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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.

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.

We present the implementation of trajectory surface hopping nonadiabatic dynamics for a polarizable embedding QM/MM formulation. The time-dependent density functional theory has been used as the quantum mechanical level of theory, whereas the molecular mechanics description has involved the polarizable AMOEBA force field. This implementation has been obtained by integrating the surface-hopping program Newton-X NS with an interface between the Gaussian 16 and Tinker suites of codes to calculate QM/AMOEBA energies and forces. The implementation has been tested on a photoinduced electron-driven proton-transfer reaction involving pyrimidine and a hydrogen-bonded water surrounded by a small cluster of water molecules and within a large water droplet.

Xanthophylls are an important class of oxygen containing carotenoids, which play a fundamental role both in light harvesting pigment-protein complexes and in many other photo-responsive proteins. The complexity of the manifold of the electronic states and the large sensitivity to the environment still prevent a clear and coherent interpretation of their pho-tophysics and photochemistry. In this Letter, we first apply cutting-edge ab-initio methods (CC3, DMRG/NEVPT2) on model C2h keto-carotenoids to critically asses the performances +of single and multi-reference methods. We then lift symmetry restrictions and extend the tested methods to time dependent DFT and Semiempirical CI (SECI). From this analysis, we demonstrate that SECI can indeed represent an optimal method for describing light-induced processes of xanthophylls in biologically relevant systems. As an example, we investigate canthaxanthin in the Orange Carotenoid Protein showing that the conical intersections between excited states ...

Light-harvesting in photosynthesis is accompanied by photoprotective processes. In cyanobacteria, the photoprotective role is played by a specialized complex, the Orange Carotenoid Protein which is activated by strong blue-green light. This photoactivation involves a unique series of structural changes which terminate with an opening of the complex into two separated domains, one of which acts as a quencher for the light-harvesting complexes. Many experimental studies have tried to reveal the molecular mechanisms through which the energy absorbed by the carotenoid finally leads to the large conformational change of the complex. Here for the first time, these mechanisms are revealed by simulating at atomistic level the whole dynamics of the complex through an effective combination of enhanced sampling techniques. On the basis of our findings, we can conclude that the carotenoid does not act as a spring that, releasing its internal strain, induces the dissociation, as it was previously proposed but as a "latch" locking together the two domains. The photochemically triggered displacement of the carotenoid breaks this balance, allowing the complex to dissociate.

Orange carotenoid protein (OCP) is a carotenoid-binding protein involved in photo-protection mechanisms of cyanobacteria. Upon exposure to high light, OCP interconverts from an orange resting form (OCPO) to a red active one (OCPR); the mechanism of this interconversion, even if extensively studied, has still not been fully elucidated. In this work, we use multiscale atomistic models ranging from classical to hybrid quantum-classical (QM/MM) molecular dynamics to give a comprehensive molecular explanation of the drastic spectroscopic changes observed upon interconversion. The findings are finally used to formulate a new hypothesis on the role of the protein in the photoactivation mechanism.

Light-harvesting in photosynthesis is accompanied by photoprotective processes. In cyanobacteria, the photoprotective role is played by a specialized complex, the Orange Carotenoid Protein which is activated by strong blue-green light. This photoactivation involves a unique series of structural changes which terminate with an opening of the complex into two separated domains, one of which acts as a quencher for the light-harvesting complexes. Many experimental studies have tried to reveal the molecular mechanisms through which the energy absorbed by the carotenoid finally leads to the large conformational change of the complex. Here for the first time, these mechanisms are revealed by simulating at atomistic level the whole dynamics of the complex through an effective combination of enhanced sampling techniques. On the basis of our findings, we can conclude that the carotenoid does not act as a spring that, releasing its internal strain, induces the dissociation, as it was previously proposed but as a "latch" locking together the two domains. The photochemically triggered displacement of the carotenoid breaks this balance, allowing the complex to dissociate.

An enantioselective electrophilic amination of 3-substituted-2-oxindoles is reported, using bis(2,2,2-trichloroethyl)azo-dicarboxylate and commercially available Cinchona alkaloid organocatalysts. The best results were obtained in the reaction of 3-aryl substrates, with high to excellent yields (75% to quantitative) and good stereoselectivity (64–77% ee). Facile reductive conversion of the protected 3-hydrazino fragment into the corresponding primary amine was also demonstrated, to expand the synthetic flexibility of asymmetric electrophilic amination with azo-dicarboxylic esters en route to enantioenriched 3-amino-2-oxindoles. The absolute configuration of 3-amino-3-phenyl-2-oxindole was independently established by electronic circular dichroism (ECD), combined with time-dependent density functional theory (TDDFT).

Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light- harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.