Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study

Yavuz Ekincioğlu

doi:10.33435/tcandtc.1013238

Araştırma Makalesi

Yıl 2022, Cilt: 6 Sayı: 1, 31 - 41, 15.06.2022

Yavuz Ekincioğlu

https://doi.org/10.33435/tcandtc.1013238

Cited By: 7

Öz

Kaynakça

[1] D.D. Hackney, When Is Weaker Better? Design of an ADP Sensor with Weak ADP Affinity, but Still Selective against ATP, Journal of the American Chemical Society (2010) 353-354.
[2] D.M. Hayes, G.L. Kenyon, P.A. Kollman, Theoretical calculations of the hydrolysis energies of some" high-energy" molecules. 2. A survey of some biologically important hydrolytic reactions, Journal of the American Chemical Society 100 (14) (1978) 4331-4340.
[3] P. Hansia, N. Guruprasad, S. Vishveshwara, Ab initio studies on the tri-and diphosphate fragments of adenosine triphosphate, Biophysical chemistry 119 (2) (2006) 127-136.
[4] M. O'keeffe, B. Domenges , G.V. Gibbs, Ab initio molecular orbital calculations on phosphates: comparison with silicates, The Journal of Physical Chemistry 89(11) (1985) 2304-2309.
[5] V.G. Machado V.G, Nome F, Energy-rich phosphate compounds, Química Nova 22(3) (1999) 351-357.
[6] M.J. Hwang, P.Y. Chu, J.C. Chen, I. Chao, Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate, Journal of computational chemistry 20(16) (1999) 1702-1715.
[7] H.M. Kalckar, The Nature of Energetic Coupling in Biological Syntheses, Chemical Reviews 28(1) (1941) 71-178.
[8] P. Oesper P, Sources of the high energy content in energy-rich phosphates, Archives of biochemistry 27(2) (1950) 255-270.
[9] R.E. Alving, K. Laki, Energy and electron orbitals in adenosine phosphates, Journal of theoretical Biology 34(2) (1972) 199-214.
[10] M.L. Atkinson, R.K. Morton, Free energy and the biosynthesis of phosphates, Comparative biochemistry 2 (2012) 1.
[11] B. Pullman, A. Pullman, Electronic structure of energy-rich phosphates, Radiation Research Supplement 2 (1960) 160-181.
[12] K. Laki, M. Seel, J. Ladik, (1977) Conformation of triphosphate and lysine-triphosphate-arginine complex, Journal of theoretical biology 67(3) (1977) 489-498.
[13] T. Gustavsson, R. Improta, D. Markovitsi, NA/RNA: building blocks of life under UV irradiation, The Journal of Physical Chemistry Letters 1(13) (2010) 2025-2030.
[14] L. Serrano-Andres, M. Merchan, Are the five natural DNA/RNA base monomers a good choice from natural selection?: A photochemical perspective, Journal of Photochemistry and Photobiology C: Photochemistry Reviews 10(1) (2009) 21-32.
[15] C. Ma, C.C.W. Cheng, C.T.L. Chan, R.C.T. Chan, W.M. Kwok, Remarkable effects of solvent and substitution on the photo-dynamics of cytosine: a femtosecond broadband time-resolved fluorescence and transient absorption study, Physical Chemistry Chemical Physics 17(29) (2015) 19045-19057.
[16] I. Conti, M. Bonfanti, A. Nenov, I. Rivalta, M. Garavelli, Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies, Challenges and Advances in Computational Chemistry and Physics QM/MM Studies of Light-responsive Biological Systems Springer (2020) 77-142.
[17] K. Kleinermanns, D. Nachtigallová, M.S. de Vries, Excited state dynamics of DNA bases, International Reviews in Physical Chemistry 32(2) (2013) 308-342.
[18] R. Improta, F. Santoro, L. Blancafort, Quantum mechanical studies on the photophysics and the photochemistry of nucleic acids and nucleobases, American Chemical Society Chemical Reviews 116(6) (2016) 3540-3593.
[19] D. Tuna, A.L. Sobolewski, W. Domcke, Mechanisms of ultrafast excited-state deactivation in adenosine, The Journal of Physical Chemistry A 118(1) (2014) 122-127.
[20] R. Improta, V. Barone, Excited states behavior of nucleobases in solution: insights from computational studies. Photoinduced Phenomena in Nucleic Acids I Springer (2014) 329-357.
[21] M.K. Shukla, J. Leszczynski, Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study, Molecular Physics 108(21-23) (2010) 3131-3146.
[22] C.B. Harrison, K. Schulten, Quantum and classical dynamics simulations of ATP hydrolysis in solution, Journal of Chemical Theory and Computation 8(7) (2012) 2328-2335.
[23] Y. Yang, Q. Cui, The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state, The Journal of Physical Chemistry A 113(45) (2009) 12439-12446.
[24] H. Sigel, Metal ion-assisted stacking interactions and the facilitated hydrolysis of nucleoside Di-and triphosphates, Journal of Inorganic Biochemistry 67(1-4) (1997) 290-290.
[25] Y. Lian, H. Jiang, J. Feng, X. Wang, X. Hou, P. Deng, Direct and simultaneous quantification of ATP, ADP and AMP by 1H and 31P Nuclear Magnetic Resonance spectroscopy, Talanta 150 (2016) 485-492.
[26] P. Cardiano, C. Foti, F. Giacobello, O. Giuffrè, S. Sammartano, Study of Al3+ interaction with AMP, ADP and ATP in aqueous solution, Biophysical chemistry 234 (2018) 42-50.
[27] A.T. Blades, Y. Ho, P. Kebarle, Free Energies of Hydration in the Gas Phase of Some Phosphate Singly and Doubly Charged Anions:(HO) 2PO2-(Orthophosphate),(HO) O2POPO2 (OH) 2-(Diphosphate), Ribose 5-Phosphate, Adenosine 5 ‘-Phosphate, and Adenosine 5 ‘-Diphosphate, The Journal of Physical Chemistry 100(6) (1996) 2443-2446.
[28] A.T. Blades, Y. Ho, P. Kebarle, Hydration in the Gas Phase of the Orthophosphate Anion,(HO) 2PO2-, and the Conversion of the Orthophosphate to the Metaphosphate, PO3-, Ion, Journal of the American Chemical Society 118(1) (1996) 196-201.
[29] F. Schinle, P.E. Crider, M. Vonderach, P. Weis, O. Hampe, M.M. Kappes, Spectroscopic and theoretical investigations of adenosine 5′-diphosphate and adenosine 5′-triphosphate dianions in the gas phase, Physical Chemistry Chemical Physics 15(18) (2013) 6640-6650.
[30] R.M. Burke, J.K. Pearce, W.E. Boxford, A. Bruckmann, C.E. Dessent, Stabilization of Excess Charge in Isolated Adenosine 5 ‘-Triphosphate and Adenosine 5 ‘-Diphosphate Multiply and Singly Charged Anions, The Journal of Physical Chemistry A 109(43) (2005) 9775-9785.
[31] R. Cini, C. Pifferi, Dalton Transactions, Supramolecular networks via hydrogen bonding and stacking interactions for adenosine 5′-diphosphate. Synthesis and crystal structure of diaqua (2, 2′∶ 6′, 2 ″-terpyridine) copper (II)[adenosine 5′-diphosphato (3–)](2, 2′∶ 6′, 2 ″-terpyridine) cuprate (II) adenosine 5′-diphosphate (1–) hexadecahydrate and density functional geometry optimization analysis of copper (II)-and zinc (II)-pyrophosphate complexes, Journal of the Chemical Society, Dalton Transactions (5) (1999) 699-710.
[32] O. Kennard, N.W. Isaacs, W.D.S. Motherwell, J.C. Coppola, D.L. Wampler, A.T. Larson, D.G. Watson, The crystal and molecular structure of adenosine triphosphate, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences 325(1562) (1971) 401-436.
[33] E. Dieguez, J.M. Cabrera, F. Agulló‐López, Optical absorption and luminescence induced by x rays in KDP, DKDP, and ADP, The Journal of chemical physics 81(8) (1984) 3369-3374.
[34] J. Gao, K. Kuczera, B. Tidor, M. Karplus, Hidden thermodynamics of mutant proteins: a molecular dynamics analysis, Science 244(4908) (1989) 1069-1072.
[35] D.R. Phillips, J.A. McCloskey, A comprehensive study of the low energy collision-induced dissociation of dinucleoside monophosphates, International journal of mass spectrometry and ion processes 128(1-2) (1993) 61-82.
[36] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, D.J. Fox , Gaussian 09, Revision D. 01, Gaussian Wallingford, CT, USA (2009).
[37] A.D. Becke AD, Correlation energy of an inhomogeneous electron gas: A coordinate‐space model, The Journal of chemical physics 88(2) (1988) 1053-1062.
[38] A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Physical review A 38(6) (1988) 3098.
[39] B. Mennucci, Polarizable continuum model, Wiley Interdisciplinary Reviews: Computational Molecular Science 2(3) (2012) 386-404.
[40] D.A. Adamiak, W. Saenger, Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP. 2H2O, Acta Crystallographica Section B: Structural Crystallography and Crystal Chemistry 36(11) (1980) 2585-2589.
[41] E.P. Gibson, J.H. Turnbull, Luminescence characteristics of adenosine and its phosphates, Journal of Photochemistry 11(5) (1979) 313-319.

Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study

Yıl 2022, Cilt: 6 Sayı: 1, 31 - 41, 15.06.2022

Yavuz Ekincioğlu

https://doi.org/10.33435/tcandtc.1013238

Cited By: 7

Öz

This paper has reported some theoretical results for the geometry optimization in ground state (S0) and the first excited state (S1), the frontier molecular orbitals, the global chemical reactivity descriptor, the excited states, the absorption and emission spectra in gas phase and aqueous solution of protonated Adenosine diphosphate molecule. Also, the excited state intramolecular proton transfer process was reported between O37-H38∙∙∙N13 bonds. Then, the results obtained have been compared with the experimental data reported and, therefore, available in literature. All calculations were carried out using density functional theory and time-dependent density functional theory method with B3LYP functional with 6-311+G (d, p) basis set. As well as, the solvent effects were investigated using Polarizable Continuum Model. As a conclusion, it has been indicated that the theoretical results obtained in this work are all in well agreement with experimental counterparts taken from literature.

Anahtar Kelimeler

Key words: ADP, PCM/TD-DFT, Excited states, Absorption, Emission

Kaynakça

[1] D.D. Hackney, When Is Weaker Better? Design of an ADP Sensor with Weak ADP Affinity, but Still Selective against ATP, Journal of the American Chemical Society (2010) 353-354.
[2] D.M. Hayes, G.L. Kenyon, P.A. Kollman, Theoretical calculations of the hydrolysis energies of some" high-energy" molecules. 2. A survey of some biologically important hydrolytic reactions, Journal of the American Chemical Society 100 (14) (1978) 4331-4340.
[3] P. Hansia, N. Guruprasad, S. Vishveshwara, Ab initio studies on the tri-and diphosphate fragments of adenosine triphosphate, Biophysical chemistry 119 (2) (2006) 127-136.
[4] M. O'keeffe, B. Domenges , G.V. Gibbs, Ab initio molecular orbital calculations on phosphates: comparison with silicates, The Journal of Physical Chemistry 89(11) (1985) 2304-2309.
[5] V.G. Machado V.G, Nome F, Energy-rich phosphate compounds, Química Nova 22(3) (1999) 351-357.
[6] M.J. Hwang, P.Y. Chu, J.C. Chen, I. Chao, Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate, Journal of computational chemistry 20(16) (1999) 1702-1715.
[7] H.M. Kalckar, The Nature of Energetic Coupling in Biological Syntheses, Chemical Reviews 28(1) (1941) 71-178.
[8] P. Oesper P, Sources of the high energy content in energy-rich phosphates, Archives of biochemistry 27(2) (1950) 255-270.
[9] R.E. Alving, K. Laki, Energy and electron orbitals in adenosine phosphates, Journal of theoretical Biology 34(2) (1972) 199-214.
[10] M.L. Atkinson, R.K. Morton, Free energy and the biosynthesis of phosphates, Comparative biochemistry 2 (2012) 1.
[11] B. Pullman, A. Pullman, Electronic structure of energy-rich phosphates, Radiation Research Supplement 2 (1960) 160-181.
[12] K. Laki, M. Seel, J. Ladik, (1977) Conformation of triphosphate and lysine-triphosphate-arginine complex, Journal of theoretical biology 67(3) (1977) 489-498.
[13] T. Gustavsson, R. Improta, D. Markovitsi, NA/RNA: building blocks of life under UV irradiation, The Journal of Physical Chemistry Letters 1(13) (2010) 2025-2030.
[14] L. Serrano-Andres, M. Merchan, Are the five natural DNA/RNA base monomers a good choice from natural selection?: A photochemical perspective, Journal of Photochemistry and Photobiology C: Photochemistry Reviews 10(1) (2009) 21-32.
[15] C. Ma, C.C.W. Cheng, C.T.L. Chan, R.C.T. Chan, W.M. Kwok, Remarkable effects of solvent and substitution on the photo-dynamics of cytosine: a femtosecond broadband time-resolved fluorescence and transient absorption study, Physical Chemistry Chemical Physics 17(29) (2015) 19045-19057.
[16] I. Conti, M. Bonfanti, A. Nenov, I. Rivalta, M. Garavelli, Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies, Challenges and Advances in Computational Chemistry and Physics QM/MM Studies of Light-responsive Biological Systems Springer (2020) 77-142.
[17] K. Kleinermanns, D. Nachtigallová, M.S. de Vries, Excited state dynamics of DNA bases, International Reviews in Physical Chemistry 32(2) (2013) 308-342.
[18] R. Improta, F. Santoro, L. Blancafort, Quantum mechanical studies on the photophysics and the photochemistry of nucleic acids and nucleobases, American Chemical Society Chemical Reviews 116(6) (2016) 3540-3593.
[19] D. Tuna, A.L. Sobolewski, W. Domcke, Mechanisms of ultrafast excited-state deactivation in adenosine, The Journal of Physical Chemistry A 118(1) (2014) 122-127.
[20] R. Improta, V. Barone, Excited states behavior of nucleobases in solution: insights from computational studies. Photoinduced Phenomena in Nucleic Acids I Springer (2014) 329-357.
[21] M.K. Shukla, J. Leszczynski, Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study, Molecular Physics 108(21-23) (2010) 3131-3146.
[22] C.B. Harrison, K. Schulten, Quantum and classical dynamics simulations of ATP hydrolysis in solution, Journal of Chemical Theory and Computation 8(7) (2012) 2328-2335.
[23] Y. Yang, Q. Cui, The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state, The Journal of Physical Chemistry A 113(45) (2009) 12439-12446.
[24] H. Sigel, Metal ion-assisted stacking interactions and the facilitated hydrolysis of nucleoside Di-and triphosphates, Journal of Inorganic Biochemistry 67(1-4) (1997) 290-290.
[25] Y. Lian, H. Jiang, J. Feng, X. Wang, X. Hou, P. Deng, Direct and simultaneous quantification of ATP, ADP and AMP by 1H and 31P Nuclear Magnetic Resonance spectroscopy, Talanta 150 (2016) 485-492.
[26] P. Cardiano, C. Foti, F. Giacobello, O. Giuffrè, S. Sammartano, Study of Al3+ interaction with AMP, ADP and ATP in aqueous solution, Biophysical chemistry 234 (2018) 42-50.
[27] A.T. Blades, Y. Ho, P. Kebarle, Free Energies of Hydration in the Gas Phase of Some Phosphate Singly and Doubly Charged Anions:(HO) 2PO2-(Orthophosphate),(HO) O2POPO2 (OH) 2-(Diphosphate), Ribose 5-Phosphate, Adenosine 5 ‘-Phosphate, and Adenosine 5 ‘-Diphosphate, The Journal of Physical Chemistry 100(6) (1996) 2443-2446.
[28] A.T. Blades, Y. Ho, P. Kebarle, Hydration in the Gas Phase of the Orthophosphate Anion,(HO) 2PO2-, and the Conversion of the Orthophosphate to the Metaphosphate, PO3-, Ion, Journal of the American Chemical Society 118(1) (1996) 196-201.
[29] F. Schinle, P.E. Crider, M. Vonderach, P. Weis, O. Hampe, M.M. Kappes, Spectroscopic and theoretical investigations of adenosine 5′-diphosphate and adenosine 5′-triphosphate dianions in the gas phase, Physical Chemistry Chemical Physics 15(18) (2013) 6640-6650.
[30] R.M. Burke, J.K. Pearce, W.E. Boxford, A. Bruckmann, C.E. Dessent, Stabilization of Excess Charge in Isolated Adenosine 5 ‘-Triphosphate and Adenosine 5 ‘-Diphosphate Multiply and Singly Charged Anions, The Journal of Physical Chemistry A 109(43) (2005) 9775-9785.
[31] R. Cini, C. Pifferi, Dalton Transactions, Supramolecular networks via hydrogen bonding and stacking interactions for adenosine 5′-diphosphate. Synthesis and crystal structure of diaqua (2, 2′∶ 6′, 2 ″-terpyridine) copper (II)[adenosine 5′-diphosphato (3–)](2, 2′∶ 6′, 2 ″-terpyridine) cuprate (II) adenosine 5′-diphosphate (1–) hexadecahydrate and density functional geometry optimization analysis of copper (II)-and zinc (II)-pyrophosphate complexes, Journal of the Chemical Society, Dalton Transactions (5) (1999) 699-710.
[32] O. Kennard, N.W. Isaacs, W.D.S. Motherwell, J.C. Coppola, D.L. Wampler, A.T. Larson, D.G. Watson, The crystal and molecular structure of adenosine triphosphate, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences 325(1562) (1971) 401-436.
[33] E. Dieguez, J.M. Cabrera, F. Agulló‐López, Optical absorption and luminescence induced by x rays in KDP, DKDP, and ADP, The Journal of chemical physics 81(8) (1984) 3369-3374.
[34] J. Gao, K. Kuczera, B. Tidor, M. Karplus, Hidden thermodynamics of mutant proteins: a molecular dynamics analysis, Science 244(4908) (1989) 1069-1072.
[35] D.R. Phillips, J.A. McCloskey, A comprehensive study of the low energy collision-induced dissociation of dinucleoside monophosphates, International journal of mass spectrometry and ion processes 128(1-2) (1993) 61-82.
[36] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, D.J. Fox , Gaussian 09, Revision D. 01, Gaussian Wallingford, CT, USA (2009).
[37] A.D. Becke AD, Correlation energy of an inhomogeneous electron gas: A coordinate‐space model, The Journal of chemical physics 88(2) (1988) 1053-1062.
[38] A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Physical review A 38(6) (1988) 3098.
[39] B. Mennucci, Polarizable continuum model, Wiley Interdisciplinary Reviews: Computational Molecular Science 2(3) (2012) 386-404.
[40] D.A. Adamiak, W. Saenger, Structure of the monopotassium salt of adenosine 5'-diphosphate dihydrate, KADP. 2H2O, Acta Crystallographica Section B: Structural Crystallography and Crystal Chemistry 36(11) (1980) 2585-2589.
[41] E.P. Gibson, J.H. Turnbull, Luminescence characteristics of adenosine and its phosphates, Journal of Photochemistry 11(5) (1979) 313-319.

Toplam 41 adet kaynakça vardır.

Ayrıntılar

Birincil Dil	İngilizce
Konular	Kimya Mühendisliği
Bölüm	Research Article
Yazarlar	Yavuz Ekincioğlu 0000-0002-8610-1245
Erken Görünüm Tarihi	15 Mart 2022
Yayımlanma Tarihi	15 Haziran 2022
Gönderilme Tarihi	21 Ekim 2021
Yayımlandığı Sayı	Yıl 2022 Cilt: 6 Sayı: 1

Kaynak Göster

APA	Ekincioğlu, Y. (2022). Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study. Turkish Computational and Theoretical Chemistry, 6(1), 31-41. https://doi.org/10.33435/tcandtc.1013238
AMA	Ekincioğlu Y. Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study. Turkish Comp Theo Chem (TC&TC). Haziran 2022;6(1):31-41. doi:10.33435/tcandtc.1013238
Chicago	Ekincioğlu, Yavuz. “Theoretical Analysis of ADP Molecule in Gas Phase and Aqueous Solution: A DFT and PCM/TD-DFT Study”. Turkish Computational and Theoretical Chemistry 6, sy. 1 (Haziran 2022): 31-41. https://doi.org/10.33435/tcandtc.1013238.
EndNote	Ekincioğlu Y (01 Haziran 2022) Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study. Turkish Computational and Theoretical Chemistry 6 1 31–41.
IEEE	Y. Ekincioğlu, “Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study”, Turkish Comp Theo Chem (TC&TC), c. 6, sy. 1, ss. 31–41, 2022, doi: 10.33435/tcandtc.1013238.
ISNAD	Ekincioğlu, Yavuz. “Theoretical Analysis of ADP Molecule in Gas Phase and Aqueous Solution: A DFT and PCM/TD-DFT Study”. Turkish Computational and Theoretical Chemistry 6/1 (Haziran 2022), 31-41. https://doi.org/10.33435/tcandtc.1013238.
JAMA	Ekincioğlu Y. Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study. Turkish Comp Theo Chem (TC&TC). 2022;6:31–41.
MLA	Ekincioğlu, Yavuz. “Theoretical Analysis of ADP Molecule in Gas Phase and Aqueous Solution: A DFT and PCM/TD-DFT Study”. Turkish Computational and Theoretical Chemistry, c. 6, sy. 1, 2022, ss. 31-41, doi:10.33435/tcandtc.1013238.
Vancouver	Ekincioğlu Y. Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study. Turkish Comp Theo Chem (TC&TC). 2022;6(1):31-4.