M. Elena Martín

Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology

The ASEP/MD method has been employed for studying the solvent effect on the conformational equilibrium of the alanine dipeptide in water solution. MP2 and density functional theory (DFT) levels of theory were used and results were compared. While in gas phase cyclic structures showing intramolecular hydrogen bonds were found to be the most stable, the stability order is reversed in water solution. Intermolecular interaction with the solvent causes the predominance of extended structures as the stabilizing contacts dipeptide-water are favoured. Free-energy differences in solution were calculated and PPII, α(R), and C5 conformers were identified as the most stable at MP2 level. Experimental data from Raman and IR techniques show discrepancies about the relative abundance of α(R) y C5, our results support the Raman data. The DFT level of theory agrees with MP2 in the location and stability of PPII and α(R) forms but fails in the location of C5. MP2 results suggest the possibility of finding traces of C7eq conformer in water solution, in agreement with recent experiments.

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.

Retinal Models: Comparison of Electronic Absorption Spectra in the Gas Phase and in Methanol Solution

An accurate study on several models of the 11-cis-retinal protonated Schiff base (PSB) has been performed both in vacuo and in methanol solution. Condensed phase calculations have been carried out making use of the ASEP/MD method, which permits the employment of the same high-level ab initio calculations usually applied in gas phase studies as well as a detailed description of the solvent structure around the solute through molecular dynamics simulations of the complete system. The solute structure was completely optimized in vacuo and in solution at the CASSCF level and/or MP2 level, and the CASPT2 method was applied for the calculation of the vertical transition energies and solvent shift values. Our results reproduce and explain the main features of the experimental absorption spectra of the 11-cis-retinal PSB. Two well-resolved bands can be identified in vacuo (separated by roughly 1.0 eV), whereas only a single broad band is observed in solution. This fact is explained by the existence of two almost degenerate excited states in methanol. The inclusion of two methyl groups at the iminium end of the system permits the reproduction of the experimental solvent shift value.

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.

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.

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.

Conformational Changes of the Alanine Dipeptide in Water-Ethanol Binary Mixtures.

Experimental work developed in the last years has evidenced the capacity of alcohols and polyalcohols to modify the energy landscape of peptides and proteins. However, the mechanism underlying this effect is not clear. Taking as a model system the alanine dipeptide (AD) we perform a QM/MM study in water, ethanol, and a 40-60% in volume water-ethanol mixture. The AD molecule was described at the MP2/aug-cc-pVDZ level. In polar solution, only αR and PPII conformers contribute in an appreciable way to the conformational equilibrium. The final in solution αR-PPII free energy difference is determined from the interplay between the internal energy of the dipeptide and the solute-solvent interaction free energy. Internal energy favors the formation of PPII, whereas, on the contrary, solute-solvent interaction is favorable to αR, so any factor that decreases the solute-solvent interaction free energy will increase the PPII population. The addition of ethanol increases the stability of the PPII conformer. Our results point to the presence of preferential solvation in this system, the composition of the first solvation shell in the binary mixture being dominated by water molecules. Remarkably, this fact does not affect the differential conformational stability that is controlled by long-range interactions. From the analysis of solvent density maps it is concluded that, in the water-ethanol mixture, ethanol molecules are more likely found around the alanine side chain and the carbonyl group, but while in PPII ethanol molecules interact mainly with the carbonyl group of the N-terminal end, in C5 the interaction is with the carbonyl group of the C-terminal end. In αR, ethanol interacts with both carbonyl groups.

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 CIβ 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.

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.

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.