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TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids (77 visite)

Fahleson T, Kauczor J, Norman P, Santoro F, Improta R, Coriani S

J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic), 2015; 119(21): 5476-5489.

Tipo di articolo: Journal Article,

Impact factor: 2.883

Impact factor a 5 anni: 2.709

Parole chiave: Aromatic Compounds, Biomolecules, Continuum Mechanics, Nucleic Acids, Solvents, Spectroscopy, Computational Studies, Energy Differences, Explicit Water Molecules, Magnetic Circular Dichroism Spectra, Polarizable Continuum Model, Qualitative Shapes, Wavelength Regions,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84930634429&partnerID=40&md5=04295d70e7ef5dbf6018b9a767931b53

We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π∗ transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π∗ excitations, but they are too weak to be observed in the experiment. © 2015 American Chemical Society.
*** IBB - CNR ***

Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden

Istituto di Chimica Dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, Pisa, Italy

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

Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via L. Giorgieri 1, Trieste, Italy

Aarhus Institute of Advanced Studies, Aarhus University, Aarhus C, Denmark
Mason, W.R., (2007) A Practical Guide to Magnetic Circular Dichroism Spectroscopy, , Wiley: New Yor

Voelter, W., Records, R., Bunnenberg, E., Djerassi, C., Magnetic Circular Dichroism Studies. VI. Investigation of Some Purines, Pyrimidines, and Nucleosides (1968) J. Am. Chem. Soc., 90, p. 6163

Djerassi, C., Bunnenberg, E., Elder, D.L., Organic Chemical Applications of Magnetic Circular Dichroism (1971) Pure Appl. Chem., 25, pp. 57-90

Coriani, S., Jørgensen, P., Ruud, K., Rizzo, A., Olsen, J., Ab Initio Determinations of Magnetic Circular Dichroism (1999) Chem. Phys. Lett., 300, pp. 61-68

Coriani, S., Hättig, C., Jørgensen, P., Helgaker, T., Gauge-Origin Independent Magneto-Optical Activity within Coupled Cluster Response Theory (2000) J. Chem. Phys., 113, pp. 3561-3572

Kjærgaard, T., Jansik, B., Jørgensen, P., Coriani, S., Michl, J., Gauge-Origin-Independent Coupled Cluster Singles and Doubles Calculation of Magnetic Circular Dichroism of Azabenzenes and Phosphabenzene using London Orbitals (2007) J. Phys. Chem. A, 111, pp. 11278-11286

Seth, M., Ziegler, T., Banerjee, A., Autschbach, J., Van Gisbergen, S.J.A., Baerends, E.J., Calculation of the A Term of Magnetic Circular Dichroism Based on Time Dependent-Density Functional Theory I. Formulation and Implementation (2004) J. Chem. Phys., 120, pp. 10942-10954

Solheim, H., Frediani, L., Ruud, K., Coriani, S., An IEF-PCM Study of Solvent Effects on the Faraday B Term of MCD (2008) Theor. Chem. Acc., 119, pp. 231-244

Solheim, H., Ruud, K., Coriani, S., Norman, P., Complex Polarization Propagator Calculations of Magnetic Circular Dichroism Spectra (2008) J. Chem. Phys., 128, p. 094103

Seth, M., Krykunov, M., Ziegler, T., Autschbach, J., Application of Magnetically Perturbed Time-Dependent Density Functional Theory to Magnetic Circular Dichroism. II. Calculation of A Terms (2008) J. Chem. Phys., 128, p. 234102

Kjærgaard, T., Jørgensen, P., Thorvaldsen, A., Saek, P., Coriani, S., Gauge-Origin Independent Formulation and Implementation of Magneto-Optical Activity within Atomic-Orbital-Density Based Hartree-Fock and Kohn-Sham Response Theories (2009) J. Chem. Theory Comput., 5, pp. 1997-2020

Kjærgaard, T., Kristensen, K., Kauczor, J., Jørgensen, P., Coriani, S., Thorvaldsen, A., Comparison of Standard and Damped Response Formulations of Magnetic Circular Dichroism (2011) J. Chem. Phys., 135

Kjærgaard, T., Coriani, S., Ruud, K., Ab Initio Calculation of Magnetic Circular Dichroism (2012) Wiley Interdiscip. Rev.: Comput. Mol. Sci., 2, pp. 443-455

Fahleson, T., Kauczor, J., Norman, P., Coriani, S., The Magnetic Circular Dichroism Spectrum of the C60 Fullerene (2013) Mol. Phys., pp. 1401-1404

Krykunov, M., Seth, M., Ziegler, T., Autschbach, J., Calculation of the Magnetic Circular Dichroism B Term from the Imaginary Part of the Verdet Constant Using Damped Time-Dependent Density Functional Theory (2007) J. Chem. Phys., 127, p. 244102

Lee, K.-M., Yabana, K., Bertsch, G.F., Magnetic Circular Dichroism in Real-Time Time-Dependent Density Functional Theory (2011) J. Chem. Phys., 134, p. 144106

Stepanek, P., Bour, P., Computation of Magnetic Circular Dichroism by Sum-Over-States Summations (2013) J. Comput. Chem., 34, pp. 1531-1539

Stepanek, P., Straka, M., Andrushchenko, V., Bour, P., Communication: Fullerene Resolution by the Magnetic Circular Dichroism (2013) J. Chem. Phys., 138, p. 151103

Honda, Y., Hada, M., Ehara, M., Nakatsuji, H., Michl, J., Theoretical Studies on Magnetic Circular Dichroism by the Finite Perturbation Method with Relativistic Corrections (2005) J. Chem. Phys., 123, p. 164113

Norman, P., Bishop, D.M., Jensen, H.J.A., Oddershede, J., Nonlinear Response Theory with Relaxation: The First-Order Hyperpolarizability (2005) J. Chem. Phys., 123, p. 194103

Tomasi, J., Mennucci, B., Cammi, R., Quantum Mechanical Continuum Solvation Models (2005) Chem. Rev., 105, p. 2999

Zgierski, M.Z., Vibronic Structure of MCD Spectra. I. Non-Condon Effects in Molecules with Nondegenerate Electronic States (1985) J. Chem. Phys., 83, pp. 2170-2185

Lin, N., Solheim, H., Zhao, X., Santoro, F., Ruud, K., First Principles Studies of the Vibrationally Resolved Magnetic Circular Dichroism Spectra of Biphenylene (2013) J. Chem. Theory Comput., 9, pp. 1557-1567

Crespo-Hernandez, C.E., Cohen, B., Hare, P.M., Kohler, B., Ultrafast Excited-State Dynamics in Nucleic Acids (2004) Chem. Rev., 104, pp. 1977-2020

Middleton, C.T., De La Harpe, K., Su, C., Law, Y.K., Crespo-Hernandez, C.E., Kohler, B., DNA Excited-State Dynamics: From Single Bases to the Double Helix (2009) Annu. Rev. Phys. Chem., 60

Gustavsson, T., Improta, R., Markovitsi, D., DNA/RNA: Building Blocks of Life under UV Irradiation (2010) J. Phys. Chem. Lett., 1, pp. 2025-2030

Santoro, F., Improta, R., Fahleson, T., Kauczor, J., Norman, P., Coriani, S., Relative Stability of the La and Lb States in Adenine and Guanine: Direct Evidence from TD-DFT Salculations of MCD Spectra (2014) J. Phys. Chem. Lett., 5, pp. 1806-1811

Szalay, P., Watson, T., Perera, A., Lotrich, V., Bartlett, R., Benchmark Studies on the Building Blocks of DNA. 1. Superiority of Coupled Cluster Methods in Describing the Excited States of Nucleobases in the Franck-Condon Region (2012) J. Phys. Chem. A, 116, pp. 6702-6710

Hare, P.M., Crespo-Hernández, C.E., Kohler, B., Internal Conversion to the Electronic Ground State Occurs via Two Distinct Pathways for Pyrimidine Bases in Aqueous Solution (2007) Proc. Natl. Acad. Sci. U. S. A., 104, pp. 435-440

Santoro, F., Barone, V., Gustavsson, T., Improta, R., Solvent Effect on the Singlet Excited-State Lifetimes of Nucleic Acid Bases: A Computational Study of 5-Fluorouracil and Uracil in Acetonitrile and Water (2006) J. Am. Chem. Soc., 128, pp. 16312-16322

Improta, R., Barone, V., Lami, A., Santoro, F., Quantum Dynamics of the Ultrafast ππ/nπ∗ Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile (2009) J. Phys. Chem. B, 113, pp. 14491-14503

Picconi, D., Avila Ferrer, F.J., Improta, R., Lami, A., Santoro, F., Quantum-Classical Effective-Modes Dynamics of the ππ→ nπ∗ Decay in 9H-Adenine. A Quadratic Vibronic Coupling Model (2013) Faraday Discuss., 163, pp. 223-242

Biemann, L., Kovalenko, S.A., Kleinermanns, K., Mahrwald, R., Markert, M., Improta, R., Excited State Proton Transfer Is Not Involved in the Ultrafast Deactivation of Guanine-Cytosine Pair in Solution (2011) J. Am. Chem. Soc., 133, pp. 19664-19667

Spata, V., Matsika, S., Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations (2014) J. Phys. Chem. A, 118, pp. 12021-12030

Plasser, F., Aquino, A.J.A., Hase, W.L., Lischka, H., UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions (2012) J. Phys. Chem. A, 116, pp. 11151-11160

Plasser, F., Lischka, H., Electronic Excitation and Structural Relaxation of the Adenine Dinucleotide in Gas Phase and Solution (2013) Photochem. Photobiol. Sci., 12, pp. 1440-1452

Rizzo, A., Coriani, S., Ruud, K., (2012) Computational Strategies for Spectroscopy. from Small Molecules to Nano Systems, pp. 77-135. , In

Barone, V. John Wiley and Sons: Hoboken, NJ, Chapter 2

Buckingham, A.D., Stephens, P.J., Magnetic Optical Activity (1966) Annu. Rev. Phys. Chem., 17, p. 399

Stephens, P.J., Theory of Magnetic Circular Dichroism (1970) J. Chem. Phys., 52, p. 3489

Ganyushin, D., Neese, F., First-Principles Calculations of Magnetic Circular Dichroism Spectra (2008) J. Chem. Phys., 128, p. 114117

Bolvin, H., Theoretical Determination of the Excited States and of g -Factors of the Creutz-Taube Ion, [(NH3)5-Ru-pyrazine-Ru-(NH3)5]5 (2007) Inorg. Chem., 46, p. 417

Cammi, R., Mennucci, B., Tomasi, J., Ruud, K., Multiconfigurational Self-Consistent Field Linear Response for the Polarizable Continuum Model: Theory and Application to Ground and Excited-State Polarizabilities of Paranitroaniline in Solution (2003) J. Chem. Phys., 119, pp. 5818-5827

Frediani, L., Ågren, H., Ferrighi, L., Ruud, K., Second-Harmonic Generation of Solvated Molecules Using Multiconfigurational Self-Consistent-Field Quadratic Response Theory and the Polarizable Continuum Model (2005) J. Chem. Phys., 123, p. 144117

Milne, B.F., Norman, P., Resonant-Convergent PCM Response Theory Calculations of Second Harmonic Generation in Makaluvamines A-V

Pyrroloiminoquinone Marine Natural Products from Poriferans of Genus Zyzzya (2015) J. Phys. Chem. A

Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Petersson, G.A., (2009) Gaussian 09, , Revision C.3

Gaussian Inc. Wallingford, CT

(2013), http://daltonprogram.org/, DALTON, a molecular electronic structure program, Release Dalton2013 and LSDalton2013. seeAidas, K., Angeli, C., Bak, K.L., Bakken, V., Bast, R., Boman, L., Christiansen, O., Dahle, P., The Dalton Quantum Chemistry Program System (2014) Wiley Interdiscip. Rev.: Comput. Mol. Sci., 4, pp. 269-284

Rohatgi, A., (2014) WebPlotDigitizer, , http://arohatgi.info/WebPlotDigitizer, Version 3.3

Hunter, J.D., Matplotlib: A 2D Graphics Environment (2007) Comput. Sci. Eng., 9, p. 90

Sutherland, J.C., Holmquist, B., Magnetic Circular Dichroism of Biological Molecules (1980) Annu. Rev. Biophys. Bioeng., 9, pp. 293-326

Sutherland, J.C., Griffin, K., Magnetic Circular Dichroism of Adenine, Hypoxanthine, and Guanosine 5′-Diphosphate to 180 nm (1984) Biopolymers, 23, pp. 2715-2724

Kaito, A., Hatano, M., Ueda, T., Shibuya, S., CNDO treatment for Faraday B terms of some azaheterocycles (1980) Bull. Chem. Soc. Jpn., 53, pp. 3073-3078

Kistler, K., Matsika, S., Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method (2009) J. Phys. Chem. A, 113, pp. 12396-12403

Blancafort, L., Migani, A., Water Effect on the Excited-state Decay Paths of Singlet Excited Cytosine (2007) J. Photochem. Photobiol., A, 190, pp. 283-290

Bazso, G., Tarczay, G., Fogarasi, G., Szalay, P.G., Tautomers of Cytosine and Their Excited Electronic States: A Matrix Isolation Spectroscopic and Quantum Chemical Study (2011) Phys. Chem. Chem. Phys., 13, pp. 6799-6807

Ferrer, F.J.A., Santoro, F., Improta, R., The Excited State Behavior of Cytosine in the Gas Phase: A TD-DFT Study (2014) Comput. Theor. Chem., pp. 186-194

Corni, S., Cammi, R., Mennucci, B., Tomasi, J., Electronic Excitation Energies of Molecules in Solution within Continuum Solvation Models: Investigating the Discrepancy between State-Specific and Linear-Response Methods (2005) J. Chem. Phys., 123, p. 134512

Improta, R., (2012) Computational Strategies for Spectroscopy. from Small Molecules to Nano Systems, pp. 39-76. , In

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18 Records (15 escludendo Abstract e Conferenze).
Impact factor totale: 83.902 (77.885 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 90.449 (81.264 escludendo Abstract e Conferenze).

Interrogazione bibliografica effettuata: (([btitle] "Aromatic Compounds" OR [btitle] "Biomolecules" OR [btitle] "Continuum Mechanics" OR [btitle] "Nucleic Acids" OR [btitle] "Solvents") AND NOT [id] = 52792)

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