Hydration of porphyrin and Mg–porphyrin: ab initio quantum mechanical charge field molecular dynamics simulations

Abstract

Ab initio QMCF-MD simulations were performed for porphyrin (POR) and magnesium-porphyrin (Mg-POR) immersed in water to study their structural and dynamical properties. The observed hydration behaviour of these solutes representing biomimetic models is in fair agreement with structural and dynamical features of their biological analogues, protoporphyrin IX (PPIX) and chlorophyll (CHl). Structural data obtained from the radial, angular and spatial distribution functions as well as the angular-radial distributions have a consensus on possessing a contrasting hydration behaviour of POR and Mg-POR. Flexibility of the ring in both solutes described by the improper torsional distribution and root mean square fluctuation showed an influence on H-bond interactions between the nitrogen atoms and water molecules that are also reflected in the respective dynamics. An axial water molecule coordinated to the Mg(ii) ion indicates the penta-coordinated Mg-POR to be stable along the simulation. It was also shown that complexation of the Mg(ii) ion to the porphyrin influences the hydration patterns significantly compared to the porphyrin itself, which is further supported by the vibrational power spectra evaluated for both solutes. Free energy of binding and solvent accessible surface area calculations also confirmed that these two solutes have distinct hydration behaviour. Detailed knowledge of the individual hydration patterns is expected to be of particular benefit.

Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9

“…Our optimized partial charge of the magnesium ion, 1.17e (Fig. 6A), is very close to the average value of 1.18 ± 0.1e derived by Moin and Hofer based on HF/MM simulations of a magnesiumporphyrin compound in water [25].…”

The hydration properties of Gd(III) and Tb(III): An ab initio quantum mechanical molecular dynamics study

“…In this study the ab initio quantum mechanical charge-field molecular dynamics (QMCF-MD) approach [2,3] has been used as it had already yielded accurate insight into the hydration properties of a wide range of cations [4][5][6] and anions [7], as well as complexes [8][9][10]. In particular, a number of trivalent cations of the lanthanoide [11][12][13][14][15] and actinoide series [16] have already been successfully investigated, the results being in very good agreement with experimental data where available.…”

A Conceptual DFT Study of the Chemical Reactivity of Magnesium Octaethylporphyrin (MgOEP) as Predicted by the Minnesota Family of Density Functionals

“…1 Porphyrins generally act as carrier molecules for divalent cations such as Fe(II) in heme, myoglobin and many other heme-containing enzymes like cytochrome and catalase, as well as Mg(II) in chlorophylls. 2 Conceptual Density Functional Theory (DFT) or Chemical Reactivity Theory (as it is also known) is a powerful tool for the prediction, analysis and interpretation of the outcome of chemical reactions. [3][4][5][6] Following the pioneering work of Parr and others, 3 a useful number of concepts have been derived from the analysis of the density of any molecular system through DFT.…”