Ultrafast Vibrational Dynamics of Hydrogen-Bonded Base Pairs and Hydrated DNA

.................................................................................................................................... 4 1 Hydrogen bonding ............................................................................................................... 7 1.1 The nature of the hydrogen bond ................................................................................... 7 1.2 Subject of the thesis ...................................................................................................... 10 2 Oneand two-dimensional linear vibrational spectroscopy in studying hydrogenbonded systems .................................................................................................................. 11 2.1 Vibrational Hamiltonian of polyatomic molecule. Effects of anharmonicity .............. 11 2.2 Vibrational spectra........................................................................................................ 13 2.3 Vibrational spectroscopy of hydrogen-bonded systems ............................................... 14 2.4 Vibrational coupling mechanisms ................................................................................ 16 2.5 Two-dimensional correlation spectroscopy .................................................................. 20 3 Nonlinear spectroscopy ..................................................................................................... 28 3.1 Optical polarization ...................................................................................................... 28 3.2 The quantum mechanical polarization .......................................................................... 30 3.3 The nonlinear optical response functions ..................................................................... 31 3.4 Feynman diagrams ....................................................................................................... 33 3.5 The reduced density matrix and thermal averaging ..................................................... 34 3.6 The role of dephasing processes ................................................................................... 35 3.7 Vibrational relaxation .................................................................................................. 36 3.8 Line broadening mechanisms ....................................................................................... 36 3.9 The dynamics of hydrogen-bonded systems ................................................................ 37 3.10 Theory of pump-probe spectroscopy ............................................................................ 38 3.11 Polarizationresolved pump-probe spectroscopy ........................................................ 42 4 Experimental techniques ................................................................................................... 45 4.1 Generation of mid-IR laser pulses ................................................................................ 45 4.2 The laser system ........................................................................................................... 46 4.3 Optical frequency conversion and amplification .......................................................... 47 4.4 Pump-probe spectroscopy – experimental realisation .................................................. 49 4.5 Characterisation of ultrashort pulses ............................................................................ 50 5 2-pyridone dimer: a DNA model system ......................................................................... 53