Structural and Dynamic Effects in Physico-chemical Properties of Biomolecules: An Integrated Computational Approach.
Stendardo, Emiliano (2010) Structural and Dynamic Effects in Physico-chemical Properties of Biomolecules: An Integrated Computational Approach. [Tesi di dottorato] (Inedito)
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In this thesis we present an integrated computational approach for the accurate prediction of magnetic properties of medium to large molecular systems in vacuo and in condensed phases. The strategy adopted relies on the integration of sophisticated quantum mechanical models with tailored force field methods; the results obtained show that, in the specific context of magnetic parameters, the approach provides answers that are as accurate as even the highest-level full quantum mechanics calculations, at a fraction of the computational cost. In particular, the extension of the popular AMBER force field to medium-large organic free radical nitroxides in vacuo and in condensed phase is presented. New atom types have been introduced whose parameters were fitted on the geometry, vibrational frequencies and potential energy surfaces (PES) derived by density functional theory (DFT) calculations on selected classes of nitroxides. Force field parameterization has been extended to include specific structural features that are often present alongside the paramagnetic center, e.g. in α-amino acidic nitroxides. This required the development of a force-field description for the peptide bonds of strongly helicogenic residues with serious steric restrictions. The resulting molecular mechanical method has been employed in an integrated computational characterization of the role of structural, environmental and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of nitroxide spin probes, with results that are quite comparable with the available experimental counterparts.
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