Excited state dynamics and spectroscopic proprieties of natural and synthetic DNA/RNA derivatives in solvent environment

Author(s)

Danillo Pires Valverde

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Física (IF/SBI)
• Defense date: 2020-12-14

Examining board members

Sylvio Roberto Accioly Canuto; Lucy Vitoria Credidio Assali; Lucas Colucci Ducati; Tertius Lima da Fonseca; André Luiz Barboza Formiga

• Advisor: Sylvio Roberto Accioly Canuto

Abstract

Photophysics and Photochemistry of molecular systems represent a wide area of physical chemistry, which is concerned with the effects of light on molecules. In this context, modified nucleobases may exhibit photophysical relaxation paths quite distinct from those observed for their respective natural analogues, which are not fluorescent and have an ultrafast excited-state lifetime. The objective of this thesis is to elucidate the main deactivation pathways after the absorption of light of modified bases of DNA/RNA in gas phase. Solvent effects are also considered, either by implicit solvation (Polarizable Continuum Model (PCM) and Solvent Model Density (SMD)) or by explicit solvation extracting the configurations from Classical Molecular Dynamics Simulations and Monte Carlo Metropolis sampling. Static approach and non-adiabatic dynamics are performed in order to explain the feasible photophysical paths. The first system studied consists of a promising fluorescent ribonucleoside alphabet. All compounds in this alphabet fluoresce from the structure ¹($\\pi\\pi$*)min, but the explanation why these molecules are fluorescent depends on the molecule. In the case of purine molecules, the fluorescence occurs due to a red shift in the electronic absorption spectrum, avoiding the accessibility to the conical intersection with the ground state (¹(gs/$\\pi\\pi$*)CI). In turn, the ¹(gs/$\\pi\\pi$*)CI structure for the pyrimidine molecules is located in a high energy region. Subsequently, it is studied the effects of solvent on the properties of the excited electronic states of 2-aminopurine (2AP), a well-known analogue of adenine. The ASEC-FEG approach, which combines the Sequential Quantum Mechanics/Molecular Mechanics methodology and the free energy gradient method, correctly describes the spectroscopic properties (absorption, emission and fluorescence) of this molecule in all solvents employed. In relation to previous theoretical works, a better solvatochromic shift from 1,4-dioxane to water was reached for the Stokes shift. Additionally, the difference in free energy between both tautomers of the 2AP in the ground and first excited states ¹($\\pi\\pi$*)min is estimated in ethanol and aqueous solution. Finally, a simple substitution of guanine that suppresses the internal conversion to the ground state and amplifies the intersystem crossing with the triplet states is studied. The system initially populates the S2 singlet state and quickly transfers the population to the S1 state. This electronic state acts as a doorway for the population transfer into triplet states. The transient absorption spectrum (TAS) is simulated in order to compare with the available experimental data. Two time-constants are extracted from the simulated TAS spectrum, which are in agreement with experimentally estimated results. An explanation of why this molecule has a shorter lifetime of the triplet state in comparison with its thiobase analogue is also described in detail. (AU)

• FAPESP's process: 17/02612-4 - Dynamics of excited states and spectroscopic properties of natural and synthetic DNA and RNA derivatives in solvent environment
• Grantee: Danillo Pires Valverde
• Support Opportunities: Scholarships in Brazil - Doctorate