Accepted Manuscript Vibrational spectroscopy, Ab Initio calculations and Frontier Orbital analysis of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one C.E.S. Nogueira, P.E.S. Caselli, P.T.C. Freire, A.M.R. Teixeira, I.M.M. Oliveira, R.R.F. Bento, J.L.B. Faria, G.O.M. Gusmão, L.E. Silva PII: DOI: Reference:

S1386-1425(15)00528-4 http://dx.doi.org/10.1016/j.saa.2015.04.056 SAA 13607

To appear in:

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy

Received Date: Revised Date: Accepted Date:

18 December 2014 13 April 2015 20 April 2015

Please cite this article as: C.E.S. Nogueira, P.E.S. Caselli, P.T.C. Freire, A.M.R. Teixeira, I.M.M. Oliveira, R.R.F. Bento, J.L.B. Faria, G.O.M. Gusmão, L.E. Silva, Vibrational spectroscopy, Ab Initio calculations and Frontier Orbital analysis of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2015), doi: http://dx.doi.org/10.1016/j.saa.2015.04.056

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Vibrational spectroscopy, Ab Initio calculations and Frontier Orbital analysis of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one C.E.S. Nogueiraa*, P.E.S. Casellib , P.T.C. Freireb, A.M.R. Teixeiraa, I.M.M. Oliveiraa, R.R.F. Bentoc, J.L.B. Fariac, G.O.M. Gusmãod,b, L.E. Silvae a

Departamento de Física, Universidade Regional do Cariri, 63010-970, Brazil

b c

Departamento de Física, Universidade Federal do Ceará, 60455-760, Brazil

Departamento de Física, Universidade Federal de Mato Grosso, 78060-900, Brazil d e

Universidade Estadual do Piauí, Teresina-PI, 64002-150, Brazil

Universidade Federal do Paraná, Setor Litoral - Matinhos, 83260-000, Brazil

ABSTRACT In this work we present a study of the vibrational spectra of 4,5,6,8,9-pentachloropyrimido[1,2-a][1,8]naphthyridin-10-one, C11H2Cl5N3O, a substance belonging to the important pharmacological class of 1,8-naphthyridine derivatives. The Fourier transform infrared and the Fourier transform Raman spectra of the crystal were recorded at room temperature in the regions 400 cm−1 to 4000 cm−1 and 50 cm−1 to 4000 cm−1, respectively. Vibrational wavenumbers were predicted using density functional theory calculations with the B3LYP functional on 6-31G(d,p) and 6-311++G(d,p) basis sets. The descriptions of the normal modes were made after calculating the potential energy distribution. Additionally, potential reaction sites were evaluated through Mulliken population and Frontier Orbital analysis. Keywords: Raman scattering; IR spectroscopy; DFT; C11H2Cl5N3O crystal

*

Corresponding author. Phone: 55-88-9985 6159, Fax: 55-88-3102 1294.

E-mail address: [email protected] (C.E.S. Nogueira). 1

1. Introduction The synthesis of isolated pure substances has become a tool of great importance to the development of drugs with enhanced pharmacological properties. The importance of the 1,8-naphthyridine derivatives is well established in pharmaceutical chemistry [1]. In fact, studies have identified activities such as anti-inflammatory [2], analgesic [2], antiparasitic [3], anticancer [4] antibacterial [5], antitumor [6], antihypertensive [7] antiallergenic [8] and antimalarial [9]. Many heterocyclic derivatives of 1,8-naphthyridine have been prepared and studied from the synthetic, pharmacological and structural point of view [10], and, as part of our efforts to develop new compounds aimed at the therapy of parasitic infections, we synthesized and assayed several chlorinated 1,7- and 1,8-naphthyridines [3]. In particular, the synthetic compound 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one, of molecular formula C11H2Cl5N3O, was achieved by using the derived 5-methoxymethylene Meldrum's acid as the precursor for the formation of naphthyridines. This synthetic protocol has attracted attention for providing the opportunity to obtain several naphthyridine derivatives and thus broaden the spectrum of biological activity, besides serving as intermediary for the synthesis of molecular structures of greater complexity [1]. By one hand, halonaphthyridines are prone to nucleophilic aromatic substitution; this makes them important precursors for the introduction of a wide variety of groups containing nucleophilic heteroatoms. On the other hand, a variety of pyrimido[1,2a][1,8]naphthyridines are of biological interest because of their antimicrobial and antihypertensive activities. In addition, naphthyridines containing the pyrimidine moiety, such as pyrimido[2,1-f ][1,6]naphthyridines, have shown tracheal muscle relaxation activity Our efforts in studying this type of structure was firstly focused on their antiparasitic properties such as antileishmanial activity and trypanosomiase diseases [3] and now on their spectroscopy properties. Although there are many experiments related to the development of new compounds, the vibrational properties of these substances have not received the same attention. In order to fill this gap, in this study, we report the characterization of 4,5,6,8,9pentachloropyrimido-[1,2-a][1,8] naphthyridin-10-one crystals by means of Fourier 2

Transform infrared attenuated total reflectance (FTIR-ATR) and Fourier Transform Raman (FT-Raman) spectroscopy. In addition, Density Functional Theory (DFT) calculations were performed with the objective of gaining insight about the normal modes of the material. We have used programs such as Gaussian [11] for carrying out DFT calculations to obtain the structural and vibrational properties of a single molecule of this crystal. The description of the normal modes of vibration was analyzed in terms of the potential energy distribution (PED) using VEDA [20] software. Finally, Mulliken population analysis was performed in order to suggest possible reactive sites for the molecule.

2. Experimental The compound 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one was synthesized as following: a solution of pyridonaphthyridinone (0.54 g, 2.53 mmol), phosphoryl oxychloride (20 ml) and phosphorus pentachloride (3.00 g, 14.38 mmol) was refluxed for 18 hours under Nitrogen atmosphere. The resulting solution was cooled, poured onto ice±water (40 ml) and neutralized with NH4OH until the pH reached 7. The precipitate was collected by filtration, washed with water, dried and purified by silica-gel chromatography with hexane/ethyl acetate (4:1). Single crystals suitable for X-ray data collection were obtained by slow evaporation from a hexane/ethylacetate solution (4:1) [yield 0.80 g, 85%; m.p. 493 K (yellow crystalline solid)]. H1 NMR(CDCl3) δ= 7.65 (d, J= 4.8 Hz, 1H); 8.63 (d, J= 4,8 Hz,1H).13C NMR (CDCl3) δ= 116.69; 119.10; 128.23; 131.05; 137.05; 143.31; 144.59; 146.21; 148.35; 148.70; 153.17; 156.31. The investigation by FT-Raman and FTIR-ATR spectroscopy was performed on a crystalline sample obtained by preparation of halonaphthyridines whose crystal structure was determined and reported elsewhere [12]. The same sample used to obtain the FTRaman spectra was used to record the spectra by FT-IR transmittance. In order to record the Raman spectrum we have used slightly compacted powder of the sample in the sample holder of a Bruker RAM II FT-Raman module coupled to the VERTEX FT-IR spectrometer as well as a liquid nitrogen cooled high-sensitivity Ge detector. The samples were excited with the 1064 nm line of a Nd:YAG laser and we 3

obtained a typical resolution of ~ 4 cm-1 with accumulation of 60 scans per spectra and a nominal laser power of 150 mW. FTIR-ATR spectrum was recorded at room temperature in the wavenumber range from 600 to 4000 cm-1 through the use of a spectrometer Bruker Vertex 70, with an accessory to diffuse reflectance; a resolution of 4 cm-1 and accumulating 32 scans per spectrum was used. A Globar lamp was used as radiation source and the detection was done through a DLaTGS detector with KBr window.

3. Computational Details DFT calculations were performed using the Gaussian 03 program [11]. Geometrical coordinates of the 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8] naphthyridin-10-one crystal, obtained through X-ray diffraction experiments were optimized using the Density Functional Theory (DFT) method with the B3LYP exchange-correlation functional [13] using two different basis sets: 6-31G(d,p) and 6-311++G(d,p). Default optimization specifications were used. Vibrational modes were then calculated analytically by the software [14] and theoretical Raman harmonic frequencies were scaled using two scaling factors. Regarding the calculations done on 6-31G(d,p) basis, for frequencies below 1800 cm-1 a scaling factor of 0.987 was used. Above that, the scaling factor was assumed to be 0.959. On calculations done using 6-311++G(d,p), the scaling factors were 0.994 and 0.984 for the same range of frequencies. These were obtained by least-square fits. The scaling factors were used in this study to offset the systematic error caused by neglecting anharmonicity, electron density and basis set truncation effects [15-17]. The upper wavenumber region, above 1800 cm-1, contains vibrations composed largely of localized hydrogen stretchings, whereas the region below 1800 cm-1 contains heavy atom in-plane stretchings and bendings, out-of-plane and torsional modes. High-energy modes can be expected to be more anharmonic, leading to greater errors because of the harmonic approximation [18, 19]. Therefore, dual scaling factors were utilized in order to improve the agreement between computed and observed frequencies. Vibrational modes were

4

analyzed in terms of Potential Energy Distribution (PED) contributions using the VEDA program [20]. Theoretical Raman Intensities (RI) were derived from Raman Activities obtained with the Gaussian program through the use of the following relationship obtained from basic Raman scattering theory [21]:

RIi = C(v0 – vi)4 · vi-1 · Bi · Si,

(1)

in which C is a scaling constant taken as 10-13, v0 is the excitation frequency of the Nd:YAG laser described before, vi is the calculated frequency for the ith normal mode and Si is the corresponding activity. The Bi factor accounts for the contribution of excited vibrational states to the intensities: Bi = (1 – exp(-h·vi·c/kT))

(2)

where h, k, c, and T represent the Planck and Boltzmann constants, the speed of light and the temperature in Kelvin. Raman intensities were calculated for room temperature (300K). For the plots of calculated spectra, Lorentzian band shapes with band width of 10cm-1 were used.

4. Results and Discussion 4.1. Structural analysis At temperature T = 193 K, the crystal structure of 4,5,6,8,9-pentachloropyrimido[1,2-a][1,8]naphthyridin-10-one (C11H2Cl5N3O) has monoclinic symmetry with space group P21/c (C2h5) with eight molecules per unit cell and lattice parameters a = 16.453 Å, b = 7.1730 Å, c = 22.368 Å and β = 107.26o [12].

5

► Figure 1

The labeling in Figure 1 describes the atom identification used in Tables 1 and 2. Figure 2 shows the overlap of the optimized molecule on B3LYP/6-31G(d,p) and of the molecule in the crystal as determined by X-ray diffraction measurements. The comparison of the two conformations reveals an excellent agreement between them. The optimized and the experimental geometrical parameters are listed in Table 1. The highest deviation in bond lengths when comparing the optimized structure with the crystallographic one are in the C–H bonds, which are, on average, 0.13Å larger in the optimized structure compared to what was measured in the crystal form. Other bond lengths are practically the same in both structures. Angle variations between said structures are also quite small, as both structures differ very little and thus are not worth mentioning. C-C bond lengths on related compound 1,8-naphthyridine [23] are, on average, 1.38 Å in length, while C-N bonds are 1.36 Å in length. Calculated bond lengths for title compound vary from 1.414 to 1,350 Å for C-C bond lengths, and from 1.420 to 1.307 Å for C-N. Thus, as can be seen from Table 1, the average calculated values for 4,5,6,8,9pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one are very close to those of 1,8naphthyridine.

► Figure 2 ► Figure 3 ► Table 1 Experimental and calculated (scaled) FT-Raman and FT-IR spectra of the 4,5,6,8,9pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one are shown in Figure 3 and Figure 4, 6

respectively. From these figures we observe the occurrence of several modes that will be analyzed in the next paragraphs.

► Figure 3 ► Figure 4

4.2. Vibrational analysis

The C11H2Cl5N3O molecule has 22 atoms and the coupling of vibrations due to the presence of eight molecules in the unit cell gives rise to 528 normal modes of vibrations in the crystal. The 528 vibrations can be decomposed in the irreducible representations of the factor group C2h as 132 (Ag + Bg + Au + Bu), where Ag and Bg are Raman active and Au and Bu are IR active; additionally, 1 Au and 2 Bu modes belong to the acoustic branch and the others are optical modes. Table 2 lists the assignments of the molecular vibrations of the 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one provided by PED analysis.

► Table 2 From this point on we indicate by pcp-napy the compound 4,5,6,8,9pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one in order to facilitate the discussion of our results. As we have written in the Introduction the number of vibrational studies on naphthyridine compounds is small. Carrano & Wait did a tentative assignment of 1,8naphthyridine (napy) in a paper from 1973 [23]. Griffith & Koh took a more modern approach in 1995, reporting assignment for napy and two of its silver complexes [24]. As those articles differ in some attributions, we will compare our results with both works. C–H Vibrations 7

We begin the discussion by analyzing the high wavenumber modes. The pcp-napy Raman spectrum exhibits two peaks with wavelengths above 3000 cm-1, namely 3100 and 3065 cm-1. As one should expect these bands must be associated with stretching vibration of CH, υ(C–H), and, in fact, PED analysis shows that these are related to υ(C–H) modes, involving the C4 and C2 atoms, respectively. These are in good accordance with other references, such as Ref. [23], that attributed two Raman peaks of the 1,8-naphthyridine, at 3110 and 3089 cm-1, to C–H stretching vibrations, υ(C–H). C–O Vibrations On one hand, Raman spectrum of pcp-napy shows a low intensity line attributed to carbonyl stretching mode at 1710 cm-1. On the other hand, in the IR spectrum this band has very strong intensity and it is observed at 1703 cm-1. This fact is very well known in the literature because the electronegativity differences between C and O atoms produce a large dipole moment and a very intense band in the IR spectrum. As a consequence, we can affirm that the strong band at 1703 cm-1 appearing in the pcp-napy IR spectrum is associated with the stretching vibration of carbonyl group [19].

C–N and C–C Vibrations There are two strong Raman bands ranging from 1600 to 1500 cm-1 in the pcp-napy spectrum: 1566 and 1535cm-1. Our PED analysis shows that these frequencies actually originate from a mix of both υ(C–N) and υ(C–C) stretching vibrations, as can be seen in Table 2. Carrano & Wait [23] assigned the Raman band of napy at 1565 cm-1 as a C–N stretching mode. Griffith & Koh [24], on the other hand, assigned the same band (1560 cm1

) as due to a C–C stretching vibration. Our mixed assignment comprises both. It is

interesting to observe the bands observed between 1500 and 1600 cm-1 in the IR spectrum, although of high intensity, are less intense than the band assigned to the stretching of the carbonyl group. This agrees with the fact that nitrogen has a lower electronegativity than oxygen and, consequently, because C–N bonds have a smaller dipole moment than C–O 8

bonds, we expect IR bands associated with stretching C–N less intense than the C-O stretching. The most intense Raman peak of pcp-napy is found at 1489 cm-1, it is a mixing of υ(C–N), υ(C–C) and the deformation δ(H–C–N) modes. It corresponds to a strong peak at 1491 cm-1 observed in the Ref. [24] in napy spectrum, where it was assigned as a combination of υ(C–C) and δ(C–C–H) modes. In the IR spectrum a band observed at 1498 cm-1 appears with strong intensity, which is compatible with stretching vibration of C–N, among others. Pcp-napy presents five prominent Raman bands ranging from 1300 to 1200 cm-1. The peak at 1302 cm-1 was assigned as a mixing of υ(C–N) and υ(C–C) vibrations. Griffith & Koh [24] assigned a similar peak at 1294 cm-1 as a pure υ(C–C) mode; other peaks in this region were assigned by them as υ(C–C) and δ(C–C–H) modes. We found out that, in addition to the presence of the modes mentioned in Ref. [24], there are also significant contributions from vibrations involving the nitrogen atoms in this region; in fact, our calculations show that the C–N stretching vibration contributes to the peaks at 1224 and 1276 cm-1 and the δ(N–C–H) vibration also contributes to the band observed at 1276 cm-1. In the region between 1100 and 1000 cm-1 there are two Raman bands, observed at 1068 and 1026 cm-1, which were assigned as υ(C–N) and τ(C–C–H), respectively. Bands found below 1000 cm-1 are not much pronounced and are related to the pyrimide ring and thus could not be compared with the bands of 1,8-naphthyridine. Cl Vibrations Raman bands ranging from 950 to 375 cm-1 are complex modes consisting of υ(Cl–C), out-of-plane vibration, γ(N–C–N–C), and torsion τ(Cl–C–C–N) vibrations, among others. The IR spectrum of pcp-napy shows some bands of strong intensity in the region between 950 and 600 cm-1. The most intense IR band in this spectral range is observed at 938 cm-1 and corresponds to a stretching mode of the Cl19–C8 atoms and a deformation of C10–N15–C11 atoms.

9

It is worth mentioning that in the Raman spectrum of pcp-napy in the 600 to 550 cm-1 range there are two relatively prominent peaks, at 581 and 567 cm-1. These bands were assigned as stretching Cl-C, υ(Cl–C), and deformations of the pyridine ring, δ(C–C–N), the latter contributing with a higher percentage in the PED. Bayrak [25] reports that a peak around 554 cm-1 of 4-amino-2,6-dihydroxypyrimidine complex could also be assigned as bending mode of the ring. Another worth-mentioning band is a relatively salient one at 375 cm-1. It consists of υ(Cl–C) and δ(C–C–N). In the Ref. [25] it was reported that peaks around 370 cm-1 should be assigned as a C–N bending mode. In summary, we were able to identify most of the normal modes of the material we have observed in both Raman and infrared spectra.

4.3. Molecular electrostatic potential maps and Mulliken charges Mulliken population analysis [26] provides an estimative of partial atomic charges. These partial charges are quantitative indicators of the electronic charge distribution of a compound from which dipole moment can be calculated. It also serves as indicators of possible reactive sites. Molecular Electrostatic Potential (MEP) maps, on the other hand, can be used as a qualitative representation of nucleophilic and electrophilic reaction sites [28]. Together, they can be used to determine the most probable interaction sites with other molecules.

► Table 3 The Mulliken atomic charges of pcp-napy are shown in Table 3. Mulliken atomic charges were computed using the DFT/B3LYP method with 6-311++G(d,p) basis set. Molecular electrostatic potential (MEP) at a point on an isosurface around a molecule indicates the net electrostatic effect produced at that point by the charge distributions of the compound. The color-coded MEP for pcp-napy is shown in Figure 5. The electrostatic potential increases from red to blue. As seen on Table 3, Mulliken analysis points C1 and O17 as the most electronegative atoms. Chlorine-bonded carbons are all positively charged, 10

with the exception of C12. The molecular electrostatic potential map, however, points the oxygen atom O17 as the only possible electrophilic reaction site since other negative atoms are not as exposed. The negatively signed site located near O17 has a potential of 6.497x10-2 a.u.

► Figure 5

4.4. Frontier orbital analysis HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) form the frontier molecular orbitals. HOMO is the highest molecular orbital occupied by electrons and LUMO is the unoccupied orbital with the lowest energy. Together they determine most of electric, optical and chemical properties of a molecule. The HOMO-LUMO energy gap, for example, is a good indicator of molecular reactivity [28]. For the pcp-napy calculated at 6-311++G(d,p) the highest occupied molecular orbital HOMO (Figure 6, bottom) lying at -6.696 eV is mostly delocalized along the pcp-napy rings, spanning through several atoms. The LUMO at -3.050 eV (Figure 6, top) exhibits a similar but less pronounced delocalization.

► Figure 7 Figure 7 also shows the HOMO-LUMO energy gap, calculated as 3.646 eV. This is in agreement with the energy gap found for similar compound 4,4'-(1,8-naphthyridine-2,4diyl)bis(N,N-dimethylaniline) [29]. The HOMO-LUMO energy gap is an indicator of molecular stability [28] as it increases with the gap. Also, one can find whether the molecule is hard or soft. The soft molecules are more polarizable than the hard ones because they need small energy to excitation. The molecular hardness of pcp-napy, which is half the HOMO-LUMO gap, was evaluated as 1.823 eV.

11

5. Conclusions A

study

on

vibrational

properties

of

4,5,6,8,9-pentachloropyrimido-[1,2-

a][1,8]naphthyridin-10-one crystal was performed using the FT-IR and FT-Raman spectroscopy as well as quantum chemical calculations on DFT level. Comparisons between calculated geometry parameters and structure obtained from X-ray diffraction data shows good agreement. The experimental and calculated (scaled) vibrational spectra were compared, showing a good correspondence. These results and the description of the normal modes followed by mean of the PED were useful to elucidate the vibrational wavenumber assignments of this synthetic substance. Finally, using the Mulliken population analysis as well as the Molecular Electrostatic Potential map it was possible to show the O17 oxygen atom of 4,5,6,8,9-Pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one is the only viable electrophilic reaction site.

Acknowledgments We thank CENAPAD-SP for the use of the GAUSSIAN 03 software package and for computational facilities made available through the project “proj373”. Financial support from FUNCAP, CNPq and CAPES is also acknowledged.

References

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[1] J. Saunders., Top Drugs: Top Synthetic Routes, University Press, Oxford, 2000, pp. 8087. [2] G. Roma, et al., J. Med. Chem. 43 (2008), 1665-1680. [3] L. E Silva, et al., Letters in Drug Design & Discovery 4 (2007), 154-159. [4] M. Atanasova, S. Ilieva, B. Galabov, B. Eur. J. Med. Chem. 42 (2007), 1184-1192. [5] Y. Kuramoto, et al., J. Med. Chem. 46 (2003), 1905-1917. [6] K. Chen, et al., J. Med. Chem. 40 (1997), 2266-2275. [7] P. Ferrarini, et al., Eur. J. Med. Chem. 35 (2000), 815-826. [8] M. Sherlock, et al., J. Med. Chem. 31 (1988), 2108-2121. [9] G. B. Barlin, et al., J. Chem. 37 (1984), 1065-1073. [10] S.-H. Ahn, et al., Korean Chem. Soc. 32 (2011), 3145-3147. [11] M. J. Frisch, et al., Gaussian, Inc., Gaussian 03, Revision C.02. Wallingford CT, 2004. [12] A. Bortoluzzi, et al., Acta Crystallographica C 61(2005), 1–3. [13] K. Burke, Electronic Density Functional Theory: Recent Progress and New Directions, Springer, New York, 1998. [14] B. G. Johnson, M. J. Frisch, Journal of Chemical Physics 100 (1994), 7429-7442. [15] C.E. Blom, C. Altona, Molecular Physics 31 (1976), 1377-1391. [16] G. Rauhut, P. Pulay, The Journal of Physical Chemistry 99 (1995), 3093-3100. [17] J. Baker, A.A. Jarzecki, P. Pulay, The Journal of Physical Chemistry A 102 (1998), 1412-1424. [18] J.P. Merrick, D. Moran, L. Radom, The Journal of Physical Chemistry A 111 (2007), 11683-11700. [19] D. Lin-Vien, et al, The Handbook of Infrared and Raman Characteristic Frequencies of Organic Molecules, Academic Press, San Diego, 1991, pp. 117-154. [20] M. H. Jamroz, Spectrochimica Acta Part A 114 (2013), 220–230. [21] J. Tang, A. C. Albrecht, Raman Spectroscopy, Vol. 2, Plenum Press, New York, 1970, pp. 33-68. [22] D. Michalska, R. Wysokinski, Chemical Physics Letters 403 (2005), 211–217 [23] J. T. Carrano, Samuel T. Wait, Journal of Molecular Spectroscopy 46 (1973), 40-418 [24] W. P. Griffith, T. Y. Koh, Journal of Raman Spectroscopy 26 (1995), 1067-1070 [25] C. Bayrak, Hacettepe Journal of Biology and Chemistry 40 (2012), 419-426 13

[26] R.S. Mulliken, J. Chem. Phys. 23 (1955), 1833-1846. [27] E. Scrocco, J. Tomasi, Adv. Quantum Chem. 11 (1979), 115. [28] N. T. Anh., Frontier Orbitals: a pratical manual, John Wiley and Sons, Chichester, 2007. [29] A.E.E.A Elrahim , M. E. Mohamed, Journal of Applied and Industrial Sciences 2 (2014), 174-180,

CAPTIONS FOR THE FIGURES

Figure 1: Optimized molecular structure of 4,5,6,8,9-pentachloropyrimido-[1,2a][1,8]naphthyridin-10-one with the atoms identification. Figure 2: Structure of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one molecule in the crystal (green) and optimized structure (blue). Figure 3: Experimental and calculated (scaled) Raman scattering spectra of 4,5,6,8,9pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one in the region of 1800 cm-1 to 50 cm-1. The inset shows the Raman spectra in the region of 3150 cm-1 to 3000 cm-1. The arrow correspond to Raman band ωFT-Raman=1489 cm−1 Figure 4: FTIR-ATR spectrum of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin10-one in the regions, 3600 cm-1 to 2800 cm-1 and 1900 cm-1 to 600 cm-1. The arrow correspond to infrared band ωFT-IR=1498 cm−1.

14

Figure 6: Molecular electrostatic potential maps of 4,5,6,8,9-pentachloropyrimido-[1,2a][1,8]naphthyridin-10-one calculated at B3LYP/6-311++G(d,p) level. Figure 7: Molecular orbital surfaces and energy levels for the HOMO and LUMO of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one computed at B3LYP/6311G++(d,p) level.

TABLE CAPTIONS Table 1. Comparison of geometric parameters of molecular structure 4,5,6,8,9pentachloropyrimido-[1,2 a][1,8]naphthyridin-10-one. Table 2. Calculated vibrational wavenumbers (in cm-1) unscaled and scaled. Scale factors for the 6-31G(d,p) and 6-311++G(d,p) are, respectively, 0.9870 and 0.9840, for 0–1750 cm-1 and 0.994 and 0.959, for 2800–3500 cm-1. Raman and FT-IR experimental bands in units of cm-1 and assignment of vibrational modes. Table 3. Mulliken charge distribution of 4,5,6,8,9-pentachloropyrimido-[1,2 a][1,8]naphthyridin-10-one calculated at B3LYP/6-311++G(d,p) level.

15

16

17

18

19

20

21

22

Table 1

Table 1: Comparison of geometric parameters of molecular structure C11H2Cl5N3O. Bond lengths

Exp. (Å)

C1-C5 C1-N1 C1-N3 C2-H1 C2-C3 C2-N1 C3-H2 C3-C4 C4-C5 C4-Cl1 C5-C6 C6-C7

1.414 1.329 1.420 0.951 1.380 1.331 0.950 1.383 1.415 1.721 1.459 1.350

Bond angle

Exp. ( º)

C5-C1-N1 C5-C1-N3 C1-C5-C4 C1-C5-C6 N1-C1-N3 C1-N1-2 C1-N3-C8 C1-N3-C11 H1-C2-C3 H1-C2-N1 C3-C2-N1 C2-C3-H2 C2-C3-C4 H2-C3-C4 C3-C4-C5 C3-C4-Cl1 C5-C4-Cl1 C4-C5-C6 C5-C6-C7

125.5 119.9 114.3 117.0 114.6 117.4 120.8 119.8 118.4 118.4 123.2 120.5 119.0 120.5 120.2 115.7 124.1 128.4 120.3

Calc. (Å)

Calc. (Å)

6-31G(d,p)

6-311++G(d,p)

1.432 1.326 1.414 1.087 1.392 1.325 1.083 1.388 1.423 1.747 1.457 1.368

1.430 1.328 1.419 1.090 1.393 1.330 1.087 1.387 1.425 1.748 1.455 1.369

Calc. (Å)

Calc. (Å)

6-31G(d,p)

6-311++G(d,p)

125.0 119.8 114.2 117.3 115.1 118.5 121.0 120.2 120.6 116.5 122.9 121.1 118.9 120.0 120.4 114.7 124.9 128.4 120.0

125.0 119.7 114.2 117.3 115.2 118.4 120.6 120.5 120.4 116.7 122.8 120.7 118.8 120.4 120.5 114.6 124.8 128.3 119.9

Bond lengths

C6-Cl2 C7-C8 C7-Cl3 C8-N2 C8-N3 C9-C10 C9-N2 C9-Cl4 C10-C11 C10-Cl5 C11-N3 C11-O1

Exp. (Å)

Calc. (Å)

6-31G(d,p)

6-311++G(d,p)

1.734 1.452 1.726 1.307 1.386 1.372 1.346 1.741 1.458 1.726 1.473 1.206

1.733 1.446 1.731 1.315 1.383 1.373 1.340 1.744 1.449 1.732 1.455 1.220

1.717 1.446 1.715 1.316 1.378 1.353 1.349 1.722 1.439 1.716 1.453 1.209

Calc. (Å)

Bond angle

C5-C6-Cl2 C7-C6-Cl2 C6-C7-C8 C6-C7-Cl3 C8-C7-Cl3 C7-C8-N2 C7-C8-N3 N2-C8-N3 C8-N2-C9 C8-N3-C11 C10-C9-N2 C10-C9-Cl4 C9-C10-C11 C9-C10-Cl5 N2-C9-Cl4 C11-C10-Cl5 C10-C11-N3 C10-C11-O1 N3-C11-O1

Exp. (Å)

121.9 117.8 122.3 122.0 115.6 119.1 117.0 123.8 116.8 119.1 124.1 120.5 120.7 123.0 115.3 116.1 111.9 126.2 121.9

Calc. (Å)

Calc. ( º)

6-31G(d,p)

6-311++G(d,p)

122.0 118.0 121.6 122.3 116.1 119.6 117.2 123.1 118.8 118.8 123.4 121.5 119.8 124.0 115.0 116.1 112.0 126.0 121.9

122.2 117.9 121.6 122.1 116.3 119.7 117.4 122.8 118.7 118.9 123.4 121.4 119.4 123.7 115.1 116.7 112.9 125.0 122.0

Table 2

Table 2: Calculated vibrational wavenumbers (in cm-1) unscaled and scaled. Scale factors for the 6-31G(d,p) and 6311++G(d,p) are, respectively, 0.987 and 0.994, for 0–1750 cm-1 and 0.959 and 0.984, for 2800–3500 cm-1. Raman and FTIR experimental bands in units of cm-1 and assignment of vibrational modes. Theoretical 6-31G(d,p) ωcalc ωscal

Theoretical 6-311++G(d,p) ωcalc ωscal

Experimental 

FT-Raman



Assignment with PED*,** [%]

FT-IR

19 42 52 74 112 142 180 192 200 213 233 251 272 275

19 41 51 73 111 140 178 190 197 210 230 248 268 271

18 42 54 75 113 144 181 192 201 212 232 250 272 275

18 42 54 75 112 143 180 191 200 211 231 249 270 273

85 s 106 s 145 m 165 w 184 w 196 m 211 m 239 m 258 w 280 w 314 w

309 331 359 368

305 327 354 363

309 332 358 363

307 330 356 361

341 w 375 w 427 w 454 w

373 419 450 505 517 565 578 590 616

368 414 444 498 510 558 570 582 608

374 419 448 504 519 565 580 593 619

372 417 445 501 516 562 577 590 616

505 w 528 w 567 w 581 m 589 m 611 w 628 w 646 w 674 w

633

625

633

629

700 vw

694 s

679 700 716 748 767 780 834 852 862 942 953 985

670 691 707 738 757 770 823 841 851 930 941 972

672 702 720 747 766 787 827 851 866 933 958 992

668 698 716 743 762 783 822 846 861 928 953 986

713 w 721 vw 738 vw 745 vw 767 vw 783 w 832 w 851 w 866 vw 894 vw 955 vw 1026 w

707 s 715 s 735 s 745 s 762 s 777 vs

606 s 641 s 666 s

847 vs 891 s 938 vs

[C1N16C10C9] (14) +[C8C7C6Cl18] (24) +[C6C7C1N16] (38) [C7C8C9C10] (28) +[C9C10N15C11] (39) + [C11C12C13N16] (10) [C10N15C11C12] (34) + [N16C10C9Cl20] (10) [C7C8C9C10] (12) + [C11C12C13N16] (31) + [N16C10C9Cl20] (11) [C11C12C13N16] (16) + [N16C10C9Cl20] (18) [C9C10N15] (10) +[C11C12C13N16] (11) [C12C11Cl21] (23) + [C10N15C11C12] (10) + [C2C4C6C7] (10) [C8C9Cl20] (12) + [C11C12Cl22] (15) [C8C9Cl20] (14) + [C11C12Cl22] (29) + [C4C6Cl18] (13) [C10N16C1N14] (30) [C9C8Cl19] (17) [C8C9Cl20] (26) + [C9C8Cl19] (37) [C12C11N15] (24) [C10N16C1N14] (12) + [Cl22C11C13C12] (26) + [N16C10C9Cl20] (19) [Cl19C8] (18) + [C1N16C10] (14) [N16C13O17] (14) + [Cl22C11C13C12] (15) [N16C10] (12) + [Cl20C9] (23) [C1N16C10C9] (22) + [Cl22C11C13C12] (11) + [N16C10C9Cl20] (11) [Cl21C11] [12) + [N16C13O17] (12) [Cl18C6] (15) + [C4C6Cl18] (27) [Cl18C6] (11) + [C12C13N16] (13) [C7C1N16] (12) + [C6C4C2N14] (23) [C7C1N16] (18) + [C6C4C2N14] (13) [Cl19C8] (13) + [Cl21C11] (16) + [C2C4C6] (12) [C12C13N16] (20) [C12C13N16] (14) + [Cl21C12C15N11] (10) [C2C4C6C7] (18) + [Cl19C7C9C8] (18) +[C8C7C6Cl18] (19) + [C6C7C1N16] (16) [C10N15C11C12] (10) + [O17C12N16C13] (11) + [Cl21C12C15N11] (43) [Cl20C9] (10) + [Cl22C12] (12) + [C2C4C6] (12) [N16C13O17] (10) + [N15C9N16C10] (14) [O17C12N16C13] (17) + [N15C9N16C10] (22) [O17C12N16C13] (28) + [N15C9N16C10] (11) [Cl18C6] (10) + [O17C12N16C13] (18) [C6C7C1N14] (50) + [C6C4C2N14] (10) [Cl19C8] (12) [H3C2C4H5] (10) +[H5C4C2N14] (74) [Cl20C9] (18) + [C4C2N14] (12) [Cl19C8] (10) + [Cl21C11] (19) + [C12C11N15] (13) [Cl19C8] (16) + [C10N15C11] (18) [H3C2C4H5] (85) + [H5C4C2N14] (10)

1050 1087 1146 1198 1218 1272 1296 1312 1331 1360 1438

1036 1073 1131 1182 1202 1255 1279 1295 1314 1342 1419

1054 1087 1145 1203 1212 1272 1284 1312 1328 1354 1434

1048 1081 1139 1196 1205 1265 1277 1305 1321 1346 1426

1052 w 1068 w 1132 vw 1201 m 1224 w 1247 s 1276 s 1302 s 1318 m 1330 m 1361 w

1046 vs 1169 s 1123 s 1183 s 1220 s 1243 s

1476 1526 1576

1457 1506 1556

1466 1504 1561

1458 1496 1552

1414 w 1446 m 1489 vs

1406 s 1441 s 1498 s

1295 s 1323 s 1362 s

[C4C6C7] (10) + [C9C10N16] (11) [N14C1] (10) + [N15C11] (10) + [N16C10] (11) [C2C4] (29) + [H5C4C2] (21) [C9C10] (11) + [C12C13] (31) [C6C7] (13) + [N16C1] (14) + [H5C4C2] (11) + [C4C6C7] (10) [C4C6] (24) + [C7C8] (31) [N14C1] (17) + [N15C11] (15) + [H3C2N14] (19) [N15C11] (20) + [C6C7] (10) + [N16C10] (18) [N16C10] (10) + [C9C10] (12) + [N16C1] (13) + [C1C7] (37) [N14C2] (22) + [C9C10] (12) + [N16C1] (12) + [H3C2N14] (12) [N14C1] (10) + [C9C10] (11) + [C7C8] (10) + [C1C7] (10) + [H3C2N14] (22) [C6C7] (18) + [H5C4C2] (26) [C8C9] (19) + [C11C12] (40) [N15C10] (10) + [C8C9] (24) + [C11C12] (11) + [N15C11] (11) + [H3C2N14] (10) [N15C10] (37) + [C11C12] (18) [C8C9] (29) + [N14C2] (16) [N14C1] (20) + [N14C2] (13) + [C4C6] (21) [O17C13] (87) [C2H3] (98) [C4H5] (98)

1590 1569 1573 1564 1535 s 1530 vs 1603 1582 1593 1584 1566 s 1548 vs 1628 1607 1615 1606 1582 m 1577 vs 1825 1801 1724 1714 1710 w 1703 vs 3188 3057 3124 2996 3065 m 3061 m 3240 3107 3156 3027 3100 m 3095 m * Only PED values greater that 10 % are gives. ** PED calculated at B3LYP/6-311++G(d,p) level. Nomenclature: =torsion; sc=scissoring; =deformation; =out of plane deformation; =stretching. vs=very strong ; s=strong; m=medium; w=weak; vw=very weak.

Table 3

Table 3. Mulliken charge distribution of 4,5,6,8,9-pentachloropyrimido-[1,2a][1,8]naphthyridin-10-one calculated at B3LYP/6-311++G(d,p) level. Atom C1 C2 H3 C4 H5 C6 C7 C8 C9 C10 C11 C12 C13 N14 N15 N16 O17 Cl18 Cl19 Cl20 Cl21 Cl22

Charge -1.458 0.041 0.207 0.292 0.224 0.272 0.102 0.072 0.032 -0.586 -0.109 0.553 -0.140 -0.173 -0.062 0.040 -0.501 0.338 0.361 0.224 0.035 0.230

23

Highlights

FT-IR and Raman of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one Optimized geometry and vibrational frequencies by DFT. Experimental and theoretical vibrational spectra comparison Potential Energy Distribution (PED) Analysis Frontier Orbitals Analysis

24

Vibrational spectroscopy, ab initio calculations and Frontier Orbital analysis of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one.

In this work we present a study of the vibrational spectra of 4,5,6,8,9-pentachloropyrimido-[1,2-a][1,8]naphthyridin-10-one, C11H2Cl5N3O, a substance ...
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