1,721,224 research outputs found
Modelling Complex Molecular and Biomaterial Systems: Simulation of Reactive Processes, Methodological Advances and Interplay with the Experiments
No full textIL RUOLO DELLA CHIMICA TEORICA NELLA FOTOFISICA E NELLA FOTOCHIMICA
No full textLa fotofisica e la fotochimica costituiscono
due importanti discipline scientifiche che trattano
lo studio dell’interazione luce-materia.
Diversi processi biologici fondamentali,
quali la fotosintesi clorofilliana ed i meccanismi
alla base della visione, rientrano nel loro campo
di ricerca. Con il presente contributo viene discusso
il ruolo chiave svolto dalla chimica teorica
e dalla sua implementazione pratica nella chimica
computazionale, per la previsione,
caratterizzazione e comprensione
di fenomeni fotoindotti, portando come esempio
significativo la caratterizzazione fotofisica
e fotochimica della molecola indolo, cromoforo
dell’amminoacido essenziale triptofan
Double Thionated Pyrimidine Nucleobases: Molecular Tools with Tunable Photoproperties
Full text linkSulfur-substitutednucleobases are DNA and RNA base derivativesthat exhibit extremely efficient photoinduced intersystem crossing(ISC) dynamics into the lowest-energy triplet state. The long-livedand reactive triplet states of sulfur-substituted nucleobases arecrucial due to their wide range of potential applications in medicine,structural biology, and the development of organic light-emittingdiodes (OLEDs) and other emerging technologies. However, a comprehensiveunderstanding of non-negligible wavelength-dependent changes in theinternal conversion (IC) and ISC events is still lacking. Here, westudy the underlying mechanism using joint experimental gas-phasetime-resolved photoelectron spectroscopy (TRPES) and theoretical quantumchemistry methods. We combine 2,4-dithiouracil (2,4-DTU) TRPES experimentaldata with computational analysis of the different photodecay processes,which are induced by increasing excitation energies along the entirelinear absorption (LA) ultraviolet (UV) spectrum. Our results showhow the double-thionated uracil (U), i.e., 2,4-DTU, appears as a versatilephotoactivatable instrument. Multiple decay processes can be initiatedwith different ISC rates or triplet-state lifetimes that resemblethe distinctive behavior of the singly substituted 2- or 4-thiouracil(2-TU or 4-TU). We obtained a clear partition of the LA spectrum basedon the dominant photoinduced process. Our work clarifies the reasonsbehind the wavelength-dependent changes in the IC, ISC, and triplet-statelifetimes in doubly thionated U, becoming a biological system of utmostimportance for wavelength-controlled applications. These mechanisticdetails and photoproperties are transferable to closely related molecularsystems such as thionated thymines
Modeling solvent effects and convergence of 31P‐NMR shielding calculations with COBRAMM
Full text linkSolvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems
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Soft X‑ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes
Full text linkMultireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core-electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra
DFT Study of the Reactions between Singlet-Oxygen and a Carotenoid Model
No full textCarotenoids such as beta-carotene are one of the most efficient singlet-oxygen (O-1(2)) quenchers. They quench catalytically O-1(2) (a highly reactive and toxic form of oxygen) through an almost diffusion-controlled energy transfer process (physical pathway): O-1(2) + carotenoid --> O-3(2) + (3)carotenoid --> O-3(2) + carotenoid (+ heat) (eq 1). In contrast to physical quenching, less efficient but concomitant processes exist, involving real chemical reactions. For example. chemical oxidation reactions, which result in the destruction of carotenoids and thus in the loss of antioxidant protection, have been observed (chemical pathway): O-1(2) + carotenoid --> chemical pathway (eq 2). To obtain more detailed information about the reactions between carotenoids and singlet-oxygen, we have performed a DFT computational study of the reaction mechanisms involved in the attack of O-1(2) to the all-trans-decaottanonaene (P-9), a polyene with 9 conjugated double bonds, chosen as carotenoid model. We have found that, together with the main energy transfer pathway (eq 1) which is almost barrierless, there are secondary but concomitant reactions (eq 2) with low-energy barriers leading to biradical intermediates via direct addition of O-1(2) to P-9. These biradicals may give ring closure to form 1,2-addition dioxetane products whose decomposition leads to the observed carbonyl chain cleavage oxidation fragments. However, these biradicals seem to be also responsible, through an S-0 --> T-1 intersystem crossing, of an alternative chemically mediated catalytic quenching of the singlet-oxygen which is returned to its triplet deactivated ground state through a dissociation process on T-1
Azobenzene cis-trans Photoisomerization Mechanism: Characterization of the Decay Ways from the Lowest pipi* Absorbing Singlet State
No full textIn this paper, we analyze the photoisomerization processes of azobenzene after its excitation in the bright S(ππ*). By state of the art/ ab initio / Complete Active Space calculations followed by perturbative corrections (CASPT2//CASSCF) we have identified the critical structures, the Minimum Energy Paths originating on the bright S(ππ*) and on other relevant excited states including the state S1(nπ*). The seams of conical intersections that are important in guiding the photoreaction are determined. We aim at establishing the mechanism of decay and of photoisomerization for the S(ππ*) state and at explaining the difference between the quantum yields found for the two lowest energy S1(nπ*) and S(ππ*) excited states. We found that an excited state based on the πN = NπN = N→π*N = Nπ*N = N configuration is a photoreaction intermediate that plays a very important role in the decay the bright S(ππ*). This doubly excited state, by driving the photoisomerization along the torsion path and by inducing a fast internal conversion to the S1(nπ*) occurring in a variety of geometries, explains all the most important features of the S(ππ*) azobenzene photoisomerization
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