Ricard Gelabert

Semiclassical description of quantum coherence effects and their quenching: A forward-backward initial value representation study

The forward–backward (FB) version of the semiclassical (SC) initial value representation (IVR) is used to study quantum coherence effects in the time-dependent probability distribution of an anharmonic vibrational coordinate and its quenching when coupled to a thermal bath. It is shown that the FB-IVR accurately reproduces the detailed quantum coherent structure in the weak coupling regime, and also describes how this coherence is quenched with an increase of the system–bath coupling and/or the bath temperature. Comparisons are made with other approximations and the physical implications are discussed.

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a (pi,pi( *)) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet (pi,pi( *)) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.

Semiclassical description of diffraction and its quenching by the forward–backward version of the initial value representation

It is shown that the forward–backward (FB) version of the semiclassical (SC) initial value representation (IVR) is able to describe quantum interference/coherence (i.e., diffraction) of particles transmitted by a two-slit potential. (In contrast, the linearized approximation to the SC-IVR, which leads to the classical Wigner model, is unable to do so.) FB-IVR calculations are also used to describe the (partial) quenching of this interference structure (i.e., “de-coherence”) when the two-slit potential is coupled to a bath of harmonic oscillators.

Operation of the Proton Wire in Green Fluorescent Protein. A Quantum Dynamics Simulation

A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent protein has been carried out on a high-quality, high-dimensionality potential energy surface describing the photoactive pipi* excited state, and including motion of both the three protons and of the donor and acceptor atoms of the hydrogen bonds in a closed proton wire. The results of the simulations show that proton transfer along the wire is essentially concerted, synchronous, and very fast, with a substantial amount of the green fluorescent species forming within several tens of femtoseconds. In this regard, analysis of the population of the fluorescent species indicates that at least two dynamical regimes are present for its formation. Within the first hundreds of femtoseconds, dynamics is very fast and impulsive. Later on, a slower pace of formation appears. It is discussed that the two largest decay times for the protonated chromophore reported experimentally (Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8362-8367) might correspond to some irreversible process occurring after formation of the fluorescent species, rather than to cleavage of the chromophores phenolic O-H bond.

Are there really low-barrier hydrogen bonds in proteins? The case of photoactive yellow protein.

For a long time, low-barrier hydrogen bonds (LBHBs) have been proposed to exist in many enzymes and to play an important role in their catalytic function, but the proof of their existence has been elusive. The transient formation of an LBHB in a protein system has been detected for the first time using neutron diffraction techniques on a photoactive yellow protein (PYP) crystal in a study published in 2009 (Yamaguchi, S.; et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 440-444). However, very recent theoretical studies based on electronic structure calculations and NMR resonance experiments on PYP in solution (Saito, K.; et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 167-172) strongly indicate that there is not such an LBHB. By means of electronic structure calculations combined with the solution of the nuclear Schrödinger equation, we analyze here under which conditions an LBHB can exist in PYP, thus leading to a more reasonable and conciliating understanding of the above-mentioned studies.

Electronic and quantum dynamical insight into the ultrafast proton transfer of 1-hydroxy-2-acetonaphthone.

The ultrafast proton-transfer dynamics of 1-hydroxy-2-acetonaphthone has been theoretically analyzed in the ground and first singlet excited electronic states by density functional theory calculations and quantum dynamics. The potential energies obtained in the ground electronic state reveal that the proton-transfer process does not lead to a stable keto tautomer unless the transfer of the hydrogen from the enol form is accompanied by an internal rotation of the newly formed O-H bond. Calculations in the first singlet excited electronic state point to a very low barrier for the formation of the keto tautomer. The analysis of the calculated frequencies of the two tautomers in the excited state unveils a coupling of the skeletal motions (low frequency modes) with the proton-transfer process, as it has been stated from time-resolved experiments. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform an exact quantum dynamics study of the process. Our results show that the proton-transfer process is completed within 25.5 fs, in remarkable good agreement with experiments.

Unveiling how an archetypal fluorescent protein operates: theoretical perspective on the ultrafast excited state dynamics of GFP variant S65T/H148D.

Green fluorescent protein variant S65T/H148D has been reported to host a photocycle involving the photoinduced proton transfer reaction between the chromophore and residue Asp148 under 50 fs and without a measurable kinetic isotope effect, and experimental evidence is suggestive of the existence of a highly delocalized proton between these residues. The blinding speed at which this biological system undergoes proton transfer has been ascribed to the extreme increase of acidity of the GFP chromophore in the electronic excited state where proton transfer takes place. This work strives to present a coherent, complete, and balanced description of the dynamics of this specific variant of GFP in which it will be shown that this increase of acidity is insufficient to explain the behavior observed. This study tracks the behavior of this photosystem to the delicate interplay between structure and dynamics shown in the presence of solvent. In this way, it has been found that the dynamics of this protein intertwines its structure with the intervening solvent to give rise to effectively degenerate situations in what concerns the reactants and products of the proton transfer reaction in ground and, most importantly, photoexcited state, in terms of potential energy profiles associated with the proton migration. Under these conditions, proton transfer can occur in accordance with the experimental data available. This set of characteristics is possibly common to a host of other proton transfer based fluorescent proteins, and helps promoting GFP S65T/H148D to a case of archetypal significance. Thus, our results can be useful to understand the way many fluorescent proteins work and, more generally, the molecular basis for proton transfer reactions in proteins.

How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima

The absorption spectrum of a fluorescent protein is determined by its chromophore, but the residues that surround it also have a remarkable role, leading to noticeable spectral shifts. We have theoretically analyzed the monomeric protein Keima (mKeima), a red fluorescent protein most remarkable for an outstanding difference between the absorption and emission frequencies, and potentially suited for multicolor imaging applications. In the present work, we have performed excited state electronic calculations on the chromophore with an increasing number of atoms surrounding it, and we have compared these results with the excited states calculations on an ensemble of structures obtained from a molecular dynamics simulation of the complete protein. The importance of the inclusion of the effects of the whole protein in the electronic calculations has been proved, and it is concluded that only with the consideration of the thermal effects can the absorption spectra of the protein be properly characterized.

Peek at the potential energy surfaces of the LSSmKate1 and LSSmKate2 proteins.

To determine the energetic feasibility of the mechanisms involved in the generation of the fluorescent species in red fluorescent proteins LSSmKate1 and LSSmKate2 developed by Piatkevich et al. (Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5369-5374 and J. Am. Chem. Soc. 2010, 132, 10762-10770), a potential energy scan for the respective reaction coordinates was performed in large cluster models including the surroundings of the chromophores, based on the respective crystallographic structures, using DFT and TDDFT. The predicted absorption wavelengths agree to within 5 nm with experiment, thus confirming the accuracy of the calculational level and modeling done. In both proteins, it was found that the adiabatic electronic state with the largest oscillator strength at the Franck-Condon region was not the one from which fluorescence could occur in the products. A diabatization procedure was used to determine an approximate photoactive state, based on selecting the state with the largest oscillator strength throughout. For LSSmKate1, this led to a rather flat potential energy profile but still did not predict a minimum in the product side. It is suggested that relaxation processes, absent from the model, could bring about such a minimum. LSSmKate2, on the other hand, clearly displays a favorable exoergic process in the photoactive state, and its double-proton transfer can be described as concerted but highly asynchronous, involving a barrier in the transfer of the first proton. In this way, the model provides strong support for the mechanism proposed for LSSmKate2.

Exploring the effects of intramolecular vibrational energy redistribution on the operation of the proton wire in green fluorescent protein.

The operation of the proton wire in Green Fluorescent Protein has been simulated by quantum dynamics and considering the coupling to the protein environment by means of a bath of harmonic oscillators. The simulation consists of 36 explicit and fully quantum degrees of freedom: 6 degrees of freedom represent the configuration of the proton wire, which are coupled to 30 bath coordinates. Regimes of weak and strong coupling have been studied. It is found that presence of the bath induces a fast energy transfer from the proton wire to the bath, with characteristic times under 400 fs. This internal vibrational redistribution happens at the expense of the potential energy content of the proton wire, deformed through the interaction to the bath from its uncoupled state. Strong coupling induces a slowing-down of the operation of the wire because it hinders to some extent the approaching of donor and acceptor atoms to distances in which proton transfer can occur. Internal vibrational energy redistribution affects the dynamics, but from our simulations we conclude that it cannot be the only cause responsible for the experimentally reported fluorescence rise times.