Density functional theory and FTIR spectroscopic study of carboxyl group

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1 Indian Journal of Pure & Applied Physics Vol. 43, December 2005, pp Density functional theory and FTIR spectroscopic study of carboxyl group Medhat Ibrahim 1, Abdallah Nada 2, & Diaa Eldin Kamal 1 1 Spectroscopy Department, National Research Center, Dokki, Cairo, Egypt 2 Cellulose and Paper Department, National Research Center, Dokki, Cairo, Egypt Received 29 March 2005;revised 7 September 2005;accepted 30 September 2005 Both molecular modelling and FTIR have been used to study carboxyl group among acetic acid, potassium and sodium acetate, glycine, sodium salicylate, salicylic acid and cellulose acetate. Molecular modelling was used to study formic acid, carboxylic acids R-COOH, monovalent alkali carboxylate CH 3 COO-M, alanine, benzoic acid as well as naphthalene. Each structure was optimized using VWN/DZVP then vibrational spectra were further calculated at the same level of theory. The comparison between both calculated and experimental spectra showed good agreement with each other. Except for formic acid and free carboxyl, the characteristic band is shifted towards lower frequency. Keywords: FTIR spectroscopy, Density functional theory, Carboxyl group, Cellulose acetate IPC Code: G01J3/28 1 Introduction Studying carboxyl group (COOH) and its interactions is very important in many areas of science: such as surface science 1-2, electrochemistry 3-4, and biology 5,6. In environment, COOH of humic acid plays a crucial role in speciation, transport and deposition of metal ions It is one of the important groups leading to the reactivity of humic substances Furthermore, trace metals could interact with humic substances as a result of electrostatic attraction and/or formation of a chelate structure to a charged COO group 12. COOH of both formic and carboxylic acids possess potentially two proton binding sites namely OH and C=O groups. Proton bound clusters are known to form hydrogen bounded networks 14. Many proton bounded clusters have been investigated experimentally 15,16 as well as througth molecular modelling 17,18. The existence of COO ν as around 1535 cm -1 and ν s around 1424 cm -1 is a characteristic feature of Ca ++ bounded Calmodulin and Parvalbumin The spectra of K, Na, Mg and Ca caroxylate were studied earlier, experimentally as well as via molecular modelling 22. Molecular modelling was used to study COOH among different structures. The model B3LYP/6-31G(d,P) was used to obtain the vibrational spectra of carboxyl in case of acetic acid, polyacrylic acid as well as benzoic acid 23. Ab initio calculations were used to study the interface between titanium oxide and amino acid in solution 24. Both ab initio and Density Functional Theory (DFT) were used to predict the 1:1 complexes of formic acid with pyrrole or imazole 25. Both FTIR and DFT were used to study the spectra of monomeric glycolic acid 26. Twelve triple complexes of nine adenine tautomers with carboxylate ion of acetic acid and sodium ion were studied by DFT method 27. Both infrared and ab initio of the hydrogen bonding between formic acid and water were studied. The complex formation resulted in red shifts in the C=O and O-H stretching vibrations and a blue shift in the C-O stretching vibration of formic acid 28. Vibrational mode analysis on mechanism of the pyrolysis of formic acid in the gas-phase catalyzed by water dimer or formic acid itself was proposed 29. Infrared spectra of bicyclic and tricyclic amidine derivatives of alanine were computed. The correlation between the calculated and experimental vibrational frequencies was characterized by the coefficients of for DFT methods; and for HF (Ref.30). The geometric and electronic structure of 1,8-bis(dimethylamino)-4-cyano-naphthalene and its mono-protonated cation have been investigated by DFT and time dependent density functional theory methods 31 (TD-DFT). Both IR and Raman spectroscopic studies of salicylic and salicylate derivatives in aqueous solution were conducted 32, and results were compared with DFT. The intramolecular hydrogen bonding of salicylic acid was further studied 33. Both kinetic and chemical modification analysis suggested that carboxylate and carboxyl groups are involved directly in the enzymatic reaction of -glucosidases Enzyme avoids

2 912 INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005 unstable charged intermediates in reaction by having groups appropriately located to donate or accept a proton 36. In almost all cases, a proton is abstracted from a carbon adjacent to carbonyl, carboxylic acid or carboxylate anion group by an active site residue because the -protons are acidic by virtue of the resonance stabilization of the enolic intermediate 37. In this work, both FTIR and DFT are utilized to study carboxyl group in case of acetic acid, potassium and sodium acetate, glycine, sodium salicylate, salicylic acid and cellulose acetate. Furthermore, carboxyl group of formic acid, carboxylic acids R-COOH, monovalent alkali carboxylate CH 3 COO- M, alanine, benzoic acid and naphthalene have been investigated using DFT. 2 Experimental Details Glycine was delivered from BDH, England. Both sodium salicylate and salicylic acid were produced from VEB, Germany. Acetic acid 95.0% solution and cellulose acetate powder are the products of Sigma- Aldrich, Germany. Both potassium and sodium carboxylates were obtained from the reaction of acetic acid with their hydroxides at ph 6.0. The IR-spectra of acetic acid, potassium, sodium carboxylates and salicylic acid are measured with BRUKER EQUINOX 55 Fourier Transform Interferometer, with a direct attachment of diffuse reflectance infrared fourier transform spectroscopy (DRIFT), at Juelich Research Center, Germany. The spectral range of which is cm -1. The remaining spectra were recorded using KBr pellet, with a fourier transform IR spectrometer JASCO, FTIR- 300 E, its spectral range is cm -1, at National Research Center, Egypt. All calculations were performed with the Cache program, at Spectroscopy Department, National Research Center, Egypt. The geometries were optimized using Local Spin Density treatment of Vosko, Wilk and Nusair VWN-LDA, with DZVP basis set. Thereafter a force constant calculation was performed to obtain the infrared frequencies and the corresponding infrared intensities (vibrational spectra were performed in the harmonic approximation). Furthermore, the assignment of the vibrational modes was performed by visualization of the eigenvectors. The errors within this type of calculations including a significant part of anharmonicity corrections, can be avoided using empirical scale factor Results and Discussion Carboxyl group was studied experimentally in case of acetic acid, potassium and sodium acetates, salicylic acid, sodium salicylate, glycine as well as cellulose acetate. It is important to point out that band assignment is achieved by comparing the eigenvectors and intensities of the calculated bands with those observed by FTIR. DRIFT spectroscopy was used to study liquid phase to avoid interference due to moisture (water molecules) over the range 1520 to 1700 cm -1. Furthermore, the KBr discs were dried before analyses for the same reason. Figure 1(a) presents the infrared spectra of acetic acid in liquid phase. The assignment of acetic acid has been discussed elsewhere 23. The main spectral characteristics of acetic acid are two sharp bands at 1276 cm 1 corresponding to C-C vibration and at 1709 cm 1 corresponding to C=O symmetric stretching. A band at 1440 cm 1 is assigned as C-H in-plane bending and C-H out-of-plane bending at 960 cm 1. Figure 1(b) presents the infrared spectra of both Fig. 1 FTIR spectrum of a carboxylic acid liquid phase and b- potassium and sodium acetate liquid phase

3 IBRAHIM et al.: DFT AND FTIR SPECTROSCOPIC STUDY OF CARBOXYL GROUP 913 sodium and potassium acetates. Smith 39 stated that, as alkali metal bonded to carboxyl instead of hydrogen bonding, the resulting arrangement is becoming unusual producing two-bond and half-linkages which can stretch asymmetrically and symmetrically producing two intense bands. The asymmetric COO stretching is obtained at , cm 1 and the symmetric COO is obtained at , cm 1 for both Na and K acetates, respectively. It is worth mentioning that the intensity of both COO bands is due to the strong dipole moment of the carbon-oxygen bonds. Figure 2(a) presents the infrared spectra of salicylic acid. From Fig.2(a) we can notice the O-H stretching of the acid at 3300 cm 1, the aromatic C-H appears at 3064 cm 1, two C=O stretching at both 1753 cm 1 and 1668 cm 1, followed by two aromatic ring modes at 1604 cm 1 and 1575 cm 1. Then, the in-plane O-H bending for the acid appears at 1418 cm 1, the methyl umbrella mode at 1369 cm 1, C-O stretch at 1305 cm 1, the saturated ester C-C-O at 1188 cm 1 followed by O-C-O at 1094 cm 1 and the O-H bending out-of-plane of the acid, at 917 cm 1, and finally, the out-of-plane C-H bending aromatic at 755 cm 1. The infrared spectrum of sodium salicylate is illustrated in Fig. 2(b). Special interest is directed to the symmetric and asymmetric COO bands at cm 1 and cm 1, respectively. The shift from 1753 cm 1 (C=O) to cm 1 (COO) is corresponding to changing the carboxyl group into carboxylate with a change in its bond arrangement into one and half linkage. The recorded shift agrees with those shifts in case of acetic acid and both Na and K acetate. This assignment is in a good agreement with Brian s 39. Glycine is the simplest amino acid and is quite abundant in various proteins and enzymes. Glycine in its solid form is studied in the spectral range cm -1. Figure 3(a) illustrates the spectrum of glycine. A weak band corresponding to symmetric CH stretching appears at 2898 cm 1, followed by a combination band (697 and 1413 cm 1 ) at 2123 cm 1. C=O stretching plus other vibrations are seen at 1703 cm 1. The band NH 2 scissoring appeared at 1610 Fig. 2 Vibrational spectrum of a Salicylic acid and b- Sodium salicylate Fig. 3.Infrared vibrational spectrum of a Glycine and b - Cellulose acetate

4 914 INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005 cm 1. CH 2 bending beside OH bending at 1521 cm 1. CH 2 scissoring appeared at 1413 cm 1. A band consists of both NH 2 twist and CH 2 twist at 1333 cm 1. A band at 1033 cm 1 can be assigned to the C-N stretch in addition to C-C vibration. Again, a band at 892 cm 1 appears with two vibrations namely NH 2 twist and CH 2 twist. Finally, a band at 698 cm 1 is assigned to NH 2 bending. The band assignment of glycine is in good agreement with Kumar et al. 40 assignment. Figure 3(b) presents the infrared spectrum of cellulose acetate. A strong broad band at cm 1 is assigned to OH stretching. The band at cm 1 is C-H stretching of CH 3 which is followed by a weak band at 2891 cm 1 corresponding to C-H stretching of CH 2. The band can be assigned to the acetyl group on the polymeric chain at cm 1 (of the C=O) followed by the asymmetric stretching of C=O at cm 1. The medium intensity band at 1382 cm 1 is related to the angular distortion of the CH in the ester methyl group 41. The C-O symmetric stretching appears at cm 1 and the asymmetric C-O-C band at cm 1. Finally, two bands appear at and cm 1 assigned to C-O and C-H, respectively. 3.1Calculated vibrational spectra of carboxyl group Table 1 presents the calculated infrared spectra of carboxyl group. Carboxyl group is first optimized then vibrational spectrum is calculated both at VWN/DZVP level. In Table 1, there are six vibrational modes corresponding to the carboxyl group. The bands are obtained at the frequencies, 574.1, 660.3, , , and finally at cm 1. The vibrational modes are assigned to C-OH torsion, C=O out-of-plane bending, OCO deformation, C-O stretching, C=O stretching and OHstretching, respectively. All the vibrational modes are corresponding to A symmetry, except the mode OCO deformation which is corresponding to A symmetry. The calculated infrared intensities were 32.17, , , 1.18, and km/mole. The calculated infrared intensity indicates that C=O symmetric stretching is the characteristic band of the carboxyl group which is in good agreement with experimental results. As a result, the spectroscopic behaviour of the carboxyl group will be discussed in terms of the characteristic band. Figure 4 shows the studied structures, which contains carboxyl group. In Table 1 Infrared vibrational frequency in cm -1, infrared intensity in km/mole and the band assignment of free carboxyl group which weere calculated using VWN/DVZP model Frequency, cm -1 Infrared intensity Assignment A C-OH torsion A C=O op-bend A OCO deform A C-O stretch A C=O stretch A OH stretch Fig. 4 Schematic diagram of the studied structures that contain carboxyl group namely: a Formic acid, b Carboxylic acid R-COOH, c Alkali metal acetate d Benzoic acid, e Glycine, f Alanine, g Naphthalene and h Salicylic acid. Where R= CH 3, CH 3 CH 2, CH 3 (CH 2 ) 2, CH 3 (CH 2 ) 3, CH 3 (CH 2 ) 4 and M =Li, Na, K, Rb, Cs and Fr respectively

5 IBRAHIM et al.: DFT AND FTIR SPECTROSCOPIC STUDY OF CARBOXYL GROUP 915 Table 2 Calculated C=O symmetric stretching in cm -1 for formic acid, and carboxylic acid R-COOH using VWN/DZVP model Structure C=O stretching, cm -1 HCOOH COOH CH 3 COOH CH 3 CH 2 COOH CH 3 CH 2 CH 2 COOH CH 3 CH 2 CH 2 CH 2 COOH CH 3 CH 2 CH 2 CH 2 CH 2 COOH Table 3 Calculated C=O symmetric stretching in cm -1 for glycine, alanine, benzoic acid, naphthalene and salicylic acid using VWN/DZVP model Structure C=O stretching, cm -1 Free carboxyl Alanine Benzoic acid Naphthalene Salicylic acid and Glycine the case of free carboxyl, each structure is optimized and the vibrational frequencies are calculated using VWN/DZVP model. Carboxyl group is optimized in case of formic acid, as well as carboxylic acids R-COOH, where R varies from CH 3 to CH 3 (CH 2 ) 4, respectively. Generally, the optimized carboxylic acids structures are C s symmetry. The characteristic band C=O is compared with that of free carboxyl. As in Table 2, C=O of carboxyl group is at cm 1, the band is shifted up to cm 1 in case of formic acid. C=O showed a shift from cm 1 to cm 1 ongoing from CH 3 COOH to CH 3 (CH 2 ) 4 COOH, which means that only 9.9 cm 1 shift is regarded as a result of hydrocarbon chain effect on carboxyl group of R-COOH, while the shift is 31.6 cm 1 as compared with C=O of free carboxyl. Table 3 shows C=O of carboxyl in case of another five structures namely: Glycine, alanine, benzoic acid, naphthalene and salicylic acid. A noticeable change in the C=O is recorded in case of alanine, which is shifted to 29.6 cm 1. Another shift of 56.1 cm 1 corresponds to benzoic acid. While the characteristic band in case of naphthalene is calculated at cm 1 with a shift of about 61.7 cm 1. Finally, salicylic acid has two bands at and cm 1. Then C=O of glycine is cm 1 with a shift of cm 1. It is clear that C=O of the studied structure is shifted to lower frequencies as compared with free carboxyl. It is worth to mention that, at VWN/DZVP level of theory negative frequencies were obtained for Table 4 Effect of alkalies on the characteristic band of carboxyl group Structure Asymmetric COO stretching Symmetric COO stretching CH 3 COO-Li CH 3 COO-Na CH 3 COO-K CH 3 COO-Rb CH 3 COO-Fr CH 3 COO-Cs C 6 H 4 (OH)-COO-Na C 6 H 5 COO-Na HCOO-Na CH 3 CH(NH 2 )-COO-Na CH 3 CH 2 COO-Na CH 3 CH 2 CH 2 COO-Na Table 5 Effect of hydrocarbon chain and aromatic cycle on the characteristic band of carboxyl ions Structure C=O stretching, cm -1 C 6 H 4 (OH)-COO 1745 and CH 3 CH(NH 2 )-COO CH 3 COO C 10 H 8 -COO C 6 H 5 COO cellulose acetate. The negative sign indicates that the vibrational spectrum is calculated for the transition state not for the optimum structure. Accordingly, the vibrational spectra of cellulose acetate is not considered at this level of theory. The effect of six monovalent alkalis on COOH vibrations was studied. The results of COO of the studied alkali carboxylate are given in Table 4. The frequency of asymmetric COO is increasing slightly from Li up to Cs. COO symmetry shows the same behaviour with an exception that Na and Cs show higher values. Another effect on COOH is tested as sodium is coordinated instead of hydrogen to formic acid, alanine, benzoic acid, salicylic acid and two R-COOH structures. The calculated data are compared with COO of sodium carboxylate which are cm 1 and cm 1, respectively. Results in Table 4 indicate a shift of 19.0 cm 1 in symmetric COO while going from HCOO-Na to CH 3 CH 2 -Na, followed by a shift in case of CH 3 (CH 2 ) 2 - Na at about 2.6 cm -1. COO asymmetric stretching of alanine is cm -1 which is similar to that of sodium carboxylate, while COO symmetric is lower than that of sodium carboxylate by 11.8 cm -1. Regarding both salicylic and benzoic acids, COO asymmetric stretching shows a respective shift of 54.8 and 45.6 cm -1 towards high frequency. The COO symmetric stretchings are in contrast to those showing a respective shift towards lower frequency.

6 916 INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005 Table 6 Comparison between experimental spectra in cm -1 of glycine with their VWN/DZVP calculated values Experimental IR Calculated IR Assignment CH symmetric stretching Combined band C=O stretching NH 2 scissoring CH 2 bend + OH bend CH 2 scissoring NH 2 twist + CH 2 twist C-N stretching + C-C vibrations NH 2 twist + CH 2 twist NH 2 bend Table 5 presents the results of carboxylate ion in case of acetic acid, alanine naphthalene and salicylic acid. Negative frequencies were obtained in case of glycine, this indicates that the glycine structure is a transition state hence the optimum structure was not found at this level of theory. Generally, the results show that, C=O values of the carboxylate ion are lower as compared to carboxyl group of the same structures. Furthermore, carboxylate ion frequencies can be arranged according to the following decreasing order: Salicylic acid > alanine> acetic acid > Naphthalene>benzoic acid. 3.2Comparison between experimental and calculated spectra Table 6 presents both calculated and experimental vibrational modes of glycine. The optimized glycine molecule has Cs symmetry. Comparison of the results reveals that calculated vibrational modes are in good agreement with the FTIR results. Furthermore, modelling with DFT is considered to be a good tool for the bands assignment of molecules containing carboxyl group. 4 Conclusion Carboxyl group was subjected to both experimental as well as modelling study. Hydrocarbon chain like R- COOH has a shift in their characteristic band of carboxyl group slightly towards lower frequency. As compared with acetic acid (with the exception of both formic acid and free carboxyl group), all structures show a shift in their characteristic bands towards lower frequencies. This shift is slightly noticeable for R-COOH, alanine, benzoic acid and for naphthalene, while decrease is more in case of salicylic acid and glycine, and becomes significant in case of carboxylate ion. Alkali acetate shows a shift of about 200 cm -1 towards the lower frequency as a carboxyl ion is transformed into carboxylate. The calculated frequencies for some bands may be considered as of slightly overestimated values and the difference may be related to the anharmonic effect, which is avoided by scaling the calculated frequencies with empirical scale factor. In spite of this, calculation based on the DFT method shows good agreement with experimental results. Hence, it could be concluded that, COOH in both aliphatic and/or aromatic structures acts as a model system to verifying the usefulness of DFT method of calculation. References 1 Smith D A, Wallwork M L, Zhang J, Kirkham J, Robinson C, Marsh A & Wong M, J Phys Chem B, 104 ( 2000) Kokkoli E & Zukoski C F, Langmuir, 17 (2001) Boubour E & Lennox R B, Langmuir, 16 (2000) Sugihara K, Shimazu K & Uosaki K, Langmuir, 16 (2000) Franco M, Nealy P F, Campbell S, Teixeria A I & Murphy C J, J Biomed Mater Res, 52 (2000) Chapman R G, Ostuni E, Yan L & Whitesides G M, Langmuir, 16 (2000) MacCarthy P, Aquatic humic substances and their influence in the fate and treatment of pollutants. Edited by I. H. Suffet and P. MacCarthy [American Chemical Society. Washington, DC], (1989) pp Livens F R, Environ Pollut, 70 (1991) Pandey A K, Pandey S D & Misra V, Ecotoxicology and Enivronmental Safey, 47 (2000) Tsutsuki K & Kuwatsuka S, Soil Sci Plant Nutr, 24 ( 1978) Perdue E M, Reuter J H & Ghost M, Geochim Cosmochim Acta, 44 (1980) Stevenson F J, Humns Chemistry: Genesis, Composition, Reactions, 2 nd editions, [John Wiely & Sons, Inc., New York] (1994). 13 Lifshitz C & Louage F, J Phys Chem, 93 ( 1989) Feng W Y & Lifshitz C, J Phys Chem, 98 (1994) Lifshitz C & Feng W Y, Int J Mass Spectrom Ion Processess, 146 ( 1995) Hirata S & Iwata S, J Phys Chem B, 102 ( 1998) Colomins C, Teixido J, Cemeli J, Luque F J & Orozco F L, J Phys Chem B, 102 ( 1998) Zhang R Q, Wong N B, Lee S T, Zhu R S & Han K L, Chem Phys Lett, 319 ( 2000) Nara M, Tasumi M, Tanokura M, Hiraoki T, Yazawa M & Tsutsumi A, FEBS Lett, 349 ( 1994) Nara M, Tasumi M, Tanokura M, Hiraoki T, Yazawa M & Tsutsumi A, Biospectroscopy, 1 (1995) Nara M, Torii H & Tasumi M, J Phys Chem, 100 (1996) Ibrahim M & Koglin E, Bull NRC Egypt, 29 (2004) Ibrahim M & Koglin E, Acta Chim Slov, 51 (2004) Langel W & Menken L M, Surface Sci, 538 ( 2003) Minyaev R M, Minkin V L, Gribanova T N & Starikov A G, Mendeleev Communications, 5 (2003) 1.

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