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 carbonyl stretch modes, to the base pairing and stacking configurations. Our research focuses on developing theoretical schemes that accurately and efficiently predict the spectral features of nucleic acids based on their structure and dynamics, which bridge molecular dynamics simulations and spectroscopy experiments. Our methods enable the interpretation of complex experimental spectra in the 1600 -- 1800 cm-1 region at the atomic level, and allow 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.
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. Our research aims to elucidate the structure, dynamics and functional roles of these short hydrogen bonds, 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.
Adsorptive and optical properties of hybrid materials. Nanomaterials have superior adsorptive and optical properties. In collaboration with experimental groups at CCB, we combine molecular simulations and density functional theory calculations to elucidate the key forces and mechanisms of molecular adsorption on an inorganic nanoscaffold that has recently been designed as carriers for cellular regulatory molecules, and determine the main chemical species that give rise to the luminescent properties of inorganic-organic hybrid materials for novel LED devices.
- S. Zhou, Y. Liu, S. Wang and L. Wang, "Chemical Features and Machine Learning Assisted Predictions of Protein-Ligand Short Hydrogen Bonds", Sci. Rep., 13, 13741 (2023)
- W. Meng, H. Peng, Y. Liu, A. Stelling and L. Wang, "Modeling the infrared spectroscopy of oligonucleotides with 13C isotope labels", J. Phys. Chem. B, 127, 2351 (2023)
- X. Zhang, S. Zhou, F. M. Leonik, L. Wang and D. Kuroda, "Quantum mechanical effects in acid–base chemistry", Chem. Sci., 13, 6998 (2022)
- S. Zhou, Y. Liu, S. Wang and L. Wang, "Effective prediction of short hydrogen bonds in proteins via machine learning method", Sci. Rep., 12, 469 (2022)
- S. Zhou and L. Wang, "Quantum effects and 1H NMR chemical shifts of a bifurcated short hydrogen bond", J. Chem. Phys., 153, 114301 (2020)
- Y. Jiang and L. Wang, "Modeling the vibrational couplings of nucleobases", J. Chem. Phys., 152, 084114 (2020)
- S. Zhou and L. Wang, "Symmetry and 1H NMR chemical shifts of short hydrogen bonds: Impact of electronic and nuclear quantum effects", Phys. Chem. Chem. Phys., 22, 4884 (2020)
- S. Zhou and L. Wang, "Unraveling the structural and chemical features of biological short hydrogen bonds", Chem. Sci., 10, 7734 (2019)
- Y. Jiang and L. Wang, "Development of vibrational frequency maps for nucleobases", J. Phys. Chem. B, 123, 5791 (2019)