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Modellizzazione molecolare multiscala del meccanismo fotosintetico di ossidazione dell'acqua
No full textIl complesso delle reazioni legate alla fotosintesi è forse uno dei campi di ricerca più vasti ed prolifici del panorama scientifico modero. Il processo di fotosintesi in batteri, alghe e piante, permette la conversione dell’energia luminosa in energia potenziale chimica immagazzinata come carboidrati e rilascia come prodotto di scarto ossigeno molecolare. La reazione avviene in un complesso proteico, il Fotosistema-II (PSII), all'interno del quale, l’assorbimento dei fotoni permette la conversione dell’acqua in ossigeno e idrogeno. Questa reazione avviene all'interno di cluster metallico di manganese attraverso un processo catalitico composto da 5 fasi, denominate da S0 a S4, e chiamato ciclo di Kok-Joliot. Gli studi sperimentali e teorici ad oggi presenti sull'argomento sono numerosi e spesso contraddittori, lasciando un dibattito aperto e acceso sull'effettivo processo molecolare del ciclo catalitico.
Questo progetto di ricerca fa uso di metodologie computazionali per la modellizzazione delle proprietà strutturali ed elettroniche cosiddette multiscala, ovvero in cui una parte del sistema, la più importante, è studiata a livello di meccanica quantistica, mentre la parte restante è descritta tramite meccanica classica.
Il primo obbiettivo del lavoro di dottorato è la definizione dei meccanismi molecolari legati alle ultime fasi del ciclo di Kok-Joliot all0interno del centro di reazione del PSII, il cluster Mn4CaO5. In queste fasi finali, due atomi substrato di ossigeno si vanno a legare formando un intermedio perossido e dopo di che sono rilasciati sotto forma di ossigeno molecolare in stato di tripletto. Il ciclo catalitico è quindi completato dalla rigenerazione de cluster mediante l’inserimento di una nuova molecola d’acqua la quale farà da substrato per il ciclo di fotolisi successivo. L’analisi della stabilità degli intermedi è stata fatta utilizzando simulazioni multiscala quantistico-classiche (QM/MM) di dinamica molecolare per valutare l’evoluzione temporale di strutture molecolari ed elettroniche. D’altro canto la descrizione dei profili di energia associati alle conversioni tra i vari stati intermedi è stata fatta tramite il calcolo del percorso di minima energia su modelli interamente quantistici QM estratti dalle simulazioni di dinamica molecolare.
Ulteriore obiettivo è quello di fornire una guida all’interpretazione dei dati sperimentali di spettroscopia differenziale Fourier-Transform Infra-Red relativi alle transizione tra i vari stati S il cui significato è ancora dibattuto. Il metodo utilizzato per studiare questi aspetti è stata la dinamica molecolare multiscale QM/MM insieme a modelli completamente QM. Il metodo di decomposizione dello spettro da dinamica QM/MM non era mai stato applicato a modelli così estesi, inoltre è stato applicata una procedura di scomposizione nuova atta a permettere un maggior controllo sulla reale identità dei picchi. Questo approccio inoltre ha permesso di avvalorare le precedenti ipotesi sperimentali e confermare la precedente assegnazione dei range di frequenze fatta per ligandi carbossilici fatta con il metodo dell’analisi dei modi normali NMA. In ultimo, è stato possibile usare questo approccio di decomposizione spettrale per ottenere informazioni sulle proprietà vibrazionali low-IR principalmente originate dal cluster di manganese ottenendo un’ottima sovrapposizione con il dato sperimentale
Early-stage formation of (hydr)oxo bridges in transition-metal catalysts for photosynthetic processes
No full textVibrational fingerprints of the Mn4CaO5 cluster in Photosystem II by mixed quantum-classical molecular dynamics
Full text linkA detailed knowledge of the structures of the catalytic steps along the Kok-Joliot cycle of Photosystem II may help to understand the strategies adopted by this unique enzyme to achieve water oxidation. Vibrational spectroscopy has probed in the last decades the intermediate states of the catalytic cycle, although the interpretation of the data turned out to be often problematic. In the present work we use QM/MM molecular dynamics on the S2 state to obtain the vibrational density of states at room temperature. To help the interpretation of the computational and experimental data we propose a decomposition of the Mn4CaO5 moiety into five separate parts, composed by “diamond” motifs involving four atoms. The spectral signatures arising from this analysis can be easily interpreted to assign experimentally known bands to specific molecular motions. In particular, we focused in the low frequency region of the vibrational spectrum of the S2 state. We can therefore identify the observed bands around 600–620 cm− 1 as characteristic for the stretching vibrations involving Mn1-O1-Mn2 or Mn3-O5 moieties
Mechanism of Water Delivery to the Active Site of Photosystem II along the S(2) to S(3) Transition
Full text linkThe two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S-2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the duster during the transition between the S-2 and S-3 states, which has been recently revealed to have the Mn4CaO5 catalytic cluster arranged in an open cubane fashion. In this Letter, by means of ab initio calculations, we investigated the possible pathways for the binding of the upcoming water molecule. Upon the four different possibilities checked in our calculations, the binding of the crystallographic water molecule, originally located nearby the Cl- binding site, showed the lowest activation energy barrier. Our findings therefore support the view in which the W2 hydroxyl group and the O5 oxygen act as substrates for the oxygen evolution. Within this framework the role of the open and closed Mn4CaO5 conformers is clarified as well as the exact mechanistic events occurring along the S-2 to S-3 transition
Unravelling Mn4Ca cluster vibrations in the S1, S2 and S3 states of the Kok–Joliot cycle of photosystem II
Full text linkVibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok-Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To better analyze the computational data and assign spectral peaks, we introduce an approach based on dipole-dipole correlation function of cluster moieties of the reaction center. Our analysis reveals variation in the infrared signature of the Mn4Ca cluster along the Kok-Joliot cycle, attributed to its increasing symmetry and rigidity resulting from the rising oxidation state of the Mn ions. Furthermore, we successfully assign the debated contributions in the frequency range around 600 cm−1. This computational methodology provides valuable insights for deciphering experimental infrared spectra and understanding the water oxidation process in both biological and artificial systems
On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II
No full textUnderstanding the structural modification experienced by the Mn4CaO5 oxygen‐evolving complex of photosystem II along the Kok‐Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S‐states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S2/S1 infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra
Evolution from S<sub>3</sub> to S<sub>4</sub> States of the Oxygen-Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics
No full textWater oxidation in the early steps of natural photosynthesis is fulfilled by photosystem II, which is a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of photosystem II, which consists of a Mn4Ca metal cluster, at which, after the accumulation of four oxidising equivalents through five steps (S0-S4) of the Kok-Joliot cycle, two water molecules are split into electrons, protons, and molecular oxygen. In recent years, by combining experimental and theoretical approaches, new insights have been achieved into the structural and electronic properties of different steps of the catalytic cycle. Nevertheless, the exact catalytic mechanism, especially concerning the final stages of the cycle, remains elusive and greatly debated. Herein, by means of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, from the structural, electronic, and magnetic points of view, the S3 state before and upon oxidation has been characterised. In contrast with the S2 state, the oxidation of the S3 state is not followed by a spontaneous proton-coupled electron-transfer event. Nevertheless, upon modelling the reduction of the tyrosine residue in photosystem II (TyrZ ) and the protonation of Asp61, spontaneous proton transfer occurs, leading to the deprotonation of an oxygen atom bound to Mn1; thus making it available for O-O bond formation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“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
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