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Light-harvesting (LH) complexes are used by photosynthetic organisms to increase the overall efficiency of photosynthesis. This is accomplished by harvesting light energy and funneling it to the reaction center, where it is converted into electrochemical potential. Dinoflagellates, unicellular algae constituting one of the most important classes of phytoplankton, use a water-soluble LH complex called peridinin-chlorophyll-a-protein (PCP) with a 4:1 peridinin/chlorophyll ratio. The presence of peridinin molecules in the PCPs enables the organism to collect light in the visible spectral region where chlorophyll poorly absorbs. The peridinins of PCPs are also able to play a photoprotective role by efficient quenching of the chlorophyll triplet states, which may occasionally be populated, thus preventing the formation of the highly toxic singlet oxygen.
Infrared spectroscopy, and in particular time-resolved IR difference spectroscopy is a well-established technique which has been successfully used to investigate photophysical phenomena and photochemical reactions taking place in photosynthetic reaction center and LH complexes. This technique allows reaction-induced changes in both the protein and the cofactors to be monitored. In both static and time-resolved IR band assignment remains a difficult task. Vibrational frequencies can be obtained from theoretical calculations performed at molecular level such that the band assignment can be subsequently performed. A detailed and complete characterization of peridinin vibrational modes appears highly desirable also as a general purpose. In fact, it has been demonstrated that with a microspectroscopic Resonance Raman (RR) approach peridinin can be visualized directly in vivo.
In studying IR signal, for both singlet and triplet states, a key signature is provided by the carbonyl function of the lactone ring. In particular the effect of different protein environments of the four peridinins present in PCP complex, was evocated to understand IR spectroscopy.
Based on this motivation, a set of IR and RR experiments is going to be performed by Dr. A.Mezzetti of the University of Lille (France) to understand environmental effects on vibrational properties of peridinin. At this end three prototypical solvents were used in simulations: 1) an apolar/aprotic solvent, like cyclohexane; 2) a polar/aprotic solvent, like deuterated acetonitrile; 3) a polar/protic solvent like ethanol.
Ab-initio molecular dynamics should help for the band assignment. Using a mixed QM/MM approach, we studied the vibrational spectroscopy of a peridinin molecule, treated at DFT level, immersed in different classical solvents. This is achieved by using the CPMD package coupled with Gromos96. The active collaboration with prof. L. Guidoni of University of L’Aquila (former at University of Rome) the HPC fellowship was fundamental for the realization of the project.
From the resulting dynamics we obtained the vibrational signatures of the system, calculating the vibrational density of states by Fourier Transform (FT) of the velocity-velocity autocorrelation function. The IR absorption spectrum and the Raman spectrum are also calculated by FT of the dipole-dipole correlation function and the polarizabiliy-polarizability correlation function, respectively. All the resulting spectra will directly take into account anharmonic effects that should play a big role in such flexible molecule, in particular in solution. Also temperature effects are directly accounted for since molecular dynamics are performed at the same finite temperature of corresponding experiments. The assignment of vibrational bands will be done using the recently developed public license code based on the work of M.-P. Gaigeot and co-workers to analyze finite temperature equilibrium dynamics in terms of effective normal modes.
 Mezzetti A. and Spezia, R. 2008. Spectroscopy: Int. J., 22, 235-250.
This project is the continuation of the Application Num.10. Here we end up simulations doing that in the other solvents.
We have now vibrational signature of peridinin in apolar/aprotic solvent (cicloexane), polar/aprotic solvent (acetonitrile) and polar/protic solvent (methanol).
Their effect on vibrational properties is relevant and our simulations are able to correctly reproduce available experimental data in different environments.
The aim of this work is to implement density functional theory (DFT) calculations that provide atomistic information on the morphology, electronic structure, and optical response of small CdSe quantum dots and related semiconductor cluster capped by different types and numbers of ligands. The goal of these calculations is the understanding of the basic properties of these systems, in particular the nature of the exciton peak.
To do this, the UV-Vis absorption spectrum, of model systems, has been calculated at the Time Dependent Density Functional Theory (TDDFT) level, providing an accurate (state of art) theoretical description of the exciton phenomena. In this way, it is possible to analyze the charge redistribution involved in this excitation, and so, going beyond the effective mass model, to a better description of the spectroscopic properties of the quantum dots, that takes into account the surface reconstruction and the role of the ligands.
The model systems, suitable to reproduce the real nanoparticles, are obtained from experimental information on the structure , reaction formation mechanism  and surface passivation  of semiconductor nanocrystals. In particular, the study has been focused on the (CdSe)33 cluster with ∼1.3 nm diameter, which represents the smallest CdSe nanocrystal that has been isolated and experimentally identified with mass spectroscopy .
From a computational point of view, these systems are still challenging and their modeling needs high performance computing and efficient quantum chemistry computer codes. In these terms, the other purpose of this work, is to explore the performance of the available softwares implemented in supercomputer facilities, with the aim to reach that region of cluster of nanometric size which opens the opportunities to study quantum confinement effects in realistic models of quantum dots.
Our simulated spectra, show that, the nature of the excitonic peak, for nanoparticles with diameter less than 2.0 nm, is related to three intense transitions. These three transition are highlighted in figure 3b as the three vertical lines that lay under the first peak. The composition of these transitions are strongly dominated by a single excitation between a linear combination of surface selenium p orbitals (HOMO, HOMO-1 and HOMO-2) to a linear combination of core cadmium s orbitals (LUMO).
For these clusters the ligands play two important roles: stabilize the structure, saturating the surface dangling bonds, and keep the geometry of the clusters close to the wurtzite one.
The calculated TDDFT spectra are in good agreement with those obtained experimentally for cluster with the same dimension capped with the same type of ligands, this suggest that our structures are realistic models of the actual quantum dots.