Because of their availability, lower cost, biodegradability, respect for health, environmental standards and their extremely high efficiency [Benmessaoud Left D, Zertoubi M, Irhzo A, Azzi M, Revue: Huiles et extraits de plantes comme inhibiteurs de corrosion pour différents métaux et alliages dans le milieu acide chlorhydrique, J Mater Environ Sci 4:855–866, 2013], the green corrosion inhibitors are currently the most sought after candidates. The ultimate aim of this work is to study the selectivity and reactivity of a series of three molecules, namely Cytisine, Dehydro-Cytisine and N-methyl Cytisine which are the major constituents of Retama monosperma seeds alkaloid extract (AERS) as eco-friendly inhibitors of corrosion of carbon steel in acidic medium HCl (1M), using the density functional theory (DFT) at B3LYP/aug-cc-pvdz levels. Indeed, this alkaloid extract AERS has proven experimentally its corrosion inhibitory power for carbon steel in 1 M HCl even at lower concentration (94.42% at 400[Formula: see text]mg/L). Besides, its adsorption on the steel surface in 1 M HCl solution followed Langmuir’s isotherm [El Hamdani N, Fdil R, Tourabi M, Jama C, Bentiss F, Alkaloids extract of Retama monosperma (L.) Boiss. seeds used as novel eco-friendly inhibitor for carbon steel corrosion in 1 M HCl solution: Electrochemical and surface studies, Appl Surf Sci 357:1294–1305, 2015, doi: 10.1016/j.apsusc.2015.09.159; El Hamdani N, Contribution a la valorisation des parties aériennes de Retama Monosperma, phytochimie, activités antimicrobiennes et propriétés anticorrosives, Universite Chouaib Doukkali Faculte des sciences El jadida, 2015]. Herein, the major aim of this work is to investigate the likelihood of the carbon steel corrosion being inhibited by the protonated species in the aqueous acidic solution. For this purpose, after proving that the most favorable protonation site for protonation was N9, we have evaluated the structural, global and local reactivity descriptors, partial atomic charge in terms of Natural bond orbital (NBO) of the three protonated inhibitors at the level of N9, which are the most stable in the aqueous acidic solution. NBO analysis and the thermodynamic properties such as entropy, enthalpy, heat capacity and Gibbs free energy were also done. In conclusion, it was observed that three protonated molecules showed a high propensity to adsorb to the mild steel surface with a priority of the molecule d-CytN9H+.