Synthesis, Structure and Quantum Mechanical Calculations of Methyl 2-(5-((Quinolin-8-yloxy)-methyl)-1,3,4-oxadiazol-2-ylthio)-acetate

AAMER SAEEDFOUZIA PERVEENNAEEM ABBASSIDRA JAMALULRICH FL?RKEc(Deprtment of Chemistry, Quid-I-Azm University, Islmd 45320, Pkistn)(Reserch Center for Modeling nd Simultions, Ntionl University

of Sciences and Technology, H-12 Campus, Islamabad, Pakistan)c(Department Chemie, Fakult?t fur Naturwissenschaften, Universit?t Paderborn, Warburgerstrasse 100, D-33098 Paderborn, Germany)

Synthesis, Structure and Quantum Mechanical Calculations of Methyl 2-(5-((Quinolin-8-yloxy)-methyl)-1,3,4-oxadiazol-2-ylthio)-acetate

AAMER SAEEDa①FOUZIA PERVEENbNAEEM ABBASaSIDRA JAMALaULRICH FL?RKEca(Department of Chemistry, Quaid-I-Azam University, Islamabad 45320, Pakistan)b(Research Center for Modeling and Simulations, National University

of Sciences and Technology, H-12 Campus, Islamabad, Pakistan)c(Department Chemie, Fakult?t fur Naturwissenschaften, Universit?t Paderborn, Warburgerstrasse 100, D-33098 Paderborn, Germany)

The title compound was synthesized by the base catalyzed reaction of 5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2(3H)-thione with methyl chloroacetate.The structure was supported by the spectroscopic data and unambiguously confirmed by single-crystal X-ray diffraction studies.It crystallizes from a methanol solution in the triclinic space group P1 with unit cell dimensions a = 7.4509(9), b = 10.2389(12), c = 12.2299(15) ?, α = 74.771(2), β = 77.956(2), γ = 69.263(2)°, V = 834.98(17) ?3 and Z = 2.In order to gain some valuable insights into the molecular structure, the quantum mechanical calculations were performed using both HF and time-dependent density functional theory at the B3LYP/6-31G(d,p) level.The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set.The calculated results show that the DFT and HF can well reproduce the structure of the title compound.The energetic behavior of the title compound was examined using the B3LYP method with the 6-31G(d) basis set.The harmonic vibrational frequencies calculated have been compared with the experimental FTIR and FT-Raman spectra.The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the13C and1H NMR chemical shifts of the title compound.Moreover, molecular electrostatic potential and thermodynamic parameters of the title compound were investigated by theoretical calculations.

methyl 2-(5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-ylthio)acetate, crystal structure, conformer, quantum chemical calculations, vibrational studies;

1 INTRODUCTION

1,3,4-Oxadiazol-2H-thiones are amongst the most important scaffolds in medicinal chemistry and versatile intermediates in organic synthesis.1,3,4-Oxadiazoles exhibit a range of biological activities like antitumor, anti-inflammatory, hypoglycemic, antifungal, and antibacterial activities[1,2].Sub-stituted 1,3,4-oxadiazol-2-thioesters are widely used for the treatment of pain and inflammation, particularly arthritis and also active components of nonsteroidal anti-inflammatory drugs[3,4].These are the common intermediates in different biosynthetic reactions and play an important role in the tagging of protein.Compounds containing 1,3,4-oxadiazol ring and thioester could provide antitumor activity and adhesive ability[5].The title compound was prepared to synthesize as a precursor towards a diversity of quinoline linked heterocylic systems for biological and theoretical studies.

By means of increasing the development of computational chemistry in the past decade, the research on theoretical modeling of drug design, functional material design, etc., has become much more mature than ever.Many important chemical and physical properties of biological and chemical systems can be predicted from the first principles by various computational techniques[6,7].

In recent years, density functional theory (DFT) has been a shooting star in theoretical modeling.The development of better and better exchange-correlation functionals made it possible to calculate many molecular properties with comparable accuracies to the traditionally correlated ab initio methods, with more favorable computational costs.The literature survey revealed that the DFT has a greater accuracy in reproducing the experimental values of geometry, dipole moment and vibrational frequency[8-12].

In this paper, we report the synthesis, characterization and crystal structure of the compound methyl 2-(5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-ylthio)acetate as well as the theoretical studies on it by using the HF/6-31G(d) and DFT/B3LYP/6-31G(d) methods.The properties of structural geometry, molecular electrostatic potential (MEP) and thermodynamic properties, nonlinear optical properties of the title compound at the B3LYP/6-31G(d) level were studied.These calculations are valuable for providing insight into the molecular properties of the title compound.The aim of the present work was to study the one electron properties of thiones using DFT methods.

2 EXPERIMENTAL

Synthesis and characterization

The melting points were recorded using a digital Gallenkamp (SANYO) model MPD.BM 3.5 apparatus1H and13C NMR spectra were recorded in CDCl3at 300 and 75 MHz respectively with a Bruker 300 MHz spectrophotometer.FTIR spectra were recorded on an IR Shimadzu 460 spectrophotometer as KBr pellets and elemental analyses were conducted using a LECO-183 CHNS analyzer.

2.1 Synthesis of methyl 2-(quinolin-8-yloxy)acetate (2)

Methyl chloroacetate (2.17 mL, 20 mmol) was added dropwise during 5 min.To a solution of 8-hydroxyquinoline (1, 3 g, 20 mmol) in 15 mL of DMF, the reaction mixture was heated for 12 h.The reaction mixture was poured into ice cold water and precipitates obtained were recrystallized from ethanol (yield 86%, m.p: 70～73 ℃).

2.2 Synthesis of 2-(quinolin-8-yloxy)acetohydrazide (3)

Hydrazine hydrazide (1.2 mL, 40 mmol) was added dropwise in an ethanolic solution of methyl 2-(quinolin-8-yloxy)acetate (2, 4.5 g, 20 mmol) and the reaction mixture was refluxed for 24 h.The progress of the reaction was monitored by TLC.Upon completion of the reaction, the solvent was evaporated and the precipitate was recrystallized from ethanol (yield 89%, m.p: 138～140 ℃).

2.3 Synthesis of 5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2(3H)-thione (4)

2-(Quinolin-8-yloxy)acetohydrazide (3, 2.1 g, 10 mmol) was dissolved in ethanol.To this solution KOH (0.5 g, 10 mol) was added on heating and carbon disulfide (18.5 mL, 10 mmol) was added dropwise.The reaction mixture was refluxed for 3 h.On completion, the reaction mixture was poured into water and the pH was adjusted to 6.The solid appeared was filtered and recrystallized from ethanol (yield 86%, m.p: 224 ℃).1H NMR (300MHz, CDCl3δ, ppm): 14.7 (broad, 1H, NH), 8.88～8.90 (dd, 1H, J = 6.6, 3.0Hz, Ar-H), 8.35～8.38 (dd, 1H, J = 8.4, 1.5Hz, Ar-H), 7.52～7.64 (m, 3H, Ar-H), 7.36～38 (m, 1H, Ar-H), 5.47 (s, 2H, CH2)13C NMR (75MHz, CDCl3, δ, ppm) 61.0 (CH2), 111.9, 122.0, 122.5, 127.0, 129.6, 136.5, 139.9, 149.9, 153.2, 160.0, 178.6.

2.4 Synthesis of methyl 2-(5-((quinolin-8-yloxy)-methyl)-1,3,4-oxadiazol-2-ylthio)acetate (5)

Anhydrous K2CO3(1.72 g, 10 mmol) was added to a stirred solution of 5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2(3H)-thione (3 g, 10 mmol) in 20 mL of DMF.Methyl chloroacetate (2.17 mL, 20 mmol) was added dropwise during 5 min and the reaction mixture was heated for 20 h.The progress of the reaction was monitored by TLC.Upon completion of the reaction, the reaction mixture was poured into ice cold water and the solid obtained was recrystallized from methanol to afford as colorless crystals (yield 89%, m.p: 75 ℃).1H NMR (300 MHz, CDCl3δ, ppm): 8.87～8.88 (m, 1H, Ar-H), 8.34～8.37 (m, 1H, Ar-H), 7.51～7.63 (m, 3H, Ar-H), 7.36～7.38 (m, 1H, Ar-H), 5.61 (s, 2H, OCH2), 4.27 (s, 2H, SCH2), 3.67 (s, 3H, OCH3)13C NMR (75MHz, CDCl3, δ, ppm) 34.0 (OCH3), 53.2 (SCH2), 60.8 (OCH3) 111.8, 121.9, 122.5, 127.0, 129.6, 136.4, 140.1, 149.9, 153.3, 164.3, 164.7, 168.5.

2.5 X-ray data collection and structure refinement

Colorless single crystal C15H13N3O4S, 2H2O, Mr= 367.38, size 0.42mm ′ 0.38mm ′ 0.20mm, triclinic, space group P1, a = 7.4509(9), b = 10.2389(12), c = 12.2299(15) ?, α = 74.771(2), β = 77.956(2), γ = 69.263(2)°, Z = 2, ρcalc= 1.461 mg/cm3, μ = 0.232 mm?1and F(000) = 384.Data were collected at 130(2) K on a Bruker[13]AXS SMART APEX CCD diffractometer using MoKα radiation; 7936 reflections collected in the range of 1.74<θ<27.88°.Structure solved by direct methods[14], full-matrix leastsquares refinement[14]on F2 and 241 parameters for 3965 unique intensities.All but H atoms were refined anisotropically, and H atoms from difference Fourier maps were refined on the idealized positions with Uiso= 1.2Ueq(C) or 1.5Ueq(C methyl/O water) and C–H distances of 0.95～0.99 ?, H(water)-positions were refined with DFIX O–H 0.84 and H··H 1.4 ?.H(Cmethyl) were allowed to rotate but not to tip.Selected bond lengths and bond angles are given in Table 1.In general, here are no unexpected geometric parameters.

Table 1.Selected Bond Lengths (?) and Torsion Angles (°)

3 RESULTS AND DISCUSSION

3.1 Synthesis and characterization

Methyl 2-(5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-ylthio)acetate (5) was synthesized in four steps starting from commercial 8-hydroxyquinoline (1) according to the route depicted in Scheme 1.Thus, 5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2(3H)thione (4) was obtained from 1 via corresponding acetate (2) and hydrazide (3) followed by base-catalyzed cyclization using carbon disulphide.Treatment of 4 with methyl cholroacetate in the presence of K2CO3in dry DMF afforded the title ester (5) in excellent yield.

Formation of ester was indicated in FTIR spectrum by stretchings at 1724 cm-1for C=O, at 1601 cm-1for C=N as well as others at 1160 cm-1for C–O–C.1H-NMR spectrum showed signals at δ7.3～8.8 ppm for aromatic protons, and two 2H singlets δ 5.61 and 4.27 indicated the presence of OCH2and SCH2, and a 3H singlet at δ 3.67 suggested the presence of the ester methyl group.

Scheme 1 Synthetic route to 2-(5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-ylthio)acetate

3.2 X-ray molecular structure

The molecular structure of the title compound is depicted in Fig.1; the unit cell with intermolecular H-bonding pattern is shown in Fig.2a.Tables 1 and 2 give selected geometric parameters.The molecule is almost planar with torsion angles O(2)–C(3)–C(2)–N(2) 5.5(2)°, N(1)–C(1)–S(1)–C(13) –5.7(2)°, and O(4)–C(14)–O(3)–C(15) –0.5(2)°.The geometry of the oxadiazole moiety is similar to that of the CSD entries XARGII and XARGOO[15].The enclosed solvent water molecules are part of intermolecular O(water)-H××N(oxadiazole), O(water)-H××N(quinoline) and O(water)–H××O(water) hydrogen bond interactions given in Table 2 and depicted in Fig.2a.π-π interactions (Fig.2b) between oxadiazole and the C6part of quinoline planes result in 2-D stacking of the molecules in sheets with a separation of 3.499(2) ?.

Table 2.Intermolecular Hydrogen Bonds (? and °)

Fig.1.Molecular structure of (5).Anisotropic displacement ellipsoids are drawn at the 50% probability level

Fig.2a.Crystal packing of (5) viewed along the b-axis with intermolecular hydrogen bonding pattern shown as dotted lines.H atoms not involved are omitted

Fig.2b.Crystal packing appr.viewed along [011].Water molecules and all H-atoms are omitted.Dashed lines indicate the π-π stacking of oxadiazole and quinoline-C6-ring planes

3.3 Computational investigations

3.3.1 Molecular geometry

Optimized structure with electronic charge distribution is shown in Fig.3.The optimized structural parameters of the title compound B3LYP/6-31G (d,p) are listed in Table 3 in accordance with the atom numbering scheme given in Fig.3.As experimental values of some geometric parameters of the title compound are known from X-ray analysis, the theoretically calculated values may supply an insight into the verification of geometric parameters of the compound and also give an idea that how the geometry of the molecule changes from the ab initio method of calculation and the DFT-B3LYP method of calculation.

A statistical treatment of these data shows that, for the bond length measurement, DFT B3LYP/6-31G(d,p) method is better than the RHF/6-31G(d,p)because interatomic bond lengths and bond angles calculated from the DFT B3LYP method are closer to the values obtained from experimental XRD data.The agreement for bond angles is not as good as that for the bond distances.

Fig.3.Optimized structure of methyl 2-(5-((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-ylthio)acetate using the DFT/B3LYP functional and the 6-31G(d,p) basis set

Table 3.Selected Comparison between the Calculated and Experimental Values of Geometrical Parameters of Methyl 2-(5-((Quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2-ylthio)acetate

3.3.2 Electronic properties

Qualitative Molecular Orbital theory is a fascinating aspect of organic chemistry that can provide a remarkable insight into the workings of organic reactions based on how orbitals interact to control the outcome of reactions.The energies of the important molecular orbitals of the compound, the lowest unoccupied molecular orbitals (LUMO) and the highest occupied molecular orbitals (HOMO) were calculated and are provided in Figs.4 and 5,respectively.It is interesting to see that both orbitals are substantially distributed over the conjugation plane.

Fig.4.HOMO’s for methyl 2-(5-((quinolin-8-yloxy) methyl)-1,3,4-oxadiazol-2-ylthio) acetate ELUMO= 0.011 eV

Fig.5.LUMO’s for methyl 2-(5-((quinolin-8-yloxy) methyl)-1,3,4-oxadiazol-2-ylthio) acetate EHOMO= –0.090 eV

ELUMOis proportional to reduction potential or the electron affinity and EHOMOto oxidation or the ionization potential of the compound.The HOMO and LUMO values for methyl 2-(5-((quinolin-8-yloxy) methyl)-1,3,4-oxadiazol-2-ylthio) acetate were found to be –0.090 and 0.011 eV, respectively with the band gap of 0.079.The lower values in the HOMO and LUMO energy gaps explain the eventual charge transfer interaction taking place within the molecule.

HOMO and LUMO were obtained in order to determine which part of the compound is involved in oxidation or reduction respectively from their delocalization behavior.The band gap measures the extent of excitation of the frontier orbitals and is directly proportional to the reactivity.Orbital shapes of HOMO and LUMO are respectively displayed in Figs.4 and 5.It is clear from Fig.4 that HOMO’s are delocalized on planar aromatic ring, implying that this part may be involved in the reduction process.Fig.5 shows that LUMO’s are delocalized on a five-membered ring including planar aromatic ring and S atom, which may be involved in oxidation process.However, O atoms are not involved in the reduction or oxidation process of methyl 2-(5-((quinolin-8-yloxy) methyl).A consideration of symmetry shows that a molecule can not have a dipole moment if it possesses a center of symmetry.The dipole moment, which is the first derivative of the energy with respect to an applied electric field asa measure of asymmetry in the molecular charge distribution, was found to be 7.3600 Debye which shows that the molecule is asymmetric with C1 point group.Hardness of the molecule calculated from the information of band gap is 0.0395 eV.Chemical Potential was found to be 0.050 eV.

3.3.3 Natural population analyses

The calculation of effective atomic charges plays a dominant role in the application of quantum mechanical calculations to molecular systems.Our interest here is in the computation of electron distribution in the title compound as broad as possible.The calculated natural atomic charge values from the natural population analysis (NPA) and Mulliken population analysis (MPA) procedures using the DFT methods are listed in Table 4.According to Reed et al.[16], NPA scheme shows greater numerical stability and better describes the electron distribution in compounds of high ionic character.So, we also concluded that NPA from the NBO method is better than the MPA scheme.Table 4 compares the atomic charge site of the title compound from both MPA and NPA methods.Moreover, we see that C(2) has a positive value in MPA, whereas negative in NPA because the surrounding atoms, O(18), C(1) (negative) will not give a positive value for the C(2) atom.Similarly, C(3) has positive value in MPA whereas negative NPA because the surrounding atoms N(16) and C(4) (negative) will not give a positive value for C(3).These are two of the evidences that NPA is better than MPA.The NPA of the title compound shows that the presence of three nitrogen atoms (N(16) =?0.519, N(24) = ?0.44978, N(26) = 0.22672) imposes large positive charges on the carbon atoms (C(3) = 0.15777, C(12) = 0.21014, C(21) = 0.11151, C(22) = 0.34330).However, the nitrogen atoms N(16), N(24) and N(26) possess large negative charges, resulting in the positive charges on the carbon atoms C(3), C(12), C(21) and C(22).

Table 4.Natural Atomic Charges and Mullikan Atomic Charges of Methyl 2-(5-((Quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2-ylthio)acetate

To be continued

3.3.4 Molecular electrostatic potential

The MEP is related to the electronic density and is a very useful descriptor in determining the sites for electrophilic and nucleophilic reactions as well as hydrogen bonding interactions[17,18].The electrostatic potential V(r) is also well suited for analyzing processes based on the 'recognition’ of one molecule by another, as in drug-receptor and enzyme-substrate interactions, because it is through their potentials that the two species first “see” each other[19].Being a real physical property, V(r) can be determined experimentally by diffraction or by computational methods[21].To predict reactive sites for electrophilic and nucleophilic attack for the investigated molecule, the MEP at the B3LYP/ 6-31G(d) optimized geometry was calculated.The negative (red and yellow) regions of MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in Fig.4.As can be seen from the figures, this molecule has many possible sites for electrophilic attack.Negative regions are mainly localized over the O(18), O(23), S(28), O(33) and O(38) atoms.Also, a negative electrostatic potential region is observed around the C(1), C(2), C(5) and C(6) atoms of the benzene ring.The negative V(r) values are ?9.860 e-2a.u.However, a maximum positive region is localized on C(11), C(12) and N(16) with a value of 9.860 e-2a.u., indicating a possible site for the nucleophilic attack.According to these calculated results, the MEP map shows that the negative potential sites are on electronegative O atoms as well as the positive potential sites are around the carbon and hydrogen atoms.These sites give information about the region from which the compound can have intermolecular interactions.Fig.8 confirms the existence of intermolecular C–H··O and C–H··S interactions.

3.3.5 Vibrational spectra C-H vibrations

Harmonic vibrational frequencies of the title compound were calculated using the DFT/B3LYP with the 6-31G(d) basis set.The vibrational band assignments were made using the Gauss-View molecular visualization program.In order to facilitate assignment of the observed peaks, we analyzed the vibrational frequencies.According to theoretical calculations, the title compound has a non-planar structure of C1 point group symmetry.The molecule has 38 atoms and 108 normal modes of vibration active in IR.The IR spectrum of the title compound is shown in Fig.7.The aromatic structure shows the presence of C–H stretching vibrations in the region of 2900～150 cm-1, which is the characteristic region for the identification of C–H stretching vibrations.In this region, the bands are not appreciably affected by the nature of the substituent.The C–H aromatic stretching mode was calculated at 3150 cm-1for B3LYP.

N-H vibrations

The infrared spectrum of the title compound is present in Fig.7.In all the heterocyclic compounds, the N–H stretching vibrations occur in the 3,500～3,000 cm-1region[20].Fig.8 shows the high frequency region, where CH and NH stretchingmodes are expected to be observed.However, not all the observed bands are associated with fundamental vibrations, since some overtones and combinations of lower-energy modes originating in anharmonic effects are usually present in this region.Thus, the band placed around 3,260 cm-1may be assigned to the worst overtone of ν(C=O).Some contribution of the bands around 3,236 cm-1may be associated with the only ν(NH) mode expected in the title compound.

Fig.6.Molecular electrostatic potential map calculated at the B3LYP/6-31G (d) level

Fig.7.FT-IR spectrum of the title compound calculated from Gaussian 03 package

Fig.8.NMR spectra of methyl 2-(5-((quinolin-8-yloxy) methyl)-1,3,4-oxadiazol-2-ylthio)acetate calculated from Gaussian 03 package

C-N vibrations

The C–N stretching frequency is a very difficult task since it falls in a complicated region of the vibrational spectrum, i.e., mixing of several bands is possible in this region[20].C–N stretching absorption appears in the 1,386～1,266 cm-1region for aromatic amines.The IR bands appearing at 1,298 and 1,272 cm-1have been assigned to the C–N stretching vibration.

3.3.613C and1H NMR chemical shift assignment

The13C NMR spectrum theoretically with the aid of the Gaussian software program is shown in Fig.8.

3.3.7 Thermodynamic properties

The total energy of a molecule is the sum of translational, rotational, vibrational, and electronic energies, i.e., E = Et + Er + Ev + Ee.Thus, the molecular partition function is the product of translational, rotational, vibrational, and electronic partition functions of the molecule[21].The relations between partition functions and various thermodynamic functions were used to evaluate the latter due to the translational, vibrational, and rotational degrees of the freedom of molecular motions.The statistical thermochemical analysis of the title compound is carried out considering the molecule to be at room temperature of 298.15 K and under atmospheric pressure.In the present analysis using B3LYP, the contributions due to internal rotations are not considered.The free energy of the molecule is calculated including zero-point vibrational energy.The values of zero-point energy of the molecule were 141.17830 kcal/mol by DFT method and 148.14892 kcal/mol by RHF method, respectively.Microscopically, the thermal energy is the kinetic energy of a system's constituent particles, which may be atoms, molecules, electrons, or particles in plasmas.Table 5 summarizes the calculated thermodynamic parameters, namely heat capacity, entropy, rotational constants, and dipole moments of the title compound.Knowledge at the permanent dipole moment of a molecule provides a wealth of information to determine the exact molecular conformation.The total dipole moment of the title compound by DFT-B3LYP is 7.8940 and by HF is 7.3600.

4 CONCLUSION

An efficient synthesis of a novel thiourea-biphenyl hybrid compound 1 is described.It is not only a versatile ligand for complexation but also an intermediate towards the synthesis of a range of heterocycles.The structural assignment was supported by spectroscopy, elemental analysis data and the crystallographic studies.

Table 5.Calculated Thermodynamic Parameters of Methyl 2-(5-((Quinolin-8-yloxy)methyl)-1,3,4-oxadiazole-2-ylthio)acetate

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10.14102/j.cnki.0254-5861.2010-1491

25 April 2014; accepted 9 April 2015 (CCDC 935330)

① Corresponding author.aamersaeed@yahoo.com