Density functional theory and molecular dynamic simulations were used to understand the microscopic-level interactions of pectin-based thin films with moisture (H2O), carbon dioxide (CO2), and oxygen (O2). Galacturonic acid (GA), which forms ~65% of the smooth region of pectin polymer, was chosen for the current study. The electrostatic potential and Fukui function maps indicate that oxygen atoms of –OH groups of GA are the most reactive sites for electrophilic attack and hydrogen atoms on the carboxylic group (–COOH) are the reactive sites for nucleophilic attack. The GA molecule has shown strong interaction via hydrogen bonding with H2O (E= ~ 40 kJ/mol) followed by CO2 (E = ~ −13 kJ/mol). Nucleophilic O2 showed insignificant interaction with GA. Surface interaction, adsorption, and diffusion of sorbate molecules on the GA film followed the order of H2O >CO2 > O2. Molecular interaction studies provided atomistic insights into the weak moisture and high gas barrier properties of pectin films. © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.