lattice packing, and which characterize clear signatures in the 2D fingerprint plots. In turn, the crystal packing in 2 is stabilized by intermolecular N-H···S hydrogen bonds. Moreover, the H···H and C···H interactions also play significant role in assembling the molecules into an organized framework. It has been shown that the analysis of the Hirshfeld surface, for both compounds, is well correlated to the spectroscopic studies. By the analysis used here, it has been proven that forming the hydrogen bonds shift the νN-H bands towards lower frequencies. It should be noted that the infrared spectroscopy in

9

ACCEPTED MANUSCRIPT polarized light of hydrogen-bonded molecular crystals is able to provide crucial experimental data in the area of the hydrogen bond research [37]. In turn, the temperature effect is also very helpful and important, because it differentiates the properties of the shorter-wave band branches from the longer-wave ones in the case of the analyzed amide and thioamide. We believe that the information on the hydrogen bonding abilities of compound 1 and 2 will be helpful in understanding the selected biochemical processes. The HOMO–LUMO energy gap

RI PT

calculated at the B3LYP/6-311++G(d,p)/6-311++(3df,2pd) level reveals the chemical activity of the molecules.

Acknowledgement This work was founded by the grant of the Institute of Mechanized Construction and Rock Mining (No 19-70/411-02/2015). All of the calculations were performed with the aid of hardware and software

SC

at the Wrocław Centre for Networking and Supercomputing WCSS, Wrocław, Poland.

References 1.

M.J. Márquez, M.B. Márquez, P.G. Cataldo, S.A. Brandán, Open J Synthesis Theory Appl 4 (2015) 1– 19.

2.

M AN U

Conflict of Interest The authors declare that they have no conflict of interest.

A.B. Raschi, E. Romano, M.V. Castillo, P. Leyton, C. Paipa, L.M. Maldonado, S.A. Brandán, Vib. Spectrosc. 70 (2014) 100–109.

M.B. Márquez, S.A. Brandán, Int. J. Quant. Chem. 114 (2014) 209–221.

4.

F.E. Chain, P. Leyton, C. Paipa, M. Fortuna, S.A. Brandán, Spectrochim. Acta Part A 138 (2015) 303– 313.

A.A. Ibrahim, A.E.-S. Abdel-Megied, M.S. Selim, H.H. Darweesh, M.M. Ayoub, New polymeric

EP

5.

TE D

3.

admixture for cement based on hyperbranched poly amide-ester with pentaerythritol core. International

6. 7. 8. 9.

AC C

Scholarly Research Notices (ISRN) (2013). Doi:10.1155/2013/270987. T.T. Tran, H. Treutlein, A.W. Burgess, J. Comput. Chem. 22 (2001) 1026–1037. S. Ilieva, B. Hadjieva, G. Galabov, J. Mol. Struct. 508 (1999) 73–80. H.J. Lee, Y.S. Choi, K.B. Lee, J. Park, Ch.J. Yoon, J. Phys. Chem. A 106 (2002) 7010-7017.

H. Adalsteinsson, A.H. Maulitz, T.C. Bruice, J. Am. Chem. Soc. 118 (1996) 7689–7693.

10. Z.S. Derewenda, L. Lee, U.J. Derewenda, Mol. Biol. 252 (1995) 248–262. 11. W. Śmiszek-Lindert, O. Lindert, M. Nowak, J. Kusz, Acta Crystallogr. Sec. C 64 (2008) 599–603. 12. W. Śmiszek-Lindert, M. Nowak, J. Kusz, Acta Crystallogr. Sec. E 63 (2007) 4161. 13. H.T. Flakus, W. Śmiszek-Lindert, K. Stadnicka, Chem. Phys. 335 (2007) 221–232.

10

ACCEPTED MANUSCRIPT 14. S.K. Wolff, D.J. Grimwood, J.J. McKinnon, D. Jayatilaka, M.A. Spackamn, Crystal Explorer 3.0 (2007) University of Western Australia, Perth. 15. J. J. McKinnon, D. Jayatilaka, M. A. Spackman, Chem. Commun. (2007) 3814–3816. 16. M.A. Spackman, J.J. McKinnon, Cryst. Eng. Comm. 4 (2002) 378–392. 17. Gaussian 09, Revision A.02, M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R.

RI PT

Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A.

SC

Montgomery, J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J.

M AN U

Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, O. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, Fox DJ (2009) Gaussian Inc, Wallingford CT.

18. A.D. Becke, J. Chem. Phys. 98 (1993) 5648–5652.

TE D

19. C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1998) 785–789. 20. S.K. Seth, G.Ch. Maity, T. Kar, J. Mol. Struct. 1000 (2011) 120–126. 21. A. Bondi, J. Phys. Chem. 68 (1964) 441–447.

EP

22. B. Schatschneider, J.J. Liang, J. Chem. Phys. 135 (2011) 164508. 23. B.C. Smith, Infrared Spectral Interpretation: A Systematic Approach, CRC Press, Boca Raton, FL,

AC C

USA, 1999.

24. M. Hesse, H. Meier, B. Zeeh, Spectroscopic Methods in Organic Chemistry, Thieme, Stuttgart, New York, 2007.

25. H.T. Flakus, Pol. J. Chem. 77 (2003) 489–517. 26. T. Zielinski, J. Jurczak, Tetrahedron 61 (2005) 4081–4089. 27. S. Ilieva, B. Hadjieva, B. Galabov, J. Mol. Struct. 508 (1999) 73–80. 28. K.B. Wiberg, P.R. Rablen, J. Am. Chem. Soc. 117 (1995) 2201–2209. 29. A.B. Lopes, E. Miguez, A.E. Kümmerle, V.M. Rumjanek, C.A. Fraga, E.J. Barreiro, Molecules 18 (2013) 11683–11704.

11

ACCEPTED MANUSCRIPT 30. A.M. Asiri, M. Karabacak, M. Kurt, K.A. Alamry, Spectrochim. Acta A 82 (2011) 444–455. 31. B. Kosar, C. Albayrak, Spectrochim. Acta A 78 (2011) 160–167. 32. K. Fukui, Acc. Chem. Res. 4 (1971) 57–64. 33. I. Fleming, Frontier orbitals and organic chemical reactions, John Wiley & Sons, 1976. 34. R.G. Pearson, Coord. Chem. Rev. 100 (1990) 403–425.

RI PT

35. V. Arjunan, L. Devi, R. Subbalakshmi, T. Rani, S. Mohan, Spectrochim. Acta A 130 (2014) 164–177. 36. O.A. El-Gammal, T.H. Rakha, H.M. Metwally, G.M. Abu El-Reash, Spectrochim. Acta A 127 (2014) 144–156.

SC

37. B. Ivanova, T.S. Kolev, Linearly Polarized IR spectroscopy: Theory and Applications for Structural Analysis, in: Effects in the Infrared Spectra of Crystals, CRC Press, Taylor & Francis Group, Boca

AC C

EP

TE D

M AN U

Raton, London, New York, 2012.

12

ACCEPTED MANUSCRIPT Table Captions Table 1 Selected bond lengths, bond angles and torsion angles for m-acetotoluidide [11] with the optimized geometry values

RI PT

Table 2 Comparison of selected calculated geometry parameters of compound 2 [12] with the experiment Table 3 Selected band assignments of the experimental and calculated infrared spectrum for m-acetotoluidide and m-thioacetotoluidide

AC C

EP

TE D

M AN U

SC

Table 4 HOMO-LUMO energy values calculated by DFT/B3LYP/6-311++G(d,p)/6-311++(3df,2pd) method

13

ACCEPTED MANUSCRIPT Table 1

1.400(14) 1.391(15) 1.504(16) 1.396(15) 1.387(16) 1.390(15) 1.400(14) 1.411(13) 1.357(13) 1.231(13) 1.505(15)

1.404 1.392 1.510 1.401 1.390 1.395 1.398 1.413 1.378 1.218 1.521

1.400 1.389 1.507 1.397 1.387 1.391 1.395 1.409 1.374 1.215 1.518

121.23(9) 120.21(10) 121.29(10) 118.50(10) 120.54(10) 121.15(10) 118.82(9) 119.76(9) 124.06(9) 128.04(9) 123.17(9) 115.35(9) 121.48(9)

121.61 120.96 120.67 118.37 120.17 121.54 118.73 119.57 123.54 129.34 124.03 114.54 121.43

121.65 120.88 120.75 118.36 120.17 121.56 118.73 119.53 123.57 129.47 124.06 114.57 121.37

-0.71(15) 179.54(10) -179.86(10) 0.39(15) 0.13(16) -0.33(15) 0.02(15) 178.35(9) 15.95(16) -0.09(16) 179.68(9)

0.00 180.00 -180.00 0.00 0.00 0.00 0.00 -180.00 0.00 0.00 179.99

0.17 -179.06 179.06 -0.17 0.06 0.06 -0.06 179.82 -0.01 -0.09 179.83

EP

M AN U

SC

RI PT

6-311++G(3df,2pd)

AC C

Bond lengths (Å) C1-C2 C2-C3 C3-C7 C3-C4 C4-C5 C5-C6 C6-C1 C1-N N-C8 C8=O C8-C9 Angles (°) C1-C2-C3 C2-C3-C7 C7-C3-C4 C2-C3-C4 C3-C4-C5 C4-C5-C6 C5-C6-C1 C6-C1-C2 C6-C1-N C1-N-C8 N-C8-O N-C8-C9 O-C8-C9 Dihedral angles (°) C1-C2-C3-C4 C1-C2-C3-C7 C7-C3-C4-C5 C2-C3-C4-C5 C3-C4-C5-C6 C4-C5-C6-C1 C5-C6-C1-C2 C5-C6-C1-N C6-C1-N-C8 C1-N-C8-O C1-N1-C8-C9

Theoretical 6-311++G(d,p)

TE D

Experimental (XRD) [11]

14

ACCEPTED MANUSCRIPT Table 2

1.389(2) 1.382(2) 1.497(2) 1.364(2) 1.384(2) 1.396(2) 1.372(2) 1.424(18) 1.328(18) 1.657(15) 1.499(2)

1.396 1.401 1.510 1.395 1.396 1.386 1.405 1.416 1.358 1.662 1.517

1.393 1.398 1.507 1.391 1.392 1.382 1.402 1.411 1.355 1.653 1.515

118.66(15) 119.85(16) 122.30(15) 120.38(16) 121.77(15) 117.85(15) 120.47(15) 120.84(14) 121.43(14) 128.77(13) 125.40(11) 114.90(12) 119.68(11)

120.38 119.42 121,11 119.47 120.26 120.29 120.07 119.53 115.62 134.32 127.58 112.27 120.12

119.43 122.45 121.08 119.46 120.24 120.31 120.10 119.45 115.69 134.49 127.69 111.59 120.72

-1.3(2) 2.2(2) -179.86(15) -0.2(2) 1.0(2) -0.1(2) -1.4(2) -178.95(12) -47.40(2) -3.10(2) 178.70(13)

0.07 -179.66 179.62 -0.10 0.06 0.02 -0.04 -179.97 -179.09 0.87 -177.37

0.12 -179.42 179.41 -0.11 0.03 0.04 -0.04 179.79 -179.40 -0.42 178.97

EP

M AN U

SC

RI PT

6-311++G(3df,2pd)

AC C

Bond lengths (Å) C1-C2 C2-C3 C5-C7 C3-C4 C4-C5 C5-C6 C6-C1 C1-N N-C8 C8=S C8-C9 Angles (°) C1-C2-C3 C2-C3-C7 C7-C4-C5 C2-C3-C4 C3-C4-C5 C4-C5-C6 C5-C6-C1 C6-C1-C2 C6-C1-N C1-N-C8 N-C8-S N-C8-C9 S-C8-C9 Dihedral angles (°) C1-C2-C3-C4 C1-C2-C3-C6 C7-C3-C4-C5 C2-C3-C4-C5 C3-C4-C5-C6 C4-C5-C6-C1 C5-C6-C1-C2 C5-C6-C1-N C6-C1-N-C8 C1-N-C8-S C1-N1-C8-C9

Theoretical 6-311++G(d,p)

TE D

Experimental (XRD) [12]

15

ACCEPTED MANUSCRIPT Table 3 Assignment

N-H stretch

(Ar)C-H bend

N-H bend (amide II band) C=O stretch (amide I band) C-C(Ar) bend C-C ring stretch C-N stretch

m-Thioacetotoluidide 3572 3501* 3150-3168 3087-3105* 1631 1598* 1325 1299* 1562 1530* 1145 1122*

N-H stretch (Ar)C-H stretch C-C ring stretch N-C stretch N-H bend C-C=S stretch

AC C

EP

TE D

* The calculated frequencies have been scaled by the scaling factor 0.98

M AN U

* The calculated frequencies have been scaled by the scaling factor 0.96

~3242-2818 ~3100-2900 ~1636 ~1253 ~1541 ~1139

RI PT

(Ar)C-H stretch

SC

Frequencies (cm-1) Experimental Theoretical DFT/B3LYP/6-311++G(3df,2pd) m-Acetotoluidide ~3290 3626 3480* ~3057 3117 2992* ~3083 3141 3016* ~3113 3162 3037* ~1327-1000 1436 1379* 1352 1298* 1117 1072* ~1570 1628 1564* ~1664 1754 1684* ~1619 1652 1586* ~1505-1406 ~1397-1500 1649 1583* ~1555 ~1327-1260 1347-1298 1293-1246*

16

ACCEPTED MANUSCRIPT Table 4 Parameters

DFT/B3LYP/ 6-311++G(d,p)

6-311++(3df,2pd)

-6.2430 -0.7521 -5.4909

-6.2511 -0.7415 -5.5096

-5.8378 -1.5620 -4.2758

-5.8318 -1.5549 -4.2769

m-Acetotoluidide EHOMO (eV) ELUMO (eV) ∆E HOMO-LUMO gap (eV)

AC C

EP

TE D

M AN U

SC

EHOMO (eV) ELUMO (eV) ∆E HOMO-LUMO gap (eV)

RI PT

m-Thioacetotoluidide

17

ACCEPTED MANUSCRIPT Figure Captions Fig. 1 Ortep view and atom numbering scheme of 1 (a) and 2 (c) with the displacement ellipsoid at the 50 % probability level. Hirshfeld surfaces mapped with the dnorm range of -0.557 to 1.513 Å and -0.404 to 1.199 Å for 1 (b) and 2 (d), respectively. The colour scheme: red – distances shorter than sum of van der Waals (vdW) radii;

RI PT

white – is used for contacts around the vdW separation; blue – distances longer than sum of vdW radii

Fig. 2 The crystal packing of the m-acetotoluidide (a) and m-thioacetotoluidide (b) along b axis showing the

SC

selected intermolecular interactions (indicated by dashed lines)

Fig. 3 Fingerprint plot of the m-acetotoluidide; (a) full and resolved (b) C···H, (c) O···H and (d) H···H contacts showing the percentages of contacts contributed to the total HS area of molecules. de the distance from the point

M AN U

to the nearest nucleus external to the surface, and di the distance to the nearest nucleus internal to the surface

Fig. 4 Fingerprint plot of the m-thioacetotoluidide; (a) full and resolved (b) S···H, (c) H···H and (d) C···H contacts showing the percentages of contacts contributed to the total HS area of molecules

TE D

Fig. 5 Electrostatic potential of compound 1 (a) and 2 (b) mapped on the Hirshfeld surface. Red region corresponds to negative electrostatic potential and blue to positive electrostatic potential

EP

Fig. 6 The IR spectrum of polycrystalline sample of 1 (a) and 2 (c) measured at 298 K by the KBr pellet technique and the Raman spectrum for identification of the C-H bond vibration lines. A part of the molecular

AC C

framework of the analyzed amide (b) and thioamide (d) (viewed along the a and b axis, respectively), showing the hydrogen-bonded chains. The spectrum of a single crystals of 1 (e) and 2 (f) measured at 77 K.

Fig. 7 Comparison of B3LYP calculated IR and Raman spectrum of 1 (a) and (c), respectively as well as 2 (b) and (d), respectively with the experiment

Fig. 8 Relative energy of isolated molecules of the m-acetotoluidide and m-thioacetotoluidide as a function of the torsion angle C2–C1–N1–C8 (relative to the lowest energy of the structure)

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

AC C

EP

TE D

M AN U

SC

RI PT

ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT Highlights •

FT-IR and FT-Raman investigations (experimentally and theoretically) of macetotoluidide and m-thioacetotoluidide were carried out. The vibrational properties of the molecule have been studied.

•

The optimized geometry and vibrational wavenumbers were computed using DFT

RI PT

•

methods.

EP

TE D

M AN U

SC

The HOMO–LUMO energy gap was theoretically predicted.

AC C

•