Investigation of intermolecular hydrogen bonding in 2,3,4,5,6 pentafluorobenzoic acid through molecular structure and vibrational analysis – A DFT approach

Accepted Manuscript Investigation of intermolecular hydrogen bonding in 2, 3, 4, 5, 6 Pentafluorobenzoic acid through molecular structure and vibrational analysis - A DFT Approach G. Subhapriya, S. Kalyanaraman, N. Surumbarkuzhali, S. Vijayalakshmi, V. Krishnakumar PII: DOI: Reference:

S0022-2860(14)01139-9 http://dx.doi.org/10.1016/j.molstruc.2014.11.033 MOLSTR 21111

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Journal of Molecular Structure

Received Date: Revised Date: Accepted Date:

7 August 2014 10 November 2014 13 November 2014

Please cite this article as: G. Subhapriya, S. Kalyanaraman, N. Surumbarkuzhali, S. Vijayalakshmi, V. Krishnakumar, Investigation of intermolecular hydrogen bonding in 2, 3, 4, 5, 6 Pentafluorobenzoic acid through molecular structure and vibrational analysis - A DFT Approach, Journal of Molecular Structure (2014), doi: http:// dx.doi.org/10.1016/j.molstruc.2014.11.033

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Investigation of intermolecular hydrogen bonding in 2, 3, 4, 5, 6 Pentafluorobenzoic acid through molecular structure and vibrational analysis - A DFT Approach G.Subhapriyaa, S.Kalyanaramana*, N.Surumbarkuzhalib, S.Vijayalakshmia and V.Krishnakumarc a

PG & Research Department of Physics, Sri Paramakalyani College, Alwarkurichi 627412, India. b Department of Physics, Government Arts College (Autonomous), Salem 636 007, India c Department of Physics, Periyar University, Salem 636 011, India

Abstract The density functional theory (DFT) and Hatree-Fock (HF) method was performed at 6–311++G** level to derive the equilibrium geometry, vibrational wavenumbers, infrared intensities and Raman scattering activities of 2,3,4,5,6 pentafluorobenzoic acid molecule (PFBA). The conformer study of the monomer PFBA was also undertaken. The possibility of intermolecular hydrogen bonding and the dimeric form of the molecule was predicted using vibrational analysis of the monomer. The effects of molecular association through O–H· · O hydrogen bonding have been described in the dimer structure using geometrical structure analysis, Natural bond orbital analysis (NBO), Molecular electrostatic potential (MEP) maps and Mulliken charge analysis. Keywords: Pentafluorobenzoic acid, DFT, vibrational analysis, intermolecular hydrogen bonding

* Tel: +91 9500603015 Fax: +91 4634283560. E-mail: [email protected]

1. Introduction Benzoic acid (BA) is one of the most commonly used preservatives in cosmetics, preservation of foodstuffs, and drug preparations, against fungus [1]. It is also used in the treatment of bacterial infections and combined with other chemicals to create products like repellents and perfumes. It occurs widely in the tissues of plants and animals along with vitamin B-complex [2, 3]. Moreover, BA has been identified as a good metal surface absorber from surface enhanced Raman scattering (SERS) studies [4]. Because of its wide applications, not only BAs but also its derivatives have been extensively investigated. Fluorinated benzoic acids have been used as water tracers in ground and soil water applications and in petroleum reservoirs [5]. When the numbers of fluorine atoms in a benzene molecule are increased, its toxicity and physiological activity get decreased. Fluorine is highly electronegative and hence they withdraw the electrons from the ring wherein change in ionization potential, electronic affinity and excitation energies of the system result [6]. Mehmet Karabacak et al., [7] studied the FTIR and FT-Raman of 2,3-difluorobenzoic acid and 2,4-difluorobenzoic acid along with their hydrogen bonded dimers. Mukherjee et al. investigated the vibrations of the 2,3,4-trifluorobenzoic acid [8], 2,3,6-trifluorobenzoic acid [9] and 2,4,5- and 3,4,5-trifluorobenzoic acid [10] molecules in optimum energy conformation and analyzed the influence of fluorine atoms on the geometry and the different modes of benzoic acid molecule. Recently, they also went on to investigate the vibrational analysis, optimized geometry and NBO analysis of 2,4,6-tri-fluorobenzoic acid and its hydrogen bonded dimer [11]. Hydrogen bonding plays a vital role in the design of organized structures and supra molecular devices. It is also an important type of non-covalent interaction that exists in many chemical and biological systems [12]. Owing to its extensive significance, the present study was focussed on the analysis of intermolecular hydrogen bonding in 2,3,4,5,6 pentafluorobenzoic acid (PFBA) employing molecular structural properties and vibrational characterization. The optimized geometry has been calculated and compared at HF/631G, B3LYP/631G**, B3LYP/6311G**, B3LYP/6311+G** and B3LYP/6311++G** basis sets for PFBA monomer. The dimer calculations have been carried out at the B3LYP/6311++G** basis set. A detailed vibrational analysis has also been attempted. In addition, natural bond orbital (NBO) analysis, molecular electrostatic potential (MEP) and Mulliken charge analysis have been carried out to estimate the nature of hydrogen bonding.

2. Experimental details The fine polycrystalline sample of pentafluorobenzoic acid was procured from SigmaAldrich Company, UK, with a stated purity of 98% and used as such for spectral measurements without further purification. The room temperature infrared spectrum of the compound in KBr pellet method was recorded with JASCO FTIR 4100 in the region 400– 4000 cm-1 with the maximum resolution of 0.9 cm-1. Raman spectrum of powder sample was recorded using a Renishaw Invia micro Raman spectrometer with 514 nm laser excitation in the region 30-4000 cm-1. 3. Computational details All theoretical calculations have been performed on B3LYP (Becke’s three parameter hybrid functional using the LYP correlation functional) at 6-311++G(d,p) basis set using Gaussian 03W Program suit [13] and Gauss view to visualize the program. The optimum geometry was determined by minimizing the energy with respect to all geometrical parameters without imposing molecular symmetry constraints in various basis sets. In the optimized structure of the molecule, no imaginary frequency modes were observed for geometry wherein a true minimum on the potential energy was found. In order to understand the most optimized symmetry, the energy calculations were accomplished for PFBA monomer, using the B3LYP/6–31G** basis set for various possible conformers. The computationally predicted possible conformers obtained for the molecule are shown in Fig. 1. The total energy distribution (TED) corresponding to each of the observed frequency calculations were done on MOLVIB V7.0 - G77 version written by Sundius which depicted the reliability and accuracy of the spectral analysis. The Raman activities (Si) calculated by Gaussian 03 program were suitably adjusted by the scaling procedure with MOLVIB and subsequently converted to relative Raman intensities (Ii) using the following relationship derived from the basic theory of Raman scattering [14–16]. ௜ 

଴  ௜ ସ ௜ ௜ 1  exp 

ି௛௖௩೔ ௄்



Where υ0 is the exciting wave number (in cm-1units), υi the vibrational wave number of the ith normal mode, h, c, and k are the universal constants and f is a suitably chosen common normalization factor for all peak intensities. Vibrational wavenumbers were calculated only for the most stable conformer at DFT/B3LYP level of theory using 6-31G**

basis set. Normal coordinate analysis was performed to provide complete assignments of the fundamental vibrational wavenumber of the molecules. For this purpose, the full set of 56 standard internal coordinates defined for PFBA are given in ST 1. From these, a nonredundant set of 56 local symmetry coordinates were constructed using suitable linear combinations of internal coordinates following the recommendations of Fogarasi and Pulay [17, 18]. These coordinates are summarized in ST 2. The title molecule is composed of 15 atoms with 39 fundamental modes of vibrations which are distributed as 27 in plane vibrations and 12 out of plane vibrations under C1 point group symmetry. All vibrations have been found to be active both in IR and Raman. The visual comparisons between the observed and simulated FTIR and Raman spectra are presented in Figs. 2 and 3 respectively. The experimental assignments of FTIR and Raman for different vibrational frequencies of PFBA are shown in Table 1. The root mean square (RMS) values of wave numbers were obtained using the following expression: ௡

1 ௘௫௣   

V୧ୡୟ୪ ௜ ଶ  1 ௜

The RMS error of wave numbers (unscaled /B3LYP/6-31G**) obtained for PFBA was found to be 43.5 cm-1. In order to reproduce the observed wave numbers, refinement of scaling factors were applied and optimized via least square refinement algorithm which resulted in a RMS deviation of 5.5 cm-1. To predict the strength of the hydrogen bonds, natural bonding orbital (NBO) method has been utilized. A useful aspect of the NBO method is that it gives information about the interactions both in filled and virtual orbital spaces which could enhance the analysis of intraand intermolecular interactions. The second-order Fock matrix was carried out to evaluate the donor–acceptor interactions in the NBO analysis. The interactions resulted in the loss of occupancy from the localized NBO of the idealized Lewis structure into an empty non-Lewis orbital. For each donor (i) and acceptor (j), the stabilization energy E(2) associated with the delocalization i → j was estimated from, 2  ∆௜௝  ௜

,  ଶ ௜  ௝

Where qi is the donor orbital occupancy,

i

and

j

are diagonal elements and F(i,j) is the off

diagonal NBO Fock matrix element [19, 20]. In order to support the NBO analysis, molecular electrostatic potential (MEP) calculations were undertaken. The MEP is plotted onto the constant electron density surface for mapping or whose potential surfaces illustrate the charge distributions of molecules three dimensionally. These maps allow us to visualize the variably charged regions of a molecule. Knowledge of the charge distribution can thus be used to determine the level of molecular interactions with one another. It can also simultaneously display the molecular shape and size, as well as the reactive sites within a molecule [21, 22]. The MEP maps allow us to visualize the variably charged regions of a molecule in terms of colour grading. Areas of low potential, red (negative MEP) are generally characterized by the abundance of electrons or greatest electron density. A portion of a molecule that has a negative electrostatic potential are susceptible to electrophilic attack; the more negative the better. Areas of high potential, blue (positive MEP), can be characterized by the relative absence of electrons. This area is the region of nucleophilic attack. 4. Results and Discussions 4.1. Conformer Study The total energies obtained for conformers are enlisted in Table 2. It is discernible that the DFT structural optimizations of the conformer from Fig.1(b) produces a global minimum energy with a negative frequency. This could be because of the steric effect offered by the highly electro negative substitution of fluorine atom and oxygen atom in the carboxyl group. The structure becomes optimized further following the rotation of the oxygen atoms with respect to C7-C1-C2 plane. The dihedral angles of the plane of atoms O8-C7-C1-C2 are represented by t8 and that of O9-C7-C1-C2 by t9. The initial torsional angles chosen were 1800 and 00 for t8 and t9 respectively. Rotation of the planes was undertaken by every 200 for t8 by and t9 and computations were carried out to obtain a global minimum energy for every particular case. The profile for the stable structure of PFBA molecule was obtained at 134.60 for t8 and -45.80 for t9. Vibrational analysis performed for every optimized structure at the same level showed positive harmonic vibrations only (Nimag=0) indicating stability of the structure. The above computations were done by keeping the torsion angles of all atoms in the molecule as frozen except the oxygen atoms of the carboxyl group.

4.2. Comparison of Basis sets The molecular structure and the numbering scheme of pentafluorobenzoic acid molecule are presented in Fig. 4. Since the crystal structure of the exact title molecule was not available, the optimized structural parameters were only compared with other similar known systems. The energies obtained by the HF and DFT methods are listed in Table 3 and it, revealed that the B3LYP/6-311++G** method could produce a fair amount of global minimum energy. The Global minimum energy obtained for dimer was -1834.5028 Hartrees by DFT method and the corrected intermolecular energy was -1834.5011 Hartrees in BSSE method. The energy difference was only 0.00165715 Hartrees confirming that in the present case both methods seemed to be compatible. The optimized geometrical parameters determined by

various methods were compared with the experimental data [23], and are exhibited in Table 4. Fig. 4 illustrates the numbering of atoms. The mean absolute deviations between the calculated and experimental bond lengths were also determined to investigate the performance and limits of the different theoretical methods which are presented in Table 5. Due to the lack of exchange and correlation energy, the HF method showed a higher deviation from the experimental analysis, whereas DFT based B3LYP method displayed a moderate deviation. The inclusion of diffuse and polarization functions improved the level of computation highly exhibiting the minimum deviation from the XRD analysis. The values obtained from DFT/B3LYP/6-311++G** methods are in agreement with the experimental values, which were further confirmed by the vibrational spectra. (Figs. 2 and 3) 4.3. Vibrational analysis 4.3.1. Ring vibrations The ring stretching vibrations in the vibrational spectra of benzene and its derivatives were very prominent, due to double bond conjugation within the ring. The carbon-carbon stretching modes of the phenyl group can be expected to be in the ranges of 1625–1590, 1590–1575, 1540–1470, 1465–1430 and 1380–1280 cm−1 with variable intensities [24]. The actual positions of these modes are determined by the nature of the substituents. C-C stretching vibrations occur at 1600, 1580, 1490, 1440 cm-1 due to the heavy substituent like fluorine atom [25]. In the present work, the wavenumbers observed in the FT-IR spectrum at 1654, 1424, 911 cm-1and Raman bands at 1665, 1534, 1519, 1318, 1310 cm-1 could be ascribed to the C-C stretching vibrations. The theoretically computed values at 1670, 1649,

1533, 1514, 1428, 1314, 1312 and 908 cm-1 (in monomer) emphasized an excellent agreement with experimental data. These mixed modes contribute to C-F in-plane bending vibration and C-C stretching vibrations. The band detected at 911 cm-1 could be assigned to the ring breathing vibration. Vibrations responsible for the ring deformation bending were found at 589, 510 and 449 cm-1 which coincided well with the DFT computed values. 4.3.2. Carboxylic acid vibration The vibrational bands of -COOH group consists of C-O, C=O, and O-H vibrational modes. Among the vibrational bands of –COOH, the C=O stretching band generally appears stronger at the region of 1660–1715 cm-1 and depends on the physical state, electronic and mass effects of neighbouring substituents, conjugations and intramolecular and intermolecular hydrogen bondings [26, 27]. The C= O stretching band is strong in FTIR but with a diminished intensity in the Raman spectrum. In the PFBA molecule the band observed at 1719 cm-1 in FTIR was a very strong band and could be assigned to the C=O stretching. The computed value (1720 cm-1) of C=O stretching vibration of the monomer was in better agreement with the experimental data. The O–H in carboxylic acid group presents three vibrations (stretching, in-plane and out-of-plane bending vibrations) which are more sensitive to the environment; and hence pronounced shifts observed in the spectra of the hydrogen bonded species can be visualised [26]. The O–H stretching in the current study was characterized by a very broad band appearing approximately at 3400 cm-1. A broad-shoulder that was observed at 3415 cm-1 in the FT-IR spectra in the solid phase appears to have its origin from the O–H stretching vibration. According to PED results, the O–H stretching is a pure mode contributing to 100%. This stretching mode sometimes gets superimposed on the sharp C-H stretching bands. The O-H bending vibration band appeared in the range of 1440 - 1395 cm-1 and the band for out-of-plane bending was found at 960 - 875 cm-1. The strong band appearing at 1180 cm-1 can be assigned to the O-H in plane bending. The theoretically computed value of 1182 cm-1 seems to be in very good agreement for the O-H in-plane bending vibration. The out-of-plane vibration observed at 559 cm-1 in Raman spectrum displayed a good correlation with the theoretically calculated value of 558 cm-1. 4.3.3. C - F vibrations

The ring C–F stretching vibrations appeared to be in the region at 1360–1000 cm-1. Mono fluorinated compounds have a strong band between 1000 and 1110 cm-1. Moreover, when more than one fluorine atom exists the band then splits into two bands namely symmetric and asymmetric [7]. In this study, the corresponding C-F peaks were observed at 1389, 1155, 1110 and 1009 cm-1 under FT-IR and Raman. The C-F bending vibrations were identified at 365, 306, 292, 278 and 265 cm-1. Bending of the ring-halogen bond of aromatic fluoro compounds portrayed a band of variable intensity from 420-375 cm-1 with the in-plane bending frequency appearing in the region of 250–350 cm-1. 4.4. Investigation of hydrogen bonding The existence of inter or intra molecular hydrogen bonding were identified through spectroscopic studies and interpreted through the analysis of geometrical parameters, Natural bond orbital analysis, Molecular electrostatic potential maps (MEP) and Mulliken atomic charges. 4.4.1. Spectroscopic Study It is discernible from the experimental FTIR spectrum of Fig. 2 that a very broad band in the region of 3400 cm-1exists which is characteristic of a dimeric structure. Literature studies revealed that, in general, intermolecular hydrogen bonded amino and hydroxyl groups exhibit a strong band in the region of 3100 – 2800 cm-1 arising from O-H stretching vibrations [25, 28]. This was found to be in excellent consistency with the experimental results obtained. Generally, stretching vibrations of the carbonyl group prompt the finger print of its substituted compounds between 1740-1700 cm−1. In the present case, it appeared at 1719 cm−1 in FTIR spectra. Since the intermolecular hydrogen bonding existed among the carbonyl group and hydroxyl group, the double bond character of the carbonyl group gets decreased making the force constant to reduce in strength resulting in a lowering of wavenumber with a corresponding increase in bond length ensuingly [25]. All these criterions were clearly notable and confirming the existence of strong inter and intra molecular hydrogen bonding in the PFBA. The occurrence of inter molecular hydrogen bonding also made the respective bands of hydroxyl and amino group to appear in the lower wavenumber region 3300 - 3000 cm-1. 4.4.2. Analysis of geometrical parameters

On comparing the bond lengths of hydroxyl and carbonyl groups of benzoic acids it was noticed that the present molecular structure exhibited appreciable elongation in the bond lengths of hydroxyl (1.20 Å) and carbonyl group (0.97Å). The elongations of these bonds are an evidence for the formation of Hydrogen Bridge. The longer the bond, the stronger is the intermolecular attraction. Similarly, shortening of C1-C7 and C7-O9 bond lengths were also noticed supporting the existence of hydrogen bonding. The computationally found endocyclic angles such as C6-C1-C2, C1-C2-C3, C2-C3-C4, C4-C5-C6 and C5-C6-C1 are enlisted in Table.4. All the endocyclic angles of PFBA were approximately of 120° except for C2-C1C6. This deviation could be attributed to the inductive effect offered by fluorine substitution and the steric effect by the substitution of carboxylic acid. Typically, the sp2 hybridization of carboxylic acid such as C-C=O and C-C-O possessed exocyclic angles around 120°. On the contrary, the values found through computational prediction were 124.170 for C1-C7-O8, 111.740 for C1-C7-O9 and 107.440 for C7-O9-H10 for PFBA in the monomer form. These changes are quite possible due to the electron withdrawing nature among highly electronegative oxygen. But at the same time in dimer structures, the values found were 121.4°, 113.4° and 1100, where the hydrogen bonding reduced the electronegativity of oxygen atoms. The hydrogen bonded distances are depicted in Fig. 5. The hydrogen bonded distances O8 - H25 = 1.68 Å and O23 - H10 = 1.68 Å were much lesser than the sum of Van der Wall’s radii (2.7 Å for O…H ) which strongly validate the presence of intermolecular H-bridges. 4.4.3. Natural Bond Orbital Analysis The selected transitions of the dimer are given in Table 6. The NBO results confirmed that in the dimer the electron delocalization takes place from the oxygen of the carbonyl group of first molecule to the hydrogen of the carbonyl group in second molecule and vice versa. It can be construed from the Table that the atoms involved in dimerization obviously have higher delocalization. The larger E(2) value vividly indicates that there is much intensive interaction between electron donors and electron acceptors. In the dimer, transition from unit 1 to unit 2 takes place from LP1 (O8) → σ* (O24-H25) with the energy of 8.66 KCal/mol and LP2 (O8) → σ* (O24-H25) with the energy of 18.93 Kcal/mol. The transition from unit 2 to unit 1 takes place from LP1 (O23) → σ* (O9-H10) and LP2 (O23) → σ* (O9-H10) which have the stabilization energies of 8.65 and 18.91 Kcal/mol respectively. These evidences strongly support the existence of intermolecular hydrogen bonding. The changes in electron density in the lone pairs (O8) with the antibonding (σ*, π*) orbitals during the formation of PFBA dimer were also evident (Table 7). The antibonding σ*(C1-C7) and σ*(C7-O9) showed

a larger decrease in the electron density, thereby resulting in the strengthening of the C1-C7 and C7-O9 bonds and subsequently a decrease in the bond distances (Table 4). However, we noticed an increase in the electron density of the antibonding orbital σ*(O-H) and (C=O) which in turn weakens the respective bonds resulting in lengthening of the bond [29, 30]. This was concomitant with a red shift in the stretching of wavenumbers of respective groups. It could be extrapolated that the changes in the bond distances are certainly due to the hydrogen bond formation confirmed here by natural bond orbital (NBO) analysis. 4.4.4. Molecular Electrostatic Potential In order to predict the reactive sites for electrophilic and nucleophilic attack on the investigated molecule the MEP study was carried out by B3LYP using 6-311++G** basis set. It can be construed from Fig. 6. that the negative (red and yellow) regions of the MEP were found to be related to electrophilic reactivity while the positive (blue) regions to nucleophilic reactivity, for monomer and dimer respectively. In the case of monomer Fig. 6.a negative regions were mainly localized over the oxygen atoms (O8) of the carboxyl moiety. The maximum positive regions were localized on the hydrogen atom (H10) of the carboxylic acid group indicating a possible site for nucleophilic attack. These sites confirm the region where the molecule can have intermolecular interactions. Thus, the possibility of the oxygen atom (O8) to be the most reactive site for electrophilic attack and hydrogen atom (H10) as the reactive site for nucleophilic attack provide an enhancement for dimer formation [31]. The MEP diagram of dimer Fig.6.b clearly illustrates the loss of colour in the reactive sites of oxygen due to the presence of donor-acceptor interactions. 4.4.5. Mulliken charge analysis Mulliken atomic charges can be estimated by determining the electron population of each atom as defined by their basis function and calculated at various basis sets HF/6-31G**, B3LYP/6-31G**, B3LYP/6-311G**, B3LYP/6-311++G**. The values for various basis sets of monomer and dimer are documented in Table 8. C1 atom in both the molecules presented negative charges, whereas C2, C3, C4, C5, C6 and C7 exhibited positive charges. C1 atom in both molecules were found to be attached to non electronegative carbon atom which could be the reason for their negative charges while the C atoms (C2, C3, C4, C5 and C6) were attached to high electronegative fluorine atom bearing the positive charge. The C7 atom attached to the oxygen atom possessed the maximum positive charge. The observed Mulliken charge value of

O8 oxygen decreased in dimer with respect to monomer in all basis sets revealing the presence of intermolecular hydrogen bond in dimer. 5. Summary and Conclusion DFT studies on pentafluorobenzoic acid were performed to obtain the stable molecular structure and conformational properties. The potential energy curve was obtained by the rotation of carboxylic acid at B3LYP/6-31G** level of theory and the analyses of the profile indicated stable structure of PFBA molecule at rotation angles of 134.60 and -45.80. Further, the optimization was carried out at various levels of theory for the most stable conformer structure including the HF method. The results showed that the geometrical parameters which were computed in B3LYP/6311++G** level of theory was found to be closer to the experimental one. A characteristic broad band of OH stretching that appeared around 3000 cm-1 in the Fourier transform infrared spectrum clearly showed the presence of inter molecular attraction. Presence of carboxylic group leads to the formation of a dimer. Geometrical optimization was done at DFT/B3LYP/6-311++G** level theory for dimer structure, which fairly exhibited a H-bridge between the two molecules of PFBA. The confirmation of dimer through intermolecular hydrogen bonding was further established by the electron density decrease of antibonding O-H and larger delocalization of hydrogen bonded O---H-O through NBO analysis. Molecular electrostatic potential maps were able to indicate the possible regions of dimerization. In dimer structure, both in electrophilic and nucleophilic regions the colour intensity was found to drop as compared to monomer confirming the intermolecular interaction. The charge of O atom participating in the intermolecular hydrogen bonding decreased in all basis sets for dimer when compared with the monomer indicating the formation of hydrogen bond. Acknowledgement The authors thank Dr. T. R. Ravindran (Materials Science Group, IGCAR, Kalpakkam) for carrying out Raman measurement. My thanks are also to The Principal, Secretary, and the management of Sri Paramakalyani College, Alwarkurichi for providing the fecilities. References [1]

http://www.ehow.com/about_5435322_uses-benzoic-acid.html

[2]

V. Balachandran, S. Lalitha, S. Rajeswari, V.K. Rastogi, Spectrochim Acta A 121 (2014) 575-585.

[3]

S. Conrad, S. Dawso, E. Hubbard, T. Meyers, K. Strothkamp, Biochemistry 33 (1994) 5739–5744.

[4]

Jiao Gao, Yongjun Hu, Shaoxin Li, Yanjiao Zhang, Xue Chen, Spectrochim. Acta A, 104 (2013) 41-47

[5]

C.U. Galdiga, T. Greibrokk, Fresen. J. Anal. Chem. 361 (1998) 797.

[6]

V. Krishnakumar, N. Mathammal J. Raman Spectrosc. 40 (2009) 1104-1109.

[7]

Mehmet Karabacak, Zeliha Cinar, Mehmet Cinar, Spectrochim. Acta A, 79 (2011) 1511-1519.

[8]

V. Mukherjee, N.P. Singh, R.A. Yadav, Spectrochim. Acta A 74 (2009) 1107–1114.

[9]

V. Mukherjee, N.P. Singh, R.A. Yadav, Spectrochim. Acta A 77 (2010) 787–794.

[10]

V. Mukherjee, N. P. Singh, R. A. Yadav Vib. Spectrosc . 52 (2010) 163–172.

[11]

V. Mukherjee, N.P. Singh, R.A. Yadav, J. Mol. Struct. 988 (2011) 24–34.

[12]

V. Krishnakumar, K. Murugeswari, N. Surumbarkuzhali, Spectrochim. Acta A 114 (2013) 410- 420.

[13]

M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheesman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann Jr., J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N.Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, N. Roga, P. Salvador, J.J. Dannenberg, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. AL-Laham, C.Y. Penng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W.

Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, J.A. Pople, Gaussian 98, Revision A. 11.4, Gaussian Inc., Pittsburgh, PA, 2003. [14]

T. Sundius, Vib. Spectrosc. 29 (2002) 89–95.

[15]

T. Sundius, MOLVIB (v.7.0); Calculation of Harmonic Force Fields and Vibraional Modes of Molecules, QCPE, Program No. 807, 2002.

[16]

T. Sundius, MOLVIB: a program for harmonic force felds calculations, CPE Program No. 604, J. Mol. Struct. 218 (1990) 321–326.

[17] G. Fogarasi, P. Pulay, in: J.R. Durig (Ed.), Vibrational Spectra and Structure, vol. 14, Elesevier, Amsterdam, 1985, 125 (Chapter 3). [18] G. Fogarasi, X. Zhov, P.W. Taylor, P. Pulay, J. Am. Chem. Soc.114 (1992) 8191– 8201. [19]

A.E. Reed, L.A. Curtiss, F. Weinhold, Chem. Rev. 88 (1988) 899–926.

[20]

C. James, A. Amal Raj, R. Reghunathan, I. Hubert Joe, V.S. Jayakumar, J. Raman Spectrosc. 37 (2006) 1381-1392.

[21]

E. Scrocco, J. Tomasi, Adv. Quantum Chem. 11 (1978) 115.

[22]

J.S. Murray, K. Sen, Molecular Electrostatic, Potentials Concepts and Applications, Elsevier, Amsterdam, 1996.

[23]

G.A. Sim, J.M. Robertson, T.H. Goodwin, Acta Crystallogr.8 (1955) 157.

[24]

G. Varsanyi, Vibrational Spectra of Benzene Derivative, Academic Press, New York, 1969.

[25]

George Socrates, Infrared and Raman Characteristic Group Frequencies–Tables and Charts (3rd edition), John Wiley & Sons, Chichester 2001.

[26]

S. Chandra, H. Saleem, N. Sundaraganesan, S. Sebastian, Spectrochim. Acta A 74 (2009) 704-713.

[27]

R.M. Silverstein, F.X. Webster, Spectroscopic Identification of Organic Compound, 6th ed., John Wiley & Sons, New York, 1998.

[28] D.N. Sathyanarayana, Vibrational Spectroscopy Theory and Application, New Age International Publishers, New Delhi, 1996. [29] C. Ravikumar, L. Padmaja, I. Hubert Joe, Spectrochim.Acta A 75 (2010) 859–866. [30] Shruti Maheshwary, U. Lourderaj, N. Sathyamurthy, J. Phys. Chem. A 110 (2006) 12662-12669. [37] A.R. Katritzky, A.F. Pozharski, Handbook of Heterocyclic Chemistry, second ed., Elsevier, Pergamon, 2000.

Figure caption Fig. 1. Stable conformations of pentafluorobenzoic acid Fig. 2. FTIR spectra of pentafluorobenzoic acid Fig. 3. Raman spectra of pentafluorobenzoic acid Fig. 4. Optimized structure of pentafluorobenzoic acid obtained by B3LYP/6-311++G** density functional calculations along with numbering of atoms Fig. 5. Optimized structure of pentafluorobenzoic acid dimer obtained by B3LYP/6311++G** density functional calculations along with numbering of atoms. Fig. 6. MEP for (a) monomer and (b) dimer PFBA

(a)

(b)

(c)

(d) Fig. 1.

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6.a

Fig. 6.b

Table caption Table 1. Observed and B3LYP/6-31G** level calculated vibrational frequencies (in cm-1) Table 2. PFBA conformer energies in Hartrees Table 3. Energies of PFBA obtained by HF method at 6-31G along with B3LYP/6-31G**, B3LYP/6-311g**, B3LYP/6-311+g**, B3LYP/6-311++g** calculations. Table 4. Geometrical parameters of PFBA by density functional theory calculations Table 5. The mean absolute deviations between the calculated and experimental geometrical parameters of PFBA. Table 6. Occupancies of bonding and antibonding orbitals, Table 7. Electron density changes of selected atoms. Table 8. Mulliken atomic charges of PFBA

Observed frequency -1

(cm )

Calculated frequency (cm-1) with B3LYP/631G** force field

S.No

IR

Raman

Unscale

Scaled

IRa(Ai)

Ramanb

d

TED (%) among type of internal coordinatesc

(Ii)

1

3415

-

3755

3415

97.68

157.04

υ OH

2

1719

-

1824

1720

382.59

36.1

υ C=O ( 67), bCO ( 10), υ CC ( 8), υ CO ( 5)

3

-

1665

1672

1670

81.05

38.39

υ CC ( 70), bring ( 13), bCF ( 9), υ CF ( 7)

4

1654

1658

1652

1649

14.88

4.87

υ CC ( 65), bring ( 13), υ CF ( 10), bCF ( 7)

5

1528

1534

1540

1533

136.94

0.5

υ CC ( 50), υ CF ( 38), bCF ( 11)

6

1491

1519

1522

1514

395.45

2.37

υ CC ( 49), υ CF ( 34), bCF ( 7), bCC ( 6)

7

1424

1410

1434

1428

56.28

22.32

υ CC ( 51), υ CF ( 42)

8

-

1389

1383

1385

145.85

2.86

υ CF(21), bring (17), CO (17), bCOH (16), υ CC(14), bC=O (10)

9

1319

1318

1318

1314

6.27

2.27

υ CC ( 77), υ CF ( 7), bring ( 6)

10

-

1310

1306

1312

7.81

1.06

υ CC ( 35), υ CF ( 26), bring ( 20), bCOH ( 10)

11

1257

1180

1185

1182

365.68

11.03

bCOH ( 33), υ CO ( 28), υ CF ( 13), υ CC ( 13), bC=O ( 5)

12

1155

1155

1163

1159

1.97

0.87

υ CF ( 77), bring ( 12), υ CC ( 9)

13

1110

-

1115

1111

31.42

2.99

υ CF ( 47), υ CO ( 20), υ CC ( 11), bring ( 9)

14

997

1009

1013

1008

248.69

0.45

υ CF ( 61), υ CC ( 14), bCF ( 12), bCC

15

911

914

911

908

44.21

2.26

υ CC ( 39), υ CF ( 26), bCF ( 14), υ CO ( 12), bring ( 6)

16

821

820

824

822

23.64

0.32

gCO( 40), bCF ( 29), bCC ( 10), gCC ( 7), tring ( 6)

17

777

775

770

765

11.94

0.12

bCF(28), tring (19), gCO (12), gCF(11), gCC (11), bC=O (8)

18

713

678

678

670

92.17

4.73

Tring(25), gCF(19), bCO (14), bC=O (10), bring (8), bCOH (7)

19

-

663

669

667

26.77

1.47

tring ( 48), gCF

20

-

658

665

650

0.78

0.41

gCF

( 64), tring ( 36) ( 50), tring ( 36), tOH ( 9)

(100)

21

-

641

650

636

29.14

0.86

22

-

589

582

586

3.95

9.87

bring ( 36), υ CF ( 36), υ CC ( 24)

23

-

559

568

558

53.72

5.85

tOH

24

-

510

504

506

3.57

10.44

bring ( 36), υ CC ( 35), υ CF ( 18), bC=O ( 6)

( 39), gCF ( 29), tring ( 18), gCO

25

465

449

447

453

0.3

5.42

bring ( 75), υ CF ( 9), υ CC ( 9)

26

-

439

439

435

2.68

0.36

bCO

( 37), bC=O ( 98)

( 42), υ CC ( 26), bring ( 18)

( 9)

( 27), gCF ( 17)

27

-

394

396

388

0.37

3.25

gCF

28

-

365

366

365

1.29

2.6

bCF

gCF (33), bCF ( 22), gCC(11), bCO ( 9), tring ( 9), bC=O (7)

29

-

313

324

320

2.67

0.99

30

-

306

306

304

1.09

0.69

bCF 44), gC ( 16), bC=O ( 11), υ CC ( 8), bCO ( 8)

31

-

292

298

296

1.09

1.3

bCF( 37), υ CC ( 26), bCO ( 14), bring ( 11), gCF ( 7)

32

-

278

281

279

0.06

0.26

bCF ( 77), bring ( 21)

33

-

265

274

271

0.1

0.09

bCF ( 87), bring ( 10)

34

-

188

208

205

1.78

0.05

gCF

35

-

163

170

168

0.49

0.65

bCC ( 62), tring ( 6), gCO ( 5), gCC ( 5), bC=O (5)

36

-

156

161

162

0.22

0.04

tring ( 77), gCC (6), bCC ( 6)

37

-

126

129

130

0.01

0.04

tring ( 98)

38

-

78

80

80

0.28

0.12

tring ( 43), gCC

( 30), bC=O ( 8), bCO ( 8), gCO (5)

39

-

41

45

42

1.77

1.23

tCO

( 9)

( 67), tring ( 19), gCC

( 73), bCF

Relative absorption intensities normalized with highest peak absorption equal to 1.0. Relative Raman intensities calculated by Eq. (2) and normalized to 100. c For the notations used see ST4 b

( 38)

gCF

Abbreviations: υ - Stretching, b - Bending, g - Wagging, t - Toorsion a

( 6)

( 11)

Conformer

Eneergy in Hartrees

a

-907.5379033900

b

-916.7090561800

c

-916.7090561900

d

-907.3597309300

Computational methods

Energy in Hartrees

HF/6-31G

-912.1948581

B3LYP/6-31g**

-916.9461768

B3LYP/6-311g**

-917.209632

B3LYP/6-311+g**

-917.2390484

B3LYP/6-311++g**

-917.2391103

C1-C2 C2-C3 C3-C4 C4-C5 C5-C6 C6-C1 C1-C7 C7-O8 C7-O9 O9-H10 C2-F11 C3-F12 C4-F13 C5-F14 C6-F15

HF/6-31G 1.395 1.376 1.374 1.373 1.377 1.394 1.486 1.208 1.340 0.955 1.349 1.353 1.347 1.354 1.349

B3LYP/631G** 1.403 1.392 1.392 1.393 1.392 1.404 1.495 1.210 1.350 0.973 1.335 1.336 1.332 1.336 1.332

B3LYP/6311G** 1.398 1.389 1.389 1.389 1.389 1.399 1.498 1.201 1.347 0.969 1.334 1.335 1.331 1.334 1.332

B3LYP/6311+G** 1.397 1.389 1.39 1.390 1.389 1.398 1.499 1.202 1.347 0.970 1.335 1.334 1.330 1.334 1.333

C1-C2-C3 C2-C3-C4 C3-C4-C5 C4-C5-C6 C5-C6-C1 C6-C1-C2 C7-C1-C2 C7-C1-C6 C1-C7-O8 C1-C7-O9 O8-C7-O9 C7-O9-H10 C1-C2-F11 C3-C2-F11 C2-C3-F12 C4-C3-F12 C3-C4-F13 C5-C4-F13 C4-C5-F14 C6-C5-F14 C5-C6-F15 C1-C6-F15

121.97 120.07 119.51 120.35 121.65 116.45 119.83 123.72 124.52 113.55 121.93 113.52 121.76 116.27 120.11 119.82 120.25 120.24 119.70 119.95 115.73 122.62

121.55 119.81 119.92 119.77 121.57 117.38 123.14 119.46 124.32 112.43 123.24 105.81 121.35 117.1 120.3 119.89 120.02 120.06 119.91 120.32 117.33 121.09

121.41 119.75 120.00 119.72 121.41 117.71 122.71 119.55 124.29 111.96 123.75 106.50 121.14 117.43 120.40 119.85 119.99 120.01 119.85 120.42 117.65 120.91

121.51 119.65 120.01 119.65 121.49 117.69 122.39 119.89 124.17 111.75 124.08 107.44 120.78 117.68 120.48 119.87 119.98 120.01 119.86 120.49 117.85 120.63

B3LYP/6311++G** 1.397 1.389 1.39 1.390 1.389 1.398 1.499 1.202 1.347 0.970 1.335 1.334 1.330 1.334 1.333 121.51 119.65 120.01 119.65 121.49 117.69 122.39 119.89 124.17 111.75 124.08 107.44 120.78 117.68 120.48 119.87 119.98 120.01 119.86 120.49 117.85 120.63

Dimer B3LYP/6311++G** 1.398 1.389 1.39 1.390 1.389 1.398 1.497 1.222 1.315 0.998 1.334 1.334 1.330 1.334 1.333 121.48 119.67 120.02 119.66 121.49 117.67 122.07 120.24 121.46 113.43 125.11 110.16 120.84 117.64 120.46 119.87 120.00 119.98 119.86 120.48 117.77 120.71

BAa 1.39 1.42 1.36 1.37 1.41 1.39 1.48 1.24 1.29 120.0 122.0 118.0 123.0 118.0 119.0 122.0 -

HF/6-31G

B3LYP/ 6-31G**

B3LYP/ 6-311G**

B3LYP/ 6-311+G**

B3LYP/ 6- 311++G**

C1-C2 C2-C3 C3-C4 C4-C5 C5-C6 C6-C1 C1-C7 C7-O8 C7-O9

0.005 -0.044 0.014 0.003 -0.033 0.004 0.006 -0.032 0.050

0.013 -0.028 0.032 0.023 -0.018 0.014 0.015 -0.030 0.059

0.008 -0.031 0.029 0.019 -0.021 0.009 0.018 -0.039 0.057

0.007 -0.031 0.03 0.020 -0.021 0.008 0.019 -0.038 0.057

0.007 -0.031 0.03 0.020 -0.021 0.008 0.019 -0.038 0.057

Dimer B3LYP/ 6-311++G** 0.008 -0.031 0.030 0.020 -0.021 0.008 0.017 -0.018 0.025

C1-C2-C3 C2-C3-C4 C3-C4-C5 C4-C5-C6 C5-C6-C1 C6-C1-C2 O8-C7-O9

1.972 -1.926 1.507 -2.649 3.650 -2.554 -0.068

1.551 -2.194 1.921 -3.232 3.572 -1.619 1.240

1.405 -2.254 2.002 -3.277 3.410 -1.293 1.752

1.511 -2.353 2.010 -3.352 3.492 -1.315 2.076

1.511 -2.353 2.010 -3.352 3.492 -1.315 2.076

1.481 -2.33 2.016 -3.339 3.49 -1.326 3.106

Donor NBO

Type of bond

Occupancy

Acceptor NBO

Type of bond

Occupancy

Energy

Kcal/mol From unit 1 to unit 2 O8

n(2)

1.84431

O24-H25

σ* (1)

0.06523

18.93

O8

n(1)

1.95936

O24-H25

σ* (1)

0.06523

8.66

From unit 2 to unit 1 O23

n(2)

1.84431

O9-H10

σ* (1)

0.06518

18.91

O23

n(1)

1.95935

O9-H10

σ* (1)

0.06518

8.65

NBO

Changes of electron density

O8 LP (1)

0.02061

O8 LP (2)

0.00814

C7- O8 (σ*)

0.00085

C7- O8 (π*)

0.00074

O9- H10 (σ*)

0.00254

C7- O9 (σ*)

0.0004

Atoms C1 C2 C3 C4 C5 C6 C7 O8 O9 H10 F11 F12 F13 F14 F15

Dimer HF/631G** B3LYP/631G** B3LYP/6311G** B3LYP/6311++g** B3LYP/6311++g** -0.401 -0.098 -0.253 1.778 1.509 0.481 0.307 0.28 -0.908 -0.956 0.352 0.257 0.189 0.323 0.315 0.39 0.275 0.202 0.189 0.12 0.35 0.256 0.186 0.309 0.32 0.463 0.305 0.266 -0.966 -0.976 1.034 0.555 0.393 0.189 0.562 -0.583 -0.441 -0.302 -0.232 -0.304 -0.718 -0.471 -0.305 -0.136 -0.289 0.429 0.332 0.263 0.296 0.527 -0.354 -0.254 -0.184 -0.149 -0.144 -0.364 -0.262 -0.189 -0.182 -0.182 -0.358 -0.254 -0.181 -0.177 -0.168 -0.365 -0.261 -0.188 -0.183 -0.184 -0.357 -0.247 -0.177 -0.152 -0.15

Highlights  Geometrical properties of PFBA were optimised using B3LYP/6-311++G**  A complete assignment of observed fundamentals has been dealt with based on PED  A correlation of theoretical and experimental data  Identification and confirmation of intermolecular hydrogen bond in the dimer of PFBA