Quantum chemical characterization of Biomolecules in the gas phase and on surfaces of metal oxides

During the four years of my PhD study, I performed systematic studies of the conformations of biomolecules ranging from a small amino acid (e.g. glycine) to a medium-sized nucleoside (e.g. 2’-deoxycytidine). To better account for possible effects brought by explicit environments (e.g. radiation, aqueous solution, and so on), we studied biomolecules in different phases, including neutral and charged species, in the gas phase and solid state, and neutral on solid surface. The work being presented in this thesis is original as: (1) A tool which can automatically generate libraries of conformations for a systematic search of the conformational space of a molecule was developed. When combined with tools developed by our colleagues, our toolbox facilitates a combinatorial computational chemical study of some small biomolecules; (2) A new method which can suppress barriers between different local minima on a molecular potential energy surface (PES) was developed, and with this new deformed PES, a lot of other techniques (e.g. Monte Carlo and simulated annealing) could be adopted to search for the global minima structure in a much more efficient way; (3) We performed a highly accurate study of two conformers of glycine up to the coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) with basis sets up to aug-cc-pVQZ level of theory, and we found that the treatment at the CCSD(T) level of theory is necessary to achieve numerical stability of the relative energies with respect to different basis sets at different geometries; (4) Through a thorough search of the conformational space of 2’-deoxycytidine, we found that its conformations in the gas phase are quite different from those in the solid state, and hopefully this finding could correct some of the previous approaches, in which structural information extracted from solid state experiments was used in computational studies of molecules in the gas phase; (5) Adsorptions of hydrogen, methanol and glycine on different types of solid surfaces (conductive and semiconductive) were studied, and catalytic performances of these surfaces on breaking chemical bonds were discussed. The current thesis not only covers the main applications of computational chemistry tools in the conformational study of biomolecules, it also includes discussions on accuracy and methodology which is involved in these studies. We definitely did not intend to solve all of the problems which people have met in their conformational studies of biomolecules. We just hope that the work being presented here was performed in a much more systematic way, and we hope these studies can give people some insights which might be helpful in their further studies

Photodissociation of Gas-Phase Ions Investigated Using Combined Mass-Spectrometry, Ion- Mobility and Laser Spectroscopy

The photophysics and photochemistry of molecules are dependent on the interplay between multiple quantum states, which is challenging to model and especially challenging to control. This lack of control impedes development of photoinitiators, phototherapies and next-generation mass spectrometry tools. In this thesis, the influence of charge on the photodissociation of gas-phase ions is investigated using combined ion-mobility (field asymmetric ion-mobility spectrometry), photodissociation action spectroscopy and massspectrometry techniques along with quantum chemistry methods. Target molecules range from fundamental chromophores, photoinitiators and biologically relevant ions

Outer valence orbital response to proton positions in prototropic tautomers of adenine

Orbital response to proton positions in the prototropic tautomers of adenine (Ade-N1, Ade-N3, Ade-N7 and Ade-N9) has been studied in position space and momentum space using dual space analysis (DSA). Based on the electronic structures of our previous density functional theory (DFT-BP86/TZ2P and BP86/QZ4P) study of adenine tautomers (J. Phys. Chem. A, 110(2006)4012), variations in properties such as ring perimeters, dipole moments, Hirshfeld charges, vertical ionization spectra and orbital theoretical momentum distributions (MDs) of these tautomers are compared, in order to understand the impact of the mobile proton positions in the purine ring. It is found that the proton relocation causes only small perturbations in isotropic properties such as geometries and vertical ionization energies in the outer valence space of adenine. Molecular polarity and dipole moments differentiate the tautomers. Hirshfeld charges divide the nitrogen sites of the tautomers into amino (single bonds) and imino (at least one double bond) nitrogen sites. Adenine tautomerization is essentially a σ-bonding phenomenon with little perturbation to the π-bonding framework. That is, the π (or a'') orbitals, including the frontier orbitals such as the highest occupied molecular orbital (HOMO), 6a'', and the third HOMO (HOMO-2), 5a'', do not respond apparently to the proton relocation (note that the next HOMO (HOMO-1) is 29a', a σ orbital). Only relevant σ or a' orbitals residing within the purine plane, such as 21a'–24a' and orbital 27a', respond significantly to the proton positions. The present study demonstrates that the tautomer electronic structures depend not only on three dimensional geometries but also on the electron density distributions