First principle computation of biomolecule -ligand interaction
Abstract
We have determined the calibration constants for the SDFT prediction of 57Fe Mössbauer parameters. The calibration constants are basis set and exchange-correlation functional specific. The basis set is 6-311G* whereas the exchange-correlation functional are UB3LYP, UBLYP, UBPW91, and UMPW1PW91. This method is used to predict the binding conformation of a dioxygen molecule to the P intermediate of methane monooxygenase whose experimental binding structure is presently unknown. When O2 binds to the diiron cluster in a μ-1,2-peroxo fashion, the associated theoretical Mössbauer parameters are in good agreement with the experimental values. An efficient method for locating minimum energy crossing points is introduced and tested on the phenyl cation. An agreement of the present method and previous works is satisfactory. The convergence rate obeys a logarithmic law and is verified on the phenyl cation. Due to its rapid convergence rate, the method is suitable for a large molecular system. As an application of the new methodology, the crossing points of the cation of [Fe(ptz)6](BF4) 2 were studied in order to identify the geometrical parameters of the spin crossing points between S=0 ↔ S=1, and S=1 ↔ S=2. The calculation shows that the transition from a singlet ground state to the triplet intermediate state is accompanied by almost 0.3Å bond length elongation of the axial ligands. We have implemented an approximation scheme that allows one to study protein system such as a ligand-protein binding conformation and a protein active site geometry optimization. The scheme, named E-MFCC, is a significant improvement over the previous MFCC approximation originally put forth by Zhang et al. The geometry optimization of some small test systems utilizing the E-MFCC scheme introduces an error on the order of 10-2Å as compared to the all-atom calculation.
Degree
Ph.D.
Advisors
Rodriguez, Purdue University.
Subject Area
Physics|Biophysics
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