Biomedical Engineering Reference
In-Depth Information
When
f
k
(2)
> 0 the process is driven by a nucleophilic attack on atom k and
then that atom acts an electrophilic species; conversely, when
k
(2)
< 0 the
process is driven by an electrophilic attack over atom
k
and therefore atom
k
acts as a nucleophilic species.
7.3
Results and Discussion
All computational studies were performed with the Gaussian 09 [33] series
of programs with density functional methods as implemented in the com-
putational package. h e equilibrium geometries of the molecules were
determined by means of the gradient technique. h e force constants and
vibrational frequencies were determined by computing analytical frequen-
cies on the stationary points obtained at er the optimization to check if
there were true minima. h e basis set used in these works was MIDIY+,
which is the same basis set as MIDI! with a polarization function added
to the hydrogen atoms and a dif use sp-set added to non-hydrogen atoms.
h e MIDI! basis is a small double-zeta basis with polarization functions on
N-F, Si-Cl, Br, and I [34-39].
7.3.1 Molecular Structures
For the calculation of the molecular structure and properties of the studied
system, we have chosen the hybrid meta-GGA density functionals M06,
M06L, M06-2X and M06HF [40], which consistently provide satisfactory
results for several structural and thermodynamic properties. Solvation
energies were computed by the Integral Equation Formalism-Polarizable
Continuum Model (IEF-PCM) [41], including the UAKS model and etha-
nol as a solvent.
h e molecular structure of BFPF Green Fluorescent Protein Chromophore
was pre-optimized by starting with the readily available PDB structure, and
i nding the most stable conformer by means of the Conformers module
of Materials Studio through a random sampling with molecular mechanics
techniques and a consideration of all the torsional angles. h e structure of
the resulting conformer was then optimized with the M06, M06L, M06-2X
and M06-HF density functionals in conjunction with the MIDIY+ basis set.
h e optimized molecular structure of the BFPF Green Fluorescent Protein
Chromophore molecule calculated with the four density functionals is
shown in Figures 7.1 to 7.4, while the bond distances (in Å) and the bond
angles (in degrees) calculated with the M06, M06L, M06-2X and M06-HF
functionals in conjunction with the MIDIY+ basis set are presented in
