1,720,964 research outputs found
Understanding Charge Dynamics in Dense Electronic Manifolds in Complex Environments
No full text[Image: see text] 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 “N3(4–)”, 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
Watching the Interplay between Photoinduced Ultrafast Charge Dynamics and Nuclear Vibrations
No full text: Here is presented the ultrafast hole-electron dynamics of photoinduced metal to ligand charge-transfer (MLCT) states in a Ru(II) complex, [Ru(dcbpy)2(NCS)2]4- (dcbpy = 4,4'-dicarboxy-2,2'-bipyridine), a photoactive molecule employed in dye sensitized solar cells. Via cutting-edge computational techniques, a tailored computational protocol is here presented and developed to provide a detailed analysis of the electronic manifold coupled with nuclear vibrations to better understand the nonradiative pathways and the resulting overall dye performances in light-harvesting processes (electron injection). Thus, the effects of different vibrational modes were investigated on both the electronic levels and charge transfer dynamics through a theoretical-computational approach. First, the linear response time-dependent density functional (LR-TDDFT) formalism was employed to characterize excitation energies and spacing among electronic levels (the electronic layouts). Then, to understand the ultrafast (femtosecond) charge dynamics on the molecular scale, we relied on the nonperturbative mean-field quantum electronic dynamics via real-time (RT-) TDDFT. Three vibrational modes were selected, representative for collective nuclear movements that can have a significant influence on the electronic structure: two involving NCS- ligands and one involving dcbpy ligands. As main results, we observed that such MLCT states, under vibrational distortions, are strongly affected and a faster interligand electron transfer mechanism is observed along with an increasing MLCT character of the adiabatic electronic states approaching closer in energy due to the vibrations. Such findings can help both in providing a molecular picture of multidimensional vibro-electronic spectroscopic techniques, used to characterize ultrafast coherent and noncoherent dynamics of complex systems, and to improve dye performances with particular attention to the study of energy or charge transport processes and vibronic couplings
An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning
No full textElectronic 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
Photophysics of a nucleic acid–protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study
No full text: We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Unveiling the structure of a novel artificial heme-enzyme with peroxidase-like activity: A theoretical investigation
No full textFe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix–heme–α-helix “sandwich” motif. Up to now, no detailed MC6 structural characterization is available. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)-MC6 structural features and to validate the de novo designed fold. Key structural elements were analyzed to achieve indirect insight relevant to understand Fe(III)-MC6 catalytic performances in solution. Extensive MD simulations showed a partial stability of the “sandwich” fold in water solution. The smaller peptide chain bonded to the heme revealed a high conformational freedom, which promoted the exposition of the heme distal side to the solvent. Regarding the accessibility of water molecules, even in Fe(III)-MC6 “closed” structure the heme cavity appeared hydrated, suggesting an easy accessibility by exogenous ligands. Fe(III)-MC6 structure in both high and low spin states was then further characterized through hybrid QM/MM optimizations. In particular, an accurate description of the active site structure was obtained, allowing a direct comparison of Fe(III)-MC6 coordination environment with that observed in the Horseradish Peroxidase crystal structures. Our results suggest a structural similarity between Fe(III)-MC6 and the natural enzyme. This study supports the interpretation of data from experimental Fe(III)-MC6 structural and functional characterization and the rational design of new artificial mimics with improved catalytic performances
Electronic and Vibrational Manifold of Tetracyanoethylene–Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics
No full text[Image: see text] 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 [ R. A. Mathies; et al. J. Phys. Chem. A2018, 122 ( (14), ), 359429558802] 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(+)
Ultrafast photo-induced processes in complex environments: The role of accuracy in excited-state energy potentials and initial conditions
Get PDFLight 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
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
- …
