Theoretical examinations of diammonium hydrogen citrate compound by density functional theory method at B3LYP/6-31G(d,p) level of theory

Year 2019, Volume: 1 Issue: 2, 1 - 19, 31.12.2019

Asaf Tolga Ülgen , Tahsin Turğay , Bahadır Akkurt , Gurcan Yıldırım

Abstract

This study aims to point out a strong strategy between the fundamental characteristic features as
regards such as chemical reactivity, stable, electronic acceptor ability,
bioactivity, kinetic stability, polarizability and intramolecular charge transfer
regions, and the potential application fields of the diammonium hydrogen
citrate compound by means of theoretical findings founded on density functional
theory (DFT) method at the standard B3LYP/6-31G(d,p) calculation level for the
first time. In this respect, we determine the optimized molecular structures,
total energies, atomic charges, thermodynamic constants, lowest unoccupied
molecular orbital (LUMO), highest occupied molecular orbital (HOMO), electrostatic
potential surface map (MEP), molecular electrostatic potential (ESP) contour
map and evaluated data (band-gap energy, chemical hardness, global softness,
electronegativity, chemical potential and electrophilicity index parameters) for
the diammonium hydrogen citrate molecule. According to the results obtained,
non-uniform charge distribution is observed on the various atoms, leading to
both the electrophilic (electronegative) and nucleophilic (electronic donor
ability) regions in the structure. Hence, the molecule can be not only bonded
metallically but interacted intermolecularly. Moreover, it is found that the
atomic position in the skeleton of compound plays an important role on the
electron engagements, conjugative effects, strong intra-molecular charge
transfer regions, valence electron cloud effects and σ-bonds between the atoms
in the diammonium hydrogen citrate.

Keywords

Diammonium hydrogen citrate; B3LYP/6-31G(d, Calculation level; Electrophilic; Nucleophilic region; MEP; ESP.

Supporting Institution

Şırnak Üniversitesi Bilimsel Araştırma Proje Koordinasyon Birimi

Project Number

2017.03.03.02

Thanks

This study is totally supported by Sirnak University Scientific Research Project Coordination Unit (Project No: 2017.03.03.02).

Diamonyum hidrojen sitrat bileşiğinin B3LYP / 6-31G (d, p) teorisi düzeyinde yoğunluk fonksiyonel teori yöntemiyle incelenmesi

Abstract

Bu çalışma, kimyasal reaktivite, kararlı, elektronik alıcı yeteneği, biyoaktivite, kinetik stabilite, polarize edilebilirlik ve intramoleküler yük aktarma bölgeleri ve diamonyum hidrojen sitrat bileşiğinin potansiyel uygulama alanları gibi temel karakteristik özellikler arasında güçlü bir stratejiye işaret etmeyi amaçlamakta ve standart B3LYP / 6-31G (d, p) hesaplama düzeyinde yoğunluk fonksiyonel teorisi (DFT) yöntemi üzerine kurulan teorik bulgular vasıtasıyla incelenmiştir. Bu bağlamda, optimize edilmiş moleküler yapıları, toplam enerjileri, atom yüklerini, termodinamik sabitleri, en düşük boş moleküler orbital (LUMO), en yüksek işgal edilmiş moleküler orbital (HOMO), elektrostatik potansiyel yüzey haritası (MEP), moleküler elektrostatik potansiyelleri (ESP), diamonyum hidrojen sitrat molekülü için dağılım haritası ve değerlendirilmiş verileri (bant aralığı enerjisi, kimyasal sertlik, küresel yumuşaklık, elektronegatiflik, kimyasal potansiyel ve elektrofiliklik indeksi parametreleri) belirledik. Elde edilen sonuçlara göre, yapıdaki hem elektrofilik (elektronegatif) hem de nükleofilik (elektronik donör yeteneği) bölgelere yol açan çeşitli atomlarda düzgün olmayan yük dağılımı gözlenmektedir. Dolayısıyla, moleküller arası etkileşime girebiliyor olsada molekül sadece metalik olarak bağlanabilir. Dahası, bileşiğin iskeletindeki atom pozisyonunun, elektron bağları, konjuge etkiler, güçlü moleküler içi yük transfer bölgeleri, değerlik elektron bulutu etkileri ve diamonyum hidrojen sitrattaki atomlar arasındaki σ-bağları üzerinde önemli bir rol oynadığı bulunmuştur.

Keywords

Diamonyum hidrojen sitrat; B3LYP / 6-31G, Nükleofilik bölge; MEP; ESP.

Project Number

2017.03.03.02

References

• References[1] Frank, H. V. (2005), Citric Acid, Ullmann's Encyclopedia of Industrial Chemistry. Weinheim: Wiley-VCH.[2] Standard Specification for Chemical Passivation Treatments for Stainless Steel Parts, Publishing ASTM web: https://www.astm.org/Standards/A967.htm. 22.07.2019[3] Srivastava, A, (2017) Optical Materials, Volume 64, February, 1-8[4] Nair, S-L., Krishan, R., Vijayan, S., WilsonP., Prabhakaran, K., (2019), MgO calcination for easy direct coagulation casting of aqueous alumina slurries, Ceramics International Volume 45, Issue 5, 1 April, 5717-5723[5] Khan, W. U, Wang D., Zhang, W., Tang, Z., Ma, X., Ding, X., Du, S., Wang Y., (2017), High Quantum Yield Green-Emitting Carbon Dots for Fe(ІІІ) Detection, Biocompatible Fluorescent Ink and Cellular Imaging, Scientific Reports 7, Article Number: 14866, 01November, 1-9[6] Mufidah, E.,Wakayama, M., (2016), Optimization of d-lactic acid production using unutilized biomass as substrates by multiple parallel fermentation, 3 Biotech, Springer, December, 6:186 [7] Idzkowska, A., Sato, K., Sakka, Y., Szafran, M., (2015), Deflocculation and stabilization of Ti3SiC2 ceramic powder in gelcasting process, Journal of the Ceramic Society of Japan, vol.123, No.1443, November, 1010-1017 2015[8] Dunn, J. D.,Watson, J. T., Bruening, M.L., (2006), Detection of Phosphopeptides Using Fe(III)−Nitrilotriacetate Complexes Immobilized on a MALDI Plate, Analytical Chemistry, vol.78, 1574-1580[9] Huang, Q. L., Zhu, X., S., (2014), Synthesis and Characterization of SERS-Active Silver Nanomaterial, Chinese Journal of Inorganic Chemistry, Volume: 30 (2), 442-450[10] Taira, S., Osaka, I., Shimma, S., Kaneko, D., Hiroki, T., Kawamura-Konishi, Y., Ichiyanagi, Y., (2006), Oligonucleotide analysis by nanoparticle-assisted laser desorption/ionization, mass spectrometry, Analyst, vol.137, issue.9, 2006-2010. [11] Berlinger, B., Náray, M., Sajó, I., Záray, G.,(2009), Critical Evaluation of Sequential Leaching Procedures for the Determination of Ni and Mn Species in Welding Fumes, The Annals of Occupational Hygiene, Vol.53, Issue 4, June, 333–340.[12] Dunn, J.D., Allison J., (2007), Detection of Multiply Charged Dyes Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for the Forensic Examination of Pen Ink Dyes Directly From Paper, Journal of Forensic Sciences Vol.52, Issue:5, September, 1205-1211. [13] Zhang, Z., Zhou, L., Zhao, S., Deng., H., (2006), 3-Hydroxycoumarin as a New Matrix for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry of DNA, Journal of The American Society for Mass Spectrometry, Vol.17 Issue: 12 Pages: 1665-1668.[14] U. Soykan, S. Cetin, B. Ozturk, F. Karaboga, Y. Zalaoglu, M. Dogruer, G. Yildirim, C. Terzioglu, (2013), Synthesis and characterization of p-benzophenoneoxycarbonylphenyl acrylate by means of experimental measurements and theoretical approaches, and bulk melt polymerization, J. Mol. Struct. Vol.1049, 479-487.[15] Durig, J. R.; Ganguly, A.; El Defrawy, A. M.; Guirgis, G. A.; Gounev, T. K.; Herrebout, W. A.; van der Veken, B. J. (2009), Conformational stability, r0 structural parameters, barriers to internal rotation and vibrational assignment of cyclobutylamine, J. Mol. Struct. Vol.918, 64-76[16] Sun, Y.X., Hao, Q. L, Lu, L. D., Wang, X., Yang, X. J., (2010), Vibrational spectroscopic study of o-, m- and p-hydroxybenzylideneaminoantipyrines, Spectrochim Acta A Mol Biomol Spectrosc. Vol.75, 203–211.[17] Breda, S., Reva, I., Fausto, R., (2008), Molecular structure and vibrational spectra of 2(5H)-furanone and 2(5H)-thiophenone isolated in low temperature inert matrix J. Mol. Struct. 887 (2008) 75.[18] Foresman, J.B, Frisch, A., (1996). Exploring Chemistry with Electronic StructureMethods: a Guide to Using Gaussian, second ed., Gaussian, Pittsburgh.[19] Scott, A.P., Radom, L., Harmonic Vibrational Frequencies: An Evaluation of Hartree-Fock, Møller-Plesset,Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors, J. Phys. Chem. Vol.100, 16502-16513.[20] Durig, J.R., El-Defrawy, A.M., Ganguly, A., Panikar, S.S., Soliman, M.S., (2011), Conformational Stability from Variable-Temperature Infrared Spectra of Xenon Solutions, r0 Structural Parameters, and Vibrational Assignment of Pyrrolidine, J. Phys. Chem. A vol.115 7473-7483.[21] Miehlich, B., Savin, A., Stoll, H., Preuss H., (1989), Results obtained with the correlation energy density functionals of becke and Lee, Yang and Parr, Chem. Phys. Lett. Vol.157, Issue3, 200-206.[22] M. Alcolea Palafox, G. Tardajos, A. Guerrero-Martínez, V.K. Rastogi, D. Mishra, S.P. Ojha, and W. Kiefer (2007) FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil, Chemical Physics, vol.340, 17-31. [23] Handy, N.C., Masley, P.E., Amos, R.D., Andrews, J.S., Murray, C.W., Laming, G., (1992), The harmonic frequencies of benzene, Chem. Phys. Lett. Vol.197, ıssues4-5, 506-515.[24] Frisch, M.J., Trucks, G.W., Schlegel, H.B., et al., (2010), Gaussian 09, Revision B.01, Gaussian Inc., Wallingford, CT.[25] Kohn, W., Sham, L.J., (1965), Self-Consistent Equations Including Exchange and Correlation Effects Phys. Rev. vol.140, A1133-A1138.[26] Becke, A.D., (1993), Density‐functional thermochemistry. III. The role of exact exchange J. Chem. Phys. Vol.98, issue7, 5648-5652.[27] Lee, C., Yang, W., Parr, R.G., (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B vol.37, 785-789.[28] Jaronczyk, M., Cz Dobrowolski, J.,(2008), On isomers and tautomers of Nitro-1-deazapurine: A DFT study, J. Mol. Struct. Theochem. Vol.858, issues 1-3, 77-84.[29] Merrick, J.P., Moran, D., Radom, L., (2007), An evaluation of harmonic vibrational frequency scale factors, J. Phys Chem A, vol.111, 11683-11700.[30] Foresman, J.B., Frisch, A., (1995) Exploring Chemistry with Electronic Structure Methods, 2nd Ed. Gaussian, Inc., Pittsburgh, PA.[31] Keresztury, G., Holly, S., Varga, J., Besenyei, G., Wang, A.Y., Durig, J.R., (1993), Vibrational spectra of monothiocarbamates-II. IR and Raman spectra, vibrational assignment, conformational analysis and ab initio calculations of S-methyl-N, N-dimethylthiocarbamate, Spectrochimica Acta Part A: Molecular Spectroscopy, vol.49, issue 13-14, 2007-2026.[32] Keresztury, G., (2002), Raman spectroscopy: theory, in: J.M. Chalmers, P.R. Griffith (Eds.), Handbook of Vibrational Spectroscopy, John Wiley & Sons, New York. [33] Politzer, P., Truhlar, D.G., (Eds.), (1981), Chemical Applications of Atomic and Molecular Electrostatic Potentials, Springer Science+Business Media New York.[34] Arjunan, V., Santhanam, R., Rani, T., Rosi, H., Mohan, S., (2013), Conformational, vibrational, NMR and DFT studies of N-methylacetanilide, Spectrochim Acta A Mol Biomol Spectrosc. Vol.104, 182-196.[35] Dennington, R.D., Keith, T.A., Millam, J.M., GaussView 5 0 9, Gaussian Inc., 2008.[36] Prasad, O., Sinha, L., Misra, N., Narayan, V., Kumar, N., (2010), Molecular structure and vibrational study on 2,3-dihydro-1H-indene and its derivative 1H-indene-1,3(2H)-dione by density functional theory calculations, J. Mol. Struct. Vol.940, 82–86.[37] S. Subashchandrabose, H. Saleem, Y. Erdogdu, O. Dereli, V. Thanikachalam, J.Jayabharathi, (2012), Structural, vibrational and hyperpolarizability calculation of (E)-2-(2-hydroxybenzylideneamino)-3-methylbutanoic acid, Spectrochim. Acta A 86, 231–241.[38] Dhas, D.A., Joe, I.H., Roy, S.D.D., Balachandran, S., (2011), Nonplanar property study of antifungal agent tolnaftate-spectroscopic approach, Spectrochim. Acta A vol.79, 993–1003.[39] Tezer, N., Karakus, N., (2009), Theoretical study on the ground state intramolecular proton transfer (IPT) and solvation effect in two Schiff bases formed by 2-aminopyridine with 2-hydroxy-1- naphthaldehyde and 2-hydroxy salicylaldehyde. J. Mol. Model. Vol.15, issue3, 223–232. [40] Peng, X.J., Song, F.L., Lu, E., Wang, Y.N., Zhou, W., Fan, J.L., Gao, Y.L., (2005), Heptamethine Cyanine Dyes with a Large Stokes Shift and Strong Fluorescence:  A Paradigm for Excited-State Intramolecular Charge Transfer, J. Am. Chem. Soc. Vol.127 4170–4171.[41] Qian, G., Zhong, Z., Luo, M., Yu, D., Zhang, Z., Ma, D., Wang, Z.Y., (2009) Synthesis and Application of Thiadiazoloquinoxaline-Containing Chromophores as Dopants for Efficient Near-Infrared Organic Light-Emitting Diodes, J. Phys. Chem. C vol.113, 1589–1595.[42] J.V. Prasad, S.B. Rai, S.N. Thakur, Chem. Phys. Lett. 164 (1989) 629–634.[43] M.K. Ahmed, B.R. Henry, J. Phys. Chem. 90 (1986) 1737–1739.[44] L.G. Wade Jr., Organic Chemistry, sixth ed., Pearson Prentice Hall, New Jersey, 2006.[45] D.A. Dhas, I.H. Joe, S.D.D. Roy, T.H. Freeda, Spectrochim. Acta A 77 (2010) 36–44. [46] V. Arjunana, S.T. Govindarajab, S. Sakiladevic, M. Kalaivania, S. Mohand, Spectrochim. Acta A 84 (2011) 196–209.[47] P. J. Stephens; K. J. Jalkanen; R. W. Kawiecki (1990). "Theory of vibrational rotational strengths: comparison of a priori theory and approximate models". J. Am. Chem. Soc. 112 (18): 6518–6529. [48] G. Gece, Corros. Sci. 50 (2008) 2981–2992.[49] K. Fukui, Theory of Orientation, Stereoselection, 1st ed., Springer-Verlag, Berlin, 1975.[50] I. Fleming, Frontier Orbitals, Organic Chemical Reactions, John Wiley and Sons, New York, 1976.[51] P.K. Chattaraj, U. Sarkar, D.R. Roy, Chem. Rev. 106 (2006) 2065.[52] T.A. Koopmans, Physica 1 (1933) 104.[53] R.G. Parr, L. von Szentpaly, S. Liu, J. Am. Chem. Soc. 121 (1999) 1922.[54] R.G. Parr, P.K. Chattraj, J. Am. Chem. Soc. 113 (1991) 1854. [55] P. Politzer, J.S. Murray, Theor. Chem. Acc. 108 (2002) 134–142.