UV-visible absorption

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Table of contents

I Acknowledgments/Remerciements 
II Outreach activities 
0.1 Introduction
0.2 Pretexte
0.3 Esperluette
0.4 MT180
III List of publications
IV Introduction générale 
V General introduction 
VI Main concepts and systems 
1 Photochemical and photophysical processes 
1.1 Photochemistry
1.2 Spectroscopies
1.2.1 UV-visible absorption
1.2.2 Circular dichroism
1.2.3 Fluorescence
1.3 Photosensitization
1.4 Photodynamic therapy
2 DNA 
2.1 Introduction
2.2 Fundamental building blocks of DNA
2.3 Double helix
2.4 DNA structural parameters
2.5 DNA photosensitivity
2.6 DNA photolesions
2.7 Repair processes
VII Methods 
3 Molecular Mechanics 
4 Molecular Dynamics 
4.1 Integration of equations of motion
4.2 Periodic Boundary Conditions (PBC)
4.3 Ewald summation and Particule Mesh Ewald (PME)
4.4 Biased Molecular Dynamics
4.5 Alchemical simulations
5 Quantum chemistry 
5.1 The six postulates of quantum mechanics
5.1.1 Postulate 1: the wave function
5.1.2 Postulate 2: Hermitian operators
5.1.3 Postulate 3: eigenstates and eigenvalues
5.1.4 Postulate 4: expectation of the wave function
5.1.5 Postulate 5: Time dependent Schrödinger equation
5.1.6 Postulate 6: wave function collapse
5.2 The Schrödinger equation in quantum chemistry
5.3 Born-Oppenheimer approximation
5.3.1 Variational Principle
5.4 Ground state
5.4.1 Hartree-Fock approximation
5.4.2 Density Functional theory (DFT)
5.4.2.1 Principle
5.4.2.2 The electronic density
5.4.2.3 The Hohenberg-Kohn theorems
5.4.2.4 The Kohn-Sham equations
5.4.2.5 LDA
5.4.2.6 GGA
5.4.2.7 meta-GGA
5.4.2.8 Hybrid GGA and hybrid meta-GGA
5.4.2.9 Double hybrids
5.5 Excited states
5.5.1 Time Dependent-Hartree Fock (TDHF)
5.5.2 Time Dependent-Density Functional Theory (TDDFT)
5.5.2.1 The Runge-Gross theorem
5.5.2.2 Time-Dependent Kohn-Sham equation
5.5.3 Frenkel excitons theory
6 QM/MM 
6.1 QM/MM energy
6.1.1 QM/MM embeddings
6.1.1.1 Mechanical Embedding (ME)
6.1.1.2 Electrostatic Embedding (EE)
6.1.1.3 Polarisable Embedding (PE)
6.2 QM/MM boundary
6.2.1 Link Atom (LA)
VIII Results and discussions 
7 Introduction 
8 Electronic Circular Dichroism (ECD) modeling 
8.1 ECD of B-DNA
8.2 ECD of G-quadruplexes
9 Binding free energy of Benzophenone 
10 Photosensitization of DNA 
10.1 Benzophenone: Hydrogen abstraction
10.2 Nile Blue, Nile Red: Electron transfer
10.3 BMEMC: Radical species
10.4 Pyo: Triplet-Triplet Energy Transfer (TTET)
11 Damaged DNA: structure and recognition 134
11.1 Cluster abasic sites
11.1.1 Recognition by APE1
11.2 64-PP and CPD
XI Appendices 
A DNA structural parameters 
B ECD of B-DNA 
C ECD of G-quadruplexes 
D Binding free energy of Benzophenone 
E Benzophenone: Hydrogen abstraction 
F Nile Blue, Nile Red: Electron transfer 
G BMEMC: Radical reactive species 
H Pyo: Triplet-Triplet Energy Transfer (TTET) 
I Cluster abasic sites 
J 6-4PP and CPD