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Year 2021, , 576 - 585, 24.09.2021

Rebaz Omer , Pelin Koparır , Ibrahim Nazem Qader , Lana Ahmed

https://doi.org/10.17776/csj.881654
Cited By: 12

Abstract

References

  • [1] Matthews D. E., An overview of phenylalanine and tyrosine kinetics in humans, The Journal of Nutrition, 6(137) (2007) 1549-1555.
  • [2] Selvarani K., Mahalakshmi R., A Review on Physical and Chemical Properties of L-Phenylalanine Family of NLO Single Crystals, Journal of Chem. Tech. Research, 1(9) (2016) 113.
  • [3] Omar R., Koparir P., Koparir M., Synthesis of 1, 3-Thiazole derivatives, Indian Drugs; 1(58) (2021) 1.
  • [4] Freire P. T., Barboza F. M., Lima J. A., Melo F. E., Mendes Filho J., Raman spectroscopy of amino acid crystals, Raman Spectroscopy and Applications, (2017) 201.
  • [5] Kumar K., Analysis of Tryptophan and Tyrosine in the Presence of Other Bioactive Molecules Using Generalized Rank Annihilation Method on Excitation-emission Fluorescence Spectroscopic Data Sets, Journal of Fluorescence, (2020) 1-6.
  • [6] Kinsey R. A., Kintanar A., Oldfield E., Dynamics of amino acid side chains in membrane proteins by high field solid state deuterium nuclear magnetic resonance spectroscopy. Phenylalanine, tyrosine, and tryptophan, Journal of Biological Chemistry, 17(256) (1981) 9028-9036.
  • [7] Moreno J. R. A., Moreno M. d. M. Q., Ureña F. P., González J. J. L., Conformational preference of short aromatic amino acids from the FT-IR, FT-Raman and Far-IR spectroscopies, and quantum chemical calculations: l-phenylalanine and l-tyrosine, Tetrahedron: Asymmetry, 14(23) (2012) 1084-1092.
  • [8] Palafox M. A., Rastogi V., Tanwar R., Mittal L., Vibrational frequencies and structure of 2-thiouracil by Hartree–Fock, post-Hartree–Fock and density functional methods, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 11(59) (2003) 2473-2486.
  • [9] Mohan S., Sundaraganesan N.,Mink J., FTIR and Raman studies on benzimidazole, Spectrochimica Acta Part A: Molecular Spectroscopy, 8(47) (1991) 1111-1115.
  • [10] Ten G., Nechaev V., Pankratov A., Berezin V., Baranov V., Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine, Journal of Structural Chemistry, 5(51) (2010) 854-861.
  • [11] Qader I. N., Mohammad A., Azeez Y. H., Agid R. S., Hassan H. S., Al-Nabawi S. H. M., Chemical Structural and Vibrational Analysis of Potassium Acetate: A Density Function Theory Study, Journal of Physical Chemistry and Functional Materials, 1(2) 22-24.
  • [12] Cansız A., Orek C., Koparir M., Koparir P., Cetin A., 4-Allyl-5-pyridin-4-yl-2, 4-dihydro-3H-1, 2, 4-triazole-3-thione: Synthesis, experimental and theoretical characterization, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, (91) (2012) 136-145.
  • [13] Koparir P., Sarac K., Orek C., Koparir M., Molecular structure, spectroscopic properties and quantum chemical calculations of 8-t-buthyl-4-methyl-2H-chromen-2-one, Journal of Molecular Structure, (1123) (2016) 407-415.
  • [14] Frisch M., Trucks G., Schlegel H. B., Scuseria G., Robb M., Cheeseman J., Scalmani G., Barone V., Mennucci B., Petersson G., GAUSSIAN 09. Revision D. 01. Gaussian Inc. Wallingford, CT, USA; (2009).
  • [15] Lee C., Yang W., Parr R. G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical review B, 2(37) (1988) 785.
  • [16] Beck A. D., Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 7(98) (1993) 5648-6.
  • [17] Fortenberry R. C., Novak C. M., Lee T. J., Bera P. P., Rice J. E., Identifying Molecular Structural Aromaticity for Hydrocarbon Classification, ACS omega, 11(3) (2018) 16035-16039.
  • [18] Ahmed L., Omer R., Kebiroglu H., A theoretical study on Dopamine molecule, Journal of Physical Chemistry and Functional Materials, 2(2) (2019) 66-72.
  • [19] Celikezen, F., Orek C., Parlak A., Sarac K., Turkez H., Tozlu Ö. Ö., Synthesis, structure, cytotoxic and antioxidant properties of 6-ethoxy-4-methylcoumarin, Journal of Molecular Structure, (1205) (2020) 127577.
  • [20] Amalanathan M., Rastogi V., Joe I. H., Palafox M., Tomar R., Density functional theory calculations and vibrational spectral analysis of 3, 5-(dinitrobenzoic acid), Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 5(78) (2011) 1437-1444.
  • [21] Rebaz O., Koparir P., Ahmed L., Koparir M., Computational determination the reactivity of salbutamol and propranolol drugs, Turkish Computational and Theoretical Chemistry, 2(4) (2020) 67-75.
  • [22] Koparir M., Orek C., Alayunt N., ParlakA. E., Koparir, P., Sarac K., Dastan S. D., Cankaya N., Synthesis, Structure Investigation, Spectral Characteristics and Biological Activitie of 4-Benzyl-3-(2-Hydroxyphenyl)-1H-1, 2, 4-Triazole-5 (4H)-Thione, Communications in Computational Chemistry, 3(1) (2013) 244-268.
  • [23] Omer R. A., Ahmed L. O., Koparir M., Koparir P., Theoretical analysis of the reactivity of chloroquine and hydroxychloroquine, Indian Journal of Chemistry-Section A (IJCA), 12(59) (2020) 1828-1834.
  • [24] Perdew J. P., Levy M., Physical content of the exact Kohn-Sham orbital energies: band gaps and derivative discontinuities, Physical Review Letters, 20(51) (1983) 1884.
  • [25] Janak J. F., Proof that∂ E∂ n i= ε in density-functional theory, Physical Review B, 12(18) (1978) 7165.
  • [26] Koopmans T., Ordering of wave functions and eigenenergies to the individual electrons of an atom, Physica, 1 (1933) 104-113.
  • [27] Parr R. G., Pearson R. G., Absolute hardness: companion parameter to absolute electronegativity, Journal of the American chemical society, 26(105) (1983) 7512-7516.
  • [28] Pearson R. G., Absolute electronegativity and hardness correlated with molecular orbital theory, Proceedings of the National Academy of Sciences, 22(83) (1986) 8440-8441.
  • [29] Adamo C., Jacquemin D., The calculations of excited-state properties with Time-Dependent Density Functional Theory, Chemical Society Reviews, 3(42) (2013) 845-856.
  • [30] Scuseriaa R., a. GE, An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules, J. Chem. Phys., 19(109) (1998) 8218-8224.
  • [31] Arjunan V., Sakiladevi S., Marchewka M., Mohan S., FTIR, FT-Raman, FT-NMR and quantum chemical investigations of 3-acetylcoumarin, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 109 (2013) 79-89.
  • [32] Joseph L., Sajan D., Reshmy R., Sasi B. A., Erdogdu Y., Thomas K. K., Vibrational spectra, structural conformations, scaled quantum chemical calculations and NBO analysis of 3-acetyl-7-methoxycoumarin, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 99 (2012) 234-247.
  • [33] Palafox, M. A., Bhat, D., Goyal, Y., Ahmad, S., Joe, I. H., and Rastogi, V., FT-IR and FT-Raman spectra, MEP and HOMO–LUMO of 2, 5-dichlorobenzonitrile: DFT study. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 136 (2015) 464-472.
  • [34] Ahmed L., Rebaz O., Spectroscopic properties of Vitamin C: A theoretical work, Cumhuriyet Science Journal, 41(4) (2020) 916-928.
  • [35] Jeyavijayan S., Arivazhagan, M., Vibrational spectral investigation, NBO, first hyperpolarizability and UV–Vis spectral analysis of 3, 5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 136 (2015) 234-246.
  • [36] Omer, L. A., Rebaz O., Computational Study on Paracetamol Drug, Journal of Physical Chemistry and Functional Materials, 1(3) 9-13.
  • [37] Reed A. E., Weinstock R. B., Weinhold F., Natural population analysis, The Journal of Chemical Physics, 2(83) (1985) 735-746.
  • [38] Mulliken R. S., Electronic population analysis on LCAO–MO molecular wave functions I., The Journal of Chemical Physics, 10(23) (1955) 1833-1840.

Structure reactivity analysis for Phenylalanine and Tyrosine

Year 2021, , 576 - 585, 24.09.2021

Rebaz Omer , Pelin Koparır , Ibrahim Nazem Qader , Lana Ahmed

https://doi.org/10.17776/csj.881654
Cited By: 12

Abstract

Phenylalanine (Phe) is one of the amino acids that cannot be produced in the body and must be ingested through diet. Tyrosine (Tyr) is also a non-essential amino acid and can be produced by Phe hydroxylation in the liver when the dietary intake of Tyr is low. Structure analysis is very important to know the correct synthesis and the reactivity of the molecule. In this study, the characterization of Phe and Tyr molecules were investigated using quantum chemical calculations. The molecular geometry for both molecules was determined using density functional theory (B3LYP) by handling the 6-311++G(d,p) basis set. The method of TD-DFT which is based on the B3LYP/6-31++G(d,p) level, was utilized in ethanol solvent to find the electronic absorption spectra. In addition, frontier molecular orbitals, electrostatic potential and molecular charge distributions analysis were carried out by B3LYP/6-311++G(d,p) theory. The energy differences between HOMO and LUMO for Phe were obtained as 0.19851 eV, which have a good argument with the reactivity compared with tyrosine, and energy band gap was 0.20501 eV

Keywords

Phenylalanine Tyrosine DFT HOMO LUMO

References

  • [1] Matthews D. E., An overview of phenylalanine and tyrosine kinetics in humans, The Journal of Nutrition, 6(137) (2007) 1549-1555.
  • [2] Selvarani K., Mahalakshmi R., A Review on Physical and Chemical Properties of L-Phenylalanine Family of NLO Single Crystals, Journal of Chem. Tech. Research, 1(9) (2016) 113.
  • [3] Omar R., Koparir P., Koparir M., Synthesis of 1, 3-Thiazole derivatives, Indian Drugs; 1(58) (2021) 1.
  • [4] Freire P. T., Barboza F. M., Lima J. A., Melo F. E., Mendes Filho J., Raman spectroscopy of amino acid crystals, Raman Spectroscopy and Applications, (2017) 201.
  • [5] Kumar K., Analysis of Tryptophan and Tyrosine in the Presence of Other Bioactive Molecules Using Generalized Rank Annihilation Method on Excitation-emission Fluorescence Spectroscopic Data Sets, Journal of Fluorescence, (2020) 1-6.
  • [6] Kinsey R. A., Kintanar A., Oldfield E., Dynamics of amino acid side chains in membrane proteins by high field solid state deuterium nuclear magnetic resonance spectroscopy. Phenylalanine, tyrosine, and tryptophan, Journal of Biological Chemistry, 17(256) (1981) 9028-9036.
  • [7] Moreno J. R. A., Moreno M. d. M. Q., Ureña F. P., González J. J. L., Conformational preference of short aromatic amino acids from the FT-IR, FT-Raman and Far-IR spectroscopies, and quantum chemical calculations: l-phenylalanine and l-tyrosine, Tetrahedron: Asymmetry, 14(23) (2012) 1084-1092.
  • [8] Palafox M. A., Rastogi V., Tanwar R., Mittal L., Vibrational frequencies and structure of 2-thiouracil by Hartree–Fock, post-Hartree–Fock and density functional methods, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 11(59) (2003) 2473-2486.
  • [9] Mohan S., Sundaraganesan N.,Mink J., FTIR and Raman studies on benzimidazole, Spectrochimica Acta Part A: Molecular Spectroscopy, 8(47) (1991) 1111-1115.
  • [10] Ten G., Nechaev V., Pankratov A., Berezin V., Baranov V., Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine, Journal of Structural Chemistry, 5(51) (2010) 854-861.
  • [11] Qader I. N., Mohammad A., Azeez Y. H., Agid R. S., Hassan H. S., Al-Nabawi S. H. M., Chemical Structural and Vibrational Analysis of Potassium Acetate: A Density Function Theory Study, Journal of Physical Chemistry and Functional Materials, 1(2) 22-24.
  • [12] Cansız A., Orek C., Koparir M., Koparir P., Cetin A., 4-Allyl-5-pyridin-4-yl-2, 4-dihydro-3H-1, 2, 4-triazole-3-thione: Synthesis, experimental and theoretical characterization, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, (91) (2012) 136-145.
  • [13] Koparir P., Sarac K., Orek C., Koparir M., Molecular structure, spectroscopic properties and quantum chemical calculations of 8-t-buthyl-4-methyl-2H-chromen-2-one, Journal of Molecular Structure, (1123) (2016) 407-415.
  • [14] Frisch M., Trucks G., Schlegel H. B., Scuseria G., Robb M., Cheeseman J., Scalmani G., Barone V., Mennucci B., Petersson G., GAUSSIAN 09. Revision D. 01. Gaussian Inc. Wallingford, CT, USA; (2009).
  • [15] Lee C., Yang W., Parr R. G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical review B, 2(37) (1988) 785.
  • [16] Beck A. D., Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 7(98) (1993) 5648-6.
  • [17] Fortenberry R. C., Novak C. M., Lee T. J., Bera P. P., Rice J. E., Identifying Molecular Structural Aromaticity for Hydrocarbon Classification, ACS omega, 11(3) (2018) 16035-16039.
  • [18] Ahmed L., Omer R., Kebiroglu H., A theoretical study on Dopamine molecule, Journal of Physical Chemistry and Functional Materials, 2(2) (2019) 66-72.
  • [19] Celikezen, F., Orek C., Parlak A., Sarac K., Turkez H., Tozlu Ö. Ö., Synthesis, structure, cytotoxic and antioxidant properties of 6-ethoxy-4-methylcoumarin, Journal of Molecular Structure, (1205) (2020) 127577.
  • [20] Amalanathan M., Rastogi V., Joe I. H., Palafox M., Tomar R., Density functional theory calculations and vibrational spectral analysis of 3, 5-(dinitrobenzoic acid), Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 5(78) (2011) 1437-1444.
  • [21] Rebaz O., Koparir P., Ahmed L., Koparir M., Computational determination the reactivity of salbutamol and propranolol drugs, Turkish Computational and Theoretical Chemistry, 2(4) (2020) 67-75.
  • [22] Koparir M., Orek C., Alayunt N., ParlakA. E., Koparir, P., Sarac K., Dastan S. D., Cankaya N., Synthesis, Structure Investigation, Spectral Characteristics and Biological Activitie of 4-Benzyl-3-(2-Hydroxyphenyl)-1H-1, 2, 4-Triazole-5 (4H)-Thione, Communications in Computational Chemistry, 3(1) (2013) 244-268.
  • [23] Omer R. A., Ahmed L. O., Koparir M., Koparir P., Theoretical analysis of the reactivity of chloroquine and hydroxychloroquine, Indian Journal of Chemistry-Section A (IJCA), 12(59) (2020) 1828-1834.
  • [24] Perdew J. P., Levy M., Physical content of the exact Kohn-Sham orbital energies: band gaps and derivative discontinuities, Physical Review Letters, 20(51) (1983) 1884.
  • [25] Janak J. F., Proof that∂ E∂ n i= ε in density-functional theory, Physical Review B, 12(18) (1978) 7165.
  • [26] Koopmans T., Ordering of wave functions and eigenenergies to the individual electrons of an atom, Physica, 1 (1933) 104-113.
  • [27] Parr R. G., Pearson R. G., Absolute hardness: companion parameter to absolute electronegativity, Journal of the American chemical society, 26(105) (1983) 7512-7516.
  • [28] Pearson R. G., Absolute electronegativity and hardness correlated with molecular orbital theory, Proceedings of the National Academy of Sciences, 22(83) (1986) 8440-8441.
  • [29] Adamo C., Jacquemin D., The calculations of excited-state properties with Time-Dependent Density Functional Theory, Chemical Society Reviews, 3(42) (2013) 845-856.
  • [30] Scuseriaa R., a. GE, An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules, J. Chem. Phys., 19(109) (1998) 8218-8224.
  • [31] Arjunan V., Sakiladevi S., Marchewka M., Mohan S., FTIR, FT-Raman, FT-NMR and quantum chemical investigations of 3-acetylcoumarin, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 109 (2013) 79-89.
  • [32] Joseph L., Sajan D., Reshmy R., Sasi B. A., Erdogdu Y., Thomas K. K., Vibrational spectra, structural conformations, scaled quantum chemical calculations and NBO analysis of 3-acetyl-7-methoxycoumarin, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 99 (2012) 234-247.
  • [33] Palafox, M. A., Bhat, D., Goyal, Y., Ahmad, S., Joe, I. H., and Rastogi, V., FT-IR and FT-Raman spectra, MEP and HOMO–LUMO of 2, 5-dichlorobenzonitrile: DFT study. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 136 (2015) 464-472.
  • [34] Ahmed L., Rebaz O., Spectroscopic properties of Vitamin C: A theoretical work, Cumhuriyet Science Journal, 41(4) (2020) 916-928.
  • [35] Jeyavijayan S., Arivazhagan, M., Vibrational spectral investigation, NBO, first hyperpolarizability and UV–Vis spectral analysis of 3, 5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy; 136 (2015) 234-246.
  • [36] Omer, L. A., Rebaz O., Computational Study on Paracetamol Drug, Journal of Physical Chemistry and Functional Materials, 1(3) 9-13.
  • [37] Reed A. E., Weinstock R. B., Weinhold F., Natural population analysis, The Journal of Chemical Physics, 2(83) (1985) 735-746.
  • [38] Mulliken R. S., Electronic population analysis on LCAO–MO molecular wave functions I., The Journal of Chemical Physics, 10(23) (1955) 1833-1840.
There are 38 citations in total.

Details

Primary Language English
Subjects Pharmacology and Pharmaceutical Sciences
Journal Section Natural Sciences
Authors

Rebaz Omer 0000-0002-3774-6071

Pelin Koparır 0000-0002-3981-9748

Ibrahim Nazem Qader 0000-0003-1167-3799

Lana Ahmed 0000-0003-2181-1972

Publication Date September 24, 2021
Submission Date February 16, 2021
Acceptance Date July 16, 2021
Published in Issue Year 2021

Cite

APA Omer, R., Koparır, P., Qader, I. N., Ahmed, L. (2021). Structure reactivity analysis for Phenylalanine and Tyrosine. Cumhuriyet Science Journal, 42(3), 576-585. https://doi.org/10.17776/csj.881654

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