Density Functional Theory Computation and Machine Learning Studies of Interaction between Au₃ Clusters and 20 Natural...

The optimal adsorption sites and the binding energies of neutral Au₃ clusters with 20 natural amino acids under the gas phase and water solvation were systematically investigated based on density functional theory (DFT) calculations. The calculation results showed that in the gas phase Au₃ tends to bind with N atoms of amino groups in amino acids, except methionine, which tends to bind with Au₃ through S atoms. Under water solvation, Au₃ clusters tended to bind to N atoms of amino groups and N atoms of side chain amino groups in amino acids. However, methionine and cysteine bind more strongly to the gold atom through the S atom. Based on the binding energy data of Au₃ clusters and 20 natural amino acids under water solvation calculated by DFT, a machine learning model (gradient boosted decision tree) was proposed to predict the optimal binding Gibbs free energy (ΔG) of the interaction between Au₃ clusters and amino acids. The main factors affecting the strength of the interaction between Au₃ and amino acids were uncovered by the feature importance analysis.