Contacts:
Supervisors:
Dr. Fabrizio Santoro
Title:
Quantum Dynamics of decay processes in photoexcited nucleobases and small oligomers: toward the simulation of time resolved spectra.
Abstract:
The aim of this PhD project is the study of photoinduced processes in DNA nucleobases and small oligomers by means of a full quantum dynamical (QD) description of the decay mechanisms after photoexcitation. DFT/TD-DFT and post- HF methods will be used to characterize the potential energy surfaces whereas different methodologies like Multi-Configurational Time-Dependent Hartree (MCTDH) and Mixed Quantum Classical models will be exploited to simulate the nonadiabatic transitions and how they are affected by the environment. After studying the photodecay of the single nucleobases in different environments and for different excitation wavelengths we will focus on collective decay processes in small oligomers. We plan to study the interplay between charge-tranfer, exciton localization and excimer formation in Adenine staked oligomers and the proton coupled electron transfer in Cytosine-Guanine base-pair in different solvents. We also aim to obtain an explicit QD simulation of the outcome of pump-probe experiments so to establish a direct bridge between the picture of the decay process arising from experiments and calculations.
Publications:
1) Yaghoubi Jouybari, M., Liu, Y., Improta, R. and Santoro, F., 2020. Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study. Journal of Chemical Theory and Computation, 16(9), pp.5792-5808.
2) Jouybari, M.Y., Liu, Y., Improta, R. and Santoro, F., 2020. Quantum dynamics of the ππ*/nπ* decay of the epigenetic nucleobase 1, 5-dimethyl-cytosine in the gas phase. Physical Chemistry Chemical Physics, 22(45), pp.26525-26535.
3) Aleotti, F., Aranda, D., Yaghoubi Jouybari, M., Garavelli, M., Nenov, A. and Santoro, F., 2021. Parameterization of a linear vibronic coupling model with multiconfigurational electronic structure methods to study the quantum dynamics of photoexcited pyrene. The Journal of Chemical Physics, 154(10), p.104106.
4) Green, J.A., Jouybari, M.Y., Aranda, D., Improta, R. and Santoro, F., 2021. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules, 26(6), p.1743.
Oral communications at congress:
1) 11th Symposium on Computing π-conjugated Compounds (Zagreb, Croatia 30th January - 1st February, 2020).“ ππ*/nπ* Internal conversion in Cytosine Derivation in Gas Phase and Polar Solvent. A Quantum Dynamics study base on TD-DFT and LVC Hamiltonian”.
2) 12th European Symposium on Computing π-conjugated Compounds (18th January -20th January2021). “ Quantum dynamics of ultrafast decay of the excited states of Cytosine and its derivatives in the gas phase based onTD-DFT and LVC Hamiltonians”.
Poster communications at congress:
1) Yaghoubi Jouybari, Martha; Esmaeilzadeh, Mahdi ; Hamidreza Simchi “Magnetic targeting in cancer photothermal therapy using cobalt doped molybdenum disulfide nanoparticles” , based on my master thesis in Chemistry for the Future International Conference, University of Pisa, Pisa, Italy, July 2019, (Best Poster).
2) SYMPOSIUM ON PROGRESS IN ORGANIC OPTOELECTRONICS AND ENERGY CONVERSION (Malaga-Spain, December 2019). “ Substituent, solvent and excitation wavelength effects on the ultrafast decay of Cytosine derivatives. A Quantum dynamical study”.
