1
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The role of intramolecular interactions on the stability of the conformers of a spiropyran derivative. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Ortiz-Rodríguez LA, Ortiz-Zayas G, Pollum M, Hoehn SJ, Jockusch S, Crespo-Hernández CE. Intramolecular Charge Transfer in the Azathioprine Prodrug Quenches Intersystem Crossing to the Reactive Triplet State in 6-Mercaptopurine †. Photochem Photobiol 2021; 98:617-632. [PMID: 34480764 DOI: 10.1111/php.13513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
The thiopurine prodrugs 6-mercaptopurine and azathioprine are among the world's essential medications for acute lymphoblastic leukemia, immunosuppression and several autoimmune conditions. Thiopurine prodrugs are efficient UVA absorbers and singlet oxygen generators and the long-term treatment with these prodrugs correlates with a high incidence of sunlight-induced skin cancer in patients. In this contribution, we show that the electronic relaxation mechanisms and photochemical properties of azathioprine are remarkably different from those of 6-mercaptopurine upon absorption of UVA radiation. UVA excitation of 6-mercaptopurine results in nearly 100% triplet yield and up to 30% singlet oxygen generation, whereas excitation of azathioprine with UVA leads to triplet yields of 15-3% depending on pH of the aqueous solution and <1% singlet oxygen generation. While photoexcitation of 6-mercaptopurine and other thiopurine prodrugs can facilitate oxidatively generated cell damage, azathioprine's poor photosensitization ability reveals the use of interchromophoric charge-transfer interactions for the molecular design of photostable prodrugs exhibiting a remarkable reduction in photocytotoxic side effects before drug metabolization.
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Affiliation(s)
| | | | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
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3
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Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO2 group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers.
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4
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Miguez FB, Menzonatto TG, Netto JFZ, Silva IM, Verano-Braga T, Lopes JF, De Sousa FB. Photo-dynamic and fluorescent zinc complex based on spiropyran ligand. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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F Reis I, Miguez FB, Vargas CAA, Menzonatto TG, Silva IMS, Verano-Braga T, Lopes JF, Brandão TAS, De Sousa FB. Structural and Electronic Characterization of a Photoresponsive Lanthanum(III) Complex Incorporated into Electrospun Fibers for Phosphate Ester Catalysis. ACS APPLIED MATERIALS & INTERFACES 2020; 12:28607-28615. [PMID: 32463219 DOI: 10.1021/acsami.0c03571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Herein, we present the light-induced synthesis and characterization of a La3+/spiropyran derivative complex (LaMC) and its application as a catalyst when incorporated into electrospun polycaprolactone (PCL) fibers. In addition to experimental methods, computational calculations were also essential to better understand the structure and electronic characteristics of LaMC. The LaMC complex was identified as a 10-coordinated structure with the La3+ ion coordinated by four oxygens from the phenolate and the carbonyl of the carboxyl acid group from both MC ligands and by six oxygens from three nitrate ligands. In addition, LaMC was capable of getting reversibly isomerized by UV or visible light cycling. All PCL fibers were successively obtained, and their morphologies, surface properties, and catalytic behavior were studied. Results showed that PCL/LaMC fibers were capable of catalyzing bis(2,4-dinitrophenyl)phosphate degradation efficiently. Complete hydrolysis was accomplished in only 1.5 days relative to the half-life time of 35 days for the uncatalyzed hydrolysis at pH 8.1 and 25 °C.
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Affiliation(s)
- Izadora F Reis
- Laboratório de Sistemas Poliméricos e Supramoleculares (LSPS) -Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 Minas Gerais, Brazil
| | - Flávio B Miguez
- Laboratório de Sistemas Poliméricos e Supramoleculares (LSPS) -Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 Minas Gerais, Brazil
| | - Carlos A Amaya Vargas
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Thiago G Menzonatto
- Laboratório de Química Computacional (LaQC)-Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 Minas Gerais, Brazil
| | - Igor M S Silva
- Departamento de Fisiologia e Biofísica-Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Thiago Verano-Braga
- Departamento de Fisiologia e Biofísica-Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Juliana Fedoce Lopes
- Laboratório de Química Computacional (LaQC)-Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 Minas Gerais, Brazil
| | - Tiago A S Brandão
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Frederico B De Sousa
- Laboratório de Sistemas Poliméricos e Supramoleculares (LSPS) -Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 Minas Gerais, Brazil
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6
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Raczyńska ED, Gal JF, Maria PC, Kamińska B, Igielska M, Kurpiewski J, Juras W. Purine tautomeric preferences and bond-length alternation in relation with protonation-deprotonation and alkali metal cationization. J Mol Model 2020; 26:93. [PMID: 32248379 PMCID: PMC7256107 DOI: 10.1007/s00894-020-4343-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/05/2020] [Indexed: 11/03/2022]
Abstract
Quantum chemical calculations were carried out for deprotonated (P-) and protonated purine (PH+) and for adducts with one alkali metal cation (P-M+ and PM+, where M+ is Li+ or Na+) in the gas phase {B3LYP/6-311+G(d,p)}, a model of perfectly apolar environment, and for selected structures in aqueous solution {PCM(water)//B3LYP/6-311+G(d,p)}, a reference polar medium for biological studies. All potential isomers of purine derivatives were considered, the favored structures indicated, and the preferred sites for protonation/deprotonation and cationization reactions determined. Proton and metal cation basicities of purine in the gas phase were discussed and compared with those of imidazole and pyrimidine. Bond-length alternations in the P, PH+, P-M+, and PM+ forms were quantitatively measured using the harmonic oscillator model of electron delocalization (HOMED) indices and compared with those for P. Variations of the HOMED values when proceeding from the purine structural building blocks, pyrimidine and imidazole, to the bicyclic purine system were also examined. Generally, the isolated NH isomers exhibit a strongly delocalized π-system (HOMED > 0.8). Deprotonation slightly increases the HOMED values, whereas protonation and cationization change the HOMED indices in different way. For bidentate M+-adducts, the HOMED values are larger than 0.9 like for the largely delocalized P-. The HOMED values correlate well in a comprehensive relationship with the relative Gibbs energies (ΔG) calculated for individual isomers whatever the purine form is, neutral, protonated, or cationized. When PCM-DFT model was utilized for P-, PH+, PM+, and P-M+ (M+ = Li+) both electron delocalization and relative stability are different from those for the molecules in vacuo. The solvation effects cause a slight increase in HOMEDs, whereas the ΔEs decrease, but in different ways. Hence, contribution of particular isomers in the isomeric mixtures of PH+, PM+, and P-M+ also varies. HOMED variations for the favored neutral, deprotonated, protonated, and lithiated forms of purine in the gas phase and aqueous solution.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland.
| | - Jean-François Gal
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Pierre-Charles Maria
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108, Nice, France
| | - Beata Kamińska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Małgorzata Igielska
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Julian Kurpiewski
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
| | - Weronika Juras
- Department of Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776, Warszawa, Poland
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7
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DFT investigation on the intramolecular and intermolecular proton transfer processes in 2-aminobenzothiazole (ABT) in the gas phase and in different solvents. Struct Chem 2019. [DOI: 10.1007/s11224-019-01395-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Zhou Z, Wang X, Chen J, Xu J. Direct observation of an intramolecular charge transfer state in epigenetic nucleobase N6-methyladenine. Phys Chem Chem Phys 2019; 21:6878-6885. [PMID: 30887998 DOI: 10.1039/c9cp00325h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
N6-Methyladenine (6MeAde), the most abundant internal modification in mRNA, has proved to be an important epigenetic biomarker for gene regulation just like 5-methylcytosine in DNA. Recently, a unique UV-induced response of 6MeAde was reported, which makes it instructive and intriguing to reveal the excited state relaxation mechanism in this methylated adenine and its derivatives. In this work, we investigated 6MeAde and its ribose species N6-methyladenosine (6MeAdo) by using femtosecond time-resolved fluorescence up-conversion (FUC) and broadband transient absorption (TA) spectroscopy. Both 6MeAde and 6MeAdo exhibit a hundreds of femtoseconds lifetime, which originates from the efficient depletion of the ππ* (La) state. A several picoseconds lifetime is also observed and it should be attributed to the ππ* (Lb) state. Surprisingly, dual peak fluorescence emission is observed in 6MeAde and the long wavelength emission is ascribed to an intramolecular charge transfer (ICT) state. The lifetime of this ICT state is determined to be 107 ps. The kinetic isotope effect shows that the ICT state is closely associated with the solute-solvent H-bonding in aqueous solution. In 6MeAdo, the ICT state is apparently quenched and adenine-like excited state dynamics suggests that DNA/RNA containing such modification could still possess excellent photostability under UV irradiation. Our results contain an important insight for understanding excited state properties in epigenetic modified DNA/RNA.
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Affiliation(s)
- Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
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9
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Brovarets’ OO, Hovorun DM. Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research. J Biomol Struct Dyn 2019; 37:2716-2732. [DOI: 10.1080/07391102.2018.1495577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
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10
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Brovarets' OO, Voiteshenko IS, Hovorun DM. Physico-chemical profiles of the wobble ↔ Watson-Crick G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) tautomerisations: a QM/QTAIM comprehensive survey. Phys Chem Chem Phys 2018; 20:623-636. [PMID: 29227488 DOI: 10.1039/c7cp05139e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This study is intended to clarify in detail the tautomeric transformations of the wobble (w) G*·2AP(w) and A·2AP(w) nucleobase mispairs involving 2-aminopurine (2AP) into the Watson-Crick (WC) G·2AP(WC) and A*·2AP(WC) base mispairs (asterisks denote mutagenic tautomers of the DNA bases), respectively, by quantum-mechanical methods and Bader's Quantum Theory of Atoms in Molecules. Our previously reported methodology has been used, which allows the evolution of the physico-chemical parameters to be tracked along the entire internal reaction coordinate (IRC), not exclusively in the stationary states of these reactions. These biologically important G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) w ↔ WC tautomerisations, which are involved in mutagenic tautomerically-conformational pathways, determine the origin of the transitions and transversions induced by 2AP. In addition, it is established that they proceed through planar, highly stable, zwitterionic transition states and they exhibit similar physico-chemical profiles and stages of sequential intrapair proton transfer, followed by spatial rearrangement of the nucleobases relative to each other within the base pairs. These w ↔ WC tautomerisations occur non-dissociatively and are accompanied by a significant alteration in geometry (from wobble to Watson-Crick and vice versa) and redistribution of the specific intermolecular interactions, which can be divided into 10 patterns including AHB H-bonds and loosened A-H-B covalent bridges along the IRC of tautomerisation. Based on the redistribution of the geometrical and electron-topological parameters of the intrapair hydrogen bonds, exactly 9 key points have been allocated to characterize the evolution of these reactions.
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Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str., 03680 Kyiv, Ukraine.
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11
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
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12
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Brovarets' OO, Pérez-Sánchez H. Whether the amino–imino tautomerism of 2-aminopurine is involved into its mutagenicity? Results of a thorough QM investigation. RSC Adv 2016. [DOI: 10.1039/c6ra24277d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2AP* mutagenic tautomer is able to induce only one incorporation error – transversion – by pairing through the H-bonds into the G·2AP* mispair.
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Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Horacio Pérez-Sánchez
- Computer Science Department
- Bioinformatics and High Performance Computing (BIO-HPC) Research Group
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
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13
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Brovarets' OO, Pérez-Sánchez H, Hovorun DM. Structural grounds for the 2-aminopurine mutagenicity: a novel insight into the old problem of the replication errors. RSC Adv 2016. [DOI: 10.1039/c6ra17787e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutagenic pressure of the 2AP molecule on DNA during its replication is realized via the more intensive generation of the T* mutagenic tautomers through the reaction 2AP·T(WC) → 2AP·T*(w).
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Affiliation(s)
- Ol'ha O. Brovarets'
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
| | - Horacio Pérez-Sánchez
- Computer Science Department
- Bioinformatics and High Performance Computing (BIO-HPC) Research Group
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- 03680 Kyiv
- Ukraine
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14
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15
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The influence of intermolecular halogen bonds on the tautomerism of nucleobases. I. Guanine. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
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Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
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17
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Raczyńska ED, Makowski M, Hallmann M, Kamińska B. Geometric and energetic consequences of prototropy for adenine and its structural models – a review. RSC Adv 2015. [DOI: 10.1039/c4ra17280a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.
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Affiliation(s)
- Ewa D. Raczyńska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | | | - Małgorzata Hallmann
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | - Beata Kamińska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
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18
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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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19
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Thermal racemization of spiropyrans: implication of substituent and solvent effects revealed by computational study. Struct Chem 2013. [DOI: 10.1007/s11224-013-0374-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Kadam SS, Maier L, Kostakis I, Pouli N, Toušek J, Nečas M, Marakos P, Marek R. Synthesis and Tautomerism of Substituted Pyrazolo[4,3-c]pyrazoles. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Raczyńska ED, Kamińska B. Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM). J Mol Model 2013; 19:3947-60. [PMID: 23832652 PMCID: PMC3744648 DOI: 10.1007/s00894-013-1926-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/16/2013] [Indexed: 11/25/2022]
Abstract
Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Live Science (SGGW), 02-776, Warszawa, Poland.
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22
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Abou-Zied OK. Effect of NH2 rotation on the fluorescence of 2-aminopurine in solution. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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23
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Stasyuk OA, Szatyłowicz H, Krygowski TM. Effect of the H-bonding on aromaticity of purine tautomers. J Org Chem 2012; 77:4035-45. [PMID: 22448684 DOI: 10.1021/jo300406r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F(-) and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (-14.12 and -10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to -14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N(-)···HF type are stronger by ~10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N(-)···HF energies in pyrrole and imidazole are -32.28 and -30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability.
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Affiliation(s)
- Olga A Stasyuk
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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Sinha RK, Lobsiger S, Leutwyler S. Isomer- and Species-Selective Infrared Spectroscopy of Jet-Cooled 7H- and 9H-2-Aminopurine and 2-Aminopurine·H2O Clusters. J Phys Chem A 2012; 116:1129-36. [DOI: 10.1021/jp2077177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
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25
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Lobsiger S, Sinha RK, Trachsel M, Leutwyler S. Low-lying excited states and nonradiative processes of the adenine analogues 7H- and 9H-2-aminopurine. J Chem Phys 2011; 134:114307. [DOI: 10.1063/1.3567090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Sinha RK, Lobsiger S, Trachsel M, Leutwyler S. Vibronic Spectra of Jet-Cooled 2-Aminopurine·H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations. J Phys Chem A 2011; 115:6208-17. [DOI: 10.1021/jp111469n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Maria Trachsel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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27
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Bravaya KB, Kostko O, Dolgikh S, Landau A, Ahmed M, Krylov AI. Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra. J Phys Chem A 2010; 114:12305-17. [DOI: 10.1021/jp1063726] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oleg Kostko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stanislav Dolgikh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Musahid Ahmed
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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28
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Raczyńska ED, Kamińska B. Prototropy and π-electron delocalization for purine and its radical ions - DFT studies. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1668] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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29
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Hassan WMI, Chung WC, Shimakura N, Koseki S, Kono H, Fujimura Y. Ultrafast radiationless transition pathways through conical intersections in photo-excited 9H-adenine. Phys Chem Chem Phys 2010; 12:5317-28. [DOI: 10.1039/b926102h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Sheng Y, Bean HD, Mamajanov I, Hud NV, Leszczynski J. Comprehensive Investigation of the Energetics of Pyrimidine Nucleoside Formation in a Model Prebiotic Reaction. J Am Chem Soc 2009; 131:16088-95. [DOI: 10.1021/ja900807m] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yinghong Sheng
- Department of Chemistry and Mathematics & Whitaker Center, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Boulevard South, Fort Myers, Florida 33965, School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, and Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, P.O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Heather D. Bean
- Department of Chemistry and Mathematics & Whitaker Center, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Boulevard South, Fort Myers, Florida 33965, School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, and Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, P.O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Irena Mamajanov
- Department of Chemistry and Mathematics & Whitaker Center, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Boulevard South, Fort Myers, Florida 33965, School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, and Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, P.O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Nicholas V. Hud
- Department of Chemistry and Mathematics & Whitaker Center, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Boulevard South, Fort Myers, Florida 33965, School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, and Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, P.O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Department of Chemistry and Mathematics & Whitaker Center, College of Arts & Sciences, Florida Gulf Coast University, 10501 FGCU Boulevard South, Fort Myers, Florida 33965, School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, and Interdisciplinary Nanotoxicity Center, Department of Chemistry, Jackson State University, P.O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
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31
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Reynisson J, Steenken S. One-electron reduction of 2-aminopurine in the aqueous phase. A DFT and pulse radiolysis study. Phys Chem Chem Phys 2009; 7:659-65. [PMID: 19787883 DOI: 10.1039/b417343k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electron affinity and the subsequent proton affinity of the electron adducts of 2-aminopurine (abbreviated 2AP) and adenine (A) are calculated with density functional theory (DFT). According to these calculations 2AP*- and A*- have similar thermochemical parameters leading to the conclusion that their reaction pathways should be close to analogous. Using the pulse radiolysis technique 2AP*- is formed by reaction with the hydrated electron (e(-)aq) and the resulting transient absorption spectrum is assigned to 2AP(NH)*. Additionally, it was found, employing the laser flash photolysis technique, that the excited singlet state of 2AP is incapable of oxidizing guanine in the aqueous phase. However, the one-electron oxidized 2AP (2AP*+) has sufficient energy to ionize guanine according to the DFT results in agreement with experimental data from the literature.
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32
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Bartl T, Zacharová Z, Sečkářová P, Kolehmainen E, Marek R. NMR Quantification of Tautomeric Populations in Biogenic Purine Bases. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Butler RS, Cohn P, Tenzel P, Abboud KA, Castellano RK. Synthesis, Photophysical Behavior, and Electronic Structure of Push−Pull Purines. J Am Chem Soc 2008; 131:623-33. [DOI: 10.1021/ja806348z] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roslyn S. Butler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Pamela Cohn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Phillip Tenzel
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Khalil A. Abboud
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Ronald K. Castellano
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
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34
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Kenfack CA, Piémont E, Ben Gaied N, Burger A, Mély Y. Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes. J Phys Chem B 2008; 112:9736-45. [PMID: 18646799 DOI: 10.1021/jp8028243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
8-Vinyl-deoxyadenosine (8VA) has been recently introduced as a fluorescent analogue of adenosine that is less perturbing and less quenched than the well-established 2-amino-deoxyribosylpurine (2AP) probe when inserted in oligonucleotides. To further validate 8VA as a fluorescent substitute of A, we compared the ability of 8VA and 2AP in sequences of the type d(CGT TTT XNX TTT TGC) (with N=8VA or 2AP and X=T and C) to discriminate the nature of the opposite base (Y) in duplexes. For both probes, systematic variations in the amplitudes of the short- and long-lived lifetimes of the fluorescence intensity decays as well as in the amplitude of the fast rotational correlation time of the fluorescence anisotropy decays were observed as a function of the nature of Y. From these parameters, we inferred a stability order 8VA-T > 8VA-G > 8VA-A > 8VA-C, similar to the stability order with the native A base, but different from the stability order with 2AP. Using a combination of molecular mechanics and ab initio calculations, we found that the time-resolved parameters of 8VA, but not the 2AP ones, correlate well with the geometry and the strength of the A-Y base-pairing interaction. This may be rationalized by the smaller structural and electronic perturbations induced by the vinyl group in position 8 as compared to the amino group at position 2. As a consequence, substitution of A by 8VA in a base pair was found to only minimally modify the structure and interaction energy of the base pair. Thus, 8VA can be used as a fluorescent substitute of the natural A, to straightforwardly discriminate the nature of the opposite base. This may find interesting applications notably in the elucidation of the mechanisms and dynamics of the DNA mismatch repair system.
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Affiliation(s)
- Cyril A Kenfack
- Photophysique des Interactions Biomoleculaires, UMR 7175 CNRS, Institut Gilbert Laustriat, Faculte de Pharmacie, Universite Louis Pasteur, Strasbourg 1, 74, Route du Rhin, 67401 Illkirch Cedex, France.
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35
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Mohamed AA, El-Harby AW. Amino–imino tautomerism of mono- and diaminothiazoles: Quantum chemical study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.04.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Wood NJ, Brannigan JA, Duckett SB, Heath SL, Wagstaff J. Detection of Picomole Amounts of Biological Substrates by para-Hydrogen-Enhanced NMR Methods in Conjunction with a Suitable Receptor Complex. J Am Chem Soc 2007; 129:11012-3. [PMID: 17711281 DOI: 10.1021/ja074286k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicholas J Wood
- Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
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37
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Abo-riziq A, Crews BO, Compagnon I, Oomens J, Meijer G, Von Helden G, Kabelac M, Hobza P, de Vries MS. The mid-IR spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine. J Phys Chem A 2007; 111:7529-36. [PMID: 17625809 DOI: 10.1021/jp072183i] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the mid-IR (400-1800 cm(-1)) spectra of 9-ethyl guanine, guanosine, and 2-deoxyguanosine measured by IR-UV double-resonance spectroscopy. We compare the recorded mid-IR spectra with the spectra of the most stable structures obtained from RI-MP2 and RI-DFT-D calculations. The results confirm the enol form for all structures and demonstrate the efficacy of a new approach to DFT calculations that includes dispersion interactions.
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Affiliation(s)
- Ali Abo-riziq
- Department of Chemistry and Biochemistry, University of California Santa Barbara, California 93106-9510, USA
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39
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Abstract
The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S(0), S(1), and S(2) states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S(2) and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S(1), S(2), and S(3) states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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40
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Neely RK, Magennis SW, Parsons S, Jones AC. Photophysics and X-ray Structure of Crystalline 2-Aminopurine. Chemphyschem 2007; 8:1095-102. [PMID: 17385756 DOI: 10.1002/cphc.200600593] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: pi-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H-7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that pi-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.
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Affiliation(s)
- Robert K Neely
- School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK
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41
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Affiliation(s)
- S. Perun
- a Polish Academy of Sciences , Warsaw
| | | | - W. Domcke
- b Technical University of Munich , Germany
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42
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Theoretical study of the regioselectivity of the cycloaddition reaction between cyclopentadiene and methyleneketene. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.04.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Raczyńska ED, Kosińska W, Ośmiałowski B, Gawinecki R. Tautomeric Equilibria in Relation to Pi-Electron Delocalization. Chem Rev 2005; 105:3561-612. [PMID: 16218561 DOI: 10.1021/cr030087h] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Wan C, Xia T, Becker HC, Zewail AH. Ultrafast unequilibrated charge transfer: A new channel in the quenching of fluorescent biological probes. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.06.101] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Perun S, Sobolewski AL, Domcke W. Ab Initio Studies on the Radiationless Decay Mechanisms of the Lowest Excited Singlet States of 9H-Adenine. J Am Chem Soc 2005; 127:6257-65. [PMID: 15853331 DOI: 10.1021/ja044321c] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms that are responsible for the rapid deactivation of the (1)npi and( 1)pipi excited singlet states of the 9H isomer of adenine have been investigated with multireference ab initio methods (complete-active-space self-consistent-field (CASSCF) method and second-order perturbation theory based on the CASSCF reference (CASPT2)). Two novel photochemical pathways, which lead to conical intersections of the S(1) excited potential-energy surface with the electronic ground-state surface, have been identified. They involve out-of-plane deformations of the six-membered aromatic ring via the twisting of the N(3)C(2) and N(1)C(6) bonds. These low-lying conical intersections are separated from the minimum energy of the lowest ((1)npi) excited state in the Franck-Condon region by very low energy barriers (of the order of 0.1 eV). These properties of the S(1) and S(0) potential-energy surfaces explain the unusual laser-induced fluorescence spectrum of jet-cooled 9H-adenine, showing sharp structures only in a narrow energy interval near the origin, as well as the extreme excess-energy dependence of the lifetime of the singlet excited states. It is suggested that internal-conversion processes via conical intersections, which are accessed by out-of-plane deformation of the six-membered ring, dominate the photophysics of the lowest vibronic levels of adenine in the gas phase, while hydrogen-abstraction photochemistry driven by repulsive (1)pisigma states may become competitive at higher excitation energies. These ultrafast excited-state deactivation processes provide adenine with a high degree of intrinsic photostability.
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Affiliation(s)
- Serhiy Perun
- Institute of Physics, Polish Academy of Sciences, PL-02668 Warsaw, Poland
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46
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Transitions to high tautomeric states can be induced in adenine by interactions with carboxylate and sodium ions: DFT calculation data. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.05.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Hou B, Lim EK, Higgins GS, Bowles DJ. N-Glucosylation of Cytokinins by Glycosyltransferases of Arabidopsis thaliana. J Biol Chem 2004; 279:47822-32. [PMID: 15342621 DOI: 10.1074/jbc.m409569200] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytokinins are plant hormones that can be glucosylated to form O-glucosides and N-glucosides. The glycoconjugates are inactive and are thought to play a role in homeostasis of the hormones. Although O-glucosyltransferases have been identified that recognize cytokinins, the enzymes involved in N-glucosylation have not been identified even though the process has been recognized for many years. This study utilizes a screening strategy in which 105 recombinant glycosyltransferases (UGTs) of Arabidopsis have been analyzed for catalytic activity toward the classical cytokinins: trans-zeatin, dihydrozeatin, N(6)-benzyladenine, N(6)-isopentenyladenine, and kinetin. Five UGTs were identified in the screen. UGT76C1 and UGT76C2 recognized all cytokinins and glucosylated the hormones at the N(7) and N(9) positions. UGT85A1, UGT73C5, and UGT73C1 recognized trans-zeatin and dihydrozeatin, which have an available hydroxyl group for glucosylation and formed the O-glucosides. The biochemical characteristics of the N-glucosyltransferases were analyzed, and highly effective inhibitors of their activities were identified. Constitutive overexpression of UGT76C1 in transgenic Arabidopsis confirmed that the recombinant enzyme functioned in vivo to glucosylate cytokinin applied to the plant. The role of the N-glucosyltransferases in cytokinin metabolism is discussed.
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Affiliation(s)
- Bingkai Hou
- CNAP, Department of Biology, University of York, York YO10 5DD, United Kingdom
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Neely RK, Magennis SW, Dryden DTF, Jones AC. Evidence of Tautomerism in 2-Aminopurine from Fluorescence Lifetime Measurements. J Phys Chem B 2004. [DOI: 10.1021/jp0490857] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert K. Neely
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - Steven W. Magennis
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - David T. F. Dryden
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
| | - Anita C. Jones
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Centre (COSMIC), The University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ, United Kingdom
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Sheng Y, Leszczynski J, Garcia AA, Rosario R, Gust D, Springer J. Comprehensive Theoretical Study of the Conversion Reactions of Spiropyrans: Substituent and Solvent Effects. J Phys Chem B 2004. [DOI: 10.1021/jp0488867] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Sečkářová P, Marek R, Maliňáková K, Kolehmainen E, Hocková D, Hocek M, Sklenář V. Direct determination of tautomerism in purine derivatives by low-temperature NMR spectroscopy. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.06.088] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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