Application of density functional theory and continuum solvation to reactions and response properties of biological molecules.

摘要

In this work density functional calculations and continuum solvation methods are applied to various biomolecular systems spanning a wide range of sizes. Gas phase calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level of theory are used in conjunction with extensive experimental data collected by collaborators to derive a comprehensive infrared spectral fingerprint of redox active tyrosine. This same level of theory, which we denote as QCRNA, in combination with various continuum solvation methods, is used to characterize the structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas-phase and in solution. In related work, various multilevel methods and density functionals are benchmarked against experimental proton affinities and gas phase basicities. These benchmark results are then used to predict proton affinities and gas phase basicities of molecules important in the study of biological phosphoryl transfer for which experimental data are not available. Finally, a Green's function approach based on a linear-scaling smooth conductor-like screening model of continuum solvation is combined with Monte-Carlo sampling of counterion condensation to make an estimate of the contribution of phosphate-phosphate repulsions to the free energy of DNA bending.