Costantino Zazza, Andrea Amadei, Amedeo Palma, Nico Sanna, Simone Tatoli, Massimiliano Aschi,
In this paper, by using the perturbed matrix method (PMM) in combination with basic statistical mechanical relations both based on nanosecond time-scale molecular dynamics (MD) simulations, we quantitatively address the thermodynamics of compound 0 (Cpd 0) formation in horseradish peroxidase (HRP) enzyme. Our results, in the same trend of low-temperature experimental data, obtained in cryoenzymology studies indicate that such a reaction can be described essentially as a stepwise spontaneous process: ...
Tópico(s): Photosynthetic Processes and Mechanisms
2008 - American Chemical Society | The Journal of Physical Chemistry B
Riccardo Spezia, Costantino Zazza, Amedeo Palma, Andrea Amadei, Massimiliano Aschi,
The electronic properties of peridinin (Per) are investigated using density functional theory (DFT) with a time dependent (TD) treatment for transitions from the ground state to the low-lying electronic excited states. The use of a TD-DFT approach was first tested on the simpler β-carotene molecule in order to see the performances of different functionals. It turns out from the present study that a TD-DFT approach provides a rather good qualitative picture for the electronic properties of this system ...
Tópico(s): Photochemistry and Electron Transfer Studies
2004 - American Chemical Society | The Journal of Physical Chemistry A
Costantino Zazza, Amedeo Palma, Andrea Amadei, Nico Sanna, Simone Tatoli, Massimiliano Aschi,
In this study the question as to whether and to what extent horseradish peroxidase (HRP) enzyme structural flexibility affects the free energy barrier for the formation of the key intermediate compound 0 (Cpd0) is addressed by the use of a combined application of molecular dynamics simulations and perturbed matrix method calculations. Results are intriguing and indicate that, within the simulated conditions, free energy profiles are substantially affected by structural fluctuations of the whole surrounding ...
Tópico(s): Photochemistry and Electron Transfer Studies
2009 - Royal Society of Chemistry | Faraday Discussions