The effect of microhydration on ionization energy and proton transfer in nucleobases. Analysis and method development.

摘要

In this thesis we use quantum mechanics to study basic properties of microhydrated nucleobases---essential building blocks of DNA. Water plays a central role in chemistry and biology by mediating the interactions between molecules, altering energy levels of solvated species, modifying potential energy profiles along reaction coordinates, and facilitating efficient proton transport through ion channels and interfaces. The effect of hydration on different properties of molecules and chemical reactions has been intensively studied for many years both theoretically and experimentally. Numerous solvation models were developed in an effort to simulate the properties and reactions in the bulk water. However, even the interaction between several water molecules are not completely understood. This work demonstrates how microhydration can affect such properties as ionization energies and control proton transfer mechanisms. It explains the experimental results and proposes mechanisms of observed effects.;In Chapter 2 a combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron VUV radiation. The onsets of the PIE curves are 8.85+/-0.05, 8.60+/-0.05, 8.55+/-0.05, and 8.40+/-0.05 eV for thymine, thymine mono-, di-, and tri-hydrates, respectively. The computed (EOM-IP-CCSD/cc-pVTZ) AIEs are 8.90, 8.51, 8.52, and 8.35 eV for thymine and the lowest isomers of thymine mono-, di-, and tri-hydrates. Due to large structural relaxation, the Franck-Condon factors for the 0←0 transitions are very small shifting the apparent PIE onsets to higher energies. Microsolvation strongly affects IEs of thymine---addition of each water molecule reduces the first vertical IE by 0.10-0.15 eV. The adiabatic IE decreases even more (up to 0.4 eV). The magnitude of the effect varies for different ionized states and for different isomers. For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule.;In Chapter 3 proton transfer in a model system comprising dry and microhydrated clusters of nucleobases is investigated. Experiments with mass spectrometry and tunable vacuum ultraviolet synchrotron radiation show that water shuts down ionization-induced proton transfer between nucleobases, which is very efficient in dry clusters. Instead, a new pathway opens up in which protonated nucleobases are generated by proton transfer from the ionized water molecule and elimination of a hydroxyl radical. Electronic structure calculations reveal that the shape of the potential energy profile along the proton transfer coordinate depends strongly on the character of the molecular orbital from which the electron is removed, i.e., the proton transfer from water to nucleobases is barrierless when an ionized state localized on water is accessed. The computed energetics of proton transfer is in excellent agreement with the experimental appearance energies. Possible adiabatic passage on the ground electronic state of the ionized system, while energetically accessible at lower energies, is not efficient. Thus, proton transfer is controlled electronically, by the character of the ionized state, rather than statistically, by simple energy considerations. Proton transfer from ionized outer water to nucleobases in dihydrated cluster through the Grotthuss-like mechanism is barrierless and the most energetically favorable mechanism.;Chapter 4 describes an implementation of coupled-cluster (CC) post-Hartree-Fock ab initio quantum chemistry methods, which are widely used in the research, including the research described in previous chapter, on GPU with CUDA C language. The implementation of these methods is based on the ccman2 and libtensor libraries and is part of the Q-Chem 4 electronic structure package. These libraries use layered modular architecture which allows relatively easy addition and replacement of low-level modules without changing high-level code (such as CC equations). Developed layered architecture make possible a fast adaptation of the existing code in the ccman2 library to other languages and technologies, such as OpenCL with AMD GPUs or Intel Xeon Phi coprocessor. The development of CC code for new massively parallel architectures is crucial for future research of larger systems with higher accuracy and for QM/MM methods. (Abstract shortened by UMI.).