Ionizable lipids relevant to known formulations for LNP's have been parameterized for implementation into CpHMD simulations with a Hamiltonian replica exchange methodology. For validation, in silico titrations of self-assembled LNP formulations were performed, and the theoretical apparent pKa values were compared to experimental values measured using TNS assays. The simulations reproduced the acidic shift in pKa values observed for LNP formulations when compared to their watersoluble analogues and show good agreement (MAE = 0.50 pKa units) with the experimental apparent pKa values of the ionizable lipids in the LNPs. Furthermore, each formulation demonstrated pH-dependent structures, emphasizing the importance of lipid protonation in LNP formulations. Simulations performed in acidic environments resulted in mesoporous structures, with RNA residing in water-filled pores, a phenomenon that has been observed previously by SAX experiments. Additionally, neutral pH environments show the mRNA incorporating with the lipids. These results provide a potential explanation for the increased loading and transfection efficiency that are observed with bleb structures, which are highly polar macrostructures known to efficiently incorporate mRNA. Under acidic conditions, in which blebs are formed, the protonated mesoporous lipid structures strongly interact with mRNA to increase loading efficiency. Upon dialysis to a more neutral pH, the mRNA incorporates with the lipids to increase stability and improve transfection efficiency. In general, the ability to accurately model the dynamic protonation of ionizable lipids coexisting in different LNP microenvironments using CpHMD models, along with the influence of an mRNA payload, provides unprecedented accuracy and physical insight into the protonation and charge-state distributions of LNPs loaded with prototypical RNA substrates. We anticipate that these new models will further enhance our understanding of the fundamental structure-function relationships of LNPs in the future, helping to guide the rational design of new lipid formulations and deepening our understanding of protonation-dependent lipid properties and interactions.