Project of the month

Riccardo Spezia is a CNRS researcher (CR2) in the Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, UMR 8587 CNRS in the Université d’Evry Val d’Essonne (France). He graduated in 2004 in the University of Rome with prof. A.Di Nola on computational methods for coupling molecular dynamics with calculations of electronic properties. During the PhD he spent 7 months with a Marie-Curie fellowship in the Laboratoire de Chimie Physique, Université de Paris Sud working with dr. A.Boutin on hydrated electron dynamics. Then in 2004 he was post-doctoral researcher in the ENS-Paris in the group of prof. J.T.Hynes on modeling ultrafast processes in solution. In 2005 moved to Evry where he has now a CNRS permanent position, working on molecular dynamics for understanding molecular spectroscopy (ESI-MS/MS, EXAFS, IR mainly).

Mixed Quantum/Classical Molecular Dynamics for Simulating Vibrational Spectroscopy of Peridinin in Solution

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 particular it is used to investigate triplet-state formation in several photosynthetic reaction centers. 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 outside the framework of investigation of the photoprotective mechanism of PCP. In fact, it has been demonstrated that with a microspectroscopic Resonance Raman approach peridinin can be visualized directly in vivo.

In studying IR signal, for both singlet and triplet state, 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 Resonance Raman 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 are used: 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 that is a particularly important task to rationalize all those experiments. We have recently shown that DFT can be successfully used for vibrational properties of peridinin [1] and ab-initio molecular dynamics in gas phase, both using a Born-Oppenheimer (BO) or a Car-Parrinello (CP) scheme [2] is also doable on this system.

Nowadays DFT-based molecular dynamics can be combined with classical molecular dynamics, as successfully achieved by coupling CPMD and Gromos96 packages. This CPMD/Gromos96 coupling was successfully used by us to study peridinin in cyclohexane by using CINECA supercomputers. The active collaboration with prof. L. Guidoni of University of L’Aquila (former at University of Rome) was fundamental for the realization of the project. We are studying solvation effects on peridinin vibrational dynamics by such a QM/MM scheme where a peridinin model is treated at DFT level and solvent is treated classically.
A molecular dynamics simulation of peridinin model in ciclohexane solution was already produced.
From the resulting dynamics we can obtain the vibrational signature of the system, directly from Fourier transform (FT) of the velocity-velocity correlation function, and also the IR absorption spectrum, from FT of the dipole-dipole correlation function and Raman spectrum, from FT of the polarizabiliy-polarizability correlation function. 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. Thus the assignment of vibrational bands will be done by 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 [3].
HPC-Europa program was very useful to provide computing time needed for this QM/MM simulations and we will hope to have more computing time for simulating also the other solvents in the next calls.

Peridinin model (in solid sticks) studied with DFT-based molecular dynamics in liquid ciclohexane. Some of the solvent molecules are shown.

References
[1] Mezzetti A. and Spezia, R. 2008. Spectroscopy: Int. J., 22, 235-250.
[2] Spezia, R., Zazza, C., Palma, A., Amadei, A. and Aschi, M. 2004. J. Phys. Chem. A, 108, 6763-6770.
[3] Martinez, M., Gaigeot, M.-P., Borgis, D. and Vuilleumier, R. 2006. J. Chem. Phys. 125, 144106.