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Vibrational Biospectroscopy

Experimental vibrational spectroscopy (such as InfraRed and Raman) is also an extremely active and fast-developing field, which is evolving towards the possibility to perform precise and time-resolvent measurements. Accurate experimental determination of spectroscopic properties of biomolecules, in combination with structural information from X-Ray or NMR are currently providing the ingredients to theoretical biophysicists and biochemists for ab-initio modelling of biospectroscopy. First principle molecular dynamics allow us to calculate vibrational properties of molecules using esplicit solvent/environment and including finite temperature effects. The direct comparison with the experimental data may eventually lead to the understanding of the relationships between the molecular structure, the environment and the spectroscopic signal.


Infra Red Multiple Photon Spectroscopy

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Vibrational spectroscopy has been applied for decades as a powerful probe of polypeptide and protein secondary structures. The underlying assumption is that the function of biological molecules is related to the three-dimensional stucture. While linear infrared and Raman vibrational spectroscopies are well established and largely applied in the condensed phase, the past decade was witnessed the development of several experimental set-ups in order to probe the vibrational properties of polypeptides in the gas phase. For ionic molecules, an emerging gas phase technique at room temperature is based on action spectroscopy either using a messenger method (IR-PD infrared photon dissociation) or multiple photon dissociation (IR-MPD infrared multiple photon dissociation).

These techniques are based on the detection by mass spectrometry of ionic fragments that comes from the parent molecules upon (multiple) photon fragmentation processes.

With the growth in complexity of the biomolecules under scrutiny, with these new experimental set-ups, theoretical calculations have become more essential in order to understand the conformations that are responsible for the experimental spectroscopic fingerprints.

The most common approach has involved comparing IRMPD spectra to harmonic frequency calculations at the density-fuctional theory (DFT) level of theory. 

In collaboration with the group of Prof. Simonetta Fornarini and Prof. Maria Elisa Crestoni we are investigating the lowest energy equilibrium conformations for S-nitroso glutathione and S-nitroso cysteine. In order to answers as to which isomers can be responsible for the experimental vibrational signatures we are using a combination of classical Molecular Dynamics and Quantum Chemistry calculations.



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)


Hydration of hydrophobic solutes

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The  hydrophobic interaction is responsible for several important biological and chemical processes: aggregation of amphiphilic molecules and micelles, protein folding, aggregation of protein subunits into multi-subunit quaternary structure[P. Ball, Chem. Rev. 108, 74–108 (2008)]. Experimental results show that hydration structure changes with shape and size of  solute. In presence of  small  hydrophobic solutes the possible configuration of water hydrogen bonds can be restricted, but the overall number of  hydrogen bonds is the same. For large hydrophobic solutes, as surface, water molecules cannot maintain unchanged and this energetic effect drives segregation between water and hydrophobic solutes [D. Chandler, Nature 437, 640-647 (2005)]. Interaction between water molecules and hydrophobic solute affects also structural, dynamic and vibrational properties of water [M. Sharma, D. Donadio, E. Schwegler and G. Galli, Nano Let. 130, No 9, 2959-2962 (2008)].

In the present work we study the structural, dynamical and spectroscopic properties of water around a methane molecule using Car-Parrinello molecular dynamics. The infrared spectra, obtained by the Fourier transform of the dipole autocorrelation function, has been decomposed into the contribution due to the first-shell and to the bulk. The analysis revealed significant differences between the bulk and the first-shell signal in several regions of the spectra. Our findings suggest the presence of previously undetected spectroscopic fingerprints of liquid water at the interface with small hydrophobic solutes.



(Fig1. A methane in a box of 63 water molecules)






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