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Fontanini RE, Flores-Moreno R, Zúñiga-Gutiérrez BA, Kaya S, Katin KP, Maslov MM, Kochaev A. Semiempirical Approach to the Fukui Function Analysis of Uric Acid under Different pH Conditions. J Phys Chem A 2023; 127:8228-8237. [PMID: 37751600 DOI: 10.1021/acs.jpca.3c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Analytic Fukui functions calculated at a first-principles level are combined with experimental pKa values and the calculation of tautomerization energies to obtain the effective regioselectivity of uric acid toward electron-transfer reactions under different pH conditions. Second-order electron binding energies are also computed to determine which of the tautomers is more likely to participate in the electron transfer. A comparison of vertical and adiabatic proton detachment energies allows us to conclude that tautomerization is not mediating deprotonation and that two monoanionic species are of comparable relevance. The main difference between these monoanionic species is the ring that has been deprotonated. Both monoanionic species are produced from a single neutral tautomer and mainly produce a single dianionic tautomer. As a method for the analysis of systems affected by pH such as uric acid, we propose to plot condensed Fukui functions versus pH, allowing us to draw the effect of pH on the regioselectivity of electron transfer in a single image.
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Affiliation(s)
- Roberto E Fontanini
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Roberto Flores-Moreno
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Bernardo A Zúñiga-Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, Guadalajara Jal. C. P, 44430 Mexico
| | - Savas Kaya
- Sivas Cumhuriyet University, Health Services Vocational School, Department of Pharmacy, 58140 Sivas, Turkey
| | - Konstantin P Katin
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Nanoengineering in Electronics Spintronics and Photonics Institute, National Research Nuclear University "MEPhI", Kashirskoe Shosse 31, Moscow 115409, Russia
| | - Mikhail M Maslov
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Nanoengineering in Electronics Spintronics and Photonics Institute, National Research Nuclear University "MEPhI", Kashirskoe Shosse 31, Moscow 115409, Russia
| | - Aleksey Kochaev
- Laboratory of Computational Design of Nanostructures Nanodevices and Nanotechnologies, Research Institute for the Development of Scientific and Educational Potential of Youth, Aviatorov str. 14/55, Moscow 119620, Russia
- Research and Education Center "Silicon and Carbon Nanotechnologies", Ulyanovsk State University, 42 Leo Tolstoy Str, Ulyanovsk 432017, Russia
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Saigusa H, Oyama A, Kitamura S, Asami H. Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase. J Phys Chem A 2021; 125:7217-7225. [PMID: 34433270 DOI: 10.1021/acs.jpca.1c05219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.
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Affiliation(s)
- Hiroyuki Saigusa
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Ayumi Oyama
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Saki Kitamura
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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Asami H, Saigusa H, Kohno JY. Conformation of protonated guanine nucleotides via infrared multiphoton dissociation spectroscopy: Observation of rotamers in the anti-conformation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Asami H, Kawabata R, Kawauchi N, Kohno JY. Photodissociation Spectroscopy of Hydrated Myoglobin Ions Isolated by IR-laser Ablation of a Droplet Beam: Recovery from pH-denatured Structure by Gas-phase Isolation. CHEM LETT 2019. [DOI: 10.1246/cl.180884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Rina Kawabata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Norishi Kawauchi
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Jun-ya Kohno
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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Saigusa H, Nakamura D, Urashima SH. Hydrogen-bonding interactions of uric acid complexes with water/melamine by mid-infrared spectroscopy. Phys Chem Chem Phys 2015; 17:23026-33. [PMID: 26271289 DOI: 10.1039/c5cp03494a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen (H)-bonding interactions of uric acid (UA) with water have been investigated via IR-UV double resonance measurements in the mid-IR region. Comparison of the present results with those obtained previously in the near-IR region enables us to examine microscopic hydration effects that are specific to the H-bonding acceptor sites of UA. It is shown that hydration of the C8O site promotes the mode coupling of this stretch with the C2O stretch. The occurrence of this coupling is manifested in the IR intensity pattern, in which the transition associated with the in-phase contribution C8O + C2O is significantly suppressed, whereas the corresponding out-of-phase contribution gives rise to a strong peak. We also measured the mid-IR spectra of the 1 : 1 complex formed between UA and melamine (MEL) and carried out a structural analysis using the spectroscopic signature of the H-bonding derived from the result of the monohydrated cluster. It is shown that the complex possesses a triple H-bonding structure with the C2O acceptor site of UA H-bonded to MEL. Furthermore, the IR-depleted UV spectroscopy technique was employed in order to ascertain whether other structural isomers are present in the probe UV spectra.
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Affiliation(s)
- Hiroyuki Saigusa
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan.
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Asami H, Saigusa H. Multiple Hydrogen-Bonding Interactions of Uric Acid/9-Methyluric Acid with Melamine Identified by Infrared Spectroscopy. J Phys Chem B 2014; 118:4851-7. [DOI: 10.1021/jp502635w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroya Asami
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University , 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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Yamazaki S, Urashima SH, Saigusa H, Taketsugu T. Ab initio studies on the photophysics of uric acid and its monohydrates: role of the water molecule. J Phys Chem A 2014; 118:1132-41. [PMID: 24446809 DOI: 10.1021/jp411880z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photophysical behavior of three lowest-energy tautomers of uric acid and seven most stable isomers of uric acid monohydrate is comprehensively studied by ab initio calculations. Ground-state energies are calculated with the CCSD(T) method, while excitation and ionization energies as well as excited-state potential energy profiles of photoinduced processes are calculated with the CC2 method. For the (1)ππ* state, it is found that the excitation energy of the monohydrate cluster is significantly lower than that of isolated uric acid when the water molecule is hydrogen-bonded at a specific carbonyl group. The calculated excited-state potential energy profiles suggest that some monohydrate isomers can undergo a migration of the water molecule from one site to another site in the (1)ππ* state with a small energy barrier. It is also found for both uric acid and its monohydrate that nonradiative decay via the NH bond dissociation in the (1)πσ* state is likely to occur at higher excitation energies. On the basis of the computational results, possible mechanisms for the absence of specific isomers of uric acid monohydrate from the resonant two-photon ionization spectrum are discussed.
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Affiliation(s)
- Shohei Yamazaki
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University , Hirosaki 036-8561, Japan
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Urashima SH, Miyazaki M, Fujii M, Saigusa H. IR–UV Double Resonance Spectroscopy as Implemented by Polarized Laser Schemes: Probing Orientations of Vibrational Transition Dipole Moments. CHEM LETT 2013. [DOI: 10.1246/cl.130425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shu-hei Urashima
- Graduate School of Bio- and Nanosystem Sciences, Yokohama City University
| | - Mitsuhiko Miyazaki
- Chemical Spectroscopy Division, Chemical Resources Laboratory, Tokyo Institute of Technology
| | - Masaaki Fujii
- Chemical Spectroscopy Division, Chemical Resources Laboratory, Tokyo Institute of Technology
| | - Hiroyuki Saigusa
- Graduate School of Bio- and Nanosystem Sciences, Yokohama City University
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Asami H, Urashima SH, Tsukamoto M, Motoda A, Hayakawa Y, Saigusa H. Controlling Glycosyl Bond Conformation of Guanine Nucleosides: Stabilization of the anti Conformer in 5'-O-Ethylguanosine. J Phys Chem Lett 2012; 3:571-575. [PMID: 26286151 DOI: 10.1021/jz300081e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nucleosides that consist of base and sugar moieties can adopt two main conformations, syn and anti, about the glycosidic bond. We have investigated the conformational properties of guanine nucleosides in the gas phase by using laser desorption combined with IR-UV double resonance spectroscopy. In guanosine, syn conformation is preferred as a result of internal hydrogen bonding between the 5'-OH group of the sugar and the N3 site of the guanine moiety. We have therefore employed a chemically modified nucleoside 5'-O-ethylguanosine, in which possible glycosyl bond conformations are restricted upon ethylation of the 5'-OH group. The result shows that anti conformer is stabilized by the formation of hydrogen bonding involving the 2'-OH group.
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Affiliation(s)
- Hiroya Asami
- †Graduate School of Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Shu-Hei Urashima
- †Graduate School of Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Masaki Tsukamoto
- ‡Graduate School of Information Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Ayaka Motoda
- ‡Graduate School of Information Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Yoshihiro Hayakawa
- §Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, 1247 Yachigusa, Yakusa Cho, Toyota 470-0392, Japan
| | - Hiroyuki Saigusa
- †Graduate School of Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
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