How Methylation Modifies the Photophysics of the Native All- trans-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol.

A comparison between the free-energy surfaces of the all- trans-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 S1 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- cis and 11- cis isomers are stabilized while that yielding the 13- cis isomer is destabilized; in fact, it becomes inaccessible by excitation to S1. Furthermore, the planar S1 minimum is not present in the methylated compound. The solvent notably stabilizes the S2 excited state at the FC geometry. Therefore, if the S2 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.

Excited-states of a rhenium carbonyl diimine complex: solvation models, spin-orbit coupling, and vibrational sampling effects.

We present a quantum-chemical investigation of the excited states of the complex [Re(CO)3(Im)(Phen)]+ (Im = imidazole; Phen = 1,10-phenanthroline) in solution including spin-orbit couplings and vibrational sampling. To this aim, we implemented electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) in the Amsterdam Density Functional program suite, suitable for time-dependent density functional calculations including spin-orbit couplings. The new implementation is employed to simulate the absorption spectrum of the complex, which is compared to the results of implicit continuum solvation and frozen-density embedding. Molecular dynamics simulations are used to sample the ground state conformations in solution. The results demonstrate that any study of the excited states of [Re(CO)3(Im)(Phen)]+ in solution and their dynamics should include extensive sampling of vibrational motion and spin-orbit couplings.

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 p-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 trans-cis 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 trans ground state without emission.

Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore.

In an attempt to shed light on the environmental effects on the deactivation channels of the PYP chromophore, radiative and non-radiative deactivation mechanisms of the anionic p-coumaric acid methyl ester (pCE-) in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level and, when necessary, at the CASPT2//CASPT2/cc-pVDZ level. We find that the solvent produces dramatic modifications on the free energy profile of the S1 state. Two twisted structures that are minima in the gas phase could not be localized in aqueous solution. Furthermore, the relative stability of minima and conical intersections (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 trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond and the non-radiative, non-reactive, 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 lower energy, while in solution the CIß structure, characterized by a large charge separation, is strongly stabilized by interactions with water molecules and becomes the structure with the lowest energy on S1. These facts explain the low fluorescence signal of pCE- in aqueous solution and the presence of partial trans-cis photoisomerization in this system.

UV-Induced Adenine Radicals Induced in DNA A-Tracts: Spectral and Dynamical Characterization.

Adenyl radicals generated in DNA single and double strands, (dA)20 and (dA)20·(dT)20, by one- and two-photon ionization by 266 nm laser pulses decay at 600 nm with half-times of 1.0 ± 0.1 and 4 ± 1 ms, respectively. Though ionization initially forms the cation radical, the radicals detected for (dA)20 are quantitatively identified as N6-deprotonated adenyl radicals by their absorption spectrum, which is computed quantum mechanically employing TD-DFT. Theoretical calculations show that deprotonation of the cation radical induces only weak spectral changes, in line with the spectra of the adenyl radical cation and the deprotonated radical trapped in low temperature glasses.

Excited State Pathways Leading to Formation of Adenine Dimers.

The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).

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 cis-trans 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 cis-trans 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 CN═NC 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 (S1), but it has a larger effect on the ππ* surface (S2) that, in polar solvents, gets closer to S1. In fact, the S2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S2 is appreciably affected by the solvent, but in this case a blue shift is found.

Energy flow in the cryptophyte PE545 antenna is directed by bilin pigment conformation.

Structure-based calculations are combined with quantitative modeling of spectra and energy transfer dynamics to detemine the energy transfer scheme of the PE545 principal light-harvesting antenna of the cryptomonad Rhodomonas CS24. We use a recently developed quantum-mechanics/molecular mechanics (QM/MM) method that allows us to account for pigment-protein interactions at atomic detail in site energies, transition dipole moments, and electronic couplings. In addition, conformational flexibility of the pigment-protein complex is accounted for through molecular dynamics (MD) simulations. We find that conformational disorder largely smoothes the large energetic differences predicted from the crystal structure between the pseudosymmetric pairs PEB50/61C-PEB50/61D and PEB82C-PEB82D. Moreover, we find that, in contrast to chlorophyll-based photosynthetic complexes, pigment composition and conformation play a major role in defining the energy ladder in the PE545 complex, rather than specific pigment-protein interactions. This is explained by the remarkable conformational flexibility of the eight bilin pigments in PE545, characterized by a quasi-linear arrangement of four pyrrole units. The MD-QM/MM site energies allow us to reproduce the main features of the spectra, and minor adjustments of the energies of the three red-most pigments DBV19A, DBV19B, and PEB82D allow us to model the spectra of PE545 with a similar quality compared to our original model (model E from Novoderezhkin et al. Biophys. J.2010, 99, 344), which was extracted from the spectral and kinetic fit. Moreover, the fit of the transient absorption kinetics is even better in the new structure-based model. The largest difference between our previous and present results is that the MD-QM/MM calculations predict a much smaller gap between the PEB50/61C and PEB50/61D sites, in better accord with chemical intuition. We conclude that the current adjusted MD-QM/MM energies are more reliable in order to explore the spectral properties and energy transfer dynamics in the PE545 complex.

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-cis-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-cis-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 para-Coumaric Acid Chromophore in Its Different Protonation Forms.

The effects of the solvent and protonation state on the electronic absorption spectrum of the para-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-cis, s-trans, syn, and anti 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.

Using molecular dynamics and quantum mechanics calculations to model fluorescence observables.

We provide a critical examination of two different methods for generating a donor-acceptor 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.

Photosynthetic light-harvesting is tuned by the heterogeneous polarizable environment of the protein.

In photosynthesis, special antenna proteins that contain multiple light-absorbing molecules (chromophores) are able to capture sunlight and transfer the excitation energy to reaction centers with almost 100% quantum efficiencies. The critical role of the protein scaffold in holding the appropriate arrangement of the chromophores is well established and can be intuitively understood given the need to keep optimal dipole-dipole interactions between the energy-transferring chromophores, as described by Förster theory more than 60 years ago. However, the question whether the protein structure can also play an active role by tuning such dipole-dipole interactions has not been answered so far, its effect being rather crudely described by simple screening factors related to the refractive index properties of the system. Here, we present a combined quantum chemical/molecular mechanical approach to compute electronic couplings that accounts for the heterogeneous dielectric nature of the protein-solvent environment in atomic detail. We apply the method to study the effect of dielectric heterogeneity in the energy migration properties of the PE545 principal light-harvesting antenna of the cryptomonad Rhodomonas CS24. We find that dielectric heterogeneity can profoundly tune by a factor up to ∼4 the energy migration rates between chromophore sites compared to the average continuum dielectric view that has historically been assumed. Our results indicate that engineering of the local dielectric environment can potentially be used to optimize artificial light-harvesting antenna systems.

Solvent Effects on the Structure and Spectroscopy of the Emitting States of 1-Phenylpyrrole.

Theoretical calculations of absorption and fluorescence properties of 1-phenylpyrrole have been performed, at the CASPT2//CASSCF level, in the gas phase and in acetonitrile solution, using in the latter case the ASEP/MD method. In addition to a locally excited state, it was also possible to identify a candidate intramolecular charge transfer state that could explain the second red-shifted fluorescence band that appears in polar solvents. In the gas phase, the charge transfer state is found to lie higher in energy than the locally excited state and the Franck-Condon absorption state, making it unlikely to be reached under these conditions. In acetonitrile solution, the charge transfer state is stabilized and lies much closer to the locally excited state, becoming accessible after absorption. The results indicate that the free-energy surface of the charge transfer state is very flat in solution, and several geometries are possible, ranging from almost planar to twisted and bent. Solvent caging and transition probabilities favor emission from structures with a small twist angle between the rings and without a pyramidal atom.

Dual Fluorescence of Fluorazene in Solution: A Computational Study.

The fluorazene molecule presents dual fluorescence in polar solvents. Its absorption and emission properties in gas phase and in acetonitrile solution have been studied theoretically using the complete active space second-order perturbation//complete active space self-consistent field quantum methodology and average solvent electrostatic potential from molecular dynamics for the solvent effects. In gas phase, two optimized excited-state geometries were obtained, one of them corresponds to a local excitation (LE), and the other is an intramolecular charge transfer (ICT) and lies higher in energy. In acetonitrile solution, a second ICT structure where the molecule remains planar is found, and the energy differences are reduced. Fluorescence energies from LE and the planar ICT have a good agreement with the experimental bands, but emission from the bent ICT has too low an energy.

Solvent Effects on the Radiative and Nonradiative Decay of a Model of the Rhodopsin Chromophore.

The radiative and nonradiative decay of a model with five double bonds of the 11-cis-retinal protonated Schiff base was studied both in vacuum and in methanol solution using an extended version of the averaged solvent electrostatic potential from molecular dynamics data (ASEP/MD) method that allows the location of crossing points between free energy surfaces both in equilibrium and in frozen solvent conditions. The multireference quantum method CASSCF was used for the description of the states of interest, while the solvent structure was obtained from molecular dynamics simulations. Electron dynamic correlation corrections to the energy were included at CASPT2 level. Unlike in gas phase, where only two states seem to be implicated, in methanol solution, three states are necessary to describe the photoisomerization process. At the Franck-Condon point the S1 and S2 states are almost degenerate; consequently, the S1 surface has a region with an ionic character ((1)Bu-like) and another one with a covalent character ((2)Ag-like). Emission from the ionic minima is responsible for the low-frequency part of the fluorescence band, while emission from the covalent minima originates the high-frequency part. The ionic minimum is separated from the conical intersection yielding the all-trans isomer by an energy barrier that was estimated in 0.7 kcal/mol. The geometry of the optimized conical intersection was found at a torsion angle of the central double bond close to 90° both in vacuum and in methanol solution. This large torsion in addition to the accompanying charge displacements forces a strong solvent reorganization during the de-excitation process which slows down the photoisomerization kinetics in methanol with respect to the gas phase. Solvent fluctuations modulate the minima depth and the barrier height and could explain the multiexponential relaxation time observed in the experiments.

What is solvatochromism?

Solvatochromism is commonly used in many fields of chemical and biological research to study bulk and local polarity in macrosystems (membranes, etc.), or even the conformation and binding of proteins. Despite its wide use, solvatochromism still remains a largely unknown phenomenon due to the extremely complex coupling of many different interactions and dynamical processes which characterize it. In this study we analyze the influence of different solvents on the photophysical properties of selected charge-transfer probes (4-AP, PRODAN, and FR0). The purpose is to achieve a microscopic understanding of the intermolecular effects which govern the absorption and fluorescence properties of solvated molecular probes, such as solvent-induced structural modifications, polarization effects, solubility, solute-solvent hydrogen-bonding interactions, and solute aggregation. To this aim we have exploited a time dependent density functional theory (TDDFT) approach coupled to complementary solvation approaches (continuum, discrete and mixed discrete and continuum). Such an integration has allowed us to clearly disentangle the complex interplay between specific and nonspecific interactions of the solvent with the probes and show that strong H-bonding effects not only can lead to large solvatochromic shifts but also can affect the nature of the emitting species with resulting reduction of the quantum yield.

Which strategy for molecular probe design? An answer from the integration of spectroscopy and QM modeling.

With this study we show that the maturity reached by quantum-mechanical (QM) modeling has allowed a new analytical approach to the design of molecular probes. In this approach, the strategy is to integrate suited computational tools with multi-spectroscopic measurements to identify specific signals for the characterization of the molecular probe with respect to the perturbation used and the environmental conditions applied. The application of the strategy to a typical optical probe (2-acetylanthracene) has allowed the identification of specific IR and NMR signals for the characterization of the conformational states in both solid and solution states. This analysis has been successively extended to the investigation of specific optical signals. In particular we have shown that the introduction of a substituent in specific positions of the aromatic structure induces a different perturbation in the different excited states of the precursor anthracene with consequent differentiations of the states with respect to their solvent sensitivity (both in terms of bulk and specific effects). Finally, the integration of simulated and experimental emission spectra has revealed a possible isomerization in the excited state with resulting change of the conformational state in the absorbing and the emitting species.

Theoretical study of the competition between intramolecular hydrogen bonds and solvation in the Cys-Asn-Ser tripeptide.

A study of the competition between intra- and intermolecular hydrogen bonds and its influence on the stability of the Cys-Asn-Ser tripeptide in aqueous solution was performed by using the averaged solvent electrostatic potential from molecular dynamics method (ASEP/MD). The model combines a DFT-B3LYP/6-311+G(d) quantum treatment in the description of the solute molecule with NVT molecular dynamics simulations in the description of the solvent. In gas phase, the most stable structure adopts a C5 conformation. Somewhat higher in energy are found the PP(II) and C7eq structures. In solution, the stability order of the different conformers is reversed: the PP(II) structure becomes the most stable, and the C5 structure is strongly destabilized. The conformational equilibrium is shifted toward conformations in which the intramolecular hydrogen bonds (IHB) have been substituted with intermolecular hydrogen bonds with the water molecules. The solvent stabilizes extended structures without IHBs that are not stable in vacuum. The effect of the protonation state on the conformational equilibrium was also analyzed.

A Subsystem TDDFT Approach for Solvent Screening Effects on Excitation Energy Transfer Couplings.

We present a QM/QM approach for the calculation of solvent screening effects on excitation-energy transfer (EET) couplings. The method employs a subsystem time-dependent density-functional theory formalism [J. Chem. Phys. 2007, 126, 134116] and explicitly includes solvent excited states to account for the environmental response. It is investigated how the efficiency of these calculations can be enhanced in order to treat systems with very large solvation shells while fully including the environmental response. In particular, we introduce a criterion to select solvent excited states according to their approximate contribution weight to the environmental polarization. As a model system, we investigate the perylene diimide dimer in a water cluster in comparison to a recent polarizable QM/MM method for EET couplings in the condensed phase [J. Chem. Theory Comput. 2009, 5, 1838]. A good overall agreement in the description of the solvent screening is found. Deviations can be observed for the effect of the closest water molecules, whereas the screening introduced by outer solvation shells is very similar in both methods. Our results can thus be helpful to determine at which distance from a chromophore environmental response effects may safely be approximated by classical models.

Fretting about FRET: failure of the ideal dipole approximation.

With recent growth in the use of fluorescence-detected resonance energy transfer (FRET), it is being applied to complex systems in modern and diverse ways where it is not always clear that the common approximations required for analysis are applicable. For instance, the ideal dipole approximation (IDA), which is implicit in the Förster equation, is known to break down when molecules get "too close" to each other. Yet, no clear definition exists of what is meant by "too close". Here we examine several common fluorescent probe molecules to determine boundaries for use of the IDA. We compare the Coulombic coupling determined essentially exactly with a linear response approach with the IDA coupling to find the distance regimes over which the IDA begins to fail. We find that the IDA performs well down to roughly 20 A separation, provided the molecules sample an isotropic set of relative orientations. However, if molecular motions are restricted, the IDA performs poorly at separations beyond 50 A. Thus, isotropic probe motions help mask poor performance of the IDA through cancellation of error. Therefore, if fluorescent probe motions are restricted, FRET practitioners should be concerned with not only the well-known kappa2 approximation, but also possible failure of the IDA.