1
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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2
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Russel NS, Kodali G, Stanley RJ, Narayanan M. Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study. J Phys Chem B 2023; 127:7858-7871. [PMID: 37698525 DOI: 10.1021/acs.jpcb.3c03618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.
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Affiliation(s)
- Nadim Shahriar Russel
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- GlowDNA LLC., Malvern, Pennsylvania 19355, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Madhavan Narayanan
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, Illinois 60532, United States
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3
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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4
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Exploring the nature of interaction and stability between DNA/RNA base pairs and defective & defect-dopant graphene sheets. A possible insights on DNA/RNA sequencing. Int J Biol Macromol 2020; 146:387-404. [DOI: 10.1016/j.ijbiomac.2020.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/07/2019] [Accepted: 01/01/2020] [Indexed: 01/29/2023]
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5
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Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
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6
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Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
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Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
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7
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Bull GD, Thompson KC. Proton Transfer and Tautomerism in 2-Aminopurine-Thymine and Pyrrolocytosine-Guanine Base Pairs. Biochemistry 2018; 57:4547-4561. [PMID: 30024730 DOI: 10.1021/acs.biochem.8b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.
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Affiliation(s)
- Graham D Bull
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
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8
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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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9
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Saha S, Quiney HM. Solvent effects on the excited state characteristics of adenine–thymine base pairs. RSC Adv 2017. [DOI: 10.1039/c7ra03244g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A systematic analysis of the excited state characteristics of the DNA base pair adenine–thymine in stacked and Watson–Crick hydrogen bonded configurations has been carried out in this study.
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Affiliation(s)
- S. Saha
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
| | - H. M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging
- Theoretical Condensed Matter Physics Group
- School of Physics
- The University of Melbourne
- Australia
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10
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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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11
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Abstract
Depending on where it binds, a water molecule may change the excited-state lifetime of 2-aminopurine by a factor of 100. We explain why?
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Hans Lischka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
- Institute for Theoretical Chemistry
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12
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Switching on the fluorescence of 2-aminopurine by site-selective microhydration. Nat Chem 2014; 6:989-93. [DOI: 10.1038/nchem.2086] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/11/2014] [Indexed: 11/08/2022]
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13
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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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14
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Trachsel MA, Lobsiger S, Schär T, Leutwyler S. Low-lying excited states and nonradiative processes of 9-methyl-2-aminopurine. J Chem Phys 2014; 140:044331. [DOI: 10.1063/1.4862913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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15
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16
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Lobsiger S, Sinha RK, Leutwyler S. Building Up Water-Wire Clusters: Isomer-Selective Ultraviolet and Infrared Spectra of Jet-Cooled 2-Aminopurine (H2O)n, n = 2 and 3. J Phys Chem B 2013; 117:12410-21. [DOI: 10.1021/jp407127c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Lobsiger
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Rajeev K. Sinha
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Atomic and Molecular Physics, Manipal University, Manipal-576104, Karnataka, India
| | - Samuel Leutwyler
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
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17
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Liang J, Nguyen QL, Matsika S. Exciplexes and conical intersections lead to fluorescence quenching in π-stacked dimers of 2-aminopurine with natural purine nucleobases. Photochem Photobiol Sci 2013; 12:1387-400. [PMID: 23625036 PMCID: PMC5006741 DOI: 10.1039/c3pp25449f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 03/29/2013] [Indexed: 12/26/2022]
Abstract
Fluorescent analogues of the natural DNA bases are useful in the study of nucleic acids' structure and dynamics. 2-Aminopurine (2AP) is a widely used analogue with environmentally sensitive fluorescence behavior. The quantum yield of 2AP has been found to be significantly decreased when engaged in π-stacking interactions with the native bases. We present a theoretical study on fluorescence quenching mechanisms in dimers of 2AP π-stacked with adenine or guanine as in natural DNA. Relaxation pathways on the potential energy surfaces of the first excited states have been computed and reveal the importance of exciplexes and conical intersections in the fluorescence quenching process.
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Affiliation(s)
- JingXin Liang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Quynh L. Nguyen
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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18
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Gedik M, Brown A. Computational study of the excited state properties of modified RNA nucleobases. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Reichardt C, Wen C, Vogt RA, Crespo-Hernández CE. Role of intersystem crossing in the fluorescence quenching of 2-aminopurine 2′-deoxyriboside in solution. Photochem Photobiol Sci 2013; 12:1341-50. [DOI: 10.1039/c3pp25437b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Dierckx A, Miannay FA, Ben Gaied N, Preus S, Björck M, Brown T, Wilhelmsson LM. Quadracyclic adenine: a non-perturbing fluorescent adenine analogue. Chemistry 2012; 18:5987-97. [PMID: 22437923 DOI: 10.1002/chem.201103419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Indexed: 12/26/2022]
Abstract
Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Gothenburg, Sweden
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Nachtigallová D, Aquino AJA, Szymczak JJ, Barbatti M, Hobza P, Lischka H. Nonadiabatic Dynamics of Uracil: Population Split among Different Decay Mechanisms. J Phys Chem A 2011; 115:5247-55. [DOI: 10.1021/jp201327w] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Adélia J. A. Aquino
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
| | - Jaroslaw J. Szymczak
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim, Germany
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Hans Lischka
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
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Liang J, Matsika S. Pathways for fluorescence quenching in 2-aminopurine π-stacked with pyrimidine nucleobases. J Am Chem Soc 2011; 133:6799-808. [PMID: 21486032 DOI: 10.1021/ja2007998] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fluorescent analogues of nucleobases are very useful as probes to study DNA dynamics, because natural DNA does not fluoresce significantly. In many of these analogues, such as 2-aminopurine (2AP), the fluorescence is quenched when incorporated into DNA through processes that are not well understood. This work uses theoretical studies to examine fluorescence quenching pathways in 2AP-containing dimers. The singlet excited states of π-stacked dimer systems containing 2AP and a pyrimidine base, thymine or cytosine, have been studied using ab initio computational methods. Computed relaxation pathways along the excited-state surfaces reveal novel mechanisms that can lead to fluorescence quenching in the π-stacked dimers. The placement of 2AP on the 5' or 3' terminus of the dimers has different effects on the excitation energies and the relaxation pathways on the S(1) excited state. Conical intersections between the ground and first excited states exist when 2AP is placed at the 3' side, whereas the placement of 2AP at the 5' side leads to the switching of a bright state to a dark state. Both of these processes can lead to fluorescence quenching and may contribute to the fluorescence quenching observed in 2AP when incorporated in DNA.
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Affiliation(s)
- Jingxin Liang
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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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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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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Barbatti M, Aquino AJA, Szymczak JJ, Nachtigallová D, Lischka H. Photodynamical simulations of cytosine: characterization of the ultrafast bi-exponential UV deactivation. Phys Chem Chem Phys 2011; 13:6145-55. [DOI: 10.1039/c0cp01327g] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Gengeliczki Z, Callahan MP, Svadlenak N, Pongor CI, Sztáray B, Meerts L, Nachtigallová D, Hobza P, Barbatti M, Lischka H, de Vries MS. Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurine. Phys Chem Chem Phys 2010; 12:5375-88. [PMID: 20379571 DOI: 10.1039/b917852j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To explore the excited state dynamics of pyrimidine derivatives, we performed a combined experimental and theoretical study. We present resonant two-photon ionization (R2PI) and IR-UV double resonance spectra of 2,4-diaminopyrimidine and 2,6-diaminopurine seeded in a supersonic jet by laser desorption. For 2,4-diaminopyrimidine (S(0)-->S(1) 34,459 cm(-1)), we observed only the diamino tautomer with an excited state lifetime bracketed between experimental limits of 10 ps and 1 ns. For 2,6-diaminopurine, we observed two tautomers, the 9H- (S(0)-->S(1) 34,881 cm(-1)) and 7H- (S(0)-->S(1) 32,215 cm(-1)) diamino forms, with excited state lifetimes of 6.3±0.4 ns and 8.7±0.8 ns, respectively. We investigated the nature of the excited state of 2,4-diaminopyrimidine by means of multi-reference ab initio methods. The calculations of stationary points in the ground and excited states, minima on the S(0)/S(1) crossing seam and connecting reaction paths show that several paths with negligible barriers exist, allowing ultrafast radiationless deactivation if excited at energies slightly higher than the band origin. The sub-nanosecond lifetime found experimentally is in good agreement with this finding.
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Affiliation(s)
- Zsolt Gengeliczki
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Smolarek S, Rijs AM, Buma WJ, Drabbels M. Absorption spectroscopy of adenine, 9-methyladenine, and 2-aminopurine in helium nanodroplets. Phys Chem Chem Phys 2010; 12:15600-6. [DOI: 10.1039/c0cp00746c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Kodali G, Kistler KA, Narayanan M, Matsika S, Stanley RJ. Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study. J Phys Chem A 2009; 114:256-67. [DOI: 10.1021/jp908055h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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Szymczak JJ, Barbatti M, Soo Hoo JT, Adkins JA, Windus TL, Nachtigallová D, Lischka H. Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State. J Phys Chem A 2009; 113:12686-93. [DOI: 10.1021/jp905085x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Jason T. Soo Hoo
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Jaclyn A. Adkins
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Theresa L. Windus
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Dana Nachtigallová
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
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31
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Feng K, Engler G, Seefeld K, Kleinermanns K. Dispersed Fluorescence and Delayed Ionization of Jet-Cooled 2-Aminopurine: Relaxation to a Dark State Causes Weak Fluorescence. Chemphyschem 2009; 10:886-9. [DOI: 10.1002/cphc.200800816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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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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Mburu E, Matsika S. An Ab Initio Study of Substituent Effects on the Excited States of Purine Derivatives. J Phys Chem A 2008; 112:12485-91. [DOI: 10.1021/jp807145c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Elizabeth Mburu
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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35
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Yamazaki S, Domcke W. Ab initio studies on the photophysics of guanine tautomers: out-of-plane deformation and NH dissociation pathways to conical intersections. J Phys Chem A 2008; 112:7090-7. [PMID: 18613658 DOI: 10.1021/jp802759v] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radiationless decay mechanisms of the S1 excited states of the 7H-keto-amino, 7H-enol-amino, and 7H-keto-imino tautomers of guanine have been investigated with the CASPT2//CASSCF method. Out-of-plane deformation of the six-membered ring or the imino group as well as dissociation of NH bonds have been considered as photochemical pathways leading to conical intersections with the electronic ground state. It has been found that all three tautomers can reach S0-S1 conical intersections by out-of-plane deformation. However, only in the 7H-keto-amino tautomer the reaction path leading to the conical intersection is barrierless. This tautomer also has the lowest energy barrier for hydrogen detachment via the (1)pi sigma* state, whose potential energy surface intersects that of the (1)pi pi* state as well as that of the ground state. The other tautomers of guanine exhibit substantial energy barriers on their S1 potential energy surfaces with respect to both reaction mechanisms. These findings suggest that the 7H-keto-amino tautomer exhibits the shortest excited-state lifetime of the three tautomers due to particularly fast nonradiative deactivation processes through S0-S1 conical intersections. The computational results explain the remarkable observation that the energetically most stable 7H-keto-amino tautomer is missing in the resonant two-photon ionization spectrum of guanine in a supersonic jet. The results also explain that the energetically less stable 7H-enol-amino and 7H-keto-imino tautomers have longer excited-state lifetimes and are thus detectable by resonant two-photon ionization.
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Affiliation(s)
- Shohei Yamazaki
- Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany.
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36
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Vibrationally mediated photodissociation of ammonia: product angular distributions from adiabatic and nonadiabatic dissociation. Mol Phys 2008. [DOI: 10.1080/00268970802245192] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Piryatinski A, Tretiak S, Chernyak VY. Dynamical variational approach to non-adiabatic electronic structure. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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38
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Kodali G, Kistler KA, Matsika S, Stanley RJ. 2-Aminopurine Excited State Electronic Structure Measured by Stark Spectroscopy. J Phys Chem B 2008; 112:1789-95. [DOI: 10.1021/jp076374x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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40
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Muchová E, Slavícek P, Sobolewski AL, Hobza P. Glycine in an Electronically Excited State: Ab Initio Electronic Structure and Dynamical Calculations. J Phys Chem A 2007; 111:5259-69. [PMID: 17530834 DOI: 10.1021/jp071483x] [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: 02/07/2023]
Abstract
The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.
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Affiliation(s)
- Eva Muchová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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41
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Barbatti M, Lischka H. Can the Nonadiabatic Photodynamics of Aminopyrimidine Be a Model for the Ultrafast Deactivation of Adenine? J Phys Chem A 2007; 111:2852-8. [PMID: 17388405 DOI: 10.1021/jp070089w] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction path for the ultrafast deactivation of 6-aminopyrimidine (6AP) has been investigated by means of ab initio surface-hopping dynamics. The electronic vertical excitation spectrum, excited-state S1 minima, and minima on the crossing seam of 6AP resemble well those found for adenine. The deactivation from the S1 to the S0 state takes place at the ultrafast time scale of 400 fs and involves the out-of-plane ring deformation of the C4 atom, a position that is sterically restricted in adenine by the imidazole ring. Mechanical restrictions have been used to simulate in a simple way the role of the imidazole group in adenine. As a result, deactivation via out-of-plane ring deformation of the C2 and N3 atoms are observed in good agreement with predictions for adenine. These dynamics results show that the previously suggested ring puckering deactivation paths really exist at a time scale, which is compatible with experimentally observed life times. The electronic structure of the crossing seam has been shown to have the same nature as those of simple biradicaloid systems, a feature which seems to be valid for any cyclic system.
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Affiliation(s)
- Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria.
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42
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Marian CM. The Guanine Tautomer Puzzle: Quantum Chemical Investigation of Ground and Excited States. J Phys Chem A 2007; 111:1545-53. [PMID: 17274608 DOI: 10.1021/jp068620v] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined density functional and multireference configuration interaction methods have been employed to explore the ground and low-lying electronically excited states of the most important tautomeric and rotameric forms of guanine with the purpose of resolving the conflicting assignments of IR-UV bands found in the literature. The calculations predict sharp 1(pi-->pi*) origin transitions for the RN1 rotamer of the 7H-amino-hydroxy species and the RN7 rotamer of the 9H-amino-hydroxy species. The other 9H-amino-hydroxy rotamer, RN1, undergoes ultrafast nonradiative decay and is thus missing in the UV spectra. Because of its very small Franck-Condon factor and the presence of a conical intersection close by, it appears questionable, whether the 1(pi-->pi*) origin transition of 9H-amino-oxo-guanine can be observed experimentally. Vibrational overlap is more favorable for the 1(pi-->pi*) origin transition of the 7H- amino-oxo form, but also this tautomer is predicted to undergo ultrafast nonradiative decay of the 1(pi-->pi*) population. The good agreement of calculated IR frequencies of the amino-oxo species with recent IR spectra in He droplets and their mismatch with peaks observed in IR-UV spectra indicate that none of the bands stem from 7H- or 9H-amino-oxo guanine. Instead, our results suggest that these bands originate from 7H-imino-oxo guanine tautomers. In the excited-state dynamics of the biologically relevant 9H-amino-oxo tautomer, a diffuse charge transfer state is predicted to play a significant role.
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Affiliation(s)
- Christel M Marian
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
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43
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Credo Chung W, Lan Z, Ohtsuki Y, Shimakura N, Domcke W, Fujimura Y. Conical intersections involving the dissociative1πσ* state in 9H-adenine: a quantum chemical ab initio study. Phys Chem Chem Phys 2007; 9:2075-84. [PMID: 17464388 DOI: 10.1039/b618745e] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conical intersections of the dissociative 1pisigma* excited state with the lowest 1pipi* excited state and the electronic ground state of 9H-adenine have been investigated with multireference electronic structure calculations. Adiabatic and quasidiabatic potential energy surfaces and coupling elements were calculated as a function of the NH stretch coordinate of the azine group and the out-of-plane angle of the hydrogen atom, employing MultiReference Configuration-Interaction (MRCI) as well as Complete-Active-Space Self-Consistent-Field (CASSCF) methods. Characteristic properties of the 1pipi*-1pisigma* and 1pisigma*-S0 conical intersections, such as the diabatic-to-adiabatic mixing angle, the geometric phase of the adiabatic electronic wavefunctions, the derivative coupling, as well as adiabatic and diabatic transition dipole moment surfaces were investigated in detail. These data are a prerequisite for future quantum wavepacket simulations of the photodissociation and internal-conversion dynamics of adenine.
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Affiliation(s)
- Wilfredo Credo Chung
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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