Our group utilizes theoretical and computational tools to elucidate the structure, spectroscopy and quantum effects of condensed phase systems.

Theoretical vibrational spectroscopy of nucleic acids

Linear and non-linear vibrational spectroscopy has been widely used to probe the structure and dynamics of nucleic acids due to the sensitivity of specific normal modes, in particular the base C=O stretch modes, to the base pairing and stacking configurations. We have recently developed a theoretical strategy that accurately and efficiently predicts the spectral features of nucleic acids based on their structure and dynamics, which bridge molecular dynamics simulations and spectroscopy experiments. Our methods enables the interpretation of complex experimental spectra in the 1600 - 1800 cm-1 region at the atomic level, and allows for the prediction of distinct spectral changes in biological processes that can be validated by experiments. The techniques of interest include linear and 2D IR, Raman and sum-frequency generation spectroscopy.
TOC couplingTOC map

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Short hydrogen bonds in biological systems

Hydrogen bonds with very short donor-acceptor heavy atom distances (R < 2.7 Å) are commonly observed in proteins. The close proximity of the heavy atoms results in a unique electrostatic environment in the protein interior and modulates the ionization of amino acid side chains. In addition, shortening R can lead to proton delocalization between the hydrogen bonding partners by making the barrier of proton transfer comparable to the zero point energy of the O-H or N-H bond. We have recently conducted a statistical analysis of the Protein Data Bank and revealed that short hydrogen bonds are prevalent in proteins, protein-ligand complexes and nucleic acids. From simulating model compounds that mimic the structures of biological short hydrogen bond, we unravel the origin of their downfield 1H NMR chemical shifts. We will elucidate the structure, dynamics and functional roles of these short hydrogen bonds in biological systems, for which we will use a hierarchy of techniques ranging from simulations with classical force fields and methods that explicitly include the quantum nature of both the electrons and nuclei.
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Related publications

Adsorptive and optical properties of nanomaterials

In recent year, surface-enhanced Raman scattering (SERS) has become a sensitive and quantitative sensing and analysis tool. In collaboration with the research group of Professor Laura Fabris, we have used molecular dynamics simulations to reveal the geometry and strength of the interactions between the nanoparticles and analytes, which are directly related to their SERS enhancements.

The Scanning Tunneling Microscope-based Break Junction (STMBJ) technique provides a powerful sensing method to probe the structures of single molecule-metal junctions. In collaboration with Professor Masha Kamenetska at Boston University, we have carried out electronic structure calculations to identify the binding geometries of adenine on the gold tip in the STMBJ experiments.






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