Simulations of photoinduced processes with the exact factorization: state of the art and perspectives.

This perspective offers an overview of the applications of the exact factorization of the electron-nuclear wavefunction to the domain of theoretical photochemistry, where the aim is to gain insights into the ultrafast dynamics of molecular systems simulations of their excited-state dynamics beyond the Born-Oppenheimer approximation. The exact factorization offers an alternative viewpoint to the Born-Huang representation for the interpretation of dynamical processes involving the electronic ground and excited states as well as their coupling through the nuclear motion. Therefore, the formalism has been used to derive algorithms for quantum molecular-dynamics simulations where the nuclear motion is treated using trajectories and the electrons are treated quantum mechanically.

Exact factorization of the photon-electron-nuclear wavefunction: Formulation and coupled-trajectory dynamics.

We employ the exact-factorization formalism to study the coupled dynamics of photons, electrons, and nuclei at the quantum mechanical level, proposing illustrative examples of model situations of nonadiabatic dynamics and spontaneous emission of electron-nuclear systems in the regime of strong light-matter coupling. We make a particular choice of factorization for such a multi-component system, where the full wavefunction is factored as a conditional electronic amplitude and a marginal photon-nuclear amplitude. Then, we apply the coupled-trajectory mixed quantum-classical (CTMQC) algorithm to perform trajectory-based simulations, by treating photonic and nuclear degrees of freedom on equal footing in terms of classical-like trajectories.

Electronic Vector Potential from the Exact Factorization of a Complex Wavefunction.

We generalize the definitions of local scalar potentials named and , which are relevant to properly describe phenomena such as molecular dissociation with density-functional theory, to the case in which the electronic wavefunction corresponds to a complex current-carrying state. In such a case, an extra term in the form of a vector potential appears which cannot be gauged away. Both scalar and vector potentials are introduced via the exact factorization formalism which allows us to express the given Schrödinger equation as two coupled equations, one for the marginal and one for the conditional amplitude.

Exploring Exact-Factorization-Based Trajectories for Low-Energy Dynamics near a Conical Intersection.

We study low-energy dynamics generated by a two-dimensional two-state Jahn-Teller Hamiltonian in the vicinity of a conical intersection using quantum wave packet and trajectory dynamics. Recently, these dynamics were studied by comparing the adiabatic representation and the exact factorization, with the purpose to highlight the different nature of topological-phase and geometric-phase effects arising in the two theoretical representations of the same problem. Here, we employ the exact factorization to understand how to accurately model low-energy dynamics in the vicinity of a conical intersection using an approximate description of the nuclear motion that uses trajectories.

The metabolic domestication syndrome of budding yeast.

Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales.

Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases.

Polarizable force fields are an essential component for the chemically accurate modeling of complex molecular systems with a significant degree of fluxionality, beyond harmonic or perturbative approximations. In this contribution we examine the performance of such an approach for the vibrational spectroscopy of the alanine amino acid, in the gas and condensed phases, from the Fourier transform of appropriate time correlation functions generated along molecular dynamics (MD) trajectories. While the infrared (IR) spectrum only requires the electric dipole moment, the vibrational circular dichroism (VCD) spectrum further requires knowledge of the magnetic dipole moment, for which we provide relevant expressions to be used with polarizable force fields.

Nonadiabatic dynamics with classical trajectories: The problem of an initial coherent superposition of electronic states.

Advances in coherent light sources and development of pump-probe techniques in recent decades have opened the way to study electronic motion in its natural time scale. When an ultrashort laser pulse interacts with a molecular target, a coherent superposition of electronic states is created and the triggered electron dynamics is coupled to the nuclear motion. A natural and computationally efficient choice to simulate this correlated dynamics is a trajectory-based method where the quantum-mechanical electronic evolution is coupled to a classical-like nuclear dynamics.

Investigating the Photodynamics of -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 -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.

On the Nature of Geometric and Topological Phases in the Presence of Conical Intersections.

The observable nature of topological phases related to conical intersections in molecules is studied. Topological phases should be ubiquitous in molecular processes, but their elusive character has often made them a topic of discussion. To shed some light on this issue, we simulate the dynamics governed by a Jahn-Teller Hamiltonian and analyze it employing two theoretical representations of the molecular wave function: the adiabatic and the exact factorization.

Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics.

Through approximating electron-nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy.

Influence of the environment on the infrared spectrum of alanine: An effective mode analysis.

The vibrational spectrum of the alanine amino acid was computationally determined in the infrared range 1000-2000 cm, under various environments encompassing the gas, hydrated, and crystalline phases, by means of classical molecular dynamics trajectories, carried out with the Atomic Multipole Optimized Energetics for Biomolecular Simulation polarizable force field. An effective mode analysis was performed, in which the spectra are optimally decomposed into different absorption bands arising from well-defined internal modes. In the gas phase, this analysis allows us to unravel the significant differences between the spectra obtained for the neutral and zwitterionic forms of alanine.

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy.

The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1).

Adiabatic and Nonadiabatic Dynamics with Interacting Quantum Trajectories.

We present a quantum dynamics method based on the propagation of interacting quantum trajectories to describe both adiabatic and nonadiabatic processes within the same formalism. The idea originates from the work of Poirier [ 4-14] and Schiff and Poirier [ 031102] on quantum dynamics without wavefunctions. It consists of determining the quantum force arising in the Bohmian hydrodynamic formulation of quantum dynamics using only information about quantum trajectories.

Exact Factorization Adventures: A Promising Approach for Non-Bound States.

Modeling the dynamics of non-bound states in molecules requires an accurate description of how electronic motion affects nuclear motion and vice-versa. The exact factorization (XF) approach offers a unique perspective, in that it provides potentials that act on the nuclear subsystem or electronic subsystem, which contain the effects of the coupling to the other subsystem in an exact way. We briefly review the various applications of the XF idea in different realms, and how features of these potentials aid in the interpretation of two different laser-driven dissociation mechanisms.

Describing the photo-isomerization of a retinal chromophore model with coupled and quantum trajectories.

The exact factorization of the electron-nuclear wavefunction is applied to the study of photo-isomerization of a retinal chromophore model. We describe such an ultrafast nonadiabatic process by analyzing the time-dependent potentials of the theory and by mimicking nuclear dynamics with quantum and coupled trajectories. The time-dependent vector and scalar potentials are the signature of the exact factorization, as they guide nuclear dynamics by encoding the complete electronic dynamics and including excited-state effects.

Quantum dynamics with curvilinear coordinates: models and kinetic energy operator.

In order to simplify the numerical solution of the time-dependent or time-independent Schrödinger equations associated with atomic and molecular motions, the use of well-adapted coordinates is essential. Usually, this set of curvilinear coordinates leads to a Hamiltonian operator that is as separable as possible. Although their corresponding kinetic energy operator (KEO) expressions can be derived for small systems or special kinds of coordinates, a and approach allows one to compute them in terms of sophisticated curvilinear coordinates.

A Photochemical Reaction in Different Theoretical Representations.

The Born-Oppenheimer picture has forged our representation and interpretation of photochemical processes, from photoexcitation down to the passage through a conical intersection, a funnel connecting different electronic states. In this work, we analyze a full in silico photochemical experiment, from the explicit electronic excitation by a laser pulse to the formation of photoproducts following a nonradiative decay through a conical intersection, by contrasting the picture offered by Born-Oppenheimer and that proposed by the exact factorization. The exact factorization offers an alternative understanding of photochemistry that does not rely on concepts such as electronic states, nonadiabatic couplings, and conical intersections.

Nonadiabatic Dynamics with Coupled Trajectories.

In this paper, we discuss coupled-trajectory schemes for molecular-dynamics simulations of excited-state processes. New coupled-trajectory strategies to capture decoherence effects, revival of coherence and nonadiabatic interferences in long-time dynamics are proposed, and compared to independent-trajectory schemes. The working framework is provided by the exact factorization of the electron-nuclear wave function, and it exploits ideas emanating from various surface-hopping schemes.

Electronic Structure and Excited States of the Collision Reaction O(P) + CH: A Multiconfigurational Perspective.

We present a study of the O(P) + CH scattering reaction, a process that takes place in the interstellar medium and is of relevance in atmospheric chemistry as well. A comprehensive investigation of the electronic properties of the system has been carried out based on multiconfigurational ab initio CASSCF/CASPT2 calculations, using a robust and consistent active space that can deliver accurate potential energy surfaces in the key regions visited by the system. The paper discloses detailed description of the primary reaction pathways and the relevant singlet and triplet excited states at the CASSCF and CASPT2 level, including an accurate description of the critical configurations, such as minima and transition states.

Choice of access route for artificial nutrition in cancer patients: 30 y of activity in a home palliative care setting.

Objectives: Malnutrition negatively affects the quality of life, survival, and clinical outcome of patients with cancer. Home artificial nutrition (HAN) is an appropriate nutritional therapy to prevent death from cachexia and to improve quality of life, and it can be integrated into a home palliative care program. The choice to start home enteral nutrition (HEN) or home parenteral nutrition (HPN) is based on patient-specific indications and contraindications.

Quantum-classical nonadiabatic dynamics of Floquet driven systems.

We develop a trajectory-based approach for excited-state molecular dynamics simulations of systems subject to an external periodic drive. We combine the exact-factorization formalism, allowing us to treat electron-nuclear systems in nonadiabatic regimes, with the Floquet formalism for time-periodic processes. The theory is developed starting with the molecular time-dependent Schrödinger equation with the inclusion of an external periodic drive that couples to the system dipole moment.

Multiomics Analysis Provides Insight into the Laboratory Evolution of toward the Metabolic Usage of Fluorinated Indoles.

Organofluorine compounds are known to be toxic to a broad variety of living beings in different habitats, and chemical fluorination has been historically exploited by mankind for the development of therapeutic drugs or agricultural pesticides. On the other hand, several studies so far have demonstrated that, under appropriate conditions, living systems (in particular bacteria) can tolerate the presence of fluorinated molecules (e.g.

Relaxation dynamics through a conical intersection: Quantum and quantum-classical studies.

We study the relaxation process through a conical intersection of a photo-excited retinal chromophore model. The analysis is based on a two-electronic-state two-dimensional Hamiltonian developed by Hahn and Stock [J. Phys.