Home Research Locations About us Organization Staff Contacts Education Login Documents IT
Projects highlights

INCIPIT

ISTAPCA (871 views)

Euro-BioImaging

Instruct-IT

Fondazione Veronesi

Fondo Europeo Pesca (280 views)

 INMiND (942 views)

 PRIN (1047 views)

 eHealthNet (869 views)

  Ponrec (825 views)

MFAG Grant (896 views)

(20 views)


Links

 |<  < >  >| 

    Export to BibTeX    Export to EndNote

Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case (57 views)

Santoro F, Barone V, Improta R

J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic, 0192-8651linking), 2008 Apr 30; 29(6): 957-964.

Abstract
By using calculations rooted in the time dependent density functional theory (TD-DFT) we have investigated how the lowest energy excited states of a face-to-face π-stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S 1)2. TD-PBEO, TD-LC-ωPBE, and TD-M05-2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S1)2 has a minimum for R ∼ 3Å, with a binding energy of ∼0.5 eV, whereas TD-B3LYP, TD-CAM-B3LYP, and TD-PBE understimate the binding energy. However, independently of the functional employed, no low-energy spurious charge transfer transitions are predicted by TD-DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD-DFT for studying the excited state of π -stacked nucleobases. © 2007 Wiley Periodicals, Inc.

Affiliations ▼
*** IBB - CNR Affiliation

Istituto per i Processi Chimico-Fisici, CNR, Area della Ricerca del CNR, Via Moruzzi, 1, I-56124 Pisa, Italy

Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy

Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 6, I-80134 Napoli, Italy

Details ▼
Impact factor: 3.39, 5-year impact factor: 5.364

Paper type: Journal Article, Comparative Study,

Keywords: Cytosine, Excited States, Nucleic Acids, Stacking, Time-Dependent Density Functional Theory, Charge Transfer, Cytosine Dimers, Stacked Nucleobases, Polymer, Article, Chemical Model, Chemical Structure, Chemistry, Comparative Study, Dimerization, Quantum Theory, Molecular,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-41549147727&partnerID=40&md5=23d21a3e3af53f7b66043cf8b5bb06c1

References ▼
Hobza, P., Selzle, H.L., Schlag, E.W., (1994) Chem Rev, 94, p. 176

Meyer, E.A., Castellano, R.K., Diederich, F., (2003) Angew Chem Int Ed, 42, p. 1210

McGaughey, G.B., Gagne, M., Rappe, A.K., (1998) J Biol Chem, 273, p. 15458

Muller-Dethlefs, K., Hobza, P., (2000) Chem Rev, 100, p. 143

Kim, K.S., Tarakeshwar, P., Lee, J.Y., (2000) Chem Rev, 100, p. 4145

Hobza, P., Sponer, J., (1999) Chem Rev, 99, p. 3247

Yakovchuk, P., Protozanova, E., Frank-Kamenetskii, M.D., (2006) Nucleic Acids Res, 34, p. 564

Luo, R., Gilson, H.S., Potter, M.J., Gilson, M.K., (2001) Biophys J, 80, p. 140

(1996) J-Aggregates, , Kobayashi, T, Ed, World Scientific: Singapore

Crespo-Hernandez, C.E., Cohen, B., Kohler, B., (2005) Nature, 436, p. 1141

Tretiak, S., Mukamel, S., (2002) Chem Rev, 102, p. 3171

Akins, D.L., Ozcelik, S., Zhu, H.R., Guo, C., (1996) J Phys Chem, 100, p. 14390

Ohno, O., Kaizu, Y., Kobayashi, H., (1993) J Chem Phys, 99, p. 4128

Chen, P., Tomov, I.V., Dvovnikov, A.S., Nakashima, M., Roach, J.F., Alabram, D.M., Rentzepis, P.M., (1996) J Phys Chem, 100, p. 17507

Rebane, A. J Opt Soc Am B 2003, 20, 321(1995) Recent Advances in Density Functional Methods, 1. , Casida, M. E, Chong, D. P, Eds, World Scientific

Dreuw, A., Head-Gordon, M., (2005) Chem Rev, 105, p. 4009

Wanko, M., Garavelli, M., Bernardi, F., Niehaus, T.A., Frauenheim, T., Elstner, M., (2004) J Chem Phys, 120, p. 1674

Dreuw, A., Weisman, J.L., HeadGordon, M., (2003) J Chem Phys, 119, p. 2943

Tozer, D.J., Amos, R.D., Handy, N.C., Roos, B.O., Serrano-Andres, L., (1999) Mol Phys, 97, p. 859

Santoro, F., Barone, V., Improta, R., (2007) Proc Nat Acad Sci USA, 104, p. 9931

Scalmani, G., Frisch, M.J., Mennucci, B., Tomasi, J., Cammi, R., Barone, V., (2006) J Chem Phys, 124, p. 094107

Improta, R., Barone, V., Santoro, F., (2007) Angew Chem Int Ed, 46, p. 405

Santoro, F., Improta, R., Lami, A., Bloino, J., Barone, V., (2007) J Chem Phys, 126, p. 084509

J Chem Phys 2007, 126, 169903 (erratum)

Santoro, F., Lami, A., Improta, R., Barone, V., (2007) J Chem Phys, 126, p. 184102

Rocha-Rinza, T., De Vico, L., Veryazov, V., Roos, B.O., (2006) Chem Phys Lett, 426, p. 268

Olaso-Gonzalez, G., Roca-Sanjuan, D., Serrano-Andrés, L., Merchán, M., (2006) J Chem Phys, 125, p. 231102

Boys, S.F., Bernardi, F., (1970) Mol Phys, 19, p. 553

Perdew, J.P., Burke, K., Ernzerhof, M., (1996) Phys Rev Lett, 77, p. 3865

Becke, A.D., (1993) J Chem Phys, 98, p. 5648

Adamo, C., Barone, V., (1999) J Chem Phys, 110, p. 6158

Enzerhof, M., Scuseria, G.E., (1999) J Chem Phys, 110, p. 5029

Vydrov, O.A., Scuseria, G.E., (2006) J Chem Phys, 125, p. 234109

Yanai, T., Tew, D.P., Handy, N.C., (2004) Chem Phys Lett, 393, p. 51

Tawada, Y., Tsuneda, T., Yanagisawa, S., Yanai, T., Hirao, K., (2004) J Chem Phys, 120, p. 8425

Truhlar, D. G. J Chem Theory Comput 2006, 2, 364Adamo, C., Scuseria, G.E., Barone, V., (2000) J Chem Phys, 111, p. 2889

Gustavsson, T., Banyasz, A., Lazzarotto, E., Markovitsi, D., Scalmani, G., Frisch, M.J., Barone, V., Improta, R., (2006) J Am Chem Soc, 128, p. 607

Frisch, M. J, Tracks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Vreven, T. Jr, Scalmani, G, Kudin, K. N, Iyengar, S. S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Rega, N, Petersson, G. A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Li, X, Hratchian, H. P, Peralta, J. E, Izmaylov, A. E

Heyd, J. J, Brothers, E, Staroverov, V, Zheng, G, Kobayashi, R, Normand, J, Burant, J. C, Millam, J. M, Klene, M, Knox, J. E, Cross, J. B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R, Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A, Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels, A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G, Clifford, S, CiMerchan, M., Serrano-Andrés, L., (2003) J Am Chem Soc, 125, p. 8108

Kistler, K.A., Matsika, S., (2007) J Phys Chem A, 111, p. 2650

Ismail, N., Blancafort, L., Olivucci, M., Kohler, B., Robb, M., (2002) J Am Chem Soc, 124, p. 6818

Sobolewski, A.L., Domcke, W., (2004) Phys Chem Chem Phys, 6, p. 2763

Tomic, K., Jörg, T., Marian, C.M., (2005) J Phys Chem A, 109, p. 8410

Fuelscher, M.P., Roos, B.O., (1995) J Am Chem Soc, 117, p. 2089

Kamiya, M., Tsuneda, T., Hirao, K., (2002) J Chem Phys, 117, p. 6010

Hirao, K. J ChemPhys 1999, 110, 10664Wu, X., Vargas, M.C., Nayak, S., Lotrich, V., Scoles, G., (2001) J Chem Phys, 115, p. 8748

Weber, J. J Phys Chem A 1997, 101, 7818Zhang, Y

Yang, W. J Chem Phys 1997, 107, 7921Lacks, D.J., Gordon, R.G., (1993) Phys Rev A, 47, p. 4681

Levy, M., Perdew, J.P., (1993) Phys Rev B, 48, p. 11638

Lieb, E.H., Oxford, S., (1981) Int J Quantum Chem, 19, p. 427

Cai, Z.L., Crossley, M.J., Reimers, J.R., Kobayashi, R., Amos, R.D., (2006) J Phys Chem B, 110, p. 15624

Peach, M.J.G., Helgaker, T., Salek, P., Keal, T.W., Lutnaes, O.B., Tozer, D.J., Handy, N.C., (2006) Phys Chem Chem Phys, 8, p. 558

Zheng, J.J., Zhao, Y., Truhlar, D.G., (2007) J Phys Chem A, 111, p. 4632

Meyer, E. A., Castellano, R. K., Diederich, F., (2003) Angew Chem Int Ed, 42, p. 1210

McGaughey, G. B., Gagne, M., Rappe, A. K., (1998) J Biol Chem, 273, p. 15458

Kim, K. S., Tarakeshwar, P., Lee, J. Y., (2000) Chem Rev, 100, p. 4145

Luo, R., Gilson, H. S., Potter, M. J., Gilson, M. K., (2001) Biophys J, 80, p. 140

(1996) J-Aggregates, , Kobayashi, T, Ed, World Scientific: Singapore

Akins, D. L., Ozcelik, S., Zhu, H. R., Guo, C., (1996) J Phys Chem, 100, p. 14390

Chen, P., Tomov, I. V., Dvovnikov, A. S., Nakashima, M., Roach, J. F., Alabram, D. M., Rentzepis, P. M., (1996) J Phys Chem, 100, p. 17507

Tozer, D. J., Amos, R. D., Handy, N. C., Roos, B. O., Serrano-Andres, L., (1999) Mol Phys, 97, p. 859

Boys, S. F., Bernardi, F., (1970) Mol Phys, 19, p. 553

Perdew, J. P., Burke, K., Ernzerhof, M., (1996) Phys Rev Lett, 77, p. 3865

Becke, A. D., (1993) J Chem Phys, 98, p. 5648

Vydrov, O. A., Scuseria, G. E., (2006) J Chem Phys, 125, p. 234109

Yanai, T., Tew, D. P., Handy, N. C., (2004) Chem Phys Lett, 393, p. 51

Kistler, K. A., Matsika, S., (2007) J Phys Chem A, 111, p. 2650

Sobolewski, A. L., Domcke, W., (2004) Phys Chem Chem Phys, 6, p. 2763

Tomic, K., J rg, T., Marian, C. M., (2005) J Phys Chem A, 109, p. 8410

Fuelscher, M. P., Roos, B. O., (1995) J Am Chem Soc, 117, p. 2089

Lieb, E. H., Oxford, S., (1981) Int J Quantum Chem, 19, p. 427

Cai, Z. L., Crossley, M. J., Reimers, J. R., Kobayashi, R., Amos, R. D., (2006) J Phys Chem B, 110, p. 15624

Peach, M. J. G., Helgaker, T., Salek, P., Keal, T. W., Lutnaes, O. B., Tozer, D. J., Handy, N. C., (2006) Phys Chem Chem Phys, 8, p. 558

Zheng, J. J., Zhao, Y., Truhlar, D. G., (2007) J Phys Chem A, 111, p. 4632


Related activities ▼
No results.

Related papers ▼
Amyloid Beta monomers regulate cyclic adenosine monophosphate response element binding protein functions by activating type-1 insulin-like growth factor receptors in neuronal cells (public domain) (4 views)
Fluoxetine Prevents Ab1-42-Induced Toxicity via a Paracrine Signaling Mediated by Transforming-Growth- Factor-b1 (public domain) (47 views)

Related bibliography ▼

Content: [X]
Extended

Authors: [X]
AND Paper type: [X]

AND Start date: End date: [X]   AND Site:    AND  IBB affiliation

[Clear form]

<=2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018   ALL YEARS

Sort by: date    title    journal    authors      impact factor

* Vibronic approach to the calculation of the decay rate of the photoexcited charge-transfer state of Guanine-Cytosine stacked dimer in water solution (15 views)
Cerezo J, Martinez-fernandez L, Improta R, Santoro F
Theoretical Chemistry Accounts, 2016 Sep; N/D: N/D-N/D.

View    Export to BibTeX    Export to EndNote    Upload PDF
* Stabilization of mixed frenkel-charge transfer excitons extended across both strands of guanine-cytosine DNA duplexes (65 views)
Huix-Rotllant M, Brazard J, Improta R, Burghardt I, Markovitsi D
J Phys Chem Lett (ISSN: 1948-7185, 1948-7185electronic), 2015; 6(12): 2247-2251.

View    Export to BibTeX    Export to EndNote    Upload PDF
* Effect of C5-methylation of cytosine on the photoreactivity of DNA: A joint experimental and computational study of TCG trinucleotides (64 views)
Esposito L, Banyasz A, Douki T, Perron M, Markovitsi D, Improta R
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2014 Sep 6; 136(31): 10838-10841.

View    Export to BibTeX    Export to EndNote    Upload PDF
* Excited state proton transfer is not involved in the ultrafast deactivation of Guanine-cytosine pair in solution (41 views)
Biemann L, Kovalenko SA, Kleinermanns K, Mahrwald R, Markert M, Improta R
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2011 Dec 14; 133(49): 19664-19667.

View    Export to BibTeX    Export to EndNote    Upload PDF


4 Records (4 excluding Abstracts and Conferences).
Total impact factor: 32.365 (32.365 excluding Abstracts and Conferences).
Total 5-year impact factor: 29.295 (29.295 excluding Abstracts and Conferences).



Your bibliography query: (([btitle, keywords, abstract] CYTOSINE AND [btitle, keywords, abstract] EXCITED AND [btitle, keywords, abstract] STATES)) AND NOT [id] = 9140



Last modified by Marco Comerci on Friday 26 May 2017, 11:20:11
57 views. Last viewed on Monday 06 November 2017, 13:51:08


Webmaster and developer: Marco Comerci
For problems and suggestions: adminibb.cnr.it
Last updated: Monday 20 November 2017, 11:36:46