The Theoretical Investigation of Molecular Structure, Vibrational Spectra and Electronic Properties of Palmitoleic Acid
Öz
In this study, the molecular structure, vibrational spectroscopic and electronic properties of Palmitoleic Acid (cis-9-Hexadecenoic acid, C16:1, POA) were investigated using the Gaussian 09 package program at DFT/B3LYP/6-311++G(d,p) level. Since the crystal structure of POA has not been determined yet, the optimized geometric parameters (bond length, bond angles and dihedral angles) were compared with experimental geometric parameters of Oleic acid (OA) which is isomorphous to the POA. The harmonic vibrational frequencies of the POA were calculated and compared with the experimental vibrational frequencies which obtained from the literature. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The calculated structural parameters and vibrational frequencies of POA are in good agreement with the experimental data. The electronic properties of the molecule were defined on the basis of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The high energy gap between HOMO-LUMO energies shows that the molecule has chemical stability and low reactivity. Molecular electrostatic potential (MEP) surface map, mulliken atomic charges and quantum chemical descriptors such as hardness, softness, electronegativity, chemical potential, ionization potential, electron affinity, electrophilic index, dipole moment were calculated to determine interaction sides in the molecule. Besides, the thermodynamic properties such as heat capacity, entropy, and enthalpy of POA at different temperatures were calculated in gas phase. All thermodynamic parameters increased with increasing temperature.
Anahtar Kelimeler
Palmitoleic Acid Density Functional Theory (DFT) Vibrational Analysis HOMO LUMO
Kaynakça
- Gennis, R.B. (1989). Biomembranes: Molecular Structure and Function Springer-Verlag, New York,.533.
- Small, D.M. (1986). The physical chemistry of lipids : from alkanes to phospholipids1th ed. Springer, London, 692.
- Jakobsen, M.U., Overvad, K., Dyerberg, J., Schroll, M., & Heitmann, B.L. (2004). Dietary fat and risk of coronary heart disease: Possible effect modification by gender and age. American Journal of Epidemiology, 160, 141–149.
- Yamamoto, Y., Kawamura, Y., Yamazaki, Y., Kijima, T., Morikawa, T., & Nonomura, Y. (2015). Palmitoleic Acid Calcium Salt: A Lubricant and Bactericidal Powder from Natural Lipids. Journal of Oleo Science, 64, 283–288.
- Yoon, W.-J., Kim, M.-J., Moon, J.-Y., Kang, H.-J., Kim, G.-O., & Lee, N.H. (2010). Effect of Palmitoleic Acid on Melanogenic Protein Expression in Murine B16 Melanoma. Journal of Oleo Science, 59, 315–319.
- Fischer, C.L., Drake, D.R., Dawson, D. V., Blanchette, D.R., Brogden, K.A., & Wertz, P.W. (2012). Antibacterial Activity of Sphingoid Bases and Fatty Acids against Gram-Positive and Gram-Negative Bacteria. Antimicrobial Agents and Chemotherapy, 56, 1157–1161.
- Wille, J.J. & Kydonieus, A. (2003). Palmitoleic Acid Isomer (C16:1Δ6) in Human Skin Sebum Is Effective against Gram-Positive Bacteria. Skin Pharmacology and Physiology, 16, 176–187.
- Çimen, I., Kocatürk, B., Koyuncu, S., Tufanlı, Ö., Onat, U.I., Yıldırım, A.D., et al. (2016). Prevention of atherosclerosis by bioactive palmitoleate through suppression of organelle stress and inflammasome activation. Science Translational Medicine, 8, 358ra126.
- Cimen, I., Yildirim, Z., Dogan, A.E., Yildirim, A.D., Tufanli, O., Onat, U.I., et al. (2019). Double bond configuration of palmitoleate is critical for atheroprotection. Molecular Metabolism, 28, 58–72.
- Kaneko, F., Yano, J., &Sato, K. (1998). Diversity in the fatty-acid conformation and chain packing of cis-unsaturated lipids. Current Opinion in Structural Biology, 8, 417–425.
- Kaneko, F., Yamazaki, K., Kobayashi, M., Sato, K., & Suzuki, M. (1994). Vibrational spectroscopic study on polymorphism of erucic acid and palmitoleic acid: γ1→α1 and γ→α reversible solid state phase transitions. Spectrochimica Acta Part A: Molecular Spectroscopy, 50, 1589–1603.
- Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J.,Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Peralta Jr, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J., Gaussian 09, Revision A.0.2, Gaussian, Inc., Wallingford CT, 2009.
- Sundaraganesan, N., Ilakiamani, S., Saleem, H., Wojciechowski, P.M., & Michalska, D. (2005). FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 61, 2995–3001.
- Jamróz M H (2010) Vibrational Energy Distribution Analysis VEDA 4, Warsaw.
- Dennington, R.,Keith, T.A., & Millam, J.M. (2008). Gaussview 5.0.8,Gaussian Inc., Wallingford, CT.
- Abrahamsson, S. & Ryderstedt-Nahringbauer, I. (1962). The crystal structure of the low-melting form of oleic acid. Acta Crystallographica, 15, 1261–1268.
- Kaneko, F., Yamazaki, K., Kobayashi, M., Kitagawa, Y., Matsuura, Y., Sato, K., et al. (1993). Structure of the γ phase of erucic acid. Acta Crystallographica Section C Crystal Structure Communications, 49, 1232–1234.
- Copyright © 2012-2018 Bio-Rad Laboratories, Inc. All Rights Reserved. https://spectrabase.com/spectrum/8R37FJJlI3H
- Machado, N.F.L., De Carvalho, L.A.E.B., Otero, J.C., & Marques, M.P.M. (2012). The autooxidation process in linoleic acid screened by Raman spectroscopy. Journal of Raman Spectroscopy, 43, 1991–2000.
- Gocen, T., Haman Bayarı, S., & Guven, M. H. (2017). Linoleic acid and its potassium and sodium salts: A combined experimental and theoretical study. Journal of Molecular Structure, 1150, 68–81.
- Lewandowski, W., Kalinowska, M., & Lewandowska, H. (2005). The influence of halogens on the electronic system of biologically important ligands: Spectroscopic study of halogenobenzoic acids, halogenobenzoates and 5-halogenouracils. Inorganica Chimica Acta, 358, 2155–2166.
- Silverstein, R.M., Bassler, G.C. & Morrill, T.C. (1976). Spectrometric identification of organic compounds, 3rd edition. Journal of Molecular Structure, 30, 424–425.
- Lewis, D.F. V., Ioannides, C., & Parke, D. V. (1994). Interaction of a series of nitriles with the alcohol-inducible isoform of P450: Computer analysis of structure—activity relationships. Xenobiotica, 24, 401–408.
- Pearson, R.G. (1988). Electronic spectra and chemical reactivity. Journal of the American Chemical Society, 110, 2092–2097.
- Zhan, C.-G., Nichols, J.A., & Dixon, D.A. (2003). Ionization Potential, Electron Affinity, Electronegativity, Hardness, and Electron Excitation Energy: Molecular Properties from Density Functional Theory Orbital Energies. The Journal of Physical Chemistry A, 107, 4184–4195.
- Sheela, N.R., Muthu, S., & Sampathkrishnan, S. (2014). Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4′-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 120, 237–251.
- Koopmans, T. (1934). Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms. Physica, 1, 104–113.
- Parr, R.G., Szentpály, L. V., & Liu, S. (1999). Electrophilicity Index. Journal of the American Chemical Society, 121, 1922–1924.
- Eşme, A. & Sağdınç, S.G. (2017). Spectroscopic (FT–IR, FT–Raman, UV–Vis) analysis, conformational, HOMO-LUMO, NBO and NLO calculations on monomeric and dimeric structures of 4–pyridazinecarboxylic acid by HF and DFT methods. Journal of Molecular Structure, 1147, 322–334.
- Chidangil, S. & Mishra, P.C. (1997). Structure-Activity Relationship for Some 2′,3′-Dideoxynucleoside Anti-HIV Drugs Using Molecular Electrostatic Potential Mapping. Journal of Molecular Modeling, 3, 172–181.
- Mishra, P.C. , Kumar, A., Murray, J.S., & Sen, K.D. (1996). Theoretical and Computational Chemistry Book Series. in: Mol. Electrost. Potentials Concepts Appl. Elsevier, Amsterdam, 257.
- Gupta, V.P., Sharma, A., Virdi, A., & Ram, V. (2006). Structural and spectroscopic studies on some chloropyrimidine derivatives by experimental and quantum chemical methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 64, 57–67.
- Mulliken, R.S. (1955). Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I. The Journal of Chemical Physics, 23, 1833–1840.
- Karthikeyan, N., Joseph Prince, J., Ramalingam, S.,& Periandy, S. (2014). Vibrational spectroscopic [FT-IR, FT-Raman] investigation on (2,4,5-Trichlorophenoxy) Acetic acid using computational [HF and DFT] analysis. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 124, 165–177.
- Bopp, F., Meixner, J., & Kestin, J. (1967). Thermodynamics and Statistical Mechanics Academic Press Inc., New York, 420.
Palmitoleik Asidin Moleküler Yapısı, Titreşim Spektrumları ve Elektronik Özelliklerinin Teorik Olarak İncelenmesi
Öz
Bu çalışmada, Palmitoleik Asit (cis-9-Hekzadekanoik asit, C16:1, POA) ’in moleküler yapısı, titreşimsel spektroskopik ve elektronik özellikleri Gaussian 09 paket programı kullanılarak DFT/B3LYP/6-311++G(d,p) seviyesinde incelenmiştir. POA’ nın kristal yapısının henüz belirlenmediğinden, optimize edilmiş geometrik parametreleri (bağ uzunluğu, bağ açıları ve dihedral açılar), POA’ ya izomorf olan Oleik asidin (OA) deneysel geometrik parametreleriyle karşılaştırılmıştır.POA’ nın harmonik titreşim frekansları hesaplanmış ve literatürden elde edilen deneysel titreşim frekansları ile karşılaştırılmıştır. Titreşim frekanslarının işaretlemeleri, VEDA 4 programı kullanılarak potansiyel enerji dağılımı (PED) analizi ile gerçekleştirilmiştir. POA’ nın hesaplanan yapısal parametreleri ve titreşim frekansları deneysel verilerle uyumludur. Molekülün elektronik özellikleri, en yüksek dolu moleküler orbital (HOMO) ve en düşük boş moleküler orbital (LUMO) temeline dayanılarak belirlenmiştir. HOMO-LUMO enerjileri arasındaki yüksek enerji aralığı molekülün kimyasal kararlılığa ve düşük reaktiviteye sahip olduğunu gösterir. Moleküler elektrostatik potansiyel (MEP) yüzey haritası, mulliken atomik yükleri ve sertlik, yumuşaklık, elektronegatiflik, kimyasal potansiyel, iyonizasyon potansiyeli, elektron afinitesi, elektrofilik indeks, dipol moment gibi kuantum kimyasal tanımlayıcıları moleküldeki etkileşim bölgelerini belirlemek için hesaplanmıştır. Ayrıca, POA’ nın ısı kapasitesi, entropi ve entalpi gibi termodinamik özellikleri farklı sıcaklıklarda hesaplanmıştır. Tüm termodinamik parametreler, artan sıcaklıkla birlikte artmıştır.
Anahtar Kelimeler
Palmitoleik asit Yoğunluk Fonksiyoneli Teorisi (DFT) titreşimsel analiz HOMO LUMO
Kaynakça
- Gennis, R.B. (1989). Biomembranes: Molecular Structure and Function Springer-Verlag, New York,.533.
- Small, D.M. (1986). The physical chemistry of lipids : from alkanes to phospholipids1th ed. Springer, London, 692.
- Jakobsen, M.U., Overvad, K., Dyerberg, J., Schroll, M., & Heitmann, B.L. (2004). Dietary fat and risk of coronary heart disease: Possible effect modification by gender and age. American Journal of Epidemiology, 160, 141–149.
- Yamamoto, Y., Kawamura, Y., Yamazaki, Y., Kijima, T., Morikawa, T., & Nonomura, Y. (2015). Palmitoleic Acid Calcium Salt: A Lubricant and Bactericidal Powder from Natural Lipids. Journal of Oleo Science, 64, 283–288.
- Yoon, W.-J., Kim, M.-J., Moon, J.-Y., Kang, H.-J., Kim, G.-O., & Lee, N.H. (2010). Effect of Palmitoleic Acid on Melanogenic Protein Expression in Murine B16 Melanoma. Journal of Oleo Science, 59, 315–319.
- Fischer, C.L., Drake, D.R., Dawson, D. V., Blanchette, D.R., Brogden, K.A., & Wertz, P.W. (2012). Antibacterial Activity of Sphingoid Bases and Fatty Acids against Gram-Positive and Gram-Negative Bacteria. Antimicrobial Agents and Chemotherapy, 56, 1157–1161.
- Wille, J.J. & Kydonieus, A. (2003). Palmitoleic Acid Isomer (C16:1Δ6) in Human Skin Sebum Is Effective against Gram-Positive Bacteria. Skin Pharmacology and Physiology, 16, 176–187.
- Çimen, I., Kocatürk, B., Koyuncu, S., Tufanlı, Ö., Onat, U.I., Yıldırım, A.D., et al. (2016). Prevention of atherosclerosis by bioactive palmitoleate through suppression of organelle stress and inflammasome activation. Science Translational Medicine, 8, 358ra126.
- Cimen, I., Yildirim, Z., Dogan, A.E., Yildirim, A.D., Tufanli, O., Onat, U.I., et al. (2019). Double bond configuration of palmitoleate is critical for atheroprotection. Molecular Metabolism, 28, 58–72.
- Kaneko, F., Yano, J., &Sato, K. (1998). Diversity in the fatty-acid conformation and chain packing of cis-unsaturated lipids. Current Opinion in Structural Biology, 8, 417–425.
- Kaneko, F., Yamazaki, K., Kobayashi, M., Sato, K., & Suzuki, M. (1994). Vibrational spectroscopic study on polymorphism of erucic acid and palmitoleic acid: γ1→α1 and γ→α reversible solid state phase transitions. Spectrochimica Acta Part A: Molecular Spectroscopy, 50, 1589–1603.
- Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J.,Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Peralta Jr, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J., Gaussian 09, Revision A.0.2, Gaussian, Inc., Wallingford CT, 2009.
- Sundaraganesan, N., Ilakiamani, S., Saleem, H., Wojciechowski, P.M., & Michalska, D. (2005). FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 61, 2995–3001.
- Jamróz M H (2010) Vibrational Energy Distribution Analysis VEDA 4, Warsaw.
- Dennington, R.,Keith, T.A., & Millam, J.M. (2008). Gaussview 5.0.8,Gaussian Inc., Wallingford, CT.
- Abrahamsson, S. & Ryderstedt-Nahringbauer, I. (1962). The crystal structure of the low-melting form of oleic acid. Acta Crystallographica, 15, 1261–1268.
- Kaneko, F., Yamazaki, K., Kobayashi, M., Kitagawa, Y., Matsuura, Y., Sato, K., et al. (1993). Structure of the γ phase of erucic acid. Acta Crystallographica Section C Crystal Structure Communications, 49, 1232–1234.
- Copyright © 2012-2018 Bio-Rad Laboratories, Inc. All Rights Reserved. https://spectrabase.com/spectrum/8R37FJJlI3H
- Machado, N.F.L., De Carvalho, L.A.E.B., Otero, J.C., & Marques, M.P.M. (2012). The autooxidation process in linoleic acid screened by Raman spectroscopy. Journal of Raman Spectroscopy, 43, 1991–2000.
- Gocen, T., Haman Bayarı, S., & Guven, M. H. (2017). Linoleic acid and its potassium and sodium salts: A combined experimental and theoretical study. Journal of Molecular Structure, 1150, 68–81.
- Lewandowski, W., Kalinowska, M., & Lewandowska, H. (2005). The influence of halogens on the electronic system of biologically important ligands: Spectroscopic study of halogenobenzoic acids, halogenobenzoates and 5-halogenouracils. Inorganica Chimica Acta, 358, 2155–2166.
- Silverstein, R.M., Bassler, G.C. & Morrill, T.C. (1976). Spectrometric identification of organic compounds, 3rd edition. Journal of Molecular Structure, 30, 424–425.
- Lewis, D.F. V., Ioannides, C., & Parke, D. V. (1994). Interaction of a series of nitriles with the alcohol-inducible isoform of P450: Computer analysis of structure—activity relationships. Xenobiotica, 24, 401–408.
- Pearson, R.G. (1988). Electronic spectra and chemical reactivity. Journal of the American Chemical Society, 110, 2092–2097.
- Zhan, C.-G., Nichols, J.A., & Dixon, D.A. (2003). Ionization Potential, Electron Affinity, Electronegativity, Hardness, and Electron Excitation Energy: Molecular Properties from Density Functional Theory Orbital Energies. The Journal of Physical Chemistry A, 107, 4184–4195.
- Sheela, N.R., Muthu, S., & Sampathkrishnan, S. (2014). Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4′-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 120, 237–251.
- Koopmans, T. (1934). Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den Einzelnen Elektronen Eines Atoms. Physica, 1, 104–113.
- Parr, R.G., Szentpály, L. V., & Liu, S. (1999). Electrophilicity Index. Journal of the American Chemical Society, 121, 1922–1924.
- Eşme, A. & Sağdınç, S.G. (2017). Spectroscopic (FT–IR, FT–Raman, UV–Vis) analysis, conformational, HOMO-LUMO, NBO and NLO calculations on monomeric and dimeric structures of 4–pyridazinecarboxylic acid by HF and DFT methods. Journal of Molecular Structure, 1147, 322–334.
- Chidangil, S. & Mishra, P.C. (1997). Structure-Activity Relationship for Some 2′,3′-Dideoxynucleoside Anti-HIV Drugs Using Molecular Electrostatic Potential Mapping. Journal of Molecular Modeling, 3, 172–181.
- Mishra, P.C. , Kumar, A., Murray, J.S., & Sen, K.D. (1996). Theoretical and Computational Chemistry Book Series. in: Mol. Electrost. Potentials Concepts Appl. Elsevier, Amsterdam, 257.
- Gupta, V.P., Sharma, A., Virdi, A., & Ram, V. (2006). Structural and spectroscopic studies on some chloropyrimidine derivatives by experimental and quantum chemical methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 64, 57–67.
- Mulliken, R.S. (1955). Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I. The Journal of Chemical Physics, 23, 1833–1840.
- Karthikeyan, N., Joseph Prince, J., Ramalingam, S.,& Periandy, S. (2014). Vibrational spectroscopic [FT-IR, FT-Raman] investigation on (2,4,5-Trichlorophenoxy) Acetic acid using computational [HF and DFT] analysis. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 124, 165–177.
- Bopp, F., Meixner, J., & Kestin, J. (1967). Thermodynamics and Statistical Mechanics Academic Press Inc., New York, 420.
Ayrıntılar
| Birincil Dil | Türkçe |
|---|---|
| Bölüm | Makaleler |
| Yazarlar | |
| Yayımlanma Tarihi | 30 Aralık 2020 |
| Gönderilme Tarihi | 22 Mayıs 2020 |
| Kabul Tarihi | 20 Ekim 2020 |
| Yayımlandığı Sayı | Yıl 2020 Cilt: 7 Sayı: 2 |