Quantum Mechanical Insights into Biological Processes at the Electronic Level - Computational Modeling of Biological Systems - page 150

species and the initial species. Then, excited electronic states for the ionized species
have to be found, and the excitation energies have to be added to the first VDE
to obtain VDEs corresponding to the electron detachment from the MOs deeper
than the HOMO. Calculated VDEs can be compared to experimental photoelectron
spectra, and good agreement (within 0.1-0.2 eV) would be a structural probe for the
molecule.

4.2 Examples of Applications

Ab initio calculations of excited states can be done with chemical accuracy, to
explain or challenge existing experiments, and to make predictions. For example,
ionization energies of aqueous nucleic acids have been calculated at TD-DFT and
CASPT2 with implicit solvation, and compared to experimental values [ 28 ]. The
lowest vertical ionization energies of aqueous cytidine and deoxythymidine were
determined experimentally to be 8.3 eV, corresponding to an electron detaching
from the base. Calculations were in quantitative agreement with the experiment.
A dramatic effect of the aqueous environment was revealed by the ab initio
computations. Namely, bulk water not only modestly lowers the ionization potential
of the DNA bases but also makes it insensitive to the presence of sugar or phosphate.
This is a very different situation from that observed in the gas phase, where the other
DNA components (phosphate in particular) strongly influence the ionization process
at the base.
Krylov and coworkers conducted a very detailed study of the electronic structure
of the chromophore in the green fluorescent protein (GFP), and its changes upon
one and two-electron oxidation [ 29 ]. The purpose of this work was to elucidate
the mechanism of oxidative redding of the protein. The chromophore in GFP, 4 0 -
hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI),(Fig. 13 a) is widely used
in bioimaging. Structural changes upon oxidation were minor but sufficient to dif-
ferentiate the species by their IR absorption spectra. MOs illustrating the electronic
changes upon electron detachments are shown in Fig. 13 b. Electronic states of
relevant species were characterized by the SOS-CIS(D), multireference perturbation
theory, and EOM-CCSD calculations, and results obtained with different methods
were in a fairly good agreement. The one- and two-electron oxidation processes for
deprotonated HBDI were considered. Figure 13 c shows an overall energy diagram
for the three considered forms of HBDI. Adiabatically, the doubly oxidized form
is 9.98 eV above the ground state of the anion. The respective value of VDE
corresponding to removing two electrons is 10.37 eV. The adiabatic ionization
energy from the ground state of the doublet radical is 7.59 eV computed using the
anion's VDE value of 2.54 and 0.15 eV relaxation energy of the neutral radical.
Another relevant value is the energy gap between the excited states D 1 and D 2 of
the doublet radical and the cation. Using the same values of vertical detachment
and relaxation energies, and 1.52 and 3.37 eV for the vertical D 0 ! D 1;2 excitation
energies, the authors estimated the ionization energy of the electronically excited