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International audience; Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems. K E Y W O R D S density based indexes, density functional theory, electronic adiabaticity degree, non adiabatic coupling, proton coupled electron transfer

We study the absorption and emission electronic spectra in an aqueous solution of N-methyl-6-oxyquinolinium betaine (MQ), an interesting dye characterized by a large change of polarity and H-bond ability between the ground (S0) and the excited (S1) states. To that end we compare alternative approaches based either on explicit solvent models and density functional theory (DFT)/molecular-mechanics (MM) calculations or on DFT calculations on clusters models embedded in a polarizable continuum (PCM). In the first approach (ClMD), the spectrum is computed according to the classical Franck-Condon principle, from the dispersion of the time-dependent (TD)-DFT vertical transitions at selected snapshots of molecular dynamics (MD) on the initial state. In the cluster model (Qst) the spectrum is simulated by computing the quantum vibronic structure, estimating the inhomogeneous broadening from state-specific TD-DFT/PCM solvent reorganization energies. While both approaches provide absorption and emission spectral shapes in nice agreement with experiment, the Stokes shift is perfectly reproduced by Qst calculations if S0 and S1 clusters are selected on the grounds of the MD trajectory. Furthermore, Qst spectra better fit the experimental line shape, mostly in absorption. Comparison of the predictions of the two approaches is very instructive: the positions of Qst and ClMD spectra are shifted due to the different solvent models and the ClMD spectra are narrower than the Qst ones, because MD underestimates the width of the vibrational density of states of the high-frequency modes coupled to the electronic transition. On the other hand, both Qst and ClMD approaches highlight that the solvent has multiple and potentially opposite effects on the spectral width, so that the broadening due to solute-solvent vibrations and electrostatic interaction with bulk solvent is (partially) counterbalanced by a narrowing of the contribution due to the solute vibrational modes. Qst analysis evidences a pure quantum broadening effect of the spectra in water due to vibronic progressions along the solute/solvent H-bonds.

The fascinating world of Excited State Proton Transfer (ESPT) reactions is experiencing a renewed enthusiasm due to the advance of techniques such as the femtosecond stimulated Raman spectroscopy.[1] The theoretical-computational chemistry is challenged by this progress, and it is called for a new effort to interpret and, when possible, to forecast the experimental results. The simulations of excited and ground state PT share difficulties and limits related to the classical or quantum treatment of the proton dynamics, especially when methods rooted in Density Functional Theory (DFT) are considered. Moreover, other problems emerging from the photo-induced nature of the ESPT can be envisaged. These reactions are in fact triggered by the electronic and/or nuclear rearrangements upon excitation, and can be competitive with radiative and/or non radiative decay processes. This complexity can be critical for many ingredients of the modeling, starting from a proper characterization of different potential energy surfaces. This contribution is a flavor of our investigations of different ESPT reactions treated by time-dependent DFT. Our work is focused on two aspects of the ESPT simulation: the use of excited state ab-initio dynamics, and the set up of new kind of analysis capable to individuate promoting forces activated by the electronic excitation.[2,3] These tools exploit the definition of electronic density based indices, ad hoc designed to follow ESPT in a simple and effective manner.[3] Examples of application will be photo acid-base reactions in solvent and the excited state proton shuttle in fluorescent proteins.

This paper describes the extension of our computational strategy for pK predictions of small molecules to large solutes. The basic computational tool results from the coupling of quantum mechanical methods rooted in the density functional theory with the most recent version of the Polarizable Continuum Model. However, a third level is introduced, which includes solute regions far from the reactive center, which are described at a simplified level. This partition, together with the recent implementation of fast cavity generation, powerful iterative solvers, and fast multipole technology, allows us to tackle solutes of the dimension of a small protein. The problems and perspectives of this methodology are analyzed with special reference to the behavior of different Polarizable Continuum Model versions on the challenging playground represented by the pK's of the different histidine residues occurring in the human prion protein.

Photoinduced charge transfer (CT) excited states and their relaxation mechanisms can be highly interdependent on the environment effects and the consequent changes in the electronic density. Providing a molecular interpretation of the ultrafast (subpicosecond) interplay between initial photoexcited states in such dense electronic manifolds in condensed phase is crucial for improving and understanding such phenomena. Real-time time-dependent density functional theory is here the method of choice to observe the charge density, explicitly propagated in an ultrafast time domain, along with all time-dependent properties that can be easily extracted from it. A designed protocol of analysis for real-time electronic dynamics to be applied to time evolving electronic density related properties to characterize both in time and in space CT dynamics in complex systems is here introduced and validated, proposing easy to be read cross-correlation maps. As case studies to test such tools, we present the photoinduced charge-transfer electronic dynamics of 5-benzyluracil, a mimic of nucleic acid/protein interactions, and the metal-to-ligand charge-transfer electronic dynamics in water solution of [Ru(dcbpy)2(NCS)2]4-, dcbpy = (4,4'-dicarboxy-2,2'-bipyridine), or "N34-", a dye sensitizer for solar cells. Electrostatic and explicit ab initio treatment of solvent molecules have been compared in the latter case, revealing the importance of the accurate modeling of mutual solute-solvent polarization on CT kinetics. We observed that explicit quantum mechanical treatment of solvent slowed down the charge carriers mobilities with respect to the gas-phase. When all water molecules were modeled instead as simpler embedded point charges, the electronic dynamics appeared enhanced, with a reduced hole-electron distance and higher mean velocities due to the close fixed charges and an artificially increased polarization effect. Such analysis tools and the presented case studies can help to unveil the influence of the electronic manifold, as well as of the finite temperature-induced structural distortions and the environment on the ultrafast charge motions.

Fluorescent Proteins are widely studied for their multiple applications in technological and biotechnological fields. Despite this, they continue to represent a challenge in terms of a complete understanding of all the non-equilibrium photo-induced processes that rule their properties. In this context, a theoretical-computational approach can support experimental results in unveiling and understanding the processes taking place after electronic excitation. A non-standard cyan fluorescent protein, psamFP488, is characterized by an absorption maximum that is blue-shifted in comparison to other cyan fluorescent proteins. This protein is characterized by an extended Stokes shift and an ultrafast (170 fs) excited state proton transfer. In this work, a theoretical-computational study, including excited state ab initio dynamics, is performed to help understanding the reaction mechanism and propose new hypotheses on the role of the residues surrounding the chromophore. Our results suggest that the proton transfer could be indirect toward the acceptor (Glu167) and involves other residues surrounding the chromophore, despite the ultrafast kinetics.

Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.

Light induces non-equilibrium time evolving molecular phenomena. The computational modeling of photo-induced processes in large systems, embedded in complex environments (i.e., solutions, proteins, materials), demands for a quantum and statistical mechanic treatment to achieve the required accuracy in the description of both the excited-state energy potentials and the choice of the initial conditions for dynamical simulations. On the other hand, the theoretical investigation on the atomistic scale of times and sizes of the ultrafast photo-induced reactivity and non-equilibrium relaxation dynamics right upon excitation requests tailored computational protocols. These methods often exploit hierarchic computation schemes, where a large part of the degrees of freedom are required to be treated explicitly to achieve the right accuracy. Additionally, part of the explicit system needs to be treated at ab initio level, where density functional theory, using hybrid functionals, represents a good compromise between accuracy and computational cost, when proton transfers, non-covalent interactions, and hydrogen bond dynamics play important roles. Thus, the modeling strategies presented in this review stress the importance of hierarchical quantum/molecular mechanics with effective non-periodic boundary conditions and efficient phase-sampling schemes to achieve chemical accuracy in ultrafast time-resolved spectroscopy and photo-induced phenomena. These approaches can allow explicit and accurate treatment of molecule/environment interactions, including also the electrostatic and dispersion forces of the bulk. At the same time, the specificities of the different case studies of photo-induced phenomena in solutions and biological environments are highlighted and discussed, with special attention to the computational and modeling challenges.

By coupling an enhanced sampling algorithm with an orbital-localized variant of Car-Parrinello molecular dynamics, the so-called atomic centered density matrix propagation model, we reconstruct the free energy profiles along reaction pathways using different density functional approximations (DFAs) ranging from locals to hybrids. In particular, we compare the computed free energy barrier height of proton transfer (PT) reactions to those obtained by a more traditional static approach, based on the intrinsic reaction coordinate (IRC), for two case systems, namely malonaldehyde and formic acid dimer. The obtained results show that both the IRC profiles and the potentials of mean force, derived from biased dynamic trajectories, are very sensitive to the density functional approximation applied. More precisely, we observe that, with the notable exception of M06-L, local density functionals always strongly underestimate the reaction barrier heights. More generally, we find that also the shape of the free energy profile is very sensitive to the density functional choice, thus highlighting the effect, often neglected, that the choice of DFA has also in the case of dynamics simulations.

The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results [Mathies, R. A.; et al. J. Phys. Chem. A 2018, 122 (14), 3594] was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the C═C axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central C═C and C≡N bonds, compared to the isolated case. An important red shift of the C═C stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear C═C axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.

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.

Advances in time resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab-initio molecular dynamics within a hybrid quantum mechanical/molecular mechanics framework and a time resolved vibrational analysis based on the wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm-1. We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm-1and the deformation at 280 cm-1are photoactivated since the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favouring the step preparatory for the photoreactivity.

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.

We simulated for the first time the oxygen-oxygen bond formation in a synthetic calcium-tetra manganese complex recently developed by Zhang and co-workers. In spite of promising structural similarities to the native oxygen evolving complex (OEC) in Photosystem II, several uncertainties on the mimic stability in water and on its potential catalytic activity still persist. Here, we characterized at density functional theory level the electronic and structural features of the Sn states of the complex, along with the oxygen-oxygen bond formation reaction, proposing a reasonable model for the hydrate complex. As a main finding, both the synthetic compound and the natural OEC show very close energetic barriers for the oxo-oxyl coupling process, suggesting that key electronic features of the natural OEC reactivity are well reproduced. This result strongly encourages the use of this synthetic complex in combination with other molecular assemblies for the design of successful artificial leaves.

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S0) and first singlet excited state (S1), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S1, the GFP proton transfer becomes favored, with respect to S0, as suggested by the experimental evidence. As an important finding, this change is strictly related to the rearrangement of the hydrogen bond network composing the reaction path, which, in S1, relaxes to a tighter and planar configuration, as a consequence of the photoinduced relaxation in the GFP chromophore structure, thus prompting more effectively for the proton shuttle. Therefore, we give an unprecedented direct proof of the key role played by the photoinduced structural relaxation of the GFP on the chromophore photoacidity, validating, in particular, the hypothesis of Fang and co-workers [Nature 2009, 462, 200].

The formation of polaron pairs is one of the important photophysical processes that take place after the excitation in semiconducting organic polymers. First-principles Ehrenfest excited-state dynamics is a unique tool to investigate ultrafast photoinduced charge carrier dynamics and related nonequilibrium processes involving correlated electron-nuclear dynamics. In this work the formation of polaron pairs and their dynamical evolution in an oligomer of seven thiophene units is investigated with a combined approach of first-principles exciton-nuclear dynamics and wavelet analysis. The real-time formation of a polaron pair can be observed in the dipole evolution during the excited-state dynamics. The possible driving force of the polaron pair formation is investigated through qualitative correlation between the structural dynamics and the dipole evolution. The time-dependent characteristics and spectroscopic consequences of the polaron pair formation are probed using the wavelet analysis.

The growing production of biodiesel as a promising alternative and renewable fuel led as the main problem the dramatic increase of its by-product: glycerol. Different strategies for glycerol derivatization have been reported so far, some more efficient or sustainable than others. Herein, we report a very promising and eco-friendly transformation of glycerol in nontoxic solvents and chemicals (i.e., solketal, ketals), proposing three new families of Fe(III) compounds capable of catalysing glycerol acetalization with unpublished turn over frequencies (TOFs), and adhering most of the principles of green chemistry. The comparison between the activity of complexes of formula [FeCl3(1-R)] (1-R = substituted pyridinimine), [FeCl(2-R,R′)] (2-R,R′ = substituted O,O′-deprotonated salens) and their corresponding simple salts reveals that the former are extremely convenient because they are able to promote solketal formation with excellent TOFs, up to 105 h–1. Satisfactory performances were shown with respect to the entire range of substrates, with results being competitive to those reported in the literature so far. Moreover, the experimental activity was supported by an accurate and complete ab initio study, which disclosed the fundamental role of iron(III) as Lewis acid in promoting the catalytic activity. The unprecedented high activity and the low loading of the catalyst, combined with the great availability and the good eco-toxicological profile of iron, foster future applications of this catalytic process for the sustainable transformation of an abundant by-product in a variety of chemicals.

The detailed knowledge of excited state proton transfer mechanisms in complex environments is of paramount importance in chemistry. However, the definition of an effective reaction coordinate and the understanding of the driving force of the reaction can be difficult from both the experimental and the theoretical points of view. Here we analyzed by theoretical approaches the mechanism and the driving forces of the excited state proton transfer reaction occurring between the 7-hydroxy-4-(trifluoromethyl)coumarin photoacid and the 1-methylimidazole base molecules in toluene solution. In particular, we compared the intrinsic and the dynamical reaction pathways, obtained by integrating the reaction coordinate, and by performing ab initio simulations of molecular dynamics, respectively. Time-dependent density functional theory and polarizable solvation continuum models were adopted to define the excited state potential energy surface. Results were analyzed by means of the D(CT) electronic density based index. Our findings suggest that the reaction coordinate is mainly composed of several intra- and intermolecular modes of the reactants. An analysis of both the intrinsic coordinate and the dynamical results shows that the charge transfer induced by electronic excitation of the coumarin molecule is the main proton transfer driving force. With regards to the methodological validation, the combination of ab initio molecular dynamics with time-dependent density functional theory appears to be feasible and reliable to study excited state proton transfer reactions in the condensed phase.

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.

The excited state proton transfer (ESPT) reaction taking place between 7-hydroxy-4-(trifluorometyl)coumarin and 1-methylimidazole, recently experimentally characterized, has been here considered as a case study to illustrate the possibility of using theoretical approaches rooted in density functional theory (DFT) and time-dependent DFT (TD-DFT) for the description of complex reactions occurring at the excited state. In particular, beside identifying all stable species occurring at the ground and excited state during the ESPT reaction, a quantitative characterization of their photophysical properties, such as absorption and emission, is obtained by properly including solvent effects. More interestingly, a computational protocol enabling one to locate possible reaction pathways for the ESPT is here proposed. This protocol is based on the use of density based indices purposely developed to characterize the properties of vertical and relaxed excited states which allow one to discriminate the most favorable reaction paths on potential energy surfaces that are in the case of ESPT intrinsically very flat and difficult to characterize based on sole energy criteria, thus opening a new scenario for the description of photoinduced proton transfer reactions.

In this study, we analyze the photophysics of the N-methyl-6-oxyquinolinium betaine (MQ) solvatochromic dye in aqueous solution, focussing on the important structural rearrangement of its first solvation shell following the electronic excitation, which is characterized by a strong charge transfer. To this aim, we compare the results provided by ground- and excited-state ab-initio molecular dynamics with that of full QM calculations on clusters including a small number of solvent molecules (from 1 to 4), taking into account bulk solvent effects by the Polarizable Continuum Model. The two methods agree in predicting that while in the ground electronic state between three and four water molecules are strongly coordinated to the oxygen atom of MQ, in the excited state two water molecules are present in the first solvation layer of the MQ oxygen. Vertical excitation and emission energies computed on the structures provided by the two approaches allow for estimates of the Stokes shift consistent with the experimental results. On the ground of the present results, some general considerations on the advantages and limitations of the dynamical and static approaches in describing a photoactivated process in solution are proposed.

A new descriptor tool enabling to qualitatively identify excited-state potential energy regions with high decay probability is here disclosed and applied to analyze a photoinduced ring-opening reaction already well characterized from the experimental and theoretical point of view. The analysis based on such descriptor allows one to highlight a high probability of excited-state deactivation within the Franck–Condon region, in agreement with experiments, and to qualitatively indentify the main mechanisms providing efficient pathways of photoreactivity.

The photophysical signature of the tautomeric species of the asymmetric (N,N-dimethylanilino)-1,3-diketone molecule are investigated using approaches rooted in density functional theory (DFT) and time-dependent DFT (TD-DFT). In particular, since this molecule, in the excited state, can undergo proton transfer reactions coupled to intramolecular charge transfer events, the different radiative and nonradiative channels are investigated by making use of different density-based indexes. The use of these tools, together with the analysis of both singlet and triplet potential energy surfaces, provide new insights into excited-state reactivity allowing one to rationalize the experimental findings including different behavior of the molecule as a function of solvent polarity.

In spite of the detailed information provided by advanced time-resolved spectroscopy, the understanding of the excited-state proton transfer (ESPT) reactivity remains difficult to obtain at molecular level. In this work we studied three photoacids showing different strength: the 8-hydroxy-1,3,6-pyrenetrisulfonate weak photoacid, the N-methyl-6-hydroxyquinolinium strong photoacid and the phenol-carboxyether dipicolinium cyanine (QCy9) superphotoacid, focusing on the intermolecular ESPT toward a solvent molecule or a base molecule in aqueous solution. To this aim, the ground and the first singlet excited-state potential energy surfaces of the three systems were characterized by means of the time-dependent density functional theory and a hybrid implicit/explicit model of the solvent. Main structural and photophysical features of the photoacids were assessed and satisfactorily compared with the experimental data. Energy profiles along the PT coordinate were analyzed in both the electronic states. We reproduced many important features of the photoacidity experimentally observed. The results suggest that the relative strength is mainly due to the different extent of charge transfer caused by the electronic transition in proximity of the acid group. Remarkably, we found that even in the case of the strongest photoacid (QCy9), showing a ESPT rate as rapid as to escape the solvent dynamics control, the PT is modulated and supported by the first solvation shell of the proton-accepting molecule. However, a complete understanding of this fascinating field needs the full account for the electronic and the molecular dynamics in play at different timescales.

In the present work, the general liquid optimized boundary (GLOB) model, which is a discrete/continuum approach for molecular simulations of liquids and solutions, has been extended to include a pressure coupling algorithm based on an extended phase-space scheme. To this end, a definition of the instantaneous pressure for a microscopic system has been derived from the minimum energy principle for the Helmholtz free energy. Applications to a pure liquid, such as water, and an aqueous solution of myoglobin are presented and the results are compared to those obtained using standard periodic boundary conditions (PBC).

In this work, the GLOB model, an effective and reliable computational approach well suited for ab initio and QM/MM molecular dynamics simulations of complex molecular systems in solution, has been applied to study two representative open-shell systems, the cobalt(II) ion and the glycine radical in aqueous solution, with special reference to their structural and magnetic properties. The main structural features of the solvent cage around the cobalt ion and the hydrogen bonding patterns around the neutral and zwitterionic forms of the glycine radical have been investigated in some detail. The general good agreement with experiments supports the use of the present model to investigate more challenging and biological/technological relevant open-shell systems.

Semi-empirical correction to density functional theory for dispersion (DFT-D) has been implemented for energies, analytical gradients, and Hessians in order to explore potential energy surfaces by means of a complete set of first-principle methods. The impact of non-bonding interactions on structures, binding energies and zero-point energy contributions as well as on ab initio molecular dynamics trajectories have been investigated for the well known case of benzene dimer. While the static results are in remarkable agreement with the most sophisticated post-Hartree–Fock approaches, the low cost of DFT-D allows to unravel dynamical aspects too, which are mandatory for situations ruled by weak interactions.