Dynamics of excited states and spectroscopic properties of natural and synthetic DNA and RNA derivatives in solvent environment

• Grant number: 17/02612-4
• Support type: Scholarships in Brazil - Doctorate
• Effective date (Start): May 01, 2017
• Effective date (End): October 31, 2020
• Field of knowledge: Physical Sciences and Mathematics - Physics - Atomic and Molecular Physics
• Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal researcher: Sylvio Roberto Accioly Canuto
• Grantee: Danillo Pires Valverde
• Home Institution: Instituto de Física (IF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 19/04413-4 - Photophysical properties of heavy atom modified nucleobases, BE.EP.DR

Abstract

The nucleic bases are know to be few fluorescent, making them higly stable photochemically. However, small chemical modifications in the nucleic bases can generate highly fluorescent compounds. The emissive analogues have significant applications in the biotechnology field when used as fluorescence probe. The solvent effects are taking account through of the combined use of the sequential QM/MM method with electrostatic mean field approximation and the Free Energy Gradient, which it has been successful in describing the electronic properties both in the ground as excited state od molecules in solution. The advantage is that it permits the use of an atomistic level , in contrast to continuum models. Furthermore, it is less computationally expensive than ab initio and conventional QM/MM simulations, even allowing the employment of more sophistacted electronic structure methods. In this work, we will study the solvent effects on the eletronic and conformational properties of RNA and DNA derivatives, and the effects on the spectroscopic properties (absorption and fluorescence). We will use classical atomic simulation (Monte Carlo orMolecular Dynamics) and sequentially quantum mechanics calculations. The Free Energy Gradient will be used for obtain geometry of the solute in solvent environment. Moreover, the quantum mechanics method CASPT2 will be employed for obtain the absorption and fluorescence spectra of the solute in solution. (AU)

Scientific publications

(8)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

FANG, YE-GUANG; VALVERDE, DANILLO; MAI, SEBASTIAN; CANUTO, SYLVIO; BORIN, ANTONIO CARLOS; CUI, GANGLONG; GONZALEZ, LETICIA. Excited-State Properties and Relaxation Pathways of Selenium-Substituted Guanine Nucleobase in Aqueous Solution and DNA Duplex. Journal of Physical Chemistry B, v. 125, n. 7, p. 1778-1789, FEB 25 2021. (14/50983-3, 19/04413-4, 18/19454-5, 17/02612-4)

DE ARAUJO, ADALBERTO VASCONCELOS SANCHES; VALVERDE, DANILLO; CANUTO, SYLVIO; BORIN, ANTONIO CARLOS. Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: (tz)A, (tz)G, and I-tz. Journal of Physical Chemistry A, v. 124, n. 34, p. 6834-6844, AUG 27 2020. (17/02612-4, 14/50983-3, 18/19454-5)

VALVERDE, DANILLO; SANCHES DE ARAUJO, ADALBERTO VASCONCELOS; CANUTO, SYLVIO; BORIN, ANTONIO CARLOS. Photophysics of Emissive C-tz[Isothiazolo-Cytidine] and U-tz[Isothiazolo-Uridine] Pyrimidine Analogues. CHEMPHOTOCHEM, v. 3, n. 9, SI, p. 916-924, SEP 2019. (17/02612-4, 14/50983-3)

LUDWIG, VALDEMIR; DA COSTA LUDWIG, ZELIA M.; VALVERDE, DANILLO; GEORG, HERBERT C.; CANUTO, SYLVIO. Free energy gradient for understanding the stability and properties of neutral and charged L-alanine molecule in water. JOURNAL OF MOLECULAR LIQUIDS, v. 319, DEC 1 2020. (17/02612-4)

VALVERDE, DANILLO; MAI, SEBASTIAN; SANCHES DE ARAUJO, ADALBERTO VASCONCELOS; CANUTO, SYLVIO; GONZALEZ, LETICIA; BORIN, ANTONIO CARLOS. On the population of triplet states of 2-seleno-thymine. Physical Chemistry Chemical Physics, v. 23, n. 9, p. 5447-5454, MAR 7 2021. (18/19454-5, 14/50983-3, 19/04413-4, 17/02612-4)

VALVERDE, DANILLO; DE ARAUJO, ADALBERTO V. S.; BORIN, ANTONIO CARLOS. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules, v. 26, n. 17, SEP 2021. (18/19454-5, 17/02612-4)

VALVERDE, DANILLO; DA COSTA LUDWIG, ZELIA MARIA; DA COSTA, CELIA REGINA; LUDWIG, VALDEMIR; GEORG, HERBERT C.. Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures. Journal of Chemical Physics, v. 148, n. 2, JAN 14 2018. (17/02612-4)

VALVERDE, DANILLO; SANCHES DE ARAUJO, ADALBERTO VASCONCELOS; BORIN, ANTONIO CARLOS; CANUTO, SYLVIO. Electronic structure and absorption spectra of fluorescent nucleoside analogues. Physical Chemistry Chemical Physics, v. 19, n. 43, p. 29354-29363, NOV 21 2017. (17/02612-4)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

VALVERDE, Danillo Pires. Excited state dynamics and spectroscopic proprieties of natural and synthetic DNA/RNA derivatives in solvent environment. 2020. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Física (IF/SBI) São Paulo.