8 research outputs found
Simultaneous Solvent and Counterion Effects on the Absorption Properties of a Model of the Rhodopsin Chromophore
The ASEP/MD (averaged solvent electrostatic
potential from molecular dynamics) method was employed in studying
the environment effects (solvent and counterion) on the absorption
spectrum of a model of the 11-<i>cis</i>-retinal protonated
Schiff base. Experimental studies of the absorption spectra of the
rhodopsin chromophore show anomalously large solvent shifts in apolar
solvents. In order to clarify their origin, we study the role of the
counterion and of the solute–solvent interactions. We compare
the absorption spectra in the gas phase, cyclohexane, dichloromethane,
and methanol. The counterion effect was described from both a classical
and quantum point of view. In the latter case, the contribution of
the chromophore-counterion charge transfer to the solvent shift could
be analyzed. To the best of our knowledge, this is the first time
that counterion and solvent effects on the absorption properties of
the 11-<i>cis</i>-retinal chromophore have been simultaneously
examined. We conclude that the counterion–solute ionic pair
in the gas phase is not a good model to represent the solvent shift
in nonpolar solvents, as it does not account for the effect that the
thermal agitation of the solvent has on the geometry of the ionic
pair. In contrast to nonpolar solvents, the experimental solvent shift
values in methanol can be exclusively explained by the polarity of
the medium. In dichloromethane, the presence of the counterion does
not modify the solvent shift of the first absorption band, but it
affects the position of the second excited state. In the three solvents
considered, the first two excited states become almost degenerate
Solvent Effects on the Absorption Spectra of the <i>para</i>-Coumaric Acid Chromophore in Its Different Protonation Forms
The effects of the
solvent and protonation state on the electronic
absorption spectrum of the <i>para</i>-coumaric acid (pCA),
a model of the photoactive yellow protein (PYP), have been studied
using the ASEP/MD (averaged solvent electrostatic potential from molecular
dynamics) method. Even though, in the protein, the chromophore is
assumed to be in its phenolate monoanionic form, when it is found
in water solution pH control can favor neutral, monoanionic, and dianionic
species. As the pCA has two hydrogens susceptible of deprotonation,
both carboxylate and phenolate monoanions are possible. Their relative
stabilities are strongly dependent on the medium. In gas phase, the
most stable isomer is the phenolate while in aqueous solution it is
the carboxylate, although the population of the phenolate form is
not negligible. The s-<i>cis</i>, s-<i>trans</i>, <i>syn</i>, and <i>anti</i> conformers have
also been included in the study. Electronic excited states of the
chromophore have been characterized by SA-CAS(14,12)-PT2/cc-pVDZ level
of theory. The bright state corresponds, in all the cases, to a π
→ π* transition involving a charge displacement in the
system. The magnitude and direction of this displacement depends on
the protonation state and on the environment (gas phase or solution).
In the same way, the calculated solvatochromic shift of the absorption
maximum depends on the studied form, being a red shift for the neutral,
carboxylate monoanion, and dianionic chromophores and a blue shift
for the phenolate monoanion. Finally, the contribution that the solvent
electronic polarizability has on the solvent shift was analyzed. It
represents a very important part of the total solvent shift in the
neutral form, but its contribution is completly negligible in the
mono- and dianionic forms
QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore
Substituent
and solvent effects on the excited state dynamics of
the Photoactive Yellow Protein chromophore are studied using the average
solvent electrostatic potential from molecular dynamics (ASEP/MD)
method. Four molecular models were considered: the ester and thioester
derivatives of the <i>p</i>-coumaric acid anion and their
methylated derivatives. We found that the solvent produces dramatic
modifications on the free energy profile of the S1 state: 1) Two twisted
structures that are minima in the gas phase could not be located in
aqueous solution. 2) Conical intersections (CIs) associated with the
rotation of the single bond adjacent to the phenyl group are found
for the four derivatives in water solution but only for thio derivatives
in the gas phase. 3) The relative stability of minima and CIs is reverted
with respect to the gas phase values, affecting the prevalent de-excitation
paths. As a consequence of these changes, three competitive de-excitation
channels are open in aqueous solution: the fluorescence emission from
a planar minimum on S1, the <i>trans–cis</i> photoisomerization
through a CI that involves the rotation of the vinyl double bond,
and the nonradiative, nonreactive, de-excitation through the CI associated
with the rotation of the single bond adjacent to the phenyl group.
In the gas phase, the minima are the structures with the lower energy,
while in solution these are the conical intersections. In solution,
the de-excitation prevalent path seems to be the photoisomerization
for oxo compounds, while thio compounds return to the initial <i>trans</i> ground state without emission
How Methylation Modifies the Photophysics of the Native All-<i>trans</i>-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol
A comparison between
the free-energy surfaces of the all-<i>trans</i>-retinal
protonated Schiff base (RPSB) and its 10-methylated
derivative in gas phase and methanol solution is performed at CASSCF//CASSCF
and CASPT2//CASSCF levels. Solvent effects were included using the
average solvent electrostatic potential from molecular dynamics method.
This is a QM/MM (quantum mechanics/molecular mechanics) method that
makes use of the mean field approximation. It is found that the methyl
group bonded to C10 produces noticeable changes in the solution free-energy
profile of the S<sub>1</sub> excited state, mainly in the relative
stability of the minimum energy conical intersections (MECIs) with
respect to the Franck–Condon (FC) point. The conical intersections
yielding the 9-<i>cis</i> and 11-<i>cis</i> isomers
are stabilized while that yielding the 13-<i>cis</i> isomer
is destabilized; in fact, it becomes inaccessible by excitation to
S<sub>1</sub>. Furthermore, the planar S<sub>1</sub> minimum is not
present in the methylated compound. The solvent notably stabilizes
the S<sub>2</sub> excited state at the FC geometry. Therefore, if
the S<sub>2</sub> state has an effect on the photoisomerization dynamics,
it must be because it permits the RPSB population to branch around
the FC point. All these changes combine to speed up the photoisomerization
in the 10-methylated compound with respect to the native compound
Theoretical Study of Solvent Effects on the Ground and Low-Lying Excited Free Energy Surfaces of a Push–Pull Substituted Azobenzene
The
ground and low-lying excited free energy surfaces of 4-amino-4′-cyano
azobenzene, a molecule that has been proposed as building block for
chiroptical switches, are studied in gas phase and a variety of solvents
(benzene, chloroform, acetone, and water). Solvent effects on the
absorption and emission spectra and on the <i>cis–trans</i> thermal and photo isomerizations are analyzed using two levels of
calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced
using a polarizable continuum model and a QM/MM method, which permits
one to highlight the role played by specific interactions. We found
that, in gas phase and in agreement with the results found for other
azobenzenes, the thermal <i>cis–trans</i> isomerization
follows a rotation-assisted inversion mechanism where the inversion
angle must reach values close to 180° but where the rotation
angle can take almost any value. On the contrary, in polar solvents
the mechanism is controlled by the rotation of the CNNC angle.
The change in the mechanism is mainly related to a better solvation
of the nitrogen atoms of the azo group in the rotational transition
state. The photoisomerization follows a rotational pathway both in
gas phase and in polar and nonpolar solvents. The solvent introduces
only small modifications in the nπ* free energy surface (<i>S</i><sub>1</sub>), but it has a larger effect on the ππ*
surface (<i>S</i><sub>2</sub>) that, in polar solvents,
gets closer to <i>S</i><sub>1</sub>. In fact, the <i>S</i><sub>2</sub> band of the absorption spectrum is red-shifted
0.27 eV for the <i>trans</i> isomer and 0.17 eV for the <i>cis</i>. In the emission spectrum the trend is similar: only <i>S</i><sub>2</sub> is appreciably affected by the solvent, but
in this case a blue shift is found
Using Molecular Dynamics and Quantum Mechanics Calculations To Model Fluorescence Observables
We provide a critical examination of two different
methods for generating a donoracceptor electronic coupling
trajectory from a molecular dynamics (MD) trajectory and
three methods for sampling that coupling trajectory, allowing
the modeling of experimental observables directly from the MD
simulation. In the first coupling method we perform a single
quantum-mechanical (QM) calculation to characterize the
excited state behavior, specifically the transition dipole moment,
of the fluorescent probe, which is then mapped onto the configuration space sampled by MD. We then utilize these transition dipoles within the ideal dipole approximation (IDA) to determine the electronic coupling between the probes that mediates the transfer of energy. In the second method we perform a QM calculation on each snapshot and use the complete transition densities to calculate the electronic coupling without need for the IDA. The resulting coupling trajectories are then sampled using three methods ranging from an independent sampling of each trajectory point (the independent snapshot method) to a Markov chain treatment that accounts for the dynamics of the coupling in determining effective rates. The results show that the IDA significantly overestimates the energy transfer rate (by a factor of 2.6) during the portions of the trajectory in which the probes are close to each other. Comparison of the sampling methods shows that the Markov chain approach yields more realistic observables at both high and low FRET efficiencies. Differences between the three sampling methods are discussed in terms of the different mechanisms for averaging over structural dynamics in the system. Convergence of the Markov chain method is carefully examined. Together, the methods for estimating coupling and for sampling the coupling provide a mechanism for directly connecting the structural dynamics modeled by MD with fluorescence observables determined through FRET experiments