The optical properties of adenine cation in different oligonucleotides: a PCM/TD‑DFT study (195 views) (PDF public 106 views)
Theor Chem Acc (ISSN: 1432-881x), 2018; 137(3): N/D-N/D.
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Paper type: Journal Article,
Impact factor: 1.545, 5-year impact factor: 2.551
Url: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042532232&doi=10.1007%2fs00214-018-2223-2&partnerID=40&md5=35bbb68400b8af601c786a63f98a8958
Keywords: Dna, Hole Delocalization, Td-Dft,
Affiliations:
*** IBB - CNR ***
LIDYL, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, Naples, 80134, Italy
Área de Didáctica de las Ciencias Experimentales, University of Extremadura, Avda. de la Universidad, Cáceres, 10071, Spain
References:
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Barber, J., Tran, P.D., From natural to artificial photosynthesis (2013) J R Soc Interface, 10 (81), p. 20120984
Dadashi-Silab, S., Doran, S., Yagci, Y., Photoinduced electron transfer reactions for macromolecular syntheses (2016) Chem Rev, 116 (17), pp. 10212-10275. , COI: 1:CAS:528:DC%2BC28XhtVGlsr8%3D
D’Souza, F., Ito, O., Photosensitized electron transfer processes of nanocarbons applicable to solar cells (2012) Chem Soc Rev, 41 (1), pp. 86-96
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Lou, Z., Li, P., Han, K., Redox-responsive fluorescent probes with different design strategies (2015) Acc Chem Res, 48 (5), pp. 1358-1368. , COI: 1:CAS:528:DC%2BC2MXntVCns7g%3D
Banyasz, A., Ketola, T.-M., Muñoz-Losa, A., Rishi, S., Adhikary, A., Sevilla, M.D., Martinez-Fernandez, L., Markovitsi, D., UV-induced adenine radicals induced in DNA A-tracts: spectral and dynamical characterization (2016) J Phys Chem Lett, 7 (19), pp. 3949-3953. , COI: 1:CAS:528:DC%2BC28XhsFamsrjO
Marguet, S., Markovitsi, D., Talbot, F., One- and two-photon ionization of DNA single and double helices studied by laser flash photolysis at 266 nm (2006) J Phys Chem B, 110 (23), pp. 11037-11039. , COI: 1:CAS:528:DC%2BD28XkslKhurc%3D
Crespo-Hernández, C.E., Arce, R., Near threshold photo-oxidation of dinucleotides containing purines upon 266 nm nanosecond laser excitation. The role of base stacking, conformation, and sequence (2003) J Phys Chem B, 107 (4), pp. 1062-1070
Banyasz, A., Martínez-Fernández, L., Balty, C., Perron, M., Douki, T., Improta, R., Markovitsi, D., Absorption of low-energy UV radiation by human telomere G-quadruplexes generates long-lived guanine radical cations (2017) J Am Chem Soc, 139 (30), pp. 10561-10568. , COI: 1:CAS:528:DC%2BC2sXht1Slt73L
Schroeder, C.A., Pluhařová, E., Seidel, R., Schroeder, W.P., Faubel, M., Slavicek, P., Winter, B., Bradforth, S.E., Oxidation half-reaction of aqueous nucleosides and nucleotides via photoelectron spectroscopy augmented by ab initio calculations (2015) J Am Chem Soc, 137 (1), pp. 201-209. , COI: 1:CAS:528:DC%2BC2cXitVSju7zE
Zhang, Y., de La Harpe, K., Beckstead, A.A., Improta, R., Kohler, B., UV-induced proton transfer between DNA strands (2015) J Am Chem Soc, 137 (22), pp. 7059-7062. , COI: 1:CAS:528:DC%2BC2MXptVGmt7k%3D
Zhang, Y., Dood, J., Beckstead, A.A., Li, X.B., Nguyen, K.V., Burrows, C.J., Improta, R., Kohler, B., Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide (2014) Proc Natl Acad Sci, 111 (32), pp. 11612-11617. , COI: 1:CAS:528:DC%2BC2cXht1amsLfN
Bucher, D.B., Pilles, B.M., Carell, T., Zinth, W., Charge separation and charge delocalization identified in long-living states of photoexcited DNA (2014) Proc Natl Acad Sci, 111 (12), pp. 4369-4374. , COI: 1:CAS:528:DC%2BC2cXkt1Wjtr8%3D
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Doorley, G.W., McGovern, D.A., George, M.W., Towrie, M., Parker, A.W., Kelly, J.M., Quinn, S.J., Picosecond transient infrared study of the ultrafast deactivation processes of electronically Excited B-DNA and Z-DNA forms of [poly(dG-dC)]2 (2009) Ang Chem Int Ed, 48 (1), pp. 123-127. , COI: 1:CAS:528:DC%2BD1MXosFKksg%3D%3D
Doorley, G.W., Wojdyla, M., Watson, G.W., Towrie, M., Parker, A.W., Kelly, J.M., Quinn, S.J., Tracking DNA excited states by picosecond-time-resolved infrared spectroscopy: signature band for a charge-transfer excited state in stacked adenine-thymine systems (2013) J Phys Chem Lett, 4 (16), pp. 2739-2744. , COI: 1:CAS:528:DC%2BC3sXhtFOqtLnF
Keane, P.M., Wojdyla, M., Doorley, G.W., Kelly, J.M., Parker, A.W., Clark, I.P., Greetham, G.M., Quinn, S.J., Long-lived excited states in i-motif DNA studied by picosecond time-resolved IR spectroscopy (2014) Chem Commun, 50 (23), pp. 2990-2992. , COI: 1:CAS:528:DC%2BC2cXivFOrt7c%3D
Kawai, K., Majima, T., Hole transfer kinetics of DNA (2013) Acc Chem Res, 46 (11), pp. 2616-2625. , COI: 1:CAS:528:DC%2BC3sXhtVWhu7zI
Vura-Weis, J., Wasielewski, M.R., Thazhathveetil, A.K., Lewis, F.D., Efficient charge transport in DNA diblock oligomers (2009) J Am Chem Soc, 131 (28), pp. 9722-9727. , COI: 1:CAS:528:DC%2BD1MXnslehu70%3D
Renaud, N., Harris, M.A., Singh, A.P.N., Berlin, Y.A., Ratner, M.A., Wasielewski, M.R., Lewis, F.D., Grozema, F.C., Deep-hole transfer leads to ultrafast charge migration in DNA hairpins (2016) Nat Chem, 8, p. 1015. , COI: 1:CAS:528:DC%2BC28XhtlChsrrK
Slinker, J.D., Muren, N.B., Renfrew, S.E., Barton, J.K., DNA charge transport over 34 nm (2011) Nat Chem, 3 (3), pp. 228-233. , COI: 1:CAS:528:DC%2BC3MXit1Wru7g%3D
Choi, J., Park, J., Tanaka, A., Park, M.J., Jang, Y.J., Fujitsuka, M., Kim, S.K., Majima, T., Hole trapping of G-quartets in a G-quadruplex (2013) Ang Chem Int Ed, 52 (4), pp. 1134-1138. , COI: 1:CAS:528:DC%2BC38XhslKntL7O
Roca-Sanjuán, D., Merchán, M., Serrano-Andrés, L., Modeling hole transfer in DNA: low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer (2008) Chem Phys, 349 (1), pp. 188-196
Arnold Anna, R., Grodick Michael, A., Barton Jacqueline, K., DNA charge transport: from chemical principles to the cell (2016) Cell Chem Biol, 23 (1), pp. 183-197. , COI: 1:STN:280:DC%2BC28jmt1WlsA%3D%3D
Genereux, J.C., Barton, J.K., Mechanisms for DNA charge transport (2010) Chem Rev, 110 (3), pp. 1642-1662. , COI: 1:CAS:528:DC%2BD1MXhsVKhsL3F
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Theor Chem Acc (ISSN: 1432-881x), 2018; 137(3): N/D-N/D.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 1.545, 5-year impact factor: 2.551
Url: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042532232&doi=10.1007%2fs00214-018-2223-2&partnerID=40&md5=35bbb68400b8af601c786a63f98a8958
Keywords: Dna, Hole Delocalization, Td-Dft,
Affiliations:
*** IBB - CNR ***
LIDYL, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, Naples, 80134, Italy
Área de Didáctica de las Ciencias Experimentales, University of Extremadura, Avda. de la Universidad, Cáceres, 10071, Spain
References:
Ponseca, C.S., Chábera, P., Uhlig, J., Persson, P., Sundström, V., Ultrafast electron dynamics in solar energy conversion (2017) Chem Rev, 117 (16), pp. 10940-11024. , COI: 1:CAS:528:DC%2BC2sXhtlSlu7r
Barber, J., Tran, P.D., From natural to artificial photosynthesis (2013) J R Soc Interface, 10 (81), p. 20120984
Dadashi-Silab, S., Doran, S., Yagci, Y., Photoinduced electron transfer reactions for macromolecular syntheses (2016) Chem Rev, 116 (17), pp. 10212-10275. , COI: 1:CAS:528:DC%2BC28XhtVGlsr8%3D
D’Souza, F., Ito, O., Photosensitized electron transfer processes of nanocarbons applicable to solar cells (2012) Chem Soc Rev, 41 (1), pp. 86-96
Liu, Z., Qi, W., Xu, G., Recent advances in electrochemiluminescence (2015) Chem Soc Rev, 44 (10), pp. 3117-3142. , COI: 1:CAS:528:DC%2BC2MXltVaiurc%3D
Lou, Z., Li, P., Han, K., Redox-responsive fluorescent probes with different design strategies (2015) Acc Chem Res, 48 (5), pp. 1358-1368. , COI: 1:CAS:528:DC%2BC2MXntVCns7g%3D
Banyasz, A., Ketola, T.-M., Muñoz-Losa, A., Rishi, S., Adhikary, A., Sevilla, M.D., Martinez-Fernandez, L., Markovitsi, D., UV-induced adenine radicals induced in DNA A-tracts: spectral and dynamical characterization (2016) J Phys Chem Lett, 7 (19), pp. 3949-3953. , COI: 1:CAS:528:DC%2BC28XhsFamsrjO
Marguet, S., Markovitsi, D., Talbot, F., One- and two-photon ionization of DNA single and double helices studied by laser flash photolysis at 266 nm (2006) J Phys Chem B, 110 (23), pp. 11037-11039. , COI: 1:CAS:528:DC%2BD28XkslKhurc%3D
Crespo-Hernández, C.E., Arce, R., Near threshold photo-oxidation of dinucleotides containing purines upon 266 nm nanosecond laser excitation. The role of base stacking, conformation, and sequence (2003) J Phys Chem B, 107 (4), pp. 1062-1070
Banyasz, A., Martínez-Fernández, L., Balty, C., Perron, M., Douki, T., Improta, R., Markovitsi, D., Absorption of low-energy UV radiation by human telomere G-quadruplexes generates long-lived guanine radical cations (2017) J Am Chem Soc, 139 (30), pp. 10561-10568. , COI: 1:CAS:528:DC%2BC2sXht1Slt73L
Schroeder, C.A., Pluhařová, E., Seidel, R., Schroeder, W.P., Faubel, M., Slavicek, P., Winter, B., Bradforth, S.E., Oxidation half-reaction of aqueous nucleosides and nucleotides via photoelectron spectroscopy augmented by ab initio calculations (2015) J Am Chem Soc, 137 (1), pp. 201-209. , COI: 1:CAS:528:DC%2BC2cXitVSju7zE
Zhang, Y., de La Harpe, K., Beckstead, A.A., Improta, R., Kohler, B., UV-induced proton transfer between DNA strands (2015) J Am Chem Soc, 137 (22), pp. 7059-7062. , COI: 1:CAS:528:DC%2BC2MXptVGmt7k%3D
Zhang, Y., Dood, J., Beckstead, A.A., Li, X.B., Nguyen, K.V., Burrows, C.J., Improta, R., Kohler, B., Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide (2014) Proc Natl Acad Sci, 111 (32), pp. 11612-11617. , COI: 1:CAS:528:DC%2BC2cXht1amsLfN
Bucher, D.B., Pilles, B.M., Carell, T., Zinth, W., Charge separation and charge delocalization identified in long-living states of photoexcited DNA (2014) Proc Natl Acad Sci, 111 (12), pp. 4369-4374. , COI: 1:CAS:528:DC%2BC2cXkt1Wjtr8%3D
Pilles, B.M., Bucher, D.B., Liu, L.Z., Gilch, P., Zinth, W., Schreier, W.J., Identification of charge separated states in thymine single strands (2014) Chem Commun, 50 (98), pp. 15623-15626. , COI: 1:CAS:528:DC%2BC2cXhvVSiu7bP
Doorley, G.W., McGovern, D.A., George, M.W., Towrie, M., Parker, A.W., Kelly, J.M., Quinn, S.J., Picosecond transient infrared study of the ultrafast deactivation processes of electronically Excited B-DNA and Z-DNA forms of [poly(dG-dC)]2 (2009) Ang Chem Int Ed, 48 (1), pp. 123-127. , COI: 1:CAS:528:DC%2BD1MXosFKksg%3D%3D
Doorley, G.W., Wojdyla, M., Watson, G.W., Towrie, M., Parker, A.W., Kelly, J.M., Quinn, S.J., Tracking DNA excited states by picosecond-time-resolved infrared spectroscopy: signature band for a charge-transfer excited state in stacked adenine-thymine systems (2013) J Phys Chem Lett, 4 (16), pp. 2739-2744. , COI: 1:CAS:528:DC%2BC3sXhtFOqtLnF
Keane, P.M., Wojdyla, M., Doorley, G.W., Kelly, J.M., Parker, A.W., Clark, I.P., Greetham, G.M., Quinn, S.J., Long-lived excited states in i-motif DNA studied by picosecond time-resolved IR spectroscopy (2014) Chem Commun, 50 (23), pp. 2990-2992. , COI: 1:CAS:528:DC%2BC2cXivFOrt7c%3D
Kawai, K., Majima, T., Hole transfer kinetics of DNA (2013) Acc Chem Res, 46 (11), pp. 2616-2625. , COI: 1:CAS:528:DC%2BC3sXhtVWhu7zI
Vura-Weis, J., Wasielewski, M.R., Thazhathveetil, A.K., Lewis, F.D., Efficient charge transport in DNA diblock oligomers (2009) J Am Chem Soc, 131 (28), pp. 9722-9727. , COI: 1:CAS:528:DC%2BD1MXnslehu70%3D
Renaud, N., Harris, M.A., Singh, A.P.N., Berlin, Y.A., Ratner, M.A., Wasielewski, M.R., Lewis, F.D., Grozema, F.C., Deep-hole transfer leads to ultrafast charge migration in DNA hairpins (2016) Nat Chem, 8, p. 1015. , COI: 1:CAS:528:DC%2BC28XhtlChsrrK
Slinker, J.D., Muren, N.B., Renfrew, S.E., Barton, J.K., DNA charge transport over 34 nm (2011) Nat Chem, 3 (3), pp. 228-233. , COI: 1:CAS:528:DC%2BC3MXit1Wru7g%3D
Choi, J., Park, J., Tanaka, A., Park, M.J., Jang, Y.J., Fujitsuka, M., Kim, S.K., Majima, T., Hole trapping of G-quartets in a G-quadruplex (2013) Ang Chem Int Ed, 52 (4), pp. 1134-1138. , COI: 1:CAS:528:DC%2BC38XhslKntL7O
Roca-Sanjuán, D., Merchán, M., Serrano-Andrés, L., Modeling hole transfer in DNA: low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer (2008) Chem Phys, 349 (1), pp. 188-196
Arnold Anna, R., Grodick Michael, A., Barton Jacqueline, K., DNA charge transport: from chemical principles to the cell (2016) Cell Chem Biol, 23 (1), pp. 183-197. , COI: 1:STN:280:DC%2BC28jmt1WlsA%3D%3D
Genereux, J.C., Barton, J.K., Mechanisms for DNA charge transport (2010) Chem Rev, 110 (3), pp. 1642-1662. , COI: 1:CAS:528:DC%2BD1MXhsVKhsL3F
Wagenknecht, H.-A., (2006) Charge transfer in DNA: from mechanism to application, , (ed), Wiley-VCH, Weinheim
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The optical properties of adenine cation in different oligonucleotides: a PCM/TD‑DFT study
The absorption spectra of several systems containing an adenine (A) cation are computed in water by TD-DFT calculations, using three different functionals and including solvent effects by a mixed discrete–continuum approach. Our calculations well reproduce the experimental absorption spectrum of deoxyadenosine nucleoside cation (dA+), which provides an intense peak at 350 nm and a weaker one at 600 nm, allowing its assignment. M052X and CAM-B3LYP predict that the hole is essentially localized on a single A base also in the cationic forms of dApdA dinucleotide, both in single and in double strand, and of (dApdT) duplex, exhibiting absorption spectra similar to that of dA+. For all these compounds, B3LYP predicts instead the delocalization of the hole over two A bases. On this ground, it is possible to propose which would be the spectral signature of partial hole delocalization. Vertical and adiabatic ionization potentials for the compounds under investigation are also computed, providing values in good agreement with the available experimental results. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
The absorption spectra of several systems containing an adenine (A) cation are computed in water by TD-DFT calculations, using three different functionals and including solvent effects by a mixed discrete–continuum approach. Our calculations well reproduce the experimental absorption spectrum of deoxyadenosine nucleoside cation (dA+), which provides an intense peak at 350 nm and a weaker one at 600 nm, allowing its assignment. M052X and CAM-B3LYP predict that the hole is essentially localized on a single A base also in the cationic forms of dApdA dinucleotide, both in single and in double strand, and of (dApdT) duplex, exhibiting absorption spectra similar to that of dA+. For all these compounds, B3LYP predicts instead the delocalization of the hole over two A bases. On this ground, it is possible to propose which would be the spectral signature of partial hole delocalization. Vertical and adiabatic ionization potentials for the compounds under investigation are also computed, providing values in good agreement with the available experimental results. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
The optical properties of adenine cation in different oligonucleotides: a PCM/TD‑DFT study
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