Computational study of the solvation of protoporphyrin IX and its Fe²⁺ complex

Abstract

Molecular dynamics (MD) simulations of a well known hydrophobic structure, the heme (ferroprotoporphyrin IX) and its precursor in the heme synthesis, protoporphyrin IX (PPIX) are presented. The objective of the present study is to determine the stability of both structures in an aqueous medium, as well as the structure-solvent relation, hydration shells, and discuss their implications for biological processes. The density functional theory (DFT) is used for the electronic and structural characterization of both PPIX and its Fe 2ϩ complex. A classical approach based on the Gromacs package is used for the MD. The radial distribution function g(r) is used to examine the allocation of water molecules around different regions of the porphyrins. The calculations demonstrate the heterogeneous character of the porphyrins with respect to the affinity with water molecules, the general hydrophobic character of the porphyrin ring bonded or not to the ion Fe, the hydrophilic character of the carboxylic oxygen that is unchanged upon iron binding, and the low hydrophilicity of Fe 2ϩ in the heme.

Solvation of anionic water‐soluble porphyrins: A computational study

“…3). Despite the strong anionic character with charge −4, the profile is very similar to that of the heme porphyrin [4], with charge −2. The hydrophobic character is responsible for porphyrin H-aggregation processes [15].…”

“…The following shells are localized at 0.31, 0.41, and 0.54 nm around each SO − 3 group. Despite, hydration shells are better defined than for the caboxyl groups of the PPIX and heme [4], the degree of local hydrophilicity is not larger, according to the height of the first peak (hydration shell).…”

“…5), with a first peak more pronounced than for the SO − 3 group as a whole. Similarly, in heme porphyrins [4], hydrophilicity is concentrated on the oxygens of CO − 2 groups. The first peak is higher in the latter case because of the favorable ratio of water hydrogens per carboxyl oxygen.…”

“…The preparation of the systems previous to MD simulations was made according to the same standard protocol previously used for protoporphyrin IX (PPIX) and heme [4]. For self-containedness, let us summarize the steps.…”

“…In previous computational work [4], the solvation properties of the protoporphyrin XI and its Fe 2+ complex, the heme, were analyzed. The global hydrophobicity and local heterogeneous solute-water affinity were characterized in such case.…”