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.
Related publications
- Development of vibrational frequency maps for nucleobases
Y. Jiang and L. Wang, J. Phys. Chem. B, 123, 5791 (2019) - Modeling the vibrational couplings of nucleobases
Y. Jiang and L. Wang, J. Chem. Phys., 152, 084114 (2020) - Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction
C. R. Baiz, B. Blasiak, J. Bredenbeck, M. Cho* et al, Chem. Rev., 120, 7152 (2020) - Modeling the infrared spectroscopy of oligonucleotides with 13C isotope labels
W. Meng, H. Peng, Y. Liu, A. Stelling and L. Wang, J. Phys. Chem. B, 127, 2351 (2023) - Unraveling the Structure-Spectrum Relationship of Yeast Phenylalanine Transfer RNA: Insights from Theoretical Modeling of Infrared Spectroscopy
C. Qian and L. Wang, Biochemistry, 63, 2075 (2024) - Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes
C. Qian,‡ Y. Liu,‡ W. Meng,‡ Y. Jiang, S. Wang and L. Wang (‡ These authors contributed equally to this paper), J. Chem. Theory Comput., 20, 10080 (2024)
Short hydrogen bonds in biological systems and liquids
Hydrogen bonds with very short donor-acceptor heavy atom distances (R ≤ 2.7 Å) are commonly observed in condensed phase systems, such as proteins and organic acid-base mixtures. For example, we have recently conducted a statistical analysis of the Protein Data Bank and revealed that short hydrogen bonds are prevalent in proteins and protein-ligand complexes. 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 for biological functions. We have also demonstrated that short hydrogen bonds can significantly alter the nature of acid-base interactions in non-aqueous environments, replacing classical proton transfer reactions by quantum mechanical proton delocalization.
Short hydrogen bonds often display distinctive spectroscopic features. Using first-principles simulations that incorporate the quantum mechanical nature of both the electrons and nuclei, we have elucidated how proton delocalization gives rise to their downfield 1H NMR chemical shifts and broad IR absorption bands in the 2000 - 2700 cm-1 range. Short hydrogen bonds exhibit significant quantum mechanical characters, in stark contrast to standard electrostatic description of hydrogen bonding interactions. 
Related publications
- Unraveling the structural and chemical features of biological short hydrogen bonds
S. Zhou and L. Wang, Chem. Sci., 10, 7734 (2019) - Symmetry and 1H NMR chemical shifts of short hydrogen bonds: Impact of electronic and nuclear quantum effects
S. Zhou and L. Wang, Phys. Chem. Chem. Phys., 22, 4884 (2020) - Quantum kinetic energy and isotope fractionation in aqueous ionic solutions
L. Wang, M. Ceriotti and T. E. Markland, Phys. Chem. Chem. Phys., 22, 10490 (2020) - Quantum effects and 1H NMR chemical shifts of a bifurcated short hydrogen bond
S. Zhou and L. Wang, J. Chem. Phys., 153, 114301 (2020) - Effective prediction of short hydrogen bonds in proteins via machine learning method
S. Zhou,‡ Y. Liu,‡ S. Wang and L. Wang (‡ These authors contributed equally to this paper), Sci. Rep., 12, 469 (2022) - Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds
S. Zhou,‡ Y. Liu,‡ S. Wang and L. Wang (‡ These authors contributed equally to this paper), Sci. Rep., 13, 13741 (2023) - Short hydrogen bonds in proteins
S. Zhou and L. Wang, Comprehensive Computational Chemistry (First Edition), Volume 4, Pages 735-754 (2024) - Quantum mechanical effects in acid–base chemistry
X. Zhang, S. Zhou, F. M. Leonik, L. Wang and D. Kuroda, Chem. Sci., 13, 6998 (2022) - pKa Matching Enables Quantum Proton Delocalization in Acid-1-Methylimidazole Binary Mixtures
R. Zhang,‡ D. Ye,‡ A. Gurung,‡ R. Warmuth, D. G. Kuroda and Lu Wang (‡ These authors contributed equally to this paper), J. Chem. Inf. Model., ASAP (2025)
Reaction mechanisms and adsorptive properties of materials
Integrating molecular dynamics simulations, electronic structure calculations and ab initio molecular dynamics simulations, we have computationally examined reaction mechanisms and adsorptive properties of a series of materials. These projects involve close collaborations with experimental experts at Rutgers University and other institutions. For example, we have elucidated the mechanisms of inverse-electron-demand Diels–Alder reactions of C60 and C70, shedding light on their unusual reactivity and regioselectivity. We have also studied molecular interactions in Scanning Tunneling Microscope-based Break Junction (STMBJ) experiments, which provides a powerful sensing method to probe the structures of single molecule-metal junctions.
Related publications
- Benzylic trifluoromethyl accelerates 1,6-elimination toward rapid probe activation
L. Wang, A. Sivakumar, R. Zhang, S. Cho, Y. Kim, T. Aggarwal, L. Wang and E. C. Izgu, bioRxiv, 2024.05.30.596105 - Synthesis of [60]- and [70]fullerene-fused tetrahydroquinoxaline derivatives by oxidative [4 + 2] cycloaddition with Unusual Reactivity and regioselectivity
Y. Sun, C. Qian, T. J. Emge, Y. Li, W. M. Kopcha, L. Wang and J. Zhang, Org. Lett., 24, 6417 (2022) - Concentration and surface chemistry dependent analyte orientation on nanoparticle surfaces
K. M. R. Scher, Z. Wang, A. Nair, Y. Wu, M. Bartoli, M. Rovere, A. Tagliaferro, S. Rangan, L. Wang and L. Fabris, J. Phys. Chem. C, 126, 16499 (2022) - Atomically precise binding conformations of adenine and its variants on gold using single molecule conductance signatures
X. Pan, C. Qian, L. Wang and M. Kamenetska, J. Chem. Phys., 157, 234201 (2022) - Computational characterization of adsorptive desulfurization using metal-organic frameworks
Y. Wu and L. Wang, J. Phys. Chem. C, 126, 18822 (2022)
