Simulation of the Resonance Raman Spectra For Uracil and its Derivatives

  • Author / Creator
    Sun, Shuai
  • In this thesis, we simulated the resonance Raman spectra of uracil and its derivatives, including 5-halogenated (F, Cl, Br) uracils and thymine, using the Herzberg-Teller short-time dynamics formalism. The electronic structure calculations are carried out using density functional theory (DFT) for ground states and time-dependent density functional theory (TD-DFT) for excited states. As the resonance Raman spectra are governed by the ground state normal modes and the excited state Cartesian gradient, the resulting spectra are examined in terms of these two factors. In the simulation of the resonance Raman spectrum for uracil, the performance of different functionals is investigated. The ground state geometry is optimized at the levels of PBE0/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ, respectively. The gradient of the bright excited state is computed using Time Dependent Density Functional Theory (TD-DFT) and Spin Flip Time Dependent Density Functional Theory (SF-TD-DFT). The excited state calculations are carried out in both the gas phase and implicit water using the conductor-like Polarizable Continuum (C-PCM) Model. The ground state equilibrium structure is found to impact the resulting resonance Raman spectrum significantly. The simulated resonance Raman spectrum using the long range corrected functionals, i.e., CAMB3LYP and LC-BLYP, and based on the PBE0/aug-cc-pVTZ optimized ground state structure shows better agreement with the experimental spectrum than using standard hybrid functionals, i.e., PBE0 and B3LYP. The solvation effect leads to a change in the energetic order of the n→π* and π→π* excited states, and it improves the agreement with the experimental spectrum, especially with regard to the relative intensities of the peaks with frequencies greater than 1600 cm-1. The resonance Raman spectra of the 5-halogenated (F, Cl, and Br) uracils are simulated, and the effects of halogen substitution are investigated through the comparison between the spectra of the three 5-halogenated uracils. The gradient of the S1 excited state is computed at the CAMB3LYP/aug-cc-pVTZ level of theory in implicit water (C-PCM), based on the equilibrium geometry determined using PBE0/aug-cc-pVTZ in implicit water (C-PCM). The simulated resonance Raman spectra show good agreement with the experimental spectra both in terms of peak positions and intensities. The differences in the normal mode eigenvectors and excited state Cartesian gradients between 5-fluorouracil and 5-chlorouracil are used to interpret the dissimilarity between their resonance Raman spectra. Meanwhile, the similarity between the spectra of 5-chlorouracil and 5-bromouracil is explained by the correspondence between their normal modes and excited state gradients. The effects of explicit hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine are also investigated computationally. The three bonding sites in uracil and thymine that form lowest energy uracil- H2O and thymine- H2O complexes are examined. The ground state structures of the three uracil- H2O and corresponding thymine- H2O complexes are optimized at the PBE0/aug-cc-pVTZ level of theory in H2O (C-PCM), and the gradients of the bright excited state (S1) are computed at the TD-CAMB3LYP/aug-cc-pVTZ level of theory in H2O (C-PCM). Explicit hydrogen bonding to water is found to cause significant changes in the resonance Raman spectra of uracil and thymine when compared to the isolated molecules. The effect of hydrogen boding is primarily on the ground state normal mode character, especially for the high frequency modes (>1600 cm-1), rather than on the excited state Cartesian gradients. Different hydrogen bonding sites are found to have different contributions in the resulting resonance Raman spectra, and inclusion of explicit hydrogen bonding on the carbonyl bond opposite to the ring nitrogen is necessary to obtain good agreement between the simulated and experimental resonance Raman spectra of uracil and thymine. While accomplishing the research in this thesis, an interface of the resonance Raman computer code in ORCA (orca_asa) to GAMESS-US and Gaussian was developed. The resulting software can be used as a general tool for computing resonance Raman spectra. Therefore, in principle any electronic structure method that can determine a (numerical or analytical) Hessian can be used to compute the ground state. Meanwhile, a variety of methods could be used to determine the excited state gradients either analytically, or, in a much more computationally expensive fashion, numerically. Where available, solvation effects can be accounted for via polarizable continuum models (PCM) or, if specific solute-solvent interactions are important, with explicit solvent + PCM.

  • Subjects / Keywords
  • Graduation date
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
  • Institution
    University of Alberta
  • Degree level
  • Department
    • Department of Chemistry
  • Supervisor / co-supervisor and their department(s)
    • Brown, Alex (Chemistry)
  • Examining committee members and their departments
    • Loppnow, Glen (Chemistry)
    • Brown, Alex (Chemistry)
    • Peslherbe, Gilles (Chemistry)
    • Klobukowski, Mariusz (Chemistry)
    • Cairo, Christopher (Chemistry)