Two isomeric anions used in Li-ion conducting electrolytes, TFSI and FPFSI, have been compared through quantum-chemical calculations. The FPFSI anion has more low-energy conformers, and its asymmetry leads to an increased number of possible structures of FPFSI–Li complexes. The preferred geometry of the anion–Li ion pair for both anions is the bidentate coordination of the cation through two oxygen atoms; the binding effect is slightly weaker for the FPFSI anion. Ab initio molecular dynamics simulations for salt solutions in tetraglyme have revealed that the amount of cation-to-solvent coordination increases in the LiFPFSI electrolytes. Analysis of the vibrational spectra of anions and ion pairs and the IR spectra of electrolytes obtained from the simulations have indicated that the S–F stretching vibration of the FPFSI anion above 600 cm–1 can be used in experimental conditions to monitor the FPFSI interactions with lithium cations.