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Solvent Effects on Peridinin Vibrational Properties

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Vibrational spectroscopy is a valuable experimental probe to investigate the static and dynamical behaviour of biomolecules in their complex environments. In this respect, mixed Quantum Mechanics/Molecular Mechanics (QM/MM) ab initio molecular dynamics methods offer a computational tool to help the interpretation of the experimental data. Within the QM/MM scheme, the quantum mechanical calculations performed by density functional theory, which represents the most computationally demanding part, can be restricted to the portion of the system that is directly involved in the vibrations, whereas all the rest of the system is treated at the classical force-field level.

Vibrational frequencies and effective normal modes can be obtained directly from QM/MM dynamics at finite temperature using the approach described in reference [1]. It consists in looking for an optimal localized decomposition of the power spectrum, that leads to collective modes, resonating at the same frequency, so defined effective normal modes.

We applied the above methodology to calculate Infrared and Raman scattering frequencies of the Peridinin molecule by first principles QM/MM dynamics at room temperature. Peridinin molecules are Light-harvesting (LH) complexes, involved in the light collection process into the peridinin-chlorophyll-a-protein (PCP).

Step-scan FTIR results in the PCP protein [2] have pinpointed the difficulties in the precise assignment of bands of peridinin in the complex. One strategy is to rely on comparison with IR or Raman data for isolated peridinin and to study the effect of the surrounding environment on band positions. To this aim we studied three different Peridinin solutions: Perdinin in cyclohexane (an apolar/aprotic solvent), in acetonitrile (a polar/aprotic solvent), and in methanol (a polar/protic solvent).

On the basis of our calculations we are able to assign effective normal modes to the peaks of the vibrational spectra. In addition solvent effects are obtained. Special attention is paid to the more sensitive carbonyl frequency, that is red-shifted in the two polar solvents, the shift being  larger for methanol than acetonitrile, despite the two solvents have comparable polarity. We summarize in figure some result to show electronic polarization of whole peridinin due to the solvent mean field and, focusing on carbonyl, we show the solvent structuration that leads to greater polarization effect under the influence of methanol's local field.

Radial pair distribution function centered on the peridinin carbonyl’s oxygen (left column) and difference density map between the peridinin in solution and in vacuo (right column), positive difference in green and negative one in blue. Scrolling down from a) the apolar solvent to b) the polar and c) the protic one, solvent structuration (left column) and electronic polarization (right column) arise.

[1] M.Martinez, M.-P.Gaigeot, D.Borgis and R. Vuilleumier. J. Chem. Phys. 125, 144106. (2006)

[2] A.Mezzetti and R.Spezia. Spectroscopy: Int. J.22, 235. (2008)

 

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