Study on Thermophysical Properties of Arginine and Glutamic Acid in Water Using Ab Initio Methods

Year 2015, Volume: 43 Issue: 1, 17 - 32, 01.03.2015

Farhoush Kiani Azam Yousefi Fardad Koohyar

Abstract

Gibbs free energy and acidic dissociation constants are two important thermodynamic properties of mo- lecules. A combination of ab initio with the density functional theory DFT and the polarized continuum model PCM of Tomasi’s method were utilized to calculate the acidic dissociation constants of arginine and glutamic acid in water. We applied the basis set at the B3LYP/6-31+G d level of theory for accurate theoretical predictions of pKa values. Furthermore, we have evaluated the molecular conformations and solute-solvent interactions of these molecules by the electronic structure theory commonly DFT method . It was found that in alkaline aqueous solutions the cation, anion, and neutral species of arginine and glutamic acid are solvated with one, two, three, and four molecules of water, respectively. There are intermolecular hydrogen bonds bet- ween the existent species and water molecules. The atomic charges were investigated to analyze the reaction mechanism. In this study, it can be seen that there is a good correlation between experimental attained pKa values and the theoretical computed pKa values.

Keywords

Arginine, Glutamic Acid, DFT Method, Acidic Dissociation Constant

Ab İnitio Yöntemler Kullanılarak Sudaki Arjinin ve Glutamik Asitin Termofiziksel Özellikleri Üzerine Bir Çalışma

Abstract

G ibbs serbest enerji ve asidik ayrışma sabiti, moleküllerin iki önemli termodinamik özellliğidir. Ab initio’nun yoğunluk fonksiyonel teori DFT ile kombinasyonu ve Tomasi’nin polarize olmuş sürekli dizi modelinden PCM yararlanılarak sudaki arjinin ve glutamik asitin asidik ayrışma sabitleri hesaplanmıştır. pK değerinin teorik tahmini için B3LYP/6-31+G d teori seviyesi uygulaması kullanılmıştır. Ayrıca elektronik yapı teorisiyle geleneksel DFT yöntemi bu moleküllerin moleküler konformasyonları ve çözünen-çözücü etkileşimleri incelenmiştir. Elde edilen bulgulara gore alkali sulu çözeltilerde arjinin ve glutamik asitin katyon, anyon ve nötral türleri, sırasıyla, bir, iki, üç ve dört su molekülü ile çözünmüştür. Varolan türler ile su molekülleri arasında molekül içi hidrojen bağları vardır. Tepkime mekanizmasını analiz etmek için atomik değişimler araştırılmıştır. Bu çalışmada, deneysel pK değerleri ile teorik pK değerleri arasında iyi bir ilişki olduğu görülmektedir

Keywords

Arjinin, Glutamik asit, DFT yöntemi, Asidik ayrışma sabiti

References

• M.A. Meyers, P.Y. Chen, A.Y.M. Lin, Y. Seki, Biological materials: Structure and mechanical properties, Prog. Mat. Sci., 53 (2008) 1.
• B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter, Molecular Biology of the Cell. 4th ed. Garland Science, New York (2002).
• Z.E. Sikorski, Chemical and Functional Properties of Food Proteins. Boca Raton: CRC Press., (2001) 242.
• X. Hao, B. Sun, L. Hu, H. Lahdesmaki, V. Dunmire, Y. Feng, S.W. Zhang, H. Wang, C. Wu, H. Wang, G.N. Fuller, W.F. Symmans, I. Shmulevich, W. Zhang, Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis, Cancer., 100 (2004) 1110.
• H. Scott, V.M. Panin, The role of protein N-glycosylation in neural transmission, Glycobiology., 24 (2014) 407.
• J.M. Beaulieu, R.R. Gainetdinov, The Physiology, signaling, and pharmacology of dopamine receptors, Pharmacol. Rev., 63 (2011) 182.
• S.A. Blandin, E.A. Levashina, Phagocytosis in mosquito immune responses, Immunol. Rev., 219 (2007) 8.
• G. Esteso, M.I. Mora, J.J. Garrido, F. Corrales, A. Moreno, Proteomic analysis of the porcine platelet proteome and alterations induced by thrombin activation, J. Proteomics., 71 (2008) 547.
• A. Berg, T.J. Meza, M. Mahiα, T. Thorstensen, K. Kristiansen, R.B. Aalen, Ten members of the Arabidopsis gene family encoding methylαCpGαbinding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development, Nucleic Acids Res., 31 (2003) 5291.
• R.E. Wyse, E. Komor, Mechanism of aminoacid uptake by sugarcane suspension cells, Plant Physiol., 76 (1984) 865.
• M. Zhao, H.B. Wang, L.N. Ji, Z.W. Mao, Insights into metalloenzyme microenvironments: biomimetic metal complexes with a functional second coordination sphere, Chem. Soc. Rev., 42 (2013) 8360.
• D.W. Newton, R.B. Kluza, pK values of medicinal a compounds in pharmacy practice, Ann. Pharmacother., 12 (1978) 546.
• F. Kiani, R. Taherinasab, H. Tahermansouri, F. Koohyar, Determination of acidic dissociation constants of glutamine and isoleucine in water using ab initio methods, Turk. J. Biochem., 39 (2014) 503.
• T. N . Brown, N . Mora-Diez, Computational determination of aqueous pK values of protonated benzimidazoles (Part 1), J. Phys. Chem. B., 110 (2006) 9270. a
• A.S. Yang, M.R. Gunner, R. Sampogna, Sharp K and Honig B. On the calculation of pKs in proteins, Proteins: Struct., Funct., Genet., 15 (1993) 252. a
• J. Gordon, J.B. Myers, T. Folta, V. Shoja, L.S. Heath, A. Onufriev, H++: a server for estimating pKs and adding missing hydrogens to macromolecules, Nucleic Acids Res., 33 (2005) 368. a
• A.M. Magill, B.F. Yates, An assessment of theoretical protocols for calculation of the pKa values of the prototype imidazolium cation, Aust. J. Chem., 57 (2004) 1205.
• J.R. Pliego, J.M. Jr Riveros, Theoretical calculation of pKa using the cluster-continuum model., J. Phys. Chem. A., 106 (2002) 7434.
• M. Tanaka, D. Ariga, Y. Takahash, Estimation of pKa of selenic acid by the correlation of experimental pKa values with those estimated by DFT calculation for inorganic oxoacids, Chem. Lett., 42 (2013) 912.
• D. Elmali, Calculation of acidity constants of some substituted thiazole derivatives using DFT and UV spectroscopic methods, J. Art. Sci., 8 (2007) 23.
• M. αmiechowski, Theoretical pKa prediction of O-phosphoserine in aqueous solution, Chem. Phys. Lett., 501 (2010) 123.
• E. Koort, K. Herodes, V. Pihl, I. Leito, Estimation of uncertainty in pKa values determined by potentiometric titration, Anal. Bioanal. Chem., 379 (2004) 720.
• M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman et al. GAUSSIAN 98, Gaussian. Inc., Pittsburgh PA (1998).
• K. Kim, K.D. Jordan, Comparison of density functional and MP2 calculations on the water monomer and dimer, J. Phys. Chem., 98 (1994) 10089.
• P.J. Stephens, F.J. Devlin, C.F. Chabalowski, M.J. Frisch, Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields, J. Phys. Chem., 98 (1994) 11623.
• S . M i e r t u s , E . J . To m a s i , A p p r o x i m a t e evaluations of the electrostatic free energy and internal energy changes in solution processes, Chem. Phys., 65 (1982) 239.
• Z.K. Jia, D.M. Du, Z.Y. Zhou, A.G. Zhang, R.V. Hou, Accurate pKa determinations for some organic acids using an extended cluster method, Chem. Phys. Lett., 4-6 (2007) 374.
• G.A. Jeffrey An Introduction to Hydrogen Bonding; Oxford University Press: Oxford (1997).