Research Article
PDF EndNote BibTex RIS Cite

L-Piroglutamik Asit Molekülünün TD-DFT ve NBO Analizleri

Year 2018, Volume 5, Issue 2, 64 - 74, 28.12.2018

Abstract

Bu çalışmada, L-piroglutamik asit (L-PGA) molekülünün konformasyonları yoğunluk fonksiyon teorisi (DFT) B3LYP/6-311++G(d,p) seti yaklaşımı ile optimize edilmiş ve potansiyel enerji dağılımı ile bariyer enerjileri hesaplanmıştır. L-PGA, minimum enerjiye sahip dört konformasyona sahip olup, I. Konformasyon en kararlı yapıdadır. Molekülün II, III ve IV. konformasyonlarının bağıl elektronik enerjileri farkı, sırasıyla 3,5, 12,6 ve 25,6 kJ mol−1 değerindedir. Konformasyonlardan en düşük enerjiye sahip molekül cis formunda, diğer ikisi trans formunda karboksilik asit grubuna sahiptir. Fock matris denklemleri ile donör akseptör etkileşimleri, doğal bağ orbital (NBO) analizi ile Gaussian programına entegre NBO 3.1 programı ile incelenmiştir. Zamana-bağlı yoğunluk fonksiyon teorisi (TD-DFT) hesaplarında, L-PGA molekülünün dalga fonksiyonu Schrödinger kuantum mekanik denklemleri ile çözülerek, uyarılma durum enerjileri hesaplanmıştır.

References

  • [1] Van Der werf, P., Meister, A. “The metabolic formation and utilization of 5-oxo-L-proline (L-pyroglutamate, L-pyrorolidone carboxylate),” in: Advances in Enzymology and Related Areas of Molecular Biology, vol. 43, (Ed. Meister, A.), pp. 519–566, 1975, John Wiley & Sons, Inc, USA.
  • [2] Lacey, J. M., Wilmore, D. W. “Is Glutamine a Conditionally Essential Amino Acid?” Nutrition Reviews, vol. 48, pp. 297–309, 1990.
  • [3] Oono, S., Kurimoto, T., Nakazawa, T., Miyoshi, T., Okamoto, N., Kashimoto, R., Tagami, Y., Ito, Y., Mimura, O. “Pyroglutamic Acid Promotes Survival of Retinal Ganglion Cells after Optic Nerve Injury”, Current Eye Research, vol. 34, pp. 598–605, 2009.
  • [4] Wegmuller, M., Von der Weid, J. P., Oberson, P., Gisin, N. “Synthesis of pyroglutamic acid fatty esters through lipase-catalyzed esterification with medium chains alcohols,” Enzyme and Microbial Technology, vol. 33, pp. 79–84, 2003.
  • [5] Abraham, G. N., Podell, D. N. “Pyroglutamic acid non-metabolic formation, function in proteins and peptides, and characteristics of the enzymes effecting its removal,” Mol. Cell Biochem., vol. 38, pp. 181–190, 1981.
  • [6] Bauer, K., Schomburg, L., Heuer, H., Schafer, M.K. “Thyrotropinreleasing hormone (TRH), the TRH-receptor and the TRHdegrading ectoenzyme; three elements of a peptidergic signaling system”, Results Prob. Cell Differ., vol. 26, pp. 13–42, 1999.
  • [7] Drago, F., Continella, G., Valerio, C., D’Agata, V., Astuto, C., Spadaro, F., Continella, G., Scapagnini, U. “Pyroglutamic acid improves learning and memory capacities in old rats,” Funct. Neurol., vol. 3, pp. 137–143, 1988.
  • [8] Issa, T. B., Sayari, F., Ghalla, H., Benhamada, L. “Synthesis, crystal structure, DFT calculations and molecular docking of L-pyroglutamic acid,” Journal of Molecular Structure, in press, 10.1016/j.molstruc.2018.10.033, 2018.
  • [9] 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.
  • [10] Reed, A. E., Curtiss, L. A., Weinhold, F. “Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint”, Chem. Rev., vol. 88, pp. 899–926, 1988.
  • [11] Bauernschmitt, R., Ahlrichs, R. “Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory,” Chem. Phys. Lett., vol. 256, pp. 454–464, 1996.
  • [12] Stratmann, R. E., Scuseria, G. E., Frisch, M. J. “An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules,” J. Chem. Phys., vol. 109, pp. 8218–8224, 1998.
  • [13] Weinhold, F., Landis, C. R. Valency and Bonding. A Natural Bond Orbital Donor-Acceptor Perspective. Cambridge University Press: New York, 2005.
  • [14] Kuş, N., Sagdinc, S., Fausto, R. “Infrared spectrum and UV-induced photochemistry of matrix isolated 5-Hydroxyquinoline,” J. Phys. Chem. A, vol. 119, pp. 6296-6308, 2015.

Year 2018, Volume 5, Issue 2, 64 - 74, 28.12.2018

Abstract

References

  • [1] Van Der werf, P., Meister, A. “The metabolic formation and utilization of 5-oxo-L-proline (L-pyroglutamate, L-pyrorolidone carboxylate),” in: Advances in Enzymology and Related Areas of Molecular Biology, vol. 43, (Ed. Meister, A.), pp. 519–566, 1975, John Wiley & Sons, Inc, USA.
  • [2] Lacey, J. M., Wilmore, D. W. “Is Glutamine a Conditionally Essential Amino Acid?” Nutrition Reviews, vol. 48, pp. 297–309, 1990.
  • [3] Oono, S., Kurimoto, T., Nakazawa, T., Miyoshi, T., Okamoto, N., Kashimoto, R., Tagami, Y., Ito, Y., Mimura, O. “Pyroglutamic Acid Promotes Survival of Retinal Ganglion Cells after Optic Nerve Injury”, Current Eye Research, vol. 34, pp. 598–605, 2009.
  • [4] Wegmuller, M., Von der Weid, J. P., Oberson, P., Gisin, N. “Synthesis of pyroglutamic acid fatty esters through lipase-catalyzed esterification with medium chains alcohols,” Enzyme and Microbial Technology, vol. 33, pp. 79–84, 2003.
  • [5] Abraham, G. N., Podell, D. N. “Pyroglutamic acid non-metabolic formation, function in proteins and peptides, and characteristics of the enzymes effecting its removal,” Mol. Cell Biochem., vol. 38, pp. 181–190, 1981.
  • [6] Bauer, K., Schomburg, L., Heuer, H., Schafer, M.K. “Thyrotropinreleasing hormone (TRH), the TRH-receptor and the TRHdegrading ectoenzyme; three elements of a peptidergic signaling system”, Results Prob. Cell Differ., vol. 26, pp. 13–42, 1999.
  • [7] Drago, F., Continella, G., Valerio, C., D’Agata, V., Astuto, C., Spadaro, F., Continella, G., Scapagnini, U. “Pyroglutamic acid improves learning and memory capacities in old rats,” Funct. Neurol., vol. 3, pp. 137–143, 1988.
  • [8] Issa, T. B., Sayari, F., Ghalla, H., Benhamada, L. “Synthesis, crystal structure, DFT calculations and molecular docking of L-pyroglutamic acid,” Journal of Molecular Structure, in press, 10.1016/j.molstruc.2018.10.033, 2018.
  • [9] 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.
  • [10] Reed, A. E., Curtiss, L. A., Weinhold, F. “Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint”, Chem. Rev., vol. 88, pp. 899–926, 1988.
  • [11] Bauernschmitt, R., Ahlrichs, R. “Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory,” Chem. Phys. Lett., vol. 256, pp. 454–464, 1996.
  • [12] Stratmann, R. E., Scuseria, G. E., Frisch, M. J. “An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules,” J. Chem. Phys., vol. 109, pp. 8218–8224, 1998.
  • [13] Weinhold, F., Landis, C. R. Valency and Bonding. A Natural Bond Orbital Donor-Acceptor Perspective. Cambridge University Press: New York, 2005.
  • [14] Kuş, N., Sagdinc, S., Fausto, R. “Infrared spectrum and UV-induced photochemistry of matrix isolated 5-Hydroxyquinoline,” J. Phys. Chem. A, vol. 119, pp. 6296-6308, 2015.

Details

Primary Language Turkish
Journal Section Articles
Authors

Nihal KUŞ> (Primary Author)
FEN FAKÜLTESİ
0000-0003-4162-7152
Türkiye


Saliha ILICAN>
FEN FAKÜLTESİ
0000-0003-4064-4364
Türkiye

Publication Date December 28, 2018
Application Date October 19, 2018
Acceptance Date November 13, 2018
Published in Issue Year 2018, Volume 5, Issue 2

Cite

APA Kuş, N. & Ilıcan, S. (2018). L-Piroglutamik Asit Molekülünün TD-DFT ve NBO Analizleri . Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi , 5 (2) , 64-74 . Retrieved from https://dergipark.org.tr/en/pub/bseufbd/issue/41708/472411