“Theoretical Modeling of Quantum Effects and Vibrational Spectroscopy of Biomolecules”
The three-dimensional architecture of proteins often creates specialized structural elements, notably short hydrogen bonds that have donor-acceptor distances below 2.7 Å. In the first part of the presentation, I will discuss our recent statistical analysis of the Protein Data Bank to identify the chemical features and quantum effects of short hydrogen bonds in biological macromolecules. We further use a series of small molecules to mimic these biological short hydrogen bonds, and carry out first principles simulations that incorporate the quantum mechanical nature of both the electrons and nuclei to identify how the 1H NMR chemical shifts follow a universal relation with the proton positions.
Vibrational spectroscopy is a powerful tool to probe the structure and dynamics of nucleic acids because specific normal modes, in particular the nucleobase carbonyl stretch modes, are highly sensitive to the patterns of base paring and base stacking. In the second part of the presentation, I will provide a theoretical framework that allows one to efficiently calculate the linear and nonlinear vibrational spectra of nucleic acids directly from molecular dynamics simulations. In particular, we have developed the first frequency maps and coupling schemes for the base carbonyl stretches, and demonstrated that the predicted infrared spectra of a variety of model systems are in good agreement with experimental measurements.
~Coffee/tea will be served prior to lecture~