Modelizations and Simulations of Nano Devices in nanok calculus

International audienceWe develop a process calculus - the nanok calculus - for modeling, analyzing and predicting the properties of molecular devices. The nanok calculus is equipped with a simple stochastic model, that we use to model and simulate the behavior of a molecular shuttle, a basic nano device currentfly used for building more complex systems

The protein environment restricts the intramolecular charge transfer character of the luciferine/luciferase complex

The electronic characterization of the luciferine/luciferase complex is fundamental to tune its photophysical properties and develop more efficient devices based on this luminiscent system. Here, we apply molecular dynamics simulations, hybrid quantum mechanics/molecular mechanics (QM/MM) calculations and transition density analysis to compute the absorption and emission spectra of luciferine/luciferase and analyze the nature of the relevant electronic state and its behaviour with the intramolecular and intermolecular degrees of freedom. It is found that the torsional motion of the chromophore is hampered by the presence of the enzyme, reducing the intramolecular charge transfer nature of the absorbing and emitting state. In addition, such a reduced charge transfer character does not correlate in a strong way neither with the intramolecular motion of the chromophore nor with the chromophore/amino-acid distances. However, the presence of a polar environment around the oxygen atom of the thiazole ring of the oxyluciferin, coming from both the protein and the solvent, enhances the charge transfer character of the emitting stateWe thank the support of the Spanish Ministry of Science and Innovation through the project PID2020-117806GA-I00 funded by MCIN/AEI/10.13039/501100011033, the Comunidad de Madrid through the Attraction of Talent Program (Grant ref 2018-T1/ BMD-10261) and the Universidad Autónoma de Madrid through the Ayudas para el Fomento de la Investigación en Estudios de Master program and the predoctoral Contract Formación de Personal Investigador (FPI-UAM). The work has been performed under the Project HPC-EUROPA3 (INFRAIA2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme and the CINECA computing center. D.A. and M.G thank funding from the European Union’s Horizon 2020 research and innovation program under the H2020-NMBP-TO-IND-2018-2020/DT-NMBP-09-2018 grant agreement No. 814492 (SIMDOME

The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations

A computational protocol based on the complete and restricted active space self-consistent field (CASSCF/RASSCF) methods and their second-order perturbation theory extensions (CASPT2/RASPT2) is employed to benchmark the highly excited-state manifold of the DNA/RNA canonical purine nucleobase guanine in vacuo. Several RASPT2 schemes are tested, displaying a steady convergence of electronic transition energies and dipole moments upon active space enlargement toward the reference values. The outcome allows calibrating and optimizing computational efforts by considering cheaper and more approximate RAS schemes that could enable the characterization of the excited-state manifolds of multi-chromophoric systems, such as DNA/RNA nucleobase dimers or multimers. Simulations of two-dimensional electronic spectra show similar trends to those observed on the other purine nucleobase adenine, deviating from this and other pyrimidine nucleobases in featuring its main excited-state absorption signal, embodied by sizable double HOMO to LUMO excitation contributions, in the UV probing window

Risk of congenital anomalies around a municipal solid waste incinerator: a GIS-based case-control study

<p>Abstract</p> <p>Background</p> <p>Waste incineration releases into the environment toxic substances having a teratogenic potential, but little epidemiologic evidence is available on this topic. We aimed at examining the relation between exposure to the emissions from a municipal solid waste incinerator and risk of birth defects in a northern Italy community, using Geographical Information System (GIS) data to estimate exposure and a population-based case-control study design. By modelling the incinerator emissions, we defined in the GIS three areas of increasing exposure according to predicted dioxins concentrations. We mapped the 228 births and induced abortions with diagnosis of congenital anomalies observed during the 1998–2006 period, together with a corresponding series of control births matched for year and hospital of birth/abortion as well as maternal age, using maternal address in the first three months of pregnancy to geocode cases and controls.</p> <p>Results</p> <p>Among women residing in the areas with medium and high exposure, prevalence of anomalies in the offspring was substantially comparable to that observed in the control population, nor dose-response relations for any of the major categories of birth defects emerged. Furthermore, odds ratio for congenital anomalies did not decrease during a prolonged shut-down period of the plant.</p> <p>Conclusion</p> <p>Overall, these findings do not lend support to the hypothesis that the environmental contamination occurring around an incineration plant such as that examined in this study may induce major teratogenic effects.</p

Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates

A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry

Ultrafast Carotenoid to Retinal Energy Transfer in Xanthorhodopsin Revealed by the Combination of Transient Absorption and Two-Dimensional Electronic Spectroscopy

By comparing two-dimensional electronic spectroscopy (2DES) and Pump-Probe (PP) measurements on xanthorhodopsin (XR) and reduced-xanthorhodopsin (RXR) complexes, the ultrafast carotenoid-to-retinal energy transfer pathway is revealed, at very early times, by an excess of signal amplitude at the associated cross-peak and by the carotenoid bleaching reduction due to its ground state recovery. The combination of the measured 2DES and PP spectroscopic data with theoretical modelling allows a clear identification of the main experimental signals and a comprehensive interpretation of their origin and dynamics. The remarkable velocity of the energy transfer, despite the non-negligible energy separation between the two chromophores, and the analysis of the underlying transport mechanism, highlight the role played by the ground state carotenoid vibrations in assisting the process

Ultra-broadband 2D electronic spectroscopy of carotenoid-bacteriochlorophyll interactions in the LH1 complex of a purple bacterium

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A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils

Photoinduced processes in thiouracil derivatives have lately attracted considerable attention due to their suitability for innovative biological and pharmacological applications. Here, sub-20 fs broadband transient absorption spectroscopy in the near-UV are combined with CASPT2/MM decay path calculations to unravel the excited-state decay channels of water solvated 2-thio and 2,4-dithiouracil. These molecules feature linear absorption spectra with overlapping ππ* bands, leading to parallel decay routes which we systematically track for the first time. The results reveal that different processes lead to the triplet states population, both directly from the ππ* absorbing state and via the intermediate nπ* dark state. Moreover, the 2,4-dithiouracil decay pathways is shown to be strongly correlated either to those of 2- or 4-thiouracil, depending on the sulfur atom on which the electronic transition localizes

Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan

: By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, we present a complete description of the primary photoinduced processes in solvated tryptophan. Our results shed new light on the role of the solvent in the relaxation dynamics of tryptophan. We unveil two consecutive coherent population transfer events involving the lowest two singlet excited states: a sub-50-fs nonadiabatic La → Lb transfer through a conical intersection and a subsequent 220 fs reverse Lb → La transfer due to solvent-assisted adiabatic stabilization of the La state. Vibrational fingerprints in the transient absorption spectra provide compelling evidence of a vibronic coherence established between the two excited states from the earliest times after photoexcitation and lasting until the back-transfer to La is complete. The demonstration of response to the environment as a driver of coherent population dynamics among the excited states of tryptophan closes the long debate on its solvent-assisted relaxation mechanisms and extends its application as a local probe of protein dynamics to the ultrafast time scales