Photoisomerization of Spiropyran in Solution: A Surface Hopping Investigation.

We performed a computational investigation of the photoisomerization of an unsubstituted spiropyran in solution using surface hopping molecular dynamics simulations in a semiempirical framework. To bring out the solvent effects on the excited state dynamics, we have run simulations in three different environments: chloroform, methanol, and ethylene glycol. We show that the interaction with a moderately polar solvent such as chloroform has little effect on the dynamics when compared to vacuum results previously obtained by our group. At variance, the interaction with the protic solvents considered considerably affects the reaction mechanism, the quantum yield, and the excited state lifetimes.

Investigating the Photodynamics of trans-Azobenzene with Coupled Trajectories.

In this work, we present the first implementation of coupled-trajectory Tully surface hopping (CT-TSH) suitable for applications to molecular systems. We combine CT-TSH with the semiempirical floating occupation molecular orbital-configuration interaction electronic structure method to investigate the photoisomerization dynamics of trans-azobenzene. Our study shows that CT-TSH can capture correctly decoherence effects in this system, yielding consistent electronic and nuclear dynamics in agreement with (standard) decoherence-corrected TSH. Specifically, CT-TSH is derived from the exact factorization and the electronic coefficients' evolution is directly influenced by the coupling of trajectories, resulting in the improvement of internal consistency if compared to standard TSH.

Ultrafast excited-state dynamics of Luteins in the major light-harvesting complex LHCII.

Carotenoid pigments are known to present a functional versatility when bound to light-harvesting complexes. This versatility originates from a strong correlation between a complex electronic structure and a flexible geometry that is easily tunable by the surrounding protein environment. Here, we investigated how the different L1 and L2 sites of the major trimeric light-harvesting complex (LHCII) of green plants tune the electronic structure of the two embedded luteins, and how this reflects on their ultrafast dynamics upon excitation. By combining molecular dynamics and quantum mechanics/molecular mechanics calculations, we found that the two luteins feature a different conformation around the second dihedral angle in the lumenal side. The s-cis preference of the lutein in site L2 allows for a more planar geometry of the π -conjugated backbone, which results in an increased degree of delocalization and a reduced excitation energy, explaining the experimentally observed red shift. Despite these remarkable differences, according to surface hopping simulations the two luteins present analogous ultrafast dynamics upon excitation: the bright S 2 state quickly decays (in ∼ 50 fs) to the dark intermediate S x , eventually ending up in the S 1 state. Furthermore, by employing two different theoretical approaches (i.e., Förster theory and an excitonic version of surface hopping), we investigated the experimentally debated energy transfer between the two luteins. With both approaches, no evident energy transfer was observed in the ultrafast timescale.

The radiative surface hopping (RSH) algorithm: Capturing fluorescence events in molecular systems within a semi-classical non-adiabatic molecular dynamics framework.

In this article, we present the radiative surface hopping algorithm, which enables modeling fluorescence within a semi-classical non-adiabatic molecular dynamics framework. The algorithm has been tested for the photodeactivation dynamics of trans-4-dimethylamino-4'-cyanostilbene (DCS). By treating on equal footing the radiative and non-radiative processes, our method allows us to attain a complete molecular movie of the excited-state deactivation. Our dynamics rely on a semi-empirical quantum mechanical/molecular mechanical Hamiltonian and have been run for hundreds of picoseconds, both in the gas phase and in isopropyl ether. The proposed approach successfully captures the first fluorescence processes occurring in DCS, and it succeeds in reproducing the experimental fluorescence lifetime and quantum yield, especially in the polar solvent. The analysis of the geometrical features of the emissive species during the dynamics discards the hypothesis of a twisted intramolecular charge transfer state to be responsible for the dual emission observed experimentally in some polar solvents. In a nutshell, our method opens the way for theoretical studies on early fluorescence events occurring up to hundreds of picoseconds in molecular systems.

Effect of Initial Conditions Sampling on Surface Hopping Simulations in the Ultrashort and Picosecond Time Range. Azomethane Photodissociation as a Case Study.

We tested the effect of different ways of sampling the initial conditions in surface hopping simulations, with a focus on the initial energy distributions and on the treatment of the zero point energy (ZPE). As a test case, we chose the gas phase photodynamics of azomethane, which features different processes occurring in overlapping time scales: geometry relaxation in the excited state, internal conversion, photoisomerization, and fast and slow dissociation. The simulations, based on a semiempirical method, had a sufficiently long duration (10 ps) to encompass all of the above processes. We tested several variants of methods based on the quantum mechanical (QM) distributions of the nuclear coordinates q and momenta p, which yield, at least on the average over a large sampling set, the correct QM energy, namely the ZPE when starting from the ground vibrational state. We compared the QM samplings with the classical Boltzmann (CB) distribution obtained by a thermostated trajectory, whereby thermal effects are taken into account, but the ZPE is utterly ignored. We found that most QM and CB approaches yield similar results as to short time dynamics and decay lifetimes, whereas the rate of the ground state dissociation reaction CH3NNCH3 → CH3NN + CH3 is sharply affected by the sampling method. With QM samplings a large fraction of trajectories dissociate promply (<1 ps) after decay to the ground state and with rates of the order of 10-1 ps-1 after the first ps. Instead, the CB samplings yield a much smaller fraction of prompt dissociations and much lower rates at long times. We provided evidence that the ZPE "leaks" from high frequency modes to the reactive ones (N-C bond elongations), therefore unphysically increasing the dissociation rates with QM samplings. We show that an effective way to take into account the ZPE and to avoid the "leaking" problem is to add the ZPE to the potential energy surfaces as a function of the most relevant internal coordinates. Then, Boltzmann sampling can be done as usual, so this approach is suitable also for condensed state dynamics. In the tests we present here, the ZPE correction method yields dissociation rates intermediate between QM and uncorrected Boltzmann samplings.

Dual photoisomerization mechanism of azobenzene embedded in a lipid membrane.

The photoisomerization of chromophores embedded in biological environments is of high importance for biomedical applications, but it is still challenging to define the photoisomerization mechanism both experimentally and computationally. We present here a computational study of the azobenzene molecule embedded in a DPPC lipid membrane, and assess the photoisomerization mechanism by means of the quantum mechanics/molecular mechanics surface hopping (QM/MM-SH) method. We observe that while the trans-to-cis isomerization is a slow process governed by a torsional mechanism due to the strong interaction with the environment, the cis-to-trans mechanism is completed in sub-ps time scale and is governed by a pedal-like mechanism in which both weaker interactions with the environment and a different geometry of the potential energy surface play a key role.

Frenkel exciton photodynamics of self-assembled monolayers of azobiphenyls.

We performed computational simulations of the photodynamics of a self-assembled monolayer (SAM) of an azobenzene derivative (azobiphenyl, ABPT) on a gold surface. An excitonic approach was adopted in a semiempirical framework, which allowed us to consider explicitly the electronic degrees of freedom of 12 azobenzene chromophores. The surface hopping scheme was used for nonadiabatic molecular dynamics simulations. According to our results for an all trans-ABPT SAM, the excitation energy transfer between different chromophores, very fast in the ππ∗ manifold, does not occur between nπ∗ states. As a consequence, the excitation transfer does not play an important role in the quenching of the azobenzene photoisomerization in the SAM (experimentally observed and reproduced by our calculations) which, instead, has to be attributed to steric effects.

Protein control of photochemistry and transient intermediates in phytochromes.

Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.

Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles.

Newton-X is an open-source computational platform to perform nonadiabatic molecular dynamics based on surface hopping and spectrum simulations using the nuclear ensemble approach. Both are among the most common methodologies in computational chemistry for photophysical and photochemical investigations. This paper describes the main features of these methods and how they are implemented in Newton-X. It emphasizes the newest developments, including zero-point-energy leakage correction, dynamics on complex-valued potential energy surfaces, dynamics induced by incoherent light, dynamics based on machine-learning potentials, exciton dynamics of multiple chromophores, and supervised and unsupervised machine learning techniques. Newton-X is interfaced with several third-party quantum-chemistry programs, spanning a broad spectrum of electronic structure methods.

Ultrafast Excited-State Dynamics of Carotenoids and the Role of the SX State.

Carotenoids are natural pigments with multiple roles in photosynthesis. They act as accessory pigments by absorbing light where chlorophyll absorption is low, and they quench the excitation energy of neighboring chlorophylls under high-light conditions. The function of carotenoids depends on their polyene-like structure, which controls their excited-state properties. After light absorption to their bright S2 state, carotenoids rapidly decay to the optically dark S1 state. However, ultrafast spectroscopy experiments have shown the signatures of another dark state, termed SX. Here we shed light on the ultrafast photophysics of lutein, a xanthophyll carotenoid, by explicitly simulating its nonadiabatic excited-state dynamics in solution. Our simulations confirm the involvement of SX in the relaxation toward S1 and reveal that it is formed through a change in the nature of the S2 state driven by the decrease in the bond length alternation coordinate of the carotenoid conjugated chain.

Surface Hopping Dynamics with the Frenkel Exciton Model in a Semiempirical Framework.

We present an implementation of the Frenkel exciton model in the framework of the semiempirical floating occupation molecular orbitals-configuration interaction (FOMO-CI) electronic structure method, aimed at simulating the dynamics of multichromophoric systems, in which excitation energy transfer can occur, by a very efficient approach. The nonadiabatic molecular dynamics is here dealt with by the surface hopping method, but the implementation we proposed is compatible with other dynamical approaches. The exciton coupling is computed either exactly, within the semiempirical approximation considered, or by resorting to transition atomic charges. The validation of our implementation is carried out on the trans-azobenzeno-2S-phane (2S-TTABP), formed by two azobenzene units held together by sulfur bridges, taken as a minimal model of multichromophoric systems, in which both strong and weak exciton couplings are present.

Photoisomerization dynamics of spiropyran: A surface-hopping investigation.

In the present work, we performed a computational investigation of the photoisomerization of spiro[1,3-dihydroindole-2,2'-chromene] [spiropyran (SP)] to merocyanine. The electronic energies and wavefunctions were obtained from configuration interaction calculations, using the floating occupation molecular orbital method, in a semiempirical framework. The parameters of the semiempirical Hamiltonian were re-optimized to reproduce ab initio literature data for SP. In our dynamics simulations, we considered, besides S0, the excited states S1, S2, and S3, which are very close in energy in the Franck-Condon region. We obtained a singlet lifetime of 0.67 ps, in line with the experimental results. We found the photoisomerization quantum yield to depend on the electronic state initially populated.

Sampling initial positions and momenta for nuclear trajectories from quantum mechanical distributions.

We compare algorithms to sample initial positions and momenta of a molecular system for classical trajectory simulations. We aim at reproducing the phase space quantum distribution for a vibrational eigenstate, as in Wigner theory. Moreover, we address the issue of controlling the total energy and the energy partition among the vibrational modes. In fact, Wigner's energy distributions are very broad, quite at variance with quantum eigenenergies. Many molecular processes depend sharply on the available energy, so a better energy definition is important. Two approaches are introduced and tested: the first consists in constraining the total energy of each trajectory to equal the quantum eigenenergy. The second approach modifies the phase space distribution so as to reduce the deviation of the single mode energies from the correct quantum values. A combination of the two approaches is also presented.

Multiscale Models for Light-Driven Processes.

Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.

Delocalization effects in singlet fission: Comparing models with two and three interacting molecules.

We present surface hopping simulations of singlet fission in 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene (ThBF). In particular, we performed simulations based on quantum mechanics/molecular mechanics (QM/MM) schemes in which either two or three ThBF molecules are inserted in the QM region and embedded in their MM crystal environment. Our aim was to investigate the changes in the photodynamics that are brought about by extending the delocalization of the excited states beyond the minimal model of a dimer. In the simulations based on the trimer model, compared to the dimer-based ones, we observed a faster time evolution of the state populations, with the largest differences associated with both the rise and decay times for the intermediate charge transfer states. Moreover, for the trimer, we predicted a singlet fission quantum yield of ∼204%, which is larger than both the one extracted for the dimer (∼179%) and the theoretical upper limit of 200% for the dimer-based model of singlet fission. Although our study cannot account for the effects of extending the delocalization beyond three molecules, our findings clearly indicate how and why the singlet fission dynamics can be affected.

Photochemistry in the strong coupling regime: A trajectory surface hopping scheme.

The strong coupling regime between confined light and organic molecules turned out to be promising in modifying both the ground state and the excited states properties. Under this peculiar condition, the electronic states of the molecule are mixed with the quantum states of light. The dynamical processes occurring on such hybrid states undergo several modifications accordingly. Hence, the dynamical description of chemical reactivity in polaritonic systems needs to explicitly take into account the photon degrees of freedom and nonadiabatic events. With the aim of describing photochemical polaritonic processes, in the present work, we extend the direct trajectory surface hopping scheme to investigate photochemistry under strong coupling between light and matter.

Nonadiabatic dynamics simulations of singlet fission in 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene crystals.

We present simulations of the singlet fission dynamics in 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene (ThBF), a thienoquinoid compound recently investigated experimentally by Kawata et al. The simulation model consisted of two ThBF molecules embedded in their crystal environment. The aim was to understand the singlet fission mechanism, and to predict the excited state lifetimes and the singlet fission quantum yield, hitherto unknown. The simulations were performed by the trajectory surface hopping approach with on-the-fly calculations of the electronic wave functions and energies by the semiempirical FOMO-CI method. We found that the initially photogenerated excitonic bright state decays to the lower dark state with a biexponential behaviour, essentially due to transitions to other close lying states. The dark state in turn decays with a lifetime of about 1 ps to the double triplet 1TT state, which is long-lived, as ascertained by performing a simulation with inclusion of the spin-orbit coupling. The singlet fission quantum yield is predicted to be close to the theoretical maximum of 200%. In view of using this thienoquinoid compound in photovoltaic devices, a major drawback is the low energy of the T1 state at its equilibrium geometry.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a ß-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10-15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Energy Selection in Nonadiabatic Transitions.

In this work we investigate whether and how a molecule undergoing a nonadiabatic transition can show different energy mean values and distributions in the two electronic states that are populated. We analyze three models, of which models I and II mimick the limiting cases of almost adiabatic and almost diabatic regimes, respectively, and are solvable by first-order perturbation theory. Model III represents realistically the photodissociation of a diatomic molecule and is treated numerically. The three models provide a consistent picture of the energy selection effect. For a typical avoided crossing, the wavepacket component that undegoes the transition between the two adiabatic states has a larger mean value of energy than the other component, both for upward and for downward transitions. The analysis of model II shows that the Landau-Zener rule can be deduced in a fully quantum mechanical way. We believe that the energy selection effect can be observed experimentally in the photodissociation of diatomic molecules. The effect should be particularly relevant for wavepackets endowed with a broad energy spectrum, as the result of excitation with ultrashort light pulses.

Decoding the Molecular Basis for the Population Mechanism of the Triplet Phototoxic Precursors in UVA Light-Activated Pyrimidine Anticancer Drugs.

The photosensitization of DNA by thionucleosides is a promising photo-chemotherapeutic treatment option for a variety of malignancies. DNA metabolization of thionated prodrugs can lead to cell death upon exposure to a low dose of UVA light. The exact mechanisms of thionucleoside phototoxicity are still not fully understood. In this work, we have combined femtosecond broadband transient absorption experiments with state-of-the-art molecular simulations to provide mechanistic insights into the ultrafast and efficient population of the triplet state in the UVA-activated pyrimidine anticancer drug 4-thiothymine. The triplet state is thought to act as a precursor to DNA lesions and the reactive oxygen species responsible for 4-thiothymine photocytotoxicity. The electronic-structure and mechanistic results presented in this contribution reveal key molecular design criteria that can assist in developing alternative chemotherapeutic agents that may overcome some of the primary deficiencies of classical photosensitizers.