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In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC\u2010CI and TD\u2010DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD\u2010DFT methods, have been examined regarding the photo\u2010absorption and emission spectra. The SAC\u2010CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD\u2010DFT calculations is difficult for these chromophores. Some stable structures of H\u2010aggregate system were computationally located and two of the configurations were examined for the photo\u2010absorption. The present results support for the assumption based on experimental measurement in which strong fluorescence is due to the monomer unit in nearly planar structure and its suppression of probes is to the H\u2010aggregates of two exciton units. Stokes shifts of these three chromophores were qualitatively reproduced by the theoretical calculations, while the energy splitting due to H\u2010aggregate in the hybridized probe was slightly overestimated. \u00a9 2018 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.25553","type":"journal-article","created":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T19:20:22Z","timestamp":1535138422000},"page":"127-134","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC\u2010CI and TD\u2010DFT Study"],"prefix":"10.1002","volume":"40","author":[{"given":"Takafumi","family":"Shiraogawa","sequence":"first","affiliation":[{"name":"SOKENDAI The Graduate University for Advanced Studies, Nishigonaka, Myodaiji Okazaki 444\u20108585 Japan"}]},{"given":"Gaelle","family":"Candel","sequence":"additional","affiliation":[{"name":"Institut de Recherche de Chimie Paris PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie Paris F\u201075005 France"}]},{"given":"Ryoichi","family":"Fukuda","sequence":"additional","affiliation":[{"name":"Elements Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto 615\u20108245 Japan"},{"name":"Department of Molecular Engineering Graduate School of Engineering, Kyoto University Nishikyo\u2010ku, Kyoto 615\u20108520 Japan"}]},{"given":"Ilaria","family":"Ciofini","sequence":"additional","affiliation":[{"name":"Institut de Recherche de Chimie Paris PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie Paris F\u201075005 France"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2638-2735","authenticated-orcid":false,"given":"Carlo","family":"Adamo","sequence":"additional","affiliation":[{"name":"Institut de Recherche de Chimie Paris PSL Research University, CNRS, Chimie ParisTech, 11 rue Pierre et Marie Curie Paris F\u201075005 France"},{"name":"Institut Universitaire de France 103 Boulevard Saint Michel, F\u201075005, Paris France"}]},{"given":"Akimitsu","family":"Okamoto","sequence":"additional","affiliation":[{"name":"Research Center for Advanced Science and Technology The University of Tokyo 4\u20106\u20101 Komaba, Meguro\u2010ku, Tokyo 153\u20108904 Japan"},{"name":"Department of Chemistry and Biotechnology Graduate School of Engineering, The University of Tokyo 7\u20103\u20101 Hongo, Bunkyo\u2010ku, Tokyo 113\u20108656 Japan"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2185-0077","authenticated-orcid":false,"given":"Masahiro","family":"Ehara","sequence":"additional","affiliation":[{"name":"SOKENDAI The Graduate University for Advanced Studies, Nishigonaka, Myodaiji Okazaki 444\u20108585 Japan"},{"name":"Elements Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto 615\u20108245 Japan"},{"name":"Institute for Molecular Science and Research Center for Computational Science Nishigonaka, Myodaiji, Okazaki 444\u20108585 Japan"}]}],"member":"311","published-online":{"date-parts":[[2018,8,24]]},"reference":[{"key":"e_1_2_6_1_1","doi-asserted-by":"crossref","unstructured":"(a) I. 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