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Highest occupied molecular orbital (HOMO) of a Ru2+ cation in aqueous
solution. This 4d6 transition metal aqua cation is low spin and forms
a coordination shell consisting of six H2O molecules which in
solution retains to a good approximation octahedral symmetry (as can be seen
from the near t2g symmetry of the HOMO in the picture). Oxidation of
the complex proceeds via an outer-sphere reorganization mechanism, preserving the
octahedral coordination, and the
Ru2+/Ru3+ couple is considered as a text book example
of a system to which the Marcus theory of electron transfer applies. This
system has been therefore our favourite model for the development of the
Marcus theory based method for the computation of redox and reorganization
free energies([JPCB05a, TCA05]). We have also studied the electronic absorption spectrum of aqueous Ru(II) using
TDDFT methods[JPCB05b]
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Lowest unoccupied molecular orbital (LUMO) of a Ag1+ cation in
aqueous solution (ion is in the center). Since the 4d10 configuration
of Ag(I) is closed shell, the LUMO is the 5s orbital which in solution
is hybridized with a delocalized virtual state of the solvent (water) as shown
in the picture (compare picture on the main page). The Ag1+
aquaion is also of interest because oxidation to Ag2+ increases the
coordination number (on average) by one H2O molecule. This introduces
non-linearities in the solvent response placing the Ag1+/Ag2+
outside the Marcus regime. Both these features are in contrast to Ru(II) which
is the reason that Ag(I) has become a second model system to which we have
returned repeatedly in calculations of redox [JACS04, JPCB04a, JCP06] and optical properties[JCP04].
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Two model quinones, benzoquinone (BQ) and duro quinone (DQ), forming stable radical anions. The reaction free energy
(redox potential) of the
BQ + DH•- → BQ•- + DQ redox reaction was computed by simulating the
DQ•- → DQ + e- and BQ•- → BQ + e- half reactions
and subtracting the oxidation free energies. Two different non-aqueous solvents,
methanol and acetonitrile were used and the results for the reaction and reorganization free energy compared[Angew. Chem.]
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Ab initio molecular dynamics model system used for the simulation of the BQ + e- → BQ•-
half reaction in methanol solution.
The green contours indicate the spin density of the unpaired electron in the BQ•- radical anion.
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Representative MD configuration of Cp Rubredoxin generated from a 1IRO crystal
structure as employed in the DFT calculations. The periodically repeated
simulation cell, with edges 31.136, 28.095, 30.502 A contains the
protein, 678 water molecules and 9 Na+ counterions. The orange isosurface
represents the spin density for the oxidized state (charge 0, spin 5/2) at
0.005 a.u..
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Two organosulfur compounds, tetrathiafulvalene (TTF) and tianthrene (TH), forming
stable radical cations. We computed the reaction free energy change (redox potential)
and reorganization free energy of the
TTF + TH•+ → TTF•+ + TH redox reaction in
acetonitrile solution[JPCB2005c]
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Electronic polarization of a TTF•+ radical cation created by vertical
ionization of a TTF molecule in acetonitrile solution. Picture shows the difference
of the charge density in cationic and neutral state for fixed atomic positions.
Note the polarization of the solvent molecules (green indicates
that charge has been removed).
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Spin polarization of the TTF•+ radical cation of the picture above
(so same atomic configuration).
The unpaired electron is localized exclusively on the solute.
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Model system of aqueous uracil used for the ab initio MD computation of the
infra-red absorption spectrum of this nucleic base. The spectrum was determined by
Fourier transformation of the time fluctuations of the polarization as computed
from maximally localized Wannier functions[JPCB03]. For a similar calculation of the
IR spectrum of NMA see [JCTC05].
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OH• radical in solution. This highly reactive species was
simulated using a special self-interaction corrected BLYP functional. The
corrections are applied to the unpaired electron only. Without these corrections
(using the regular BLYP functional) the radical even attacks the solvent
forming a spurious hemi-bond with the O atom of a neighbouring water. With
these corrections the OH• was found to be hydrogen bonded
to the solvent accepting two to three weak H-bonds and donating one strong
H-bond[PCCP05]
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Pentahydroxyphosphorane (P(OH)5) molecule in aqueous in solution (periodic
boundary conditions applied). Using this rather small model system we were able
to compute the relative equilibrium constants (pKa's) for axial and equatorial
acid dissociation[JACS2002]. The pKa's were obtained from the reversible work needed to transfer a proton
from a phosphorane OH group to the solvent. The challenge is now to find a method
for computation of acid dissociation constants which is consistent with our half-reaction
scheme for computing redox potentials, i.e. we will have to find a way to completely
eliminate the proton from the system or insert a proton. This will enable us to compute
reaction free energies for proton coupled redox reactions, which are the rule for redox
reactions of organic molecules.
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