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The 12-6-4 model

The Li lab is one of the primary groups that is developing the 12-6-4 model for metal ions. Dr. Li has proposed the 12-6-4 model with Dr. Merz in 2014 (J. Chem. Theory Comput. 2014, 10, 289-297.), where the additional C4 term was proposed to take the ion-induced dipole interaction into account. The 12-6-4 showed better accuracy and transferability than the 12-6 model due to its physical robustness, although with trivial additional computational costs. The 12-6-4 model has been widely employed in simulating metal ions in various chemical, biological, and materials systems, following are some represetative examples:

    (1) The cheating effect of chemical ligands: J. Am. Chem. Soc. 2018, 140, 15166-15169.

    (2) Ion binding thermodynamics in metalloproteins: J. Am. Chem. Soc. 2020, 142, 6365-6374.

    (3) Cation-pi interactions in proteins and protein-ligand interactions: J. Chem. Theory Comput. 2020, 16, 7184-7194.

    (4) Ion transport in biological ion channels: J. Chem. Inf. Model. 2024, 64, 974-982.

    (5) Lanthanide transport in MoS2 channels: Sci. Adv. 2024, 10, eadh1330.

    (6) Molecular adsorption in metal-organic frameworks: Mol. Simul. 2023, 49, 1135-1142.

For more details of the 12-6-4 model, please check Dr. Li’s Google Scholar webpage.

The MCPB.py program

Dr. Li has been a developer of the AMBER Molecular Dynamics Software Package since 2015. He is the leading developer of the pyMSMT module in AMBER, which has the MCPB.py program in it. 

The MCPB.py program has been widely used in scientific research in the bio-inorganic chemistry field, which has been employed by studies published in high-impact journals such as Science, Nature Chemistry, Nature Catalysis, Nature Chemical Biology, Nature Synthesis, Nature Communications, Science Advances, Proceedings of the National Academy of Sciences, Journal of the American Chemical Society, Angewandte Chemie,  Chemical Science, etc.

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