The invention of 4D Fingerprints (4DFP) is a breakthrough achievement of 3D and 4D Quantitative Structure-Activity Relationship (QSAR) methods since it eliminates the requirement of manual alignments through the chemical structures. In addition, it adds the dynamic consideration into 3D QSAR instead of considering only conformation in the minimum energetic state. However, the 4DFP only use traditional molecular dynamic simulation with predefined forcefields. Applying traditional molecular dynamic simulation methods to small molecules may lead to some inaccurate bonding dynamic problems, and limited applicable structures. Here we present the use of PM3 semi-empirical methods with ab initio molecular dynamics simulation to generate the 4DFP of trichothecene molecules. With contemporary computer technologies, there is no significant computational time increase by replacing traditional molecular dynamics with PM3 molecular dynamics. However, the PM3 methods can improve the accuracy of studying and applying dynamics of small molecules.

Application of ab initio molecular dynamic simulation in 4D fingerprints

2019 Spring National Meeting

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