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Laura L Perissinotti

Publications and source records attributed to Laura L Perissinotti.

4 recordsLinked to original sources
PubMed2006

Modeling heme proteins using atomistic simulations.

Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.

Computer Simulation↗
PubMed2006

A surprisingly stable S-nitrosothiol complex.

In this work we present for the first time an X-ray structure of a coordinated S-nitrosothiol obtained by reaction of the extremely reactive K[IrCl5NO] with benzylmercaptan in acetonitrile. This surprisingly stable compound, trans-K[IrCl4(CH3CN)N(O)SCH2Ph], was isolated in high yield (80%) and fully characterized by FTIR, 1H NMR, and ESI-MS. To our knowledge this is the first example of a coordinated S-nitrosothiol that has been isolated.

Journal Article↗
PubMed2005

Solvent effects on peroxynitrite structure and properties from QM/MM simulations.

We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO(-) bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties.

Computer Simulation↗