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In this work, excited state ab initio molecular dynamics together with a time resolved vibrational analysis is employed to shed light on the vibrational photoinduced dynamics of a well-known diarylethene molecule experiencing a ring opening reaction upon electronic excitation. The photoreactivity of diarylethenes is recognized to be controlled by a non-adiabatic intersection point between the ground and the first excited state surfaces. The computation of an energy scan, along a suitable reaction coordinate, allows us to identify the region of potential energy surfaces in which the ground (S0) and the first excited (S1) state are well separated. The adiabatic sampling of that region in S1 shows that in the first 3 picoseconds, the central CC bond, which is subject to break, oscillates in an antiphase with respect to the energy gap ΔE(S1 - S0). A multiresolution analysis based on the wavelet transform was then applied to the structural parameters extracted from the excited state dynamics. The wavelet maps show characteristic oscillations of the frequencies, mainly CC stretching and CCC bending localized on the central 4-ring moiety. Moreover, we have identified the main frequency (methyl wagging motion) involved in the modulation of these oscillations. The anharmonic coupling within a group of vibrational modes was therefore highlighted, in good agreement with experimental evidence. For the first time, a quantitative analysis of time resolved signals from a wavelet transform/ab initio molecular dynamics approach was performed.

Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (alpha = 1.25) and lysozyme (alpha = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Delta(tau) = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.

We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.

The mechanism of base to base intermolecular proton shuttling occurring in the excited state proton transfer reaction between 7-hydroxy-4-(trifluoromethyl)coumarin (CouOH) and concentrated 1-methylimidazole base (1-MeId) in toluene solution is disclosed here by means of a computational approach based on Density Functional Theory (DFT) and Time Dependent DFT (TD-DFT). These methods allow us to characterize both the ground and excited state potential energy surfaces along the proton shuttling coordinate, and to assess the nature of the emitting species in the presence of an excess of 1-MeId. As a result, the tautomerism of CouOH is found to be photo-activated and, from a mechanistic point of view, the calculations clearly show that the overall driving force of the entire shuttling is the coumarin photoacidity, which is responsible for both the first proton transfer event and the strengthening of the following chain mechanism of base to base proton hopping.

In-chain donor/acceptor block copolymers comprised of alternating electron rich/poor moieties are emerging as promising semiconducting chromophores for use in organic photovoltaic devices. The mobilities of charge carriers in these materials are experimentally probed using gated organic field-effect transistors to quantify electron and hole mobilities, but a mechanistic understanding of the relevant charge diffusion pathways is lacking. To elucidate the mechanisms of electron and hole transport following excitation to optically accessible low-lying valence states, we utilize mean-field quantum electronic dynamics in the TDDFT formalism to explicitly track the evolution of these photo-accessible states. From the orbital pathway traversed in the dynamics, p- and n-type conductivities can be distinguished. The electronic dynamics of the studied polymers show the time-resolved transitions between the initial photoexcited state, a tightly-bound excitonic state that is dark to the ground state, and a partially charge separated state indicated by long-lived, out-of-phase charge oscillations along the polymer backbone. The frequency of these charge oscillations yields an insight into the characteristic mobilities of charge carriers in these materials. When the barycenters of the electron and hole densities are followed during the dynamics, a pseudo-classical picture for the translation of charge carrier densities along the polymer backbone emerges that clarifies a crucial aspect in the design of efficient organic photovoltaic materials.