A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials.

Abstract

Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels. In this work, we propose a computational scheme to explore the configurational space of 12 types of sodiated pyranoses with the assistance of a neural network potential (NNP). We demonstrated that it is possible to train an NNP based on the density functional calculations extracted from a previous study on sodiated glucose (Glc), galactose (Gal), and mannose (Man). This NNP yields a better description of the other five types of aldohexoses than the four types of ketohexoses. We further show that such a discrepancy in the accuracy of NNP can be resolved by an active learning scheme where the NNP model is engaged in generating the data and has itself updated. Through this iterative process, we can locate more than 17 000 distinct local minima at the B3LYP/6-311+G(d,p) level and an NNP with an accuracy of 1 kJ mol-1 was created, which can be used for further studies.